Product of a dubious gene prediction unlikely to encode a functional protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
Does not bind calcium as one of the calcium-binding sites is lost (Asp->Arg in position 64, which corresponds to 'Arg-49' in the current nomenclature)
Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction
Although homologous to serine proteases, it has lost all essential catalytic residues and has no enzymatic activity
It is uncertain whether Met-1 or Met-9 is the initiator
It is uncertain whether Met-1 or Met-2 is the initiator. The first methionine is not conserved among other organisms, but rat. It could be rodent-specific
The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools
Was originally thought to be an inhibitor of alpha-amylase or of a protease and was known as PAPI: probable alpha-amylase/protease inhibitor
Was originally thought to be a Map2k3 protein but sequence analysis shows closer similarity to the Map2k6 proteins
Lacks the conserved Cys residue in position 81
Because the enzyme that would modify Asp-89 to 3-methylthioaspartic acid has not been found in the proteome of this organism, that modification is not predicted
Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB
The protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools
An article reported that this protein promotes microtubule reorientation in hypocotyls; however, this paper was later retracted
In E.coli K12 / MG1655 and K12 / W3110 this operon is silenced by an IS1D insertion in the promoter region
It is uncertain whether Met-1 or Met-3 is the initiator
In contrast to other members of the family, lacks the regions that come into close contact with the mRNA in the ribosomal A-site and determine the STOP codon specificity, explaining the loss of codon specificity for translation release factor activity
It is not clear if the light chain is degraded after cleavage
The gene for this protein is duplicated in strains AX3 and AX4. These strains contain a duplication of a segment of 750 kb of chromosome 2 compared to the corresponding sequence in strain AX2
Was reported to act as an endonuclease that specifically cleaves 5-hydroxymethylcytosine (5hmC)-containing DNA in vitro (PubMed:29020633). Additional experiments are however required to confirm this activity as this protein is present in many organisms that do not utilize methylcytosine for epigenetic control
This peptide is cyclic. The start position was chosen by similarity to OAK1 (kalata-B1) for which the DNA sequence is known
Young tissue from this organism is photosynthetic and contains some thylakoids, although the photosynthetic activity does not exceed the light compensation point
According to PubMed:2168892, this sequence initiates from a non-AUG codon; N-terminal ACG codon did serve as a start codon
In strain K12 / CR63, finO is interrupted by an IS3 element
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-39; H2BK34ac = acetylated Lys-40; H2BK143ub1 = monoubiquitinated Lys-147
MC degradation was originally described as sequential, three-step process catalyzed by enzymes subsequently named as MlrA, MlrB and MlrC, where MlrC catalyzes hydrolysis of tetrapeptides generated by MlrB (PubMed:8899999). It is shown later that purified MlrC hydrolyzes also linear MC (PubMed:11769251, PubMed:22591122) so it is not clear if MlrB is indispensable in this pathway
Was termed (Ref.3) RASSF3
It is uncertain whether Met-1 or Met-20 is the initiator
Product of a dubious gene prediction
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4me = methylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me = methylated Lys-10; H3S10ph = phosphorylated Ser-11; H3T11ph = phosphorylated Thr-12; H3K14ac = acetylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me = methylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me = methylated Lys-24; H3K27me = methylated Lys-28; H3S28ph = phosphorylated Ser-29; H3K36me = methylated Lys-37
Could be the product of a pseudogene
The potential active site Asp residue in position 11 is replaced by a Leu
According to PubMed:22563492, alternative splicing gives rise to an isoform (Paraplegin-2) which is identical to the sequence of the mature protein and localizes to the endoplasmic reticulum
Originally thought to be a component of PSII; based on experiments in Synechocystis, N.tabacum and barley, and its absence from PSII in T.elongatus and T.vulcanus, this is probably not true
It is uncertain whether Met-1 or Met-10 is the initiator
Part of a set of proteins in which some residues (ACT_SITE, NP_BIND, REGION and BINDING) are not conserved
Could be the product of a pseudogene. This sequence is much shorter than orthologs
It is uncertain whether Met-1 or Met-4 is the initiator
It is uncertain whether Met-1 or Met-11 is the initiator
Although assigned as a calmodulin family member by PubMed:17263873, it only contains EF-hand domains
Both N-terminus methionine truncation and retention have been observed for this protein by 2 different experiments
Tyr-9 is present instead of the conserved Cys which is expected to be the active site residue of peptidase C39. Thus they are presumed to be without peptidase activity
Was originally thought to be involved in formation of the cyclopentone ring of protochlorophyllide from Mg-protoporphyrin IX monomethyl ester
Studies from PubMed:24184420 describe a peptide with an Arg-30 instead of an Asn-30
Does not bind calcium as one of the calcium-binding sites is lost (Asp->Lys in position 48, which corresponds to 'Lys-49' in the current nomenclature)
There are several genes encoding the J region in the T cell receptor gamma locus. The peptide described in this entry is a representative for all the peptides encoded by these genes
Although it contains a PPIase FKBP-type domain, does not show peptidyl-prolyl cis-trans isomerase activity
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-6; H2AK7ac = acetylated Lys-10; H2AS128ph = phosphorylated Ser-133
Could be the product of a pseudogene. Truncated; premature stop codon
Not expected to have any kinase activity
Additional evidence for its localization to the endoplasmic reticulum membrane was found. However this paper was retracted due to manipulation of data
Nucleotide binding site is not accessible for binding to ATP-analogs
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-37; H2BK143ub1 = monoubiquitinated Lys-149
In some plant proteins and in human SARM1, the TIR domain has NAD(+) hydrolase (NADase) activity (By similarity). However, despite the presence of the catalytic Asp residue, the isolated TIR domain of human TLR4 lacks NADase activity (By similarity). Based on this, it is unlikely that Toll-like receptors have NADase activity
A mature protein with 47 amino acid residues is predicted in PubMed:17270501 (sequence of 45-91) instead of the chain proposed here (2 amino acids longer). Since the protein sequence and the predicted mass correspond exactly with proteomic data (PubMed:17270501), the 49 amino acid chain is shown
Was originally thought to be involved in copper homeostasis (PubMed:7635807), however, the copper sensitivity phenotype of the mutant was later shown to be due to the loss of MicL sRNA which leads to elevated Lpp levels (PubMed:25030700). Silent mutations in this protein that disrupt the promoter of micL are copper sensitive
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-8; H2BK6su = sumoylated Lys-8; H2BK7ac = acetylated Lys-9; H2BK7su = sumoylated Lys-9; H2BK11ac = acetylated Lys-15; H2BK16ac = acetylated Lys-26; H2BK16su = sumoylated Lys-26; H2BK17su = sumoylated Lys-27; H2BK123ub1 = monoubiquitinated Lys-135
Lacks the His residue in the RING-type domain 2 that is one of the conserved features of the family
Glyoxalase activity has been reported (PubMed:22523093). It may however reflect its deglycase activity
The protein deglycation activity is controversial. It has been ascribed to a TRIS buffer artifact by a publication and as a result of the removal of methylglyoxal by glyoxalase activity that leads to a subsequent decomposition of hemithioacetals and hemianimals due to the shift in equilibrium position by another one. However, biochemical experiments showing that PARK7 is a bona fide deglycase have been performed
Was originally thought to differ from MetX, which was assigned as a second AdoMet synthase before being shown to be identical to MetK
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-6; H2BK11ac = acetylated Lys-11; H2BK12me2 = dimethylated Lys-12; H2BK16ac = acetylated Lys-16; H2BK27ac = acetylated Lys-28; H2BK33ac = acetylated Lys-34; H2BK34ac = acetylated Lys-35; H2BK143ub1 = monoubiquitinated Lys-141
Ser-155 is present instead of the conserved Cys which is expected to be an active site residue
Was originally thought to be the site of the radC102 mutation, but it was subsequently shown that it is not the case
Contains the conserved metal-binding sites characteristic of RNA polymerases but has been shown to lack RNA polymerase activity when expressed in E.coli
The fragment sequence AC P84683 is identical to the sequence presented in this entry, but both peptides are probably different peptides, since the experimental molecular mass of AC P84683 does not correspond to theoretical mass of the peptide presented here
Gluconolactonase catalyzes a key step in ascorbic acid (vitamin C) biosynthesis, but primates lack the last enzyme in the pathway and are unable to synthesize vitamin C
For examples of full-length immunoglobulin heavy chains (of different isotypes) see AC P0DOX2, AC P0DOX3, AC P0DOX4, AC P0DOX5 and AC P0DOX6
The genomic sequence for this protein is not available, so Asp-4 may possibly be an asparagine which is known to be more labile when immediately followed by a glycine
Lacks the conserved His residue essential for phosphatase activity. Its enzyme activity is therefore unsure
Was originally (PubMed:15855155) thought to function in polyamine resistance, hence the name BRP1, but this phenotype was later (PubMed:16374585) attributed to down-regulation of PMA1
Product of a dubious CDS prediction. Encoded by the 3'-UTR of HEPACAM
The D.melanogaster ortholog of this protein has been proposed to undergo autophosphorylation on tyrosine residues which is induced in response to cell adhesion (PubMed:1371458). However as mammalian orthologs of this protein seem to lack kinase activity this protein may associate with, and be phosphorylated by, an unknown active tyrosine kinase
Was named WNK/'with no lysine(K)' because key residues for catalysis, including the lysine involved in ATP binding, are either not conserved or differ compared to the residues described in other kinase family proteins
Was initially thought to constitute the phosphatidylserine receptor, a receptor that mediates recognition of phosphatidylserine, a specific marker only present at the surface of apoptotic cells. Phosphatidylserine receptor probably participates in apoptotic cell phagocytosis. This protein was identified using phage display expressing mAb 217, an antibody that specifically recognizes phosphatidylserine receptor. However, its nuclear localization and the fact that mAb 217 antibody still recognizes the phosphatidylserine receptor in mice lacking Jmjd6, strongly suggest that it does not constitute the receptor for phosphatidylserine and is not involved in apoptotic cell removal
For expression reasons, the sequence was engineered with a Gly residue instead of a Pro at position 39
Although related to peptidase S1 family, lacks the conserved active Ser residue in position 192 which is replaced by an Ala, suggesting that it has no protease activity. Lacks also metal binding sites Glu in position 67 which is replaced by Asn and Asn in position 69 which is replaced by Lys
It is uncertain whether Met-1 or Met-83 is the initiator
Lacks the two active site residues His and Cys at position 245 and 246 which are essential for dual-specificity phosphatase activity. Lacks phosphatase activity
PubMed:11584023 reported a cytosolic, as well as nuclear subcellular location. This result was obtained using an N-terminally GFP-tagged construct which most probably affected signal peptide-driven targeting to the ER. As a consequence, the in vivo revelance of the observed interaction with APOBEC1, a nuclear protein, is dubious. This holds true for the interaction with PWP1
The products of the genes tfdR and tfdS were originally thought to be identical but in fact they differ by one residue (amino acid 264 which is Asp in tfdR and Ala in tfdS)
The most common activity assay for dermonecrotic toxins detects enzymatic activity by monitoring choline release from substrate. Liberation of choline from sphingomyelin (SM) or lysophosphatidylcholine (LPC) is commonly assumed to result from substrate hydrolysis, giving either ceramide-1-phosphate (C1P) or lysophosphatidic acid (LPA), respectively, as a second product. However, two studies from Lajoie and colleagues (2013 and 2015) report the observation of exclusive formation of cyclic phosphate products as second products, resulting from intramolecular transphosphatidylation. Cyclic phosphates have vastly different biological properties from their monoester counterparts, and they may be relevant to the pathology of brown spider envenomation
Glyoxalase activity has been reported. It may however reflect its deglycase activity
According to a report, morpholino knockdown in embryos is lethal (PubMed:25078621). Other publications report that morpholino knockdown animals are viable (PubMed:28681861, PubMed:28161523, PubMed:30016436)
Although named XerD by PubMed:11763967, it is not the ortholog of XerD and constitutes a distinct protein family. In contrast to the classic XerD protein, it does not contain the Arg-His-Arg-His (R-H-R-H) sandwich residues that are clustered with the Tyr active site. It also lacks the C-terminal region which is known to mediate the interaction with XerC. It is therefore unknown whether it has tyrosine recombinase activity or act as a regulator
Identified as having similarity to the core DENN family and referred to as DENN6B (PubMed:21330364). Prediction methods do not indicate a DENN domain for this sequence and, the exact role of the DENN or this DENN-like domain in GEF activity needs to be clarified
Mups are encoded by multiple paralogous genes which are very similar to each other, making accurate identification difficult. The recommended nomenclature used in this entry is based on that provided by the MGI database
The kinase domain has very low catalytic activity in vitro
According to a well-established model, RNF168 cannot initiate H2A 'Lys-63'-linked ubiquitination and is recruited following RNF8-dependent histone ubiquitination to amplify H2A 'Lys-63'-linked ubiquitination. However, other data suggest that RNF168 is the priming ubiquitin ligase by mediating monoubiquitination of 'Lys-13' and 'Lys-15' of nucleosomal histone H2A (H2AK13Ub and H2AK15Ub respectively). These data suggest that RNF168 might be recruited to DSBs sites in a RNF8-dependent manner by binding to non-histone proteins ubiquitinated via 'Lys-63'-linked and initiates monoubiquitination of H2A, which is then amplified by RNF8. Additional evidence is however required to confirm these data
Phosphorylation has been demonstrated on peptides which are common to both Rab7a and Rab7b
Despite its name, it does not contain any EF-hand domains
Product of a dubious CDS prediction. May be a non-coding RNA
Most probably a non-functional protein that cannot participate to the synthesis of a productive T cell receptor (TR) chain due to an altered splicing site (PubMed:9619395)
This peptide is cyclic. The start position was chosen by similarity to Oak1 (kalata B1) for which the DNA sequence is known
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK5ac = acetylated Lys-6; H2AK8ac = acetylated Lys-9; H2AK10ac = acetylated Lys-11; H2AK12ac = acetylated Lys-13; H2AK17ac = acetylated Lys-18; H2AS122ph = phosphorylated Ser-123; H2AK123ub1 = monoubiquitinated Lys-124; H2AS127ph = phosphorylated Ser-128
Could be the product of a pseudogene. YIL165C seems to be the C-terminal part of a putative nitrilase-like protein formed of NIT1/YIL164C and YIL165C
Was originally termed sox-13
The elongator complex was originally thought to play a role in transcription elongation. However, it is no longer thought to play a direct role in this process and its primary function is thought to be in tRNA modification
NLP1 carries a deletion of a single nucleotide which leads an early stop-codon. Therefore, NLP1 is assumed to be a pseudogene with a length of 345 bp and a size of 114 amino acids
Was initially reported to act as a regulator of mRNA translation efficiency by binding to m6A-containing mRNAs (PubMed:30591559). This study suggested that the 3 different paralogs (YTHDF1, YTHDF2 and YTHDF3) have unique functions with limited redundancy (PubMed:32943573). However, later studies showed that YTHDF1, YTHDF2 and YTHDF3 paralogs have redundant functions to a profound extent and directly promote degradation of m6A-containing mRNAs (PubMed:32943573). The effect on translation efficiency observed earlier is probably indirect (PubMed:32943573)
Could be the product of a pseudogene unlikely to encode a functional protein. This is the C-terminal part of L-serine dehydratase. Strain S288c has a stop codon in position 128, which disrupts the gene coding for this protein and produces two ORFs YIL167W and YIL168W. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. A contiguous sequence for L-serine dehydratase can be found in other strain backgrounds (AC P0CF23)
Could be the product of a pseudogene. Probably not expressed, due to the absence of promoter-like sequences upstream of the operon tsaMBCD2 (PubMed:11282598)
It is uncertain whether Met-1, Met-2, Met-5 or Met-8 is the initiator
Was originally thought to be a choline transporter
The experimental design does not allow to distinguish AOX1 from AOX3 in rat liver as the effector of the superoxide and nitric oxide production (PubMed:17353002, PubMed:19801639)
Although initially thought (PubMed:17846994) to be a zinc-finger protein, it was later shown (PubMed:17376863) that it binds 1 2Fe-2S cluster instead
Asn-331 is present instead of the conserved Asp which is expected to be an active site residue
It is uncertain whether Met-1 or Met-17 is the initiator
Lacks the GMN motif, which is a conserved feature of the family
B.parapertussis and B.bronchiseptica seem not to produce the pertussis toxin (S1, S2, S4, S5 and S3) and ptl proteins (PtlA, PtlB, PtlC, PtlD, PtlE, PtlF, PtlG, PtlH and PtlI) in vivo due to changes in the promoter region of the ptx-ptl operon. However, it is possible that their promoter is active under certain, as-yet-undefined conditions and that B.parapertussis and B.bronchiseptica are therefore capable of producing these proteins
Toxicity tests have been done on recombinant non-amidated toxin
Similar to plant 1-aminocyclopropane-1-carboxylate synthases but lacks a number of residues which are necessary for activity
Unlike mammalian MSRA, lacks methionine oxidase activity because Cys-232 cannot function as a resolving cysteine to perform the disulfide exchange and instead remains as a free thiol (PubMed:30529269). As a result, the active site cysteine is trapped in disulfide linkage with Cys-246 and is therefore unable to react with a second molecule of methionine sulfoxide to complete methionine oxidation (PubMed:30529269)
The PHTF domain was initially defined as an atypical homeodomain, suggesting that this protein could act as a transcription regulator (PubMed:10395808). However, the protein is not found in the nucleus and mainly localizes in the endoplasmic reticulum membrane, suggesting that it does not act as a transcription factor (By similarity)
Was originally thought to be elastase 1
Appears to have histone acetyltransferase (HAT) activity, specifically towards histones H2B and H4 in vitro (By similarity). However, it is not clear if this activity is genuine or caused by contamination with other histone acetyltransferases in the assay
Was reported to interact with UBXN6 but the corresponding article has been retracted (PubMed:18768758)
Although related to peptidase S1 family, lacks the essential His, Asp, and Ser residues of the catalytic triad at positions 83, 129 and 221 and is therefore predicted to have lost protease activity
It is uncertain whether Met-1 or Met-12 is the initiator
This protein does not undergo proteolytic processing to release the disintegrin domain. However, in experimental conditions (absence of calcium), the disintegrin domain is autoproteolytically processed from the mature protein and give the chain 208-291
Although it belongs to the protein kinase superfamily, the ATP-binding motif VAIK has an arginine instead of a lysine residue suggesting that KSR1 cannot bind ATP and therefore lacks protein kinase activity. However, KSR1 is capable of binding ATP (PubMed:21441104). Has protein kinase activity towards MAP2K1 in presence of RAF1/c-RAF in vitro (PubMed:21441104)
Note that unlike other eukaryotes, peridinin-containing dinoflagellates have a nuclear-encoded chloroplast-targeted form II RuBisCO
Four genes are encoding the same mature protein that may have different glycosylation degree. The two precursors produced differ by only one amino acid located in the signal peptide
It is uncertain whether Met-1 or Met-2 is the initiator
Nakanishi et al (PubMed:11698233) shows that the transport process is electrogenic, contrary to the conclusions of Hamdani et al (PubMed:22821889) who finds that the transport is electroneutral with a Na(+):L-glutamine stoichiometry of 1:1 (PubMed:22821889, PubMed:11698233). Hamdani et al. shows that this electrogenic transport describes by Nakanishi et al. would correspond to large uncoupled fluxes of protons (PubMed:22821889, PubMed:11698233)
There is no equivalent of this gene in strain K12 / MG1655
The sequence shown here has been extracted from PDB entry 1WAL
May be non-functional, contains only the C-terminal section of a formamidopyrimidine-DNA glycosylase and has no detectable DNA-binding activity
It is possible that trbEA and trbEB form a single orf
Both Cso2A and Cso2B were originally thought to be glycosylated (PubMed:10525740). Later experiments do not show any evidence of glycosylation (PubMed:26608811)
The humanin peptide has been shown to be biologically active but is the product of a mitochondrial gene, MT-RNR2. The mechanisms allowing the production and the secretion of humanin from the mitochondrial gene remaining unclear, the possibility exist that the physiologically active humanin peptide is encoded by one of the related genes present in the nuclear genome including the one described here (PubMed:19477263)
SKL1 does not possess shikimate kinase activity in vitro probably because it lacks the conserved active sites and substrate binding sites of the shikimate kinase family
For an example of a full-length immunoglobulin lambda light chain see AC P0DOX8
Lacks the conserved active site CXXC motif that is essential for thiol reductase activity. Its enzyme activity is therefore unsure
Maps to a duplicated region on chromosome 15; the gene is present in at least 3 almost identical copies
Although assigned as a calmodulin family member by Ref.4, it only contains EF-hand domains
This peptide is cyclic. The start position was chosen by similarity to cliotide cter-B for which the DNA sequence is known
Although related to the peptidase M24 family, this protein lacks conserved active site residues suggesting that it may lack peptidase activity
Three distinct genes (AMY1A, AMY1B and AMY1C), located in a gene cluster on 1p21, encode proteins sharing the same peptidic sequence
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK6su = sumoylated Lys-7; H2BS10ph = phosphorylated Ser-11; H2BK11ac = acetylated Lys-12; H2BK16ac = acetylated Lys-17; H2BK16su = sumoylated Lys-17; H2BK17su = sumoylated Lys-18; H2BK123ub1 = monoubiquitinated Lys-125
Although related to peptidase M14 family, lacks the active site residues and zinc-binding sites, suggesting that it has no carboxypeptidase activity
The orthologous protein is known as the alpha subunit (UreC) in most other bacteria
Was originally thought to be a subunit of PAB-dependent poly(A)-specific ribonuclease
Was originally thought to signal lymphoid cells to proliferate via thymic shared antigen 1 (PubMed:11714798). This work was later retracted (PubMed:12538725)
It has been reported that MYDGF is secreted into blood plasma and localized to the endoplasmic reticulum-Golgi intermediate compartment (PubMed:17362502, PubMed:25581518). However, another report shows resident localization to the endoplasmic reticulum and Golgi apparatus and secretion when the two most C-terminal residues of the RTEL motif are abolished (PubMed:29954947)
It is uncertain whether Met-1, Met-9, Met-13 or Met-14 is the initiator
Represents an unconventional myosin. This protein should not be confused with the conventional myosin-10 (MYH10)
There are several genes encoding the J region in the T cell receptor alpha locus. The peptide described in this entry is a representative for all the peptides encoded by these genes
Despite classification as a pseudogene, the existence of this protein is supported by unambiguous mass spectrometry evidence
Was originally (PubMed:10792723) thought to control translocation of choline-binding proteins to the cell surface but PubMed:11260480 failed to confirm this observation. The conflicting observations could be explained by the fact that the mutant strain used in PubMed:10792723 lacked capsule
As S.pyogenes is unable to produce acid from glycerol, the significance and/or function of the glpO gene in this organism is at present unknown
The conserved active site Cys (or selenocysteine) residue in position 29 is replaced by a Thr. However, as function in selenoprotein synthesis is probable, it is possible Cys-31 is the active site
The six exosome core subunits containing a RNase PH-domain are not phosphorolytically active
Once thought to be involved in copper homeostasis, experiments in E.coli have shown this is not the case
In light of strong homologies in the primary amino acid sequence, the 3 AKT kinases were long surmised to play redundant and overlapping roles. More recent studies has brought into question the redundancy within AKT kinase isoforms and instead pointed to isoform specific functions in different cellular events and diseases. AKT1 is more specifically involved in cellular survival pathways, by inhibiting apoptotic processes; whereas AKT2 is more specific for the insulin receptor signaling pathway. Moreover, while AKT1 and AKT2 are often implicated in many aspects of cellular transformation, the 2 isoforms act in a complementary opposing manner. The role of AKT3 is less clear, though it appears to be predominantly expressed in brain
Lacks the conserved Glu residue in position 477 essential for carbopeptidase activity. The mature form lacks catalytic activity towards synthetic peptide substrates
An isoform was shown to be localized to both the cytoplasm and the nucleus and to be sumoylated with SUMO1 (PubMed:19059915). The article has later been withdrawn by the authors
Although it belongs to the glycosyl hydrolase 18 family, Leu-119 is present instead of the conserved Glu which is an active site residue. Therefore this protein lacks chitinase activity
Represents an unconventional myosin. This protein should not be confused with the conventional myosin-9 (MYH9)
Does not seem to have protease activity as it lacks the zinc-binding site
Isoform 3 is predicted to be expressed at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. Contrary to expectations, it has been shown to be well expressed, and the encoded protein is detected in mitochondria (PubMed:11015561, PubMed:17940881, PubMed:22228304)
Contains a metallopeptidase domain, but the active site is not conserved, so the protein is not expected to have protease activity
The uracil binding region known from UPRTases is missing
May be the product of a chimeric cDNA as it seems that the 3'end map to chromosome 4 and the 5'end to chromosome 7
A publication reports an opposite topology (PubMed:26774479). However, 3 different articles, 2 in human and one in mouse, confirm the topology shown in this entry (PubMed:27099988, PubMed:27642048)
Could be the product of a pseudogene. A stop codon at position 188 results in a truncated and certainly non functional protein
The well-known t(6)A modification appears to be a hydrolyzed artifact of natural cyclic t(6)A (ct(6)A) that occurs during the preparation and handling of tRNA in B.subtilis and many other species (PubMed:23242255). In these species, the t(6)A modification is processed further by dehydration into ct(6)A, a reaction catalyzed by TcdA
This sequence initiates at a CTG codon
In contrast to its orthologs it harbors a signal sequence
Shares some similarity with tyrosine phosphatase proteins but it has no phosphatase activity
Could be the product of a pseudogene. Lacks the signal peptide and 2 of the 4 disulfide bonds, which are conserved features of the family
According to PubMed:12959640, T.stejnegeri was formerly named T.gramineus, supposing that this protein is the same as PLA-VII from T.gramineus. They have been kept separated, because T.gramineus and T.stejnegeri are considered as being two different species (see http://reptile-database.org)
Was originally thought to inhibit the secretion of FSH by pituitary cells
Was originally called ecpD, but ecp is now used for the ecpABCDE operon involved in E.coli common pilus (ECP) synthesis
The Zn(2)-C6 fungal-type DNA-binding domain is highly degenerated, the transcriptional regulation activity of gsfR1 is therefore doubtful
This toxin has the prefix lambda in its name (instead of kappa), since lambda is the Greek letter attributed to calcium-activated potassium (KCa) channel impairing toxins (according to the nomenclature of King et al., 2008)
It is uncertain whether Met-1 or Met-57 is the initiator
Could be the product of a pseudogene. In M.polymorpha this protein is in two parts: ORF 1068 (N-terminal) and ORF 464 (C-terminal). It also could be due to a frameshift error
It is unclear whether this protein requires a metal cofactor for catalysis. It was originally proposed to be a Zn(2+)-dependent metalloenzyme based on structural similarities to bacterial aminopeptidases and the observation that it can bind Zn(2+) ions, typically in a 1:1 stoichiometry (By similarity). However, a recent study suggests a Zn(2+)-independent catalytic mechanism (By similarity)
Was originally (PubMed:2954162) thought to control the translation of its own gene by binding to its mRNA; it now seems that discrimination against the AUU start codon is a kinetic effect (PubMed:16857585)
There is a discrepancy in nomenclature: was submitted as Bu1.4 in PubMed:20143226 but is named Bu1.3 in ConoServer
Was originally thought to be a DNA photolyase
Could be the product of a pseudogene. In strain cv. Columbia, a frameshift at position 140 results in a truncated RNR2B protein. The resulting sequence lacks the conserved features of the family. A second start codon could potentially direct the translational initiation of a second peptide homologous with TSO2 (AC Q9LSD0) at residues 141 to 332. A complete sequence for a functional RNR2B can be found in strain cv. Landsberg erecta (AC P0DKH3)
Unlike the other TEC subfamily members, TXK is activated independently of the activity of phosphatidylinositol 3-kinase, consistent with its lack of a PH domain. Membrane association is performed through palmitoylation at the N-terminus
The order of the peptides shown is unknown
Part of the residues that are essential for calcium binding are not conserved, resulting in loss of calcium binding at physiological calcium concentrations
This protein has the conserved residues necessary to bind a zinc ion as do the zinc-binding member of this family, but it is not clear if does so
Most probably a non-functional protein that cannot participate in the synthesis of a productive immunoglobulin chain due to an unusual recombination signal (RS) sequence altering V-(D)-J recombination (PubMed:9619395)
Product of a dubious CDS prediction
Does not bind calcium as three of the calcium-binding ligands are lost
This sequence is an example of a full-length TR alpha chain. Pan-cancer TRAV38-2DV8*01J31*01C*01 TR alpha chain is generated by somatic recombination of variable TRAV38-2DV8 (AC A0JD32) and joining TRAJ31 (AC A0A075B700) gene segments spliced to constant TRAC (AC P01848) gene segment
EF-Tu 1 and EF-Tu 2 differ in a single position and are no longer merged. However, many papers are found in both entries as it is not always possible to determine for each paper which of EF-Tu 1 or EF-Tu 2 was being worked upon
Originally suggested to encode a cobalamin adenosyl transferase
Could be the product of a pseudogene. This sequence is shorter than orthologs and lacks the conserved active site Glu
Variants Trp-88, Cys-152, Cys-181, Ser-343, Pro-503, Arg-514 and His-554 have original been associated with ALD. However this paper was retracted due to inconsistencies in a confirmation immunoblot that could not be validated from the originally published data
Was previously thought to be non-coding but has been shown to be translated and functional
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-5
Has low sequence similarity to characterized chitin deacetylases with an apparent lack of conserved active sites and metal binding sites, making its function difficult to predict
Was originally thought to be a chloride channel
Was originally thought to interact with acj6
Contains a degenerate basic motif not likely to bind DNA
Lacks the phospho-accepting Asp (here Glu-89), present in the receiver domain, which is one of the conserved features of two-component response regulators (ARRs) family
The term basicilin was erroneously reported in a review. Since such a letter reversal is relatively common, we thought it would be appropriate to indicate it here to facilitate the search for this protein
Lacks the active site residue so is predicted to be catalytically inactive
Lacks the conserved metal-binding residues in the NUDIX motif and is not expected to have hydrolase activity
While it is structurally defined as a knottin it lacks the conserved Cys residue in position 75
Sequence shown in this entry in copied from Fig.2, and not from Table 1, which differs
The crystal structure has erroneously been identified as HigA, the sequence submitted is in fact that of YddM
Was originally thought to originate from S.solfataricus strain P1, but the culture was contaminated with S.acidocaldarius
Shares some similarity with tyrosine phosphatase proteins but it has probably no phosphatase activity
Could be the product of a pseudogene. In strain cv. Columbia, a naturally occurring frameshift at position 277 results in a truncated MRS2-8 protein lacking the two transmembrane regions, which are conserved features of the family. A complete sequence for MRS2-8 can be found in strain cv. Landsberg erecta (AC P0CZ21)
Although assigned as a calmodulin family member by Ref.5, it only contains EF-hand domains
Product of a dubious CDS prediction. Could be the remnant of an endogenous retroviral dUTPase
This is a truncated TALA gene product. Strain AX4 has a stop codon in position 1280 which disrupts the gene and produces a truncated protein. On the other hand, strain AX2 produces a full length protein (AC P0CE95)
Could lack activity as the potential ADP-glucose binding site Arg/Lys residue in position 15 is replaced by an Ser
Although it belongs to the XPG/RAD2 endonuclease family, only two of the seven Asp residues involved in Mg(2+) binding are conserved suggesting that it has no nuclease activity
The active site contains a CPPC motif wich differs from the conserved CGPC motif
Several genes are coding for this toxin for which the structure by NMR has been determined. The cross-references to PDB can be found in entry AC P18511
Could be the product of a pseudogene. Is truncated in the N-terminal where it lacks 31 residues compared to orthologs and it has a 13 residues deletion in between Ala-325 and Pro-326
Absent from the genome of domestic mammals and New World monkeys it is found in the genome of hominids and Old World monkeys. Likely derived from retrogene insertion of an NLRP2/NLRP7-like gene, it has probably arisen recently in the mammalian genomes where it is under purifying selection
This sequence was originally thought to contain an additional peptide (PubMed:16529377). However, it was later shown that the peptide is likely to be human type II keratin, a common contaminant in proteomic analyses, so it has been removed and the remaining sequence may also contain further contaminations (PubMed:23895828)
The sequence of 1-41 of PubMed:12359730 has not been submitted
Binds calcium very weakly as one of the calcium-binding ligands is lost (Asp->Lys in position 64, which corresponds to 'Lys-49' in the current nomenclature)
Could be the product of a pseudogene. Is missing C-terminal sequences compared to its orthologs
Lacks the conserved active site 'GDSL' motif. Its enzyme activity is therefore unsure
In contrast to its ortholog from P.sojae, still has the conserved Glu residue in position 222 essential activity, but, as for P.sojae XLP1, does not show xyloglucanase activity
Was originally thought to be located in the peroxisome. However, was later shown to be cytosolic
The active site contains a CGSC motif wich differs from the conserved CGPC motif
In strain MG1655 the eut operon is interrupted by the CPZ-55 prophage, encoding 9 genes situated between eutA and eutB, which are translated in the other direction. CPZ-55 may prevent expression of the eut operon in strain MG1655. Strain W3110 does not have this prophage element and should be able to express the operon
This sequence is an example of a full-length immunoglobulin kappa light chain
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-5; H2AK7ac = acetylated Lys-8; H2AK126su = sumoylated Lys-127; H2AS128ph = phosphorylated Ser-129
Was originally thought to be MFT1, the mitochondrial fusion target protein
Tyr-13 is present instead of the conserved Cys which is expected to be the active site residue of peptidase C39. Thus this protein is presumed to be without peptidase activity
Was originally (PubMed:2793826) reported to be a transcriptional repressor of cat genes. However, further investigations have shown it to be a transcriptional activator
It is uncertain whether Met-1 or Met-52 is the initiator
Was originally erroneously termed DUSP25
Although strongly similar to formylglycine-generating enzyme, lacks the catalytic Cys residues at positions 261 and 266 that bind the catalytic copper. The catalytic copper is required to activate oxygen and catalyze oxidative C-H activation
Was originally thought to be involved in delta-aminolevulinic acid biosynthesis
Was originally thought to have a head-to-tail cyclic structure, but actually has a threaded side chain-to-backbone ring structure that is penetrated by the C-terminal tail in a noose-like motif
The assignment of paradoxin function to this sequence has been made based on sequence similarity to taipoxin and cannitoxin. The gamma chain has not yet been sequenced
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4 = Lys-5; H3K4me = methylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me = methylated Lys-10; H3S10ph = phosphorylated Ser-11; H3T11ph = phosphorylated Thr-12; H3K14 = Lys-15; H3K14ac = acetylated Lys-15; H3K18 = Lys-19; H3K18ac = acetylated Lys-19; H3K23 = Lys-24; H3K23ac = acetylated Lys-24; H3K27ac = acetylated Lys-28; H3K27me = methylated Lys-28; H3K35 = Lys-36; H3K35me = methylated Lys-36; H3K36 = Lys-37; H3K36me = methylated Lys-37
The use of this protein as a coreceptor for C.botulinum type D (BoNT/D, botD) is controversial. In double SV2A/SV2B knockout mice BoNT/D does not degrade its synaptobrevin target; introducing SV2A, SV2B or SV2C restores target cleavage (PubMed:21483489). However another group does not find a convincing interaction with SV2 (PubMed:21632541)
Apparent discrepancy in expression data: a transgenic promoter based on about 4 kb from the 5' flank of the gene, drives reporter gene expression in larval L1-L4 stages, but endogenous transcripts are not detected in L1 larvae using in-situ hybridisation
Neither O157 strain expresses urease due to a truncation of ureD, the last gene of the probable operon. Urease activity is restored in O157 / Sakai upon complementation with wild-type ureD
This region of the chromosome is duplicated in strain O157:H7 / EDL933 but not in O157:H7 / Sakai
Does not bind calcium as one of the calcium-binding sites is lost (Asp->Ser in position 47, which corresponds to 'Ser-49' in the current nomenclature)
May lack the polyribonucleotide 5'-hydroxyl-kinase and polynucleotide 5'-hydroxyl-kinase activities that are characteristic of the human ortholog
The role of p38 MAPK kinases is unclear in phosphorylation and activation of MAPKAPK5. According to some reports, it interacts and is phosphorylated by p38-alpha/MAPK14 and p38-beta/MAPK11 (PubMed:9628874, PubMed:12808055). According to other reports, it is not activated by p38-alpha/MAPK14 and p38-beta/MAPK11. An explanation for these discrepancies, might be that the interaction with p38 MAPK kinases is weak and occurs only under specific conditions
Was originally thought to be a toxin with hemolytic and cytolytic activity
Compared to its human ortholog it has lost the N-terminal DBF4-type zinc finger
For an example of a full-length immunoglobulin kappa light chain see AC P0DOX7
Unlike classical synaptotagmins, lacks Ca(2+)-binding sequences and does not bind phospholipids
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me1 = monomethylated Lys-10; H3S10ph = phosphorylated Ser-11; H3K14ac = acetylated Lys-15; H3K14me2 = dimethylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me1 = monomethylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me1 = monomethylated Lys-24; H3K27ac = acetylated Lys-28; H3K27me1/2/3 = mono-, di- and trimethylated Lys-28; H3K36ac = acetylated Lys-37; H3K36me1/2/3 = mono-, di- and trimethylated Lys-37; H3K56ac = acetylated Lys-57; H3K64ac = acetylated Lys-65; H3K79me1/2/3 = mono-, di- and trimethylated Lys-80
Was originally thought to be the ovarian carcinoma antigen CA125
Strain CNPAF512 was originally thought to originate from R.leguminosarum bv phaseoli
Topology may be in opposite way (PubMed:27335350)
The translocation involving this gene was originally published as t(X;11)(q13;23), but BRWD3 is localized to Xq21 and not to Xq13
Although this enzyme participates in the selenocysteinyl-tRNA(Sec) biosynthesis pathway in many taxa, this pathway has been shown in PubMed:30742068 to be lost in dikarya
Was originally thought to be apomucin (also known as mucin core protein; CTM-A)
Does not bind calcium as one of the calcium-binding sites is lost (Asp->Lys in position 64, which corresponds to 'Lys-49' in the current nomenclature)
Could be the product of a pseudogene. The original protein is truncated by the IS2H element which is inserted right before residue 10. The original N-terminal of this protein is not known
Has most probably no phospholipid phosphatase activity (By similarity). This is supported by the fact that the phosphatase sequence motifs as well as the His residue acting as a nucleophile in active phosphatases of the PA-phosphatase related phosphoesterase family are not conserved (By similarity)
Orthologs in other Plasmodium species contain 4 EF-hand domains instead of 3 EF-hand domains as identified for this entry, therefore it might be possible that the displayed C-terminus sequence of P.yoelii CDPK3 is incorrect
The number, localization and denomination of hydrophobic domains in the Na(+)/H(+) exchangers vary among authors
PubMed:8595899 sequence was originally thought to originate from human
Although this protein has high similarity to uridine phosphorylases, it has no detectable catalytic activity. It contains substitutions at Gly-126 and Gln-201, two conserved sites which are known to be important for uridine binding
The origin of a shorter ASP5 form with an apparent molecular weight of 55 kDa is unclear (PubMed:26576949, PubMed:26473595). One study suggests that it is a processed form of the full length protein (PubMed:26576949). However, another study suggests that it originate from a splicing event (PubMed:26473595)
Wang et al (2022) synthesized and tested activity on the short peptide 54-74. By comparison with Conotoxins SIIIA and SIIIB (AC P0DKQ2, and AC P0CE77) and according to pair of basic residues, the natural peptide may be 2 residues longer at the N-terminus (52-74), and may contain a pyrrolidone carboxylic acid at its N-terminal Gln-52
According to a report, ORAI1 has been shown to colocalize with UBQLN1 in the autophagosome as a target for autophagic degradation; ORAI1 is however not an autophagosomal protein
Juge et al. shows that SLC32A1 is a symporter of both 4-aminobutanoate or glycine or beta-alanine with Cl(-) that operates according an electrical gradient without the need for a chemical gradient (PubMed:19843525, PubMed:23919636). However Farsi et al. and Egashira et al. confirm that SLC32A1 is an antiporter that exchanges vesicular protons for cytosolic 4-aminobutanoate or glycine and exclude any coupling with chloride (By similarity)
The catalytic activity of the kinase domain is controversial
The terminology of MLL proteins in mammalia is not consistent also concerning the terminology of MLL protein-containing complexes. The decribed MLL2/MLL3 complex is commonly described as MLL3/MLL4 complex in literature
Could be the product of a pseudogene. There are 3 rpoA-like genes in this organism (found in the inverted repeat). None of them are convincing as rpoA, and it may be that the functional gene is in the nucleus
Despite its close structural homology with class I terpene cyclases, flvF lacks intact metal-binding motifs DDXX(D/E) and (N,D)D(L,I,V)X-(S,T)XXXE characteristic of all class I terpene synthases
The Rab-GAP TBC domain appears to be inactive, probably due to a lack of the essential Arg and Gln in the catalytic finger motifs
Was originally thought to originate from Chlamydia trachomatis
Was initially shown to catalyze the removal of carboxy-terminus tyrosine from alpha-tubulin (PubMed:21303978). However, later studies did not identified any detyrosinase or deglycylase activities from the carboxy-terminus of tubulin (By similarity)
Was originally thought to have detyrosinating activity from C-terminal positions on tubulin
In contrast to other members of the AGC Ser/Thr protein kinase family, lacks the AGC-kinase C-terminal domain at the C-terminus
Arg-67 is present instead of the conserved His which is expected to be an active site residue
The gene for this protein is either identical to or adjacent to that of TREX1. Some of the mRNAs that encode ATRIP also encode TREX1 in another reading frame
Lacks the conserved Cys residue necessary for ubiquitin-conjugating enzyme E2 activity
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AXS139ph = phosphorylated Ser-139
Although strongly related to the nudix NUDT16 protein, lacks the Nudix box and is therefore not related to the rest of the family. Lacks a number of residues which are necessary for hydrolase activity and does not play a role in U8 snoRNA decapping activity
The full-length coding region in cv. A3525 has been amplified by RT-PCR and sequenced, but not submitted to the EMBL/GenBank/DDBJ databases (PubMed:21478368)
PubMed:12823556 conflicts between the peptide sequence obtained by Edman degradation and that obtained from the cDNA sequence may be due to contamination of the peptide sample with hemocyanin C
Was reported by PubMed:11788770 to be an alpha-1,2-fucosidase
Was orginally thought to be a phosphatidylinositol (PI) synthase
Was reported to interact with VIM, however the paper was retracted as some results and conclusions are not reliable
Was reported to interact with RAB4 and to be induced by serotonin, however the paper was retracted as some results and conclusions are not reliable
The large subunit has no homology with other group III PA2 family members, but the small subunit does
It is not known if heme and GST are required for prostaglandin synthase activity. The protein copurifies with heme and GST when DTT is omitted during the purification procedure. The GSH-heme complex-bound enzyme has been proposed to act as a lyase and catalyze the degradation of prostaglandin E2 H2 (PGH2) to 12(S)-hydroxy-5(Z),8(E),10(E)-heptadecatrienoic acid (HHT) and malondialdehyde (MDA). According to PubMed:18198127, boiling the enzyme leads to loss of prostaglandin synthase activity, but does not eliminate the lyase activity. Besides, free heme can catalyze the formation of 12L-hydroxy-5,8,10-heptadecatrienoic acid (HHT) (PubMed:18198127). A more recent study demonstrates the GSH-dependent property of PTGES2, DTT dissociates the bound heme to produce active PGE2 synthase in vitro (By similarity). PTGES2 can only catalyzes PGE2 synthesis in the free state as an enzyme, while in vivo it forms a complex with heme and does not participate in PGE2 synthesis (By similarity). In agreement with this study, the in vivo evidence from PTGES2 deficient mice do not show that this protein is responsible for the PGE2 production under basal or pathophysiological conditions (By similarity)
Product of a dubious CDS prediction. Probable non-coding RNA
Could be the product of a pseudogene, it is missing about 320 N-terminal residues compared to orthologs
Compared to other HisH it lacks an internal segment that normally contains the Cys active site residue
It is unclear if PMVI is glycosylated as other members of the same enzyme family, i.e. PMI and PMII, are not
Seems to have a sequencing error in the C-terminal region when compared to orthologs, but the potentially correct sequence could not be inferred
Despite its name, it does not contain a PHD-type zinc finger, but contains a RING-type zinc finger. Moreover, PHD-type zinc fingers do not have any ubiquitin ligase activity
An article reported a role as negative regulator of ABA during seed germination; however, this paper was later retracted
The ligation for manganese is based on the ligation for zinc, an inhibitor, in the crystallographic structure reported in PubMed:10449417. The ligation for manganese in the active form of the enzyme may differ
Unlike other members of this family, it does not possess sterol C14 reductase activity
A truncated form of MSP9 has serine protease activity in vitro; however, it is not clear if this is physiologically relevant (By similarity). Also, the putative residues forming the catalytic triad (His-55, Asp-94, and Ser-190) are not conserved in P.vivax, P.knowlesi, and P.cynomolgi orthologs casting a doubt on the physiological relevance of the protease activity (By similarity)
It is uncertain whether Met-1 or Met-51 is the initiator
Was initially thought (Ref.1) to be a thionin
Two different genes At3g23240 and At4g17500 were assigned the same gene name ERF1
The order of the first peptide shown is unknown
The 8 variants shown here could also be shown in the 3 identical proteins (AC B1NWS4, AC P0CH46 and AC B1NWR7) encoded by the 3 different genes
The protein sequences in X55956 are all from mutants in which fusions to an internal fragment of recE have occurred
Was originally thought to be a receptor for neuropeptide Y type 3 (NPY3R) (NPY3-R). Subsequent studies indicated it does not function as receptor for neuropeptide Y
Initial characterization was derived from usage of a monoclonal antibody (A60) directed to an unknown protein called NeuN (PubMed:15605376, PubMed:1483388), but later identified as RBFOX3
Could be the product of a pseudogene. PubMed:9729295 reported that PMCHL1 mRNA may not be used as template for translation as only antisense PMCHL1 transcripts are present in brain
Strain ATCC 10014 was originally thought to originate from H.haemolyticus
Compared to other bacterial PriA, it has a very divergent helicase domain
Was originally (Ref.1) erroneously named IAA29
Represents a conventional myosin. This protein should not be confused with the unconventional myosin-2 (MYO2)
NPY has been reported to be a ligand for GPR83 (PubMed:17240481). However, a more recent study found that radiolabeled PEN binding to GPR83 is not affected by NPY concentrations below 1 mM, only very high, non-physiological concentrations causes a partial, displacement of PEN binding (By similarity)
Was originally thought to be an aspartic proteinase inhibitor (PubMed:1391774, PubMed:1515078)
The enzyme produces 15-cis-phytoene. The conversion to all-trans-phytoene is due to photoisomerisation
Was originally thought to originate from Pseudomonas denitrificans, but similarity searches show that the sequence is much closer to Sinorhizobium. The entry's taxonomy has been changed
Although it belongs to the glycosyl hydrolase 31 family, it lacks one active site residue, thus suggesting it may lack some enzyme activity
Although found extracellularly, no signal sequence is present. An alternative secretory pathway may be used
Although this protein contains the conserved Asp-246 that functions as an active site, this protein does not have proteolytic activity, and may therefore be catalytically inactive
Although it belongs to the peptidase M24 family, it does not contain metal cofactors and lacks aminopeptidase activity
It was suggested that CAHS proteins were intrinsically unstructured and show heat-dependent glass transition, which contributes to the vitrification of cells, and this further leads to desiccation tolerance (PubMed:28306513). However, more recent studies led to the conclusion that there was no evidence supporting glass transition of CAHS proteins to be contributing to the glass transition of the whole tardigrade (PubMed:33545053)
PubMed:17425806 show that the phosphorylation state does not affect protein stability, whereas PubMed:17008917 show that phosphorylation may play a role in caspase-dependent cleavage
Although originally named XLX for its homology to mammalian XIAP, a more similar Xenopus XIAP homolog (xiap) has since been identified
Two proteins (Vur-PL2A and Vur-PL2B) with different masses and detected in two different fractions have been isolated from the venom. They both seem to have the same sequence. Vur-PL2B is possibly a more stable conformer than Vur-PL2A. Since data on both proteins are very similar, information reported here mainly concerns Vur-PL2B
The high-resolution electron microscopy structures indicate that the N-terminus is cytoplasmic, followed by two short helices that dip into the membrane, but do not cross it (PubMed:26280335). In contrast, results based on mutagenesis to create N-glycosylation sites indicate that the N-terminus is lumenal (PubMed:12639958, PubMed:30598546, PubMed:30630874). Both studies indicate that the C-terminus is lumenal (PubMed:12639958, PubMed:26280335)
In C.vinosum two similar set of genes code for RuBisCO large and small chains: the RbcL-RbcS and the RbcA-RbcB pair (this entry). Under standard photoautotrophic culture conditions only the latter pair seems active, the former being probably cryptic
The gene for this protein is either identical to or adjacent to that of MEF2B. Some mRNAs that encode this protein also include MEF2B
The second enzyme involved in phosphonate degradation (PhnX, EC 3.11.1.1) is not found in this organism. The function of this enzyme is therefore uncertain
It is uncertain whether Met-1 or Met-18 is the initiator
While it is structurally defined as a knottin it lacks the conserved Cys residue in position 81
Was initially thought to mediate palmitoylation of Wnt proteins. It was later shown that instead it acts as a serine O-palmitoleoyltransferase that mediates the attachment of palmitoleate, a 16-carbon monounsaturated fatty acid (C16:1(9Z)), to Wnt proteins (PubMed:17141155, PubMed:24798332)
Product of a dubious gene prediction. The corresponding gene is on a region of chromosome 21 that is known to be an artifactual duplication of another chromosome 21 region in the GRCh38 assembly. This entry may represent an artifactual copy of AC P0DPI2
Despite sequence similarity to MED25, to date this protein has not been identified as a component of the Mediator complex
Unlike mouse protein, not able to transport adenine nucleotide in acidic condition
Product of a dubious CDS prediction. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay
The active site cysteine and glutamate residues are not conserved in this protein. Its activity is therefore unsure
Represents a conventional myosin. This protein should not be confused with the unconventional myosin-1 (MYO1)
The original start site is 14 aa downstream of the start site shown here. Experiments from PubMed:17576516 were carried out with the original sequence
The orthologs in A.thaliana catalyze the first reaction of the Smirnoff-Wheeler pathway, the major route to ascorbate biosynthesis in plants
Although strongly related to the NB-LRR family, it is shorter and lacks the LRR repeats that are present in other proteins of the family
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-35; H2BK34ac = acetylated Lys-36; H2BK143ub1 = monoubiquitinated Lys-143
Lacks the conserved His at position 67, which is expected to be an active site residue
Was originally thought to be the ortholog of human X11 (APBA1)
Was originally (Ref.1) thought to be two genes, ydcI and ydcJ
POLR1D isoform 2 lacks an RNA polymerase domain and therefore cannot have DNA-dependent RNA polymerase function
According to a study, preferentially binds to long telomeres that have a low concentration of shelterin complex (PubMed:28082411). According to another report, binds telomeres regardless of their length (PubMed:28500257)
Was originally assigned as a member of the E3 ubiquitin-protein ligase ATL subfamily
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK6su = sumoylated Lys-7; H2BK7ac = acetylated Lys-8; H2BK7su = sumoylated Lys-8; H2BS10ph = phosphorylated Ser-11; H2BK11ac = acetylated Lys-12; H2BK16ac = acetylated Lys-17; H2BK16su = sumoylated Lys-17; H2BK17su = sumoylated Lys-18; H2BK123ub1 = monoubiquitinated Lys-123
Defects in PLEKHG4 were initially thought (PubMed:16001362) to be the cause of spinocerebellar ataxia 16q22-linked. However, it was later shown (PubMed:17611710) that it is not the case. Spinocerebellar ataxia 16q22-linked, also known as spinocerebellar ataxia type 31 (SCA31), is caused by defects in BEAN gene
The truncated forms found may result from N-terminal proteolysis
The mutagenesis studies described in PubMed:8756487 and PubMed:9169449 are made with the sequence from PubMed:2383565 (see the sequence conflict in position 83-85)
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-4; H2AK7ac = acetylated Lys-6; H2AK126su = sumoylated Lys-125; H2AS128ph = phosphorylated Ser-127
Lacks the conserved residues within the catalytic triad, probably resulting in a loss of proteolytic activity
A report observed N-glycosylation at Asn-58 (PubMed:19139490). However, as the protein is not predicted to localize in an extracellular compartment of the cell, additional evidence is required to confirm this result
In mouse, Slco6c1 is an additional auxiliary subunit of the CatSper complex. It is unclear if the related SLCO6A1 protein performs the same role in non-rodent species
Some sequenced Tc1 elements display an extra base T that would give rise to another start point for Tc1 transposase. This could result in a protein of 335 AA instead of 273 AA (displayed)
RHOF2 and RHOF2B are arranged in a head-to-head orientation and share high sequence similarity (>99%). They cannot easily be distinguished and are usually analyzed as a single gene
Thr-195 is present instead of the conserved Ser which is expected to be an active site residue. It is therefore unsure if this protein has kept its catalytic activity
Was initially thought to function as a nucleotidyltransferase (PubMed:15701005). But it was later shown that it is a deacetylase (PubMed:17226887)
Was originally thought to be a pseudogene before the proof of transcription of the gene
Not regulated by serum or glucocorticoids
It is uncertain whether Met-1 or Met-89 is the initiator
SAA4 used to be called SAA5. What was SAA4 is a pseudogene which is now called SAA-ps
It is uncertain whether Met-1 or Met-30 is the initiator
Opinions are divided on whether Anemonia viridis (Forsskal, 1775) and Anemonia sulcata (Pennant, 1777) are separate species
Was initially thought to be a protease inhibitor
Membrane topology is controversial (PubMed:11601977). Membrane topology structure with endoplasmic reticulum lumen orientation of the catalytic domains while the C-terminus is in the cytosol have been suggested by one study (By similarity). Others investigators have argued for a reverse orientation, with a membrane-embedded N-terminal domain but no C-terminal transmembrane segment, and a cytosolic orientation of the catalytic domain (PubMed:11601977). These contracductoty results are probably because of differences in the assay systems
Although it belongs to the protein phosphatase 2C family, it lacks some of the conserved residues that bind manganese, suggesting it has no phosphatase activity
In contrast to the orthologous protein found in other species, the C-terminal part differs and lacks the fourth beta/gamma crystallin 'Greek key' domain. Moreover, its non-specific tissue specificity suggests that it may have lost its function (PubMed:15853812)
According to PubMed:14628042 also shows serine/threonine protein phosphatase activity
Lacks the two conserved aspartate and the histidine residues in position 106, 177 and 179 respectively, that are involved in the active site of the protein in orthologs; they are replaced by a tyrosine, a valine and an asparagine residue respectively
Although the active site residues Cys and His are conserved, appears to lack catalytic activity in vitro. This is probably due to the active site pentapeptide VCCRG being highly divergent from the canonical active site pentapeptide QAC[RQG]G present in catalytically active caspases
Several phenotypes were reported for a triple-alanine mutant. However this data was retracted as several constructs contained a C-terminal deletion instead of the reported triple-alanine mutation. Following strain regeneration, although many phenotypes were not reproducible, the central observations of the publication were confirmed
Lacks most of the conserved residues that are essential for binding the metal cofactor and hence for dihydropyrimidinase activity. Its enzyme activity is therefore unsure
The strain (Berkeley) sequenced by the collaborative genome project contains a 3' deletion and is considered a pseudogene
Product of a dubious CDS prediction. Overlap the TYMS locus in the opposite strand
According to PubMed:16861741, disruption of the gene causes increased prevalence of placental thrombosis, reduced litter size and increased pup mortality. No such effect was observed by PubMed:18755794. One possible explanation lies in the fact that PubMed:16861741 observed a remarkable 100% survival of control pups and 16% mortality for mutant pups, while PubMed:18755794 observed 16% mortality for both wild-type and mutant pups. According to PubMed:18755794, the construct used in PubMed:16861741 may lead to expression of a truncated transcript that might have deleterious effects
Although strongly related to the peptide:N-glycanase enzyme, it lacks the conserved active site Cys in position 208, which is replaced by a Ala residue suggesting that it has no activity
Zhu and Gao submitted another 'Neurotoxin MeuNaTx-6' in 2009, whose sequence highly differs from the one presented here (AC P86406)
In spite of its original name 'Pancreatic elastase 1', CELA1 is not detected in the pancreas. Elastase activity described in the pancreas may be in fact due to CELA2A (PubMed:10620133)
Has been shown to be a pseudogene in cv. Columbia (AC P0DH87) due to a frameshift mutation that introduces a premature stop codon in this strain. The sequence shown is from strains cv. Pog-0 and cv. Wei-1
Could be the product of a pseudogene. Although strongly related to DNA helicases, it lacks the helicase ATP-binding domains, suggesting that it has no helicase activity
In contrast to other members of the family, lacks the regions that come into close contact with the mRNA in the ribosomal A-site and determine the STOP codon specificity, suggesting a loss of codon specificity for translation release factor activity
YBP1 encoded by the widely used laboratory strain W303-1a is only partially functional, probably due to four amino acid substitutions
The BCR(KLHL3) complex was initially thought to act by mediating ubiquitination of SLC12A3/NCC (PubMed:22406640). However, it was later shown that effects on SLC12A3/NCC are indirect and caused by impaired ubiquitination of WNK4 (PubMed:23387299)
Although the bacteria accumulates coproporphyrinogen-III when the gene is disrupted, no oxygen-independent coproporphyrinogen-III oxidase activity or complementation have been shown. The exact role of this protein is unknown
In this second copy of HPRK/P in O.iheyensis, Ala-202 and Glu-243 are present instead of the conserved Glu and Arg which are respectively expected to be part of the active site
Was originally identified as a 1,4-beta-D-xylan xylanohydrolase (PubMed:12664153). However, further sequence comparisons and enzymatic studies showed that xynA was principally an 1,4-beta-D-glucan cellobiohydrolase (PubMed:22776993)
Could be the product of a pseudogene, it is missing the C-terminus compared to orthologs. The sequence is interrupted by an IS5Y insertion sequence which causes the frameshift and loss of C-terminus
Could be the product of a pseudogene unlikely to encode a functional protein. This is a truncated version of L-serine dehydratase. Strain S288c has a stop codon in position 128, which disrupts the gene coding for this protein and produces two ORFs YIL167W and YIL168W. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. A contiguous sequence for L-serine dehydratase can be found in other strain backgrounds (AC P0CF23)
Lacks the transmembrane domain, which is one of the conserved feature of the family
Has been reported to act as a receptor for prosaposin (PSAP). However, it has also been shown that prosaposin does not increase activity. It has been suggested that GPR37L1 is a constitutively active receptor
Was originally reported to have a protein kinase activity and to phosphorylate on Ser and Thr residues the Goodpasture autoantigen (in vitro)
The modification form of Leu-142 is subject of controversy and could be the artifactual result of sample handling
Was reported to promote CD8+ T cell immunity through effects on mitochondrial respiration (PubMed:25883318). However, the corresponding article has been retracted (PubMed:27980177)
Seems to have a defective ATP-binding region
The reference genome assembly, GRCh37, describes the non-functional copy of that gene, frameshifted at position 22, that is more frequent in human populations
Watson et al. identified this gene on chromosome 14. However, it is not currently present on the reference genome assembly (GRCh38/hg38)
In contrast to other phospholipases, it lacks the typical Asp active site (Asp->Glu in position 93)
Functional localization of the protein to the endoplasmic reticulum (ER) has been disputed. ER-localization of the enzyme may be difficult to detect in nutrient-rich or respiratory-demanding growth conditions
Could be the product of a pseudogene. Although strongly related to DNA helicases, it lacks the helicase domains, suggesting that it has no helicase activity
Was originally thought to be a GPI-anchored membrane protein
The sequence shown is that of IMGT allele TRBJ2-6*01
In the PI-PLC X-box Asn-459 is present instead of the conserved His which is one of the active site residues. It is therefore expected that this protein lacks catalytic activity
Lacks lipoate-protein ligase activity, probably due the loss of the lysine residue involved in the formation of the lipoyl-AMP reaction intermediate (PubMed:25116855). However, in some studies appears to be able to partially rescue ligase activity in E.coli lacking ligases lplA and lipB (PubMed:17244193, PubMed:18069893)
Was initially thought to be a thionin
Was initially thought to be a glyoxalase II isozyme (PubMed:9349270), but has been shown to lack glyoxalase activity (PubMed:22786886)
Although it belongs to the XPG/RAD2 endonuclease family, only one of the seven Asp residues involved in Mg(2+) binding is conserved suggesting that it has no nuclease activity
This protein, although sequenced from the genome of strain 74-OR23-1A, has only limited sequence identity to the corresponding protein produced by the locus NCU07340 determined in the complete genome sequence of Neurospora crassa 74-OR23-1A, due to extensive nucleotide sequence discrepancies mostly in the N-terminus
The molecular identity of the sigma-2 receptor has been unclear for a long time. It is now identified as TMEM97 (PubMed:28559337). Previously identified as PGRMC1 (AC O00264) (PubMed:22292588, PubMed:28007569)
This peptide has been shown to be biologically active but is the product of a mitochondrial gene. Usage of the mitochondrial genetic code yields tandem start and stop codons so translation must occur in the cytoplasm. The mechanisms allowing the production and secretion of the peptide remain unclear
Described as a member of the Mediator complex and a probable MED28 ortholog but shows very low similarity to known MED28 proteins and lacks the Pfam Med28 signature found in known MED28 proteins
PubMed:12384590 (AE005674) sequence differs from that shown due to the presence of an insertion sequence. In strain 301, this gene is probably a pseudogene
CarB is split into two genes in M.kandleri (MK0911 and MK1666)
Although it belongs to the alpha-carbonic anhydrase family, Arg-116 is present instead of the conserved His which is a zinc-binding residue. It is therefore expected that this protein lacks carbonic anhydrase activity
All S.morsitans family members described in 'Undeheim et al., 2014' have not been imported into UniProtKB. Please, refer to this paper to access them
Product of a dubious CDS prediction. May be a non-coding RNA. No experimental confirmation available
TraG is not responsible for the N-terminal acetylation of F pilin as stated by some authors
Lacks 1 of the 4 disulfide bonds, which are conserved features of the family
The selectivity for particular phosphatidylinositol lipids is under debate. According to one report (PubMed:19553671), the rat protein binds exclusively to phosphatidylinositol 4,5-bisphosphate, while the human protein has been reported (PubMed:15561769) to bind to phosphatidylinositol 3,4-bisphosphate and also to phosphatidylinositol 3-phosphate
One study reported a nucleation-promoting factor (NPF) activity towards the Arp2/3 complex using partially purified samples of the WASH complex (PubMed:19922875). In another study, the in vitro reconstituted and purified recombinant WASH core complex, consisting of WASHC3, WASHC4, WASHC5, WASHC1 and the N-terminal residues 1-356 of WASHC2, did not show activity toward Arp2/3 complex (PubMed:20498093)
Does not possess catalytic activity due to replacement of highly conserved residues in tyrosine-protein phosphatase domain
Shows no or low enzymatic activity even tough it conserves the catalytic residues. This may be due to the distorsion of the calcium binding loop
Position 67 and 84 are wrongly translated from the nucleotide sequence, it is why a feature 'unsure' is indicated. AGC (position 67) code for a Ser but a Val is indicated instead, whereas CTA (position 84) code for a Leu but a Iso is indicated instead
According to some authors, isoform 3 (truncated at the N-terminus) is not a receptor for the CD200/OX2 cell surface glycoprotein
This is a truncated version of aquaporin-2. A natural 11 bp deletion in position 109 leads to a frameshift, which disrupts the gene coding for this protein and produces two ORFs SCY_3532 and SCY_3531. A contiguous sequence for aquaporin-2 can be found in strain Sigma 1278B (AC P0CD89)
Lys-Phe-Leu-Lys residues at positions 15-18 are predicted by comparison with orthologs and according to the data of amino acid composition. Pyroglutamate residue at position 1 has been predicted by comparison with orthologs and because the pyroglutamate aminopeptidase was used to allow sequencing. It is noteworthy that the theoritical mass of the peptide does not correspond to the measured mass of 5241 Da
It is uncertain whether Met-1 or Met-5 is the initiator
Has been shown to be inactive in cv. Ler-2 (AC D9UBI3) and cv. Bl-1, cv. C24 and cv. Ct-1 (AC D9UBG0) due to naturally occurring sequence variation in these strains. The sequence shown is from strain cv. Columbia
The human genome was initially thought to contain 2 genes for UTP--glucose-1-phosphate uridylyltransferase: UGP1 and UGP2 (PubMed:8354390, PubMed:8631325). However, the sequence defined as UGP1 (PubMed:8354390) probably does not exist and corresponds to UGP2
The equivalent of tuf1 in the CIRAD genome (AC Q5FCW3) is annotated as a frameshift version requiring 2 frameshifts to produce full-length protein
It is uncertain whether Met-1 or Met-53 is the initiator
Two isoforms have been reported, however the molecular basis and sequence differences have not been determined. Both isoforms interact with components of the ERI/DICER complex and both are detected at all larval and adult stages, but only pir-1b is expressed in embryos (PubMed:33378643). Furthermore, pir-1a expression depends on drh-3 activity and pir-1b expression depends on dcr-1 activity (PubMed:33378643)
Despite the presence of a stop codon in position 243 in the fliF gene and in position 127 in the flhA gene, it has been shown that B.melitensis is able to express genes corresponding to the M ring, the hook and the filament of the flagellar apparatus in the early log phase of growth in 2YT broth. Under these conditions, a polar and sheathed flagellar structure is visible by transmission electron microscopy
The synthetic peptide described in PubMed:26948522 is one residue shorter than the mature sequence shown in this entry (44-60) (the Arg-43 is removed) and the Cys-60 is amidated
The sequence misses the N-terminal part. The correct gene model with the complete protein sequence could not be recovered from the submitted genomic sequence
Has been shown to act as a sodium/bicarbonate cotransporter in exchange for intracellular chloride (PubMed:10993873, PubMed:20566632). Has also been shown to act as a sodium/biocarbonate cotransporter which is not responsible for net efflux of chloride, with the observed chloride efflux being due to chloride self-exchange (By similarity)
Was originally thought to suppress the temperature-sensitive growth phenotype of fabA6(Ts) mutants
Was initially identified as a bi-functional protein that has an N-terminal domain with O-GlcNAcase activity and a C-terminal domain that has histone acetyltransferase activity (PubMed:15485860). The protein has apparent histone acetyltransferase activity when expressed in mammalian cells, but not when expressed in bacterial cells (PubMed:15485860), suggesting that the histone acetyltransferase activity might be due to the presence of a contaminant. Characterization of the human ortholog shows that this protein does not bind acetyl-CoA and therefore cannot have acetyltransferase activity
It is uncertain whether Met-1 or Met-14 is the initiator
Although this was cloned from strain NCIB 8253 in 1998 it was not detected as part of the complete proteome when it was sequenced in 2005
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-5; H2AK7ac = acetylated Lys-7; H2AS128ph = phosphorylated Ser-129
The unknown residue 'x' in the transmembrane isoform is probably a proline residue by similarity to mouse and rat sequences
Although related to histone H2AB1 in human (AC P0C5Y9), it is unclear whether human and mouse H2AB1 proteins are involved in similar processes. In mouse, histone H2AB1 is specifically required to direct the transformation of dissociating nucleosomes to protamine in male germ cells during spermatogenesis (PubMed:28366643). It is however unclear whether human protein, which participates in mRNA processing and is associated with active transcription, is also involved in nucleosomes to protamine replacement
Lacks a Cys at position 176 preventing the formation of a homodimer
It is uncertain whether Met-1 or Met-9 is the initiator. Orthologous sequences (mouse and chicken) have shorter N-terminus
Ala-101 is present instead of the conserved Ser which is expected to be an active site residue
Could be the product of a pseudogene. Corresponds to the C-terminal part of other plant accD proteins
The Dictyosteliida are known to produce a glycosylsphingolipidinositol anchor (GPI-like-anchor). It has not been established whether Dictyosteliida make a glycosylphosphatidylinositol anchor (GPI-anchor) also, and whether their GPI-like-anchor modifications can be interconverted with GPI-anchor modifications in a resculpting process. It has not been established that the GPI-like-anchor modification in Dictyosteliida utilizes the same sequence motif
Different sequence motifs predict both the N-glycosylation modification and the GPI- or GPI-like anchor modification for Asn-118. While it is chemically possible for both modifications to occur, it is not known whether it is enzymatically possible
Functional assignment as methanogen HACN has been made based on the presence of the YLRT motif involved in substrate specificity as discussed in PubMed:20170198
Has been originally mistaken for cellobiose dehydrogenase (CDH) due to low activity with cellobiose
The article has been retracted, because it has become clear that the thioredoxin that interacts in yeast 2-hybrid with the Cf-9 C-terminus is in fact localized in the chloroplast, rendering a role in Cf-9 signaling unlikely. All the authors agree that this paper should be withdrawn from the scientific literature
It is uncertain whether Met-1 or Met-8 is the initiator
It is uncertain whether Met-1 or Met-65 is the initiator
The C-terminal carbohydrate-binding module (CBM) extension found in some acetylxylan esterases from other species is absent
Was originally thought to be a translation initiation factor but further analysis (PubMed:19424157, PubMed:19338753) clearly suggests that it is involved in translation elongation and not translation initiation
It is uncertain whether Met-1 or Met-6 is the initiator
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK6su = sumoylated Lys-7; H2BK7ac = acetylated Lys-8; H2BK7su = sumoylated Lys-8; H2BS10ph = phosphorylated Ser-11; H2BK11ac = acetylated Lys-12; H2BK16ac = acetylated Lys-17; H2BK16su = sumoylated Lys-17; H2BK17su = sumoylated Lys-18; H2BK123ub1 = monoubiquitinated Lys-124
Was named ERF3 but it corresponds to Arabidopsis ERF4
For expression reasons, the sequence was engineered with a Gly residue instead of a Pro at position 79
Rat 3-beta-HSD type II may possess only one transmembrane domain
Several genes are coding for this toxin for which the structure by NMR has been determined. The cross-references to PDB and additional information can be found in entry AC D2Y1X9
Was originally thought to be a mitochondrial ribosomal protein
Was originally called CpsC
Medium-wave-sensitive opsin genes vary in number among individuals and, together with a single red pigment gene, reside in a head-to-tail tandem array within the X chromosome. In the GRCh38 reference genome assembly, there are 3 genes in tandem coding for identical proteins AC P04001, AC P0DN77 and P0DN78
This peptide is cyclic. The peptide order is assigned by homology with the gene sequence for alpha-amanitin from Amanita bisporigera
In peptide sequencing work prior to 1968, the residue shown in the first position was reported as a beta-methylleucine derivative that could arise by either beta-methylation of leucine or gamma-methylation of isoleucine. The correct structure has been determined to be derived from isoleucine without methylation
According to PubMed:20530728, the fimB gene contains a premature stop codon that prevents expression of this protein in strain ATCC 33277 and strain ATCC BAA-1703 / FDC 381. This is the cause for the production of abnormally long fimbriae by these strains; in vitro mutagenesis that restores the full open reading frame leads to the production of shorter fimbriae in strain ATCC 33277 (PubMed:20530728). In contrast, there is no premature stop codon in the sequence reported by PubMed:17081195
The first GAGE nomenclature was based on identified mRNA sequences, but the high identity of the GAGE members made impossible to separate products of paralogous genes from polymorph products. PubMed:18179644 presented a new GAGE gene nomenclature based on the identified genes and their products
Reported to have transcriptional repression activity in vitro. However, it is unclear whether this protein has any function in transcription in vivo
Was originally thought to have three internal disulfide bonds
Although related to the cap-specific mRNA (nucleoside-2'-O-)-methyltransferase, lacks the conserved Lys active site in position 367, which is replaced by an Asn residue, suggesting it has no methyltransferase activity
Lacks the conserved Asp residue in position 50 usually required for phosphorylation
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 1422 in the dsPTPase catalytic loop and does not have phosphatase activity (By similarity). The pocket is however sufficiently preserved to bind phosphorylated substrates, and maybe protect them from phosphatases
Has been shown to be active in cv. Columbia (AC Q9SE37) due to naturally occurring sequence variation in this strain. The sequence shown is from strain cv. Ler-2
It is uncertain whether Met-1 or Met-37 is the initiator
Despite its similarity with the UDP-N-acetylglucosamine 2-epimerase enzymes, it does not display UDP-GlcNAc 2-epimerase activity
SsrA has yet not been found in R.prowazekii, so the function of this protein is not obvious
Was initially thought (PubMed:1995329, PubMed:7705336) to be a protease inhibitor
A stretch of the chloroplast genome is duplicated within chromosome 2 resulting in the duplication of the gene. The expression of this duplicated gene has not been demonstrated
Was originally (Ref.4) thought to originate from mouse
Was originally thought to be a glucan synthase
In contrast to other A.fumigatus strains, strain ATCC MYA-4609 does not produce indole alkaloids such as fumitremorgins and verruculogen. While the biosynthetic pathway is complete, a variation in the O-methyltransferase FtmD (AC Q4WAW6) abolishes production of the tryprostatin A intermediate (PubMed:23649274)
The synthetic peptide described in PubMed:26948522 shows the toxin without C-terminal amidation
It is uncertain whether Met-1 or Met-7 is the initiator
Lacks the conserved Glu residue in position 488 essential for carbopeptidase activity. The mature form lacks catalytic activity towards synthetic peptide substrates
In psbV2 it is not clear which residue serves as the second axial ligand for the heme group
Most of the residues in the galectin domain that have been shown to be critical for carbohydrate-binding in other galectins are not conserved
Thought to palmitoylate MPP1 (PubMed:22496366). This work was later retracted due to image manipulation
May be duplicated on chromosome 8, within an intron of the ERLIN2 gene
The active site Cys-600 is replaced by a Asp residue suggesting that egg-5 may lack catalytic activity. Despite the lack of catalytic activity, egg-5 may retain the capacity to bind to phosphorylated substrates
Was originally thought to have murein hydrolase activity
Unlike many members of this family does not have peptidase activity
The sequence described initially (PubMed:9256446) corresponds to a mutant, frameshifted form named PEG-3 that frequently arises during cell transformation and does not seem to exist in normal cells. PEG-3 functions as a dominant negative of GADD34-mediated pro-apoptotic pathway and promotes cancer aggressiveness
AK6 and TAF9 were initially considered as products of the same gene since they share two exons. However, they are translated from different initiation codons and reading frames and encode unrelated proteins. This arrangement is conserved in some mammalian species
An article reported the role of autophosphorylation of Tyr-610 in brassinosteroid signaling; however, this paper was later retracted. A second article from the same group reported the role of phosphorylation; however, this paper was also retracted
It is not known if heme and GST are required for prostaglandin synthase activity. The protein copurifies with heme and GST when DTT is omitted during the purification procedure. The GSH-heme complex-bound enzyme has been proposed to act as a lyase and catalyze the degradation of prostaglandin E2 H2 (PGH2) to 12(S)-hydroxy-5(Z),8(E),10(E)-heptadecatrienoic acid (HHT) and malondialdehyde (MDA). Boiling the enzyme leads to loss of prostaglandin synthase activity, but does not eliminate the lyase activity. Besides, free heme can catalyze the formation of 12L-hydroxy-5,8,10-heptadecatrienoic acid (HHT) (By similarity). A more recent study demonstrates the GSH-dependent property of PTGES2, DTT dissociates the bound heme to produce active PGE2 synthase in vitro (By similarity). PTGES2 can only catalyzes PGE2 synthesis in the free state as an enzyme, while in vivo it forms a complex with heme and does not participate in PGE2 synthesis (By similarity). In agreement with this study, the in vivo evidence from PTGES2 deficient mice do not show that this protein is responsible for the PGE2 production under basal or pathophysiological conditions (By similarity)
Lacks the lipidation signal found in other family members, suggesting it may not be exported to the cell surface, and may not be part of the fimbriae
Was originally thought to be a transcription factor that may bind Jun homologs such as GCN4 and YAP-1, and which may inhibit DNA binding and transactivation by Jun homologs
Chambrey et al. shows that the transport mechanism differs in renal cells and suggests that SLC4A9 is a Na(+)/HCO3(-) cotransporter in mouse kidney beta-intercalated cells (PubMed:23610411). However the stoichiometry is not defined and the role of chloride ions is not clear
Despite the fact that it belongs to the cyclophilin-type PPIase family, a report has shown that it has probably no peptidyl-prolyl cis-trans isomerase activity
Although related to peptidase S1 family, lacks the conserved active Ser residue in position 665 which is replaced by a Thr, suggesting that it has no protease activity
Was initially thought to constitute the naringenin 7-O-methyltransferase (NOMT), a methyltransferase involved in the biosynthesis of the sakuranetin, an inducible defense mechanism of O.sativa against pathogen attack (PubMed:10814825). However, it was later shown that it is not the case (PubMed:22493492)
The phosphorylation site Tyr-195 is located in a predicted transmembrane region
Cellular localization of OCT1 in the intestine and the kidney remains to be finally defined. While most authors have deduced a localization at the basolateral side of enterocytes consistent with a physiological role in organic anions uptake from the blood flow and intestinal excretion (By similarity), other studies demonstrated an apical localization (By similarity), supporting a function in intestinal absorption of organic anions and drugs (By similarity). Similarly, contradictory findings have shown a localization to the basolateral side (PubMed:7990927, PubMed:9808712, PubMed:10997918, PubMed:11083459) or to the apical side (By similarity) of proximal tubules (PubMed:7990927, PubMed:9808712, PubMed:10997918, PubMed:11083459) (By similarity). Affinity and capacity of the transporter for endogenous substrates vary among orthologs (By similarity)
Was originally thought to inhibit the transcriptional activity of nuclear factor NF-kappa-B
Lacks the conserved cytochrome b5 heme-binding domain present in other sulfite oxidases
His-82, rather than His-78 in the same tryptic peptide, was identified in PubMed:7306504 as the probable site of phosphorylation. This misidentification was corrected in later work and confirmed in structural work on the enzyme from Lactococcus lactis
Despite its homology to the anaerobic sulfatase-maturating enzymes, it is not involved in Cys-type sulfatase maturation in vivo
The existence of two isoforms has been reported, and could explain the differences in sequence and kinetic parameters
Although highly similar to the deubiquitinase OTULIN, lacks the conserved active site Cys at position 136 which is replaced by an Asp residue, and does not show deubiquitinase activity
Lacks the conserved Glu residue in position 512 essential for carbopeptidase activity. The mature form lacks catalytic activity towards synthetic peptide substrates
Has been described as heme-binding protein in mouse, but His-42, a residue essential for heme binding in mouse, is not conserved in all orthologs, or in the heme-binding family member HEBP1
Has no glucosyltransferase activity
Was originally thought to be a peptidyl-prolyl isomerase (PPIase). It was shown later that even if PpiD shows sequence similarity to PPIases, it is in fact devoid of PPIase activity (PubMed:19866485)
This is a truncated version of GDP-mannose transporter 2. This strain has a stop codon in position 73, which disrupts the gene coding for this protein and produces two ORFs. A contiguous sequence for GDP-mannose transporter 2 can be found in strain Lalvin EC1118 (AC C8Z742)
An ORF (C19orf029 OS) has been described in the opposite strand of the C-terminus of this gene
Lacks the Tyr (here Asp-226), a conserved feature of the aromatic cage required for the interaction with histone H3K4me3/2
Encoded in an intron of the TRPC5 gene (opposite strand). May be a non-coding RNA
Could be the product of a pseudogene. Encoded by an intronless gene, it lacks the basic helix-loop-helix (bHLH) domain found in ID2
Was initially thought to mediate AMPylation of HSPA5/BiP at 'Ser-365' and 'Thr-366' in vitro, leading to activate HSPA5/BiP (PubMed:25601083). However, it was later shown that it mediates AMPylation of HSPA5/BiP at 'Thr-518', leading to inactivate HSPA5/BiP
Initially, this protein was identified as a carnitine/acylcarnitine transporter (By similarity). Later, a study conducted by Palmieri and coworkers demonstrated that SLC25A29 is mainly involved in the translocation of basic amino acids (By similarity)
Represents a conventional myosin. This protein should not be confused with the unconventional myosin-7 (MYO7)
Lacks the conserved His residue in position 66 and the conserved Ser residue in position 205 essential for protease activity
Postulated to act as a 3-hydroxybutyrate dehydrogenase, however its contribution to ketone body formation appears to be physiologically irrelevant since it has very low affinity for the substrate
The correspondence between the sequence (indicated in PubMed:7811255) and the function (from PubMed:11237764) has not been clearly demonstrated
PubMed:11080288 describes GST23 and GST36 as two different members of the GST family but they seem to be allelic variants of the same gene
There is a disagreement about sodium-independent transport of cationic amino acids, such as L-arginine and L-lysine (By similarity). While Hatanaka et al. shown that SLC38A4 may mediate sodium-independent transport of cationic amino acids, such as L-arginine and L-lysine (By similarity). Recent studies by Fairweather et al., using quantitative LC-MS analysis, shown any transport activity of cationic amino acids, such as L-arginine and L-lysine (By similarity)
A paper describing ATG4B tissue expression has been retracted, due to concerns of image duplication in some of the figures
Had previously been shown to interact with PELP1. However this paper was retracted as cell-based data was viewed as unreliable
Lacks 6-phosphogluconolactonase activity
The catalytic domain of GDPD2 is oriented extracellularly; Glycerophosphoinositol is hydrolyzed in the medium of cells overexpressing Gdpd2, whereas intracellular levels of glycerophosphoinositol is not affected
Leu-10 is present instead of the conserved Cys which is expected to be the active site residue of peptidase C39. Thus this protein is presumed to be without peptidase activity
Asn-18 is present instead of the conserved His which is expected to be zinc-binding residue. There is therefore some uncertainty concerning the enzymatic activity of this protein
Bioinformatics prediction programs detect only 8 instead of 10 transmembrane regions
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2A.ZK3ac = acetylated Lys-4; H2A.ZK8ac = acetylated Lys-9; H2A.ZK10ac = acetylated Lys-11; H2A.ZK14ac = acetylated Lys-15
Cys-97 is present instead of the conserved Lys which is expected to be an active site residue
An expected heme iron ligand His residue was not found at position 89 in this sequence
Lacks some conserved transmembrane domains, which are one of the features of the ABC conjugate transporter subfamily
This gene should not be confused with EIF2A, with which it shares the alias EIF2A. Although both of these proteins function in binding initiator tRNA to the 40S ribosomal subunit, the eIF2 complex requires GTP, whereas the EIF2A protein does so in a codon-dependent manner
Although related to peptidase S1 family, lacks the conserved active Ser residue in position 339 which is replaced by a Thr, suggesting that it has no protease activity
The two loci are in opposite orientation
Contains a predicted homeobox domain which is degenerated and lacks residues that are important for DNA-binding. The protein localizes in the endoplasmic reticulum and not in the nucleus, which also argues against homeobox function (PubMed:18165233)
Some prediction bioinformatics tools predict the presence of a homeobox domain (By similarity). However, the domain is degenerate and residues that are important for DNA-binding are absent (By similarity). Moreover, the protein localizes in the endoplasmic reticulum and not in the nucleus, strongly suggesting that it does not constitute a canonical homeobox domain (PubMed:18165233)
The TRIM21-mediated ubiquitinated residue is not conserved in mice, therefore it remains unclear whether the physiological role of NMI ubiquitination is preserved throughout mammals
According to PubMed:19119139, it acts as a regulator of DNA replication. According to PubMed:19854130, this effect is indirect and it rather acts as a general regulator of DNA metabolism
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-27; H2BK143ub1 = monoubiquitinated Lys-135
The gene Tgtp1 belongs to a large family of eutherian IFNG-inducible GTPases, called immunity-related p47 GTPases, which comprises a variable amount of paralogs depending upon the species studied. In C57BL/6J mice, there is over 20 genes, whereas humans have only one ortholog. Tgtp2 closest paralog is Tgtp1. Both genes encode identical proteins. At the nucleotide sequence level, their CDSs differ at only 4 positions. Consequently it is almost impossible to assign unambiguously to one gene or the other experimental data published in the literature
The C-terminus of Mocs1a was previously believed to be thiocarboxylated, but it is now known not to be the case
Was originally thought to be related to urease function
Controversial data exists concerning the repressor activity of isoform 3. A study showed that isoform 3 exhibits weak repressor activity of a NRSE motif-containing reporter construct (PubMed:11779185). Another report, however, does not observe any isoform 3 transcriptional repressor activity of a NRSE motif-containing reporter construct (PubMed:11741002). Controversial data also exists regarding the function of isoform 3 on the negative regulation of isoform 1. It was shown that isoform 3 negatively regulates the repressor activity of isoform 1 by binding to isoform 1, thereby preventing its binding to NRSE and leading to derepression of target genes (PubMed:11779185). Another study, however, did not observe any inhibitory activity of isoform 3 on the isoform 1 transcriptional repressor activity (PubMed:11741002)
Was originally (Ref.1) thought to be a lin-10 homolog
The article by Li et al was retracted by the editors after publication. Concerns were raised regarding a number of figure panels, such as partial overlap between the panels and duplication of protein gel analysis
The gene name nadA has also been given to quinolinate synthase
The amino acid sequence of this toxin was deduced to be identical with that of toxin Astrotia stokesi A on the basis of identity of the tryptic peptide 'map' and the amino acid composition of each peptide
Could be the product of a pseudogene. It corresponds to positions 370 to 439 of the complete orthologous and probably active protein in R.felis (RF_0890)
Only inflorescences, fruits, starved seedlings and stressed stem tips are green in this organism
The conserved 'Asp-464' active site is replaced by a Gly residue
Despite the fact that it belongs to the cyclophilin-type PPIase family, a report has shown that it has probably no peptidyl-prolyl cis-trans isomerase activity due to the presence of a tyrosine instead of a tryptophan at position 389
According to PubMed:12959640, T.stejnegeri was formerly named T.gramineus, supposing that this protein is the same as PLA-I from T.gramineus. They have been kept separated, because T.gramineus and T.stejnegeri are considered as being two different species (see http://reptile-database.org)
The precise function of this protein in melanin biosynthesis is still under debate. DHICA oxidase activity is controversial. The mouse protein has been shown to have DHICA oxidase activity (By similarity). In contrast, the human protein was shown lack DHICA oxidase activity, or to have DHICA oxidase activity only in the presence of Cu(2+), but not with Zn(2+) (By similarity)
Could be the product of a pseudogene, it is missing up to 110 N-terminal residues compared to orthologs
The active site contains a CASC motif wich differs from the conserved CGPC motif
Was shown to mediate palmitoylation of STAT3, leading to homodimerization and transcriptional activation of STAT3. However, this study was later retracted
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AXS139ph = phosphorylated Ser-135
Was initially reported to localize in the nucleus (PubMed:11525638). However, it was later shown to localize in the endoplasmic reticulum lumen
It is unclear if the knockout of Sh2d3c causes lethality (PubMed:20505138, PubMed:20881139). One report in genetic knockout mice suggests it is viable (PubMed:20505138). Another report in the same strain but a different genetic knockout model suggests lethality (PubMed:20881139)
A histidine residue in the pterin-binding domain interferes with substrate binding, and seems to be responsible for abolishing dihydropteroate synthase activity
Sumoylation at Lys-210 was initially reported to regulate nuclear localization and recombination efficiency of XRCC4 (PubMed:16478998). This result is however not confirmed by another study (PubMed:25934149)
Could be the product of a pseudogene. This is the C-terminal part of a DUP240 protein in strain S288c due to a naturally occurring frameshift at position 8 compared to other strains. A complete sequence for YAR023C can be found in other strain backgrounds (AC P0CI38)
Results concerning the involvement of this peptide in blood volume and blood pressure homeostasis are conflicting. Several studies utilising in vitro and heterologous expression systems show that it is able to activate cGMP and promote vasodilation and natriuresis (By similarity). However, an in vivo study found that it is not sufficient to induce any diuretic, natriuretic, nor hypotensive responses, and is unable to bind NPR1 nor increase guanylyl cyclase activity (PubMed:7831500)
Product of a dubious gene prediction. May be a non-coding RNA
The C-terminal domain thought to be required for interaction with some regulatory factors is missing from this protein
Despite its similarity with the succinyl-diaminopimelate desuccinylase enzymes, it does not display DapE activity
Two variants of the PRC2 complex have been described, termed PRC3 and PRC4. Each of the three complexes may include a different complement of EED isoforms, although the precise sequences of the isoforms in each complex have not been determined. The PRC2 and PRC4 complexes may also methylate 'Lys-26' of histone H1 in addition to 'Lys-27' of histone H3 (PubMed:15099518, PubMed:15684044), although other studies have demonstrated no methylation of 'Lys-26' of histone H1 by PRC2 (PubMed:16431907)
Might be an inactive rhomboid-type serine protease due to mismatches with the consensus active sites
It is uncertain whether Met-1 or Met-23 is the initiator
The gene has been cloned in cv. Landsberg erecta, but the tissue specificity and the induction have been determined in cv. Columbia (PubMed:11678272)
A family of highly similar proteins (GOLGA8A, GOLGA8B, GOLGA8C, GOLGA8D, GOLGA8E, GOLGA8F, GOLGA8G) are encoded by a repeated region on chromosome 15q11-15q13. Our sequences are in agreement with HGNC nomenclature
The proteins from this family have generally a signal sequence and are found in the outer membrane. This protein lacks a recognizable signal sequence
The N-terminus contains a putative primase-like domain; however the absence of the zinc binding domain and other motifs important for catalysis suggests that TWNK lacks primase activity
In vitro, can catalyze the hydrolysis of different nucleotide triphosphate (NTP) substrates with different efficiency
Despite its name, it does not contain a R3H domain
The relevance of the protein lysine acetyltransferase activity is unclear (By similarity). The publication reporting acetylation of GJA1 does not provide direct evidence of lysine acetyltransferase activity of ELP3 (PubMed:28507509)
Was isolated and reported to have peptide:N-glycanase activity (PubMed:10617595). However, its strong sequence similarity with alpha-glucosidase proteins suggest that it is not its function in vivo
In the PI-PLC X-box Thr-486 is present instead of the conserved His which is one of the active site residues. It is therefore expected that this protein lacks catalytic activity
Was originally thought to have a more extreme phenotype upon deletion; however the 100-fold reduction in virulence of the first deletion experiment, and impairment of phagosome escape seen in infected mice, is probably due to the kanamycin-cassette derivative used in that experiment
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-6; H2AK7ac = acetylated Lys-10; H2AS128ph = phosphorylated Ser-131
Lacks the conserved Tyr, which is one of four residues to bind the zinc atom
Brucella species display species-specific inactivation of flagellar genes and are consequently nonmotile
Although it belongs to the ADP-ribosylglycohydrolase family, lacks the metal-binding and substrate-binding residues, suggesting that it has no hydrolase activity
Was initially shown to catalyze the removal of carboxy-terminus tyrosine from alpha-tubulin (By similarity). However, later studies did not identified any detyrosinase or deglycylase activities from the carboxy-terminus of tubulin (By similarity)
Was first identified as gene weakly similar to Ac transposable elements, but does not code for any transposase activity
Lacks the conserved active site Arg in position 20. There is a cysteine in this position
Was originally thought to be an N(6)-adenine-specific DNA methyltransferase based on primary sequence and predicted secondary structure
Although it belongs to the glycosyl hydrolase 22 family, Thr-122 and Asn-139 are present instead of the conserved Glu and Asp which are active site residues. It is therefore expected that this protein lacks hydrolase activity
Two CRISP proteins (notescatin-a and -b) are secreted in the venom of N.scutatus. Since the N-terminal amino-acid sequence of these two proteins is identical, only one UniProtKB entry has been created (PubMed:19106157)
Contains an apparent HMA-like domain but lacks the core conserved Cys-X-X-Cys motif
Has been shown to be active in cv. Columbia (AC Q9M670) due to naturally occurring sequence variation in this strain. The sequence shown is from strains cv. Blh-1, cv. Pyl-1 and cv. Sha
In contrast to other kinesin-like proteins, residues required for ATPase activity are missing
It is uncertain whether Met-1 or Met-76 is the initiator. In the liver, the main translation initiation site may be Met-76
It is not clear which residue serves as the second axial ligand for the heme group
Represents a conventional myosin. This protein should not be confused with the unconventional myosin-3 (MYO3)
Although no clear MSS51 ortholog is encoded in mammalian genomes, the mammalian MSS51/ZMYND17 protein of unknown function is significantly similar
Lacks the Cys (here Ser-215), present in the DUF26 domain, which is one of the conserved features of the cysteine-rich repeat secretory protein family
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-8; H2BK6su = sumoylated Lys-8; H2BK7ac = acetylated Lys-9; H2BK7su = sumoylated Lys-9; H2BK11ac = acetylated Lys-15; H2BK16ac = acetylated Lys-25; H2BK16su = sumoylated Lys-25; H2BK17su = sumoylated Lys-26; H2BK123ub1 = monoubiquitinated Lys-133
Could be the product of a pseudogene. Despite its name, it does not contain a canonical C2H2-type zinc-finger and in contrast to other members of the krueppel C2H2-type zinc-finger protein family, it is much shorter and lacks the C-terminus part
All T.longicornis family members described in 'Undeheim et al., 2014' have not been imported into UniProtKB. Please, refer to this paper to access them
Lacks the conserved glutamate residue in position 447 that binds magnesium; it is replaced by an alanine residue
All E.rubripes family members described in 'Undeheim et al., 2014' have not been imported into UniProtKB. Please, refer to this paper to access them
Lacks the conserved motif Gly-Gly-x-Gly-Lys-Thr that is the consensus ATP-binding site for this enzyme
Was reported to be a protein deacetylase that removes acetyl groups on specific lysine residues in target proteins (PubMed:26716769). However, later experiments demonstrate that this protein does not have any protein deacetylase activity; the discrepancy observed seems to be due to contaminants having proteolytic activity (PubMed:29939131)
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC Q8S8U0
The gene for this protein is interrupted in position 307 by an IS6110 element
One study reported that the protein is not localized in the mitochondrion
The start codon has not been identified for this gene
Although highly homologous to the 2 other thiaminase-2 family members THI20 and THI21 in yeast, no hydroxymethylpyrimidine phosphate kinase activity could be demonstrated for this protein
PubMed:9892646 describes the wrong protein; the cDNAs used had been switched inadvertently
The authors of PubMed:3211766 originally stated that their sequence was from Frankia sp
It is not indicated if M-poneratoxin-Dq3b and M-poneratoxin-Dq3c have been predicted from the transcriptome or found as mature peptides in the peptidome. Authors indicate they have been cleaved from M-poneratoxin-Dq3a and amidated
This toxin is only expressed in some vibrio strains. Most serotype-O1 strains do not express this toxin
The rat protein was reported to play a role in DNA repair (PubMed:9406864), based on its ability to complement E.coli deficient in the DNA repair enzyme mutT that hydrolyzes oxidized guanine nucleotides. PubMed:17569023 found no such activity, neither for the human nor the rat protein
Lacks the conserved threonine and leucine residues in positions 50 and 261, respectively, which are part of the carbamoylphosphate and ornithine binding sites; they are replaced by a leucine and a glutamine residue, respectively
Was initially assigned as wee2 (PubMed:12217326). However, it corresponds to the zygotic protein WEE1 in mammals
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC Q8S8V3
This toxin precursor is identical to three other precursors (AC B1NWR6, AC B1NWS4 and AC B1NWR7). AC B1NWR6 shows 8 variants that could also be associated with this gene
In cv. Columbia and cv. Di-17, this protein is not present due to an unequal crossing over between the RPP8 and RP8HA genes that creates a unique RPP8 gene
This CDS is disrupted by an insertion sequence in strain 301
Was originally (Ref.1) thought to be AckA
Because the enzyme that would modify Asp-102 to 3-methylthioaspartic acid has not been found in the proteome of this organism, that modification is not predicted
Was originally isolated as a proteoglycan protein (explaining its name). Although not excluded, such secreted function is not clear
The HMA domain lacks the core conserved Cys-X-X-Cys motif
The RS447 megasatellite DNA is a highly polymorphic conserved tandem repetitive sequence which contains a copy of the USP17 gene. It is present with an interindividual variation in copy number, ranging from 20 to 103, and can be found in the genome on chromosome 4 and chromosome 8. The high similarity between the UPS17-like genes makes it impossible to specifically assign data to a particular gene of the family. Oligonucleotides designed in RNAi experiments are for instance not specific for a given UPS17-like gene
Sequence obtained after translation (DsM-b1) and sequence directly sequenced from protein (Dsm-b1', AA 17-27) correspond exactly. However, the mass found for the protein (14084) does not correspond to the expected mass calculated after translation (14055) (PubMed:17611171)
Could be the product of a pseudogene. Putative protein with similarity to PDZK1 C-terminus
Lacks the Cys residue in position 216 that is replaced by a Ser residue, resulting of a loss a disulfide bond. This may contribute to the lower procoagulant activity
Gln-112 is present instead of the conserved Glu which is expected to act as an active site proton donor
According to a report, displays histone acetyltransferase activity while localized in the Golgi apparatus (PubMed:21981917). May mediate acetylation of free histone H4 and promote nucleosome assembly (PubMed:21981917). Such results are however unclear in vivo and recent reports strongly suggest that it acts as a N-alpha-acetyltransferase that specifically targets N-terminal residues of transmembrane proteins (PubMed:21750686, PubMed:25732826)
Was not identified as subunit of the 26S proteasome complex (PubMed:20516081). Could be the product of a pseudogene
Missing conserved residues thought to be important for metal-binding
Weak similarity to other lysozymes and lacks the conserved active site
The D.melanogaster ortholog of this protein has been proposed to undergo autophosphorylation on tyrosine residues which is induced in response to cell adhesion (PubMed:1371458). However as mammalian orthologs of this protein seem to lack kinase activity it may be that this protein associates with, and is phosphorylated by, an unknown active tyrosine kinase
Some authors found genomic clones that have 9 or 12 consecutive glycine residues instead of 15 (AA 9-27)
Isoform 1 was reported to not have cation exchanger activity (PubMed:12080145). However, such result is unclear
Isoform 1 and isoform 2 were reported to localize to the endoplasmic reticulum membrane and cell membrane, respectively (PubMed:14625281). This result is however not supported by other studies that report localization to the mitochondrial membrane (PubMed:20018762, PubMed:24067497)
It is unclear whether this protein requires a metal cofactor for catalysis. It was originally proposed to be a Zn(2+)-dependent metalloenzyme based on structural similarities to bacterial aminopeptidases and the observation that it can bind Zn(2+) ions, typically in a 1:1 stoichiometry. However, a recent study suggests a Zn(2+)-independent catalytic mechanism
The sequence shown is derived from the best amino acid sequence data as modified by the X-ray data
Gln-172 is present instead of the conserved His which is expected to be an active site residue
As L.lactis is unable to produce acid from glycerol, the significance and/or function of the glpO gene in this organism is at present unknown
Was initially thought to play a role in DNA replication (PubMed:15684404). However, it was later shown that it is mainly involved in homologous recombination repair (PubMed:23401855)
Val-221 is present instead of the conserved Glu which is an active site in the cytidine and deoxycytidylate deaminase family of enzymes. It is suggested that this protein may act as a regulatory subunit
PubMed:8318586 sequence was originally thought to be rat caltrin. A number of peptide fragments were derived from a trypsin digest of caltrin and soybean trypsin inhibitor was used to stop the digestion. It appears that some of the inhibitor was also digested and sequenced
Was initially thought to catalytically inactive (PubMed:14715245). However, it was later shown that it is active (PubMed:21362556)
Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB (PubMed:8993314, PubMed:20503968)
It is not clear whether a synaptic vesicle protein acts as its receptor; there is evidence for and against SV2 fulfilling this function
Could be the product of a pseudogene, is missing up to 900 N-terminal residues compared to orthologs
Was initially characterized as a 3,5-epimerase in vitro (PubMed:15752721). However, it was later shown that it acts as a dTDP-6-deoxy-D-xylo-4-hexulose 3-epimerase in vivo (PubMed:16514445)
Was originally thought to be a phosphatidylinositol 4,5-bisphosphate phosphodiesterase type I (phospholipase C-alpha)
Although highly related to the citrate synthase family, lacks the conserved active His at position 264 which is replaced by an Asn residue
It is uncertain whether Met-1, Met-6 or Met-20 is the initiator
Lacks one Cys residue in the IBR-type zinc finger domain that is one of the conserved features of the family
This peptide is cyclic. The start position was chosen by similarity to chassatide C8 for which the DNA sequence is known
The protein was originally predicted to include a TKFQDFLRF-amide peptide, although TKFQDFLRF-amide has no effect on the activity of dissected pharyngeal myogenic muscle system
Ser-184 is present instead of the conserved Asp which is expected to be an active site residue
The PmrD protein from K12 strain (sequence shown) does not interact with phosphorylated BasR protein, and thus does not seem to be involved in polymyxin resistance
It is uncertain whether Met-1 or Met-55 is the initiator
The sequence shown in this entry differs from the translation of the reference genome assembly (GRCh38/hg38) due to a nonsense variant creating stop codon at position 577 in the reference genome
Was originally thought to contain an iron sulfur cluster (PubMed:8381402). It was shown later that only NrdG contains an iron sulfur center (PubMed:8621608)
According to a first report, interacts with ALK leading to stimulation of ALK tyrosine phosphorylation (PubMed:11278720). According to a second report, ALK is phosphorylated independently of a direct interaction with PTN but through PTPRZ1 which is inactivated in PTN-stimulated cells; the sites that are autophosphorylated in ALK no longer can be dephosphorylated by PTPRZ1; thus, autoactivation and tyrosine phosphorylation of ALK rapidly increase (PubMed:17681947)
Could be the product of a pseudogene. The protein is severely truncated in several ecotypes and the gene even harbors a complete retrotransposon in 3 ecotypes
PubMed:9016716 and PubMed:9440698 strain is not known and has been termed 'X' in this entry
Gln-101 is present instead of the conserved Lys which is expected to be an active site residue
It is uncertain whether Met-1 or Met-25 is the initiator
Several genes are coding for this toxin for which the structure by NMR has been determined. The cross-references to PDB and additional information can be found in entry AC P0C247
It is uncertain whether Met-1 or Met-16 is the initiator
While it is structurally defined as a knottin it lacks the conserved Cys residue in position 45
The sequences determined for the two internal peptides of Ole e 4 are identical to internal fragments of Ole e 9. However, the apparent molecular weight of the two proteins is different and they are still classified as two separate allergens (PubMed:22385802), even though we may be facing two different isoforms of the same allergen
Contains 8 disulfide bonds instead of the 4 disulfide bonds, which are conserved features of the family
Does not contain a CXXC active site motif indicating that it is a catalytically redox-inactive member of the protein disulfide isomerase family
It is uncertain whether Met-1 or a Met upstream of this sequence is the initiator
Was initially thought to constitute the phosphatidylserine receptor, a receptor that mediates recognition of phosphatidylserine, a specific marker only present at the surface of apoptotic cells, and participates in apoptotic cell phagocytosis. However, some results strongly suggest that it does not constitute the receptor for phosphatidylserine and is not involved in apoptotic cell removal
The active site contains a CGGC motif wich differs from the conserved CGPC motif
Although assigned as a calmodulin family member by Ref.3, it only contains EF-hand domains
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC A4QKX4
According to a report, has weak protein acyltransferase activity compared to protein acetyltransferase activity (PubMed:27377381). These conclusions are however not supported by subsequent studies (PubMed:29211711, PubMed:31542297)
It is uncertain whether Met-1 or Met-15 is the initiator
Two proteins (AC P60244 and AC Q9PW36) have been independently named acutolysin-C
An ORF called dsdC was originally assigned to the wrong DNA strand and thought to be a D-serine deaminase activator (PubMed:3275618). It was then resequenced and still thought to be 'dsdC', but this time to function as a D-serine permease (Ref.2). Another report showed that dsdC is another gene and that this sequence should be called dsdX (PubMed:7592420). It should also be noted that the C-terminal part of dsdX (from 338 onward) was also sequenced and was thought to be a separate ORF (don't worry, we also had difficulties understanding what happened!) (PubMed:3029015, PubMed:1659648)
Was initially thought to constitute the phosphatidylserine receptor, a receptor that mediates recognition of phosphatidylserine, a specific marker only present at the surface of apoptotic cells, and participates in apoptotic cell phagocytosis. However, its nuclear localization and the fact that it is not involved in phagocytosis during apoptosis strongly suggest that it does not constitute the receptor for phosphatidylserine and is not involved in apoptotic cell removal
PubMed:12623078 presents this protein as coming from C.viridis viridis, whereas PubMed:24707493 concludes it comes from C.oreganus abyssus due to identical sequences, very similar catalytic activity, and geographical origin
Has been shown to be inactive in cv. Ct-1 and cv. Ga-0 (AC D5K211), cv. Bl-1 and cv. Sakata (AC D9UBX6), cv. Blh-1, cv. Pyl-1 and cv. Sha (AC D9UBX4), and cv. Ge-1 (AC D9UC01) due to naturally occurring sequence variation in these strains. The sequence shown is from strain cv. Columbia
Although it belongs to the enolase family, Leu-362 is present instead of the conserved Glu which is expected to be an active site residue
Mutation in ABCD3 have been found in two individuals affected by Zellweger syndrome (PubMed:1301993). Later studies, however, showed unambiguously that a PEX1 defect was the underlying cause of the defect in peroxisome biogenesis in these patients (PubMed:9539740)
The protein in cv. Landsberg erecta and cv. Columbia (AC Q0WPN0) only differ by one residue in position 705 (a Pro and Arg residue, respectively); this variation leading to inactivate the protein in cv. Columbia (AC Q0WPN0)
It is uncertain whether Met-1 or Met-40 is the initiator
Lacks the conserved glutamate residue in position 500 that binds magnesium; it is replaced by a serine residue
Lacks the conserved aspartate residue in position 480 that binds magnesium; it is replaced by a serine residue
May be expressed in adult splenic cells (PubMed:15187158), as the antibody used could not discriminate between CD200R1 and CD200R4. May be expressed in uterus at 12.5 dpc (at protein level) (PubMed:15274657), as the antibody used could not discriminate between CD200R1 and CD200R4
According to some authors (PubMed:15187158), CD200R4 is a receptor for the CD200/OX2 cell surface glycoprotein, but it was later found (PubMed:23602662) to miss key amino-acids for binding to CD200
It is uncertain whether Met-1 or Met-26 is the initiator
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-5; H2AK7ac = acetylated Lys-9; H2AS128ph = phosphorylated Ser-128
There are two genes in human, ADAM3A and ADAM3B that are non-functional (PubMed:11439107). ADAM3A gene is deleted in infertile men and in some fertile men. ADAM3B transcripts, from testicular RNA of ADAM3A-deficient men, present many stop codons in all possible reading frames. Moreover these two proteins are neither detected in extracts from the testis of a man with the ADAM3A-positive genotype, nor of a man with a ADAM3A-deficient genotype
Morita et al. (2006) suggested that this protein inhibits collagen-induce platelet aggregation by binding to platelet glycoprotein VI, but a surface plasmon resonance experiment failed to demonstrate an interaction between these two proteins
Reported as CYP72A219 in the publication but submitted as CYP72A129
Dispensable in mitochondrial dynamics and morphology during early embryonic development (PubMed:19327994). However, another study shows that ced-9 is involved in regulating mitochondrial dynamics (PubMed:21949250)
Was originally thought not to translocate protons
The molecular identity of the sigma-2 receptor has been unclear for a long time. It is now identified as TMEM97 (PubMed:28559337). Previously identified as PGRMC1 (AC O00264)
Originally predicted to contain a coiled coil domain but shown to contain a stable SAH domain instead
Has lost two of the three essential catalytic residues and so probably has no enzymatic activity
This peptide is cyclic. The start position was chosen by similarity to cyclotide cter-A for which the DNA sequence is known
Was originally annotated as an acid phosphatase (EC 3.1.3.2)
The sequence shown in this entry is that of the functional protein expressed by the A2G strain, which is known for its unique resistance to myxovirus (influenza) infections, or Czech II strain, which derives from wild mice (PubMed:3000619, PubMed:15489334). Some other strains also express fully active Mx1 protein, such as SL/NiA (PubMed:2903437). In some inbred mouse strains however, including the strain of the reference genome C57BL/6J, Mx1 gene contains a deletion or a nonsense mutation that results in a non-functional gene product
Was originally thought to be involved in the activation of nitrogen assimilatory genes
Was previously described as the first fungal L-xylulose reductase responsible for NADPH dependent reduction of L-xylulose to xylitol in L-arabinose catabolism (PubMed:12009906). However, lxr1 forms a clade with fungal D-mannitol 2-dehydrogenases, is not induced by L-arabinose, and deletion reduces D-mannitol 2-dehydrogenase activity, suggesting that lxr1 is a D-mannitol 2-dehydrogenase and that a true L-xylulose reductase is still awaiting discovery (PubMed:19303876)
PubMed:9697413 reported that this sequence contains TPR repeats. These are not detected using our methodology
Functions as a mitochondrial uncoupling protein when expressed in yeast
Ala-192 is present instead of the conserved Val which is part of the DDVD box
Upon expression in E.coli, Rv1956 has been shown to function as a toxin inhibiting cell growth and colony formation that is neutralized by coexpression with Rv1955 (PubMed:19016878). It is not clear if these conflicting results are due to expression in a heterologous system. The gene names higA and higB have been assigned to both Rv1955 and Rv1956; we have chosen to call Rv1956 higA1 after consulting the authors
Was originally (PubMed:3312167) thought to be an outer membrane binding protein (chlanectin). The sequence was incorrect due to a cloning artifact
Could be the product of a pseudogene. In A.formosae this protein is in two parts: ORF 1031 (N-terminal) and ORF 473 (C-terminal)
The RS447 megasatellite DNA is a highly polymorphic conserved tandem repetitive sequence which contains a copy of the USP17 gene. It is present with an interindividual variation in copy number, ranging from 20 to 103, and can be found in the genome both on chromosome 4 and chromosome 8. The high similarity between the UPS17-like genes makes impossible to clearly assign data to one of the genes of the family. Oligonucleotides designed in RNAi experiments are for instance not specific of a given UPS17-like gene
Was originally thought to be a biotin sulfoxide reductase
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me1 = monomethylated Lys-10; H3S10ph = phosphorylated Ser-11; H3K14ac = acetylated Lys-15; H3K14me2 = dimethylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me1 = monomethylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me1 = monomethylated Lys-24; H3K27ac = acetylated Lys-28; H3K27me1/2/3 = mono-, di- and trimethylated Lys-28; H3K36ac = acetylated Lys-40; H3K36me1/2/3 = mono-, di- and trimethylated Lys-40; H3K56ac = acetylated Lys-60; H3K64ac = acetylated Lys-68; H3K79me1/2/3 = mono-, di- and trimethylated Lys-83
Was originally thought to be a trans-dienelactoneisomerase
The spacing between the conserved Cys residues used for the 4Fe-4S cluster is unusual (C-X11-CXXC instead of C-X3-CXXC); it is therefore unclear whether this protein will bind the cofactor
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-6; H2AK7ac = acetylated Lys-10; H2AS128ph = phosphorylated Ser-132
Lacks the conserved catalytic triad His-Tyr-Glu of the active site
Was originally (PubMed:15247229) thought to have phosphatidylinositol 5-phosphatase activity, however, it was later shown (PubMed:16039589) that it is probably not the case in vivo
According to PubMed:11877383, it is not involved in seed germination
Was thought to be an outer membrane protein as it is part of a disulfide cross-linked complex that is insoluble in the detergent Sarkosyl; however based on experiments in C.psittaci it is likely to be periplasmic
The protein contains an even number of transmembrane helices, fewer than predicted by bioinformatics tools
Was originally thought to originate from S.undulatus
Lacks the phospho-accepting Asp (here Glu-76), present in the receiver domain, which is one of the conserved features of the two-component response regulators (ARRs) family
Results concerning the involvement of this peptide in blood volume and blood pressure homeostasis are conflicting. Several studies utilising in vitro and heterologous expression systems show that it is able to activate cGMP and promote vasodilation and natriuresis (By similarity). However, an in vivo study in rat found that it is not sufficient to induce any diuretic, natriuretic, nor hypotensive responses, and is unable to bind NPR1 nor increase guanylyl cyclase activity (By similarity)
Results concerning the involvement of this peptide in blood volume and blood pressure homeostasis are conflicting. Several studies utilising in vitro and heterologous expression systems show that it is able to activate cGMP and promote vasodilation and natriuresis (By similarity). However, a heterologous and in vivo expression study in rat found that it is not sufficient to induce any diuretic, natriuretic, nor hypotensive responses, and is unable to bind NPR1 nor increase guanylyl cyclase activity (By similarity)
A second toxin (SmT-2) has been reported which has been sequenced up to residue 24 and only differs by two residues that are missing (see conflict in the feature table)
Orthologs of U2af1l4 do not appear to exist in lower eukaryotes, Drosophila, C. elegans, plants, or vertebrates such as Xenopus or zebrafish (PubMed:11739736). Existence of splicing isoforms of U2af1l4 in human and rat is not yet proven
Was originally thought to be a homohexamer
In contrast to other members of the family, lacks the conserved Ser at position 243 which is replaced by a Pro residue, suggesting it is inactive
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-27; H2BK143ub1 = monoubiquitinated Lys-134
Was originally designated as the EP2 subtype
3D-structure analysis of the human homolog indicates that the membrane topology differs from the predictions. Contrary to predictions, the N-terminus contains two short helices that dip into the membrane, but do not cross it. The C-terminus contains the single transmembrane helix. This gives rise to a topology where the N-terminus is cytoplasmic and the C-terminus is lumenal
Was originally thought to be a phosphatase
Has no glucosyltransferase activity. Concerning beta-galactosyltransferase activity, the level of CERCAM could be too low to detect any activity when tested in transfected insect cells
Sequences of mRNA encoded by the same gene but extracted from leaves (AF521191) or from endosperm (AF521190) differ at several prositions due to sequencing uncertainties
Was initially thought to mediate palmitoylation of Wnt proteins. It was later shown that instead it acts as a serine O-palmitoleoyltransferase that mediates the attachment of palmitoleate, a 16-carbon monounsaturated fatty acid (C16:1(9Z)), to Wnt proteins
The structure contains a calcium molecule but it is unclear if this is an artifact of the crystallization process or if it has a physiological role in the activity regulation/formation of the channel
It is uncertain whether Met-1, Met-2 or Met-3 is the initiator
Human C6orf211 has been reportedly associated with a protein carboxyl methyltransferase activity, but whether this protein indeed has such an activity remains to be determined (By similarity). It has been later shown to belong to a family of metal-dependent phosphatases implicated in metabolite damage-control (By similarity)
This protein is encoded by the leptin receptor (LEPR) gene, but shares with LEPR only the first two 5'-UTR exons. It therefore does not share any sequence similarity with LEPR
Contains 6 disulfide bonds instead of the 4 disulfide bonds, which are conserved features of the family
It is unclear if PMV is glycosylated as other members of the same enzyme family, ie. PMI and PMII, are not
Could be the product of a pseudogene. It is unsure wether the two stop codons at positions 140 and 230 are real or are due to sequencing errors (PubMed:15285616)
The [4Fe-4S] cluster was originally thought to be ligated by three cysteine residues, but the crystal structure establishes that it is ligated by four cysteine residues
Was indicated as B3Gal-T6 in submitted DNA entries
Lacks the conserved Tyr residue in the active site triad of Ser-Tyr-Lys necessary for dehydrogenase activity, suggesting that it has no oxidoreductase activity
A single-base error is suspected in position 1, thus masking the true initiator Met
Despite its name, it does not contain a canonical C3H1-type zinc-finger
PKD1L3 and PKD2L1 have been defined as sour taste receptor in gustatory cells based on a number of indirect evidences in mouse. Some data confirm this hypothesis in human: in 2 patients with sour ageusia that are unresponsive to sour stimuli, but show normal responses to bitter, sweet, and salty stimuli, expression of PKD1L3 and PKD2L1 is absent in the anterior part of the tongue (PubMed:19812697). However, a number of experiments have recently shown that the sour taste receptor activity is probably indirect
It is uncertain whether Met-1 or Met-27 is the initiator
Was originally (Ref.1) erroneously named IAA21
Was originally thought to be a thioether S-methyltransferase but appears to be the ortholog of human INMT
LolA1 has similarity only to the C-terminal domain of aspartate kinases, excluding the kinase active site (PubMed:15654104)
It is uncertain whether Met-1 or Met-19 is the initiator
The region of SLC9A1/NHE1 that interacts with CHP3 is conflicting: In human, interaction with SLC9A1/NHE1 has been reported via residues 507-549, the juxtamembrane region of the cytoplasmic C-terminus. However, another publication has reported interaction with SLC9A1/NHE1 via residues 637-820, the region of the cytoplasmic C-terminus more distal to the membrane
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-5; H2AK7ac = acetylated Lys-9; H2AS128ph = phosphorylated Ser-129
Although it shares high sequence similarity with GRXCR1, it does not contain a canonical glutaredoxin domain
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-28; H2BK34ac = acetylated Lys-29; H2BK143ub1 = monoubiquitinated Lys-136
Asn-335 is present instead of the conserved Asp which is expected to be an active site residue. This enzyme has been shown to be catalytically inactive
This is a truncated version of an UPF0507 family protein. Strain S288c has a frameshift in position 286, which disrupts the gene coding for this protein and produces two ORFs YML003W and YML002W. A contiguous sequence for a S.cerevisiae UPF0507 family protein can be found in strain YJM789 (AC A6ZM60)
Was initially though to be involved in the side-chain initiation step of the polyglutamylation reaction rather than in the elongation step (PubMed:17499049). However, it was later shown to be involved in both steps (PubMed:19152315)
PubMed:12968785 shows that the expression of the transcribed processed pseudogenes (TPP) Makorin1-p1 prevents the decay of functional Mkrn1 mRNAs. In contrast, PubMed:16882727 shows that Makorin1-p1 is not transcribed and that the putative transcripts represent an alternative isoform of the Mkrn1 source gene
Multiple papers report expression in the developing neural crest and a role in neural crest formation. However, PubMed:17724611 reports differences between the duplicated hes4 gene products and shows that hes4-B/hairy2b but not hes4-A/hairy2a has a role in neural crest formation, and that hes4-B/hairy2b but not hes4-A/hairy2a is expressed in the presumptive neural crest
Product of a dubious gene prediction. Partially overlaps Q0010
It is uncertain whether Met-1, Met-3 or Met-12 is the initiator
Juge et al. shows that SLC32A1 is a symporter of both 4-aminobutanoate or glycine or beta-alanine with Cl(-) that operates according an electrical gradient without the need for a chemical gradient (By similarity). However Farsi et al. and Egashira et al. confirm that SLC32A1 is an antiporter that exchanges vesicular protons for cytosolic 4-aminobutanoate or glycine and exclude any coupling with chloride (PubMed:27601664, PubMed:26912364)
Could be the product of a pseudogene. The sequence shown in this entry differs from the translation of the reference genome assembly (GRCh38/hg38) due to two nonsense variants creating stop codons at positions 16 and 168 in the reference genome
Asn-335 is present instead of the conserved Asp which is expected to be an active site residue
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-35; H2BK34ac = acetylated Lys-36; H2BK143ub1 = monoubiquitinated Lys-142
Lacks the conserved His residue in position 67 and the conserved Ser residue in position 206 essential for protease activity
Could be the product of a pseudogene unlikely to encode a functional protein. Transposon Ty2-DR2 (YLRCTy2-2) contains a 172 aa deletion at position 1540 compared to other Ty2 elements. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
It is uncertain whether Met-1 or Met-32 is the initiator
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-5; H2AK7ac = acetylated Lys-8; H2AS128ph = phosphorylated Ser-128
Could be the product of a pseudogene. The protein is missing 8 N-terminal amino acids due to a premature stop codon; when the reading frame is restored strain W3110 synthesizes cellulose. See (AC P0DP92) for a functional intact protein
The sequence of this protein is available under the NCBI RefSeq accession WP_042646516, but the source is unknown
Could be the product of a pseudogene. Much shorter than other members of the family and lacks the PI3K/PI4K catalytic domain
Was originally called HPr kinase/phosphatase, but P-Ser-HPr dephosphorylation was found to follow a quite unique mechanism (PubMed:12359880), in which Pi instead of H(2)O is used for the nucleophilic attack on the phosphoryl group. P-Ser-HPr dephosphorylation is therefore not a phosphohydrolysis but a phospho-phosphorolysis reaction, and the bifunctional enzyme was dubbed HPr kinase/phosphorylase
Could be the product of a pseudogene. The existence of a transcript at this locus is supported by only one sequence submission (PubMed:2174397)
According to experiments made in rat, this enzyme is unable to transfer GalNAc onto serine or threonine residue on the protein receptor, but instead requires the prior addition of a GalNAc on a peptide before adding additional GalNAc moieties, thereby acting as a glycopeptide transferase
Was originally thought to contain a [4Fe-4S] cluster (PubMed:7771772, PubMed:8325851). However, a more recent study in M.tuberculosis has shown that this enzyme contains a [2Fe-2S] cluster, which is unstable and subject to degradation
This copy of PsbA is missing the site cleaved by CtpA, and thus may not be able to ligate the manganese cluster
This copy of psbA is missing some conserved residues important for binding the Mn4-Ca-O5 cluster
The guanine nucleotide exchange factor (GEF) activity is controversial. One study showed GEF activity towards RALA, RAP1A and RRAS (By similarity). However, in another study, a construct containing only the Ras-GEF domain lacks GEF activity towards RAP1 (By similarity)
Was originally thought to be the H-Y antigen
It is uncertain whether Met-1, Met-14 or Met-24 is the initiator
Was originally thought to be rhodanese
Lacks the conserved Glu residue at position 70 that serves as proton acceptor in enzymes with gamma-glutamylcyclotransferase activity
Could be the product of a pseudogene. Almost identical to the N-terminus of SMG1
In contrast to other members of the family, it lacks the C-terminal ricin B-type lectin domain, which usually contributes to the glycopeptide specificity. It instead contains a motif that may retain its secretion form the endoplasmic reticulum
It is uncertain whether Met-1 or Met-43 is the initiator
It is uncertain whether Met-1 or Met-13 is the initiator
This protein lacks transmembrane domains and is probably not involved in transport
HLA-DRB3, HLA-DRB4 and HLA-DRB5 may represent a unique gene
Was originally thought to be the antitoxin component of a type II toxin-antitoxin (TA) system (PubMed:22239607). When coexpressed with cognate toxin CptA (now ygfX), the antitoxin neutralizes toxicity of CptA (PubMed:22239607). Has been suggested to be a transcriptional regulator (PubMed:22239607). The putative toxin, CptA (ygfX) has since been shown not to be toxic in E.coli or Serratia species (PubMed:23657679)
Was named ERF5 but it corresponds to Arabidopsis ERF3
Was originally thought to be a diacylglycerol kinase
Represents a conventional myosin. This protein should not be confused with the unconventional myosin-4 (MYO4)
Lacks the conserved Glu residue involved in nucleophilic attack and essential for hydrolase activity. Its enzyme activity is therefore unsure
Experimental results based on the injection of HAVCR2/TIM-3 antibodies or use of HAVCR2/TIM-3-Fc fusion proteins can reflect changes in the activity of several cell types and pathways as HAVCR2/TIM-3 is expressed by multiple immune cell types
Glu-476 was identified as the third Zn ligand (PubMed:11827531), however in other crystal structures (Aquifex aeolicus and Thermotoga maritima) the conserved equivalent residue does not bind Zn. Instead it makes a hydrogen bond with the side chain of the first catalytic Zn-binding residue and indirectly stabilizes the Zn
PubMed:1463835 originally thought that there were two genes for psaC in PCC 6803. However, the first one identified did not originate from PCC 6803 but from N.tabacum. The real psaC gene was therefore incorrectly termed psaC2
Although it belongs to peptidase S1 family, lacks the conserved Ser residue within the catalytic triad (Asp-His-Ser) which is replaced by a Gly residue, probably resulting in a loss of proteolytic activity
The strain (Berkeley) sequenced by the collaborative genome project contains a deletion of T nucleotide in position 49 leading to premature stop codon. It is therefore considered a pseudogene
Plasmid p42d was originally thought to originate from Rhizobium leguminosarum (biovar phaseoli)
Orthologs of U2AF1L4 do not appear to exist in lower eukaryotes, Drosophila, C. elegans, plants, or vertebrates such as Xenopus or zebrafish. Existence of circadian and light-inducible alternative splicing of U2AF1L4 similar to the mouse in human and rat is not yet proven
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 337 in the dsPTPase catalytic loop, suggesting that it has no phosphatase activity
Although related to reduced folate carrier family, it lacks transmembrane domains, suggesting that it has probably no transporter function
The orthologous protein is known as the gamma/beta subunit (UreAB) in most other bacteria
In PubMed:6653780 it is said that 50% of the peptides have N-methyl-Phe and 50% begin with Thr-9. N-terminal methylation produces preview during Edman degradation, which makes this appear to happen when the peptide is completely N-terminally methylated
Lacks the conserved MIT domain, which is one of the features of the spastin family
Was initially reported to display histone acetyltransferase activity, with a preference for histone H4 (PubMed:12072557). Such activity is however unsure in vivo. Histone acetyltransferase activity would be in contradiction with the function of the protein in corepressor complexes (PubMed:19061646, PubMed:22009739). Moreover, crystallographic studies demonstrated that it does not share any similarity with other acetyltransferases and instead forms a crotonase-like fold (PubMed:19507244)
Lacks one of the four calcium-binding sites found in other family members
In contrast to the human ortholog it does not have a signal sequence as it has an additional 53 residue sequence at the N-terminus. At the position of the human initiation methionine there is a leucine (Leu-54)
May not be essential for endoplasmic reticulum-to-Golgi transport
A stretch of the chloroplast genome is duplicated within chromosome 10 resulting in the duplication of the gene. The expression of this duplicated gene has not been demonstrated
This is a tentative sequence based on X-ray data
Asp-351 is present instead of the conserved His which is expected to be zinc-binding residue. There is therefore some uncertainty concerning the enzymatic activity of this protein
Most extant K-12 lines do not express O-antigen because of mutations in dTDP-rhamnose biosynthetic genes or in the rhamnosyltransferase gene wbbL
Product of a dubious CDS prediction. No homolog. May not code for a protein
The position of the proteolytic cleavage is unclear (PubMed:2007860, PubMed:12850260). One study shows a cleavage between Asn-124 and Ala-125 (PubMed:2007860). Another study shows a cleavage between Gly-123 and Asn-124 (PubMed:12850260)
This is the ortholog of mouse OASL1
The antibiotic variants could harbor other changes as whole genes were not sequenced
According to a report, can also be a component of ESCRT-I complexes containing VPS37B, VPS37C or VPS37D (PubMed:22405001). However, another publication showed that UBAP1 has specificity for complexes containing VPS37A and not VPS37 paralogs (PubMed:24284069)
Do not confuse Mt a-1 with MT A-1; these are two different proteins
In (PubMed:9545258) and in (PubMed:10051563) experimental information is given for a truncated version of TGFBRAP1 (sequence of 474-860), which was later shown to act as a dominant negative
A report observed N-glycosylation at Asn-815 (PubMed:19139490). However, as the protein is not predicted to localize in an extracellular compartment of the cell, additional evidence is required to confirm this result
There is a sequence conflict at position 79 between the sequence from NCBI (CAH64856; Leu) and the sequence shown in fig.1 (Pro) of Kauferstein et al., 2005
This organism lacks the other subunits that are necessary for ATP-independent citrate lyase activity. Even though this protein has clear similarity to citrate lyase beta subunit, it is expected to have a somewhat different enzyme activity
Was reported to have a protein kinase activity and to act as a Mn(2+)-dependent serine-threonine-specific protein kinase
In the PI-PLC X-box Asn-458 is present instead of the conserved His which is one of the active site residues. It is therefore expected that this protein lacks catalytic activity
Was previously considered as a subunit of the NADH dehydrogenase of the mitochondrial respiratory chain complex I. Due to lack of 38 of the other 40 subunits that are present in that complex in mammals, this attribution is unlikely
Ser-80 is present instead of the conserved Cys/Sec which is expected to be the active site residue
It is uncertain whether transit peptide cleavage occurs after His-61 or Ala-62. Peptides have been found for both N-termini
It is unclear if PMVII is glycosylated as other members of the same enzyme family, i.e. PMI and PMII, are not
Although related to the Ser/Thr protein kinase family, has no protein kinase activity and acts as a mannose kinase instead
Although strongly related to the Ufm1-specific proteases, it is shorter in N-terminus and lacks the conserved Cys active site, suggesting that it is probably catalytically inactive
Was originally thought to originate from C.acetobutylicum
Despite its gene name, this protein differs in domain structure from bacterial clpB. Bacterial clpB contains two AAA modules, one in the N-terminal part of the protein and one in the C-terminal part, separated by a coiled coil, while vertebrate CLPB contains a single C-terminal AAA region and an N-terminal ANK repeat region which is absent from bacterial clpB
Was originally thought to be the ubiquinone-binding protein (QP-C)
The sequence shown here is derived from an EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is preliminary data
In their assays, PubMed:11741918 could not detect any effect on activation of the ERK pathway
The region between transmembrane regions M4 and M5 and between M6 and M7 (also termed intracellular loops IL2 and IL4, respectively) seem to be localized at least in part in the membrane. The hydrophobic region H10 is proposed to be located within the membrane
The interacting region with TESC is conflicting: In human, it has been reported that SLC9A1 interacts with TESC via the juxtamembrane region of the cytoplasmic C-terminal domain, including residues 507-549. However, another publication has reported interaction with TESC via residues 637-822, the region of the cytoplasmic C-terminus more distal to the membrane
Has no enzymatic activity towards unfolded RNase B or thyroglobulin
AMPylation was initially reported to take place at Ser-365 and Thr-366 in vitro, and promote activation of HSPA5/BiP (PubMed:25601083). However, it was later shown that AMPylation takes place at Thr-518 and leads to inactivation of HSPA5/BiP
It is unsure if the enzyme has intrinsic kinase activity
Despite belonging to the type II pantothenate kinase family, the pantothenate kinase domain contains a Val residue at position 147 and a Trp residue at position 211 instead of the two conserved active site residues, Glu and Arg. Lacks pantothenate kinase activity
The nomenclature of the 3 Arabidopsis DRG genes is ambiguous; in the literature several gene names have been used for the same protein
This enzyme lacks one or more conserved metal-binding sites. It may be non-functional
The plasmid pTiTM4 carries two T-regions, the TA and TB region, both of which have an IaaH gene, with low homology between them. Only the TB-IaaH gene seems to be functional
Lacks the tyrosine conserved in bacteria and other archaea, involved in feedback inhibition
This is a truncated version of a ThrE family protein. Strain S288c has a frameshift in position 382, which disrupts the gene coding for this protein and produces two ORFs YJL107C and YJL108C. A contiguous sequence for a S.cerevisiae ThrE family protein can be found in strain YJM789 (AC A6ZQL9)
Lacks 2 conserved residues that bind magnesium; the aspartate residue in position 461 is replaced by an asparagine and the glutamate residue in position 464 is replaced by an alanine residue
In domesticated laboratory strains (168 and derivatives), lytF is not expressed in a majority of the growing cells. These cells form a subpopulation that grows in multicellular, nonmotile chains. Undomesticated strains (3610) express lytF in a majority of the population, that grows as separate individual motile cells (PubMed:19542270)
Does not seem to possess aminotransferase activity
The allele found in cv. Missouri 17 (AC A0A291LSD6) encodes an active enzyme while the allele found in cv. B73 contains a frame shift mutation
This protein is encoded by a hybrid gene consisting of a duplication of exons 5 through 10 of the CHRNA7 gene fused 3-prime to a copy of the FAM7A gene (exons A through E). The CHRFAM7A gene is in the opposite orientation to the CHRNA7 gene. It seems not to be represented on every human chromosome 15 and it is not clear whether the transcript is actually translated
Was reported to have a protein kinase activity
Called 'metalloprotease', but clearly belongs to the S1B family of serine proteases
Most probably a non-functional protein that cannot participate to the synthesis of a productive immunoglobulin chain due to an unusual recombination signal (RS) sequence altering V-(D)-J recombination (PubMed:9619395)
Conflicting data shows that it is not able to edit the amino acid moiety from incorrectly charged Ser-tRNA(Ala) in trans (PubMed:14663147). Another paper shows that this protein can edit mischarged Ser-tRNA(Ala) but not Gly-tRNA(Ala) in trans (PubMed:20010690). Experiments are not well detailed in either paper
Was reported to recruit SETDB1 during DNA replication, to form a S phase-specific complex that would facilitate methylation of H3 'Lys-9' during replication-coupled chromatin assembly and vould be at least composed of the CAF-1 subunit CHAF1A, MBD1 and SETDB1 (PubMed:15327775). The interaction with SETDB1 was also reported to be inhibited by sumoylation at Lys-499 and Lys-538 (PubMed:17066076). However, these papers have been retracted because some data, results and conclusions are not reliable (PubMed:30849389, PubMed:31612521)
According to PubMed:18060440, it is predicted to be a non-inhibitory serpin due to Val-337 and Glu-338 which differ from the conserved residues in the reactive center loop (RCL) that is involved after cleavage in covalent linking and inhibition of the target proteinase
Lacks the conserved zinc-binding motif HEXXH, which presumably renders it inactive for proteolysis
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 333 in the dsPTPase catalytic loop, suggesting that it has no carboxypeptidase activity
Sequence shown in this entry in copied from Fig.2, and not from Table 1, which differ
This organism being non-photosynthetic, the role of this protein is uncertain
Although strongly related to the peptide:N-glycanase enzyme, it lacks the conserved active site Cys in position 261, which is replaced by a Val residue suggesting that it has no activity
Represents an unconventional myosin. This protein should not be confused with the conventional myosin-1 (MYH1)
The original article describing the function has been retracted because the results of E338A and E366A mutants were reversed. The authors later submitted a corrected manuscript
Ser-107 is present instead of the conserved His which is expected to be an active site residue
It is uncertain whether Met-1 or Met-31 is the initiator
Ser-293 is present instead of the conserved Asp which is expected to be an active site residue. Low level autophosphorylation activity has been reported in PubMed:10383454, while other authors describe this as an inactive kinase
This protein is not found in the crude venom
Does not bind calcium as one of the calcium-binding sites is lost (Asp->Ser in position 64, which corresponds to 'Ser-49' in the current nomenclature)
Instead of Lys-820, Arg-820 is found at the binding site
Although it belongs to the glycosyl hydrolase 18 family, Leu-140 is present instead of the conserved Glu which is an active site residue. Therefore this protein lacks chitinase activity
Has been shown to act as a sodium/bicarbonate cotransporter in exchange for intracellular chloride (By similarity). Has also been shown to act as a sodium/biocarbonate cotransporter which is not responsible for net efflux of chloride, with the observed chloride efflux being due to chloride self-exchange (PubMed:18319254)
It is uncertain whether Met-1 or Met-214 is the initiator
HSN2 was originally thought to be an intronless gene lying within a WNK1 gene intron. It has been shown to be a nervous system-specific exon of WNK1 included in isoform 2 and isoform 3 (PubMed:18521183)
MYO1A mutations have been reported to cause autosomal dominant non-syndromic hearing loss DFNA48 (PubMed:12736868). It was later shown that MYO1A is not associated with DFNA48 (PubMed:24616153)
In contrast to PubMed:11080145, PubMed:12660153 demonstrates that OmpL actually plays no perceptible role in modulating redox potential in the periplasm of E.coli
MntS mRNA was originally thought to be an sRNA
Could be the product of a pseudogene. This sequence is shorter than orthologs
It is uncertain whether Met-1 or Met-21 is the initiator
Although it belongs to the protein kinase family, lacks the active site Asp residue which has been changed to Asn so is unlikely to be catalytically active
Was classified as a serine carboxypeptidase-like (SCPL) protein solely on the basis of the overall sequence similarity (PubMed:15908604) but it has been shown that it belongs to a class of enzymes that catalyze acyltransferase reactions (PubMed:17600138)
INPP5F has been initially described as an inositol polyphosphate 5-phosphatase
Although AknT shows significant similarity to cytochrome P450 family, it lacks the heme-binding sites. The conservation of amino acid sequence is confined primarily to the C-terminal half of the protein
Thr-291 is present instead of the conserved His which is expected to be an active site residue
Lacks the conserved Glu residue in position 489 essential for carbopeptidase activity. The mature form lacks catalytic activity towards synthetic peptide substrates
Was initially thought to mediate AMPylation of Hsc70-3/BiP at 'Thr-366' (PubMed:25395623). However, it was later shown that it catalyzes AMPylation of Hsc70-3/BiP at 'Thr-518'
Lacks the conserved Q motif, which is one of the features of the DEAD box helicase family
Was initially thought to mediate ion transport such as calcium or manganese (PubMed:12058017, PubMed:24392018). However, different publications have shown that it does not act as an ion transporter (PubMed:22745129, PubMed:32353073, PubMed:32973005). Specifically binds moderately hydrophobic transmembrane with short hydrophilic lumenal domains that misinsert into the endoplasmic reticulum (PubMed:32973005)
Was originally thought to originate from Clostridium cellulovorans and was termed endoglucanase C (engC)
PubMed:10850809 has identified a second propeptide cleavage site after Lys-68 and both possible mature proteins were found in equal quantities in a heterologous expression system in Aspergillus awamori
Does not bind calcium as one of the calcium-binding sites is lost (Asp->Ser in position 48, which corresponds to 'Ser-49' in the current nomenclature)
There are 3 copies of the NOMO gene on chromosome 16p12-p13: NOMO1, NOMO2 (AC Q5JPE7) and NOMO3 (AC P69849). All 3 are extremely similar, which makes their individual characterization difficult. Thus, most experiments probably do not discriminate between the different members. Moreover, it does not allow a clear view of which variant belongs to which of the 3 copies. The results reported in other entries may therefore apply for this protein
H2A histone demethylase activity was observed in vitro (PubMed:22961808). The relevance of such activity is however unclear and additional experimental evidence would be needed to confirm this activity in vivo
The DNA N6-methyl adenine demethylase activity is subject to discussion. While DNA N6-methyl adenine demethylase activity was observed by a report (PubMed:27027282). Another group was unable to detect clear DNA N6-methyl adenine demethylase activity in vivo (PubMed:27745969)
The existence of N(6)-methyladenosine on DNA is unclear in mammals (PubMed:32203414). According to a report, the majority of N(6)-methyladenosine in DNA originates from RNA catabolism via a nucleotide salvage pathway and is misincorporated by DNA polymerases, arguing against a role as epigenetic DNA mark in mammalian cells (PubMed:32203414). Additional evidences are therefore required to confirm the role of METTL4 as a N(6)-adenine-specific DNA methyltransferase in vivo (PubMed:32203414)
Is called bop2 in PubMed:21135094
It is unclear whether the detected peptide spanning residues 67-81 is active on its own or just constitutes the N-terminus of the predicted sequence of prothoracicotropic hormone
In contrast to other members of the family, lacks the conserved Cys active site in position 129, suggesting it is inactive
Lacks two conserved histidine residues that bind copper and zinc
Could be the product of a pseudogene. The intronless gene encoding this protein has arisen by SVA-mediated retrotransposition of the SLC35G6 gene in the primate lineage. There is no evidence for transcription (PubMed:17101974)
Was reported to be recruited by MBD1, during DNA replication, to form a S phase-specific complex that would facilitate methylation of H3 'Lys-9' during replication-coupled chromatin assembly and would be at least composed of the CAF-1 subunit CHAF1A, MBD1 and SETDB1 (PubMed:15327775, PubMed:17066076). However, these papers have been retracted because some data, results and conclusions are not reliable (PubMed:30849389, PubMed:31612521)
Was reported to trimethylate H3 'Lys-9', to interact with CHD7, NLK1 and PPARG and to be phosphorylated at Thr-796 (PubMed:17952062). However, this work was later retracted although its role in H3 'Lys-9' trimethylation is supported by other papers (PubMed:25358353)
NG36 and G9a were originally thought to derive from two separate genes
Was originally thought to be a squalene synthase (PubMed:20713508). Further characterization suggests it is actually a farnesyl diphosphate phosphatase (PubMed:25308276)
Was initially reported to act as a regulator of mRNA translation efficiency in cooperation with YTHDF1 by binding to m6A-containing mRNAs and interacting with 40S and 60S ribosome subunits (PubMed:28106072, PubMed:28106076, PubMed:28281539). These studies suggested that the 3 different paralogs (YTHDF1, YTHDF2 and YTHDF3) have unique functions with limited redundancy (PubMed:28106072, PubMed:28106076, PubMed:28281539). However, later studies showed that YTHDF1, YTHDF2 and YTHDF3 paralogs have redundant functions to a profound extent and directly promote degradation of m6A-containing mRNAs (PubMed:32492408). The effect on translation efficiency observed earlier is probably indirect (PubMed:32492408)
In contrast to other members of the family, it apparently does not use iron or other metals as cofactor
While most authors have deduced a localization at the basolateral membrane of proximal tubules, other studies demonstrated a localization to the luminal membrane in the distal tubule
Was originally thought to be a nicotinamide N-methyltransferase
Was originally thought to possess 2 RRM (RNA recognition motif) domains and to bind RNA (PubMed:22431979). It seems to be in disagreement with the supposed ion transporter function
This was previously named TMEM55 and corresponded to a 130-residue protein. However, recent evidence suggests that the wrong ORF was originally chosen for this protein and supports an upstream ORF coding for a 63-residue protein
The sequence shown here has been extracted from PDB entry 1EXM
Lacks the phospho-accepting Asp (here Glu-116), present in the receiver domain, which is one of the conserved features of two-component response regulators (ARRs) family
Was thought to be a protease inhibitor (Ref.1, PubMed:15082560, PubMed:12369816)
Was also called At1g03610 (in AAM47889)
In spite of its official gene name, this protein may be the functional ortholog of human MRGPRX2, in terms of expression pattern and pharmacology
The several steps and mechanisms that permit controlled Shh dispersion and gradient formation remain controversial. The ShhNC C-terminal domain displays an autoproteolysis activity and a cholesterol transferase activity resulting in the cleavage and covalent attachment of a cholesterol moiety to the C-terminal of the newly generated N-terminal fragment (ShhN). The protein is further modified by covalent addition of palmitate at the N-terminal of ShhN, resulting to the dual-lipidated Shh (ShhNp). ShhNp is firmly tethered to the cell membrane where it forms multimers. Further solubilization and release from the cell surface seem to be achieved through different mechanisms, including the interaction with DISP1 and SCUBE2, movement by lipoprotein particles, transport by cellular extensions called cytonemes or by proteolytic removal of both terminal lipidated peptides. Once released, the fully processed Shh can signal within embryonic tissues both at short and long-range
LCK seems to be active in all vertebrates, except in squirrel monkey T-cells, in which it is inactivated. The reason seems to be that squirrel monkeys are the natural host for Saimiriine herpesvirus 2, which is able to efficiently transform T-cells through a mechanism involving viral Tip/ host LCK interaction. Its inactivation may a mechanism that specifically counteracts the transformation effects of viral Tip
Not expressed under laboratory conditions
Has been shown to confer susceptibility to the fungus Cochliobolus victoriae by conditioning victorin-dependent (victorin is a toxin synthesized by C.victoriae) induction of defense-associated proteins in cv. Cl-0 (AC A7XGN8). In strain cv. Bay-0, 2 variations at positions 228 (Thr -> Ala) and 538 (Arg -> Ser) result in an inactive LOV1 protein regarding sensitivity to victorin. The sequence shown is from strain cv. Bay-0, a complete sequence for LOV1 can be found in strain cv. Cl-0 (AC A7XGN8)
Has been the subject of controversy surrounding its catalytic capabilities. Early characterization of PEAK1 gave a weak in vitro tyrosine kinase activity (PubMed:20534451). The crystal structure indicates that the kinase-domain contains a closed nucleotide-binding cleft that in this conformation may deleteriously affect nucleotide binding (PubMed:29212708). Furthermore PEAK1 is devoid of nucleotide binding activity, as detected by a thermal-shift assay (PubMed:24107129). So it seems probable that PEAK1 is an inactive kinase
Could be the product of a pseudogene. It corresponds to positions 451 to 491 of the complete orthologous and probably active protein in R.felis (RF_0890)
The precise function of this protein in melanin biosynthesis is still under debate. DHICA oxidase activity is controversial (PubMed:9758418, PubMed:28661582). Lacks DHICA oxidase activity (PubMed:9758418). Has DHICA oxidase activity in the presence of Cu(2+), but lacks DHICA oxidase activity with Zn(2+) (PubMed:28661582)
Was initially thought to be a potential transcription factor, localized in the nucleus
The polymorphism 'Glu58Gly' (described in PubMed:12819961) is in fact an error, the G to A change described representing a synonymous mutation that does not induce any amino acid change in Gly-32
Could be the product of a pseudogene. Compared to other members of the glycosyl hydrolase 2 family this putative protein is truncated in both the N- and C-terminal regions and thus probably lacks enzymatic activity
Lacks the phospho-accepting Asp (here Glu-80), present in the receiver domain, which is one of the conserved features of the two-component response regulators (ARRs) family
This is a full-length TALA gene product. Strain AX2 produces a full length protein. Strain AX4 has a stop codon in position 1280 which disrupts the TALA gene and produces a truncated protein (AC P0CE94)
The glutathionylation site found in orthologs is not conserved here, possibly due to a gene model error, but the protein has been shown to be glutathionylated
The measured molecular weight is 17 daltons lower than the expected one suggesting an experimental error
Initally suggested to be a protease, mutation of the protease domain active site residues does not alter its in vivo function in magnetosome formation
Was originally thought to be an isopentenyl monophosphate kinase
This putative homolog of vertebrate MBD4 DNA glycosylase is designated as MBD4L (MBD4-like) to avoid nomenclature confusion with a protein with a conserved MBD but no DNA glycosylase domain already called MBD4 (AC Q9LYB9)
Despite overall sequence similarity to the typical alpha class carbonic anhydrases, lacks one of the three conserved catalytic zinc-ligand histidines. The carbonate dehydratase activity of this protein is zinc-independent
It is uncertain whether the mature protein starts at position 22 or 23. The first residue of the N-terminus obtained by direct protein sequencing is 'Asn-22' according to PubMed:18303202, but it is 'Val-23' according to PubMed:15047697, PubMed:10552514 and PubMed:29423371
In contrast to other members of the family, it lacks the conserved zinc-binding residues
This protein is not related to the claudin family
The NMR solution structure identifies a second transmembrane helix starting with Gly-91 (PubMed:25647032). The X-ray structure clearly shows that this region is not helical and not in the membrane; instead it is part of two beta-strands (PubMed:27042935)
High sequence similarity with other vitellogenin genes means that assigning functions to individual proteins is difficult; authors sometimes refer to VITs or vitellogenins
Transposon Ty1-A (YARCTy1-1) contains a frameshift at position 610, which disrupts the ORF coding for protein TY1B. This is the truncated, C-terminal part of TY1B translated from an in-frame start codon, and it is probably not functional
Was initially shown to have low deadenylase activity that was lost when the metal-binding Glu was mutated (PubMed:12573214). Later studies showed that the purified protein lacked deadenylase activity (By similarity). Was subsequently shown to act as a phosphatase (By similarity)
Was identified as interaction partner for CCS (PubMed:30260988). Only misfolded mutant protein forms that lack part of the zinc-binding sites interact with CCS. The full-length protein does not interact with CCS. Likewise, mutant protein that lacks all four zinc-binding residues does not interact with CCS (PubMed:30260988)
This protein was originally thought to have NAD-dependent ribose 1,5-bisphosphate isomerase activity but the recombinant protein was not active in vitro (PubMed:15375115, PubMed:26919468). In contrast, another protein from M.jannaschii likely possesses this activity (MJ0122)
S.cerevisiae displays strain polymorphism with regard to Endo.SceI endouclease activity. This is due to the mitochondrion-encoded, catalytic subunit ENS2, which exhibits strain polymorphism. It can be either present as continuous ORF in the mitochondrial genome (e.g. strain IAM 4274), present but disrupted by the insertion of GC clusters (e.g. strain D273-10B/A), or completely absent in the mitochondrial genome (e.g. strain S288c)
Information taken from PubMed:20637222 and PubMed:11137545 are not linked to a specific sequence. Hence, it is not sure whether the function corresponds to this protein or to a paralog
The highly conserved N-terminal zinc-binding site of this subunit is not present in this sequence
The existence of several isoforms has been reported that may be due to either different composition or different glycosylation or by the synthesis from different genes
Was originally thought to be a calcium transporter (PubMed:2145281). However later studies indicate that it functions as a sodium/potassium exporter (PubMed:11932440, PubMed:19757095)
Could be the product of a pseudogene. Compared with other ppx it lacks 200 residues at the C-terminal region
It is uncertain whether Met-1 or Met-20 is the initiator. A 'GT' insertion (rs59214675) allows to extend the sequence in the N-terminus. The majority of mRNAs do not have this insertion and the corresponding protein sequences start at Met-20
It is uncertain whether Met-1 is the initiator or if the sequence starts further upstream
PDLPs were initially named Cysteine-rich secretory proteins based on a classification work that failed to predict the transmembrane region at the C-terminus (PubMed:11402176). However, it was later shown that PDLPs are membrane proteins
Although similar to (1R,4R,5S)-(-)-guaia-6,10(14)-diene synthase, lacks the metal binding site Asn at position 288 and does not show (1R,4R,5S)-(-)-guaia-6,10(14)-diene synthase activity. Converting Lys-288 to a asparagine restores activity
According to a well-established model, RNF8 initiate H2A 'Lys-63'-linked ubiquitination leading to recruitment of RNF168 to amplify H2A 'Lys-63'-linked ubiquitination. However, other data suggest that RNF168 is the priming ubiquitin ligase by mediating monoubiquitination of 'Lys-13' and 'Lys-15' of nucleosomal histone H2A (H2AK13Ub and H2AK15Ub respectively). These data suggest that RNF168 might be recruited to DSBs sites in a RNF8-dependent manner by binding to non-histone proteins ubiquitinated via 'Lys-63'-linked and initiates monoubiquitination of H2A, which is then amplified by RNF8. Additional evidence is however required to confirm these data
It is unclear whether this protein requires a metal cofactor for catalysis. It was originally proposed to be a Zn(2+)-dependent metalloenzyme based on structural similarities to bacterial aminopeptidases and the observation that it can bind Zn(2+) ions, typically in a 1:1 stoichiometry (PubMed:21671571). However, a recent study suggests a Zn(2+)-independent catalytic mechanism (By similarity)
The cleavage site does not match the consensus
CKS-17 sequence does not match the minimal active consensus
No predictable signal peptide
Truncated; premature stop codon upstream of the potential transmembrane domain
There is no mitochondrial-type translation initiation codon present in frame in the sequence. In PubMed:19533212, the authors suggest the presence of a novel start codon coding for either Pro or Ser in Drosophila CoI transcripts
Although strongly related to polypeptide N-acetylgalactosaminyltransferase proteins, it lacks the conserved His at position 211 which is part of the Asp-Xaa-His motif which binds the cofactor Mn(2+). This suggests that it may have lost its activity
Both termini are shown to be facing the stroma and hence a sixth transmembrane domain should be present
It is uncertain whether Met-1, Met-11, Val-26 or Met-36 is the initiator
Could be the product of a pseudogene. This locus is annotated as an authentic frame shift in the DNA submission
Shares its exons with RAB34, but the first 5'-exon is longer, and the translation occurs 443 base pairs upstream from RAB34 initiator, in another frame. May be produced by an alternative promoter
Has been given the gene name AGO3 by FlyBase based on the literature but is more similar to members of the Piwi subfamily
Inactive as a kinase due to its inability to bind ATP
The human orthologous sequence is longer in the N-terminus
As Mambaquaretin-7 and Mambaquaretin-8 (different from the single residue A27S) could not be separated from each other, the characterization was done on their mixture
PubMed:16668362 postulates a moderate inhibition of serine proteases but the sequence homology points to a cysteine protease inhibitor
Characterization of function and toxicity was performed using CpTx1, a mixture of DELTA-miturgitoxin-Cp1a, DELTA-miturgitoxin-Cp1b and DELTA-miturgitoxin-Cp1c. While it is assumed that all three are active current data cannot prove this
This peptide is cyclic. The start position was chosen by similarity to cyclotide cter-M for which the DNA sequence is known
Was originally thought to function as a chloroplast protein import receptor
The sequence was elongated in the N-terminal section, to maximize the similarity with other orthologs. We have not found a valid start site, therefore we used an GTT
The first enzyme involved in phosphonate degradation (PhnW, EC 2.6.1.37) is not found in this organism. The function of this enzyme is therefore uncertain
Product of a dubious gene prediction. Overlaps in opposite strand with BAALC
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-5; H2AK7ac = acetylated Lys-7; H2AK126su = sumoylated Lys-126; H2AS128ph = phosphorylated Ser-128
Could be the product of a pseudogene, as in E.coli K12 the nmpC open reading frame is interrupted by an IS5 insertion and generates a hybrid open reading frame that is not expressed. In strains which have undergone selection for suppressors of ompB mutations (for example, mutant strain CS384) nmpC is expressed
Originally described as a 2-lysophosphatidate/LPA phosphatase (PubMed:12730698). However, following studies suggested it does not have such activity or only a residual one (PubMed:15280885). This is further supported by the fact that the phosphatase sequence motifs as well as the His residue acting as a nucleophile in active phosphatases of the PA-phosphatase related phosphoesterase family are not conserved (PubMed:15280885)
Was originally (PubMed:2973057) thought to be a protease. However, removal of residues 165-200 (a ClpP-protease-like motif) does not alter the lysogenization process, and in vitro studies show no evidence of a protease activity for the isolated HflKC complex
Lacks the conserved active site Asp and is not expected to have phosphoribosyltransferase activity
Was originally proposed to be a calcium channel facilitator (By similarity). However, a more recent study shows that this protein regulates membrane phospholipid homeostasis (PubMed:30509349). Therefore, any effects on calcium flux are most likely a secondary consequence of defects in membrane composition or fluidity (PubMed:30509349)
Although similar to the small GTPase superfamily, lacks the conserved catalytic Gln in position 67 which is replaced by a Ser residue, possibly explaining the weak GTPase activity. In contrast to other members of the family, it is not prenylated (PubMed:22076686) and unlikely to associate directly with membranes
All C.westwoodi family members described in 'Undeheim et al., 2014' have not been imported into UniProtKB. Please, refer to this paper to access them
Was originally suggested to be a nuclease that resolves Holliday junction intermediates during genetic recombination
Was originally thought to be involved in the regulation of the labile hydrogenase activity
Lacks the Asp residue of the conserved catalytic triad Ser-Asp-His
Was originally thought to be a heat shock protein. However upon further examination the original mutants do not have a deletion in this gene (PubMed:16980444)
The gene names for receptor guanylyl cyclases are inconsistent between mouse and human. The ortholog of the mouse Gucy2d gene is a pseudogene in humans. The mouse Gucy2d is not an ortholog of the human GUCY2D gene, the latter of which encodes a retinal receptor guanylyl cyclase involved in phototransduction
It is uncertain whether Met-1 is the initiator
Despite its name, the presence of HEAT repeat is unsure and is not confirmed by repeat-detection programs
Lacks the conserved Ser at position 1000 required for covalent attachment of 4-phosphopantetheine
Could be the product of a pseudogene unlikely to encode a functional protein. This is a truncated version of a second copy of formate dehydrogenase in the yeast genome. Strains BY4741, S288c and W303 have a stop codon in position 146, which disrupts the gene coding for this protein and produces two ORFs YPL275W and YPL276W. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. A contiguous sequence for formate dehydrogenase 2 can be found in found in strain CEN.PK113-7D (AC P0CT22)
The crystal structure does not show the Schiff base that is expected to form between Lys-194 and the pyridoxal phosphate cofactor
In contrast to other cytidine and deoxycytidylate deaminase, lacks the conserved Glu active site in position 213 which is replaced by a Val residue, suggesting that it acts as a regulatory subunit
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 1410 in the dsPTPase catalytic loop, suggesting that it has no phosphatase activity
In strain CO-92 it seems to be a pseudogene. It is interrupted by frameshifts in positions 90 and 143. The sequence has been verified by the authors and is believed to be correct
Although the active site residue Ser is conserved, appears to lack catalytic activity in vitro
Lacks the conserved catalytic glutamate found in many enzymatically active members of the Gcn5-like N-acetyltransferase (GNAT) family
Surprinsingly, this toxin has also been observed to have phospholipase A2 and trypsin inhibitory activities
This protein was previously thought to be M-calpain but has since been found to be an intermediate form between the M and Mu types
Could be the product of a pseudogene. Is missing N- and C-terminal sequences compared to its orthologs
Does not bind calcium as one of the calcium-binding sites is lost (Asp->Asn in position 64, which corresponds to 'Asn-49' in the current nomenclature)
The protein characterized in PubMed:9660191 corresponds to this sequence and not to the fragment sequence described in this article
Was originally thought to be a ligand for CCR8
Probably inactive as a hydrolase due to lack of catalytic Cys and His
It is uncertain whether Met-1, Met-6, Met-110, Met-114 or Met-123 is the initiator
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-4; H2AK7ac = acetylated Lys-7; H2AS128ph = phosphorylated Ser-128
Many references talk about 'p110 isoforms' but it is not yet known if this refers to CDK11A and/or CDK11B or one/some of the isoforms of each
Could be the product of a pseudogene. RPL23 has been split into 2 overlapping ORFs in the Caryophyllales. Although these genes are transcribed, this is probably the product of a pseudogene; the protein purified with the 50S subunit is the product of a nuclear-encoded gene (AC Q9LWB5)
Lacks the dyad motif characteristic of alpha-KTx and generally associated with channel blockage
Although the beta-barrel of Cu/Zn SODs is largely preserved, SOD5 is a monomeric copper protein that lacks a zinc-binding site and is missing the electrostatic loop element proposed to promote catalysis through superoxide guidance. Without an electrostatic loop, the copper site of SOD5 is not recessed and is readily accessible to bulk solvent
Only one single gene encoding glyoxalase II has been identified in vertebrates. In yeast and higher plants, separate genes encode the cytosolic and mitochondrial forms of glyoxalase II
Thr-72 is not followed in the nucleotide sequence by the expected Gly residue required to produce amidation
Was originally reported to play a role in determining adult lifespan. However, the paper was later retracted due to errors in the data
Lacks the conserved active histidine at position 79 that mediates the phosphotransfer. Shows a conserved HPt domain that may have some alternative degenerated phosphorelay role in cell signaling
Nomenclature used in PubMed:8576224 refers to PP2A B subunit B' alpha isoform, which is cited as PP2A B subunit beta-PR61 isoform in later publications
Sequence AAQ84766 was incorrectly indicated as originating from mouse
Could be the product of a pseudogene. There seems to be a natural frameshift that produces two separate ORFs
No similarity to other species complex I subunit 2
The homodimer may have ATP-independent ubiquitin ligase activity. However, in another study, UCHL1 was shown to lack ubiquitin ligase activity
Corresponds to the C-terminal section. Unlike the other Salmonellae, the ortholog of the FliB protein may be encoded by two CDS in S.muenchen. It cannot be ruled out that sequencing errors produced two CDS instead of one
In spite of its similarity with AHCY, which catalyzes the reversible hydrolysis of S-adenosyl-L-homocysteine to adenosine and homocysteine, recombinant AHCYL1 expressed in bacteria shows no hydrolase activity, nor does it affect the enzyme activity of AHCY
Lacks the FYVE domain, necessary to efficiently target the protein to membranes containing the phosphatidylinositol-3P substrate. Therefore, its molecular function remains unknown
E.coli has 2 glycerate kinases, GK1 and GK2; it is not clear which gene encodes which enzyme. PubMed:5325263 may be a mix of GK1 and GK2
Contains the typical disintegrin-like domain of the P-III subfamily, but lacks the cysteine-rich domain like in P-II subfamily. This protein may represent an intermediate in the evolutionary pathway along the structural diversification pathway of disintegrin (PubMed:16786436)
This protein has not been detected in the venom
Was originally assigned to be ubiB
Product of a dubious gene prediction unlikely to encode a functional protein. Was originally (PubMed:7992502) thought to function in calcofluor white resistance, hence the name CWH36, but this phenotype was later (PubMed:14594803) attributed to the overlapping gene VMA9. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
Has no homology to any known proteases
Isoform 2 (PKMzeta) was initially thought to be generated by proteolysis of full-length PRKCZ (PubMed:8378304). However, PKMzeta is a bona fide isoform produced by an alternative promoter in intron 4 (PubMed:12857744)
Was originally thought to be a receptor for sphingosine 1-phosphate
This locus, comprising the single gene At5g12370 in the original reference genome assembly, contains in fact two paralogous genes in tandem, SEC10a (At5g12370) and SEC10b (At5g12365), and a sequence segment of 7 kb in length is missing from the reference genome sequence
The original paper reporting the role of LOXL2 in deamination of trimethylated 'Lys-4' of histone H3 was retracted due to inappropriate manipulation of figure data (PubMed:22483618, PubMed:27392148). However, this role was confirmed in a subsequent publication (PubMed:27735137)
Could be the product of a pseudogene unlikely to encode a functional protein. This is a truncated version of a flocculin protein family member. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
Was originally reported as originating from S.acidocaldarius
There are 2 paralogs in M.tuberculosis, in a reference this gene is called nei1
It is uncertain whether Met-1 or Met-33 is the initiator
It is uncertain whether Met-1 or Met-50 is the initiator
The sequence shown here has been extracted from PDB entry 1C52
Lacks conserved residue(s) required for the propagation of feature annotation
It is uncertain whether Met-1 or Val-27 is the initiator
Was originally thought to be pallidin
Was originally thought to be a poly(A) polymerase II
Although it contains a putative aminopeptidase domain, the critical residues for Zn(2+) binding and thus for catalytic activity are not conserved suggesting that nra-2 lacks peptidase activity
Seems to lack the C-terminal part (TM6 and TM7)
The fragment sequence AC P84691 is identical to the sequence presented in this entry, but both peptides are probably different peptides, since the experimental molecular mass of AC P84691 does not correspond to theoretical mass of the peptide presented here
The question of whether FtsL and DivIC interact directly (PubMed:16936019) or indirectly (PubMed:11994149) remains controversial
Lacks the phospho-accepting Asp (here Glu-95), present in the receiver domain, which is one of the conserved features of two-component response regulators (ARRs) family
Despite the fact that it belongs to the cyclophilin-type PPIase family, it has probably no peptidyl-prolyl cis-trans isomerase activity
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-37; H2BK143ub1 = monoubiquitinated Lys-151
Lacks the conserved Ser residue within the catalytic triad which is replaced by a Gly residue, probably resulting in a loss of proteolytic activity
Was termed TMPRSS6 (Ref.3)
Appears to have serine protease activity in vitro (PubMed:19716386). However, it is uncertain if this activity is genuine as bli-5 lacks all the catalytic features of serine proteases
Has sometimes been referred to as ADAMTS3
Was originally thought to be involved in mitochondrial import
Was originally (PubMed:15215601) thought to be a probable tetracycline dehydrogenase since it is essential to the final reaction in the biosynthesis of 6-demethyltetracycline, but enzymatic activity has not been proven. Several facts suggest it is more likely to be a coenzyme F420:L-glutamate ligase: it is a homolog of the characterized protein CofE from Methanococcus jannaschii and FbiB from Mycobacterium smegmatis which are involved in the polyglutamylation of F420-0; F420 is used for tetracycline biosynthesis, probably being necessary for the last step; the gene coding for this protein is close to a homolog of the characterized protein CofD from Methanococcus jannaschii involved in F420-0 production
Due to the high similarity between gsp-3 and gsp-4, the antibody used to study expression does not distinguish between the two proteins
An article reported regulation of transcriptional activity and hypersensitive response control by Xanthomonas type III effector XopD; however, this paper was later retracted
The protein deglycation activity has been ascribed to a TRIS buffer artifact by a publication (PubMed:27903648), which has then been rebutted by clear biochemical experiments showing that DJ-1 family deglycases are bona fide deglycases (PubMed:28013050). Deglycase activity is even strengthened by a novel article that reports nucleotide deglycation activity (PubMed:28596309)
PubMed:22447656 describes a heterodimeric snaclec (named agkisacucetin) that is presented as being another protein than agglucetin, despite the very high sequence similarity. Agkisacucetin is described as an inhibitor of platelet aggregation, but no experimental data or cited references support this description. In addition, according to PubMed:22447656, agkisacucetin cannot be tetrameric, because cysteine residues are missing. However, non-covalently linked tetramers are found in snaclecs, as exemplified by rhodocetin
The T-DNA insertion may still allow the production of a functional cytosolic form of the protein, if translation is initiated from the second initiation codon, encoding Met-63 in the full-length protein
Several peptides are generated during UQCRFS1 insertion. According to some authors, the identification of the transit peptide as the subunit 9, does not necessary imply that it must be considered as a structural subunit of the complex III dimer as additional fragments from UQCRFS1 are also present
The lack of peptide signal and first catalytic site is due to the cloning strategy (the sequence was amplified from the second ATG codon). The functional tests have been done using an incomplete recombinant protein resulting in an inactive protein. However, this functionally inactive recombinant protein behaved as a good immunogen, capable of inducing immunoprotection in test animals
Product of a dubious CDS prediction. LINC02912 may produce non-coding RNAs that regulate the expression of SIM2
Could be the product of a pseudogene. It is transcribed
Was originally thought to be membrane-associated
M.bovis (strains ATCC BAA-935 / AF2122/97 and BCG / Pasteur 1173P2) and M.marinum (strain ATCC BAA-535 / M) have a single fused pks15/1 ORF, but M.tuberculosis (strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh) have 2 separate ORFs. This is due to the natural deletion of a single base, a guanine, that causes a frameshift and thus the two ORFs, pks15 and pks1, instead of pks15/1. This frameshift led to the inactivation of Pks15/1, which in turn caused the inability of these strains to elongate the putative p-hydroxybenzoic acid precursor and thus to produce phenolphthiocerol derivatives
X-ray crystallography in other archaea shows this protein binds a 3Fe-4S cluster, although a 4Fe-4S cluster has been suggested to be present in this protein
Has not been found in the genome sequence, yet it seems to be really from D.discoideum
Cellular localization of OCT1 in the intestine and the kidney remains to be finally defined. While most authors have deduced a localization at the basolateral side of enterocytes consistent with a physiological role in organic anions uptake from the blood flow and intestinal excretion (By similarity), other studies demonstrated an apical localization (By similarity), supporting a function in intestinal absorption of organic anions and drugs (By similarity). Similarly, contradictory findings have shown a localization to the basolateral side (By similarity) or to the apical side (By similarity) of proximal tubules (By similarity). Affinity and capacity of the transporter for endogenous substrates vary among orthologs (By similarity)
In cv. Columbia (AC P0DKJ8), the sequence differs from that shown due to a deletion in the genomic sequence that remove 60 residues after the Asn-562
Was originally thought to originate from mouse
In strain IOL-207 the Cys that is thought to be palmitoylated is mutated to Ser; presumably the following Cys is acylated instead
Has no ubiquitin ligase activity on its own; may require ubiquitin-conjugating enzyme, ubc-13
Was originally (PubMed:1313413) thought to be an accessory protein required for nickel incorporation at the urease active site or for nickel transport. Actually, has been shown (PubMed:9712811) not to be required for the assembly of a catalytically active urease
In PubMed:11442825, mutational analysis indicated that His-123, His-131, and His-193 were important for acid activation of urea uptake in the Xenopus oocytes model, but in H.pylori itself His-193 seems to be the only histidine that is crucial for UreI activation at low pH
Identified as a cargo protein of vacuolar sorting receptors (PubMed:23738689). This was based on interactions with truncated vacuolar sorting receptors and their co-secretion in the culture medium (PubMed:23738689). This function is however not supported by recent evidences
Was originally thought to have endopeptidase activity (PubMed:1885539). But it could not be confirmed with orthologs purified from P.abyssi (PubMed:17766251, PubMed:21183954)
PubMed:18095347 report an endoplasmic reticulum localization and a lack of enzymatic activity, which could be a result of impaired N-glycosylation
PubMed:10988300 reports the possible existence of a secreted isoform starting at Met-119. However, they do not provide any experimental evidence
Was originally (Ref.1) thought to originate from Porphyra purpurea
Could be the product of a pseudogene. The gene coding for this protein is interrupted by a IS3B element between amino acids 486 and 487
Lacks the conserved Glu residue in position 490 essential for carbopeptidase activity. The mature form lacks catalytic activity towards synthetic peptide substrates
The first non-coding exon of CCBL2 is in common with that of RBMXL1
AOP1, AOP2 and AOP3 are found in tandem and inverted duplications on chromosome IV and encode 2-oxoglutarate-dependent dioxygenases involved in glucosinolates biosynthesis. In cv. Columbia, AOP2 (AC Q9ZTA2) cDNA contains a 5-bp deletion that leads to a non-functional protein and AOP3 (AC Q9ZTA1) is not expressed. The functional and expressed alleles for AOP2 (AC Q945B5) and AOP3 (AC Q945B4) are found in cv. Cvi and cv. Landsberg erecta, respectively. No ecotype coexpresses both AOP2 and AOP3 genes. The catalytic role of AOP1 is still uncertain (PubMed:11251105)
Lacks the calcium-binding EGF-like domain which is a conserved feature of the wall-associated receptor kinase family
Lacks the typical ATP binding site, suggesting that it may not be functional
There might be a sequencing error that fuses together two ORFs
Was originally thought not to have cytosine-5 methyltransferase activity, and this was attributed to the insertion of a Ser residue between the Pro-Cys motif found at the active site of C5 MTases (PubMed:8636983). When this serine is deleted it becomes catalytically active and recognizes and methylates the sequence CC[AT]GG. This was in agreement with S.pombe lacking m5C DNA-methylation. However, it has later been shown that it has tRNA-methyltransferase activity despite this sequence variation (PubMed:23074192)
While it is structurally defined as a knottin it lacks the conserved Cys residue in position 95
The reactive bond has a Glu in position P1 instead of an expected Arg or Lys
The guanine nucleotide exchange factor (GEF) activity is controversial. One study showed GEF activity towards RALA, RAP1A and RRAS (PubMed:10896938). However, in another study, a construct containing only the Ras-GEF domain lacks GEF activity towards RAP1 (By similarity)
A portion of this ORF was originally annotated as mcrD, and reported to inhibit mcrE restriction
Was initially proposed to transport palmitoylcarnitine, based on complementation experiments in yeast mutants lacking CRC1 and CIT2 and release of radiolabeled carnitine from mitochondria incubated with radiolabeled palmitoylcarnithine (PubMed:12882971). Later experiments done primarily with human indicate the protein functions instead as transporter of basic amino acids (By similarity)
Has been described as a LysP lysine permease, due in part to the presence of LYS elements in the regulatory region
An article showing that FANCM-MHF promotes gene conversion at blocked replication forks by fork reversal was withdrawn due to genotype mislabeling of strains. Following strain regeneration, although many phenotypes were not reproducible, the central observations of the publication were confirmed
Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction (PubMed:20503968)
In contrast to other members of the family, does not contain a prenylation domain
The subcellular locations reported need confirmation (PubMed:19682089). Components of the WMM complex are known to localize in the nucleus, and it is also the case for the CBLL1/HAKAI protein in vertebrates. It is therefore likely that this protein mainly localizes in the nucleus
SHISA7 has been reported to interact with AMPAR subunit GRIA1 in heterologous conditions and in the brain (By similarity). However, it was later demonstrated that SHISA7 does not colocalize neither interact with AMPAR, but with GABA(A)R (By similarity). Therefore additional experiments are needed to understand the discrepancy for SHISA7 function
A paper showing a role in tumorigenesis has been retracted due to panel duplication in several figures
This sequence is shorter than orthologs and has a completely different amino acid sequence after position 289 due to a single nucleotide insertion. This protein is not functional which could partially explain the failure of M.bovis derivatives to produce the full-length PGL
The oxidation forms of Trp-89, Trp-143 and Trp-197 are subject of controversy and could be the artifactual results of sample handling
Lacks the conserved Lysine residue that is involved in covalent pyridoxal phosphate binding in other members of the family
Was originally thought to be an ammonium transport protein
Has no tyrosine-protein phosphatase activity at mild acidic conditions (pH 5.5). The in vivo relevance of the low PPase activity for the human protein at acidic conditions (pH 4.5) is questioned. This catalytic activity seems to be affected by the replacement of a highly conserved residue in the tyrosine-protein phosphatase domain
Lacks 2 conserved residues that bind magnesium; the aspartate residue in position 464 is replaced by an asparagine and the glutamate residue in position 467 is replaced by a serine residue
Non-collagenous domain 1 seems to be the predominant tissue form from which endostatin is cleaved. However, the proteolytic cleavage site to generate non-collagenous domain 1 is not known. Soluble recombinant non-collagenous domain 1 amenable to biochemical studies has been used instead; its molecular weight corresponds to probable non-collagenous domain 1 immunoblot bands seen in tissue extracts
Lacks the conserved His residue that binds heme iron in the nitrobindin family
Was originally thought (PubMed:14960574) to be a mannosyltransferase involved in the biosynthesis of phosphatidylinositol mannosides (PIMs), but further in vivo and in vitro characterizations (PubMed:18585090) clearly show that inactivation of Rv1500 does not affect the expression pattern of PIMs
There are two genes for this protein in the chloroplast inverted repeat; while they are usually identical, in this organism they are not. The other copy is AC Q8S8V2
Further mature peptides might exist
Compared to other sortases, it is shorter and lacks the N-terminal membrane anchor. It may lack activity
Although it belongs to the glycosyl hydrolase 22 family, Ala-70 and Asn-87 are present instead of the conserved Glu and Asp which are active site residues. It is therefore expected that this protein lacks hydrolase activity
Lacks the conserved Glu residue in position 485 essential for carbopeptidase activity. The mature form lacks catalytic activity towards synthetic peptide substrates
It is uncertain whether Met-1 or Met-104 is the initiator. Some orthologous sequences cannot be extended
EcdB, ecdC, ecdD, ecdE and ecdF have previously been identified as being part of the echinocandin B biosynthetic cluster, but it was later realized that this was due to a genome misassembly and these 5 proteins are now considered as artifacts and not part of the cluster
S.cerevisiae displays strain polymorphism with regard to Endo.SceI endouclease activity. This is due to the mitochondrion-encoded, catalytic subunit ENS2, which exhibits strain polymorphism. It can be either present as continuous ORF in the mitochondrial genome (e.g. strain IAM 4274), present but disrupted by the insertion of GC clusters (e.g. strain D273-10B/A), or completely absent in the mitochondrial genome (e.g. strain S288c). Sequences for the 2 subunits ENS2 (AC P12294) and SSC1 (AC P0CS91) for an active Endo.SceI endonuclease can be found in strain IAM 4274
Has been shown in one study to be involved in the active efflux of the autoinducer N-(3-oxododecanoyl) homoserine lactone (PubMed:9973347). However, has been shown in another study not to be involved in efflux of this autoinducer (PubMed:32715566)
According to PubMed:15077197, it is a pseudogene. However, a peptide specific to this protein was identified by mass spectrometry (PubMed:17525332). Given that the product described by PubMed:15077197 is located downstream and on another frame of the transcript, it may explain why PubMed:15256438 could not detect this protein on a Western blot
A palmitoylation site was proposed at Cys-77, but it was later shown that this cysteine is engaged in a disulfide bond
After extraction of the protein with ammonium fluoride and hydrofluoric acid, His-137 and Cys-279 were reported to be oxidized but could be the artifactual results of sample handling. Leu-123 was also reported to be mono- and dimethylated. Despite sequence similarity with cathepsins, silicatein lacks the intra- and interchain disulfide bonds for conserved cysteines. No numeric data was provided to support the mass-spectrometric interpretations
In contrast to other members of the family, lacks the C-terminal ricin B-type lectin domain that contributes to the glycopeptide specificity, and lacks the conserved His residue in position 341. No glycosyltransferase activity has been detected in an in vitro assay (PubMed:24398516)
It is uncertain whether Met-1 or Met-28 is the initiator. Some orthologous sequences cannot be extended
According to a report, N6-methylation of MAT2A affects MAT2A mRNA stability instead of preventing splicing (PubMed:29262316). However, it was later shown that N6-methylation of MAT2A transcripts prevents recognition of their 3'-splice site by U2AF1/U2AF35, thereby inhibiting splicing and protein production (By similarity)
It is uncertain whether Met-1 or Met-97 is the initiator
Alleles mu63 and mu349 were originally reported (PubMed:9834184) as the mutations L130F and Q147STOP respectively. This is in conflict with WormBase and more recent literature (PubMed:15282167) which is represented in this entry
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-33; H2BK34ac = acetylated Lys-34; H2BK143ub1 = monoubiquitinated Lys-138
The histidine biosynthesis pathway is not functional in the dairy strain IL1403
Lacks one of the four calcium-binding sites (Gly->Ser in position 30) found in other family members
It was previously proposed that SLC39A2 operates as a Zn2(+)/HCO3(-) symport mechanism (By similarity). However in more recent studies, SLC39A2-mediated transport is independent of both HCO3(-) and H(+)-driving forces, but modulated by extracellular pH and voltage (By similarity)
The 45 kDa RNA-binding proteins identified in PubMed:7969126, PubMed:8873767 and PubMed:11087864 may correspond to elavl2/elrB
Silenced gene expression via RNA interference in PubMed:17011493 and PubMed:17960593 was simultaneously performed with DDX5 and DDX17; siRNA-resistant DDX5 expression was able to rescue the effect in muscle differentiation
Is probably not a functional DNA helicase since the N-ter is truncated and misses the ATP-binding domain
Does not bind calcium as one of the calcium-binding sites is lost (Asp->Lys which corresponds to 'Lys-49' in the current nomenclature)
The source organism was originally classified as the Bothrops neuwiedi species
Postulated to regulate KDM8 histone demethylase activity on di- and trimethylated 'Lys-36' (H3K36me2/me3) of histone H3 (PubMed:24981860). However the demethylase activity of JMJD5 is controversial, as it was later shown to rather act as an endopeptidase that cleaves monomethylated and dimethylated arginine residues of histones H2, H3 and H4. In several studies, JMJD5 was shown not to display any demethylase activity toward methylated H3K36 nor toward other methyllysines in the N-terminal tails of H3 and H4 in vitro (PubMed:28982940)
Was originally thought to be a tagatose 6-phosphate kinase
The revised sequence of AmiA now includes, in the C-terminal section, the sequence of an ORF which was previously known as AmiB
According to PubMed:12959640, T.stejnegeri was formerly named T.gramineus, implying that this protein is the same as PLA-II from T.gramineus. They have been kept separated, because T.gramineus and T.stejnegeri are considered to be two different species (see http://reptile-database.org)
Was originally proposed to code for two separate adjacent ORFs, ascA and ascB
The most common activity assay for dermonecrotic toxins detects catalytic activity by monitoring choline release from substrate. Liberation of choline from sphingomyelin (SM) or lysophosphatidylcholine (LPC) is commonly assumed to result from substrate hydrolysis, giving either ceramide-1-phosphate (C1P) or lysophosphatidic acid (LPA), respectively, as a second product. However, two studies from Lajoie and colleagues (2013 and 2015) report the observation of exclusive formation of cyclic phosphate products as second products, resulting from intramolecular transphosphatidylation. Cyclic phosphates have vastly different biological properties from their monoester counterparts, and they may be relevant to the pathology of brown spider envenomation
3D structural studies were performed with a synthetic heptapeptide that contained Cys, corresponding to position 1094, therefore the detected disulfide bridge is an artifact
Fused to a domain highly related to the dihydrofolate reductase family in its N-terminus. It is however unknown whether it contains such enzymatic activity
Could be the product of a pseudogene. Lacks the signal peptide and part of the extracellular leucine-rich repeats that are required for the specificity of the elicitor protein recognition, which are conserved features of the family
It is uncertain whether Met-1 or Met-76 is the initiator. Transcript evidence available at present time points at Met-76. In this short version of the protein, the signal peptide cannot be predicted and the irisin peptide is severely truncated. The first initiation codon corresponds to a non-AUG site, an N-terminal ATA codon. This initiation codon has been annotated as it is in good Kozak context and it is conserved in other primates, including gibbon, chimpanzee and gorilla. Although the existence of such a form has not been demonstrated in human, western blot analysis following endurance exercise shows the presence of an irisin peptide of similar size in human and mouse plasma (PubMed:22237023), suggesting the existence of full-length irisin in human, at least in some tissues. However, expression from Met-1 may be less efficient than that from Met-76 (PubMed:24040023)
Unlike mammalian homologs, does not play an essential role in the endoplasmic reticulum-associated degradation (ERAD) of inositol 1,4,5-triphosphate receptors (IP3Rs)
Was originally thought to be part of an osmoprotectant uptake system (PubMed:15251200). However, it was shown later that the complex does not mediate osmotic stress protection (PubMed:26325238)
B.parapertussis and B.bronchiseptica seem not to produce the pertussis toxin (S1, S2, S4, S5 and S3) and Ptl proteins (PtlA, PtlB, PtlC, PtlD, PtlE, PtlF, PtlG, PtlH and PtlI) in vivo due to changes in the promoter region of the ptx-ptl operon. However, it is possible that their promoter is active under certain, as-yet-undefined conditions and that B.parapertussis and B.bronchiseptica are therefore capable of producing these proteins
Amino acids thought to be required for catalysis are not conserved in ISA2, suggesting that it may not be an active debranching enzyme and acts via its interaction with ISA1
Lacks the conserved Glu residue in position 506 essential for carbopeptidase activity. The mature form lacks catalytic activity towards synthetic peptide substrates
Could be the product of a pseudogene. Transposon Ty4-P (YPLCTy4-1) contains a frameshift at position 1105, which disrupts the ORF coding for protein TY4B. It is probably not functional
The product of the reaction was originally identified as L-erythrulose 4-phosphate (PubMed:26560079). It was then corrected to L-erythrulose 1-phosphate by the same group (PubMed:26978037)
An additional N-terminally truncated cytoplasmic isoform was previously reported to exist. However, the paper was subsequently retracted due to concerns regarding duplication of panels in some figures
The sequence TLRTTTGYWTTVEKGNGTTPAANSTEKGNRPYGR described in the text of Wu et al., 2010 as Hyalomin-B1 is indicated as Hyalomin-B2 in Fig.1b. Therefore, it is uncertain whether the function described for Hyalomin-B1 is not the function of Hyalomin-B2
Was originally (Ref.1) thought to be involved in thiamine biosynthesis. However, this phenotype was probably due to an artifactual recombination event involving a portion of the adjacent thiI gene
An alternative upstream Met is found in primates and translation may initiate from the upstream Met which would give rise to a 680-residue protein. However, the upstream codon has a weak Kozak signal while the codon used for translation of the shorter 677-residue sequence has a strong Kozak signal and is widely conserved. In addition, protein sequencing indicates that this is the preferred start codon in vivo
Was originally thought to have DNA polymerase activity
A stretch of the chloroplast genome is duplicated within chromosomes 6 and 7 resulting in the duplication of the gene. The expression of these duplicated genes has not been demonstrated
Comparisons with its orthologs suggests that this protein may be full-length
Was reported that reduction/oxidation of cysteine residues Cys-23, Cys-45 and Cys-106 and a possible intramolecular disulfide bond involving Cys-23 and Cys-45 give rise to different redox forms with specific functional activities. Was reported to be secreted. However, this work was later retracted, although the roles of different redox forms in some functional activities is supported by similarity
Alternative initiation from an upstream conserved methionine cannot be fully excluded but is not experimentally supported while initiation from the displayed methionine is supported by PubMed:17323924
Lacks the conserved cysteine (here Ser-39), present in the redox-active center, which is one of the conserved features of the thioredoxin family
This protein does not undergo proteolytic processing to release the disintegrin domain
Membrane topology is controversial (PubMed:16223484, PubMed:15355969). Membrane topology structure with endoplasmic reticulum lumen orientation of the catalytic domains while the C-terminus is in the cytosol have been suggested (PubMed:16223484, PubMed:11279029). Others investigators have argued for a reverse orientation, with a membrane-embedded N-terminal domain but no C-terminal transmembrane segment, and a cytosolic orientation of the catalytic domain (PubMed:15355969). These contradictory results are probably because of differences in the assay systems
Has been reported to be located in the Golgi apparatus (By similarity). However, another study was unable to detect Golgi localization (By similarity). Has also been reported to be located in the mitochondrion (By similarity). However, no mitochondrial localization was detected in another study which reported that the protein is primarily cytoplasmic (By similarity)
There is uncertainty concerning the 2-methylcitrate stereochemistry. Brock et al. report a (2S,3S) stereochemistry, but Reddick et al. determined that the 2-methylcitrate has either (2S,3R) or (2R,3S) stereochemistry
A paper describing a role for this protein in IRAK1-independent activation of the MAPK/ERK pathway in response to IL1 has been retracted, because some of the experimental data could not be reproduced
The transcript is probably edited at the RNA level as has been shown for P.thunbergii, P.armandii, P.mugo, Larix kaempferi and Abies homolepis (see PubMed:15240834)
Was originally thought to be a ribosomal protein
Based on sequence similarity, it has been suggested that C15orf41 might encode a divalent metal-ion dependent restriction endonuclease, although nuclease activity could not be experimentally proven
Due to a recent gene duplication event, CYP3A30 and CYP3A56 are very similar. Because of this it was not possible to distinguish between the two genes when measuring the tissue expression
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 1422 in the dsPTPase catalytic loop and does not have phosphatase activity (PubMed:9537414). The pocket is however sufficiently preserved to bind phosphorylated substrates, and maybe protect them from phosphatases
Mutations in the scaffold leading to either a stop codon instead of a Glu at position 90, an Arg instead of the well conserved Trp at position 188, or a Pro instead of Ser at position 303 lead to the loss of inhibitory activity
The universally conserved zinc-binding site of this subunit is not present in this sequence
Could be the product of a pseudogene. N-terminally truncated compared to the protein-coding REXO1 gene. Originally thought to encode human GOR47-1, an antigenic epitope identified from the serum of virus infected chimpanzee (see AC P48778), which was apparently also expressed in human and used in ELISA tests to detect hepatitis C virus infection in patients. It turns out that the peptide identified in chimpanzee cannot be produced by human REXO1L1/GOR gene, due to a premature stop codon in the gene (PubMed:11472404) and therefore the basis of the tests remains unclear. However, the same authors provide evidence of the expression of a different N-terminal peptide from the human REXO1L1/GOR gene, the GOR1-125 antigen (PubMed:11472404)
The metalloprotease is also encoded by another precursor (AC Q90WC0)
Was originally thought to be the Disks lost (Dlt) protein. However, PubMed:14667407 showed that it is not the case and renamed it Patj. This drastically changes the first conclusions drawn about its essential function, since the mutant used contained defects for another protein, which is now called Dlt. If its association with proteins involved in cell polarization complexes is clear, Patj is not essential since its absence apparently does not lead to important defects
The sequence shown in this entry differs from the translation of the reference genome assembly (GRCh38/hg38) due to a missense variant at position 174 in the reference genome, that results in the loss of response to short chain fatty acids, including propionate
No in vitro nuclease activity has been observed against crRNA for this protein
The TIAF1 protein is coded in the 3'-UTR region of MYO18A
It is uncertain whether Met-1 or Met-22 is the initiator
Lacks the PABC domain, which is one of the conserved features of the PAPB family
It is unsure whether the 3rd residue is an Ile or a Leu. NMR structural calculations were carried out using only the Ile-3 form of the peptide
Was originally thought to be a sensor protein involved in the regulation of hydrogenase activity
Sequences and experimental results obtained from PubMed:16112630 and PubMed:16914147 are obtained from A.mellifera carnica and not A.mellifera
The intracellular compartmentalization of AGTX in mammalian hepatocytes is species dependent. In human and rabbit, AGTX is peroxisomal. In new world monkeys (marmoset) and rodents (rat and mouse), it is distributed approximately evenly between peroxisomes and mitochondria. In carnivores, like cat, the great majority of the enzyme is mitochondrial with only a small proportion being peroxisomal
The alternative and minor mechanism for utilizing trehalose as a carbon source provided by the MAL11/AGT1 and NTH1 system is specific to S.cerevisiae strains with constitutive and non-glucose-repressible expression of the MAL genes
In contrast to other members of this family, lacks the conserved Cys in position 69, which is replaced by an Arg
Was originally reported to catalyze the cofactor-independent decarboxylation of pyruvate (PubMed:21623357). In contrast, Kellett et al. demonstrated with computational, structural, and kinetic evidence that this enzyme does not exhibit pyruvate decarboxylase activity (PubMed:23452154)
Cannot be called ispA as this name is already used
Was originally (PubMed:2494667) thought to be vnd but further analysis (PubMed:2127912) has clearly shown that it corresponds to Appl
The authors believe the gene from which the sequence was translated to be functional although the second intron begins with 'GC' rather than the usual 'GT'
Was initially thought to be involved in chloroplast development or function against cell death (PubMed:21916894, PubMed:22180599)
PubMed:2420009 misquotes the gene name as 'CSF1'
When this sequence was assembled, the third base of codon 137 was missed, generating two ORFs instead of one
The ortholog in A.thaliana catalyzes the first reaction of the Smirnoff-Wheeler pathway, the major route to ascorbate biosynthesis in plants
Could be the product of a pseudogene. The original protein is truncated by an IS2 element which is inserted after residue 255, giving an altered C-terminus
Represents an unconventional myosin that should not be confused with the conventional myosin-1
Several experiments have been done with an amidated coprisin, although the amide donor for C-terminal amidation (usually a Gly residue) is missing in the precursor sequence
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-8; H2BK6su = sumoylated Lys-8; H2BK7ac = acetylated Lys-9; H2BK7su = sumoylated Lys-9; H2BK11ac = acetylated Lys-15; H2BK16ac = acetylated Lys-25; H2BK16su = sumoylated Lys-25; H2BK17su = sumoylated Lys-26; H2BK123ub1 = monoubiquitinated Lys-134
Sequence highly divergent from genome sequence. It could originate from another bacterial species
It was shown that proteolytic cleavage of Il15ra involves ADAM17/TACE; this publication has later been retracted
TTLL3 and TTLL8 monoglycylase-mediated glycylation of tubulin was initially reported to play a role in ependymal motile ciliary maintenance (PubMed:23897886). However, contradictory results were later observed (PubMed:33414192)
A similar protein in IS911 has been shown to only be produced upon ribosomal frameshifting. This does not seem to be the case for this protein, as DNA sequencing shows one complete open reading frame
Was originally thought to be a precorrin-8w decarboxylase
According to a first report, morpholino-mediated knockdown of kctd13 leads to increased brain size and cell proliferation (PubMed:22596160). However, it was later shown that deletion of kctd13 does not cause any change in brain size or cell proliferation (PubMed:29088697). Experimental conditions used may explain discrepancies. A possible explanation being that morpholinos used in the first study, may have affected off-targets
It is not certain that this protein has E3 ubiquitin-protein ligase activity by itself. Lacks a detectable RING-type zinc finger domain; the sequence in this region is highly divergent and lacks most of the expected Cys residues. Still, Cys-434 in this highly divergent region is required for ubiquitination of FBP1, suggesting a direct role in catalyzing ubiquitination
Lacks the conserved tripeptide Ser-Pro-Cys in position 405 necessary for the methyltransferase activity in DRM protein (AC Q9M548)
Although it belongs to the peptidase S1 family, it lacks essential His, Asp, and Ser residues of the catalytic triad and is therefore predicted to lack peptidase activity
Tyr-334 is present instead of the conserved His which is expected to be an active site residue suggesting that this protein has lost its catalytic activity
Has no detectable chitin esterase activity in purified form. Enzymatic activity is detected in the presence of CPAP3-A1, or B.mori molting fluid. However, it is unclear whether this protein functions as a chitin esterase in vivo
Was originally thought to be lysosomal
CarB is split into two genes in M.jannaschii (MJ1378 and MJ1381)
Was originally assigned to be a biotin sulfoxide reductase hence the original gene designation of bisC
Was originally thought to be inactive as a glycosylase, but recent reports demonstrate that cleavage of the initiator methionine is essential for catalytic activity
Was originally thought to be involved in the resistance to UV light and chemical DNA-damaging agents
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-35; H2BK143ub1 = monoubiquitinated Lys-148
The reading frame from which this protein is translated has no Met initiation codon near to the 5'-end. However, it is not a pseudogene. It has been shown that at least 72 residues upstream of the first in-frame start codon (Met-151) are required for function and proper subcellular location. May be translated by means of alternative initiation codon usage, programmed translational frame shifting, or mRNA editing
Product of a dubious CDS prediction. May be a long non-coding RNA
With the use of epibatidine as high affinity ligand, an alpha-2 homopentamer has been purified and crystallized. Its physiological relevance has not been proven
Differs from other KatG proteins because it has a much longer N-terminus
It is not clear if the data in PubMed:11309127 refer to MspB or MspC as they are nearly identical
Could be the product of a pseudogene. Highly similar to the C-terminus of RPL13A but lacks the N-terminal part
While it is structurally defined as a knottin it lacks the conserved Cys residue in position 39
Was originally thought to be part of the MLL5-L complex, at least composed of KMT2E, STK38, PPP1CA, PPP1CB, PPP1CC, HCFC1, ACTB and OGT (PubMed:19377461). However, the corresponding article has been retracted (PubMed:24336203)
According to the authors the mRNA described in PubMed:9600854 may be encoded by a gene different from ALOX15
PubMed:9774100 reports the association of mutation Ile93Met with Parkinson disease. However, according to PubMed:16450370 this association is uncertain and UCHL1 is not a susceptibility gene for Parkinson disease
The oxidation forms of Met-1, Met-6, Met-12, Met-124, Met-179 and Cys-220 are subject of controversy and could be the artifactual results of sample handling
The homodimer may have ATP-independent ubiquitin ligase activity (PubMed:12408865). However, in another study, UCHL1 was shown to lack ubiquitin ligase activity (PubMed:23359680)
It was found (PubMed:8227063) that in engineered, C3S-mutagenized sequence expressed in HEK293 cells there was no radiolabeling by either S- or N-palmitoylation. This result is incompatible with a prediction for N-palmitoylation unless N-palmitoylation depends on S-palmitoylation occurring first or N-palmitoylation did not occur in the experimental expression system
Was shown to interact with G protein subunit GNB1 and GNG2, the interaction was reduced by mutation of Trp-474 and Trp-477. However this paper was retracted due to a lack of clear and continous electron density in the complex structure
PubMed:11850620 suggests PTH1R involvement in multiple enchondromatosis. However, PubMed:15523647 shows evidence that this disease is not caused by PTH1R
The name echicetin has been given to 2 different proteins, this one from E.carinatus sochureki and another one for which the subspecies has not been specified (E.carinatus). Most experiments have been done on E.carinatus sochureki
Was originally thought to be a glutathione reductase
Supposed to contain a CARD domain at the N-terminus (PubMed:20434986). However, this domain is not detected by Pfam, PROSITE or SMART. Has a weak similarity with a DAPIN domain
Contains a Gly residue instead of a conserved Cys residue at position 120 in the dsPTPase catalytic loop which renders it catalytically inactive as a phosphatase (By similarity). The binding pocket is however sufficiently preserved to bind phosphorylated substrates, and may protect them from phosphatases (By similarity)
A CDS in the 3'-UTR of SPG7 mRNA had been erroneously identified as a cell matrix adhesion regulator and originally thought to be encoded by the CMAR gene. There is no experimental evidence for the production of endogenous CMAR protein
It is uncertain whether Met-1 or Met-30 is the initiator. Initiation at Met-30 is supported by sequence similarity with mammalian orthologs and by a Kozak context more favorable compared to that at Met-1
It is uncertain whether Met-1 or Met-35 is the initiator
PubMed:11748240 suggested that BAH was dependent upon Zn(2+), but according to PubMed:28235873, there is no indication of zinc in the structure: synchrotron X-ray fluorescence scans failed to detect a peak corresponding to zinc, and there was no indication of an atom with sufficient electron density in the resulting high-resolution structure. The enzyme does contain a metal cation, but the electron density identifies this cation as either Mg(2+) or Na(+) and not zinc
Was originally (PubMed:3080335, PubMed:2553401) thought to be a ferredoxin
Nucleotide sequence indicated is deduced from the source 'expression system E.coli' written in PDB 4QNN file
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK4ac = acetylated Lys-5; H2BK41ac = acetylated Lys-42; H2BK115ub1 = monoubiquitinated Lys-116
Lacks conserved active site residues, suggesting it has no catalytic activity
The role of YTHDF2 and N6-methyladenosine (m6A) in virus expression and replication is unclear (PubMed:29109479, PubMed:29447282, PubMed:29659627, PubMed:30559377). According to some reports, YTHDF2 promotes viral gene expression and replication of polyomavirus SV40 and herpesvirus (KSHV) by binding to N6-methyladenosine (m6A)-containing viral RNAs (PubMed:29447282, PubMed:29659627). Another report however suggests that YTHDF2 regulates virus expression and replication indirectly, via its ability to inhibit the type I interferon response, thereby promoting virus expression (PubMed:30559377). Indirect regulation via inhibition of type I interferon response might explain why contradictory results have been reported for its role in KSHV virus replication (PubMed:29109479, PubMed:29659627)
Previous studies suggested the 3 different paralogs (YTHDF1, YTHDF2 and YTHDF3) have unique functions with limited redundancy (PubMed:26046440). However, later studies showed that YTHDF1, YTHDF2 and YTHDF3 paralogs have redundant functions to a profound extent and directly promote degradation of m6A-containing mRNAs (PubMed:32492408)
It is not known which subunit of DmfA1 or DmfA2 possesses catalytic activity
It is uncertain whether Met-1 or Met-28 is the initiator
This sequence is an example of a full-length TR beta chain. Pan-cancer TRBV25-1*01J2S3*01C2*01 TCR beta chain is generated by somatic recombination of variable TRBV25-1 (AC A0A075B6N4) and joining TRBJ2-3 (AC A0A0B4J200) gene segments spliced to constant TRBC2*01 (AC A0A5B9) gene segment
Although highly similar to the deubiquitinase OTULIN, lacks the conserved active site Cys at position 139 which is replaced by an Asp residue, and does not show deubiquitinase activity
Was originally thought to be an endo-exonuclease
It is uncertain whether Met-1, Met-38, Met-71, Met-77 or Met-82 is the initiator
Was initially thought to have tumor suppressor function in prostate cancer. However, it was shown that it is probably not the case (PubMed:12866033)
Could be the product of a pseudogene. The N-terminus is about 750 residues shorter than orthologs, and it contains a truncated response regulatory domain
Contains 7 disulfide bonds instead of the 4 disulfide bonds, which are conserved features of the family
Was initially thought to be two separate ORFs named yitO and yitN
An expected heme iron ligand His residue was not found at position 51 in this sequence
While human FABP5 can exist as a monomer as well as a domain-swapped dimer, mouse is found only in the monomeric form
Could be the product of a pseudogene. Lacks the GED domain, which is a conserved feature of the family
Encoded by an expressed retrotransposed copy of the MT1H locus
Was originally thought to be recA; but the sequence was incorrectly assigned
Lacks the C-terminal part containing the 'disulfide through disulfide knot' structure
Was initially thought to be an integral membrane protein (PubMed:11836248). However, it was later shown that it is a soluble luminal protein localized in the endoplasmic reticulum lumen
PubMed:11168356 reported the oxidation of Met-651 to sulfoxide. This is most probably an artifact of isolation
Was originally proposed to be a calcium channel facilitator (PubMed:23673622). However, a more recent study shows that this protein regulates membrane phospholipid homeostasis (By similarity). Therefore, any effects on calcium flux are most likely a secondary consequence of defects in membrane composition or fluidity (By similarity)
Lacks the phospho-accepting Asp (here Gln-94), present in the receiver domain, which is one of the conserved features of the two-component response regulators (ARRs) family
A paper showing a role in apoptosis in neurons has been retracted due to panel duplication in several figures
Was originally thought to be the spo0F protein
Was originally thought to originate from human and was called BRAG1 (brain-related apoptosis gene 1) with a proposed role in apoptosis (PubMed:8649811). The DNA sequence of the region sequenced is more than 99% identical to that of this E.coli gene. Furthermore the claim of an 'extensive similarity to the Bcl-2 family of genes' is not correct
It is uncertain whether Met-1, Met-44 or Met-88 is the initiator
While it is structurally defined as a knottin it lacks the conserved Cys residue in position 9
This sequence is an example of a full-length immunoglobulin gamma-1 heavy chain
It is not sure if the block at the amino end is natural or artifactual
Could be the product of a pseudogene. The C-terminus is much shorter than in related proteins
Lacks the Cys residue in position 253 that is replaced by a Gly residue, resulting of a loss a disulfide bond. This may contribute to a probable lower procoagulant activity
Ref.2 refers to only one protein (TMV-D49-PLA2), but erroneously shows two sequences. The translation of AF408409 (mentioned in Ref.2 as submitted to GenBank) differs by one amino acid from the sequence shown in Fig.1 and described in the text (see the conflict at position 71)
Was originally given the gene name dsbB; however this seems to belong to a different DsbB subfamily
In strain cv. Columbia, cv. Landsberg Erecta and cv. Wassilewskija, loss-of-function mutations lead to inactive FRI protein. A complete sequence for FRI can be found in strains cv. H51 (AC P0DH90)
Was originally referred as a palmitoyl-protein thioesterase (palmitoyl-protein hydrolase)
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me1 = monomethylated Lys-10; H3K14ac = acetylated Lys-15; H3K14me2 = dimethylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me1 = monomethylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me1 = monomethylated Lys-24; H3K56ac = acetylated Lys-56; H3K64ac = acetylated Lys-64
This entry seems to be produced by an incorrect sequence that contains at least 14 frameshifts. Do not use it for any phylogenetic purpose
It is uncertain whether Met-1 or Met-47 is the initiator
Was reported to be a cytosolic prephenate dehydratase interacting with a G-protein alpha-subunit
It is uncertain whether Met-1 or Met-64 is the initiator
A C-terminal fragment of this protein (residues 1599 to 2461) was originally described as neuraxin in PubMed:2555150
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-27; H2BK143ub1 = monoubiquitinated Lys-133
In cv. Columbia, CYP74B2 (AC B3LF83) DNA sequence contains a 10-bp deletion that leads to a shorter N-terminus compared to typical other CYP74B subfamily members, and CYP74B2 is thought to be a non-functional enzyme. Functional alleles, with full N-terminus are found in cv. Landsberg erecta and cv. Wassilewskija (AC Q9ZSY9)
This protein may not be real because it is encoded on the opposite frame of insertion element IS406
The name Restin has also been used for CAP-Gly domain-containing linker protein 1 the product of the CLIP1 gene
Variants Ala-1622 and Val-1637 have been originally reported as DA2B3 pathogenic mutations (PubMed:16642020). These variants are now thought to be polymorphisms on the basis of additional family information and frequencies in large databases of control populations (PubMed:25957469)
The nucleotide accession number of this protein has been wrongly cited in a publication which is available in the nucleotide entry
Was originally shown to be localized in the inner nuclear membrane by using a truncated protein (PubMed:12514182). Was used as an inner nuclear membrane marker (PubMed:17996101, PubMed:18660802, PubMed:19369416). However, more recent studies showed that it is localized in the nuclear outer membrane, which is consistent with a function in the initiation of nuclear fusion (PubMed:19297527, PubMed:19570912)
Was originally (Ref.1) thought to be a cinnamyl-alcohol dehydrogenase
Reported to have transcriptional repression activity in vitro (PubMed:16825764, PubMed:19757162). However, it is unclear whether this protein has any function in transcription in vivo
PubMed:16055087 showns that TBC1D15 can also functions as GTPase activating for RAB11 at a lower extent than for RAB7A, however this function is not confirmed by PubMed:20363736
The PDB entry 2OSN is a reinterpretation of the PDB entry 1G2X
Was originally thought to be a suppressor of CDC26
In contrast to other serine-repeat antigen proteins (SERA) of the peptidase C1 family, contains a serine residue at the position of the canonical catalytic cysteine and has been shown to lack protease activity (By similarity). However, other studies show that it has protease activity towards synthetic peptides in vitro (By similarity)
Was originally (PubMed:8863740) thought to be a metalloprotease (PRSM1). This was based on a wrong translation of the ORF which gave rise to a putative protein of 318 AA containing a pattern reminiscent of zinc metalloproteases
Hydrophilic histidine residues that participate to zinc binding in transporters of the family are not conserved in SLC30A6
Called LivG in S.typhimurium, but we renamed it to LivF for the sake of consistency with the E.coli protein
Was originally named betaine aldehyde dehydrogenase (PubMed:9792097). Sequence similarity is higher with aldehyde dehydrogenase family 9 member A1, suggesting it has the same function and catalytic activities as other homologs
The WASH4P N-terminus differs from WASH3P for which it is shown to be required for the WASH complex assembly. Hence is association within the WASH complex is ambiguous. However, WASH4P retains the regions implicated in interaction with WASHC2 and confering in vitro NPF activity
The amino acid substitutions in both the subunits found in PubMed:24907509 might have resulted from different cultivars or growing conditions of the plant used in the study
Could be the product of a pseudogene unlikely to encode a functional protein. In strain S288c, this gene has a frameshift compared to the other IMD alleles, producing 2 ORFs YAR073W and YAR075W. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
Was originally (Ref.1) thought to be a queuine tRNA-ribosyltransferase
Despite its name, does not contain a C-type lectin domain
Was originally thought to be a UDP-sugar hydrolase
The family of genes to which Mnda belongs has undergone a rapid expansion in the mouse. As a consequence, mouse Mnda and human MNDA genes, although belonging to the same family, are not one to one orthologs
A peptide arising from positions 166 to 174 was originally termed neurotensin-related peptide (NRP) and was thought to regulate fat digestion, lipid absorption, and blood flow
Could be the product of a pseudogene. It is homologous to a middle section of two uncharacterized proteins (RF_0471 of R.felis and RBE_0759 of R.bellii)
Despite its name, it is related to the unc-93 family and not to the major facilitator superfamily
A stretch of the chloroplast genome is duplicated within chromosomes 7, 8 and 9 resulting in the duplication of the gene. The expression of these duplicated genes have not been demonstrated
Was originally thought to be a eukaryotic release factor (ERF)
Was originally thought to be involved in the transcription initiation step
Could be the product of a pseudogene unlikely to encode a functional protein. This is a truncated version of guanine nucleotide exchange factor SDC25. Strain S288c has a frameshift in position 92, which disrupts the gene coding for this protein and produces two ORFs YLL016W and YLL017W. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. A contiguous sequence for SDC25 can be found in strain W303 (AC P0CF32)
The catalytic activity is unsure despite catalytic sites being conserved
Was originally thought to have an internal disulfide bond
Juge et al. shows that SLC32A1 is a symporter of both 4-aminobutanoate or glycine or beta-alanine with Cl(-) that operates according an electrical gradient without the need for a chemical gradient (By similarity). However Farsi et al. and Egashira et al. confirm that SLC32A1 is an antiporter that exchanges vesicular protons for cytosolic 4-aminobutanoate or glycine and exclude any coupling with chloride (By similarity)
Could be the product of a pseudogene. However, proteomics data suggest the existence of the protein
It is uncertain whether Met-1, Met-2 or Met-7 is the initiator
Was reported to interact with IL15RA (PubMed:10463949). However, this work was later retracted (PubMed:21357251)
According to PubMed:16831889, it is a pseudogene
Controversial data exist concerning the topology of PRS55. One study in mouse shows that PRSS55 is a GPI-anchored protein (PubMed:30032357). An other study does not confirm the GPI-anchor status of PRSS55 (By similarity). However, as a GPI-anchor motif is detected, the possibility of a GPI-anchor instead of a single-pass type I membrane protein is probable
Lacks the conserved His residue in position 138 suggested to serve as a proton acceptor for this family, however this protein still has diacyglycerol O-acyltransferase activity in E.coli
Was originally thought to be a FoxD1 protein (PubMed:11804794, PubMed:15656969). However, further sequence comparisons clearly suggests that it belongs to the FoxD2 subclass (PubMed:10702024)
Although related to the peptidase M28 family, it lacks the conserved zinc-binding and active sites and therefore has probably lost hydrolase activity
Although initially described as a cell membrane glycoprotein, ADRM1 is intracellular and non-glycosylated, and has probably no direct role in cell adhesion
Could be the product of a pseudogene unlikely to encode a functional protein. Transposon Ty1-LR4 (YLRWTy1-4) contains a frameshift at position 753, which disrupts the ORF coding for protein TY1B. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
Does not transport any of the organic anions transported by the other multidrug resistance-associated proteins (MRPs) in vesicular transport assays, nor does it confer resistance to cytotoxic agents in intact cell assays
PubMed:11159911 show a lack of role in heart induction but PubMed:12167861 show a role in heart formation; the discrepancy may be due to duplication of Xenopus wnt11 genes
Thr-13 is present instead of the conserved Cys which is potentially a redox-active site
PubMed:12676443 describes this protein as coming from E.ramsayi, which is considered in this reference as a synonym of E.quadricolor
Lacks the conserved Glu active site in position 136, which is replaced by an Ala residue, explaining why it is inactive
Depending on the experimental set up and substrate used, NSD2 has been shown to mono-, di- or tri-methylate 'Lys-27', 'Lys-36' or 'Lys-79' of histone H3 and 'Lys-20' or 'Lys-44' of histone H4 (PubMed:19808676). However, dimethylation of nucleosomal histone H3 at 'Lys-36' (H3K36me2) is likely to be the physiological reaction catalyzed by NSD2 (PubMed:19808676, PubMed:22099308)
Originally thought to be phosphorylated by MPF during mitosis. However this paper was retracted due to falsification of data
Was originally thought to be a receptor for lysophosphatidylcholine (LPC) and sphingosylphosphorylcholine (SPC), However, this work has been retracted
Martineau M. et al. show that may function as a L-glutamate/H(+) antiporter (By similarity). However, according to Eriksen J. et al., H(+) is an allosteric activator (By similarity)
Expressed in the intestine (PubMed:18662544). However, others have been unable to detect intestinal expression (PubMed:22001047). Based on lifespan assays conducted with a putative null allele, elt-3(vp1), represses longevity caused by a daf-2(e1370) mutant background (PubMed:18662544). However, this repression could not be reproduced (PubMed:22001047). Based on further analysis, the failure to reproduce seems to be due to a novel, unknown, mutation which arose in the daf-2(e1370) mutant background in one lab, but not the other (PubMed:23262285)
Shares some similarity with tyrosine phosphatase proteins but it has probably no phosphatase activity since the potential active site Cys residue in position 65 is replaced by Gly
Lacks 2 of the 4 disulfide bonds, which are conserved features of the family
Could be the product of a pseudogene. This sequence seems to be incomplete in both termini
According to a report, the N-terminal hydrophobic region forms a transmembrane region that crosses the mitochondrion inner membrane (PubMed:28712726). According to another report, the N-terminal hydrophobic region associates with the membrane without crossing it (PubMed:28712724)
The nuclear function of SLC29A2/ENT2 is unclear. A study reported that under proliferative conditions, two SLC29A2/ENT2 nuclear isoforms recruited SLC29A2/ENT2 to the nuclear envelope in order to translocate nucleosides into the nucleus for incorporation into DNA during replication (PubMed:27271752). However, the physiological existence of these isoforms has yet to be proven
Was originally thought to be S-nitrosylated and to interact with MTA1 (PubMed:20519513). However, this work was later retracted (PubMed:28314777). Nevertheless, other publications demonstrate that it is S-nitrosylated and there are several publications in the human ortholog demonstrating its interaction with MTA1 (PubMed:18754010, PubMed:20972425)
Could lack activity as the potential active site Cys residue in position 93 is replaced by an Ala
According to a report, processing following retrotranslocation is dependent on the proteasome (PubMed:24998528). However, it was later shown that processing takes place in a proteasome-independent manner (PubMed:27676297, PubMed:27676298)
Its topology is subject to discussion. According to some groups, it has a single-pass type II membrane protein in normal conditions and is retrotranslocated into a single-pass type III membrane protein in response to stress (PubMed:24448410). According to other reports, it is integrated into the endoplasmic reticulum membrane via multiple membrane-spanning alpha-helices
Was initially thought to activate erythroid-specific, globin gene expression (PubMed:8036168). Knockout experiments in mouse however demonstrated that it is not the case
Although it belongs to the glycosyl hydrolase 18 family, Ser-148 is present instead of the conserved Glu which is an active site residue. Therefore this protein may lack chitinase activity
Although only weakly related to the S.cerevisiae SEN15 protein, it probably displays the same function within the tRNA splicing endonuclease complex
Neither Cas1 nor Cas2 are fully present in this fusion protein, however as this is the only copy of these proteins in this organism they are probably functional. The Cas1 section is much smaller than usual and it is quite atypical
Lacks two conserved zinc binding sites
Most authors have deduced a localization at the basolateral membrane of proximal tubules (PubMed:11912245). Other studies demonstrated a localization to the luminal membrane in the distal tubule (PubMed:9260930)
O-glycosylation sites are annotated in first sequence repeat only. Residues at similar position are probably glycosylated in all repeats
Submitted as Flavobacterium meningosepticum ATCC 33958 by the authors and identified as Elizabethkingia miricola by ATCC Catalog
Initially the conserved reside Thr-80 was thought to be a nucleophile (PubMed:12571243); mutagenesis in E.coli and P.falciparum indicates it is not
The name restin has also been used for CAP-Gly domain-containing linker protein 1 the product of the CLIP1 gene
Lacks some of the catalytic-important sites due to premature sequence termination compared to the close ortholog in M.jannaschii. The missing 250 amino acids or so may be retrieved through a serie of sequence corrections
Was named RRNAD1 by HGNC because a ribosomal RNA adenine dimethylase signature is detected by PROSITE. However, it probably constitutes a false positive and the ribosomal RNA adenine dimethylase signature is not conserved in orthologs
A peptide arising from positions 166 to 174 was originally (PubMed:3087352, PubMed:2437111) termed neurotensin-related peptide (NRP) or kinetensin and was thought to regulate fat digestion, lipid absorption, and blood flow
In contrast to the mouse ortholog, it does not interact with the Ras-like GTPases RAC1 and RHOA
Was originally thought to be a protein-tyrosine-phosphatase (PubMed:15995210). Was later shown to function as an arginine phosphatase in vivo and in vitro (PubMed:22517742, PubMed:23770242)
Two inactivating mutations in human TTLL10 (Ser-448 and Lys-467) are proposed to explain the lack of polyglycylation
There is some controversy about O-methyltransferase on pre-miR-145, since the dimethylation first described as the specific enzymatic activity cannot be reproduced by a more recent work which observes a monomethylation of pre-miR-145 but two orders weaker than the methylation of cytosolic histidyl tRNA
The role of the nuclear export signal (NES) motif in XPO1-mediated DDX3X export is controversial (PubMed:30131165, PubMed:31575075, PubMed:15507209). In one study, NES has been found dispensable for DDX3X export while the helicase domain mediates the interaction with XPO1 (PubMed:15507209). However, in two other studies, DDX3X nuclear export is dependent on both NES and Ran in its GTP-bound form while the helicase domain is not required (PubMed:30131165, PubMed:31575075)
Lacks the conserved glutamate residue that binds magnesium
Could be the product of a pseudogene unlikely to encode a functional protein. Transposon Ty2-GR1 (YGRCTy2-1) has a stop codon in position 28, which disrupts the ORF coding for protein TY2A, and a frameshift at position 813, which disrupts the ORF coding for protein TY2B. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
The active site contains a CPDC motif wich differs from the conserved CGPC motif
Was initially thought to have a homogentisate phytyltransferase activity and to be involved in tocopherol biosynthesis
The interaction between DSCAM, PAK1 and RAC1 has been described. This article has been withdrawn by the authors
In contrast to other members of the family, lacks the conserved iron-binding sites, suggesting that the alpha subunit has no oxidoreductase activity
Was originally thought to be a fatty acyl-CoA ligase (FACL) (PubMed:19182784). However, although FadD10 has a primary sequence similar to FACLs, it is indeed a fatty acyl-AMP ligase (FAAL) that is only able to acylate an ACP (Rv0100) rather than coenzyme A (PubMed:22451903, PubMed:23625916)
Gln-105 is present instead of the conserved Glu which is expected to act as an active site proton donor
Subsequent steps in cytosine demethylation are subject to discussion. According to a first model cytosine demethylation occurs through deamination of 5hmC into 5-hydroxymethyluracil (5hmU) and subsequent replacement by unmethylated cytosine by the base excision repair system (PubMed:21496894). According to another model, cytosine demethylation is rather mediated via conversion of 5hmC into 5fC and 5caC, followed by excision by TDG and replacement by unmethylated cytosine
As this bacterium is not an Enterobacteriaceae, this protein may not have a true dGTPase activity
In contrast to protein kinases, Ser-369 is present instead of the conserved Asp which is expected to be an active site residue
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK6su = sumoylated Lys-7; H2BK7ac = acetylated Lys-8; H2BK7su = sumoylated Lys-8; H2BS10ph = phosphorylated Ser-11; H2BK11ac = acetylated Lys-12; H2BK16ac = acetylated Lys-17; H2BK16su = sumoylated Lys-17; H2BK17su = sumoylated Lys-18; H2BK123ub1 = monoubiquitinated Lys-125
Could be the product of a pseudogene. Is missing N- and possibly C-terminal residues compared to orthologs
Has no tyrosine-protein phosphatase activity at mild acidic conditions (pH 5.5). The in vivo relevance of the low PPase activity at acidic conditions (pH 4.5) is questioned. This catalytic activity seems to be affected by the replacement of a highly conserved residue in the tyrosine-protein phosphatase domain
Lacks transmembrane domains and is probably not involved in transport
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 1284 in the dsPTPase catalytic loop and does not have phosphatase activity (By similarity). The pocket is however sufficiently preserved to bind phosphorylated substrates, and maybe protect them from phosphatases
PubMed:16484612 decribes a Naa35/Egap-containing complex as evolutionary conserved NatC complex; however, the mMak3 protein investigated in this context corresponds to mammalian NAA50 and not NAA30 and its interaction with NAA35 is ambiguous
Do not confuse myelin-oligodendrocyte glycoprotein (MOG) with oligodendrocyte-myelin glycoprotein (OMG)
Lacks the conserved His residue in position 138 suggested to serve as a proton acceptor for this family
Some prediction bioinformatics tools predict the presence of a homeobox domain (By similarity). However, the domain is degenerate and residues that are important for DNA-binding are absent (By similarity)
Contains a histidine kinase domain, but it seems to be non-functional as the highly conserved histidine residue is missing
This sequence originates from a miocene fossil leaf sample
According to PubMed:12738806, does not hydrolyze cystinyl-bis-glycine but data is not shown in paper
Tna2 is expressed in strain T but expression in strain IAM 13621 has not been proven
Was previously thought to be part of the photosystem I complex
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 388 in the dsPTPase catalytic loop, suggesting that it has no phosphatase activity
Although strongly related to the peptide:N-glycanase enzyme, it lacks the conserved active site Cys in position 243, which is replaced by a Val residue suggesting that it has no activity
Authors numbered this protein framework XXVII. Unfortunately, this number is already attributed to another Cys arrangment (C-CC-C-C-C). As a consequence, it has been renamed conotoxin GeXXVIIIA
It is unclear whether this protein requires a metal cofactor for catalysis. It was originally proposed to be a Zn(2+)-dependent metalloenzyme based on structural similarities to bacterial aminopeptidases and the observation that it can bind Zn(2+) ions, typically in a 1:1 stoichiometry (PubMed:21288892). However, a recent study suggests a Zn(2+)-independent catalytic mechanism (By similarity)
The sequences characterized in (PubMed:21829394) and crystallized in (PubMed:23236156) are actually derived from cdiA-CTo11/cdiIo11, an orphan cdiA-CT/cdiI module that only encodes the cdiA CT fragment and its associated cdiI. It is however identical to that shown in this entry, which does have the elements necessary for gene expression
The cytochrome b561 domain lacks the conserved His residue that binds iron in the heme. The reductase activity is therefore unsure in vivo
This protein lacks the conserved Cys in positions 52 and 56; they are replaced by an Asp and a Thr, respectively. It is therefore possible that the D-cluster is either altered or missing in this protein, which may not form heterotetramers
The catalytic activity is unsure despite catalytic sites being conserved (PubMed:23525007, PubMed:27836991). Lacks cholesterol esterase activity when overexpressed in S2 cells (PubMed:27836991). Lack lipolytic activity towards trioleoylglycerol, dioleoylglycerol or monooleoylglycerol when overexpressed in COS-7 cells or S2 cells (PubMed:23525007, PubMed:27836991)
Was originally thought to be a laminin receptor
Lacks the active site cysteine required for interaction with ubiquitin
In contrast to other members of the family, it lacks a canonical signal sequence; the existence of the signal sequence is therefore unsure
Was originally thought to be a lin-10 homolog
PubMed:11087666 sequence was originally thought to originate from mouse
Was shown to be S-palmitoylated by ZDHHC19, leading to STAT3 homodimerization. However, this study was later retracted
Strongly resembles the MrnC Mini-3 enzyme, but is missing a highly conserved, possibly catalytically important site at position 72
Was initially reported to mediate activation of SUMO2 in addition to UFM1 (By similarity). However, it was later shown that it is specific for UFM1 (PubMed:21304510)
Was originally thought to be GUT2, the FAD-dependent glycerol-3-phosphate dehydrogenase
Lacks the conserved Glu residue in position 467 essential for carbopeptidase activity. The mature form lacks catalytic activity towards synthetic peptide substrates
This protein sequence has been named 'Slow A' MYH14, but it also appears also as 'Slow B' MYH15 within the reference
In contrast to the human ortholog, lacks the RRM (RNA recognition motif) domain at the N-terminus
Was originally designated as the ams protein
Salusin-beta detected systemically according to PubMed:18344632 represents the putative rat salusin consisting of 40 amino acid residues or a shorter fragment produced by an unknown processing mechanism. No salusin-alpha homolog is detected in rat tissues
Lacks 2-(S)-hydroxypropyl-CoM dehydrogenase activity. Contains apparent mutations in the N-terminal region, including the lack of key NAD(+)-binding residues, which may explain the lack of activity
Was originally erroneously assigned as a beta subunit
Although strongly related to USP22, which deubiquitinates histones, lacks the N-terminal UBP-type zinc finger, suggesting it does not have the ability to deubiquitinate histones
Studies in clathrin-mediated endocytosis of ITGB1 and TFR used a siRNA mixture of ISTN1 and ISTN2 suggesting a partially overlapping role of the EH domain-containing proteins
Represents a conventional myosin. This protein should not be confused with the unconventional myosin-6 (MYO6)
The conserved zinc-binding site Asp residue in position 381 is replaced by an Asn
D-glycero-beta-D-manno-heptose 1,7-bisphosphate (HBP) was initially thought to constitute the bacterial pathogen-associated molecular pattern metabolite (PAMP) triggering the ALPK1-TIFA innate immunune response (PubMed:26068852, PubMed:28877472, PubMed:28222186). It was however shown that ADP-D-glycero-beta-D-manno-heptose (ADP-Heptose) constitutes the main PAMP that activates the kinase activity of ALPK1, promoting phosphorylation of TIFA (PubMed:30111836)
Was initially (PubMed:11209081) thought to be involved in the tryptamine pathway for the biosynthesis of indole-3-acetic acid (IAA), but it has been shown (PubMed:20974893) that this is not the case. It is now admitted (PubMed:22025724, PubMed:22108406) that the YUCCA family is implicated in the conversion of indole-3-pyruvic acid (IPA) to indole-3-acetic acid (IAA)
Has been described as GLUT10 in literature, but this gene name has already been used for SLC2A10
Was originally (PubMed:9390555, PubMed:8600032) thought to have exonuclease activity but it was later shown (PubMed:17173052, PubMed:17174896) that only DIS3/RRP44 subunit of the exosome core has this activity
Was originally (PubMed:1851993) reported to be a connexin and to contain transmembrane domains. PubMed:8400879 authors have assigned that this is not a connexin, but rather a protein kinase
Most probably a non-functional protein that cannot participate in the synthesis of a productive immunoglobulin chain due to an altered splicing site (PubMed:9619395)
Shows a different disulfide-stabilized fold, despite containing the conserved cysteine framework and disulfide connectivity of classical alpha-conotoxins
Defined as a pseudogene by MGI. However, proteomics data suggest the existence of the protein
The mature peptide is linear as it lacks the C-terminal Asp/Asn residue required for cyclization
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC A4QJX7
PubMed:16620771 does not detect acyl-CoA:lysocardiolipin acyltransferase activity
It is uncertain whether Met-1, Met-8 or Met-9 is the initiator
It is uncertain whether Met-1 or Met-44 is the initiator
Predicted to be inactive as the cysteine residue involved in the catalytic reaction is a lysine at position 223
Opinions are divided on whether Anemonia viridis (Forsskal, 1775) and Anemonia sulcata (Pennant, 1777) are separate species. Authors from PubMed:17492942 and PubMed:19609479 consider they are only one species, it is why their studies (on A.viridis) are integrated in this entry on A.sulcata
AaV-SP-I is sequenced from 25-48 and its carbohydrate contents is 9%, whereas AaV-SP-II is sequenced from 25-64 and its carbohydrate contents is 4%
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-8; H2BK6su = sumoylated Lys-8; H2BK7ac = acetylated Lys-9; H2BK7su = sumoylated Lys-9; H2BS10ph = phosphorylated Ser-12; H2BK11ac = acetylated Lys-13; H2BK16ac = acetylated Lys-18; H2BK16su = sumoylated Lys-18; H2BK17su = sumoylated Lys-19; H2BK123ub1 = monoubiquitinated Lys-125
The active site contains a CEVC motif wich differs from the conserved CGPC motif
Encoded in intron of the gene CYFIP2 (opposite strand)
Although it belongs to the peptidase M16 family, lacks the zinc-binding sites and appears to lack catalytic activity in vitro
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 346 in the dsPTPase catalytic loop, suggesting that it has no phosphatase activity
Lacks the C-terminal domain
Like its mammalian and yeast counterparts, PEX19-1 might be farnesylated and interacting transiently with the peroxisome membrane. However, this post-translational modification has not been demonstrated and only a trace of PEX19 was found associated with the peroxisome (PubMed:16923726)
It is uncertain whether Met-1, Met-18 or Met-29 is the initiator
Although strongly related to XerD, it constitutes a distinct protein family. In contrast to the classic XerD protein, it does not contain the Arg-His-Arg-His (R-H-R-H) sandwich residues that are clustered with the Tyr active site. It also lacks the C-terminal region which is known to mediate the interaction with XerC. It is therefore unknown whether it has tyrosine recombinase activity or acts as a regulator
Numerous studies suggest that the C-terminal tail of the Na(+)/H(+) exchangers assumes a cytosolic orientation and constitutes a regulatory region. This cytosolic localization is confirmed by phosphorylation analysis (PubMed:15665377, PubMed:18407956). However, residues Asn-515, Asn-550 and Asn-563 have been shown to be glycosylated and localized at the lumenal side (PubMed:11036065). These contradictory results suggest an unusual topology of the C-terminal tail which may contain membrane spans formed by beta-sheets or even may switch from one side to the other of the membrane
Was originally thought to be involved in protamine removal but this was shown to be incorrect in the subsequent published erratum
PubMed:18467340 shows that PBP1 inhibits polymerization of PYK10 complex, while in PubMed:19965874, PBP1 activates purified PYK10
In vitro experiments measuring cell viability in melanoma cell lines used siRNA specific for MAGEA3 and MAGEA6
A fairly frequent variant (Ala-64) was originally (PubMed:17970586) suggested to be responsible for some cases of rifampicin resistance. This has since been shown not to be true (PubMed:18550732), although it is a good marker for the Beijing-W clade/SCG-2 phylogenetic group
According to some authors, contains a SANT domain but this domain is not detected by any prediction tool
According to PubMed:20884799, this protein should not be regarded as a classical SR protein
Although the active site residues are conserved, lacks the conserved His residue which is normally found 9 residues before the catalytic His
Has a much lower NAD-retinol dehydrogenase activity compared to the human ortholog
No comparison between the natural toxin and the recombinant one has been done to attest that the results can be also attributed to the natural toxin (mode of action and disulfide bonds)
In contrast to other members of the family, lacks the conserved iron-binding sites, suggesting it has no oxidoreductase activity
PubMed:14736920 demonstrates a thylakoid lumen location, while PubMed:14671022 shows a mitochondrial location
Although it belongs to the glycosyl hydrolase 1 family, Asp-201 is present instead of the conserved Glu which is an active site residue. It is therefore expected that this protein lacks glycosidase activity
Was originally thought to contain a F-box domain
In strain 91001 it seems to be a pseudogene. It is interrupted by a frameshift in position 100. The sequence has been verified by the authors and is believed to be correct
It is uncertain whether cleavage occurs at Arg-172 or Glu-173
Was originally thought to be phosphorylated at Thr-120 (PubMed:19940129). However, this work has been retracted (PubMed:27825096)
This sequence initiates at a non-canonical CTG leucine codon
According to PubMed:12738806, exhibits dipeptidase activity hydrolyzing cystinyl-bis-glycine but according to PubMed:32325220, lacks this activity which may be due to the inability of serine (instead of aspartate found in DPEP1/2) at position 356 to function as the acid/base catalyst and activate the nucleophilic water/hydroxide
There is controversy about the substrate specificity of the enzyme. Next to the primary substrate UMP, PubMed:1333436 and Ref.8 report that the enzyme accepts also CMP and AMP as nucleoside monophosphates, but not GMP, whereas PubMed:2172245 and PubMed:8391780 report activity with GMP and dTMP, but not AMP or CMP
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-8; H2BK6su = sumoylated Lys-8; H2BK7ac = acetylated Lys-9; H2BK7su = sumoylated Lys-9; H2BK11ac = acetylated Lys-13; H2BK16ac = acetylated Lys-23; H2BK16su = sumoylated Lys-23; H2BK17su = sumoylated Lys-24; H2BK123ub1 = monoubiquitinated Lys-130
It is unclear whether this protein requires a metal cofactor for catalysis. It was originally proposed to be a Zn(2+)-dependent metalloenzyme based on structural similarities to bacterial aminopeptidases and the observation that it can bind Zn(2+) ions, typically in a 1:1 stoichiometry (PubMed:18072935, PubMed:21288892). However, a recent study suggests a Zn(2+)-independent catalytic mechanism (By similarity)
Lacks the isocitrate binding site which is one of the conserved features of the isocitrate dehydrogenase family
Could be the product of a pseudogene. In strain cv. Columbia, a frameshift mutation introduces a premature stop codon leading to a truncated SRK protein. A complete sequence for SRK can be found in strains cv. Pog-0 and cv. Wei-1 (AC P0DH86)
Although it belongs to the tubulin--tyrosine ligase family, the TTL domain lacks some of the ATP binding sites predicted to be essential for TTL activity (By similarity). Lacks tyrosine ligase activity in vitro (By similarity). Lacks glutamylation activity in vitro (By similarity)
Sequence obtained after translation (DsM-a2) and sequence directly sequenced from protein (Dsm-a2', AA 17-29) correspond exactly. However, the mass found for the protein (13810) does not correspond to the expected mass calculated after translation (13810) (PubMed:17611171)
There are several genes encoding the J region in the immunoglobulin heavy locus. The peptide described in this entry is a representative for all the peptides encoded by these genes. For examples of full-length immunoglobulin heavy chains (of different isotypes) see AC P0DOX2, AC P0DOX3, AC P0DOX4, AC P0DOX5 and AC P0DOX6
There are amino acid differences between the sequence shown in fig.1 (PubMed:11210180) and the sequence deposited in the database (AF026380). The sequence from fig.1 shows only 3 conflicts between PubMed:11210180 and PubMed:16141072. These are at AA positions 141, 240 and 287
This protein is missing the flavodoxin-like domain seen in orthologs
Was originally thought to be involved in transcriptional regulation
This protein is unrelated to LytR from S.aureus, which is part of a two-component regulatory system that, together with LytS, is involved in autolysis and cell wall metabolism. The B.subtilis ortholog of S.aureus LytR is LytT (AC P94514)
Product of a dubious gene prediction. Encoded in intron of ERC2
Lacks the active site aspartate
A dicopper center located in the alpha/pmoB subunit is proposed as active site, in part based on mutagenesis studies using a soluble pmoB construct in which its two cupredoxin domains have been artificially bridged. However, the construct has only 10% methane oxidation activity compared with the intact membrane-bound pMMO
This protein should not be confused with mitochondrial peptidyl-prolyl cis-trans isomerase F (PPIF) which is often referred to as cyclophilin D or CypD
The motif D/ECD-tripeptide is missing
Lacks the conserved active site Asp and has no significant phosphoribosyltransferase activity
PubMed:15635094 reported that the initiator methionine is coded by an unusual start codon, CTG
sequence Was originally thought to originate from human but appears to be from rat
The sequence reported in PubMed:8357831 was thought to originate from rat, but was later shown (PubMed:12074592, PubMed:12379742) to be derived from mouse
Lacks the phospho-accepting Asp (here Glu-133), present in the receiver domain, which is one of the conserved features of two-component response regulators (ARRs) family
This protein is smaller than usual in this organism, and may not be functional
In contrast to other fungi which have a single histidine biosynthesis trifunctional protein, 2 proteins are present in S.pombe to ensure these functions: his7 (phosphoribosyl-AMP cyclohydrolase and phosphoribosyl-ATP pyrophosphatase activities) and his2 (histidinol dehydrogenase activity)
Resembles portions of the beta' subunits of RNA polymerases from bacteria and chloroplasts. It was suggested that both the beta' subunit of RNA polymerases and L.biflexa ArgE-complementing activity possess N-acetylase or N-acetylornithinase activity. No homology with E.coli ArgE
Lacks the 4Fe-4S ferredoxin-type domain found in GltD orthologs
Was originally thought to be a glutathione peroxidase (PubMed:10480913) or a phospholipid hydroperoxide glutathione peroxidase (PubMed:11445588), but functions as an atypical 2-Cys peroxiredoxin using thioredoxin as reducing power instead (PubMed:16251189)
Was originally thought to be a receptor for sphingosylphosphorylcholine and lysophosphatidylcholine (PubMed:11535583). However, this work has been retracted
Supposed to contain a CARD domain at the N-terminus. However, this domain is not detected by Pfam, PROSITE or SMART. Has a weak similarity with a DAPIN domain
The KIR2DS1 gene is not directly represented on the GRCh38 primary reference genome assembly but on alternate loci of that assembly
Was initially thought to act as a transcriptional regulator via its interaction with TCF3/E12
The disulfide bond observed in the structure does not exist in vivo (PubMed:18390551). The enzyme reaction was initially thought to act via a redox-active disulfide bond mechanism; however the disulfide bond only takes place with inactive enzyme that lacks the copper cofactor (PubMed:25931126). The catalytic copper is required to activate oxygen and catalyze oxidative C-H activation (PubMed:25931126)
Was originally thought to be protein kinase C inhibitor 2 (PKCI-2 or 12 kDa inhibitor of protein kinase C). Later, was shown experimentally not to inhibit protein kinase C (PubMed:1868545, PubMed:1710782)
According to some reports, mediates transmembrane transport of glucose and fructose (By similarity). However, another group coud not confirm transporter activity for glucose or fructose (By similarity)
A structure of a fragment of this protein in complex with the catalytic domain of C.botulinum neurotoxin type B (BoNT/B, botB) was reported; because of the lack of clear and continuous electron density for the VAMP2 peptide in the complex structure, the paper was retracted (PubMed:10932255, PubMed:19578378). However this protein is a substrate for BoNT/B (PubMed:7803399, PubMed:22289120)
Has been suggested to play a role in the regulation of RYR2 channel activity and thereby contribute to the regulation of excitation-contraction coupling in cardiac muscle. According to PubMed:20431056, the amount of FKBP1B in rat heart is much lower than that of RYR2, suggesting that FKBP1B can play only a minor role in the regulation of RYR2 channel activity
Most strains of E.coli do not exhibit 20-ketosteroid reductase activity against steroid substrates such as 11-DOC, despite containing a full-length kduD gene. This activity is observed in the K12 / DH5-alpha strain, whose disruption of the kdgR gene leads to the constitutive expression of KduD in this strain
Was originally thought to be a D-3-phosphoglycerate dehydrogenase
Was originally thought to be a zinc uptake system
Tricorn seems to be split into two ORFs in S.tokodaii, encoded on opposite strands and separated by approximately 279 kb
Could be the product of a pseudogene. Related to NKAP
Cellular localization of OCT1 in the intestine and the kidney remains to be finally defined. While most authors have deduced a localization at the basolateral side of enterocytes consistent with a physiological role in organic anions uptake from the blood flow and intestinal excretion (PubMed:11463829), other studies demonstrated an apical localization (PubMed:23680637), supporting a function in intestinal absorption of organic anions and drugs (PubMed:11463829, PubMed:23680637). Similarly, contradictory findings have shown a localization to the basolateral side (By similarity) or to the apical side (By similarity) of proximal tubules (By similarity). While carnitine efflux is Na(+)-independent, carnitine uptake is significantly reduced in the absence of Na(+) (PubMed:28942964). Not able to uptake and choline in the liver (PubMed:24961373). Affinity and capacity of the transporter for endogenous substrates vary among orthologs (PubMed:34040533, PubMed:35469921). For endogenous compounds such as dopamine, histamine, serotonin and thiamine, mouse ortholog display higher affinity and capacity compared with human OCT1 (PubMed:35469921). In contrast with human ortholog, not involved in metformin efflux transport (PubMed:34040533)
Could be the product of a pseudogene. However, mouse (AC Q9QYL0) and rat (AC D3ZZW6) orthologs encode functional proteins
Product of a dubious CDS prediction. The MIR17HG transcript shows predominant nuclear localization and may not be efficiently translated into protein
This peptide is cyclic. The start position was chosen by similarity to cliotide T1 for which the DNA sequence is known
It is unclear whether it activates ALK as a homodimer or a monomer (PubMed:34646012, PubMed:34819673). According to a report, homodimeric ALKAL2 activates ALK (PubMed:34819673). According to a second publication, monomeric ALKAL2 binds and activates ALK (PubMed:34646012)
Could be the product of a pseudogene. Lacks 1 of the 4 disulfide bonds, which are conserved features of the family
Dodecin family members from different organisms have non-identical ligand binding specificity
One of the major routes for the degradation of L-threonine to glycine in both prokaryotes and eukaryotes takes place through a two-step biochemical pathway in mitochondria. In the first step, L-threonine is oxidized to (2S)-2-amino-3-oxobutanoate, by L-threonine 3-dehydrogenase tetramer (TDH). In the second step, mitochondrial 2-amino-3-ketobutyrate coenzyme A ligase (GCAT) catalyzes the reaction between (2S)-2-amino-3-oxobutanoate and coenzyme A to form glycine and acetyl-CoA. In human, however the enzyme thats catalyzes the fist reaction, TDH, is an expressed pseudogene encoding non-functional truncated proteins
Was originally thought to be two separate ORFs named bvgB and bvgC
There are conflicting reports on the effect the deletion of PTC7 causes in cells (PubMed:23940037, PubMed:28076776). In one report, deletion of PTC7 causes decreases in COQ6 levels, and mitochondrial defects observed are thought to be caused by disruption of the COQ6 pathway (PubMed:23940037). In another report, deletion of PTC7 causes no change in COQ6 levels and mitochondrial defects observed in mutants are not thought to be caused by changes in the COQ6 pathway (PubMed:28076776)
It was previously reported that this protein was the ortholog of rat SM-20. However, EGLN3 is now considered the true ortholog of rat SM-20 since it shows substantially greater similarity
Mass spectrometry indicates that the start site is probably Met-1, and not Met-12 as is thought to be the case in other organisms
The sequence signal is uncertain for 2 reasons. Firstly, it contains 2 consecutive basic residues (Arg) that may indicate that this segment corresponds to the message for translating an unknown third peptide or long propeptide. Secondly, it is not predicted by the predictive tools
There is confusion in the literature with phosphatidylinositol 4-phosphate 5-kinase type I nomenclature due to the fact that frequently mouse PIP5K1B is named Phosphatidylinositol 4-phosphate 5-kinase type I alpha
There are 4 nearly identical operons in various strains of P.putida. This one and the mepABC operon of strain KT2442-TOL function in solvent and antibiotic efflux; however the arpABC operon of strain S12 functions only in antibiotic efflux. This may be due to different protein expression levels. In strain KT2440 the equivalent operon does not seem to function in toluene efflux
An article reported the role of PknB in phosphorylation of PbpA, but this paper was later retracted as some figures were modified prior to publication
Was originally thought to originate from L.plantarum
The catalytic domain of Gdpd2 is oriented extracellularly; Glycerophosphoinositol is hydrolyzed in the medium of cells overexpressing Gdpd2, whereas intracellular levels of glycerophosphoinositol is not affected
This protein is about 60 residues too short at the N-terminus compared to its close orthologs
More similar by sequence similarity to the eukaryotic RNA polymerase subunits
Although clearly related the GHMP kinase family as demonstrated by the 3D-structure, it lacks many conserved feature of GHMP kinases and probably does not bind ATP, suggesting that it probably does not have kinase activity
Could be the product of a pseudogene. A frameshift removes the C-terminus. A full-length restored gene can be seen in (AC P0DP90)
Has been reported to enhance netrin-induced phosphorylation of PAK1 and FYN; and the interaction between DSCAM, PAK1 and RAC1 has been described. This article has been withdrawn by the authors
Lacks the conserved cysteine residue that is involved in the formation of the covalent thioimide linkage with the substrate; it is replaced by a glycine residue (Gly-45). The enzyme may thus be inactive
Could be the product of a pseudogene. It corresponds to positions 95 to 221 of the complete orthologous and probably active protein in R.felis (RF_0890)
Was reported that this protein is required for a proper autophagic response under stressful conditions such as prolonged starvation, based on experiments conducted on cells or mice claimed to have null alleles (PubMed:17442669). However, this paper has been retracted because of aberrations in the relevant figure (PubMed:30808006). Nevertheless, a separate experiment in the same paper suggests that the alleles are null and so the inferred function may be true
The U21 position mentioned in PubMed:11983710 corresponds in fact to U20 with the conventional numbering
It is uncertain whether Met-1 or Met-29 is the initiator
The complete sequence contains a signal peptide, a propeptide domain, and a proteinase domain at the N-terminus
A structure shows that CysB motif binds zinc but a later study has suggested it might bind 1 4Fe-4S cluster instead
Was originally thought to be a heterodimer based on the purification of the enzyme first reported from E.coli B, but results of enzyme assays in PubMed:21378189 have indicated that DadA is solely responsible for the observed dehydrogenase activity
The molecular function of NOTUM family protein has remained unclear for many years. It was initially thought to hydrolyze glycosaminoglycan (GAG) chains of glypicans, thereby affecting glypicans ability to interact with Wnt ligands. It was later reported to trigger glypican shedding, by mediating cleavage of their GPI-anchor (PubMed:22669824). It was finally shown that it requires glypicans to suppress Wnt signaling, but does not cleave their GPI-anchor. It acts by mediating depalmitoleoylation of WNT proteins, impairing WNT binding to frizzled receptors
Despite some similarity with the 'phage' integrase family, PubMed:7958912 showed that it has no recombinase activity
The sequence submitted as delta-AITX-Bcg1b (AC P86460) and renamed delta-AITX-Bcg1e is a deamidation product (at Asn-16 residue) of delta-AITX-Bcg1a (renamed delta-AITX-Bcg1d). This product does not show any activity on all Nav1 tested (Nav1.1 to Nav1.7)
ECM32 was originally identified as a DNA helicase and as component of DNA polymerase I
Was originally called CpsF
In contrast to other members of the family, it lacks one conserved zinc-binding site and the active site
The full-length coding region in cv. A3525 has been amplified by RT-PCR and sequenced, but not submitted to the EMBL/GenBank/DDBJ databases (PubMed:20679205)
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 1439 in the dsPTPase catalytic loop, suggesting that it has no phosphatase activity
Was originally thought to originate from mouse (Ref.1, PubMed:9757043)
Could be the product of a pseudogene. Created by a base pair loss in a duplication of PSBP1 (At1g06680). Not detected at the protein level in purified chloroplasts
Despite the fact that it belongs to the cyclophilin-type PPIase family, it has probably no peptidyl-prolyl cis-trans isomerase activity due to the presence of a tyrosine instead of a tryptophan at position 389
According to PubMed:16256063, this sequence exists in both japonica and indica subspecies and was submitted by the authors as a japonica cultivar nipponbare sequence. However, the corresponding sequence cannot be found in the currently available japonica nipponbare genome or japonica expressed sequence tag data, but matches perfectly in indica genome sequence. It is therefore annotated as indica sequence
Authors of PubMed:26511093 indicate an amidation at Cys-61. This amidation is improbable since no Gly follows the mature peptide region. This PTM is therefore not indicated here and we assume that electrophysiological results are obtained with an unamidated synthetic peptide
Was initially reported to act as a regulator of mRNA translation efficiency by promoting ribosome loading to m6A-containing mRNAs and by interacting with translation initiation factors eIF3 (EIF3A or EIF3B), thereby facilitating translation initiation (PubMed:30401835, PubMed:30728504, PubMed:30843071). These studies suggested that the 3 different paralogs (YTHDF1, YTHDF2 and YTHDF3) have unique functions with limited redundancy (PubMed:30401835, PubMed:30728504, PubMed:30843071). However, later studies showed that YTHDF1, YTHDF2 and YTHDF3 paralogs have redundant functions to a profound extent and directly promote degradation of m6A-containing mRNAs (PubMed:32943573). The effect on translation efficiency observed earlier is probably indirect (PubMed:32943573)
Lacks the conserved Asp active site at position 272
Was initially reported to have histone methyltransferase activity and methylate 'Lys-4' and 'Lys-36' of histone H3 (H3K4me and H3K36me) (PubMed:21832073). However, this conclusion was based on mass spectrometry data wherin mass shifts were inconsistent with a bona fide methylation event and the histone methyltransferase activity could not be confirmed (PubMed:30626964)
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 333 in the dsPTPase catalytic loop, suggesting that it has no phosphatase activity
Was initially thought to regulate chromosome segregation and mitotic spindle assembly (PubMed:16302001). However, it was later shown that its absence neither affect mitosis nor centriole duplication (PubMed:23644468)
Does not bind calcium as one of the calcium-binding sites is lost (Asp->Lys in position 64, which corresponds to 'Lys-49' in the current nomenclature). However, the hydrolytic activity is not restored by the mutant containing an Asp-64, indicating that other residues play a key role in hydrolytic activity (PubMed:11829743)
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-37; H2BK143ub1 = monoubiquitinated Lys-147
Could be the product of a pseudogene. The N-terminal region is truncated when compared to orthologs
Sequence shown in PubMed:10611289 correspond to the product of the second gene cited in PubMed:11117877
Valosin is an artifact of purification procedure, generated in vitro by cleavage of the whole protein upon acid extraction of tissues
The WASH6P N-terminus differs from WASH3P for which it is shown to be required for the WASH complex assembly. Hence is association within the WASH complex is ambiguous. However, WASH6P retains the regions implicated in interaction with WASHC2 and confering in vitro NPF activity
The biochemical characterization done in PubMed:15028873 is devoted to oleic acid, however, the preferred substrate of the enzyme is linoleic acid
Sequence shown and variants are a mixture of subunits alpha and beta, since the correspondence of each variant to each subunit is not yet defined
Although Mg(2+) has been found in crystallography study, the positions do not correspond to the correct residues
The first non-coding exon of RBMXL1 is in common with that of CCBL2
This insertion-derived sequence is found in six copies in NRC-1, one copy on the chromosome, two on plasmid pNRC100 and three on plasmid pNRC200
CarB is split into two genes in A.aeolicus (AQ_1172 and AQ_2101)
A report observed N-glycosylation at Asn-83 (PubMed:19139490). However, as the protein does not localize in an extracellular compartment of the cell, additional evidence is required to confirm this result
There are two genes termed arcA in strain O6 of E.coli, one refers to an arginine deiminase and the other to a two-component regulator
Could be the product of a pseudogene. Not expected to have protease activity
Has been shown to be active in cv. Columbia (AC Q9M670) due to naturally occurring sequence variation in this strain. The sequence shown is from strains cv. Bl-1 and cv. Sakata
The gene model predicted by TAIR differ by the presence of one additional Glu at the splice site
A truncated form of MSP9 has serine protease activity in vitro; however, it is not clear if this is physiologically relevant (PubMed:10699251). Also, the putative residues forming the catalytic triad (His-55, Asp-94, and Ser-190) are not conserved in P.vivax, P.knowlesi, and P.cynomolgi orthologs casting a doubt on the physiological relevance of the protease activity (PubMed:14630931)
Characterization did not differentiate between the two isoforms determined by protein sequencing (PubMed:22195573, PubMed:23823708)
In strain COL, lip2 is interrupted in position 645 by the insertion of the L54a prophage
It is unclear if PMIX is glycosylated as other members of the same enzyme family, i.e. PMI and PMII, are not
The PHTF domain was initially defined as an atypical homeodomain, suggesting that this protein could act as a transcription regulator (By similarity). However, the protein is not found in the nucleus and mainly localizes in the endoplasmic reticulum membrane, suggesting that it does not act as a transcription factor (By similarity)
This sequence lacks full-length transcript support
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me1 = monomethylated Lys-10; H3S10ph = phosphorylated Ser-11; H3K14ac = acetylated Lys-15; H3K14me2 = dimethylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me1 = monomethylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me1 = monomethylated Lys-24; H3K27ac = acetylated Lys-28; H3K27me1/2/3 = mono-, di- and trimethylated Lys-28; H3K36ac = acetylated Lys-39; H3K36me1/2/3 = mono-, di- and trimethylated Lys-39; H3K56ac = acetylated Lys-59; H3K64ac = acetylated Lys-67; H3K79me1/2/3 = mono-, di- and trimethylated Lys-82
It was initially thought that PDL3 has phospholipase D activity due to its HKD motifs. The second HKD motif contains Glu instead of the canonical Asp. Its enzyme activity is therefore unsure. Catalytic phospholipase D activity is still controversial (By similarity). Its closest homolog PLD4, exhibits no phospholipase activity (By similarity)
Some authors (PubMed:9560439, PubMed:10821186) suggest this protein is rps11, however rps11 is a completely different gene which encodes small ribosomal subunit protein uS11
Was originally thought to be the toxic component of a type II toxin-antitoxin (TA) system; overexpression was shown to lead to growth arrest after 5 hours, with initial elongation of cells, followed by swelling (PubMed:22239607). The toxic effects were abrogated by coexpression with antitoxin CptB (now sdhE) (PubMed:22239607). However subsequent studies have been unable to show the toxic effect upon overexpression, nor is the Serratia ortholog a toxin (PubMed:23657679)
According to some authors, has impaired kinase activity
Was originally thought to be involved in carbon catabolite repression (PubMed:8557031). It has later been demonstrated that the catabolite-regulation defect in COQ7 mutants was a secondary effect of the respiration deficiency in ubiquinone-deficient mutants and could be rescued by the addition of exogenous ubiquinone (PubMed:9452453)
Ref.5 refers to this gene as REV7. REV7 is however the adjacent gene
Lacks the transmembrane and the protein kinase domains, which are conserved features of the CRK subfamily
The proteins described here are encoded by the gene CDKN2A, but are completely unrelated in terms of sequence and function to cyclin-dependent kinase inhibitor 2A (AC P51480) which is encoded by the same gene
The subcellular location study was carried out using a rat fibroblast cell line
Probable inactive cysteine methyltransferase. In contrast to other members of the family, has a shorter C-terminus and is unable to inhibit host cell NF-kappa-B activation (PubMed:20485572)
Was originally thought to belong to the methylesterase (MES) family
Despite its official name, does not contain LRR repeats
Was originally thought to play a role in adaptive immunity through control of dendritic cell-mediated antigen transport to lymph nodes from peripheral sites (PubMed:22538615). However, this was later shown to be dependent on DOCK8 (PubMed:26605525)
In mouse, 5 genes homologous to human CD209/DC-SIGN and CD209L/DC-SIGNR have been identified
A previous study found the localization of TMEM174 in the endoplasmic reticulum (By similarity). A more recent study detected TMEM174 in cell membrane (By similarity). The difference between these two studies could be due to the use of different cell lines
Lacks the conserved active histidine at position 83 that mediates the phosphotransfer. Shows a conserved HPt domain that may have some alternative degenerated phosphorelay role in cell signaling
In cv. LA101, 9DC1 results from the rearrangement in the Cf-9 disease resistance gene cluster between Cf-9 and Hcr9-9D, both originating from the cv. Cf9
Was originally incorrectly assigned as CHB4
Was reported to have N(6)-adenine-specific DNA methyltransferase by mediating methylation of DNA on the 6th position of adenine (N(6)-methyladenosine) (PubMed:30017583). The existence of N(6)-methyladenosine on DNA is unclear in mammals (PubMed:32203414). According to a report, the majority of N(6)-methyladenosine in DNA originates from RNA catabolism via a nucleotide salvage pathway and is misincorporated by DNA polymerases, arguing against a role as epigenetic DNA mark in mammalian cells (PubMed:32203414). Moreover, subsequent studies could not confirm the role of N6AMT1 as a N(6)-adenine-specific DNA methyltransferase (PubMed:30392959, PubMed:31632689, PubMed:31636962)
An expected heme iron ligand His residue was not found at position 197 in this sequence
Could be the product of a pseudogene; it is missing regions at the N- and C-terminus compared to its paralogs
Lacks the Tyr (here Asp-204), a conserved feature of the aromatic cage required for the interaction with histone H3K4me3/2
High-capacity urate transporter that was first described as a fructose and glucose transporter. Also described in the literature as high-affinity and low-capacity glucose and fructose transporter (PubMed:18327257, PubMed:17710649, PubMed:18842065). However, another group could not confirm transporter activity for glucose or fructose (PubMed:28083649)
Could be the product of a pseudogene. The protein is truncated by the insertion of transposon Tn1000
No genomic clone corresponding to this cDNA could be found
Does not bind calcium as one of the calcium-binding sites is lost (Asp->Asn in position 48, which corresponds to 'Asn-49' in the current nomenclature)
It is uncertain whether variants in this gene are associated with Parkinson disease. Some authors mention association with the disease (PubMed:18252210). In contrast, some others do not observe any association (PubMed:19133659)
Studies in clathrin-mediated endocytosis used a siRNA mixture of EPS15 and EPS15L1
The nucleotide sequence reported in PubMed:9055413 was not that of the characterized enzyme. Inspection of the original N-terminal sequence showed that the characterized enzyme was pfkA2 (SCO5426) and not pfkA1 (SCO2119), another isozyme in S.coelicolor (PubMed:18606812)
This gene is encoded entirely within the yaaW gene on the opposite strand. Disruptions of one gene are also usually disruptions in the other
Does not seem to have protease activity as it lacks the zinc-binding sites
This protein was first known as suppressin (characterized in bovine neuroendocrine and immune cells). However, according to PubMed:9773984, it is uncertain whether it corresponds really to the suppressin also described in Ref.4. DEAF1 has been described as a nuclear dimeric protein and suppressin as a secreted monomeric protein
This peptide is cyclic. The start position was chosen by similarity to cyclotide mra4 for which the DNA sequence is known
In contrast to other fungi who have a single histidine biosynthesis trifunctional protein, 2 proteins are present in S.pombe to ensure these functions: his7 (phosphoribosyl-AMP cyclohydrolase and phosphoribosyl-ATP pyrophosphatase activities) and his2 (histidinol dehydrogenase activity)
Was originally thought to be a longer protein that encodes what is now known to be OrgA and OrgB
Was originally (PubMed:18299247) thought to belong to the ABC transporter family. Lacks the conserved ABC domain, which is one of the features of the ABC transporter family
The proteins described here are encoded by the gene CDKN2A, but are completely unrelated in terms of sequence and function to tumor suppressor ARF (AC Q8N726) which is encoded by the same gene
According to a report, interaction with FOXK2 is not dependent on phosphorylation of BAP1 (PubMed:24748658). However, it was later shown that phosphorylation at Thr-493 promotes interaction with FOXK2 (PubMed:25451922)
Met-5 is the major initiator, but Met-1 may also be used
It is uncertain whether Met-1 or Met-45 is the initiator. N-terminal sequencing in PubMed:10978616 suggests that Met-45 is used, followed by methionine initiator removal
Was originally (PubMed:11102367) named veg. However, more thorough studies (PubMed:22575127) found that the veg phenotype does not map to this protein. It is still not known which gene corresponds to the veg phenotype
Was originally thought to be a bacteriocin (PubMed:7986050); it has since been shown this is not the case (PubMed:19172747)
PubMed:16895901 reports that it is a type I membrane protein. However, no clear transmembrane region is detected by prediction methods, suggesting that its localization at the plasma membrane is unsure
Although related to peptidase S1 family, the active site residues characteristic of serine proteases appear to be absent from this protein, which may therefore lack protease activity
Was originally erroneously termed BP80E
Was initially thought to act as an inhibitor of MCU based on effects following MICU1 depletion (PubMed:20693986, PubMed:23101630). However, depletion of MICU1 also eliminates MICU2, explaining the initial conclusion. It was later shown to act as a stimulator of MCU activity instead (PubMed:24560927)
The topology is subject to discussion. According to some reports, localizes at the outer surface of the mitochondrion inner membrane (PubMed:20693986, PubMed:24332854). According to another publication, forms an intramembrane hairpin loop without crossing the membrane (PubMed:23747253). Recent studies rather suggest that it contains a transmembrane region that crosses the mitochondrial inner membrane, with the main part of the protein localized in the mitochondrial intermembrane space (PubMed:26387864, PubMed:26489515)
According to PubMed:18629938, the SIGLECP16 sequence, that was initially classified as a pseudogene, has a 4 bp deletion when compared with the sequence shown in this entry. This deletion is a polymorphism with a frequency of around 50% in the UK population. The frameshifted allele is non-functional whereas the sequence displayed here seems to be functional. The functional allele has been named SIGLEC16 in PubMed:18629938
Was reported to dephosphorylate STAT5A and STAT5B in the nucleus to negatively regulate prolactin-mediated signaling pathway (PubMed:11773439). However, the corresponding article has been retracted (PubMed:24319783)
Lacks the conserved Asp residue expected to act as the active site proton acceptor
In contrast to other members of the family, it lacks the N-terminal region
Contains two extra cysteines at two highly conserved sites. Cys-37 and Cys-54 replaces the conventional calcium-binding Gly-32 and Asp-49 respectively
Product of a dubious gene prediction. Encoded in intron of UBA1
Could be the product of a pseudogene. It is encoded in the reverse strand of the region coding for trl, a gene which has been shown to exist in a number of H.pylori strains
Was first identified because of its ability to stimulate Na(+)-dependent phosphate cotransport
Was initially thought to function as a transcriptional corepressor
Was proposed to be a ligase for bicarbonate and threonine (PubMed:21285948): in the first step, TsaD would catalyze transfer of a gamma-phosphate group from ATP to bicarbonate, yielding carboxyphosphate and ADP; carboxyphosphate would then react with the threonine amine, producing N-carbamoylthreonine and phosphate. However, the protein ortholog in B.subtilis was shown to be involved in another step of t(6)A37 biosynthesis, i.e. the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB (PubMed:23072323). The protein ortholog in yeast (QRI7) was also shown to catalyze this step, and does not require the presence of additional proteins (PubMed:23620299)
The well-known t(6)A modification appears to be a hydrolyzed artifact of natural cyclic t(6)A (ct(6)A) that occurs during the preparation and handling of tRNA in E.coli and many other species (PubMed:23242255). In these species, the t(6)A modification is processed further by dehydration into ct(6)A, a reaction catalyzed by TcdA
Lacks the conserved ATP-binding site due to Leu-43 (instead of a conserved basic residue)
Could be the product of a pseudogene; while the translated protein of the N-terminal section has been identifed, this section has not been seen by mass spectrometry
Despite a certain similarity to selA, this is not selA (see AC Q57622)
Gly-651 is present instead of the conserved Ser which is expected to be an active site residue suggesting that this protein has no peptidase activity
Could be the product of a pseudogene. Although transcribed, the gene is poorly translated probably due to a deletion in the regulatory region. PubMed:17623810 could not detect the protein by Western blot
Protein purification and mass spectrometry by PubMed:16962183 do not differentiate between the TRP4.8/polIIA and TRP5.9/polIIB gene products
Although it contains a polysaccharide deacetylase domain, the protein does not display any chitin deacetylase activity
Truncated sequence in cv. Columbia (AC F4IBJ3) N-terminus compared to cv. Landsberg erecta (AC Q6IVU7) and other members of the expansin B subfamily
There are 4 nearly identical operons in various strains of P.putida. The ttgABC operon of strain DOT-T1E and the mepABC operon of strain KT2442-TOL function in solvent and antibiotic efflux; however in strain S12 the arpABC operon functions only in antibiotic efflux. This may be due to different protein expression levels. In KT2400 this operon does not seem to function in toluene efflux
In contrast to other members of the family, lacks the active sites for palmitoleoyl-protein carboxylesterase activity, suggesting it has no activity
In strain H37Rv, PLC-D lacks the N-terminal domain. The gene is truncated and interrupted by the insertion of an IS6110 element. However, when expressed in M.smegmatis, recombinant PLC-D is detected in the cell wall fraction and shows phospholipase activity (PubMed:20736081)
It is uncertain whether Met-1 or Val-35 is the initiator
PubMed:9792670 states that both the N- and the C-terminus are located in the cytoplasm
Has no 2-lysophosphatidate/LPA phosphatase activity. This is supported by the fact that the phosphatase sequence motifs as well as the His residue acting as a nucleophile in active phosphatases of the PA-phosphatase related phosphoesterase family are not conserved
Micasin should not be confused with micasin-1, the second defensin-like peptide from A.canis, which shows low sequence similarity compared to micasin
Was originally called epsilon crystallin
It has been reported that mutant phenotypes can be rescued by tryptophan dietary supplementation, but not by methionine (PubMed:23499532). However, a later report describes successful phenotype rescue by methionine supplementation; this may be due to methodological differences (PubMed:33016879)
Despite its similarity with the trehalose-phosphate phosphatase enzymes, it does not display trehalose-phosphate phosphatase activity
Different sequence motifs predict both the N-glycosylation modification and the GPI- or GPI-like anchor modification for Asn-161. While it is chemically possible for both modifications to occur, it is not known whether it is enzymatically possible
HKT2 is found in salt-tolerant cultivar indica Pokkali. It does not exist in cultivar indica 93-11 or japonica Nipponbare
The interaction with CACNA1A is described as calcium independent in PubMed:11865310 while it is shown to be acutely calcium dependent in PubMed:14570872. PubMed:12032348 describes a stimulatory effect of CABP1 during agonist-induced intracellular calcium signaling while PubMed:14570872 and PubMed:11865310 show an inhibitory effect
Lacks the potential active site region of the MGMT family and therefore has probably lost the methyltransferase activity
CORI3 was initially isolated by Lopukhina et al (PMID:11500565) as tyrosine aminotransferase (TAT). The authors also measured a TAT activity in vitro, even though relatively weak. Jones et al (PMID:12525491) showed that CORI3 possesses cystine lyase (CL) activity, but lacks TAT activity in vitro. In addition, CL activity is not inhibited by saturation of L-tyrosine in the medium. As CORI3 should bind L-tyrosine to catalyze TAT activity, this excludes a TAT activity for CORI3. Jones et al. made the statment that TAT activity resulted probably from residual native TAT-catalyzing proteins present in the purified preparations employed by Loupokhina et al
Could be the product of a pseudogene. Highly similar to the N-terminus of GUSB but lacks the C-terminal part
A report observed N-glycosylation at Asn-493 (PubMed:19139490). However, as the protein is predicted to act as a DNA-binding transcription activator, additional evidence is required to confirm this result
Could be the product of a pseudogene. Experiments were performed with a repaired version of the protein (AC B7NGZ6) (PubMed:26162088)
Was initially thought to be considered to be a low affinity lactate transporter with negligible affinity for pyruvate (By similarity). However, it was later shown that SLC16A3 is a high affinity lactate transporter with physiologically relevant affinity for pyruvate (By similarity)
Was initially assigned as monocarboxylate transporter 3 (MCT3) (PubMed:9632638). However, it was later shown that it corresponds to monocarboxylate transporter 4 (MCT4)
This gene should not be confused with EIF2S1, frequently called eIF2-alpha in the literature, and with which it shares the alias EIF2A. EIF2S1 is the alpha subunit of the eIF2 translation initiation complex. Although both of these proteins function in binding initiator tRNA to the 40S ribosomal subunit, the EIF2A protein does so in a codon-dependent manner, whereas eIF2 complex requires GTP
The mature 9-residue peptide is expected to be found in 18-residue cyclopeptides produced by combinatorial peptide splicing either with itself or with other demidefensins. However among cyclopeptides screened for antimicrobial activity, no peptides that would have been produced from this sequence were detected
It is not sure whether OMT1 and OMT2 are really encoded by two different genes or if they represent cloning artifacts
The N-terminus is shorter than in orthologs
Was originally thought to be an RNase; when the C-terminus (residues 409-569) is expressed in E.coli it has RNase, not DNase activity, and inhibits growth upon expression in E.coli. In vitro RNase activity and in vivo growth inhibition are neutralized by cognate immunity protein YxxD, but not by immunity proteins specific to other toxins with the LXG domain. Mutation of His-548 to Ala leads to loss of growth inhibition and RNase activity in E.coli
This sequence is shorter than orthologs
PRY has multiple identical or highly similar copies on chromosome Y, some of which might be non functional pseudogenes
Was originally proposed to be inserted into either the outer or inner mitochondrial membrane (PubMed:12972421, PubMed:8089172). More recent data indicates that it is instead inserted into the ER (PubMed:19556461)
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-20; H2BK34ac = acetylated Lys-21; H2BK143ub1 = monoubiquitinated Lys-128
This protein has been N-terminally truncated based on homology to the Anabaena variabilis ortholog
It is uncertain whether Met-1, Met-14 or Met-30 is the initiator
Could be the product of a pseudogene. According to PubMed:17562432, no evidence has been tendered concerning the existence of this protein
According to PubMed:12514748, it is related to the prion family because it is found in the same genomic cluster as PRNP and PRND. However, it does not share any sequence similarity with these 2 proteins
A paper describing ATG4D tissue expression has been retracted, due to concerns of image duplication in some of the figures
Was originally thought to be a kinase on the basis of weak and non-significant similarities
Was originally thought to be an L-carnitine dehydratase
In strains K / NM522 and K12 / MG1655 the cybC gene has a 26 bp deletion and lacks the first 7 amino acids. It is not translated in those strains
Could be the product of a pseudogene. The peptide used to produce antibodies against ACOT7L matches at 85% with ACOT7 and the antibodies may not be specific to ACOT7L
Was originally thought to be CDC39 (which is in fact NOT1)
Was originally thought to be a xanthine dehydrogenase
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me1 = monomethylated Lys-10; H3S10ph = phosphorylated Ser-11; H3K14ac = acetylated Lys-15; H3K14me2 = dimethylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me1 = monomethylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me1 = monomethylated Lys-24; H3K27ac = acetylated Lys-28; H3K27me1/2/3 = mono-, di- and trimethylated Lys-28; H3K36ac = acetylated Lys-37; H3K36me1/2/3 = mono-, di- and trimethylated Lys-37; H3K56ac = acetylated Lys-57; H3K64ac = acetylated Lys-68; H3K79me1/2/3 = mono-, di- and trimethylated Lys-80
Was originally termed sox-12 (PubMed:8597594, PubMed:1614875)
Could be the product of a pseudogene unlikely to encode a functional protein. Strain S288c has a stop codon in position 142, which disrupts the gene coding for this protein and produces two ORFs. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
Could be the product of a pseudogene, in E.coli K12, an insertion sequence (IS3E) is inserted in the gatR gene in position 102
This protein is missing some of the active site residues
Found in a segmental duplication on p arm of chromosome 16 giving rise to two identical copies of this gene sharing exons with SULT1A3 and SULT1A4
None of the predicted glucanase inhibitor proteins (GIPS) has an intact catalytic triad, therefore, GIPs are proteolytically inactive
The last gene of this probable operon, ureD, gives rise to a truncated protein. Absence of ureD prevents expression of active urease. Correction of the mutation does not effect virulence in mice in any detectable fashion, suggesting urease is not important in the virulence of Y.pestis (PubMed:11119503)
Has been the subject of controversy surrounding its catalytic capabilities. Early characterization of PEAK1 gave a weak in vitro tyrosine kinase activity. The crystal structure indicates that the kinase-domain contains a closed nucleotide-binding cleft that in this conformation may deleteriously affect nucleotide bindin. Furthermore PEAK1 is devoid of nucleotide binding activity, as detected by a thermal-shift assay. So it seems probable that PEAK1 is an inactive kinase
In contrast to other metacaspases of the peptidase C14B family, the catalytic histidine and cysteine residues do not appear to be conserved
PubMed:11533064 detected some protein kinase activity and ability to phosphorylate transcription factors c-jun/JUN and ATF2. However, PubMed:15762844 showed that it does not have protein kinase activity
Despite possessing the necessary catalytic residues, this protein does not function as an enzymatically active argininosuccinate lyase
PubMed:22511981 refers the nucleotide sequence FD664509 as coming from Scorpiops tibetanus
The sequence was deposited erroneously as PPO2 (PubMed:12185078)
Ser-855 is present instead of the conserved Asp which is expected to be an active site residue
The sequence misses both the N-terminal and C-terminal parts. The correct gene model with the complete protein sequence could not be recovered from the submitted genomic sequence
Its phosphatase activity is uncertain. Lacks in vitro phosphatase activity with p-nitrophenylphosphate, even if the catalytic Cys is conserved
It is uncertain whether Met-1 or Met-14 is the initiator. However, according to some experiments, Met-14 seems to be the initiator
First thought to play a role in the regulation of apoptosis, mediating mitochondria-induced cell death in vascular smooth muscle cells through the release of cytochrome c (COX) from mitochondria and the activation of the caspase cascade (By similarity). However, recent studies show that it is not directly involved in apoptosis regulation but in the protection of COX from oxidatively induced degradation (PubMed:30552096, PubMed:25175347)
Plays a role in repressing the response to infection by the Gram-negative bacterium P.aeruginosa (PubMed:27927200). However, is also reported to play a protective role in the response to infection by P.aeruginosa (PubMed:28662060). These differences may be due to conditions of infection or perhaps genetic background
Although strongly similar to members of the ADAMTS family it lacks the metalloprotease and disintegrin-like domains which are typical of that family
Could be the product of a pseudogene unlikely to encode a functional protein. The ORF corresponds to a fragmentary flocculin piece with sequence similarity to FLO1. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
Aurein 5.2 may be a deamidated form of aurein 5.3
Although thought to contribute to D(4)-dafrachronic acid biosynthesis, the latter may not be present at physiologically relevant concentrations in C.elegans and comparative metabolomics would indicate 7-dehydrogenase activity and participation in D(7)-dafrachronic acid biosynthesis instead
To date, the intracellular localization of ABCB6 is a matter of debate, with conflicting reports suggesting mitochondrial or endolysosomal localization, therefore questioning the requirement of ABCB6 in the mitochondrial import of porphyrins
Should not be confused with rat testin which is a thiol protease homolog
YoeB, the specific toxin against which this antitoxin acts in E.coli, is not encoded in this genome
Manganese (Mn) transport by SLC40A1 remains controversial. Some in vitro studies have suggested that SLC40A1 transports minimal amounts of Mn(2+) (By similarity). Other groups have suggested that it does not. The affinity of SLC40A1 for manganese is extremely low compared with iron, implying that any SLC40A1-mediated Mn transport in vivo would likely be trivial (By similarity). A recent study examined the role of SLC40A1 in Mn homeostasis by using Tmprss6-O mice, which express high levels of hepcidin/HAMP and therefore have very low SLC40A1 levels in their tissues. These mice show frank iron deficiency and reduced iron levels in most tissues, but manganese levels are largely unaffected (By similarity). These studies suggest that manganese is propably not the physiological substrate of SLC40A1
HSN2 was originally thought to be an intronless gene lying within a WNK1 gene intron. It has been shown to be a nervous system-specific exon of WNK1 included in isoform 4 and isoform 5 (PubMed:18521183)
It is uncertain whether Met-1 or Met-214 is the initiator in isoform 4 and isoform 5
Was originally (PubMed:8383878) thought to have a N-terminal sequence signal and a C-terminal transmembrane region. Both domains do not exist in the revised sequence
Could be the product of a pseudogene. C-terminally truncated compared to orthologs
In contrast to other members of the histone H2B family, this protein is much longer and has a highly divergent N-terminus. It is therefore unclear whether it is a real histone
The order of the peptides is unknown
Conflicting results are seen for mutagenesis of Lys-173. It is seen to reduce binding to the SH3 6 domain of human DNMBP (Tuba) by surface plasmon resonance (PubMed:19767742). In the crystal structure with Tuba this reside is seen not to be in the protein-protein interface, and pull-down assays show it interacts normally with Tuba (PubMed:24332715). Two studies show this residue is important for virulence in the mouse model (PubMed:19767742, PubMed:23403554)
Was termed (PubMed:8387522, PubMed:2170109) RPTPase beta
The human genome was initially thought to contain 2 genes for PTPRZ: PTPRZ1 (on chr 7) and PTPRZ2 (on chr 1). However, PTPRZ2 probably does not exist and corresponds to PTPRZ1
Reported to bind to bacterial lipopolysaccharide (LPS) in vitro (PubMed:15158712, PubMed:27145151). However, the in vivo significance of this is uncertain since other studies indicate little or no specificity for LPS (PubMed:12920053, PubMed:25223608)
It is unclear whether it acts as an upstream kinase for polo kinase by mediating phosphorylation of plk1/plx1 or whether it is a downstream target of plk1/plx1
Although similar to members of the ADAMTS family, it lacks the metalloprotease and disintegrin-like domains which are typical of that family
Upon comparison to orthologs, this is probably a fragment
Could be the product of a pseudogene unlikely to encode a functional protein. This is a truncated part of a POL protein in the mutated, non-functional YCLWTy5-1 transposon. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
Was originally thought to be involved in molybdate transport
This protein is not an active H(+)-ATPase in its current form as there is a deletion in a conserved domain crucial for P-type ATPase function
Was initially reported to be secreted via a non-classical export pathway (PubMed:18548201). It was however later shown that it localizes to mitochondria, in agreement with other members of the family (PubMed:22746225)
Reported to be associated with components of the peptide-loading complex, TAPBP, CALR, CANX and PDIA3 (PubMed:12794138). This association in primary cells and its functional relevance is disputable, given that antigen presentation and MAIT cell activation is shown to be TAP1-TAP2 and proteasome-independent
PubMed:15368893 (AE017042) sequence differs from that shown due to the presence of an IS100 insertion sequence. This gene in strain 91001 is probably a pseudogene
The DapA family was originally thought to be dihydrodipicolinate synthases (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB. This enzyme is still named DHDPS in PubMed:22949190 and PubMed:24677246, but since DHDPS is considered as a misleading name, it was not used in this entry
Product of a dubious CDS prediction. The transcript contains several 3' non-coding exons. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay
There is controversy as to whether this protein preferentially binds Fe(2+) or Fe(3+), and also whether it is found associated with the plasma membrane or not
PubMed:10484737 describes this protein as produced by V.verutina. It is very probable that this species is a misspelled form of V.velutina
Was originally thought to be the ortholog of human HOX11
Was initially thought to be two separate ORFs named yhaJ and yhaK
Although assigned as a calmodulin family member by Ref.6, it only contains EF-hand domains
A WASHC2C construct with WASHC2A-specific sequence insertions has been used in a number of experiments; the results are included in the WASHC2C entry
Could be the product of a pseudogene. This gene is longer than the rat and mouse orthologs and also contains a RanBP2-type zinc finger which is not present in those orthologs
Was thought to be an outer membrane protein as it is part of a disulfide cross-linked complex that is insoluble in the detergent Sarkosyl. In PubMed:7532170 it was shown to likely be periplasmic
Although it belongs to the glycosyl hydrolase 18 family, Leu-167 is present instead of the conserved Glu which is an active site residue. Therefore this protein lacks chitinase activity
Although related to peptidase S1 family, lacks the conserved active Ser residue in position 342 which is replaced by a Thr, suggesting that it has no protease activity
PubMed:1371275 sequence was incorrectly thought to originate from bovine
Has been suggested to both inhibit transposition and possibly enhance transposition
Phe-155 is present instead of the conserved Tyr which is expected to be an active site residue
Leu-9 is present instead of the conserved Cys which is expected to be the active site residue of peptidase C39. Thus they are presumed to be without peptidase activity
The protein-lysine deacetylase activity using CoA as substrate is unclear as this protein belongs to a family of serine hydrolases, and that the reaction shown in the publication is not hydrolyzing H(2)O. Additional experiments are therefore required to confirm this activity in vivo
It is uncertain whether Met-1 or Met-74 is the initiator
Could be the product of a pseudogene. In K12 strains the phnE gene has an 8-bp insertion, absent from the strain B gene, which causes a frameshift mutation (PubMed:1840580). In 8 K12 derivatives selected for their ability to grow on phosphonate this repeat is no longer present, which restores an intact PhnE open reading frame (PubMed:1840580)
Lacks the conserved thioester bond that is characteristic of the alpha-2-macroglobulins
Found in a segmental duplication on p arm of chromosome 16 giving rise to two identical copies of this gene sharing exons with SLX1A and SLX1B. The ORFs of SULT1A3 and SULT1A4 differ with only a single nucleotide change that does not alter the encoded amino acid. It is not possible to determine whether any individual polymorphism is present within SULT1A3 or SULT1A4 (PubMed:15358107)
Contrary to other SET-domain containing methyltransferases, set-9 does not have the residues usually involved in cofactor binding: instead of the highly conserved XGXG, Y and NH motifs, set-9 displays AVEA (Ala-940-Ala-943), V (Val-959) and F (Phe-1055) and RR (Arg-1016-Arg-1017) motifs
This peptide is linear but closely related to cyclotides. Since in UniProtKB the primary structure is preferred to classify proteins, the sequence is assigned to the cyclotide family
A paper showing that the protein forms homodimers via the BTB domain has been retracted by the authors, due to concerns regarding the validity of their data. However, they still consider that their main conclusions may be correct and require further testing
Was originally thought to be a glutathione peroxidase (PubMed:10455235), but functions as an atypical 2-Cys peroxiredoxin using thioredoxin as reducing power instead (PubMed:18162174)
The homodimer was initially thought to be disulfide bonded; however it is not the case
Asn-213 is present instead of the conserved Asp which is expected to be a metal binding residue
Was previously reported to interact with ASXL1. However, this publication has been retracted
PubMed:12142430 (AE009952) sequence differs from that shown due to the presence of an IS100 insertion sequence. This gene in strain KIM5 may, therefore, be a pseudogene
Ser-301 is present instead of the conserved Lys which is expected to be the pyridoxal phosphate-binding residue which is required for activity in all known pyridoxal-dependent aminotransferases
The N-terminus is shorter than in related proteins
The conserved zinc-binding site Asp residue in position 364 is replaced by a Thr
Could be the product of a pseudogene. This sequence is interrupted by a stop codon
Could be the product of a pseudogene. In P.cenocladum this protein is in two parts: a N-terminal section of 308 AA and a C-terminal section of 1535 AA
Defined as a pseudogene by HGNC. However, proteomics data suggest the existence of the protein
Was originally assigned as UGD4
Could be the product of a pseudogene. Related to FRMD8
Due to the effects of deletion on gene expression, was originally thought to be a general transcription factor (PubMed:19679657). Further studies clearly suggest that it is involved in nuclear localization of the RNA polymerase II complex (PubMed:21504834)
Encoded in an intron of the TRAPPC9 gene
Although the complete sequence is not known with certainty, sequence shown here appears to be the most probable in accordance with the mouse sequence ortholog
Was originally thought to be involved in cobalamin biosynthesis
In contrast to human SIRT5, which has only weak deacetylation activity, CobB shows comparable lysine deacetylation and lysine deacylation activities
PubMed:10381378 has reported that this protein has a weak ADP-ribosyltransferase activity, but that is probably not its primary activity in vivo
Lacks the conserved Glu residue in position 378 necessary for the catalytic activity
Neither His-431 nor Leu-432 is followed in the nucleotide sequence by the expected Gly residue that would be required to produce amidation
Lacks one of the three transmembrane regions, which are conserved features of the family
No detectable activity
This is a truncated version of aquaporin-2. A natural 11 bp deletion in position 109 leads to a frameshift, which disrupts the gene coding for this protein and produces two ORFs EC1118_1L10_0111g and EC1118_1L10_0100g. A contiguous sequence for aquaporin-2 can be found in strain Sigma 1278B (AC P0CD89)
This is not the ortholog of human CEACAM3
Isoform 3 was originally thought to display histone methyltransferase activity only following O-glycosylation at Thr-440 (PubMed:19377461). However, the corresponding article has been retracted (PubMed:24336203). Does not exhibit histone methyltransferase towards histone H3 in vitro (PubMed:19264965, PubMed:27812132). The isolated catalytic SET domain lacks binding activity towards cofactor S-adenosyl-L-methionine; instead of the highly conserved XGXG, Y and NH motifs, KMT2E displays NKKI (Asn-339-Ile-342), F (Phe-381) and RR (Arg-408-Arg-409) motifs (PubMed:27812132). Also lacks binding activity towards histone H3 due to a poor conservation of the key residues involved in the binding and the presence of large loop which prevents the docking of the H3 'Lys-4' side chain (PubMed:27812132)
Conflicting reports about the role of ERBB4 in mediating apoptosis, differentiation, or tumor cell proliferation may be explained by the opposite functions of the different isoforms and their intracellular fragments, and by the formation of heterodimers with other EGF receptor family members (PubMed:18454307, PubMed:21811097). Thus, heterodimer formation of a kinase-dead ERBB4 mutant with ERBB2 is sufficient for the activation of AKT1, MAPK1/ERK2 and MAPK3/ERK1 (PubMed:19098003)
Lacks the conserved tripeptide Ser-Pro-Cys in position 625 necessary for the methyltransferase activity in DRM protein (AC Q9M548)
Was originally proposed to be a subunit from an L-xylulose uptake system, but PubMed:16385129 shows that it does not bind L- or D-xylulose
Product of a dubious gene prediction. Van den Eynde et al (PubMed:7544395) identified this gene on chromosome X, however it is not currently present in the reference genome assembly (GRCh38/hg38)
Defined as a pseudogene by HGNC. However the existence of the functional protein is supported by the inhibition of its expression and its function using siRNAs specifically targeting SUMO1P1/SUMO5
Despite its name it is related to the unc-93 family and not to the major facilitator superfamily
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-34; H2BK143ub1 = monoubiquitinated Lys-146
In contrast to mammalian L-gulono-1,4-lactone oxidases, the ortholog in M.tuberculosis is not a flavoenzyme
It is uncertain whether Met-1 or Met-72 is the initiator
Reported to phosphorylate STK11 leading to nuclear export of STK11, subsequent inhibition of PI3K/Akt signaling, and increased apoptosis in vein endothelial cells treated with the oxidant peroxynitrite (PubMed:18321849). However this paper was withdrawn by the authors due to concerns of image duplication in the figures. Its role in protein phosphorylation has been confirmed in other studies (PubMed:15084291, PubMed:15324659)
This protein does not seem to be able to bind zinc, which all carbonic anhydrases are thought to require
According to PubMed:16233211, SerC is not involved in pyridoxine biosynthesis in B.subtilis. In this organism, pyridoxal phosphate biosynthesis is achieved via an alternative pathway involving PdxS and PdxT
The acidic chain was originally postulated to act as an inhibitor of the basic chain
The gene coding for this protein seems to be defective in strain 91001 where it is interrupted by the insertion of an IS285 element
Was originally thought to be a putative gustatory receptor named Gr36d but further analysis suggested that this is not the case
Was shown to phosphorylate and activate DCK in vitro but probably not in vivo
According to PubMed:17258408, the major transcript has no stop-codon and is probably non protein-coding. A minor transcript is also expressed and encodes the displayed protein which misses C-terminal part compared to other mammalian orthologs
Was originally thought to be PsbN
There is a disagreement about sodium-independent transport of cationic amino acids, such as L-arginine and L-lysine. While Hatanaka et al (PubMed:11342143) shown that SLC38A4 may mediate sodium-independent transport of cationic amino acids, such as L-arginine and L-lysine (PubMed:11342143). Recent studies by Fairweather et al (PubMed:33928121), using quantitative LC-MS analysis, shown any transport activity of cationic amino acids, such as L-arginine and L-lysine (PubMed:33928121)
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 391 in the dsPTPase catalytic loop and does not have phosphatase activity
A paper reported that MCUR1 has an indirect role as a regulator of mitochondrial calcium uniporter (MCU) and is involved in cytochrome c oxidase (COX) assembly instead (PubMed:25565209). Subsequent publications however confirmed the function of MCUR1 as a regulator of MCU (PubMed:26445506, PubMed:27184846)
Expressed in the mutant strain HemA1 but expression in the wild-type strain has not been proven
This protein-coding gene has been repurposed in primates, with the presence of a new enhancer sequence that drives expression in brain in response to sensory experience, leading to restrict dendritic growth in the developing cortex (PubMed:27830782)
In some plant proteins and in human SARM1, the TIR domain has NAD(+) hydrolase (NADase) activity (PubMed:28334607). However, despite the presence of the catalytic Asp residue, the isolated TIR domain of human TLR4 lacks NADase activity (PubMed:28334607). Based on this, it is unlikely that Toll-like receptors have NADase activity
This toxin precursor is identical to three other precursors (AC B1NWR6, AC B1NWS4 and AC P0CH46). AC B1NWR6 shows 8 variants that could also be associated with this gene
The cGAS-STING pathway promotes a limited inflammatory response in bats (PubMed:29478775). This may be caused by the absence of the phosphorylation site at position 358, which is required to production of type-I interferons and other cytokines in other species (PubMed:29478775). The dampened cGAS-STING pathway may explain why bats show an increased tolerance to highly pathogenic viruses, such as coronaviruses, and serve as a virus reservoir (PubMed:29478775)
Focadhesin is predicted to contain three transmembrane domains. However, experimental data indicate that it does not localize to organelles with bilayered lipid membranes, challenging the presence of the transmembrane domains
It is uncertain whether Met-1, Met-17 or Met-19 is the initiator
Was originally (PubMed:8048925) thought to be induced by UV light and alkylating agents. The authors from PubMed:11861905 have found from further investigation that it is induced and regulated by glucose
Was originally termed SOX-8
PubMed:9837992 indicates that a number of mRNA with sequence conflict(s) are produced by RNA editing. This seems not to be the case as discussed in PubMed:10497260
Could be the product of a pseudogene. Compared to other family members it is truncated and highly divergent and thus is very unlikely to have catalytic activity
Lacks two of the six Cys residues found in other family members, resulting in the lost of one disulfide bond
Was originally proposed to be fused with ccmD
Glyoxylase activity previously reported may reflect in fact its deglycase activity
The protein deglycation activity has been ascribed to a TRIS buffer artifact by a publication, which has then been rebutted by clear biochemical experiments showing that PARK7 is a bona fide deglycase. Deglycase activity is even strengthened by a novel article that reports nucleotide deglycation activity
The S-adenosyl-L-methionine binding sites are not conserved, suggesting that this protein lacks methyltransferase activity. Likewise, the zinc-binding Cys residues in the pre-SET domain are only partially conserved
An older version of this entry represented the conceptual translation of what was thought to be HNRNPA3 but which was in fact a pseudogene (HNRPA3P1/FBRNP) located on chromosome 10
GalT is not present in P.putida strain KT2440 due to a frameshift
This has been proposed to be processed from a precursor (Ref.4); however no signal is predicted by signal sequence detection programs
Interaction with TP35 was reported to promotes TP53 'Ser-15' phosphorylation and nuclear accumulation causing cell cycle arrest and inhibition of tumor growth (PubMed:15701641). However, the publication has been retracted due to image duplication and manipulation. Interaction with TP35 has been confirmed by other studies (PubMed:12494467). The nuclear locatization has been confirmed by other studies (PubMed:10940556, PubMed:12494467, PubMed:15371550, PubMed:16166625)
Originally proposed to be a peroxisomal protein (By similarity). Recent studies have suggested its localization to the endoplasmic reticulum and within the lysosome (By similarity)
Has sometimes been referred to as ADAMTS2
Exists in some isolates as a HTH-truncated isoform. This short isoform is still able to regulate gene expression
Although the enzyme shows to be able to complement hemF hemN double mutant and to accumulate coproporphyrinogen-III when the gene is disrupted, no oxygen-independent coproporphyrinogen-III oxidase activity has been shown. The exact role of this protein is still unknown
This protein does not possess neither proline racemase nor hydroxyproline-2-epimerase activities
Could be the product of a pseudogene. Lacks 3 of the 4 disulfide bonds, which are conserved features of the family
Could be the product of a pseudogene. In contrast to other members of the family, lacks a signal sequence due to a frameshift, suggesting that it is not functional (PubMed:11322959, PubMed:11230163, PubMed:10380929)
Although related to the peptidase M28 family, it lacks some conserved zinc-binding sites involved in catalysis and therefore has probably lost hydrolase activity
Translation initiation occurs at a non-canonical CUG codon
In the crystal structure (PubMed:12588867), the metal ion is absent, probably due to the oxidation of the active site Cys-174 to sulfinic acid. In the absence of metal, positions of the coenzyme and the substrate and their interactions are all significantly altered, presumably accounting for the inactivity of this form
May not bind metals in vitro (PubMed:15165844). It is possible that some phenotypes due to mutant cu9 allele are due to deletion of predicted flanking non-coding RNA genes
Hexokinase is known to act as a monomer (PubMed:10686099). It however homodimerizes at elevated protein concentrations used for crystallizations (PubMed:9493266, PubMed:10574795)
A structure of a fragment of this protein in complex with the catalytic domain of C.botulinum neurotoxin type B (BoNT/B, botB) was reported; because of the lack of clear and continuous electron density for the VAMP2 peptide in the complex structure, the paper was retracted. One of its associated structures remains valid (PDB:1F82, light chain alone) (PubMed:10932255, PubMed:19578378)
Was originally (Ref.1) thought to be a thermostable diaphorase
Was originally thought to be an adenine nucleotide carrier
When this protein is expressed in E.coli it migrates as a 36 kDa protein; thus the sequence may be incorrect in the C-terminal section
Maps to duplicated regions on chromosome Y; the gene is present in at least 3 copies
Ref.2 (CAA41963) sequence was wrongly assigned to be a thymidylate synthase
A paper describing truncating mutations of TARBP2 in tumor cells and resultant effects on DICER1 stability and miRNA processing has been retracted, due to concerns of image duplication in some of the figures
Preliminary results in vitro suggested that Pnldc1 might act as an exonuclease that specifically cleaves precursor piRNAs (pre-piRNAs) at their 3' ends (PubMed:26919431). These results however require additional experimental evidences: another report showed that the protein mainly localizes to the endoplasmic reticulum and preferentially acts on poly(A) tails (PubMed:27515512)
Has been initially named PRMT9 and reported to act as an arginine methyltransferase that can catalyze the formation of omega-N monomethylarginine (MMA) as well as symmetrical and asymmetrical dimethylarginine (sDMA and aDMA), however no further works support these observations (PubMed:16487488). It should not be confused with official PRMT9 (AC Q6P2P2)
Strain K12 / MG1655 is deficient in both production and response to EDF, unlike strains K12 / MC4100, K12 / W3110 and K12 / K38, all of which make and respond to EDF
Was originally (PubMed:10482844) identified to be a major allergen, but a second study (PubMed:15940136) reported a very low prevalence
Lacks essential residues of the catalytic triad and is therefore predicted to have no protease activity
Was initially reported to be specifically expressed in embryonic stem cells and germ cells (PubMed:16331322). However, it was later shown by different groups that it is specifically expressed in myoblasts where it promotes myoblast fusion (PubMed:28569745, PubMed:28569755, PubMed:28386024)
Was originally thought to be a sodium/neutral amino acid cotransporter (system a neutral amino acid transporter) responsible for the sodium-dependent intake of neutral amino acids such as alanine, glycine, serine, cysteine, and proline
Was originally proposed to function in mitochondrial DNA replication and maintenance
In cv. Columbia, a naturally occurring frameshift at position 444 results in a shortened C-terminus. A complete sequence for TAN can be found in strain cv. Landsberg erecta (AC Q197W8)
The coq-4 gene is duplicated in C.briggsae to produce coq-4.1 and coq-4.2. coq-4.1 encodes a longer functional protein while coq-4.2 is shorter and may be non-functional or have acquired a different function to coq-4.1
In C.vinosum two similar set of genes code for RuBisCO large and small chains: the RbcL-RbcS (this entry) and the RbcA-RbcB pair. Under standard photoautotrophic culture conditions only the latter pair seems active, the former being probably cryptic
Was originally thought to be the miniconductance mechanosensitive channel MscM
Although it is derived from a rearrangement with the neighboring RSK3 gene, it plays a crucial role in t-haplotype cells
Was originally thought to catalyze the entire reaction from (6E)-8-oxogeranial to nepetalactol including a cyclase step, but new results have shown that the cyclase is a different enzyme and this enzyme exclusively catalyzes a reduction step
Was originally thought to have exonuclease activity but it was later shown (PubMed:17173052, PubMed:17174896) that only DIS3/RRP44 subunit of the exosome core has this activity
Was originally (Ref.1) thought to originate from human
In T.ferrooxidans two similar set of genes code for RuBisCO large and small chains: the rbcL1-rbcS1 and the rbcL2-rbcS2 sets
This gene name has also been given to glycosyltransferase GlyA (AC A0A0H2URH7) in this organism
There is no mention of the activity in PubMed:15581681. The Greek letter 'delta' in the name delta-AITX-Amc2a (which indicates an inhibition of sodium channels) has been deduced from the toxin paralytic activity to crabs
The synthetic peptide described in PubMed:26948522 is one residue shorter than the mature sequence shown in this entry (44-60) (the Gly-61 is removed) and the Cys-60 is amidated
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC Q14FB6
PubMed:15158073 experiments have been carried out in mouse
The substrate-binding sites for the inactive GTP cyclohydrolase-2 activity are conserved while several cofactor-binding sites are lost
PubMed:12230558 uses only BmKIM as the name, whereas the authors submitted sequences using KIM2 as the name
Controversial data exists concerning the repressor activity of isoform 2. A study in human showed that human isoform 3 exhibits weak repressor activity of a NRSE motif-containing reporter construct (By similarity). Another report, however, does not observe any isoform 3 transcriptional repressor activity of a NRSE motif-containing reporter construct (By similarity). Controversial data also exists regarding the function of isoform 2 on the negative regulation of full-length REST. It was shown that isoform 2 negatively regulates the repressor activity of isoform 1 by binding to isoform 1, thereby preventing its binding to NRSE and leading to derepression of target genes (PubMed:10490617, PubMed:11039732). Another study in human, however, did not observe any inhibitory activity of human isoform 3 on the isoform 1 repressor activity (By similarity)
Lacks one transmembrane, which is a conserved feature of the family
A recent genetics report associated srdA and its cluster with the biosynthesis of furanocoumarin neurosporin A, a metabolite produced by N.crassa for chemoresistance against predation by arthropod fungivores (PubMed:28485098). However, based on the gene cluster organization and predicted gene functions, this cluster is unlikely to be involved in neurosporin A biosynthesis, but instead produces compounds similar to pyriculol (PubMed:30908040)
Could be the product of a pseudogene. This sequence is much shorter than E.coli K12 DsdX
An article reported the interaction surface between C3 and CR2 (PubMed:11387479). According to a another paper, it is however an artifact and can be ascribed to the presence of zinc acetate in the buffer (PubMed:21527715)
The difference between allele C3S (C3 slow) and allele C3F (C3 fast) was reported to be caused by a an Asn at position 1216 instead of an Asp (PubMed:2473125). The paper was however retracted (PubMed:2584723)
The capacity to transport copper ions remains controversial
Was initially reported to contain a CUE domain (PubMed:19956593). However, no CUE domain is predicted by prediction tools and the CUE-like region does not show no affinity for ubiquitinated histones (PubMed:20075079)
Was originally (PubMed:2546007, PubMed:2124629) thought to be a glyceraldehyde 3-phosphate dehydrogenase, but glyceraldehyde 3-phosphate is not an efficient substrate (PubMed:7751290, PubMed:9182530)
The role in phosphatidylglycerols remodeling and cardiolipin synthesis is questioned as both processes occur in mitochondria. The monoacylglycerol acyltransferase activity is also weak and a direct role in triacylglycerol synthesis appears unlikely
Was initially shown to have low deadenylase activity that was lost when the metal-binding Glu was mutated (By similarity). Later studies showed that the purified protein lacked deadenylase activity (By similarity). Was subsequently shown to act as a phosphatase (By similarity)
Was originally proposed to function as a glutathione transporter (PubMed:20332504). However, some evidences suggest it is not the case (PubMed:24312054)
PMCHL1 mRNA may not be used as template for translation. In human only antisense PMCHL1 transcripts are present in brain
This sequence is published under the name CVIE but another peptide with a different sequence and a different pharmacological family is already published with this name (see AC P69751)
Could be the product of a pseudogene. Highly similar to PRKX in the pseudoautosomal region of the X chromosome, the transcripts specific of that gene are potential candidates for nonsense-mediated decay
The plantago asiatica mosaic virus (PlAMV)-resistant ecotypes (cv. Bay-0, cv. Ga-0, cv. Dra-2, cv. Eil-0 and cv. Is-1) encoded a full-length 157-amino-acid proteins (AC H3JUC3), whereas in the susceptible ecotypes (cv. Col-0 and cv. Ler), the presence of a stop codon in the first exon results in the production of a N-terminal 36-amino-acid fragments (PubMed:22307853). However, the identification of a small peptide spanning an alternative splice junction leads to the proposal of an alternative gene model in cv. Columbia
Was originally identified as mitochondrial large ribosomal subunit protein mL56 (MRP-L56) (PubMed:11551941), but has since been shown to localize to the mitochondrial intermembrane space where it forms filaments (PubMed:19858488)
Was originally (PubMed:8969503, PubMed:9384377) predicted to be the product of two different genes yfkA and yfkB
Martineau M. et al. show that may function as a L-glutamate/H(+) antiporter (PubMed:29273736). However, according to Eriksen J. et al., H(+) is an allosteric activator (By similarity)
Some reports could not detect a significant activity with sphingosine 1-phosphate as substrate
Was originally described as a deoxyribonuclease (PubMed:17878218), but it was later shown that PdaC has no DNase activity at all (PubMed:22277649)
Biochemical and mutational analysis assigned Cys-120 as the resolving cysteine (C(R)) (PubMed:9888818). However, crystal structures showed that Cys-120 is deeply buried within the protein and revealed formation of a disulfide bond between the peroxidatic cysteine Cys-62 and the therefore more likely C(R) Cys-31 (PubMed:22474296, Ref.21)
Has been shown to be active in cv. Columbia (AC Q9M670) due to naturally occurring sequence variation in this strain. The sequence shown is from strains cv. Ct-1 and cv. Ga-0
This sequence is an example of a full-length immunoglobulin delta heavy chain
Lacks the conserved ATP-binding site due to Leu-38 (instead of a conserved basic residue)
PubMed:680138 authors have used the name Pseudomonas ovalis for this species
In PubMed:11154066 there is uncertainty about the number of Arg residues at position 10 and whether position 25 is Pro or Tyr
Although it belongs to the kinase superfamily, lacks the residues involved in ATP binding, suggesting that it has no protein kinase activity
Was previously called At1g48610
Was originally thought to be a protein kinase C inhibitor and to bind zinc in solution. Both seem to be incorrect
Was originally thought to originate from B.lactofermentum=C.glutamicum
According to PubMed:17173052 and PubMed:17174896, only DIS3/RRP44 subunit of the exosome core has exonuclease activity
Was originally reported that TYKY1 and TYKY2 were two different genes
Gene LAMA4 was formerly called LAMA3
Could be the product of a pseudogene. This putative protein corresponds to the central region of bacterial and Trichomonas vaginalis beta-eliminating lyase-like protein and could have been acquired by horizontal transfer
Was originally proposed to be encoded from either Met-1 or Val-71 (PID CAA23521); it is now thought to start of Met-1
Was named BEX2 by some authors
It is uncertain whether Met-1, Met-44, Met-81 or Met-100 is the initiator
Was originally identified in the nucleolus (PubMed:8862517). A recent publication found it only in the endoplasmic reticulum, which agrees with its biological function and the predicted signal sequence (PubMed:23959653)
It was suggested by Lee et al that the amb cluster is involved in the biosynthesis of 2-(2-hydroxyphenyl)-thiazole-4-carbaldehyde (IQS), a cell-cell communication signal that modulates the production of AMB through the pqs and rhl quorum sensing systems (PubMed:23542643). The chemical structure of IQS indicates that this compound may be assembled from salicylate and cysteine. However, neither of the two peptide synthases encoded by the amb gene cluster present adenylation domains with a specificity for these substrates. It is thus highly implausible that IQS is specified by the amb gene cluster (PubMed:25814981)
Reported to bind to bacterial lipopolysaccharide (LPS) in vitro. However, the in vivo significance of this is uncertain since other studies indicate little or no specificity for LPS
PubMed:1863783 postulates an inhibition of trypsin but the sequence homology points to a cysteine protease inhibitor
Down-regulation of Kctd13 was initially reported to cause macrocephaly due to increased proliferation (PubMed:22596160). However, it was later shown that deletion of Kctd13 does not cause any change in brain size, embryonic cell proliferation, neurogenesis, or cortical layering/migration (PubMed:29088697). Experimental conditions used may explain discrepancies. A possible explanation being that shRNAs used in the first study, may have affected off-targets
Cleavage site of the transit peptide is likely localized before the predicted cleavage site at Val-74, probably around His-67
SPAC17G8.03c was previously identified as the homolog of budding yeast DBP3 in fission yeast. However, it was further demonstrated that SPCC16C4.22 is the true ortholog of DBP3
Was reported to probably be expressed in the AVJL and AVJR neurons (PubMed:22768843). However, this has been claimed to be an anatomical error and that expression is restricted to the AVH neurons (PubMed:34604715)
Throughout PMID:11566890, the gene name taf-11 is used instead of taf-10, based on an earlier nomenclature; readers should be aware to avoid confusion
The first GAGE nomenclature was based on identified mRNA sequences, but the high identity of the GAGE members made impossible to separate products of paralogous genes from polymorph products. PubMed:18179644 presented a new GAGE gene nomenclature based on the identified genes and their products. GAGE12B is present as fragment in GRCh37 reference genome assembly due to an unsequenced gap between two clusters in the GAGE locus
Could be the product of a pseudogene. The N-terminus is shorter than in related proteins
Could be the product of a pseudogene. The N-terminal region is truncated when compared to other members of the family
Some prediction bioinformatics tools predict the presence of a homeobox domain (By similarity). However, the domain is degenerate and residues that are important for DNA-binding are absent (By similarity). Moreover, the protein localizes in the endoplasmic reticulum and not in the nucleus, strongly suggesting that it does not constitute a canonical homeobox domain (By similarity)
Lacks the heme-binding site and is thus probably inactive (PubMed:15654104)
One study reported a nucleation-promoting factor (NPF) activity towards the Arp2/3 complex using partially purified samples of the WASH complex (PubMed:19922875). In another study, the in vitro reconstituted and purified recombinant WASH core complex, consisting of WASHC3, WASHC4, WASHC5, WASHC1 and the N-terminal residues 1-356 of WASHC2, did not show any NPF activity towards the Arp2/3 complex (PubMed:20498093)
The RING-type 2 zinc finger was initially reported to only bind 1 zinc ion instead of 2 compared to classical RING-types (PubMed:15236971). But it was later shown that it is not the case and binds 2 zinc ions (PubMed:24058416, PubMed:23707686)
Was reported to be expressed in adult skeletal muscle and fat, in fetal lung, and in gastric carcinomas and cancer cells of diverse origin (PubMed:11279086). However, this paper has been retracted because data in one figure has been falsified (PubMed:30808000)
Val-225 is present instead of the conserved Glu which is an active site in the cytidine and deoxycytidylate deaminase family of enzymes. It is suggested that this protein may act as a regulatory subunit
TPS20 in Arabidopsis ecotype Columbia lacks dolabellane-type diterpene synthase activity because of a 17 amino acid deletion and several mutations in its sequence. TPS20 protein in ecotype Cvi is functional and possesses dolabellane-type diterpene synthase activity
Product of a dubious CDS prediction. May be a long intergenic non-protein coding RNA. No experimental confirmation available
A pseudogene in strain MG1655 / ATCC 700926 due to a recent laboratory-derived single nucleotide deletion, but not its parent MG1655 / ATCC 47076
It is unclear how SCUBE2 binds the dilipidated SHH. According to a report, the SHH cholesterol-anchor, but not palmitate, seems to be both necessary and sufficient for SCUBE2-mediated SHH release from the cell membrane (PubMed:22902404). According to a second paper, palmitoylation accelerates the rate of SCUBE2-mediated release (PubMed:22677548). Cholesterol modification is sufficient for a heterologous protein to bind to SCUBE2 and to be secreted in a SCUBE2-dependent manner (PubMed:22902404)
In contrast to other phospholipases, it lacks the typical His active site (His->Gln in position 47)
Was originally (PubMed:10806476) thought to be a receptor for sphingosylphosphorylcholine (SPC). However, this work has been retracted (PubMed:16508674)
Although it belongs to the enolase family, Leu-333 is present instead of the conserved Glu which is expected to be an active site residue
Expected to lack catalytic activity
Signal and propeptide sequences are imported from ArachnoServer
Was originally thought (PubMed:9234727) to interact with HNRNPK. This apparent interaction may be mediated by the translated product of the 5'-UTR sequence of the 2-hybrid clone
Product of a dubious CDS prediction. Found in the 3'-UTR of TLE4. No homolog. Large scale identification of a phosphorylated peptide (PubMed:15302935) would require further confirmation
Unlike its ortholog in S.coelicolor, it is not seen to bind zinc
Has sequence similarities with potassium channel inhibitors, but inhibits chloride channels. It is why the systematic name 'Potassium channel toxin alpha-KTx 8.3' has been moved as alternative name
Lacks key residues involved in peptide docking, suggesting that this is a non-classical MHC class I protein which does not play a role in antigen presentation
Was originally thought to be inactive as a glycosylase (PMID:12200441,PMID:19121397), but recent reports (PMID:22569481, PMID:20185759) demonstrate that cleavage of the initiator methionine is essential for catalytic activity
Ile-198 is present instead of the conserved Val which is part of the DDVD box
This sequence may not function as a hydroxymethylbilane synthase because it lacks the cysteine residue necessary for attachment of the dipyrromethane cofactor
According to a well-established model, RNF8 initiate H2A 'Lys-63'-linked ubiquitination leading to recruitment of RNF168 to amplify H2A 'Lys-63'-linked ubiquitination (PubMed:19203578, PubMed:19203579). However, other data suggest that RNF168 is the priming ubiquitin ligase by mediating monoubiquitination of 'Lys-13' and 'Lys-15' of nucleosomal histone H2A (H2AK13Ub and H2AK15Ub respectively) (PubMed:22980979). These data suggest that RNF168 might be recruited to DSBs sites in a RNF8-dependent manner by binding to non-histone proteins ubiquitinated via 'Lys-63'-linked and initiates monoubiquitination of H2A, which is then amplified by RNF8 (PubMed:22980979). Additional evidence is however required to confirm these data
Product of a dubious gene prediction. Completely overlaps the gene coding for mitochondrial 9S RNA (RPM1)
The C-terminal Gly suggests that the peptide is amidated and is one residue shorter (residues 49-64) than that synthesized by Qiang et al., 2021
Smaller forms of 80-90kDa appear to be present in the asexual blood stage suggesting that the protein may be proteolytically cleaved (PubMed:9371731). They localize to the cytoplasm in schizonts, to organelles in all blood stages and to the host erythrocyte membrane during schizont segmentation (PubMed:9371731)
Although PubMed:12809501 report that TESC-binding results in a decrease in activity, studies with rat SLC9A1 show that TESC-binding results in the maturation and accumulation of SLC9A1 at the cell surface
The interacting region with TESC is conflicting: Interaction with TESC has been reported via the juxtamembrane region of the cytoplasmic C-terminal domain, including residues 503-545 (PubMed:11696366, PubMed:30287853). In contrast, another publication has reported interaction with TESC via residues 633-815, the region of the cytoplasmic C-terminus more distal to the membrane (PubMed:12809501)
While it is structurally defined as a knottin it lacks the conserved Cys residue in position 90
Encoded in intron of the gene GTF2E2 (opposite strand). Confirmed by numerous ESTs
The start codon has not been identified for this gene; that indicated here is a suggestion
Was originally thought to originate from human
Despite of the presence of a putative ATP-binding motif, this protein does not bind ATP, suggesting that it has no protein kinase activity
Could be the product of a pseudogene. The open reading frame is disrupted by a nonsense mutation after 8 amino acids; consequently, this gene is currently considered to be a unitary pseudogene in human even though it is functional in other mammals
Was reported to interact with SLC6A4, however the paper was retracted as some results and conclusions are not reliable
Although it belongs to the adenosylhomocysteinase family, recombinant mouse homolog AHCYL1 expressed in bacteria shows no hydrolase activity, suggesting that Drosophila AhcyL2 may also lack this activity
The sequence reported in PubMed:3004982 was thought to originate from R.sphaeroides but was later shown to be derived from R.capsulatus
The exact role in regulating T-cell function is under debate. According to (PubMed:16713976), SEMA7A-deficient mice are highly susceptible to contact hypersensitivity and experimental autoimmune encephalomyelitis. According to (PubMed:17377534) mice do not develop contact hypersensitivity, and are highly resistant to experimental autoimmune encephalomyelitis
HK1 and HK2 are incomplete as individual proteins but can complement each other's function
Was originally described as a gef leader peptide
Reported to contain a F-box domain (PubMed:16009132). Such domain is however not predicted by any detection method
PubMed:8223590 reports a cDNA predicted to encode a protein with an extended N-terminus but there is no further evidence for the existence of such a protein
Was originally thought to lack retinol dehydrogenase (RDH) activity. However, a more recent publication demonstrates a retinol dehydrogenase activity for RDH13
Was reported to form a transcriptional repressor complex with CHD7 and SETDB1 involved in PPARG repression (PubMed:17952062). However, this work was later retracted (PubMed:25358353)
Product of a dubious gene prediction. Except for the proteomic data there is no mRNA or EST supporting this predicted gene
Lacks the conserved Asp residue in position 297 essential for alpha-L-arabinofuranosidase activity. Its enzyme activity is therefore unsure
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-5; H2AK7ac = acetylated Lys-9; H2AS128ph = phosphorylated Ser-131
In contrast to family members hmit-1.1 and hmit-1.2, it is not induced by hyperosmotic stress
Human SLC6A18 has been shown to be an inactive protein
There is another gene, npl-4.2, which has a 99% identical sequence making it difficult to identify the specific function for each protein
The residue potentially involved in the covalent binding of FMN is a Ser instead of a Thr
MINAR1 topology is a matter of debate, some authors think the N-terminus is extracellular, while preliminary experimental results suggest a cytosolic location
Was reported that thymocytes isolated from a RasGRP1 mutant mouse strain show a defect in Ras activation following T-cell-receptor (TCR) engagement (PubMed:12932358). However, this paper has been retracted because the data in one figure was falsified by one of the authors (PubMed:22808526). The authors stand by the validity of the other figures, results and interpretation in this paper (PubMed:22808526). Furthermore, evidence supporting function is derived by similarity with the human ortholog, so may be true
Was originally thought to be a deoxycytidine kinase
PubMed:16527250 attributed the differences between their clones to the existence of two separate genes. This seems rather unlikely, considering that the cDNAs are 100% identical outside of this clearly delimited zone
Was originally thought to be a 2',5'-RNA ligase
PubMed:17637675 showed that COI1 interacts with the N-terminal part of the protein (1-208), but not with its C terminus
In contrast to other phospholipases, it lacks the typical Asp active site (Asp->Glu in position 62)
It is not certain that ARS and ANUP are identical proteins
It is uncertain whether Met-1, Met-3 or Met-4 is the initiator
Was originally called TEF-1, but is the ortholog of mammalian TEF-3
The subcellular location has been matter of debate. After being reported to be exclusively localized to mitochondria, demonstrations of promiscuous associations and locations were considered as artifactual due to the extremely acidic character and the use of different tagged versions of the protein (PubMed:9305894, PubMed:11493647). However, its location to multiple compartments linked to diverse functions is now accepted. The N-termini of the surface and secreted forms are identical to the reported processed mitochondrial form
This sequence is much shorter than orthologs
Ile, Leu, Gln and Lys residues were impossible to discriminate with the method employed and are all assigned by comparison with orthologs
The oxidation forms of Trp-111 are subject of controversy and could be the artifactual results of sample handling
Was originally thought to originate from a rabbit cDNA library and was known as protein phosphatase Z (PP-Z)
Unlike some other archaeal S14P proteins, this is unable to bind zinc
The cholinesterase-like (ChEL) region lacks the Ser residue of the catalytic triad suggesting that it has no esterase activity
In A.ferrooxidans two similar set of genes code for RuBisCO large and small chains: the rbcL1-rbcS1 and the rbcL2-rbcS2 sets
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following convention is used: H2AS128ph = phosphorylated Ser-151
Previously thought to be the same gene as Tagap. These are distinct loci that encode proteins with identical C-termini but each with a unique N-terminus
Although assigned as a calmodulin family member by Ref.7, it only contains EF-hand domains
Was originally thought that the I-POU homeobox is unable to bind DNA because it lacks two N-terminal basic residues
Was originally thought to interact with vvl
There is supporting proteomic evidence with peptides unique to RAP1BL suggesting it is not a pseudogene
The membrane insertion topology of the two monomers was controversial and some studies originally suggested a parallel arrangement of the two monomers in the EmrE dimer. The antiparallel dimeric structure is now the generally accepted functional topology
Lacks the phospho-accepting Asp (here Glu-114), present in the receiver domain, which is one of the conserved features of two-component response regulators (ARRs) family
Analysis of new null mutants leads to the conclusion that plants do not need ABP1 for auxin signaling and for their growth and development under normal growth conditions
Was originally thought (PubMed:11489859) to be an N(2)-acetyl-L-2-aminoadipate semialdehyde transaminase
Was initially thought to be a protease involved in deubiquitination because of its similarity with cysteine proteases (PubMed:11090361, PubMed:16301742). However, it was later shown that YopJ is an acetyltransferase that uses a dual substrate mechanism similar to the one used by papain-like proteases (PubMed:16728640)
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me3 = trimethylated Lys-10; H3S10ph = phosphorylated Ser-11; H3K14ac = acetylated Lys-15; H3K14me2 = dimethylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me1 = monomethylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me1 = monomethylated Lys-24; H3K27ac = acetylated Lys-28; H3K27me1/2/3 = mono-, di- and trimethylated Lys-28; H3K36ac = acetylated Lys-37; H3K36me1/2/3 = mono-, di- and trimethylated Lys-37; H3K56ac = acetylated Lys-57; H3K64ac = acetylated Lys-65; H3K79me1/2/3 = mono-, di- and trimethylated Lys-80
Evidence for subcellular location in the Golgi was determined in pachytene spermatocytes and spermatids in mouse testes. They observe that the ectopically expressed PLD6 protein was localized to the mitochondria in PLD6-transfected cells. Authors claim a possible explanation for the contradictory results is that previous studies have reported the localization of exogenous PLD6, but not endogenous PLD6, in cultured cells. The reason for differences observed in subcellular localization of exogenous and endogenous PLD6 is not clear but one attributable reason may be that different types of anti-PLD6 antibodies have been used in previous studies
Defined as a polymorphic pseudogene by MGI
An alternative product iASPP(RAI) has been described (PubMed:15489900, PubMed:10336463). However, it is not detected in vivo and is most probably a cloning artifact (PubMed:15489900)
Asn-157 is present instead of the conserved Asp which is expected to be an active site residue
The ability of METTL14 to have catalytic activity is unclear and a number of experimental evidence suggests that it has no methyltransferase activity by itself. According to some reports, has some methyltransferase activity in vitro (PubMed:24394384). However, other studies showed that METTL14 constitutes the RNA-binding scaffold that recognizes the substrate rather than the catalytic core. 3D-structure studies showed that METTL14 contains a degenerate active site that is unable to accommodate donor and acceptor substrates
Evolved via a duplication of Dnmt3B and was initially annotated as a pseudogene
Was originally thought to be secreted via the ESX-1 secretion system, but it was probably released in the medium via cell lysis
Some prediction bioinformatics tools predict the presence of a homeobox domain (By similarity). However, the domain is degenerate and residues that are important for DNA-binding are absent (By similarity). Moreover, the protein localizes in the endoplasmic reticulum and not in the nucleus, strongly suggesting that it does not constitute a canonical homeobox domain (PubMed:15823095)
The locus MISFA encodes two differents polypeptides Kastor and Polluks, with different transcription start sites and different ORFs
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3T3ph = phosphorylated Thr-4; H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me1/2/3 = mono-, di- and trimethylated Lys-10; H3S10ph = phosphorylated Ser-11; H3T11ph = phosphorylated Thr-12; H3K14ac = acetylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me = methylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me = methylated Lys-24; H3K27me = methylated Lys-28; H3S28ph = phosphorylated Ser-29; H3K36me = methylated Lys-37
Was initially thought to be AMPylated at 'Thr-366' by Fic (PubMed:25395623). However, it was later shown to be AMPylated at 'Thr-518'
Its phosphorylation by PKC/PRKCZ at Ser-428 is reported to promote peroxynitrite-induced nuclear export of STK11, leading to PTEN activation and subsequent inhibition of PI3K/AKT signaling and induction of apoptosis in vein endothelial cells (PubMed:18321849). However this paper was withdrawn by the authors due to concerns of image duplication in the figures. Its phosphorylation by PKC/PRKCZ has been confirmed in other studies (PubMed:18854309, PubMed:23612973)
PubMed:8288612 reports 2 different N-termini by direct protein sequencing: mature protein either starts at Ile-70 or Ser-74
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-25
Could be the product of a pseudogene. Seems to be an unlikely translation of a REP element
Was originally (PubMed:9795230) thought to be a nuclear protein that interact with nuclear receptor. However, it was shown later to be mitochondrial (PubMed:12654921), a function related to nuclear receptors being unsure
The sequence shown here has been extracted from PDB entry 1CXA
PubMed:7959731 claims that there are 3 different FOXG1 proteins, FOXG1A, FOXG1B, and FOXG1C. It was latter found that there is only one gene and the differences between these three may be sequencing errors since the protein is coded in a unique exon
Was originally thought to originate from pig (PubMed:2512577, PubMed:1396696). It was later shown that this protein in fact originates from A.suum which is present in pig intestine (PubMed:12737319)
Lacks one cysteine (here Phe-106), present in the RING domain, which is one of the conserved features of the RING-type zinc finger family
This is a truncated version of aquaporin-2. A natural 11 bp deletion in position 109 leads to a frameshift, which disrupts the gene coding for this protein and produces two ORFs C1Q_01794 and C1Q_01798. A contiguous sequence for aquaporin-2 can be found in strain Sigma 1278B (AC P0CD89)
It is unclear how SCUBE2 binds the dilipidated SHH. According to a report, the SHH cholesterol-anchor, but not palmitate, seems to be both necessary and sufficient for SCUBE2-mediated SHH release from the cell membrane (PubMed:22902404). According to a second report, SHH palmitoylation accelerates the rate of SCUBE2-mediated release (PubMed:22677548). Cholesterol modification is sufficient for a heterologous protein to bind to SCUBE2 and to be secreted in a SCUBE2-dependent manner (PubMed:22902404)
Previously identified as the mitochondrial deoxyribonucleotide carrier (PubMed:11226231). However other experiments later demonstrated that SLC25A19 is a thiamine diphosphate transporter and not a mitochondrial deoxyribonucleotide carrier (PubMed:15539640, PubMed:18280798)
There is a known reversal of the Pgm1 and Pgm2 nomenclature applied to mouse versus other vertebrates. The official name of this gene in mouse is Pgm2 but it is the ortholog of other vertebrate PGM1 genes
The DNA coding for this protein is not found in the complete genome of strain ATCC MYA-826 / Pb01
EBF4 expression was not detected in mouse NK cells and CD8(+) T-cells and there were no differences in the NK, CD8(+), and CD4(+) precursor and mature cell subsets in the thymus, spleen, or liver from a mouse EBF4 knockout (PubMed:35939714). It has been suggested, therefore, that the functions of EBF4 differ between humans and mice (PubMed:35939714)
Was reported to be induced by various cytochrome P450 inducers, including phenobarbital, dexamethasone, rifampicin and barbituric acid in its autophosphorylated state, and that carbamazepine has no effect. Was also reported to be expressed predominantly in erythroid cells, and at much lower levels, expressed in hepatocytes (at protein level). However, this paper has been retracted because of improper data manipulation, reuse, and analyses
Some authors describe two catrins (catrin-1 and -2), with different activities and masses, but no difference in sequence is described
Was originally thought to be cytoplasmic and membrane-associated and to mediate ubiquitination and subsequent degradation of STX1A
Present in the 5'-UTR of low-affinity glucose transporter HXT4, the multicopy suppression phenotype is probably due to the presence of an HXT4 regulatory element in this region
Has been classified as a the potassium channel toxin alpha-KTx 22.2 in PubMed:22230549. Since the subfamily 22 has already been attributed, this peptide should be reclassified as alpha-KTx 23.2
According to PubMed:15599508, it may be peroxisomal. There is however no experimental evidence to prove this
Called dATM in some references while it is the ortholog of ATR
The metalloproteinase domain lacks the active site
Was originally thought to be a glutamate decarboxylase (GAD)
Could be the product of a pseudogene, it is missing about 90 N-terminal residues compared to orthologs
Probably inactive because it lacks critical residues conserved in other family members, including an Asp in the motif DSDT, which is NSDI in has-rs, and an Arg residue in the motif QXXRW, which is QQTPW in has-rs. Also inactive in the functional assays of PubMed:9442026
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-8; H2BK33ac = acetylated Lys-29; H2BK34ac = acetylated Lys-30; H2BK143ub1 = monoubiquitinated Lys-134
It is uncertain whether Met-1 or Met-68 is the initiator
Was originally predicted to have poly(A) polymerase activity (EC 2.7.7.19), and its gene was named papS
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK33ac = acetylated Lys-41; H2BK34ac = acetylated Lys-42; H2BK143ub1 = monoubiquitinated Lys-149
Lacks the C-terminal part of the cytochrome b561 domain, which contains the residues coordinating the two heme molecules and 4 of the 6 conserved transmembrane regions
Was originally described as a regulatory protein involved in the regulation of the production of extracellular enzymes
Could be the product of a pseudogene. Corresponds to the C-terminal of members of this family
PubMed:10781952 has termed the gene 'STK22D' as it was then thought that there were two different closely related genes
Is called bop1 in PubMed:21135094
Experiments in mouse confirm the importance of JAGN1 in neutrophil function with some differences. Mice lacking JAGN1 do not show neutropenia and display increased susceptibility to fungal infections due to defective killing capacity of neutrophil granulocytes
This sequence seems to be incorrect, it diverges from other UxaC orthologs in position 354
Ref.1 (CAA41963) sequence was wrongly assigned to be a thymidylate synthase
Was originally thought to be the 52 kDa Ro autoantigen
PubMed:10749672 describes peptide sequences that do not match PLB1, but originate from a copurified, contaminating chitin deacetylase
Gly-141 is present instead of the conserved Asp which is expected to be an active site residue
Could be the product of a pseudogene unlikely to encode a functional protein. This is the C-terminal part of an aryl-alcohol dehydrogenase homolog of the AAD family. In strain S288c, a -1 frameshift disrupts the gene coding for this protein and produces two ORFs YFL056C and YFL057C. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 390 in the dsPTPase catalytic loop, suggesting that it has no phosphatase activity
The gene of ZNF547 share a non-coding exon with TRAPPC2P
It is uncertain whether Met-1, Met-23 or Met-45 is the initiator
The EMBL entry for PubMed:10574460 is not complete, the paper shows the rest of the sequence (residues 1 to 23)
Originally called wnt-2b by PubMed:9203142. Although PubMed:12084573 renames it as wnt-2, it is considered to be a wnt2b paralog by Xenbase
The disintegrin is also encoded by another precursor (AC Q1PBD1)
A MPS3B mutation at position 100 was erroneously reported (PubMed:9950362) as an amino acid change from Arg to His. The right amino acid change is from His to Arg
The annotated sequence does not include a start codon, because it is at the end of an incomplete sub-telomeric contig of the genomic sequence. Data from paralogs suggest an additional 28 residues at the N-terminus, consistent with the SPBC1348.02 (AC P0CU14) annotation
Was termed (Ref.2) DEFB137
Has been found in the mitochondrial ribosome large and small subunits
Neither a protein sequence nor a nucleotide sequence has been determined for this protein. This is the sequence of a model fit to electron density plots at 2.2 Angstroms resolution. The N-methylasparagine modification was omitted in the model
M.banksi is a member of the M.pilosula complex, but is clearly distinct from M.pilosula species. It is why the nomenclature proposed by Touchard et al., 2016 is slightly modified in this entry
It is uncertain whether Met-1 or Met-61 is the initiator
Although related to peptidase S1 family, lacks the essential His, Asp, and Ser residues of the catalytic triad at positions 73, 119 and 210 and is therefore predicted to have lost protease activity
Identified as a putative plastidic SufS-like protein and thus called CpNifS3 (PubMed:18978034). However, it seems to be more related to L-cysteine desulfhydrase
Was initially reported to act as a regulator of mRNA translation efficiency by promoting ribosome loading to m6A-containing mRNAs and by interacting with translation initiation factors eIF3 (EIF3A or EIF3B), thereby facilitating translation initiation (PubMed:26046440, PubMed:26593424). These studies suggested that the 3 different paralogs (YTHDF1, YTHDF2 and YTHDF3) have unique functions with limited redundancy (PubMed:26046440, PubMed:26593424). However, later studies showed that YTHDF1, YTHDF2 and YTHDF3 paralogs have redundant functions to a profound extent and directly promote degradation of m6A-containing mRNAs (PubMed:32492408). The effect on translation efficiency observed earlier is probably indirect (PubMed:32492408)
In contrast to other phospholipases, it lacks the typical Asp active site (Asp->Asn in position 75)
Although PubMed:11174199 reported this as a pseudogene, PubMed:12391231 showed it is expressed and has proteolytic activity when expressed in bacterial cells
PubMed:2823223 strain is not known and has been termed 'X' in this entry
Was originally (Ref.4) termed APH(3')IIa whereas it is APH(3')Ia
Lacks the B30.2/SPRY domain found in the human ortholog, thus may have divergent function(s)
It is uncertain whether sirS is an active short chain dehydrogenase since it lacks the conserved active sites
Unlike human OOSP2, mouse OOSP2 seems not participate in folliculogenesis and oocyte maturation
The role of the Tudor-knot domain, also named chromo barrel or chromodomain, is unclear. Based on its similarity with some chromo domains, it was first reported to bind histone H3 trimethylated on 'Lys-4' and/or 'Lys-9' (H3K4me3 and/or H3K9me3, respectively) (PubMed:19783983, PubMed:25560918). However, another group was not able to see any binding to methylated histones (PubMed:29494751). The 3D structure of the domain suggests that the inability to bind histones is caused by occlusion of the putative peptide-binding site by a basic amino acid side chain within a unique beta hairpin (PubMed:29494751)
Although no clear MSS51 ortholog is encoded in mammalian genomes, the mammalian MSS51/ZMYND17 protein is significantly similar. Considered by a number of resources to be the ortholog of yeast MSS51
MTCP1 and MTCP1NB are transcribed from the same promoter and could be considered the same gene
The DNA coding for this protein is not found in the complete genome of strain OF4
The venom of this snake was originally thought to be that of N.nigricollis
The purified enzyme was shown to contain 1.8 zinc atoms per subunit, and sequence analysis was used to predict the zinc binding site (PubMed:8449931). The crystal structure of the human ortholog indicates a lack of bound zinc ions, and shows that the residues that were predicted to bind zinc are too far apart in space to form a zinc binding site (By similarity)
It is uncertain whether Met-1 or Met-59 is the initiator
Arg-129 is present instead of the conserved Cys which is one of the two iron-sulfur binding sites
Lacks the second conserved cysteine (here Arg-129) that binds iron-sulfur cluster in orthologs
Lacks the conserved Asp residue in position 50 usually required for phosphorylation. The Glu residue in position 50 may mimic constitutive phosphorylation and allow FtcR to bypass the requirement for phosphorylation
It is uncertain whether Met-1 or Met-60 is the initiator
Lacks the conserved His residue involved in heme iron binding and essential for heme oxygenase activity. Its enzyme activity is therefore unsure
The role of this protein in Akt activation has been demonstrated in PubMed:12749859 but Iynedjian has not been able to reproduce the result in rat hepatocytes
Was also proposed to catalyze the transfer of the threonylcarbamoyl moiety of TC-AMP to the N6 group of A37 (PubMed:21285948, PubMed:21775474). However, it was shown that this reaction is catalyzed in B.subtilis by the TsaEBD proteins (PubMed:23072323)
Has been first identified as a cytoplasmic poly(A) polymerase (PAP) implicated in cell cycle checkpoint controls (PubMed:12218190). Further studies showed that cid1 had robust poly(U) polymerase activity in vitro and that is was rather an RNA uridylyltransferase (PubMed:17353264, PubMed:17449726)
Initially, no deubiquitinase activity could be detected when tested (PubMed:23827681). Other studies, show an obvious deubiquitinase activity (PubMed:21267069, PubMed:28343629, PubMed:27864334)
Besides the signal peptide, the N-terminal 32 AA may contain a propeptide sequence
Was originally thought to be a G-coupled receptor
Although related to histidine acid phosphatases, it lacks the conserved active sites, suggesting that it has no phosphatase activity
Lacks the conserved Asp residue in position 654 essential for protease activity
Initially reported to specifically promote pancreatic beta cell proliferation without insulin resistance and to promote beta cell mass expansion, thereby improving glucose tolerance (PubMed:23623304). However, this result could not be confirmed by further studies and the original paper was later retracted (PubMed:28038792). The lack of a role in beta cell proliferation was also confirmed in another study (PubMed:25417115)
Both gene predictions and some EST data suggest that there may be an additional exon at the C-terminus, adding another 10 kDa to the protein
In contrast to other members of the family, lacks the conserved Glu active site in position 449, which is replaced by a Gln residue, suggesting it is inactive
The rearrangement modifications of the Cys residues involved in the cross-links has not been described and the structure may be subject to revision
The existence of N(6)-methyladenosine on DNA is unclear in mammals (By similarity). According to a report, the majority of N(6)-methyladenosine in DNA originates from RNA catabolism via a nucleotide salvage pathway and is misincorporated by DNA polymerases, arguing against a role as epigenetic DNA mark in mammalian cells (By similarity). Additional evidences are therefore required to confirm the role of METTL4 as a N(6)-adenine-specific DNA methyltransferase in vivo (By similarity)
The Dictyosteliida are known to produce a glycosylsphingolipidinositol anchor (GPI-like-anchor). It has not been established whether Dictyosteliida make a glycosylphosphatidylinositol anchor (GPI-anchor), and whether their GPI-like-anchor modifications can be interconverted with GPI-anchor modifications in a 'resculpting process'. It has not been established that the GPI-like-anchor modification in Dictyosteliida utilizes the same sequence motif as the GPI-anchor modification
Product of a dubious gene prediction. The putative gene is located in an intron of SEPT7
The interacting region with TESC is conflicting: In human, it has been reported that SLC9A1 interacts with TESC via the juxtamembrane region of the cytoplasmic C-terminal domain, including residues 503-545. However, another publication has reported interaction with TESC via residues 633-818, the region of the cytoplasmic C-terminus more distal to the membrane
Initially the cerebellin peptide was thought to present the biological active entity
Has been shown in one study to be required for processing of sli into slit N-product and slit C-product (PubMed:27628033). However, has been shown in another study not to be required for sli cleavage with the protease required for sli cleavage being identified as tok (PubMed:27628033)
Lacks the conserved His and Cys residues that are essential for the activity of de-ubiquitinating enzymes. Lacks ubiquitin C-terminal hydrolase activity (PubMed:18728397)
Has been suggested to be found on the cell surface, but its function as an RNA helicase makes this dubious
Acetyltransferase activity toward tubulin in vitro is unclear (PubMed:28681565). Crystallographic studies with the human protein demonstrated that it does not share any similarity with other acetyltransferases and instead forms a crotonase-like fold
Was initially identified as sigma-2 receptor, which is thought to play important role in regulating cell survival, morphology and differentiation (PubMed:21730960, PubMed:22292588, PubMed:28007569). However, it was later shown that it is not the case (PubMed:28007569). The sigma-2 receptor has been identified as TMEM97 (AC Q5BJF2) (PubMed:28559337)
Was originally (PubMed:10944470) thought to be peroxisomal but was later shown (PubMed:16940157) to be mitochondrial
Was originally called CpsB
Some prediction bioinformatics tools predict the presence of a homeobox domain (By similarity). However, the domain is degenerate and residues that are important for DNA-binding are absent (By similarity). Moreover, the protein localizes in the endoplasmic reticulum and not in the nucleus, strongly suggesting that it does not constitute a canonical homeobox domain (PubMed:12912983)
PubMed:8334153 incorrectly assigned their sequence fragment as a fatty acid-binding protein
Originally thought to be a component of PSII; based on experiments in this organism, N.tabacum and barley, and its absence from PSII in T.elongatus and T.vulcanus, this is probably not true
Not only are egl-18/elt-5 and elt-6 moderately similar (46% identical) paralogous genes, but they may be transcribed both monocistronically and dicistronically in a tissue-dependent manner, so complicating interpretation of knockdown and expression experiments
Was initially (PubMed:2753038) named PLCD2 and was thought to be a new member of the PLC-delta family. It was later shown that it corresponds to PLCD4 (PubMed:15219862)
The position of the magnesium ion observed in the crystallographic structure is different from that observed in the structure of E.coli RmlA2 (RffH) and does not seem to correspond to the binding site for the catalytically essential magnesium ion. Therefore, we choose to propagate in the feature lines the positions found in the E.coli structure
The mouse ortholog has been shown to be a GPI-anchored protein but the Gly residue which is predicted to be the modified site in mouse and rat is not conserved in human
This protein lacks the conserved Cys in positions 65 and 69; they are replaced by a Gln and an Asn, respectively. It is therefore possible that the D-cluster is either altered or missing in this protein, which may not form heterotetramers
Could be the product of a pseudogene in strain CT18
Overlaps completely with ORF YGR031W
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9ac = acetylated Lys-12; H3K9me1 = monomethylated Lys-12; H3K14ac = acetylated Lys-17; H3K14me2 = dimethylated Lys-17; H3K18ac = acetylated Lys-21; H3K18me1 = monomethylated Lys-21; H3K23ac = acetylated Lys-26; H3K23me1 = monomethylated Lys-26; H3K27ac = acetylated Lys-30; H3K27me1/2/3 = mono-, di- and trimethylated Lys-30; H3K36ac = acetylated Lys-40; H3K36me1/2/3 = mono-, di- and trimethylated Lys-40; H3K56ac = acetylated Lys-62; H3K64ac = acetylated Lys-70; H3K79me1/2/3 = mono-, di- and trimethylated Lys-85
Has been given the gene name dsbB; however this is a longer form which is more closely related to the DsbI subfamily
Maps to a duplicated region on chromosome 15; the gene is present in at least 4 almost identical copies
The characterized enzyme was reported to be a monomer of approximately 45 kDa; it is not clear whether this corresponds to YdiO, YdiP or to another activity altogether
The status of C.vitulinus is unclear
DDX5 was reported to be a transcriptional coactivator of ESR1. However, this study has been retracted due to concerns of image manipulation
Was reported, in hepatocytes, to be involved in heme-mediated translational control of CYP2B and CYP3A and possibly other hepatic P450 cytochromes. Was reported that it may also regulate endoplasmic reticulum (ER) stress during acute heme-deficient conditions. However, this paper has been retracted because of improper data manipulation, reuse, and analyses
Lacks the conserved Ser-Lys catalytic dyad essential for proteolytic activity. Its enzyme activity is therefore unsure
Could be the product of a pseudogene. In strain cv. Columbia, a naturally frameshift at position 543 results in a truncated HMA3 protein. Lacks the magnesium binding sites, suggesting that it has no cadmium/zinc-transporting ATPase activity. A complete sequence for HMA3 can be found in strain cv. Wassilewskija (AC P0CW78)
Could be the product of a pseudogene. This is the C-terminal part of a putative glutamine--fructose-6-phosphate aminotransferase. Strain S288c has a frameshift in position 258, which disrupts the gene coding for this protein and produces two ORFs YMR084W and YMR085W. A contiguous sequence for this protein can be found in strain YJM789 (AC A6ZME2)
Was initially assigned as wee1 (PubMed:7749193). However, it corresponds to the meiosis-specific protein WEE2 in mammals
This gene was called SMR13 in PubMed:24399300
The identity of the enzyme catalyzing mitochondrial mRNA N(1)-methyltransferase is unclear. According to a report, mitochondrial mRNA N(1)-methyltransferase activity is catalyzed by TRMT61B (AC Q9BVS5) (PubMed:29107537). According to a second report, it is mediated by TRMT10C (PubMed:29072297). As both reports only tested one protein (either TRMT61B or TRMT10C), it is possible that both proteins have this activity
Was originally thought to be a rubredoxin oxidoreductase
Represents an unconventional myosin. This protein should not be confused with the conventional myosin-7 (MYH7)
Originally predicted to contain a coiled coil domain but proposed to contain a stable SAH domain instead
In A.terreus strain NIH2624, ATEG_00913 misses most of its catalytic domains. This difference may be due to errors in the sequencing or the automatic annotation of genome. The protein consists of a highly reducing PKS module (KS-AT-DH-ER-KR-ACP), a single NRPS module (C-A-PCP), and C-terminal TD domain
Glyoxalase activity has been reported (PubMed:22523093, PubMed:31653696). It may however reflect its deglycase activity (PubMed:25416785)
The protein deglycation activity is controversial. It has been ascribed to a TRIS buffer artifact by a publication (PubMed:27903648) and as a result of the removal of methylglyoxal by glyoxalase activity that leads to a subsequent decomposition of hemithioacetals and hemianimals due to the shift in equilibrium position by another one (PubMed:31653696). However, biochemical experiments showing that PARK7 is a bona fide deglycase have been performed (PubMed:25416785, PubMed:28013050, PubMed:28596309)
This gene name has also been given to serine hydroxymethyltransferase (AC Q97R16) in this organism
Was reported to act as a corepressor through recruitment of KDM1A and CBX; this publication has been retracted
Was initially reported to display histone acetyltransferase activity, with a preference for histone H4 (PubMed:12072557). Such activity is however unsure in vivo. Histone acetyltransferase activity would be in contradiction with the function of the protein in corepressor complexes (PubMed:12947414). Moreover, crystallographic studies in human demonstrated that it does not share any similarity with other acetyltransferases and instead forms a crotonase-like fold
According to some authors, recombinant REF6 can demethylate H3K4me3/2 and H3K36me3/2 (PubMed:20711170). In contrast, PubMed:21642989 and PubMed:27111035 show that REF6 is an intrinsic H3K27me3/2-specific demethylase. The different activities seen may be caused by the presence of different cofactors
Strain CLIB 122 / E 150 has a defective XPR2 sequence (xpr2-322) which lacks the N-terminus (positions 1 to 34)
PubMed:12489691 finds protein expression from early oogenesis but earlier publications (PubMed:2761544, PubMed:1280105, PubMed:11274061) suggest that the protein is not present before at least the blastula stage of embryos
Lacks the conserved Glu residue acting as catalytic proton donor. Its enzyme activity is therefore unsure
Was reported to share sequence similarities with IKBKB and therefore named 'NF-kappa-B inhibitor-like protein 2' (PubMed:7738005). However, the sequence similarity is remote and effects as regulator of NF-kappa-B are probably indirect and require additional evidence (PubMed:9242696)
Lacks the conserved Glu residue in position 493 essential for carbopeptidase activity. The mature form lacks catalytic activity towards synthetic peptide substrates
Has the same mature sequence than Reg1e (AC P85011). RgIA could therefore be the precursor of Reg1e, except that RgIA does not have the C-terminal Gly residue required for C-terminal amidation of Reg1e
This is a truncated version of aquaporin-2. In strain S288c and many laboratory strains, a natural 11 bp deletion in position 109 leads to a frameshift, which disrupts the gene coding for this protein and produces two ORFs YLL052C and YLL053C. A contiguous sequence for aquaporin-2 can be found in strain Sigma 1278B (AC P0CD89)
Despite overall sequence similarity to the typical alpha class carbonic anhydrases, lacks one of the three conserved catalytic zinc-ligand histidines
Was initially thought to be a NADP-specific glutamate dehydrogenase
Was termed (Ref.1) CES5
Could be the product of a pseudogene. Related to SNX29
In PubMed:3917402 the authors propose that Cys-36 and Cys-37 are disulfide bonded because they could not be observed during peptide sequencing, but were observed after reduction by dithiothreitol and reaction with labeled iodoacetamide. The crystallographic structures do not support these cysteines being disulfide bonded. Artifactual oxidation and some other cysteine modifications might be consistent with these observations
Could be the product of a pseudogene. Lacks the signal peptide, which is a conserved features of the family
Has a stop codon at position 56, which shortens the ORF when compared to other seripauperin family members
Although PubMed:12812785 report induction by snai2/slug, PubMed:12885557 report that sox10 lies in between snai1/snail and snai2/slug in the complex sequence of inductive events required for neural crest formation
Could be the product of a pseudogene. Inactivating mutations are found throughout the sequence in cv. Wassilewskija (PubMed:20801759) and no expression of the gene is detected in cv. Columbia (PubMed:16267099)
The active site contains a CTPC motif wich differs from the conserved CGPC motif
Ala-129 is present instead of the conserved Asp which is expected to be an active site residue
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-8; H2BK33ac = acetylated Lys-24; H2BK143ub1 = monoubiquitinated Lys-131
It is uncertain whether the initial Met is cleaved or not
Although it belongs to the SDR family, Phe-218 is present instead of the conserved Tyr which is an active site residue. It is therefore expected that this protein lacks oxidoreductase activity
Although PubMed:18321853 show that TESC-binding results in the maturation and accumulation of SLC9A1 at the cell surface, previous studies with human SLC9A1 report that TESC-binding results in a decrease in activity
The interacting region with TESC is conflicting: It has been reported that SLC9A1 interacts with TESC via the juxtamembrane region of the cytoplasmic C-terminal domain, including residues 505-571 (PubMed:18321853). However, studies with human SLC9A1 report the interaction with TESC via residues 503-545 or via residues 633-815
The original paper reporting lysine deamination at Lys-5 by LOXL2 has been retracted due to inappropriate manipulation of figure data (PubMed:22483618, PubMed:27392148). However, this modification was confirmed in a subsequent publication (PubMed:27735137)
Could be the product of a pseudogene. A family of highly similar proteins (GOLGA8A, GOLGA8B, GOLGA8C, GOLGA8D, GOLGA8E, GOLGA8F, GOLGA8G) are encoded by a repeated region on chromosome 15q11-15q13. Our sequences are in agreement with HGNC nomenclature
Mistakenly referred to as AT2G04040 in PubMed:11739388
PubMed:17724611 reports that the probe used in PubMed:12774230 cross-hybridizes with hes4-A/hairy2a, so the maternal expression reported in PubMed:12774230 is in fact due to hes4-A/hairy2a and not hes4-B/hairy2b
There are two genes for this protein in the chloroplast inverted repeat; while they are usually identical, in this organism they are not. The other copy is AC Q8S8U1
TTLL3 and TTLL8 monoglycylase-mediated glycylation of tubulin was initially reported to play a role in ependymal motile ciliary maintenance (By similarity). However, contradictory results were later observed (By similarity)
It is uncertain whether Met-1 or Met-91 is the initiator. The first 90 residues are not conserved and orthologous sequences, including rat and mouse ones, contain a stop codon upstream of the conserved methionine
Surprinsingly, this protein (from the Elapidae family) shows a high similarity with phospholipases A2 from the Viperidae family, which belongs to the group II of phospholipases A2, in contrast to the Elapidae family that belongs to the group I
It is not obvious if the APS kinase domain is functional; there is an Ala-555 replacing the conserved active site Ser. Furthermore R.baltica seems to harbor a bona fide single domain APS kinase (CysC)
Lacks the conserved Glu residue in position 166 essential for chitinase activity. Its enzyme activity is therefore unsure
The interaction with mouse KPNA2 may prevent SNAI1 nuclear import
According to publications, it is related to the galactose-1-phosphate uridylyltransferase type 1 family and histidine triad superfamily (PubMed:12119013). However, such families are not detected by prediction tools such as Pfam or SUPFAM
The human, porcine and bovine orthologs have a longer N-terminal part
Has been shown to act as a sodium/bicarbonate cotransporter in exchange for intracellular chloride (By similarity). Has also been shown to act as a sodium/biocarbonate cotransporter which is not responsible for net efflux of chloride, with the observed chloride efflux being due to chloride self-exchange (By similarity)
Originally proposed to be a peroxisomal protein (PubMed:9266848). Recent studies have suggested its localization to the endoplasmic reticulum and within the lysosome (PubMed:27456980)
In contrast to other members of the family, it apparently does not inhibit the Wnt signaling pathway, suggesting that it does not mediate depalmitoleoylation of WNT proteins (PubMed:23365253). However, additional evidence is required to confirm these data
It is uncertain whether Met-1 or Val-4 is the initiator
Was reported to dephosphorylate the penicillin-binding protein PBPA. However, this publication has been retracted because the published versions of some figures were modified prior to publication
Reported to be phosphorylated by AKT2 (PubMed:12697749). However, the publication has been retracted due to image duplication in figures
Was originally thought to bind single-stranded RNA molecules and regulate GABA-B receptor expression
Could be the product of a pseudogene. Contains an internal deletion relative to its orthologs
Although related to the glycosyl hydrolase 18 family, lacks the conserved Glu active site at position 30, which is relaced by a Lys residue, suggesting it has no glycosidase activity
Lacks the conserved His residues essential for binding the catalytic zinc ion. Lacks the conserved residues important for substrate binding and catalysis. Its enzyme activity is therefore unsure
While belonging to the GST superfamily, it probably lacks glutathione transferase activity
The phosphoserine observed at Ser-996 in PubMed:17218307 undoubtedly results from the secondary neutral loss of pantetheine from the phosphodiester linked cofactor
Was initially thought to be a peroxisomal protein (PubMed:7957077). However, it was later shown in human that it is a mitochondrial protein (PubMed:16582907, PubMed:16582910)
Was originally erroneously termed AKT6
It is unclear if PMIV is glycosylated as other members of the same enzyme family, ie. PMI and PMII, are not
Was originally known as R.NgoMI
Could be the product of a pseudogene. Much shorter than related proteins
The tissue specificity and the characterization shown in PubMed:11722126 are from a soluble protein extract not making the distinction between the two proteins produced by NCS1 and NCS2
Could lack activity as the potential active site Cys residues in positions 72 and 218 are both replaced by a Ser
Lacks the N-terminal part with coiled coil domains, which are common features of the NEAP family
Although the beta-barrel of Cu/Zn SODs is largely preserved, SOD5 is a monomeric copper protein that lacks a zinc-binding site and is missing the electrostatic loop element proposed to promote catalysis through superoxide guidance. Without an electrostatic loop, the copper site of SOD5 is not recessed and is readily accessible to bulk solvent (PubMed:24711423)
It was originally suggested that BarX is likely to participate in the regulatory pathway for the production of VB, rather than in the biosynthetic pathway of VB itself
Lys-57 is present instead of the conserved Glu which is expected to bind iron
Product of a dubious CDS prediction. May encode a non-functional truncated protein
Could be the product of a pseudogene. Truncated purine permease that is probably not expressed
Product of a dubious gene prediction. Overlap the RAB4A locus
Was originally thought to bind DNA. It was probably an artifact due to the cationic nature of skp
The functional relevance of vacuolar localization is disputed
Was originally thought to be plasmid encoded
Although homologous with the vitamin K-dependent clotting factors, it has lost two of the essential catalytic residues and has no enzymatic activity
This gene should not be confused with EIF2S1, frequently called eIF2-alpha in the literature, and with which it shares the alias EIF2A. EIF2S1 is the alpha subunit of the eIF2 translation initiation complex. Although both of these proteins function in binding initiator tRNA to the 40S ribosomal subunit, the EIF2A protein does so in a codon-dependent manner, whereas eIF2 complex requires GTP. Was initially thought to constitute the ortholog of prokaryotic IF-2 (infB) protein
The active site contains a CVPC motif wich differs from the conserved CGPC motif
Was originally thought to possess lysophospholipase activity but the absence of this activity has been shown by PubMed:11834744
Eristocophin II appears to represent degradation product of EMF10B
Was originally termed CYP4A11
There is no sequence for the expressed copy of A1 in strain S288c, because this strain is of mating type alpha. A sequence for the expressed copy of A1 can be found in other strains (AC P0CY10)
Was assigned to CHC1 in PubMed:21187379
Originally described as a retinal dehydrogenase based on its ability to preferentially oxidize 9-cis-retinal (PubMed:11007799). It has been reassigned to a 2-aminomuconic semialdehyde dehydrogenase (PubMed:29703752)
Was first identified as the mitochondrial pyruvate transporter (PubMed:12887330). However, later experiments showed that was a NAD(+) transporter (PubMed:16291748)
The gene name nadA has also been given to Neisseria adhesin A, a protein used in serogroup B vaccines
This TrpB is highly divergent compared to other bacterial TrpB. As C.trachomatis seems to have lost part of the Trp biosynthetic operon, it is possible that this protein is not active
Was originally (PubMed:2179047) characterized as part of a cryptic cel operon for a cellobiose degradation system. The Cel+ phenotype is due to mutations making expression chitobiose-independent and altering the substrate specificity
Although it belongs to the kinase superfamily, contains an asparagine residue at the position of the canonical catalytic aspartic acid and is predicted to lack kinase activity. However, can bind ATP (By similarity)
An article reported the identification and characterization of this protein as zinc metalloprotease in different tissues; however, this paper was later retracted
Baed on animal models in mouse and zebrafish, it was suggested that KCTD13 is the major factor inducing the macrocephaly phenotype associated with the 16p11.2 deletion (PubMed:22596160). However, a subsequent report showed that KCTD13 does not play a role in brain size
AGTR2 has been reported to be involved in X-linked intellectual disability (PubMed:12089445). Its pathological role is however questionable (PubMed:23871722)
In contrast to other members of the family, lacks the conserved Asp at position 158, which is replaced by an Asn residue, suggesting it is inactive
This protein does not encode the conserved residues that usually bind zinc
According to a report, mice lacking Zbp1 display reductions in respiratory epithelial damage and lung inflammation (PubMed:27917412). However, the virus persists and replicates in the infected cells leading to a delay in recovery from infection, but the animals are protected from mortality (PubMed:27917412). In contrast, another article reported increased mortality in knockout mice, probably caused by increased virus burden (PubMed:27746097). However, as this study did not assess the inflammatory response in the lungs, it is difficult to compare ZBP1 regulation of lung inflammation between these two studies (PubMed:27746097)
Experimental mass obtained by mass spectrometry (2060.5 Da) is very different from the calculated average mass 1821.25 Da, even with consideration of post-translational modifications
The CWBP52 polypeptide was originally called CWBP55 based on its apparent molecular weight
Although related to the SDR family, lacks the conserved active Tyr residue in position 218 which is replaced by a Phe, suggesting that it may lack oxidoreductase activity
The mutant Gln-371 studied is still likely to be glycosylated at Asn-370, but study did not include mutagenesis of Asn-370
It is uncertain whether Met-1 or Met-40 is the initiator. Orthologous sequences cannot be extended
Was originally suggested to positively regulate sigma-E activity in vitro
Lacks the conserved serine which acts in the transient covalent linkage to DNA during strand cleavage and rejoining
Was originally thought (PubMed:1459959, PubMed:14621995, PubMed:16511076) to be a 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) synthase but further protein analysis clearly suggests that it is a 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) synthase
The mode of regulation of FOXK1 by mTORC1 is controversial. According to a first report, mTORC1 signaling promotes phosphorylation of FOXK1 and nuclear exclusion (PubMed:25402684). According to a second report, mTORC1 signaling prevents phosphorylation by GSK3 (GSK3A or GSK3B), thereby promoting translocation to the nucleus (PubMed:29861159)
Was originally (PubMed:2680969) thought to be involved in mouse virulence. It was later shown that the mutation responsible for the virulence phenotype maps to nearby genes (PubMed:8288531)
Was originally proposed to bind to DNA and act as transcription factor
Could be the product of a pseudogene. The N-terminus is shorter and lacks the signal sequence compared to the mouse sequence, suggesting it may not be functional
Was originally thought to be a glutathione peroxidase (PubMed:10480913) or a phospholipid hydroperoxide glutathione peroxidase (PubMed:11445588), but functions as an atypical 2-Cys peroxiredoxin using thioredoxin as reducing power instead (PubMed:12437921)
Although related to peptidase S1 family, lacks the conserved active Ser residue in position 364 which is replaced by a Thr
Autophosphorylation is proposed although the protein kinase domain is predicted to be catalytically inactive
Was intially thought to be allosterically stimulated by dGTP (PubMed:22056990, PubMed:24141705, PubMed:24217394). However, it was later shown that it is allosterically activated and regulated via the combined actions of GTP and dNTPs (dATP, dGTP, dTTP and dCTP), which bind two separate binding sites (PubMed:25288794, PubMed:25267621, PubMed:25760601)
Phosphorylation at Thr-592 was initially thought to impair ability to restrict infection by viruses without affecting the deoxynucleoside triphosphate (dNTPase) activity (PubMed:23601106). However, it was later shown that phosphorylation reduces the stability of the homotetramer, leading to impair the dNTPase activity (PubMed:26294762, PubMed:26431200)
Was initially thought to have 3'-5' exonuclease activity, acting on single-stranded RNA (PubMed:23364794, PubMed:25038827). A publication also reported some DNA 3'-5' exonuclease activity (PubMed:23364794). However, it was later shown that SAMHD1 does not possess DNA and/or RNA exonuclease activities and that these activities are due to contamination during the purification process that can be removed after chromatography steps (PubMed:26101257). The exonuclease activity observed was maybe due to the presence of MRE11 during the purification steps (PubMed:29670289)
Was originally assigned as UGD1
Was originally (Ref.1) thought to originate from A.thaliana
D-glycero-beta-D-manno-heptose 1,7-bisphosphate (HBP) was initially thought to constitute the bacterial pathogen-associated molecular pattern metabolite (PAMP) triggering the ALPK1-TIFA innate immunune response (PubMed:28877472, PubMed:28222186). It was however shown that ADP-D-glycero-beta-D-manno-heptose (ADP-Heptose) constitutes the main PAMP that activates the kinase activity of ALPK1 (PubMed:30111836)
Conflict in position 933 in the human genome assembly due to a frameshift
There may be second mutations present in each of mutant strains C58 and C213
Despite being nearly identical to the ttgABC operon in strain DOT-T1E and the mepABC operon in strain KT2442-TOL this operon does not function in solvent efflux. This may be due to different protein expression levels. In strain KT2440 the equivalent operon does not seem to function in toluene efflux
It is uncertain whether Met-1 or Met-2 is the initiator. Met-2 is more conserved than Met-1 among the orthologs
Was originally annotated as sucA because of sequence similarity(PubMed:9634230, PubMed:12218036). But this protein was shown not to be able to serve as the E1 component of 2-oxoglutarate dehydrogenase (ODH) (PubMed:16045627). However, it was later shown that this protein does in fact sustain ODH activity, and requires specific activation by acetyl-CoA (PubMed:21867916)
The drug propylthiouracilin was reported to bind to the distal heme-pockets of LPO (PubMed:25760705). However, the paper was retracted as some concerns were raised about the modeling
This peptide is cyclic. The start position was chosen by similarity to Voc2 (cycloviolacin-O11) for which the DNA sequence is known
Asn-183 is present instead of the conserved Asp which is expected to be an active site residue
The substrate specificity could be slightly different compared to human ELOVL1, AC Q9BW60. No activity toward octadecanoyl-CoA, for instance, is observed in vivo (PubMed:23689133)
Was originaly thought to be involved in active uptake of glycerol driven by electrogenic proton symport (PubMed:10931309), but has later been shown to be an acyltransferase and that effects on glycerol transport may be indirect (PubMed:10694878, PubMed:15381122)
The third copy of this protein is missing from the Sakai strain
Unlike other plasmepsins, one of the two catalytic aspartates, Asp-157, is replaced with histidine; however, the protein is catalytic active (PubMed:11782538). Unlikely to act as a serine protease (By similarity). His-157 may stabilizes the catalysis and Asp-337 may act as both an acid and a base during catalysis (By similarity)
It is unclear if PMIII is glycosylated as other members of the same enzyme family, ie. PMI and PMII, are not
Gln-136 is present instead of the conserved Asp which is expected to be an active site residue
Was originally known as M.NgoMI
Was originally proposed to be fused with TM_0929
Contains Gly-74 instead of the conserved Cys required for the covalent attachment of FMN in the first PAS domain
Was originally thought to originate from the sponge Geodia cydonium, but, on the basis of phylogenetic studies (Ref.2) it seems very probable that the DNA sequence coding for this protein comes from a rodent as agreed by the original authors (Ref.3)
The initiator methionine may be further downstream
While belonging to the GST superfamily, it lacks glutathione transferase activity
Despite its name, it does not contain a canonical C2H2-type zinc-finger, seems to be a partial inverted duplication of ZNF674
Lacks the conserved active site Arg in position 20. There is a histidine in this position
There are conflicting results concerning the role of ABCA7 in lipid transport. ABCA7 was described to play a role in apolipoprotein-mediated phospholipid and cholesterol efflux when expressed in HEK293 cells (PubMed:12917409, PubMed:27472885). However, another report shows that ABCA7 deficiency does not influence cholesterol and phospholipid efflux in mouse primary macrophages, but leads to lower serum HDL cholesterol levels and a reduction in fat mass in female mice (PubMed:15550377)
Production of a dubious gene prediction
Despite some similarity with the 'phage' integrase family, it has no recombinase activity
Lacks the conserved threonine residue in position 57, which is part of the carbamoylphosphate binding site; it is replaced by a leucine residue (PMIS:9346304)
Lacks the first part of the protein and the active site Ser residue which is a conserved feature of peptidase S10 family
1WQ8 PDB entry indicates an origin from V.aspis aspis, whereas PubMed:15542594 that mentions 1WQ8 indicates an origin from V.ammodytes ammodytes
Used to include what was called 'menR'
According to a report, N6-methylation of MAT2A affects MAT2A mRNA stability instead of preventing splicing (By similarity). However, it was later shown that N6-methylation of MAT2A transcripts prevents recognition of their 3'-splice site by U2AF1/U2AF35, thereby inhibiting splicing and protein production (PubMed:33930289)
Stoichiometry of the protein is unclear. According to two reports, the methyltransferase acts as a monomer (PubMed:30197299, PubMed:30197297). According to a another paper, it acts as a homodimer (PubMed:29593291)
Attempts to clone the transcript coding for this protein failed
Lacks a RING domain and has therefore no E3 ubiquitin-protein ligase activity by itself
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK5ac = acetylated Lys-6; H2AK8ac = acetylated Lys-9; H2AK10ac = acetylated Lys-11; H2AK12ac = acetylated Lys-13; H2AK17ac = acetylated Lys-18; H2AS122ph = phosphorylated Ser-123; H2AK123ub1 = monoubiquitinated Lys-124; H2AS124ph = phosphorylated Ser-125; H2AS129ph = phosphorylated Ser-130; H2AS134ph = phosphorylated Ser-135
Has been originally identified as involved in pre-tRNA splicing since its deletion accumulates pre-tRNAs (PubMed:7363329, PubMed:3031485). However, further studies have shown that it is actually a nuclear pore protein involved in transport of pre-tRNAs and mature tRNAs (PubMed:9774653)
Lacks three conserved histidine residues and one conserved aspartate residue that bind copper and zinc
PubMed:22511981 describes the 3D-structure 2LIX submitted to PDB as being secreted by Isometrus maculatus (and not by Lychas mucronatus as indicated in the PDB entry)
Was originally proposed to code for two separate adjacent ORFs, flaE and flaY
Lacks two Cys residues in the RING-type zinc finger domain 2 that are conserved features of the family
This sequence is shorter in the N-terminal part than sequences from orthologs. It is not possible to make it longer
PubMed:17906154 suggests that SfrAB is involved in acetate metabolism and does not participate directly in the reduction of Fe(3+) chelates, as was initially proposed in PubMed:11443080
This protein is inactive in the dairy strain IL1403. The histidine biosynthesis pathway is not functional in the dairy strain IL1403
This protein is unrelated to the penicillin-binding protein Pbp2a, also called MecA, that confers resistance to methicillin in several strains of S.aureus (MRSA) and is used as a marker for the identification of MRSA isolates
Has most probably no lipid phosphatase activity (By similarity). Critical residues that support the reaction mechanism in active members of that protein family, including the residues of the active site acting respectively as proton donor and nucleophile, are not conserved
Although this protein contains both EAL and GGDEF domains it is unlikely to have either c-di-GMP phosphodiesterase or diguanylate cyclase activities as amino acids known to be important to these activities are not conserved
Was initially identified as a laminin-binding protein (PubMed:3417768), but later studies indicate that this is highly unlikely (PubMed:1825466, PubMed:2302244)
Truncated; premature stop codon after the RNase H domain
Was originally thought to be WecF, the 4-alpha-L-fucosyltransferase
Has a deletion of about 30 residues in position 132 compared to all other ThiM
Was termed (PubMed:15354349, PubMed:17081983) USP31
Was originally thought to be a subunit of methylviologen hydrolase II
Was originally identified in the small subunit (28S) of mitochondrial ribosomes that were purified on sucrose gradients (By similarity). This observation has been challenged by experiments showing MRPS36 copurification with the oxoglutarate dehydrogenase complex (OGDC), also called alpha-ketoglutarate dehydrogenase complex (KGDH). Both mitochondrial ribosome 28S subunit and OGDC have a similar size and OGDC is highly abundant, therefore OGDC has been found to contaminate ribosomal preparations performed by sequential centrifugation steps (By similarity). In addition, MRPS36 could not be located in the structure of the human mitochondrial ribosome, supporting the hypothesis that it is not a mitoribosomal protein (PubMed:25838379)
The spacing between the first 2 Cys is very close; it may not bind zinc
The nomenclature for members of the GUCY2 gene family is not consistent across species. In mice the GUCY2D gene encodes the protein guanylate cyclase 2D specifically expressed in a subpopulation of olfactory sensory neurons. In rat the official name is GUCY2E for guanylate cyclase 2D. In human this gene is a pseudogene
The gene has been cloned in cv. Landsberg erecta, but the tissue specificity, developmental stage and induction have been determined in cv. Columbia (PubMed:11678272)
Lacks the conserved Glu residue in position 619 essential for glucanase activity. Its enzyme activity is therefore unsure
Was originally thought to be elastase IV
Could be the product of a pseudogene. The human MOXD2 gene lacks the last 2 terminal exons, as well as the 3'-UTR and poly(A) signal found in all other mammalian sequences. This deletion, which occured after the divergence of humans and chimpanzees, may interfere with proper mRNA processing and/or translation
Lacks the Tyr (here Asp-212), a conserved feature of the aromatic cage required for the interaction with histone H3K4me3/2
According to some reports, mediates transmembrane transport of glucose and fructose (PubMed:15033637, PubMed:16186102, PubMed:29548810). However, another group could not confirm transporter activity for glucose or fructose (PubMed:28083649)
NALCN was also originally reported to be a voltage-independent, cation-nonselective channel which is permeable to sodium, potassium and calcium ions (PubMed:17448995). However, NALCN is recently reported to be selective only for monovalent cations and to be blocked by extracellular divalent cations (By similarity). Futhemore, coexpression of NALCN, UNC79, UNC80, and NALF1 results in voltage-dependent NALCN currents (By similarity)
Encoded by the 21 C-terminal amino acids of the HcaR transcriptional activator, it is suggested to be produced by an independent promoter within the hcaR gene. However the peptide's existence has not been proven, nor has mutagenesis of HcaR itself rather than overexpression of IroK been ruled out as the cause of 3-HP resistance
Although this protein has been named voltage-gated K channel beta subunit 4.1 in Ref.1 and Ref.2, there is no evidence that it may play a role in ion transport
Was originally thought to have protein tyrosine kinase activity
An alternative isoform might be encoded by the 3'part of the transcript derived from AK228109
This is a poor transmembrane prediction
It is uncertain whether Met-1 is the initiator. Based on the lack of an in-frame AUG codon, mammalian TFIIIA may be translated from this non-AUG initiation site, which has a good Kozak context and which is well conserved among mammals
Experimental mass obtained by mass spectrometry (2145.0 Da) is very different from the calculated average mass 1817.18, even with consideration of post-translational modifications
Glu-125 is present instead of the conserved Asp which is expected to be an active site residue
O-glycosylation sites are annotated in first sequence repeat only. Residues at similar position are probably glycosylated in all repeats. Experimental sites were determined in a synthetic peptide glycosylated in vitro (PubMed:7744025, PubMed:9597769)
Low resolution structures by electron microscopy suggested the presence of six transmembrane regions (PubMed:31276439). However, high resolution structures in human and S.pombe showed that it is composed of four transmembrane and two intramembrane regions (By similarity)
Was originally thought to be a voltage-gated ClC-type chloride channel
Corresponds to the N-terminal section. Unlike the other Salmonellae, the ortholog of the FliB protein may be encoded by two CDS in S.muenchen. It cannot be ruled out that sequencing errors produced two CDS instead of one
Although strongly similar to formylglycine-generating enzyme, lacks the catalytic Cys residues that bind the catalytic copper. The catalytic copper is required to activate oxygen and catalyze oxidative C-H activation
Was originally thought to be a pore or transmembrane transporter for hemolysin
Was originally termed dappled
Could be the product of a pseudogene. Polymorphic pseudogene or segregating pseudogene, a deletion of 2 bp code for a longer protein which is conserved in other mammals and potentially functional
Does not bind calcium as one of the calcium-binding sites is lost (Asp->Lys in position 77, which corresponds to 'Lys-49' in the current nomenclature)
Authors initially considered AURKA/STK6 and STK15 as 2 different proteins (PubMed:9771714). It is clear that they are the same protein
An article that concluded that AURKA-mediated phosphorylation of BRCA1 'Ser-308' plays a role in the normal cell cycle G2/M transition was withdrawn due to data manipulation of flow cytometry data
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-11; H2BK6su = sumoylated Lys-11; H2BS10ph = phosphorylated Ser-15; H2BK11ac = acetylated Lys-19; H2BK123ub1 = monoubiquitinated Lys-137
The mouse ortholog protein is an active neutral amino acid transporter
Ref.2 sequence was originally thought to originate from Human
Was originally (PubMed:7539799, PubMed:9736737) thought to have dipeptidase activity but it was shown later to lack that activity
Was orginally thought to originate from Pseudomonas denitrificans, but similarity searches show that the sequence is much closer to Sinorhizobium. The entry's taxonomy has been changed
Nomenclature used in PubMed:8576224 refers to PP2A B subunit B' delta isoform, which is cited as PP2A B subunit epsilon-PR61 isoform in later publications
Was originally thought to be a receptor for SCYA3 and SCYA17
Unlike human or mouse orthologs, does not mediate carnitine uptake
Lacks the conserved Cys residue in position 155 and the conserved His residue in position 268 essential for carbopeptidase activity. Its enzyme activity is therefore unsure
This sequence was first thought to be an alternatively spliced isoform of PLA2G4B. It is derived from JMJD7 which is located upstream of PLA2G4B. Most tissues also express read-through transcripts from JMJD7 into the downstream PLA2G4B gene, some of which may encode fusion proteins combining the N-terminus of this protein with PLA2G4B protein
Was originally (PubMed:2092358) characterized as part of a cryptic cel operon for a cellobiose degradation system. The Cel+ phenotype is due to mutations making expression chitobiose-independent and altering the substrate specificity
Was reported to have a protein kinase activity and to autophosphorylates on Ser-385 and Thr-389
A paper showing that PRMT1-mediated arginine methylation of PIAS1 regulates STAT1 signaling has been retracted, because some of the data was found to be deliberately falsified
There are 4 nearly identical operons in various strains of P.putida. This one and the ttgABC operon of strain DOT-T1E function in solvent and antibiotic efflux; however in strain S12 the arpABC operon functions only in antibiotic efflux. This may be due to different protein expression levels. In strain KT2440 the equivalent operon does not seem to function in toluene efflux
Due to high divergence, the Zn(2)-C6 fungal-type DNA-binding domain cannot be predicted
Has been classified as a gamma-KTx toxin due to its molecular target (Kv11/ERG), but could be classified as an alpha-KTx since it shares a high level of homology in both primary and 3D structures with other alpha-KTx scorpion toxins
Product of a dubious CDS prediction. Most probably an erroneously predicted open reading frame in the 3' UTR of the SLITRK2 gene
Could be the product of a pseudogene, it is missing up to 370 N-terminal resides compared to orthologs
Could be the product of a pseudogene. It corresponds to positions 534 to 586 of the complete orthologous and probably active protein in R.felis (RF_0890)
As this protein has Gly-222 in the position that determines the specificity of the enzyme instead of the Asp found in trypsins, it could have a chymotrypsin-like activity
Do not confuse oligodendrocyte-myelin glycoprotein (OMG) with myelin-oligodendrocyte glycoprotein (MOG)
Two studies agree that egl-1 is dispensable in mitochondrial dynamics and morphology during early embryonic development (PubMed:21949250, PubMed:19327994). However, it is also reported that egl-1 can act in mitochondrial dynamics during larval development, via regulation of ced-9 (PubMed:21949250)
Was originally termed Galnt10/pp-GaNTase 10
Strain BM4361 does not express or weakly expresses aminoglycoside resistance gene and is thus aminoglycoside-sensitive. Strain BM4362 expresses it due to a chromosomal deletion leading to aminoglycoside resistance
Product of a dubious CDS prediction. May be a target of NMD. Not on genome assembly (GRCh37/hg19)
In all 3D-structures with RF2/PrfB and the 70S ribosome this protein is seen to contact 16S rRNA (PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:28077875). In most is also seen to contact 23S rRNA (PubMed:27906160, PubMed:27934701, PubMed:28077875). Contact with ribosomal protein S12 is also reported sometimes (PubMed:27906160, PubMed:27906161). These discrepancies may be due to interpretation of results
In cv. Landsberg erecta (AC P0DKJ7), the sequence differs from that shown due to an insertion in the genomic sequence that adds 60 residues after the Asn-564
Previously identified as the mitochondrial deoxyribonucleotide carrier. However other experiments later demonstrated that SLC25A19 is a thiamine diphosphate transporter and not a mitochondrial deoxyribonucleotide carrier
The identity of the enzyme catalyzing mitochondrial mRNA N(1)-methyltransferase is unclear. According to a report, mitochondrial mRNA N(1)-methyltransferase activity is catalyzed by TRMT61B (PubMed:29107537). According to a second report, it is mediated by TRMT10C (AC Q7L0Y3) (PubMed:29072297). As both reports only tested one protein (either TRMT61B or TRMT10C), it is possible that both proteins have this activity
Contradictory results have been reported for activation of this receptor by beta-ionone in human and mouse. Beta-ionone does not activate OR51E2 in mouse. This difference may depend on the different methods used for the experiment or may be due to species difference
Was initially thought to mediate palmitoylation of Wnt proteins (PubMed:24292069). It was later shown that instead it acts as a serine O-palmitoleoyltransferase that mediates the attachment of palmitoleate, a 16-carbon monounsaturated fatty acid (C16:1), to Wnt proteins
Lacks the conserved aspartate or glutamate residue in position 458 that binds magnesium; it is replaced by an alanine residue
Lacks key residues involved in peptide docking and also does not require TAP (transporter involved in antigen processing) for cell surface expression, suggesting that this is a non-classical MHC class I protein which does not play a role in antigen presentation
PubMed:11117876 showed an allyl-alcohol dehydrogenase activity on (2S,4S)-carveol while PubMed:17945329 and Ref.4 showed an exclusive enone reductase activity
Was originally (PubMed:8617361) thought to originate from Sulfolobus solfataricus, but was shown (PubMed:18157853) to stem from Sulfolobus acidocaldarius. This was due to a contamination of the S.solfataricus P1 strain isolate used for the initial cloning with the S.acidocaldarius species
This protein lacks the conserved Cys in positions 52 and 300; they are replaced by an Arg and a Glu, respectively. It is therefore possible that the C- and D-clusters are either altered or missing in this protein
Contrary to the situation in zebrafish, xenopus and drosophila, mammalian MYO1D defects have no effects on left-right body asymmetry
Although similar to the small GTPase superfamily, lacks the conserved catalytic Gln in position 79 which is replaced by a Ser residue, possibly explaining the weak GTPase activity. In contrast to other members of the family, it is not prenylated (PubMed:21505417)
PubMed:10077615 shows data confirming the peroxisomal localization of the protein, however this study was later retracted as the images were additionally used in other articles for other proteins
Although assigned as two separate genes (c20orf57 and DUSP15), it is probable that C20orf57 does not exist by itself and is a part of the DUSP15 gene
It is uncertain whether Met-1 or Leu-7 is the initiator
No signal sequence is predicted for this protein. All LptD proteins in this family possess a predicted signal sequence and are located on the bacterial outer membrane
Functional characterization has been done on a chimeric protein carrying at its C-terminus a fragment of the cloning vector instead of the levanase sequence
Although the residues involved in the catalytic activity are absent, suggesting that the kinase is inactive, some kinase activity has been detected
Could be the product of a pseudogene. It is encoded in the reverse strand of the region coding for AF_0739.1, a potential gene which belongs to the UPF0146 family
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-8; H2BK6su = sumoylated Lys-8; H2BK7ac = acetylated Lys-9; H2BK7su = sumoylated Lys-9; H2BK11ac = acetylated Lys-15; H2BK16ac = acetylated Lys-26; H2BK16su = sumoylated Lys-26; H2BK17su = sumoylated Lys-27; H2BK123ub1 = monoubiquitinated Lys-133
Lacks the typical Cys active site in position 696 that is replaced by a Ser residue, preventing the tyrosine-protein phosphatase activity
Represents a conventional non-muscle myosin. This protein should not be confused with the unconventional myosin-10 (MYO10)
Most probably a non-functional protein that cannot participate to the synthesis of a productive immunoglobulin chain due to a mutation at position 115, corresponding to the second cysteine from the disulfide bridge, potentially leading to uncorrect folding (PubMed:9619395). Watson et al (PubMed:23541343) identified this gene on chromosome 14. However, it is not currently present on the reference genome assembly (GRCh38/hg38)
The full-length coding region has been amplified by RT-PCR and sequenced, but not submitted to the EMBL/GenBank/DDBJ databases
Lacks the ATP-binding motif which is one of the conserved features of the kinesin family
This sequence originates from an organism contaminating a Chlorella sorokiniana culture, probably a bacterium
Product of a dubious CDS prediction. Overlaps in opposite strand with MED14
Despite its name, the murine TOMT protein does not contain a transmembrane region in contrast to primate orthologs
This is a pseudogene in 2 other cucumber chloroplast genomes (cv. Baekmibaekdadagi and Borszczagowski). In cv. Chipper and Gy14 there is a single base insertion that restores the reading frame
Was originally thought to be a cell wall structural protein
It is uncertain whether Met-1 or Met-24 is the initiator
A venom protein (not sequenced) was found in the specimen of from South Carolina, whereas no venom protein was found in the specimen from Iowa
Was originally identified in the small subunit (28S) of mitochondrial ribosomes that were purified on sucrose gradients (PubMed:11279123, PubMed:22015679). This observation has been challenged by experiments showing MRPS36 copurification with the oxoglutarate dehydrogenase complex (OGDC), also called alpha-ketoglutarate dehydrogenase complex (KGDH). Both mitochondrial ribosome 28S subunit and OGDC have a similar size and OGDC is highly abundant, therefore OGDC has been found to contaminate ribosomal preparations performed by sequential centrifugation steps (By similarity). In addition, MRPS36 could not be located in the structure of the human mitochondrial ribosome, supporting the hypothesis that it is not a mitoribosomal protein (By similarity)
Was originally thought to be involved in phosphate transport
Although PubMed:12809501 reports that TESC results in a decrease in transporter activity of human SLC9A1, studies with rat SLC9A1 show that TESC-binding results in the maturation and accumulation of SLC9A1 at the cell surface
The interacting region of SLC9A1/NHE1 with CHP3 is conflicting: Interaction with SLC9A1/NHE1 has been reported via residues 503-545, the juxtamembrane region of the cytoplasmic C-terminus (PubMed:11696366, PubMed:18321853, PubMed:30287853). However, another publication has reported interaction with SLC9A1/NHE1 via residues 633-815, the region of the cytoplasmic C-terminus more distal to the membrane (PubMed:12809501)
Product of a dubious gene prediction. Found in the 3'UTR of TMEM217/ AC Q8N7C4
The N-terminal region seems to be truncated when compared to orthologs
Was originally thought to have lysophosphatidic acid acyltransferase activity, but by homology with SH3GL2/endophilin A1 is unlikely to have this activity
Could be the product of a pseudogene. It lacks about 130 C-terminal residues, which corresponds to the regulatory domain
Exhibits no phospholipase activity, despite two HKD motifs
This protein is much smaller than the orthologs present in other bacteria; the NBD2 and C-terminal domains are missing. However, there is a paralog in the genome (clpB1) that encodes a protein which contains only the NBD2 and C-terminal domains
This protein lacks the conserved Gly residues in positions 90 and 93 that are potentially involved in NAD(H) binding. They are replaced by an Asn and an Ala, respectively
Although strongly related to the ABRAXAS1 protein, lacks the C-terminal pSXXF that constitutes a specific recognition motif for the BRCT domain of BRCA1
Defined as a pseudogene by HGNC. However, proteomic data on a specific peptide suggest the existence of this protein
Was originally identified as FMN-containing NADH dehydrogenase (PubMed:12417325), based on the NADH oxidase activity of the C-terminally truncated protein. Was then shown to function as sulfide:quinone reductase. The full-length protein does not have NADH oxidase activity (PubMed:19438211)
This toxin sequence resembles the beta scorpion toxin class, although patch-clamp experiments shows the induction of supplementary slow inactivation of sodium channels, which means that it behaves like an alpha scorpion toxin
Supposed to contain a SH3, a PDZ and a guanylate kinase-like domain. But none of these 3 domains are detected by PROSITE, Pfam or SMART
Could be the product of a pseudogene. TNXA is transcriptionally active in adrenal cortex but no protein product has been observed
Was originally thought to be nuclear
Initially reported to localize in the cytoplasm (PubMed:16003559). A number of studies showed that it accumulates at DNA damage sites in the nucleus (PubMed:27601467, PubMed:27723720, PubMed:27723717)
Product of a dubious gene prediction. Partially overlaps Q0017
Was originally thought to be a type II membrane protein but this is inconsistent with the results of multiple phosphorylation studies because this topology would locate the phosphorylation sites in the lumen or extracellularly rather than in the cytoplasm
Was originally thought to be part of the V-type sodium ATP synthase
Product of a dubious gene prediction. No homolog. May not code for a protein
In contrast to PubMed:10687864 and PubMed:11963654, PubMed:17418841 found that triiodothyronine (T3) did not induce expression in the embryo
It is uncertain whether Met-1, Met-3, Met-8 or Met-23 is the initiator
Lacks the conserved Glu residue in position 503 essential for carbopeptidase activity. The mature form lacks catalytic activity towards synthetic peptide substrates
Contains ten transmembrane regions, not eight as predicted
Was originally thought (PubMed:3011793) to be a high affinity ribose transport protein, but further analysis (PubMed:15060078) shows that it is a D-ribose pyranase
Encoded in an intron of the gene DPH1/OVCA1 (same strand)
In plants, methylation steps 2, 3 and 4 of wybutosine biosynthesis are probably processed by the this multifunctional enzyme, while in other eukaryotes, these steps are mediated by 3 different proteins
Lacks the conserved His residues required for metal binding. Its function must therefore be different from the metal-dependent roles proposed for other family members
It is not clear if Met-1 or Met-10 is the start codon
Lacks the signal peptide, which is one of the conserved features of the laccases
This gene differs from CFC1 by only one residue at position 78:R -> W. R78W is also thought to be a CFC1 polymorphism
Was reported as a homodimer (PubMed:11809823). However, 3D structure data show that it forms a monomer (By similarity)
Although it was initially thought to be a methyltransferase of the menaquinone pathway, PubMed:13678585 showed that it has no SAM-dependent methyltransferase activity and is not involved in the menaquinone pathway
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 403 in the dsPTPase catalytic loop, suggesting that it has no phosphatase activity
Could be the product of a pseudogene. Highly similar to the N-terminus of NCOR1, but may encode a non-functional truncated protein
It is uncertain whether Met-1 or Met-45 is the initiator. Initiation at Met-45 is supported by CAGE data but there is peptide data to support translation initiation at Met-1
In spite of its similarity to other phosphatidylinositol kinases, lacks intrinsic lipid kinase activity
An article reported a lack of interaction with LPA2; however, this paper was later retracted
The gene has been independently discovered by another group, who referred to it as aceA, causing confusion with the aceA gene which encodes a undecaprenyl-phosphate glucose phosphotransferase
Ser-137 is present instead of the conserved His which is expected to be zinc-binding residue. There is therefore some uncertainty concerning the enzymatic activity of this protein
The conserved 'Asp-461' active site is replaced by a Gly residue
Although it belongs to the enolase family, Leu-332 is present instead of the conserved Glu which is expected to be an active site residue
Could be the product of a pseudogene. It corresponds to positions 609 to 720 of the complete orthologous and probably active protein in R.felis (RF_0890)
Was originally thought to be lin-10
Reported as CYP749A22 in the publication but submitted as CYP749A20
There is a confusion with this peptide name. In the original refence Chen et al., 2006, authors attribute this sequence to Phylloseptin-11. This sequence is erroneously reproduced as 'Phylloseptin-9' in Amiche et al. 2008, in the nucleotide entry, and in the antimicrobial peptide database
Was originally thought to be the catalytic subunit of phosphoribosylaminoimidazole carboxylase, with ATPase subunit PurK
Was originally thought to be ribosomal protein L20
This fragmental protein is 100% identical to atrolysin-B (AC Q90391) and may be the same protein
In contrast to the related histone demethylases JHDM1D and PHF8, the conserved active His in position 321 is replaced by a Tyr. However, the presence of a Tyr residue neither affects binding to the catalytic iron nor abolishes demethylase activity (PubMed:21167174)
Could be the product of a pseudogene. This protein seems to be a truncated duplicated copy of csd/HI_1295. It is encoded at the border of a duplicated DNA segment and is therefore probably non-functional
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-6; H2BK6su = sumoylated Lys-6; H2BK7ac = acetylated Lys-7; H2BK7su = sumoylated Lys-7; H2BS10ph = phosphorylated Ser-10; H2BK11ac = acetylated Lys-11; H2BK123ub1 = monoubiquitinated Lys-120
PubMed:12823556 conflicts between the peptide sequence obtained by Edman degradation and that obtained from the cDNA sequence may be due to contamination of the peptide sample with hemocyanin D
Presents a truncated kinase-interacting sequence (KIS)
This enzyme was originally referred to as 'lactate oxidase' but this acetate producing enzyme is now referred to as 'lactate monooxygenase' (LMO), and 'lactate oxidase' (LOX) refers to a related flavoenzyme that converts lactate and molecular oxygen to pyruvate and hydrogen peroxide
Was originally thought to originate from B.subtilis
This is not the ortholog of rat CEACAM3
The N-terminus contains a putative primase-like domain; however the absence of the zinc binding domain and other motifs important for catalysis suggests that mtDNA-helicase lacks primase activity
There are multiple pseudogenes of this gene dispersed through the genome
The partially purified protein from strain CPN50 is approximately 70 kDa smaller than the sequence indicated here
While belonging to the class-I pyridoxal-phosphate-dependent aminotransferase family, it lacks a number of residues which are necessary for activity thus suggesting that it lacks enzymatic activity
Most tissues also express read-through transcripts from this gene into the upstream gene (Jmjd7), some of which may encode fusion proteins
Because analogs resulting of mutagenesis of Hyp-49, Asn-50, Leu-57 and Asp-59 give very low yields upon folding, the results of mutagenesis on these residues should be interpreted with caution
Formerly referred to as a v-SNARE
Was originally thought to be a protease that processes pro-LasA
The region that interacts with CEP43 is conflicting: According to a report, interacts via N-terminus (PubMed:28428259). According to another report, interacts via C-terminus (PubMed:28659385)
It is uncertain whether sirQ is an active short chain dehydrogenase since it lacks the conserved active sites
Interacting region of CEP19 is conflicting: According to a report, interacts via N-terminus (PubMed:28428259). According to another report, interacts via C-terminus (PubMed:28659385)
Was initially believed to be a subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (complex I)
The protein-lysine deacetylase activity using CoA as substrate is unclear as this protein belongs to a family of serine hydrolases, and that the reaction shown in the publication is not hydrolyzing H(2)O (By similarity). Additional experiments are therefore required to confirm this activity in vivo (By similarity)
Was originally thought to be involved in both the uptake and efflux of glutarate, thereby acting as a bidirectional organic anion:dicarboxylate exchanger (PubMed:15037815). However, another study did not show any significant uptake of glutarate by SLC22A11/OAT4 (PubMed:17229912). Although initial results showed that SLC22A11/OAT4 drove DHEA-S and E1S uptake in a Na(+)-independent manner (PubMed:10660625), further studies demonstrated that both the uptake of DHEA-S and E1S by SLC22A11/OAT4 was partly Na(+)-dependent (about 50%) (PubMed:18501590, PubMed:10660625). The mechanism of SLC22A11/OAT4-mediated transport of E1S is unclear. Most studies have demonstrated a translocation of E1S through the plasma membrane into the cytosol, which would highlight a role of SLC22A11/OAT4 in placental and renal absorption (PubMed:10660625, PubMed:15037815, PubMed:17229912, PubMed:18501590, PubMed:26277985). Instead, SLC22A11/OAT4 was later proposed to mediate both the insertion into and the extraction from the plasma membrane of E1S without being translocated into the cytosol (PubMed:28027879)
Contrary to other SET-domain containing methyltransferases, set-26 does not have the residues usually involved in cofactor binding: instead of the highly conserved XGXG, Y and NH motifs, set-26 displays AVEA (Ala-948-Ala-951), V (Val-967) and F (Phe-1063) and RR (Arg-1024-Arg-1025) motifs (PubMed:29714684). However, histone methyltransferase activity has been detected in vitro (PubMed:24685137)
Oxidation of Cys-43 to form cysteic acid is most probably an artifact generated during sample preparation
Could be the product of a pseudogene. A frameshift introducing a premature stop codon in exon 1 most probably results in the inactivation of that transcribed gene in human. However, alternative splicing may allow the production of a truncated but possibly functional protein containing 5 transmembrane domains which is shown here
Lacks the conserved threonine residue in position 60, which is part of the carbamoylphosphate binding site; it is replaced by a glycine residue
It is uncertain whether Met-1 or Met-58 is the initiator
According to a report, not degraded in response to autophagy (PubMed:20495340). However, publications have shown that KEAP1 is degraded via a proteasomal-independent process during selective autophagy (PubMed:22872865, PubMed:24011591)
The mechanism of inactivation of the BCR(KEAP1) complex by covalent modifications of reactive cysteines is unclear. Covalent modifications were initially thought to disrupt interaction between KEAP1 and NFE2L2/NRF2 (PubMed:12193649). Recent publications suggest that cysteine modifications disrupt the interaction between KEAP1 and CUL3 without affecting the interaction between KEAP1 and NFE2L2/NRF2 (By similarity)
Two forms of this protein have been cloned (NAS5-1 and NAS5-2) which seem to be identical with the exception of a 15 amino acids deletion
Enzyme activity is uncertain. Was shown to have endochitinase activity (in vitro) (PubMed:10890535). Lacks the conserved Glu residue that is essential for catalytic activity, suggesting it lacks enzyme activity
There are likely two genes coding for two slightly different proteins, NDK3 and NDK4. The characterization was made on a thylakoid lumen preparation containing probably both proteins
N-terminal sequence obtained in PubMed:8620040 was later shown to be incomplete at the N-terminus
It is uncertain whether Met-1 or Met-49 is the initiator
The two different versions of rusticyanins are most probably due to strain variations
The modification on Lys-34 was initially thought to be a spermidine residue
In strain CT18 it seems to be a pseudogene. It is interrupted by a frameshift in position 353. The sequence has been verified by the authors and is believed to be correct
Transposon Ty1-A (YARCTy1-1) contains a frameshift at position 610, which disrupts the ORF coding for protein TY1B
The protein in cv. Landsberg erecta (AC P0DM58) and cv. Columbia only differ by one residue in position 705 (a Pro and Arg residue, respectively); this variation leading to inactivate the protein in cv. Columbia
The interacting region with TESC is conflicting: In human, it has been reported that SLC9A1 interacts with TESC via the juxtamembrane region of the cytoplasmic C-terminal domain, including residues 507-549. However, another publication has reported interaction with TESC via residues 637-820, the region of the cytoplasmic C-terminus more distal to the membrane
To date, the intracellular localization of ABCB6 is a matter of debate, with conflicting reports suggesting mitochondrial (PubMed:10837493, PubMed:17006453, PubMed:17661442) or endolysosomal localization (PubMed:22655043, PubMed:25627919, PubMed:29940187, PubMed:31053883), therefore questioning the requirement of ABCB6 in the mitochondrial import of porphyrins
Lacks the conserved Glu residue in position 391 essential for carbopeptidase activity. The mature form lacks catalytic activity towards synthetic peptide substrates
In the genome of Neisseria meningitidis (serogroup B), the gene for this protein is present (NMB0066). It was introduced as part of a construct built to neutralize the virulence of the bacterium
Was originally thought to be a 5-methylaminomethyl-2-methyltransferase involved in tRNA modification
It is probable that CSTX-15 A and B chains originate from the same gene. Both chains may be separated by some amino acids
May be a cleavage product of CSTX-13
A paper reported a role in assisting chlorophyll a binding protein psbC assembly within photosystem II (PSII); however, this paper was later retracted. An article reported an interaction with LPA3; however, this paper was later retracted
Was originally thought to be a P2Y receptor
PubMed:11139336 experiments have been carried out partly in chicken and partly in human
Found in the 3'-UTR of AAK1 but there is evidence for the existence of the protein from a number of proteomics studies
Was originally thought to be a glucose 1-phosphate uridylyltransferase
Methylammonium (MeA) has been widely used to measure ammonium transport activity because the radioactive tracer [14C]MeA is commercially available. However, MeA is a poor substrate analog for AmtB, not well suited to elucidate the mechanistic details of AmtB activity
Was initially reported to have histone methyltransferase activity and methylate 'Lys-36' of histone H3 (H3K36me) (PubMed:21307598). However, this conclusion was based on mass spectrometry data wherin mass shifts were inconsistent with a bona fide methylation event and the histone methyltransferase activity could not be confirmed (By similarity)
Was initially thought to regulate chromosome segregation and mitotic spindle assembly (PubMed:16302001). However, it was later shown that its absence neither affect mitosis nor centriole duplication
The sequence was deposited erroneously as PPO1 (PubMed:12185078)
The 'mutant' Ts1-G was isolated from the venom before the last step maturation (i.e. amidation) thanks to a right purification technique (PubMed:24560880). It is indicated here as a mutant, since it does not correspond to the mature toxin
Missing the N-terminal trans-membrane domains found in paralogs
Was reported to be a protein deacetylase that removes acetyl groups on specific lysine residues in target proteins (PubMed:26716769). However, later experiments demonstrate that the protein ortholog in E.coli does not have any protein deacetylase activity; the discrepancy observed seems to be due to contaminants having proteolytic activity (PubMed:29939131)
High-capacity urate transporter that was first described as a fructose and glucose transporter. Also described in the literature as high-affinity and low-capacity glucose and fructose transporter (By similarity). However, another group could not confirm transporter activity for glucose or fructose (By similarity)
Was originally (PubMed:3267207) thought to originate from human but was later shown (PubMed:10072763) to be derived from rat
It is uncertain whether Met-1 or Met-87 is the initiator methionine
Lacks the conserved glutamate residue in position 465 that binds magnesium; it is replaced by a serine residue
There are two genes for DctA in NGR234; one on the sym plasmid, the other on the chromosome
Was originally thought to be an FMN-dependent pyridoxine 5'-phosphate oxidase
FMN and PLP are seen in the crystal structures published in PubMed:16239726, however, the enzyme does not bind these compounds in vitro, and the complexes obtained in the crystal structures may be the result of weak FMN/PLP binding that is stabilized by the crystal lattice
Although it is unknown whether it is a serine/threonine or a tyrosine protein kinase, it is strongly related to serine/threonine-protein kinase family
Could be the product of a pseudogene. According to PubMed:9760194, it is a processed pseudogene
An article reported induction by MKK1, MKK2 and MKK3 in response to drought and salt stresses; however, this paper was later retracted
The sequence shown here has been extracted from PDB entry 1KTV
3' to 5' exonuclease activity reported in PubMed:15576351 is probably artifactual, due to the presence of other nucleases in the preparation
Was previously considered as a subunit of the NADH dehydrogenase of the mitochondrial respiratory chain complex I. Due to lack of 38 of the other 40 subunits that are present in that complex in mammals, this attribution is unlikely (PubMed:1518044)
Could be inactive due to a defective ATP-binding site
Contains a Gly residue instead of a conserved Cys residue at position 120 in the dsPTPase catalytic loop which renders it catalytically inactive as a phosphatase. The binding pocket is however sufficiently preserved to bind phosphorylated substrates, and may protect them from phosphatases
Was originally thought to belong to the ABC transporter family (PubMed:18299247). Lacks the conserved ABC domain, which is one of the features of the ABC transporter family
eRF3 antibodies used in PubMed:19417104 do not differentiate between GSPT1/ERF3A and GSPT2/ERF3B
The structures described in PubMed:16403515 and PubMed:25295175 corresponds to an inactive form, and displays a conformation that alters the position and orientation of the residues that are expected to bind the substrate and the catalytic metal ions
This strain is avirulent; testing for virulence is done in strain D39
Was originally classified as an esterase D due to its apparent insensitivity to serine hydrolase inhibitors
This protein was first identified as a Trichophyton rubrum transporter and called TruMDR2, but it was further realized that the isolate used for the identification was a Trichophyton interdigitale isolate
Has a deletion of about 20 residues in between positions 79 and 80 when compared with orthologs
Could be the product of a pseudogene. Lacks 2 of the 4 disulfide bonds, which are conserved features of the family
Although it belongs to the S54 peptidase family, the active site Ser-235 is replaced by an alanine residue, suggesting that it has no serine peptidase activity
A palmitoylation site was proposed at Cys-104, but it was later shown that this cysteine is engaged in a disulfide bond
The polyclonal antibody used in PubMed:9820802 and PubMed:9874241 and initially thought to detect SLC25A4/ANT1 in interactions with Ppif/CyP-D is rather detecting SLC25A3
Was initially shown to have low deadenylase activity that was lost when the metal-binding Glu was mutated (By similarity). Later studies showed that the purified protein lacked deadenylase activity (PubMed:29860338, PubMed:30389976). Was subsequently shown to act as a phosphatase (PubMed:31147539)
In contrast to other members of the family, this protein is much shorter and lacks the VWFA domain. Defined as a pseudogene by HGNC. PubMed:10095065 reports that it is expressed and glycosylated in mammalian cells
Positions of N-glycosylation sites are unclear (PubMed:22552861). No N-glycosylation site is detected by prediction tools
Was initially identified in the synaptonemal complex (PubMed:1363622). Characterization data from human and mouse indicate the protein is in the endoplasmic reticulum, which agrees with its biological function and the predicted signal sequence
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 378 in the dsPTPase catalytic loop and does not have phosphatase activity
Although clearly a member of the adenine deaminase type 2 family, it lacks the conserved Glu active site residue in position 212 characteristic for this family. Its exact enzymatic activity is therefore unsure
Although it belongs to the glycosyl hydrolase 22 family, Gly-51 is present instead of the conserved Glu which is an active site residue. It is therefore expected that this protein lacks hydrolase activity
Could be inactive as a ligase. The potential active site Cys residue in position 88 is replaced by a Ser
Asn-306 is present instead of the conserved Asp which is expected to be an active site residue. Low level autophosphorylation activity has been reported in PubMed:12054681, while other authors describe this as an inactive kinase
Could be the product of a pseudogene. A single point mutation in the signal peptide region of the PPY2 gene introduces a premature stop codon, reducing the predicated size of the precursor to only 21 amino acids
Was initially thought to mediate manganese transport (PubMed:24392018). However, it was later shown to specifically bind moderately hydrophobic transmembrane with short hydrophilic lumenal domains that misinsert into the endoplasmic reticulum (PubMed:32973005)
Was shown to interact with VDR and with acetylated histones via its Bromo domain, but this work has later been retracted
Called Irx6 by PubMed:10704856
Could be the product of a pseudogene unlikely to encode a functional protein. In strain S288c, this gene has a frameshift compared to the other IMD alleles, producing 2 ORFs YAR073W and YAR075W. Additionally, YAR073W is not transcribed and lacks the biological functions of the other IMD genes even when artificially expressed. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
Gln-136 is present instead of the conserved Asp which is expected to be a proton acceptor in the active site
The embryo lethal disruption phenotype (PubMed:16169895) could be confirmed (PubMed:19605416)
Was originally shown to be phosphorylated at Ser-87 by PKB, protecting the protein from ubiquitination and proteasomal degradation (PubMed:14645242). However, this work was later retracted (PubMed:27825084)
Compared to other members of the family, it is shorter and lacks the WD repeats at the N-terminus
Has been reported to phosphorylate EF-Tu in vitro (on 'Thr-383') (PubMed:19150849). According to another report, does not phosphorylate EF-Tu (PubMed:19622872)
Could be the product of a pseudogene. According to PubMed:8910290, PubMed:8910373, PubMed:9013614, the human NPY6R gene is an expressed pseudogene containing a premature stop codon and encoding a non-functional truncated protein missing the last transmembrane domain. A single base pair deletion relative to the mouse ortholog, results in a truncated protein lacking the seventh transmembrane domain
Although it belongs to the XPG/RAD2 endonuclease family, only one of the seven Asp residues involved in Mg(2+) binding are conserved suggesting that it has no nuclease activity
Lacks the chitin binding type-1 domain wich is one of the conserved features of the chitinase class I and class IV subfamilies
Was originally thought to be located in the peroxisome (By similarity). However, was later shown to be cytosolic (PubMed:11725955)
Was initially thought to be a phenylacrylic acid decarboxylase (PubMed:11693915, PubMed:17766451). However, direct assays could not confirm decarboxylase activity (PubMed:12903944, PubMed:25852989). It has been shown that this enzyme synthesizes the essential cofactor for the associated decarboxylase FDC1. It is therefore thought that decarboxylation defects due to the disruption of this gene were in fact a secondary effect of inactive FDC1 decarboxylase missing its essential cofactor (PubMed:25647642)
Tyr-8 is present instead of the conserved Asp which is expected to be a metal-binding site residue
Lacks the CX6CC and the CKS-17 domains
In contrast to other aldo/keto reductase 2 proteins, it lacks the N-terminal half which contains the active site. It is therefore unlikely that it acts as a functional oxydoreductase
Although it belongs to the glycosyl hydrolase 1 family, Asp-200 is present instead of the conserved Glu which is an active site residue. It is therefore expected that this protein lacks glycosidase activity
Activity as ligand to G-protein coupled receptor npr-1 might depend on a neomorphic gain-of-function sensitivity of the receptor npr-1 associated with the Bristol N2 strains
Was originally thought to be a superoxide dismutase
Although it belongs to peptidase S1 family, the residues corresponding to the serine protease catalytic triad (Asp-His-Ser) are not conserved suggesting that SPCLIP1 lacks catalytic activity
This protein was previously referred to as T2R2 but is now considered to be an ortholog of rat TAS2R23
The article by Sureka et al was retracted by the editors after publication. Concerns were raised regarding the results presented in multiple figure panels. The raw data or replacement panels that were available did not satisfactorily address all the issues, thus questioning the integrity of the data
While mouse FABP5 is found only in the monomeric form, human FABP5 can exist as a monomer as well as a domain-swapped dimer
Nakanishi et al (PubMed:11243884) shows that the transport process is electrogenic, contrary to the conclusions of Hamdani et al (PMID:11742981) who finds that the transport is electroneutral with a Na(+):L-glutamine stoichiometry of 1:1 (PubMed:11243884). Hamdani et al (PMID:11742981) shows that this electrogenic transport describes by Nakanishi et al. would correspond to large uncoupled fluxes of protons (PubMed:11243884)
Identified as having similarity to the core DENN family and referred to as DENN6B. Prediction methods do not indicate a DENN domain for this sequence and, the exact role of the DENN or this DENN-like domain in GEF activity needs to be clarified
Represents an unconventional myosin. This protein should not be confused with the conventional myosin-6 (MYH6)
Originally predicted to contain a coiled coil domain but generally accepted to contain a stable SAH domain instead
The plasmid pTiTM4 carries two T-regions, the TA and TB region, both of which have a functional iaaM gene, with low homology between them
An article reported the phosphorylation of PbpA by PknB, but this paper was later retracted as some figures were modified prior to publication
The annotated sequence does not include a stop codon, because it is at the end of an incomplete sub-telomeric contig of the genomic sequence. RACE data from PubMed:15591066 suggests an additional 32 residues at the C-terminus, consistent with the SPBCPT2R1.08c (AC Q1RKN3) annotation
According to PubMed:11437245, PKS2 has no polyketide synthase activity
The N-terminus share sequence similarity with the dihydrodipicolinate reductase family. It however lacks the conserved C-terminal part, suggesting it has no dihydrodipicolinate reductase activity
The 21 C-terminal amino acids have been proposed to be expressed from an independent promoter within this gene and called IroK. Overexpression of IroK has been suggested to be responsible for 3-hydroxypropionic acid (3-HP) resistance. However the IroK peptide's existence has not been proven, nor has mutagenesis of HcaR itself rather than overexpression of IroK been ruled out as the cause of 3-HP resistance (PubMed:22161628)
Was reported to form, during DNA replication, a S phase-specific complex that would facilitate methylation of H3 'Lys-9' during replication-coupled chromatin assembly and vould be at least composed of the CAF-1 subunit CHAF1A, MBD1 and SETDB1 (PubMed:15327775). However, this paper has been retracted because some data, results and conclusions are not reliable (PubMed:30849389)
The active site residues characteristic of serine proteases appear to be absent from this protein, which may therefore lack catalytic activity
Although it belongs to the glycosyl hydrolase 18 family, Leu-149 is present instead of the conserved Glu which is an active site residue. Therefore this protein lacks chitinase activity
Was originally thought to have an endonuclease activity
There was previous evidence for interactions with AR, NR3C1 and ESR2. However this paper was retracted as cell-based data was viewed as unreliable
The interacting region with TESC is conflicting: In human, it has been reported that SLC9A1 interacts with TESC via the juxtamembrane region of the cytoplasmic C-terminal domain, including residues 503-545. However, another publication has reported interaction with TESC via residues 633-817, the region of the cytoplasmic C-terminus more distal to the membrane
Was originally (Ref.1) thought to be a ferripyochelin binding protein (gene fbp)
In strain cv. Columbia (AC Q9SLI6), a naturally occurring variation results in the deletion of 35 amino acids in the middle part of the protein. The sequence shown is from strain cv. Landsberg erecta
Was originally thought to be involved in Peronospora parasitica resistance (PubMed:15155873). However, the corresponding article has been retracted (PubMed:17284584)
Was initially wrongly assigned as Galnt8
Although transmembrane domains are strongly predicted, they may rather represent hydrophobic globular domains associated with microtubules
Seems to lack two of the iron-binding residues
Was originally thought to be an alpha-L-fucosidase
The nucleotide sequence (X82595) deposited at the EMBL differs from that shown in PubMed:7559605 with the same accession number
The gene Tgtp1 belongs to a large family of eutherian IFNG-inducible GTPases, called immunity-related p47 GTPases, which comprises a variable amount of paralogs depending upon the species studied. In C57BL/6J mice, there is over 20 genes, whereas humans have only one ortholog. Tgtp1 closest paralog is Tgtp2. Both genes encode identical proteins. At the nucleotide sequence level, their CDSs differ at only 4 positions. Consequently it is almost impossible to assign unambiguously to one gene or the other experimental data published in the literature
Although it shares some weak sequence similarity with the UPF0398 family, it is distinct form other members of the family
Was initially reported to specifically bind 5-hydroxymethylcytosine (5hmC)-containing DNA in stem cells (PubMed:23434322). It was later suggested to act as an endonuclease that specifically cleaves 5hmC-containing DNA (PubMed:29020633). However, recent studies question this activity: no alterations in global 5hmC levels are observed in bone marrow cells from knockout mice (PubMed:31806351)
Contradictory results show that only SV2C is the receptor; in these experiments gangliosides do not improve toxin-coreceptor interaction (PubMed:16545378)
Could be the product of a pseudogene. It is missing about 10 N-terminal amino acids compared to orthologs
PubMed:12189208 experiments have been carried out partly in rat and partly in human
Upon DNA damage, was shown to interact with SIRT6 resulting in its deacetylation. However, this study was later retracted
The protein has been shown to be 126 residues longer (PubMed:17145760), but in (PubMed:19118359) no evidence of this longer protein was seen
An article reported that transcripts can move in the phloem from leaves to shoot apex to induce flowering; however, this paper was later retracted
A stretch of the chloroplast genome is duplicated within chromosomes 4 and 8 resulting in the duplication of the gene. The expression of these duplicated genes (Os04g0236400 and Os08g0455300) has not been demonstrated
Was originally proposed to be a calcium channel facilitator (By similarity). However, a more recent study shows that this protein regulates membrane phospholipid homeostasis (By similarity). Therefore, any effects on calcium flux are most likely a secondary consequence of defects in membrane composition or fluidity (By similarity)
Lacks the conserved cysteine and leucine residues in positions 269 and 270, respectively, which are part of the ornithine binding site; they are replaced by an aspartate and a methionine residue, respectively
Was originally proposed to be fused with MdlA
Based on current literature, utilization of para-aminobenzoic acid (pABA) involving C4-deamination is still unclear, and seems not to occur in bacteria, plants and mammals where only C5 hydroxylation of HHB has been shown, even if human COQ6 is able to support C4-deamination in yeast cells lacking COQ9
It is uncertain whether Met-1 or Met-36 is the initiator
Was originally (Ref.2, PubMed:9757043) thought to originate from mouse
The same name (BpL) has been given to a lectin from Bothrops pirajai (AC P0DL30)
While it is structurally defined as a knottin it lacks the conserved Cys residue in position 79
Could be the product of a pseudogene. Neither O157 strain expresses urease. In both O157 strains this CDS is shorter than in urease producing E.coli strains, due to a premature stop codon. Urease activity can be restored in O157 / Sakai upon complementation with a wild-type ureD
Although DnrQ shows significant similarity to cytochrome P450 family, it lacks the heme-binding sites. The conservation of amino acid sequence is confined primarily to the C-terminal half of the protein
According to PubMed:15938716 binds to the UPR element (UPRE) but not to CRE or the NF-kappa-B site. Preferentially binds DNA with to the consensus sequence 5'-T[GT]ACGT[GA][GT]-3' and has transcriptional activation activity from UPRE. According to PubMed:11956138 and to PubMed:16925989 binds to NF-kappa-B site and has transcriptional activation activity from NF-kappa-B-containing regulatory elements
A palmitoylation site was proposed at Cys-93, but it was later shown that this cysteine is engaged in a disulfide bond
Was reported to be transcribed but not translated (PubMed:11890990). However, it was later shown that it is expressed at protein level (PubMed:19531736)
This is a truncated version of GDP-mannose transporter 2. Strain S288c has a stop codon in position 73, which disrupts the gene coding for this protein and produces two ORFs YER039C-A and YER039C. A contiguous sequence for GDP-mannose transporter 2 can be found in strain Lalvin EC1118 (AC C8Z742)
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-9; H2BK6su = sumoylated Lys-9; H2BS10ph = phosphorylated Ser-13; H2BK11ac = acetylated Lys-17; H2BK123ub1 = monoubiquitinated Lys-134
Was originally (Ref.1) thought to be a malate dehydrogenase or an NADH-dependent acyl-CoA reductase
Was originally thought to be the beta-2 subunit
Could be the product of a pseudogene. The original protein is interrupted by the insertion of the prophage VT2-Sakai between positions 18 and 19
The potential active site Asp residue in position 16 is replaced by a Leu
2 Cys residues are missing that are conventionnally part of disulfide bonds II and III
The active site contains a CRKC motif wich differs from the conserved CGPC motif
Could be the product of a pseudogene. In contrast to other members of the family, it is shorter at the C-terminus and lacks the heme-binding sites
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-6; H2AK7ac = acetylated Lys-10
Was originally assigned to be a glycosyltransferase
Was named ABCB1 by some authors
Previously thought to be the same gene as Tagap1. These are distinct loci that encode proteins with identical C-termini but each with a unique N-terminus
Was initially reported to localize both in cytoplasm and nucleus (PubMed:17979886). However, it was later shown it localizes in mitochondrion (PubMed:23666923). The discrepancy is probably due to the use of a fusion protein with an N-terminal tag in the initial report (PubMed:17979886)
Stoichiometry of the protein is unclear. According to a report, it forms a homodimer (PubMed:20406883). According to another publication, it is mainly monomeric (PubMed:24838397)
The sequence given here is inactive
It is uncertain whether Met-1, Met-6 or Met-70 is the initiator
PubMed:2798425 reported that there are two potential EF-hand regions, but the evidence seems weak
It is unclear whether it requires ATP: according to PubMed:8552679 and PubMed:10216955, it does not require ATP, while according to PubMed:15196029, PubMed:15554978 and PubMed:17259309, it requires ATP
The thiosulfate dehydrogenase [quinone] subunits have originally been described as components of the aa3-type terminal oxidase
The peroxidase activity using glutathione as a reducing power is controversial (PubMed:19690965, PubMed:29124185). In one study, GPX5 lacks glutathione peroxidase activity (PubMed:19690965). However, in another study, GPX5 shows glutathione peroxidase activity when cells are grown in selenium rich medium (PubMed:29124185)
It is uncertain whether Met-1 is the initiator. An alternative upstream Met is found in primates, but not in other mammalians
Could be the product of a pseudogene. It is N- and C-terminally truncated compared to othologs
Lacks a counterpart to the N-terminal domain of the TyrR protein of E.coli
Could be the product of a pseudogene. A point deletion in exon 8, which introduces a frame shift leading to a premature stop codon. Thus, a protein expressed by this gene would be soluble rather than expressed on the cell surface. This single-nucleotide deletion has been acquired after human-chimpanzee speciation, about five million years ago
Lacks phosphorylation sites present in ortholog HMGA proteins
Has been shown to be mono-ADP-ribosylated at Glu-657 and Glu-705 by PARP14 which prevents phosphorylation at Tyr-701 (PubMed:27796300). However, the role of ADP-ribosylation in the prevention of phosphorylation has been called into question (PubMed:29858569). It has been suggested that the lack of phosphorylation may be due to sumoylation of Lys-703 (PubMed:29858569)
This protein is distinct from Tes/Testin which is a LIM domain protein
Was originally thought to be proteolytically processed intracellularly
Was originally (PubMed:16557337) assigned as a member of the E3 ubiquitin-protein ligase ATL subfamily but does not display E3 catalytic activity (PubMed:16339806)
The name 'Consomatin Ma1' has also been given to a peptide from Conus maioensis. As a consequence, we have suggested to rename the peptide from Conus maioensis 'Consomatin Mao1'
Was originally thought to be rffE, the UDP-N-acetylglucosamine epimerase
It was initially shown that the substrate specificities of the enzyme natively expressed in Aspergillus niger and the recombinant enzyme expressed in E.coli were different (PubMed:17061133), and it was hypothesized that the difference may be due to a misfolding or a post-translational modification (PubMed:21210990). However, both papers were corrected (PubMed:23455586) or retracted (PubMed:23870008), because it was shown that the 2 enzymes analyzed were different in terms of their primary structure (Ref.7)
PubMed:2480957 sequence seems incorrectly to be attributed to a mouse sequence while it really seems to correspond to the rat sequence
Was originally thought to be a nuclear DNA-binding protein
Was originally (PubMed:11346655) thought to belong to the ABC transporter family. Lacks the conserved ABC domain, which is one of the features of the ABC transporter family
Lacks four Cys residues in the RING-type zinc finger domain 1 and two Cys residues in the RING-type zinc finger domain 2 that are conserved features of the family
The translation and the expression of this protein may be maintained under stress conditions thanks to the presence of the upstream ORF in transcripts
Was originally thought to function as an oligopeptidase (NUDEL-oligopeptidase or endooligopeptidase A) which could regulate peptide levels relevant to brain function
Was originally identified as the 11.3 kDa PinO protein, a calcium-binding protein synthesized in the absence of isoleucine in relA stains, which may be required for the initiation of chromosome replication (PubMed:1925011, PubMed:1938934). But GspB is predicted to be 15.9 kDa and has isoleucine residues, and there is no evidence that gspB encodes the PinO peptide or that it binds calcium
Appears to have histone acetyltransferase (HAT) activity, specifically towards histones H2B and H4 in vitro (PubMed:10821277). However, it is not clear if this activity is genuine or caused by contamination with other histone acetyltransferases in the assay
The pyrrolidone carboxylic acid reported in PubMed:11927537 probably formed artifactually from Glu-113 during the extraction procedure in 70% formic acid. In PubMed:15522881, the protein was found to have unblocked Glu at the N-terminus
Was originally thought to be the site of the radC102 mutation, but it was subsequently shown that radC102 is an allele of RecG
Was originally described as an NAD(+)-dependent alcohol dehydrogenase (ADH) (PubMed:9660191). However, BLAST alignments indicate that this fragment represents the N-terminal sequence of an aldehyde dehydrogenase. The protein characterized in this article does not correspond to the sequenced fragment but to the alcohol dehydrogenase as shown in the UniProtKB AC Q8GIX7 entry
It is uncertain whether Met-1 or Met-46 is the initiator
Was originally thought to be interferon beta-2
Shows similarity to potassium channel (Kv) toxins, but does not possess the 'functional dyad' element required for binding to Kv channels. As a consequence, it may not be a channel blocker
Could be the product of a pseudogene. The gene coding for this protein is interrupted by a IS1 element between amino acids 114 and 115. The N-terminus is shorter than orthologs
Does not seem to have protease activity as it lacks the conserved zinc-binding sites and the active site
As the DNA coding for this protein is not found in the complete genome of T.maritima. It could have originated from another bacterial species
Martineau M. et al. show that may function as a L-glutamate/H(+) antiporter (By similarity). However, according to Eriksen J. et al., H(+) is an allosteric activator (PubMed:27133463)
Despite its name, does not contain a real coiled coil domain region: predicted coiled coil regions are the result of the Glu-rich region
Unlike P.berghei CDPK1, appears to be involved in the asexual blood stage and in male gamete exflagellation prior host erythrocyte membrane rupture
It is uncertain whether Met-1 or Met-34 is the initiator
Antifungal activity was tested using a fraction containing a number of different peptides. It is not clear which peptide actually has antifungal activity
Maps to a tandemly repeated region on chromosome Y. Between 50 and 200 copies per Y chromosome are reported
The sequence shown here has been extracted from PDB entry 1DFE
Could be the product of a pseudogene. Lacks the signal peptide, which is a conserved feature of the family
Lacks the conserved glutamate residue in position 506 that binds magnesium; it is replaced by a serine residue
It is uncertain whether Met-1 or Met-95 is the initiator
Although related to the XPF family, the nuclease active site is not conserved
Lacks the Cys residue in position 255 that is replaced by a Gly residue, resulting of a loss a disulfide bond. This may contribute to a probable lower procoagulant activity
Could be the product of a pseudogene. Shares high sequence similarity with the N-terminus of the CCDC144 family. Compared to other members of the family, it is however much shorter and lacks the C-terminal part
Although related to peptidase S1 family, lacks the conserved active Ser residue in position 310 which is replaced by a Thr
Was originally called crtE
Strain ATCC 23975 was originally classified as being from Pseudomonas aeruginosa
According to a report, the spliced A3GALT2 mRNA is not detected in human tissues (PubMed:18630988). The functional activity of human A3GALT2 tested by expressing a chimeric protein containing the catalytic domain of human A3GALT2 is unable to synthesize isogloboside 3 (iGb3). Futhermore mutagenesis experiments in rat, show that the mutant 'Asn-253' of human A3GALT2 completely eliminates alpha-1,3-galactosyltransferase activity (PubMed:18630988)
Product of a dubious CDS prediction. Probable non-coding RNA. At least 6 alternative mRNA transcripts exist, with consensus splice donor and acceptor sites, but no coding potential nor murine ortholog. This protein sequence corresponds to the so-called isoforms C21orf24-6 and C21orf24-7
Although suggested, the interaction with GNBP1 has not been experimentally demonstrated
Could be the product of a pseudogene. This is the C-terminal part of an allantoate permease subfamily member protein. Strain S288c has a stop codon in position 170, which disrupts the gene coding for this protein and produces two ORFs YOL163W and YOL162W
Was originally (Ref.1) thought to be a zeatin O-glucosyltransferases and was named ZOG2
A mitochondrially-encoded gene whose putative product is 100% identical to this plastid-encoded gene is the result of gene transfer. It is not known if the mitochondrial gene is transcribed, B.vulgaris mitochondrial DNA encodes a different rps7 that is more mitochondrial-like
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC A6MMI6
The use of uridine 5'-monophosphate (UMP) as a counter-anion is disputed and needs further investigation
Was originally (PubMed:14506263) thought to be an inhibitor of type 1 phosphatases using in vitro experiments, but further in vivo experiments (PubMed:18172024) showed that it was rather an activator of these phosphatases
Was originally (PubMed:8327475, PubMed:8924413) thought to be an ultraviolet-sensitive opsin present in short single cones
Was originally thought to be ARF2
Lacks the conserved active site residues. Probably catalytically inactive
Could be the product of a pseudogene. It is encoded in the reverse strand of the region coding for TP_0409.1, a potential gene which belongs to the UPF0092 family
It has been reported that lim-4 is expressed in the SIA interneurons (PubMed:10421632). However, a subsequent report suggests that this was a mis-identification, instead indicating that the correct cell type is the SMB sensory/inter/motor neuron (PubMed:26305787)
The residues that bind the substrate in other aspartate aminotransferases are not conserved
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-8; H2BK6su = sumoylated Lys-8; H2BK7ac = acetylated Lys-9; H2BK7su = sumoylated Lys-9; H2BS10ph = phosphorylated Ser-12; H2BK11ac = acetylated Lys-13; H2BK16ac = acetylated Lys-24; H2BK16su = sumoylated Lys-24; H2BK17su = sumoylated Lys-25; H2BK123ub1 = monoubiquitinated Lys-131
It is not obvious if the molybdenum-pterin domain is functional; the conserved cysteine (position 339) is replaced by an isoleucine
Was originaly thought to be involved in active uptake of glycerol driven by electrogenic proton symport (PubMed:10931309), but has later been shown to be an acyltransferase and that effects on glycerol transport may be indirect (PubMed:15381122)
The reading frame from which this protein is translated has no Met initiation codon near to the 5'-end. However, it is not a pseudogene. It has been shown (PubMed:14761959) that at least 72 residues upstream of the first in-frame start codon (Met-151) are required for function and proper subcellular location. May be translated by means of alternative initiation codon usage, programmed translational frame shifting, or mRNA editing
Was originally thought to be involved in transcription
Lacks the conserved cysteine (here Ser-77), present in the redox-active center, which is one of the conserved features of the thioredoxin family
Could be the product of a pseudogene. As no transcript has been detected so far, this sequence could come from an incomplete and non functional gene
Was originally (PubMed:8793298) named RasGEFA, as it was the second RasGEF, after aimless, to be identified there. When aimless, aleA, was renamed gefA to make the nomenclature consistent and systematic, RasGEFA was renamed gefR
There is no equivalent of this gene in strain K12 / W3110
This peptide is cyclic. The start position was chosen by similarity to chassatide C4 for which the DNA sequence is known
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC Q14F95
Was originally (PubMed:8574415, PubMed:8969502) thought to be a longer ORF that encodes what is now known to be pxpB (kipI) and pxpC (kipA)
Experiments in human confirm the importance of JAGN1 in neutrophil function with some differences. Defects in JAGN1 cause neutropenia in human, while it is not the case in mice lacking Jagn1. Mutant mice show defects in neutrophil migration and increased susceptibility to fungal infections due to defective killing capacity of neutrophil granulocytes
Compared to other bacterial RnfG, it has a divergent N-terminal domain
According to PubMed:12370122, it has no hydrolytic activity
A stretch of the chloroplast genome is duplicated within chromosome 8 resulting in the duplication of the gene. The expression of this duplicated gene has not been demonstrated
Fused to a domain related to the dihydrofolate reductase family in its N-terminus. It is however unknown whether it contains such enzymatic activity
PubMed:9159522 mis-identifies Trp-33 as residue 32
In vitro (PubMed:19706448) and in vivo (PubMed:23016873) results on the importance of the identity of residue 148 for cleavage by RseP differ
Lacks one of the cysteines to make the disulfide bridge in isoform 1. It is replaced by Val-233
Activation by specific Wnt family members may depend on the cells used for the experiment. Contradictory results have been reported for activation by WNT7B in human and mouse
Could be the product of a pseudogene. In primates the genes coding for the enzymes for the degradation of uric acid were inactivated and converted to pseudogenes (PubMed:16462750)
Could be the product of a pseudogene. The original sequence is truncated by an IS5 element which is inserted between position 123 and 124
The nucleotide sequence submitted as Y11769 is a genomic DNA sequence and not a mRNA sequence, as mentioned in the submission
Not present in cv. Columbia. The sequence shown is from strain cv. Ms-0
Was originally thought to be a deferrochelatase, which promotes iron extraction from exogenous heme source, preserving the tetrapyrrol ring intact (PubMed:19564607). However, Dailey et al. were unable to reproduce the in vitro dechelation reaction (PubMed:22068980). They suggest that YfeX is a typical dye-decolorizing peroxidase and not a dechelatase, and that the protoporphyrin reported by Letoffe et al. to accumulate when YfeX is overexpressed likely arises from the intracellular oxidation of endogenously synthesized protoporphyrinogen and not from dechelation of exogenously supplied heme (PubMed:22068980)
Probably not an ascorbate peroxidase (APx), as it lacks the heme-binding site, the proton acceptor and the transition state stabilizer, which are conserved features of the ascorbate peroxidase
In PubMed:413571 it is said that 50% of the peptides have N-methyl-Phe and 50% begin with Thr-9. N-terminal methylation produces preview during Edman degradation, which makes this appear to happen when the peptide is completely N-terminal methylated
It is unclear whether the protein is conserved in human: no ortholog has been identified yet although antibodies against Fcor stain human tissues
Was originally (PubMed:15252046) thought to have ceramide kinase activity. Such activity is however unlikely in vivo
Was shown to be phosphorylated and activated by CSNK1D/CK1 in vitro but probably not in vivo
Was originally thought to be a nuclear protein and mutations were shown to prevent full derepression of the SUC2 (invertase) gene
Could be the product of a pseudogene. This gene is annotated as a frameshift-version of tuf in the genome; it would need 2 frameshifts to produce full-length protein
The reaction mechanism is subject to discussion. Some work suggest MICAL enzymes directly oxidize actin methionine residues to produce methionine-(R)-S-oxide. Other publications suggest that the enzyme functions as a NADPH oxidase producing H(2)O(2) (EC 1.6.3.1) and that it is the produced H(2)O(2) that is responsible for the methionine-(R)-S-oxide production
The predicted start codon is CTG
Could be the product of a pseudogene, it is missing the C-terminus compared to orthologs. An example of a full-length E.coli protein is (AC J9RX10)
The sequence shown differs from that proposed in Ref.1 due to the presence of a constitutive single-nucleotide exon
Was named previously At3g26090
Isoform 1 shares some similarity with tyrosine phosphatase proteins but it has probably no phosphatase activity
Upon DNA damage, was reported to promote DNA end resection via deacetylation of RBBP8. However, this study was later retracted
The binding-mode of MDL-801 selective activator is subject to discussion (PubMed:30374165, PubMed:33649599, PubMed:33649600). According to a group, MDL-801 binds around the acyl channel exit and acts as an allosteric activator (PubMed:30374165, PubMed:33649600). According to another group, the binding mode of MDL-801 remains undefined (PubMed:33649599)
This peptide is cyclic. The start position was chosen by similarity to cyclotide cter-B for which the DNA sequence is known
Was originally (PubMed:2350438) thought to be a serine protease. However, PubMed:18936097 showed it is not the case
Was originally thought to be located in nuclear speckles based on overexpression of the protein (PubMed:15060122). However, the endogenous protein was later shown not be expressed in nuclear speckles (PubMed:21699900)
We have changed a potential AGG for Arg-1 as ATG for Met-1
Glu-37 is present instead of the conserved Lys which is expected to be an active site residue. Lys-38 may fulfill that role
Lacks two EF-hand domains in the calmodulin-like domain, which are conserved features of the CDPK ubfamily
Could be the product of a pseudogene. This sequence is shorter than orthologs and lacks the conserved active site Glu and metal-binding site Asp residues
Has been first described as FZD3 in literature
This sequence is divergent compared to other bacterial RibF
Was initially thought (Ref.1) to be a protease inhibitor
Was originally thought to be involved in molybdenum transport
This sequence is 42 amino acid shorter than orthologs and therefore lacks two conserved residues involved in calcium binding and active site activity. The two other residues involved in calcium binding are present but it is not known if they still bind calcium
Most probably a non-functional protein that cannot participate to the synthesis of a productive T cell receptor (TR) chain due to a mutation at position 53, corresponding to a conserved amino acid, potentially leading to uncorrect folding (PubMed:9619395)
While chromophore attachment has been shown in a purified system in vitro, this chromoprotein has never been isolated in vivo
Was originally thought to play a role in inflammatory responses both as a target and as a component of the NF-kappa-B signaling, to interact with the HDAC2, and be induced by lipopolysaccharide (LPS) (PubMed:20519513). However, this work was later retracted (PubMed:28314777). Nevertheless, the interaction with HDAC2 has been demonstrated by several publications in the human ortholog
It is unsure if the sequence starts at position 1 or 2
Two N-terminal sequences could be detected after automatic Edman degradation, one is the sequence AHKPRFYYNP, that corresponds to the fragment 18-27, and the other is DH., that possibly corresponds to the fragment 2-17. Vur-KIn possibly was partially degraded into two fragments which might be kept linked by disulfide bonds during sample preparation
Was proposed to be a geranyl diphosphate synthase involved in gibberellins biosynthesis
Unlike P.falciparum CDPK1, appears not to be involved in the asexual blood stage and in male gamete exflagellation prior host erythrocyte membrane rupture
Lacks the His residue in the RING-type domain 1 that is one of the conserved features of the family
Although it belongs to the kinase superfamily, contains an asparagine residue at the position of the canonical catalytic aspartic acid and does not have kinase activity (PubMed:31148576). However, can bind ATP (PubMed:31148576)
The proteins described here are encoded by the gene CDKN2A, but are completely unrelated in terms of sequence and function to tumor suppressor ARF (AC O77618) which is encoded by the same gene
Was originally thought to activate the pilin promoter
The mature peptide AKH-1 is also encoded by another precursor (AC C0HL91)
Was originally thought to be SD
This protein could be artifactual, it seems to contain pieces of several different proteins
May be linked to snaclec alpha and beta subunits, thus forming a metalloproteinase from the P-IIId sub-subfamily
Was originally thought to be two separate ORFs named DnaX and DnaZ
Was previously assigned to At2g31870
Lacks the cysteine thought to be important for catalysis. It is replaced by Ala-288
Was initially classified as a member of the small heat shock family protein. However, it was later shown that it is not the case (PubMed:22595669)
Has been proposed to be involved in c-di-GMP turnover (PubMed:15882417), but also not be involved in its turnover (PubMed:19376870). Mutagenesis of Glu-29 in the EAL domain suggests if this protein has c-di-GMP phosphdiesterase activity it is not involved in motility regulation (PubMed:21278297). Note that (PubMed:15882417) and (PubMed:19376870) experiments were done in strain 14028, which is not an LT2 derivative
Str5 and str6 form two genes in S.tenacellus whereas they are fused in close related species
PubMed:10896159 demonstrated that CABLES1 is not associated with CDK3
It is uncertain whether Met-1 or Met-90 is the initiator
Unlike in human TRPM2, residues in the Nudix box (AEFGE) that are important for ADP-ribose pyrophosphatase activity are conserved suggesting that N.vectensis TRPM2 may have ADP-ribose pyrophosphatase activity
Could lack activity as the potential active site Cys residue in position 78 is replaced by an Ala
Was originally thought to be a putative gustatory receptor named Gr43b but further analysis suggested that this is not the case
Originally tisA and tisB were fused into one ORF by frameshift reconstruction. TisA is probably a pseudogene
Although DesVIII shows significant similarity to cytochrome P450 family, it lacks the heme-binding sites. The conservation of amino acid sequence is confined primarily to the C-terminal half of the protein
Some publications use a protein sequence that is longer at the N-terminus and is based on an artificial construct (PubMed:12732141, PubMed:27304076). The sequence used in these publications modifies a non-canonical CTG leucine codon upstream of the initiator codon into ATG, generating a protein of 1021 residues (PubMed:12732141, PubMed:27304076). The existence of this form has not been confirmed in vivo and is therefore unsure (PubMed:12732141, PubMed:27304076). Similarly, the existence of the S33 ('Ser-33') phosphorylation site described in Panayiotou et al. is unsure (PubMed:27304076)
Due to sequence microheterogeneity among zein messenger RNAs, this protein might be encoded by the same gene as AZS22-8 (AC P04699)
Has been classified as a the potassium channel toxin alpha-KTx 22.5 in PubMed:22230549. Since the subfamily 22 has already been attributed, this peptide should be reclassified as alpha-KTx 23.5
It is unclear how it participates in the recruitment of TP53BP1 at DNA damage sites. According to a first report, participates in the recruitment of TP53BP1 by promoting ubiquitination and removal of L3MBTL1 from DNA damage sites (PubMed:22120668). According to a second report, it acts by removing 'Lys-48'-linked ubiquitination from sites of DNA damage (PubMed:22020440)
Although related to histidine acid phosphatase proteins, it lacks the conserved active sites, suggesting that it has no phosphatase activity
In mouse, 5 genes homologous to human CD209/DC-SIGN and CD209L/DC-SIGNR have been identified. Mouse CD209A product was named DC-SIGN by PubMed:11581173 because of its similar expression pattern and chromosomal location in juxtaposition to CD23, but despite of the low sequence similarity
May lack kinase activity. The human ortholog has been shown to have impaired catalytic activity with an inability to undergo autophosphorylation or to phosphorylate substrates
Tyr-340 is present instead of the conserved cysteine active site residue, a key catalytic residue that is methylated in the first step of the reaction mechanism. Therefore this protein may be inactive
NAP-I was previously referred to as AP-I
It is reported in PubMed:11790834 that disulfide bonds may be in positions 4-17, 8-31 and 25-36
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4ac = acetylated Lys-5; H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me3 = trimethylated Lys-10; H3S10ph = phosphorylated Ser-11; H3K14ac = acetylated Lys-15; H3K18ac = acetylated Lys-19; H3K23ac = acetylated Lys-24; H3K27ac = acetylated Lys-28; H3K27me1/2/3 = mono-, di- and trimethylated Lys-28; H3K36ac = acetylated Lys-37; H3K36me1/3/3 = mono-, di- and trimethylated Lys-37; H3K56ac = acetylated Lys-57; H3K56me1 = monomethylated Lys-57; H3K79me1 = monomethylated Lys-80
Was originally thought to be the pancreatic lipase
Could be the product of a pseudogene. This is the C-terminal part of aquaporin-2. A natural 11 bp deletion in position 109 leads to a frameshift, which disrupts the gene coding for this protein and produces two ORFs C1Q_01794 and C1Q_01798. A contiguous sequence for aquaporin-2 can be found in strain Sigma 1278B (AC P0CD89)
Inconsistent experimental results may reflect the use of inconsistently defined redox forms. A recombinant fully reduced form has been used in a number of experiments. However, the redox states of HMGB1 administered in vivo, may interconvert among each other. Purified HMGB1 by itself has only weak pro-inflammatory activity
In contrast to other members of the family, lacks the SAP domain
Has similarity to alpha 1,2-mannosidases, but the catalytic activity of this protein is controversial. One study shows that it is important for a specific oligosaccharide trimming step from Man9GlcNAc2 to Man8GlcNAc2, suggesting activity as a mannosidase. However, another study reports that this protein has no mannosidase activity
Has been reported to be expressed in Rathke's pouch and the developing pituitary gland (PubMed:9090387). However, a later report found no expression in these tissues and speculated that earlier results may represent cross-hybridization with the very similar Nhlh1 gene (PubMed:15470499)
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK6su = sumoylated Lys-7; H2BK11ac = acetylated Lys-14; H2BK16ac = acetylated Lys-24; H2BK16su = sumoylated Lys-24; H2BK17su = sumoylated Lys-25; H2BK123ub1 = monoubiquitinated Lys-134
Was originally termed sox-11
Although related to the cytochrome P450 family, lacks the heme-binding sites
Despite its name, the zebrafish TOMT protein is not predicted to contain a transmembrane region in contrast to primate orthologs
Truncated; premature stop codon in the surface protein
DHRS7 was originally reported to be anchored in the endoplasmic reticulum membrane and facing the lumen (PubMed:24246760). However, the catalytic moiety was later shown to be facing the cytosol (PubMed:28457967)
Nomenclature used in PubMed:8576224 refers to PP2A B subunit B' gamma isoform, which is cited as PP2A B subunit delta-PR61 isoform in later publications
In strain 301 the corresponding sequence has an in-frame codon. The sequence has been checked and is believed to be correct
Could be the product of a pseudogene. Corresponds to residues 18 to 104 of the R.prowazekii RP603 whereas RC0923 corresponds to residues 290 to 407 of RP603. To reconstruct a sequence that would be similar to R.prowazekii RP603, it would be necessary to correct 4 frameshifts and to bypass a stop codon
The effect of phosphorylation at Ser-399 is unclear. According to a report, phosphorylation at Ser-399 is important for interaction with METTL3: phosphorylated Ser-399 forms a salt bridge with 'Arg-471' of METTL3 (PubMed:27281194). According to another report, phosphorylation at Ser-399 does not affect interaction with METTL3 (PubMed:29348140)
The ability of METTL14 to have catalytic activity is unclear and a number of experimental evidence suggests that it has no methyltransferase activity by itself (PubMed:27627798, PubMed:27281194, PubMed:27373337). According to some reports, has some methyltransferase activity in vitro (PubMed:24316715). However, other studies showed that METTL14 constitutes the RNA-binding scaffold that recognizes the substrate rather than the catalytic core (PubMed:27627798, PubMed:27281194, PubMed:27373337). 3D-structure studies showed that METTL14 contains a degenerate active site that is unable to accommodate donor and acceptor substrates (PubMed:27627798)
A disulfide bond between Cys-338 and Cys-388 is observed in a structure (PubMed:27627798). Its existence is however unsure in vivo
The disruption mutant used by Hendriksen et al for transcriptome analysis of the CodY regulon and for virulence studies contains additional mutations allowing survival of codY mutant cells (PubMed:20979332). Whole genome sequencing revealed additional mutations in fatC, which encodes a ferric iron permease, and amiC: this combination of mutations was confirmed to allow tolerance of codY inactivation (PubMed:20979332)
The topology shown here is that reported by PubMed:8232193. It contradicts that predicted by TM prediction programs and which has been used in orthologous entries
This is a divergent form of trpE. It is not obvious if it is active in Trp biosynthesis
Used to include what was called 'MenCF'
Lys-201 is present instead of the conserved Glu which binds a calcium ion
It has been speculated that AKR7L encodes a selenoprotein, which includes a selenocysteine (Sec) residue in lieu of a UGA translational termination codon at position 106 (PubMed:12879023). However, there is no evidence that such a protein is produced in vivo
The sequence shown in this entry differs from the translation of the reference genome assembly (GRCh38/hg38) due to a nonsense variant creating stop codon at position 106 in the reference genome
Was originally erroneously termed AKT5
Was named OAX2 but it does correspond to Arabidopsis OAX2 protein
According to PubMed:12445129, no association with a flavin cofactor is detected. Does not reduce 12-oxophytodienoic acid (OPDA) nor any other alpha,beta-unsaturated carbonyl tested
Bioinformatics programs predicts this could have a signal sequence
Due to an amino acid substitution at the processing site, the putative signal sequence is probably not cleaved and the protein is inactive
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-8; H2BK6su = sumoylated Lys-8; H2BK7ac = acetylated Lys-8; H2BK7su = sumoylated Lys-9; H2BK11ac = acetylated Lys-15; H2BK16ac = acetylated Lys-25; H2BK16su = sumoylated Lys-25; H2BK17su = sumoylated Lys-26; H2BK123ub1 = monoubiquitinated Lys-134
Product of a polymorphic gene. This sequence cannot be differentiated from this of the IGHV3-30 gene. Watson et al. identified this gene on chromosome 14. However, it is not currently present on the reference genome assembly (GRCh38/hg38)
There are 10 AA differences between the cDNA deduced sequence and the determined protein sequence. These differences are not indicated in the paper
Epitope 1, mapped in PubMed:16785532, is predicted to be buried in the membrane. Its accessibility to the extracellular space, and thus to antibody recognition, is not explained
PKD1L2 is both a gene and a pseudogene in the human population. The reference genome assembly corresponds currently to the non-functional allele while the sequence shown here is the one of the functional protein
Although related to the protein phosphatase 2C family, lacks some of the conserved residues that bind manganese, suggesting it has no phosphatase activity
Despite its name, does not contain a functional leucine zipper
Note that in PubMed:11154066 it was found that the N-terminus is blocked, whereas the mass determined in PubMed:16287167 suggests that the initiator methionine is removed. No extra mass for a blocking group was found
Results concerning the involvement of this peptide in blood volume and blood pressure homeostasis are conflicting. Several studies utilising in vitro and heterologous expression systems show that it is able to activate cGMP and promote vasodilation and natriuresis (PubMed:2825692, PubMed:7720651). However, an in vivo study in rat found that it is not sufficient to induce any diuretic, natriuretic, nor hypotensive responses, and is unable to bind NPR1 nor increase guanylyl cyclase activity (By similarity)
Results concerning the involvement of this peptide in blood volume and blood pressure homeostasis are conflicting. Several studies utilising in vitro and heterologous expression systems show that it is able to activate cGMP and promote vasodilation and natriuresis (PubMed:2825692, PubMed:7720651, PubMed:7595132). However, a heterologous expression study in rat found that it is not sufficient to induce any diuretic, natriuretic, nor hypotensive responses, and is unable to bind NPR1 nor increase guanylyl cyclase activity (PubMed:7831500)
Contains substitutions of several amino acids thought to be essential for catalytic activity. Its enzyme activity is therefore unsure
All S.alternans family members described in 'Undeheim et al., 2014' have not been imported into UniProtKB. Please, refer to this paper to access them
Binds 2 Na(+), but the precise binding sites are still uncertain and may change during the transport cycle
The orthologous human gene is a pseudogene
Was originally thought to be an ADP-ribosyltransferase
Ala-206 is present instead of the conserved Ser which is expected to be an active site residue
The antibiotic resistant variants could harbor other changes as the whole genes were not sequenced
Was initially reported to have histone methyltransferase activity and methylate 'Lys-4' and 'Lys-36' of histone H3 (H3K4me and H3K36me) (By similarity). However, this conclusion was based on mass spectrometry data wherin mass shifts were inconsistent with a bona fide methylation event (PubMed:30626964). In vitro, the protein-lysine methyltransferase activity is weak compared to the protein-histidine methyltransferase activity (PubMed:30526847)
Ser-211 is present instead of the conserved Cys which is expected to be a metal-binding residue
Isoform 4 has been previously detected in cytosol and in the nuclei of apoptotic cells and promoted apoptosis following irradiation (PubMed:12551933). However the nuclear localization and apoptosis promotion has not been confirmed in other cell types (PubMed:24073260)
M.banksi is a member of the M.pilosula complex, but is clearly distinct from M.pilosula species
The name pilosulin-3 has also been attributed by Davies et al., 2004 to an heterodimer from M.pilosula
Mass spectrometry experiment was done on the entire protein whose known sequence is incomplete (sequence of 1-18). The difference between measured (4993) and calculated (5136) mass resides in the fact that the sequence of this entire protein is maybe not identical to the sequence shown
Has sometimes been referred to as ADAMTS4
Rice plants contain two different alleles of WRKY45, WRKY45-1 (AC Q5W6D6) and WRKY45-2 (AC B8AWM1), which play similar and opposite roles in defense response, response to abscisic acid (ABA) and response to abiotic stresses
PubMed:3166520 sequence which was said to originate from chicken. It however seems to originate from pig
Could be the product of a pseudogene. The N-terminus is about 275 residues shorter than orthologs
The nucleotide accession number corresponding to this protein cited in PubMed:20950666 is wrongly indicated as being GU570565
The sequence provided in PubMed:12719779 is indicated as being Beta-fibrinogenase (VLBF)
The gene is frameshifted. However, transcriptional slippage at poly(A) may correct the reading frame, which can potentially yield full-length protein
Sequence analysis predicts this to be a membrane protein, however crystallography in complex with OrfX1 shows this is not the case
Reported as ATB2 in TAIR. The origin of the name is unclear and this protein should not be mixed with bZIP family protein ATB2
Could be the product of a pseudogene, it may be missing up to 90 N-terminal residues compared to orthologs
Nitric oxide synthase (NOS) activity is dubious
In contrast to other members of the family, the conserved Glu residue in position 94 is replaced by an Arg. Its activity is therefore unsure
Although related to the eukaryotic ATPase epsilon family, there is no evidence for a function in the ATP synthase complex
Lacks the conserved metal-binding residues in the NUDIX motif and does not have hydrolase activity
Was originally thought to be a membrane protein. Crystallography of an ortholog in complex with OrfX1 shows this is not the case (By similarity)
Was originally thought to be a high molecular weight interleukin (IL-14 or IL14)
Although strongly related to the peptidase S54 family, it lacks the conserved active sites, suggesting that it has no peptidase activity
Was reported to interact with MDM2 and USP7 and to act in a complex with VCP in cooperation with USP7 to promote MDM2 deubiquitination and stabilization. However, the corresponding article has been retracted
The measured molecular weight is 27 daltons higher than the expected one suggesting a sequence error
Lacks the conserved active serine at position 228 and does not have carboxylesterase activity
Was proposed to function as a mannose-sensitive hemagglutinin and a virulence factor, and to be involved in the utilization of sialic acid (PubMed:21873407). However, it was later shown to be probably part of a C4-dicarboxylate TRAP transporter (PubMed:21980116, PubMed:22556361)
It is uncertain whether Met-1, Met-18, Met-33 or Met-44 is the initiator
The analgesic activity produced by crotamine in Mancin et al., 1998 may be a misinterpretation (PubMed:9839677). This activity is probably due to the co-elution with the 14 amino acids crotalphine peptide (AC P08878). In that article crotamine was purified uniquely by gel filtration G-75. This single chromatographic step without going through a RP-HPLC is not sufficient to separate crotamine from other low molecular weight peptides such as the potent analgesic crotalphine peptide
Studies have shown that crotamine is present in the venom of certain specimens of C.durissus terrificus, and absent in others. This is due to geographical variations (PubMed:10484745)
The gene for this protein is part of the operon phzABCDEFG which is duplicated in P.aeruginosa. Cristallographic study (PubMed:12741825) has been arbitrarily placed in this entry (AC P0DPC1), because it is impossible to differentiate between the duplicate which has been chosen for the study, and because PhzD2 (AC P0DPC1) displays an important role in phenazine production and host infection
PubMed:15764369 initially suggested a role in targeting SLC4A1 (kidney anion exchanger 1) to the plasma membrane; it does not seem to do so as it does not interact with SLC4A1 and has no effect on SLC4A1 trafficking
Was initially reported as a potential telomeric factor as it harbors two helix-loop-helix dsDNA binding domains which are recurrently found in telomeric proteins. However, teb1 was shown to have higher affinity for the vertebrate telomere repeat, TTAGGG, than to fission yeast telomere repeats in vitro
Lacks the C-terminal region present in SsbA and thus is probably not able to participate in DNA replication and/or DNA repair
Seems to not have any beta-fructofuranosidase activity
There is another gene, npl-4.1, which has a 99% identical sequence making it difficult to identify the specific function for each protein
Suggested but not proven to function in complex with SLC3A2 rather than with SLC3A1
The initial gene disruption experiment found a less pronounced phenotype than that reported in a later study (PubMed:1317267, PubMed:11559852). Both experiments disrupt expression of isoform 1 and NGF binding (PubMed:1317267, PubMed:11559852). The differences may be due to the presence of isoform 2; its expression is disrupted in the later experiment, but not in the initial experiment (PubMed:11559852)
Was originally (PubMed:2303168, PubMed:1418626) thought to be a selenoprotein and was known as sperm mitochondrial capsule selenoprotein
Lacks the conserved His residues essential for binding the catalytic zinc ion. Its enzyme activity is therefore unsure
The subcellular location of this enzyme needs further confirmation
PubMed:9362508 cloned and sequenced SFT which consisted of UBE2D1 last coding exon along with intronic sequences on the 5'-end of this exon. A function in iron transport has been described
Due to contradictory results, it is uncertain whether tyrosine and phenylalanine act as allosteric inhibitors
PubMed:2834327 authors incorrectly assigned the protein to be part of FPR, the C-terminal of GlpX
In PubMed:17137716 the protein has been overexpressed in S.lividans, where it is incorrectly processed and has 2 additional N-terminal amino acids
In disagreement with experimental results in mouse, PubMed:22961547 reports lack of histone methyltransferase activity on core histones generally, and on histone H3 specifically
The protein was initially thought to be catalytically inactive (PubMed:27461074). It was later shown that it has aspartyl protease activity and mediates cleavage of NFE2L1/NRF1 (PubMed:27676298)
It was shown by two studies that dimerization of DEFA5 is crucial for antimicrobial activity (PubMed:17088326, PubMed:22573326). Another study, however, states that dimer formation is not indispensable for antimicrobial activity of DEFA5 (PubMed:25782105)
Although strongly related to the peptide:N-glycanase enzyme, it lacks the conserved active site Cys in position 259, which is replaced by a Val residue suggesting that it has no activity
Although strongly related to other members of the family, lacks the kinase activity. A conserved Asp/Glu residue present in other members of the family, which coordinates the Mn(2+) ion and the ion-pair Lys and is indispensable for kinase activity, is replaced by a Gln in position 258
All results of mutagenesis experiments are compared with the mutant DEL-52
In contrast to other members of the family, it is shorter at the C-terminus and lacks the heme-binding sites
There are several mRNAs and ESTs supporting this gene model. However, the genome sequence encoding the N-terminal part contains several sequence discrepancies
Could be the product of a pseudogene. Lacks the GMN motif, which is a conserved feature of the family
Could be the product of a pseudogene unlikely to encode a functional protein. YIL171W and YIL170W represent the N- and C-terminal of a putative transporter. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
Could be the product of a pseudogene, it is missing up to 140 N-terminal residues compared to orthologs
Contrary to PubMed:17011543, which shows pronephric expression during tailbud and somitogenesis stages, PubMed:18787069 report that osr1 is not expressed in kidney tissue. Similarly, in the absence of osr1, PubMed:17011543 report a complete absence of kidney tissue, and pericardial edemas characteristic of renal failure, whereas PubMed:18787069 report a segment-specific defect in the proximal nephron, with the distal nephron relatively unaffected, and a compensatory increase in angioblast cell numbers in the same trunk region
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK143ub1 = monoubiquitinated Lys-151
The mature sequence shown is shorter than the sequence proposed in PubMed:16215260 and PubMed:21656569. A comparison of jerdostatin with KTS-disintegrins and a higher potency (IC(50) of 80 nM compared to 180 nM) suggest that the C-terminal dipeptide is post-translationally removed
It is uncertain whether Met-1 or Met-54 is the initiator
Diamine acetyltransferase activity is unclear (PubMed:15283699, PubMed:12803540). According to a report, mediates acetylation of polyamines, such as norspermidine, spermidine or spermine (PubMed:12803540). However, another publication showed that such activity is weak compared to thialysine acetyltransferase activity, suggesting that polyamines are not substrates in vivo (PubMed:15283699)
Defective elastase-like serine protease which does not seem to have protease activity
It is unclear whether its ability to act as a receptor for xenotropic and polytropic murine leukemia retroviruses is relevant in vivo and whether such viruses can infect human
Contrary to the situation in zebrafish, xenopus and drosophila, rat Myo1d defects have no effects on left-right body asymmetry
Sequence AAF36406.2 was incorrectly indicated as originating from bovine
Despite its name, this protein may not be the one-to-one ortholog of TMEM184C
Has been reported as both positive and negative regulator of secondary cell wall (SCW) biosynthesis by contradictory mutants phenotypes
A C-terminal amidation at Cys-63 is suggested by authors, despite the lack of Gly residue at position 64 which should provide the amino group (-NH2)
Although strongly related to the EndA enzyme, it does not contain the conserved Tyr-His-Lys active sites, preventing tRNA-splicing activity
Was reported to be expressed predominantly in erythroid cells and at much lower levels in hepatocytes. However, this paper has been retracted because there was improper manipulation, reuse and analyses
Originally proposed to be involved in the regulation of the acid citric cycle in response to fatty acids. This was based on in vitro experiments showing that MngR was released from its DNA-binding sites by high concentration sof fatty acids and acyl-CoAs. These results could be explained by the fact that these high-concentrations of fatty acids could have denatured the MngR protein
Despite homology with xyloglucan-specific endo-beta-1,4-glucanase inhibitor proteins (XEGIPs) and T.aestivum xylanase inhibitor (TAXI-I), fails to inhibit representative fungal endo-glucanases and other cell wall-degrading enzymes
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK123ub1 = monoubiquitinated Lys-122
Lacks the conserved Glu residue in position 487 essential for carbopeptidase activity. The mature form lacks catalytic activity towards synthetic peptide substrates
The protein kinase domain is predicted to be catalytically inactive but PubMed:17194765 shows an in vitro activity
In contrast to other JHDM1 histone demethylases, it lacks the iron catalytic His in position 370 which is replaced by a Tyr residue and has no histone demethylase activity in vitro (PubMed:16362057). It therefore may not be functional in vivo
Prakash et al. cloned a cDNA corresponding to the 3'UTR of the last exon of the gene (PubMed:9809749). They have shown that a synthetic peptide derived from this sequence could stimulate fibroblasts growth in vitro, and that this protein could be a fibrogenic lymphokine, that could stimulate several biological activities related to scarring. It would be expressed in placenta, skeletal muscle, pancreas, thymus, testis, and leukocytes. However, it was not confirmed by in vivo data
While NG36 and G9a were originally thought to derive from 2 separate genes, all G9A transcripts also contain the in frame coding sequence of NG36
It is uncertain whether Met-1 or Met-21 is the initiator methionine
May have lost its catalytic activity
Lacks an insertion found in the C3ar family. It remains uncertain whether it belongs to the C3ar or the C5ar family
Glu-119 is present instead of the conserved Lys which is expected to bind the lipoyl cofactor
This protein has been described as HOS10 (high expression of osmotically responsive genes 10), a coordinating factor for responses to abiotic stress and for growth and development (PubMed:15994234). However, due to a locus misidentification, the locus responsible for the HOS10 phenotypes reported in ecotype C24 remains unknown and the paper has been retracted (PubMed:20622156)
Could be the product of a pseudogene, it is missing about 60 N-terminal residues compared to orthologs
This is a truncated version of an UPF0508 family protein. Strain S288c has a tandem insertion of a Ty1 transposon in position 742, which disrupts the gene coding for this protein and produces two ORFs YJR030C and YJR025C-A. A contiguous sequence of this protein can be found in strain YJM789 (AC A6ZPZ1)
Could be the product of a pseudogene. Contains an internal 112 amino acid deletion relative to its orthologs
Cysteine residues characteristic for this protein family are absent
Could be the product of a pseudogene. Much shorter in N-terminus than its rodent counterparts due to a stop codon insertion. However, proteomics data suggest the existence of the protein
Although initially defined as an alpha-glucosidase, it produces beta-glucose by an inverting mechanism, suggesting it rather acts as a glucan 1,4-alpha-glucosidase
Gstm7 is the putative ortholog of human GSTM2
Was originally (PubMed:12220620) thought to be a receptor for sphingosine 1-phosphate. It has been demonstrated that it is not the case (PubMed:19286662)
Lacks the phospho-accepting Asp (here Glu-102), present in the receiver domain, which is one of the conserved features of two-component response regulators (ARRs) family
Was originally (Ref.2) thought to originate from Dictyostelium discoideum
Asn-126 is present instead of the conserved Asp which is expected to be an active site residue
Could be the product of a pseudogene. Lacks the signal peptide and the transmembrane domain, which are conserved features of the family
These proteins have been named according to their molecular weight (see PubMed:11755680): BACH (also called CTE-IIa and CTE-II), LACH1 (also called MTE-II) and ACT (also called CTE-IIb). It is unknown whether ACT corresponds to another isoform
Was reported to be a 2-nitropropane dioxygenase, the previous name for nitronate monooxygenase (PubMed:16682407). However, later experiments demonstrate that this protein does not have any nitronate monooxygenase activity, the activity reported by Ha et al. was likely due to the non-enzymatic reaction of propyl-2-nitronate with oxygen (PubMed:27502282)
Subsequent steps in cytosine demethylation are subject to discussion. According to a first model cytosine demethylation occurs through deamination of 5hmC into 5-hydroxymethyluracil (5hmU) and subsequent replacement by unmethylated cytosine by the base excision repair system. According to another model, cytosine demethylation is rather mediated via conversion of 5hmC into 5fC and 5caC, followed by excision by TDG (PubMed:21817016)
It is uncertain whether sirR is an active short chain dehydrogenase since it lacks the conserved active sites
CyRPA was thought to be GPI-anchored to the merozoite membrane (PubMed:25583518). However, a subsequent report shows that this was not the case (PubMed:27374406)
CyRPA shares structural homology with sialidases, however the 3 conserved arginine residues involved in substrate binding and the nucleophilic tyrosine residue are not conserved. Does not have sialidase/neuraminidase activity in vitro
Was originally thought to be a glutathione peroxidase (PubMed:10480913) or a phospholipid hydroperoxide glutathione peroxidase (PubMed:11445588), but functions as an atypical 2-Cys peroxiredoxin using both glutathione and thioredoxin almost equally as reducing power instead (PubMed:20572871)
The leucine biosynthesis pathway is not functional in the dairy strain IL1403
Was originally thought to originate from X.laevis. However, sequence identity with X.tropicalis is much higher than with X.laevis, suggesting that the sequence is from X.tropicalis
This toxin does not seem to be a typical beta-scorpion toxin, but causes a rather alpha-scorpion toxin-like effect
By homology with the human sequence, it is uncertain whether Met-1 is the initiator
Could lack activity as the potential active sites and zinc-binding sites are missing
Lacks the conserved His residue in position 290 essential for rhamnogalacturonase activity. Its enzyme activity is therefore unsure
Was originally thought to be an oxidase, i.e. using molecular oxygen for oxidation of L-2-hydroxyglutarate and producing hydrogen peroxide. However, no O2 consumption could be detected with L2HG using the purified recombinant and active enzyme (PubMed:30498244)
The C-terminal carbohydrate-binding module (CBM) extension found in soem acetylxylan esterases from other species is absent
It is not clear whether the mature peptide starts at Ala-107 or at Val-108
Was originally thought to be a member of the cytochrome bd-I complex (PubMed:16079137). Subsequent work suggests this is not the case (PubMed:16863643)
Was originally (PubMed:9694845) thought to enhance the formation and/or stability of non-covalent complexes between the trp repressor protein and operator-bearing DNA. However, WrbA does not specifically influence the affinity or mode of binding of TrpR to its operator
According to some authors (PubMed:14759510) it does not bind to ethanol. They suggest that the avoidance triggered by high concentration of alcohols may be due to impurities, such as phthalates or structurally related compounds, present as contaminants in the ethanol used. They conclude that it may be directly and strictly required for the perception of an odorant, rather than being involved only in modulating the response to ethanol
The allele found in cv. Missouri 17 (AC K7WDC8) encodes an active enzyme while the allele found in cv. B73 contains a frame shift mutation
There may be an additional Gly residue between Lys-59 and Gly-60
Was originally thought to belong to the DNA polymerase type-B family based on conserved motifs (PubMed:12093911). Has later been shown to be unrelated to B class DNA polymerases (PubMed:12695662)
Was originally shown to localize in the mitochondrion and to play a role in mitochondrial transport (PubMed:16225668). Recent articles, however, have shown that it does not localize to mitochondria, it interacts with the cytoskeleton and does not have a role in mitochondrial function (PubMed:20621975, PubMed:23427148)
Asn-9 is present instead of the conserved Cys which is expected to be the active site residue of peptidase C39. Thus they are presumed to be without peptidase activity
Was originally thought to be a sulfo-lyase
PubMed:11238224 sequence was incorrectly assigned to originate from M.mulatta
Membrane topology is controversial (PubMed:12534290). Membrane topology structure with endoplasmic reticulum lumen orientation of the catalytic domains while the C-terminus is in the cytosol have been suggested (By similarity). Others investigators have argued for a reverse orientation, with a membrane-embedded N-terminal domain but no C-terminal transmembrane segment, and a cytosolic orientation of the catalytic domain (PubMed:12534290). These contradictory results are probably because of differences in the assay systems
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-6; H2AK7ac = acetylated Lys-8; H2AS128ph = phosphorylated Ser-128
PubMed:15969500 has erroneously named this protein oryzacystatin-3
Does not associate with the C1 complex. According to PubMed:15385675, doesn't cleave the proform of complement C1s
Was initially described as an outward slow-vacuolar (SV) ion channel (PubMed:9184204, PubMed:11821043)
Was originally thought to be the membrane-bound lytic murein transglycosylase (MLT)
Was shown to interact with AKT1 and PAK1 (PubMed:15784622). This work has later been retracted due to concerns of image manipulation
Ser-234 is present instead of the conserved Cys which is expected to be an active site residue suggesting that this protein has lost its phosphatase activity
Was originally thought to be located in the peroxisome (PubMed:11108725). However, was later shown to be cytosolic (PubMed:14972328)
Could be the product of a pseudogene. IS2E is a partial IS2 sequence which lacks the N-terminal 83 residues of InsD. Locus b1578 is not annotated in the MG1655 genome and b1578/JW1570 is probably not expressed
Strain 168 and its derivatives encode a truncated, inactive version of this protein. The sequence shown here corresponds to that of strain ATCC 21332 which is active
Originally identified from a mitochondrial tricarboxylate carrier purification (PubMed:8132491). The physiological relevance of this remains unclear (PubMed:30442778)
Author states that kinase activity observed in PubMed:11956649 may be due to sample contamination. This protein is predicted to be catalytically inactive
It has been previously shown that mediates migration of early primordial germ cells (PGCs) (PubMed:16326387). But according to PubMed:16326387, have no detectable effects on development of the germ line or on the generation of live young, hence, is not essential for PGC migration
The key substrates of OTULIN and where OTULIN acts to limit inflammation have been subject to discussion. According to some reports, OTULIN plays active roles in TNF or NOD2 receptor signaling complexes (RSCs) by directly deubiquitinating proteins in these complexes (PubMed:26997266, PubMed:27523608). A publication also suggested that OTULIN directly mediates deubiquitination of RIPK2 (PubMed:23806334). However, a publication reported that OTULIN function is restricted to homeostasis of the LUBAC complex, because it is not stably associated with TNF or NOD2 receptor signaling complexes (RSCs) (PubMed:26670046). The main function of OTULIN in deubiquitinating the LUBAC complex was confirmed by knockin experiments in mouse
Although strongly related to the 'phage' integrase family this protein lacks the conserved Tyr at position 318 suggesting it has no recombinase activity
Could be the product of a pseudogene. The sequence has been verified by the authors and is believed to be correct
PMID:10823827 shows that the transport process is electrogenic with a Na(+):L-glutamine stoichiometry of 2:1, contrary to the conclusions of Chaudhry et al (PMID:10619430) who finds that the transport is electroneutral with a Na(+):L-glutamine stoichiometry of 1:1. Chaudhry et al (PMID:11742981) shows that this electrogenic transport describes by Fei et al (PMID:10823827) would correspond to an amino acid-gated H(+) conductance that is not stoichiometrically coupled to the amino acid transport but which influences the ionic gradients that drive the amino acid transport (By similarity)
The plantago asiatica mosaic virus (PlAMV)-resistant ecotypes (cv. Bay-0, cv. Ga-0, cv. Dra-2, cv. Eil-0 and cv. Is-1) encoded a full-length 157-amino-acid proteins, whereas in the susceptible ecotypes (cv. Col-0 and cv. Ler), the presence of a stop codon in the first exon results in the production of a N-terminal 36-amino-acid fragments (AC F4I9R6) (PubMed:22307853). However, the identification of a small peptide spanning an alternative splice junction leads to the proposal of an alternative gene model in cv. Columbia
This protein is much smaller than the orthologs present in other bacteria; the N-terminal and NBD1 domains are missing. However, there is a paralog in the genome (clpB2) that encodes a protein which contains only the N-terminal and NBD1 domains
Could be the product of a pseudogene. This sequence is shorter than orthologs and lacks the NAD(P)-binding motif
In contrast to other species, in which it plays an essential role as component of the mitotic checkpoint, bub1 is predicted to be inactive in D.discoideum. Its function is therefore highly unsure
Seems to be expressed only in enteropathogenic E.coli strains; in E.coli K12 / MG1655 and K12 / W3110 this operon is silenced by an IS1D insertion in the promoter region
The initially described myosin heavy chain kinase activity is probably artifactual due to numerous errors in the sequence used for characterization
There are conflicting results in its involvement in the inflammatory network. It was first described to be a pro-inflammatory cytokine by inducing the activation of NF-kappa-B signaling pathway and up-regulates IL6 production in liver carcinoma cells (PubMed:21658842). While it seems to have the opposite effect in macrophages (PubMed:27086950)
Involvement in food intake and energy was only observed when the protein was externally administered in the brain, but not when this protein was overexpressed in vivo
It is not known if heme and GST are required for prostaglandin synthase activity. The protein copurifies with heme and GST when DTT is omitted during the purification procedure. The GSH-heme complex-bound enzyme has been proposed to act as a lyase and catalyze the degradation of prostaglandin E2 H2 (PGH2) to 12(S)-hydroxy-5(Z),8(E),10(E)-heptadecatrienoic acid (HHT) and malondialdehyde (MDA). Boiling the enzyme leads to loss of prostaglandin synthase activity, but does not eliminate the lyase activity. Besides, free heme can catalyze the formation of 12L-hydroxy-5,8,10-heptadecatrienoic acid (HHT) (By similarity). A more recent study demonstrates the GSH-dependent property of PTGES2, DTT dissociates the bound heme to produce active PGE2 synthase in vitro (By similarity). PTGES2 can only catalyzes PGE2 synthesis in the free state as an enzyme, while in vivo it forms a complex with heme and does not participate in PGE2 synthesis (By similarity). In agreement with this study, the in vivo evidence from PTGES2 deficient mice do not show that this protein is responsible for the PGE2 production under basal or pathophysiological conditions (PubMed:19010439)
Although related to peptidase S1 family, lacks the conserved active Ser residue in position 192 which is replaced by an Ala, suggesting that it has no protease activity. Lacks also metal binding sites Glu in position 67 which is replaced by Asn and Asn in position 69 which is replaced by Arg
Was originally thought to be involved in synthesis of the pyrimidine moiety of thiamine and/or in metabolism of Fe-S clusters
Has lost two of the three potential zinc-binding residues and therefore may not be active
Tyr-143 is present instead of the conserved Asp which is expected to be a magnesium-binding residue
Was initially reported to be deacetylated by Sirt5 (PubMed:19410549). However, it was later shown that Sirt5 has poor deacetylase activity and mediates desuccinylation of Cps1 instead (PubMed:22076378)
A number of sequences were reported to show high variation indicative of high levels of genetic change in Chernobyl rodents (PubMed:8614463). However, this work was later retracted although the nucleotide sequences are still available (PubMed:9363899)
Lacks the conserved Cys in position 6 which is part of a zinc-finger along with Cys-3, Cys 31 and Cys-34
The protein has been described as presenting a second isoform with a missign Lys in position 309 (PubMed:15972818). However, the paper has been retracted
Although belonging to the PA-PL1 family, does not seem to have any phospholipase activity
Has been reported to be located in the Golgi apparatus (By similarity). However, another study was unable to detect Golgi localization (By similarity). Has also been reported to be located in the mitochondrion (PubMed:18775783). However, no mitochondrial localization was detected in another study which reported that the protein is primarily cytoplasmic (By similarity)
Could be the product of a pseudogene. It is homologous to the N-terminus of two uncharacterized proteins (RF_0471 of R.felis and RBE_0759 of R.bellii)
Is not present in yeast genome
Was originally (PubMed:8251535, PubMed:3178809) thought to be identical to thyroxine deiodinase but this was later shown to be incorrect
Although it belongs to the ADP-ribosylglycohydrolase family, lacks metal-binding and substrate-binding residues, suggesting that it has no hydrolase activity
Acts as an inhibitor of cullin neddylation and SCF complex assembly in vitro (PubMed:19942853). However in vivo experiments in other organisms strongly suggest that it acts as an essential regulator of SCF complex assembly
Lacks several key residues involved in metal-binding and catalytic activity, therefore has lost phosphatase activity
Phe-23 is present instead of the conserved Tyr which is expected to be an active site residue
KCO3 shares similarity to the TPK family (2P/4TM) but lacks the conserved internal part including one pore-forming region and two transmembrane segments. As a result and according to its structure, KCO3 could also be classified as a member of the IRK family (1P/2TM)
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-5; H2BK6su = sumoylated Lys-5; H2BK7ac = acetylated Lys-6; H2BK7su = sumoylated Lys-6; H2BS10ph = phosphorylated Ser-9; H2BK11ac = acetylated Lys-10; H2BK16ac = acetylated Lys-15; H2BK16su = sumoylated Lys-15; H2BK17su = sumoylated Lys-16; H2BK123ub1 = monoubiquitinated Lys-122
The order of the last 3 peptides shown is unknown
This gene confers 4-fold increased resistance to nalidixic acid (MIC 2 ug/ml) when expressed in susceptible N.gonorrhoeae strains (PubMed:1906260). The exact mutation responsible for resistance was not identified; later analysis suggests it is probably Asn-429 which is usually Asp. Asn-429 confers resistance to AZD0914 and ciprofloxacin
Was originally (PubMed:7919993) reported to be isolated from an A.thaliana cv. Landsberg erecta cDNA library
Was originally (Ref.5) thought to be a P2Y receptor
Does not contain the conserved Gly-cisPro motif at positions 137-138 required for rejection of L-amino acids; instead it encodes Ala-Gly
PubMed:23093034 describes a peptide from Lachesana sp. Since the sequence is identical with a peptide from L.tarabaevi and the genus is the same, it is probable that the peptide is from this species
First thought to play a role in the regulation of apoptosis, mediating mitochondria-induced cell death in vascular smooth muscle cells through the release of cytochrome c (COX) from mitochondria and the activation of the caspase cascade (PubMed:16782708, PubMed:18977203). However, recent studies show that it is not directly involved in apoptosis regulation but in the protection of COX from oxidatively induced degradation (PubMed:30552096)
Was originally shown to have aminopeptidase IV activity (PubMed:10085079). Later characterization was unable to detect any significant aminopeptidase IV activity (PubMed:25752612)
PubMed:7841459 sequence was originally thought to originate from S.typhimurium, but seems to come from an unknown E.coli strain
According to PubMed:12959640, T.stejnegeri was formerly named T.gramineus, supposing that this protein is the same as PLA-VI from T.gramineus. They have been kept separated, because T.gramineus and T.stejnegeri are considered as being two different species (see http://reptile-database.org)
Was reported to be phosphorylated at Ser-34. However, the paper was retracted because some data, results and conclusions in the paper are not reliable
The Arg residue that is thought to bind ATP in this protein is missing; it probably binds ATP elsewhere
Although initial characterizations described PCA1 as a copper-transporting ATPase, subsequent experiments have demonstrated that PCA1 is capable of high affinity copper ion binding, but not active copper ion transport
Strain S288C, as well as other laboratory cadmium-sensitive strains, contain a natural Gly-970-Arg mutation which eliminates cadmium transport function. Loss of cadmium resistance provides a fitness advantage under cadmium-free conditions
Was initially identified as a component of the elastin-associated microfibrils (PubMed:1374398). More recent results indicate it is instead part of the spliceosome B complex
Was termed Unkempt
While it is structurally defined as a knottin it lacks the conserved Cys residue in position 71
It is uncertain whether Met-1 or Met-85 is the initiator
Was originally (PubMed:8096175) thought to suppress a groEL mutation and mimic the effect of groE overexpression. This was later shown (PubMed:11948170) to be probably due to an artifact
Was originally thought to be a cell surface protein involved in B-cell activation
This protein probably does not originate from A.thaliana, rather it resembles fungal GTSs
According to some authors, acts by extracting target proteins from membranes (PubMed:21642972). According to a another report, rather acts by targeting proteins to membranes (PubMed:22085962)
It has been reported that MYDGF is secreted into blood plasma (PubMed:15378209, PubMed:25581518). However, another report studying human MYDGF shows resident localization to the endoplasmic reticulum and Golgi apparatus and secretion when the two most C-terminal residues of the RTEL motif are abolished (By similarity)
Was originally characterized as ATP-dependent phosphofructokinase (PubMed:9055413). However, inspection of the original N-terminal sequence showed that the characterized enzyme was not pfkA1 (SCO2119), but pfkA2 (SCO5426) instead, another isozyme in S.coelicolor (PubMed:18606812)
Lacks one of the disulfide bridges highly conserved in the class III peroxidase family
Was originally thought to be involved in gluconate metabolism and was referred to as GntY
Was originally annotated in the complete genome as thiD
Product of a dubious gene prediction. Zuker et al. identified this gene on chromosome 12. However, it is not currently present on the reference genome assembly (GRCh38/hg38)
Lacks the conserved Cys-50-Cys-66 disulfide bridge due to the replacement of Cys-50 by a Gly
Although glit-1 contains an extracellular carboxylesterase-like domain, the characteristic Ser-Glu-His catalytic triad present in acetylcholinesterase is replaced by two Asp residues and an Arg, suggesting that glit-1 lacks catalytic activity
Was originally thought to be a calmodulin-independent adenylate cyclase
A report observed N-glycosylation at Asn-349 (PubMed:19139490). However, as the protein is not extracellular, additional evidence is required to confirm this result
Lacks the conserved Glu residue in position 242, which is expected to be an active site residue
Was originally thought to be a protein from the small subunit of the ribosome
Was originally erroneously termed DUSP23
Reported to interact with SLC6A4 in its sialylated form. However, this publication was retracted due to image duplication in the figures
Contradictory results have been reported for activation by beta-ionone in human and mouse. Beta-ionone does not activate OR51E2 in mouse. This difference may depend on the different methods used for these experiments, or may be due to species difference
Conflicting results for the role of OR51E2 in the regulation of breathing and its role as a hypoxia sensor activated by lactate are reported (PubMed:26560302, PubMed:30258151). It was first described as a hypoxia sensor in the breathing circuit by sensing lactate produced when oxygen levels decline (PubMed:26560302). A recent study fails to confirm a role for OR52E2 in this pathway (PubMed:30258151). Conflicting results may reflect the use of different strain backgrounds (PubMed:30258152, PubMed:26560302, PubMed:30258151)
The role of this protein in Akt activation has been demonstrated by Du et al for the mouse ortholog but PubMed:15469416 has not been able to reproduce the result in rat hepatocytes
This ERD6-like sugar transporter is shorter than other family members and contains only 8 transmembrane domains. It may not be functional
The ability to deacetylate Uox in vivo is unclear. The anti-acetylated lysine antibody used in the assay is not fully specific and cross-reacts with some acylated lysines. It is therefore possible that it also recognizes N6-malonyllysine and N6-succinyllysine residues (PubMed:23085393)
Throughout PMID:11566890, the gene name taf-5 is used instead of taf-4, based on an earlier nomenclature; readers should be aware to avoid confusion
Variants Gln-294 and Val-485 have been originally reported as disease-causing mutations in NPDA and NPDB (PubMed:12369017, PubMed:15221801). These variants have been reclassified as benign polymorphisms (PubMed:23430512)
The third iron-binding site which is normally a His is replaced here by Asn-145
X-ray crystallography in this and other archaea shows this protein binds a 3Fe-4S cluster, although a 4Fe-4S cluster has been suggested to be present in this protein
Ref.1 indicates C21orf8 as a synonym for this orf, this is incorrect, C21orf8 is already assigned to another chromosome 21 region
Lacks the typical Glu active site in position 111 that is replaced by a His residue, preventing the hyaluronidase activity
Lacks the conserved CCT domain, which is one of the features of the CONSTANS family
Weak activity relative to mammalian poly(ADP-ribose) glycohydrolase orthologs
Lacks the conserved Glu residue in position 491 essential for carbopeptidase activity. The mature form lacks catalytic activity towards synthetic peptide substrates
There are conflicting results in its involvement in the inflammatory network. It was first described to be a pro-inflammatory cytokine by inducing the activation of NF-kappa-B signaling pathway and up-regulates IL6 production in liver carcinoma cells. While it seems to have the opposite effect in macrophages
Involvement in food intake and energy was only observed when the protein was externally administered in the brain, but not when this protein was overexpressed in vivo (PubMed:24366864)
Was originally thought to be phosphorylated on Ser-53 (PubMed:3112145); this was later shown to be wrong (PubMed:7665584)
The toxin name trachynilysin was given according to the species S.trachynis. This species has finally been reclassified as a synonym of S.horrida
It is uncertain whether Met-1, Met-171 or Met-172 is the initiator
STARD3 was reported to function in cholesterol transport to the mitochondria or to the cell membrane (PubMed:12070139, PubMed:19965586). Other reports however showed that it mediates cholesterol transport from the endoplasmic reticulum to endosomes (PubMed:11053434, PubMed:28377464). Discrepancies may be due to the different cell type used and the cellular physiological state (PubMed:28377464)
The phosphoserine observed at Ser-1003 in PubMed:17218307 may result from the secondary neutral loss of pantetheine from the phosphodiester linked cofactor
It is uncertain whether transit peptide cleavage occurs after His-62 or Ala-63. Peptides have been found for both N-termini in roughly equal amounts
Compared to other DXS it lacks a domain of about 20 residues between positions 208 and 209
There are two genes for this protein in the chloroplast inverted repeat; while are usually identical, in the sequence from PubMed:17607527 they are not
Given that these two proteins are not members of the same ribosomal subunit, and that they are not known to contact each other in the ribosome, this may be incorrectly predicted and should perhaps be two separate genes
Product of a dubious CDS prediction. Encoded in intron of the NTM gene
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK143ub1 = monoubiquitinated Lys-153
Could be the product of a pseudogene. Resulting from truncation by frameshift mutation
sequence is a contaminating peptide from a S.cerevisiae glycogen synthase purification
Was previously thought to be non-coding and described as 'non-protein coding RNA 81', abbreviated NCRNA00081
The sequence shown in this entry differs from the translation of the reference genome assembly (GRCh38/hg38) due to a nonsense variant creating stop codon at position 125 in the reference genome
The topology of the disulfide bonds differs from that of orthologs
Was originally thought to be a trifunctional enzyme but only a formyltetrahydrofolate synthetase activity was detected and not a dehydrogenase/cyclohydrogenase activity
Could be the product of a pseudogene, it is missing about 120 C-terminal residues compared to orthologs
This sequence is a fusion of the duplicated copies ccmA2 and ccmE2, however, important parts of the proteins are missing and it is therefore probably not functional
Was originally thought to be the testis determining factor (TDF)
Due to the high similarity between gas2l2.L and gas2l2.S, the morpholinos used for knockdown target both gas2l2.L and gas2l2.S RNA
The N-terminus is shorter than orthologs
Nakanishi et al (PMID:11698233) shows that the transport process is electrogenic, contrary to the conclusions of Hamdani et al (PMID:22821889) who finds that the transport is electroneutral with a Na(+):L-glutamine stoichiometry of 1:1 (By similarity). Hamdani et al. shows that this electrogenic transport describes by Nakanishi et al. would correspond to large uncoupled fluxes of protons (By similarity)
Reported to mediate ubiquitination and subsequent degradation of AGO2 (PubMed:19898466). However, this result is subject to discussion and later reports suggest that, while it interacts with AGO2, it is not involved in AGO2 ubiquitination (PubMed:22508726, PubMed:22735451)
Was originally erroneously termed LCR51 before the split of the gene model
The Forssman antigen (FORS1) is normally expressed on erythrocytes of some non-primate mammals. However, in rare cases it is expressed on human erythrocytes of histo-blood group FORS carriers
Was originally thought to be a receptor for adrenomedullin
PMID:21169637 identified the deleted gene as YP_420381.1 (equivalent to amb1018, mamY), which does not correspond to either the gene or protein sequenced by the same authors. It is not clear which gene was really deleted
There is some confusion regarding the nomenclature of this gene. In the literature, Tlr11 is frequently referred to as Tlr12 and vice-versa
Contains a predicted homeobox domain which is degenerated, lacking residues important for DNA-binding. Moreover, the protein localizes in the endoplasmic reticulum and not in the nucleus, which also argues against homeobox function (By similarity)
Gene called vmp16 in DNA submission but vlp15 in nomenclature paper
As the paper only indicates the species as 'red sea turtle', the species indicated here is therefore an inference
Was originally thought to contain a 6Fe-6S cluster as indicated
Was originally named fadF
Lacks the conserved active site Lys, and therefore lacks catalytic activity
Could be the product of a pseudogene. Lacks the region corresponding to the signal sequence and the propeptide. Has mutations in all 3 active site positions
In PubMed:22511981, this sequence erroneously refers to SjKTx32
Could be the product of a pseudogene. This sequence is much shorter in its N-terminus than orthologs
Was originally assigned as At3g12790
There are conflicts between the sequence shown here and that from PDB 1D5A
Lacks the first cysteine that binds the 2Fe-2S complex
There are conflicting results relative to ion selectivity and permeation. Initially outward rectification has been reported which makes the proposed activity as lysosymal Ca(2+) release channel unlikely. Inward rectification has been decribed in later studies supporting the Ca(2+) release activity
Could be the product of a pseudogene unlikely to encode a functional protein. Although strongly related to DNA helicases, it lacks the helicase ATP-binding domains, suggesting that it has no helicase activity. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
Was originally thought to be involved in the deamination and isomerization of D-galactosamine 6-phosphate to D-tagatofuranose 6-phosphate
The sequence shown here has been extracted from PDB entry 1SRV
Was originally thought to be an RNase; when the C-terminus (residues 449-600) is expressed in E.coli it has RNase, not DNase activity, and inhibits growth upon expression in E.coli. In vitro RNase activity and in vivo growth inhibition are neutralized by cognate immunity protein YobK, but not by immunity proteins specific to other LXG toxins. Mutation of His-562 to Ala leads to loss of growth inhibition and RNase activity in E.coli
The LCP3 and LCP4 genes on chromosome X code for identical proteins. There are also pseudogenes for both LCP3 and LCP4 on chromosome neo-Y
In contrast to FOLR1 and FOLR2, unable to bind folate
Was initially believed to be a subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (complex I). However, was not present in all complex I preparations and presence correlated with contamination by COX6B1 (PubMed:12837546)
Was originally thought to be the ATPase subunit of phosphoribosylaminoimidazole carboxylase, with catalytic subunit PurE
Was originally thought to originate from E.coli
Lacks the conserved Ser residue involved in nucleophilic attack and essential for hydrolase activity. Its enzyme activity is therefore unsure
Was originally thought to be an endonuclease subunit
Was initially identified as a component of the 26S proteasome
Has been shown to be active in cv. Columbia (AC Q9SE37) due to naturally occurring sequence variation in this strain. The sequence shown is from strains cv. Bl-1, cv. C24 and cv. Ct-1
This protein is encoded by LEPR gene, but shares with LEPR only the first two 5'-UTR exons. It therefore does not share any sequence similarity with LEPR
Could be the product of a pseudogene. Lacks the signal peptide and 1 of the 4 disulfide bonds, which are conserved features of the family
Although related to the glycosyl hydrolase 31 family, lacks the conserved active sites, suggesting it has no glycosidase activity
Could be the product of a pseudogene. According to PubMed:12499400, the human GGTA1 gene is an expressed pseudogene encoding non-functional truncated proteins containing the first four translated exons but missing the two catalytic exons. Although all exons expected to encode a functional GGTA1 of 371 residues are present in the human genome, all transcripts described encode truncated proteins that result from prematurely terminated transcription at the level of a strong transcriptional stop signal in the middle of intron 7. The premature transcriptional arrest of human GGTA1 gene leads to an ectopic splicing event and to the connection of a short intronic sequence downstream from translated exons. GGTA1 is active in marsupials, nonprimate placental mammals, lemurs and New World monkeys and synthesizes a carbohydrate antigen called 'alpha-gal epitope'. The alpha-gal epitope is present in large numbers on cell membrane glycolipids and glycoproteins. GGTA1 gene was inactivated in ancestral Old World monkeys and apes and, because of this, they lack alpha-gal epitopes and naturally produce an antibody called the 'anti-Gal antibody' which binds specifically to alpha-gal epitopes, is the most abundant antibody in humans and is responsible of rejection of mammalian xenografts
Although the cofactor binding sites are conserved, it is questioned if the catalytic activity as cystathionine beta-synthase is intact
Was originally (PubMed:14592418) thought to be a receptor for sphingosine 1-phosphate. It has been demonstrated that it is not the case in human
Was termed (Ref.2) DEFB136
Originally described as a SAM-dependent methyltransferase (PubMed:9634230), the crystal structure does not resemble other known SAM-dependent methyltransferases. The structure does resemble the phosphohistidine domain of several phosphotransfer system proteins. The protein does not bind S-adenosylmethionine cofactor or potential methyltransferase substrate molecules
According to PubMed:9049310, this sequence initiates exclusively at a GTG codon
Was originally (PubMed:12361956) assigned to be a glycosyltransferase. However, it was later shown (Ref.2 and PubMed:12464682) that it has no transferase activity and rather acts as a chaperone
This toxin probably comes from Halcurias carlgreni, although the identification is not definitive
Despite a previous report demonstrating SLC22A4/OCTN1-mediated transport of nucleosides such as the endogenous 2'deoxycytidine or the anticancer drug cytarabine, another study was unable to verify these findings
The C-terminus of MOCS1A was previously believed to be thiocarboxylated, but it is now known not to be the case
Several mechanisms of transport has been proposed, namely electroneutral NH3 transport (PubMed:15572441, PubMed:19273840) and electroneutral NH4(+)/H(+) exchange (PubMed:11861637, PubMed:19273840, PubMed:15572441). However, Caner T. et al demonstrates that RHAG is unlikely to be NH4(+)/H(+) exchanger, but transports the ionic NH4(+) and the neutral NH3 species and that the transport of NH4(+) is electrogenic (PubMed:26354748)
It is not known whether the so-called human ASE1 and human CAST proteins represent two sides of a single gene product with sharply different functional characteristics. Experiments done with the mouse homolog protein are in favor of an implication of this gene in rRNA transcription instead of T-cell receptor signaling
Could be the product of a pseudogene. The original protein is truncated by an IS1 element which is inserted right before residue 6. What was the original N-terminal of this protein is not known. Other genes of the operon were presumably also deleted by this IS1 event
An article reported the role of PprB in modulation of the quorum-sensing signal production. However, this paper was later retracted as the authors' main conclusion on the regulatory role of PprB on AHL signal production in wild type P.aeruginosa is not correct
This protein lacks the conserved Cys in position 54; it is replaced by a Trp. It is therefore possible that the D-cluster is either altered or missing in this protein, which may not form homodimers
For human, rat and golden hamster orthologs, a GPI-anchor has been predicted. However, in the case of pig and bovine, no GPI-anchor motifs have been detected, but it does not rule out the possibility of a GPI-anchor instead of a single-pass type I membrane protein
TsaC2 is probably the product of a pseudogene and is not expressed, due to the absence of promoter-like sequences upstream of the operon tsaMBCD2
Seems to be more closely related to protozoan and plant gpmI than to bacterial orthologs
In contrast to human counterpart, it lacks a signal sequence
Was initially thought to form a homodimer (PubMed:18554500). However, 3D structure of C.reinhardtii ortholog showed that it is probably not the case
The sequence shown here has been extracted from PDB entry 2CUA
Arg-34 is present instead of the conserved Trp which is expected to be C-glycosylated by mannose
The N-terminal sequence has been extracted from PDB entry 1LJ1
Was initially characterized as chloride channel, but such a function is difficult to reconcile with the single predicted transmembrane region. Other family members have been shown to stimulate channel activity
It is unclear whether the protein is involved in the piRNA metabolic process. The absence of phenotypes in flies suggests that this function is not conserved
Originally thought to be a component of PSII; based on experiments in this organism, Synechocystis and barley, and its absence from PSII in T.elongatus and T.vulcanus, this is probably not true
Lacks the canonical catalytic triad. Two of the three residues necessary for catalytic activity are mutated. Arg-67 stands instead of an His and at position Asn-206 stands instead of a Ser. As a result, the protein is not proteolytically active
While the gene symbol and protein names are indicative of the presence of LRR repeats, such repeats are not present in this protein
Was initially thought to act as an electron-transport mediator in the dissimilatory reduction of Fe(3+)
Was originally thought to be MreB
This enzyme is expected to be secreted, but there is no predicted signal sequence
Tyr-154 was proposed to be phosphorylated (PubMed:8683601) but it has been shown (PubMed:17087724) to be sulfated instead. Phosphate and sulfate groups are similar in mass and size, and this can lead to erroneous interpretation of the results
This organism being probably non-photosynthetic, the role of this protein is uncertain
Was previously erroneously called ligatin, a trafficking receptor for phosphoglycoproteins, while ligatin is actually a distinct 10 kDa filamentous membrane protein encoded by a still unidentified gene
A second transmembrane domain at positions 95-115 is predicted by three programs ESKW, MEMSAT and Phobius. However experimental evidence supports the presence of a single signal-anchor transmembrane domain at the N-terminus
The enzyme was purified from Aspergillus oryzae var. globosus M-9. The sequence does however not resemble any currently known A.oryzae aspartic protease and is most similar to an Aspergillus pseudoglaucus (E.repens) enzyme
According to a report, acts as a negative regulator of T-cell activation independently of its enzymatic activity (PubMed:28891065). However, authors of this study only tested enzyme activity via phenylalanine (Phe) deprivation and not via tryptophan (Trp). As IL4I1 immunoregulator activity is mediated via Trp degradation and subsequent activation of the transcription factor AHR, additional experiments are required to confirm this statement (PubMed:32818467, PubMed:32866000)
According to PubMed:14660436, interacts with BMP2, BMP4, BMP5, BMP6, BMP7 but not INHBA. According to PubMed:15094188, interacts with INHBA but not BMP2, BMP4 and BMP6
Ref.3 has shown that this is not a chalcone synthase, but a pyrone synthase
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2A.ZK4ac = acetylated Lys-5; H2A.ZK7ac = acetylated Lys-8; H2A.ZK10ac = acetylated Lys-11; H2A.ZK13ac = acetylated Lys-14; H2A.ZK16ac = acetylated Lys-17; H2A.ZK21ac = acetylated Lys-22
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-5; H2AK7ac = acetylated Lys-7; H2AS128ph = phosphorylated Ser-127
Could be the product of a pseudogene. YPL277C and YPL278C correspond to the N- and C-terminal regions of the uncharacterized protein YOR389W, respectively
In human, WASHC2 has undergone evolutionary duplication giving rise to highly homologous family members. A WASHC2C construct with WASHC2A-specific sequence insertions (of 2 aa and 21 aa length resulting in a construct length of 1341 aa similar to WASHC2A length) has been used to demonstrate the interaction with WASHC2 (PubMed:24643499)
Reported to be expressed in male and female germ cells, to be up-regulated at the protein level as early as 3 hours after chorionic gonadotropin treatment in the ovary, and to interact with 14-3-3 proteins (PubMed:12424248). However, the publication has been retracted due to image duplication and manipulation. The nucleotide sequence has been confirmed by other studies (PubMed:11116088)
DHRS7 was originally reported to be anchored in the endoplasmic reticulum membrane and facing the lumen (By similarity). However, the catalytic moiety was later shown to be facing the cytosol (By similarity)
Predicted to have endopeptidase activity (By similarity). However, as it is located in the outer alpha-ring, it is suggested to lack catalytic activity and preferentially interact with regulatory complexes such as PSME4/PA200
This truncated primase was identified on the basis of sequence homologies, but no information is available about whether this protein is functional
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4me = methylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me = methylated Lys-10; H3S10ph = phosphorylated Ser-11; H3T11ph = phosphorylated Thr-12; H3K14ac = acetylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me = methylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me = methylated Lys-24; H3K36me = methylated Lys-37
According to PubMed:18021396, it binds DNA and acts as a transcription factor. However, the localization in lysosomes which was confirmed by different groups and the presence of transmembrane region strongly suggests that it does not have coactivator activity
It is uncertain whether Met-1 or Met-20 is the initiator; if Met-20 then the protein would probably be secreted
Although this protein contains the conserved Asp-262 that functions as an active site, this protein does not have proteolytic activity, and may therefore be catalytically inactive
The role of human KHDC3L in the restart of replication forks is unclear as it has been shown to not be involved in the process (PubMed:31609975). However it has been shown that the KHDC3L ortholog in macaque is required for the process (By similarity)
In contrast to other members of the family, lacks the conserved Tyr active site at position 176 which is replaced by a Phe residue
Does not bind calcium as three of the calcium binding ligands are lost
This protein does probably not undergo proteolytic processing to release the disintegrin domain
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me1/2/3 = mono-, di- and trimethylated Lys-10; H3S10ph = phosphorylated Ser-11; H3T11ph = phosphorylated Thr-12; H3K14ac = acetylated Lys-15; H3K14me3 = trimethylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me3 = trimethylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me3 = trimethylated Lys-24; H3K27me1/2/3 = mono-, di- and trimethylated Lys-28; H3S28ph = phosphorylated Ser-29; H3K36 = Lys-37; H3K37 = Lys-38
The name echicetin has been given to 2 different proteins, this one from E.carinatus and another one for which the subspecies has been specified (E.carinatus sochureki). Most experiments have been done on E.carinatus sochureki
The role of autophosphorylation in RIPK2 activation is unclear: an initial studies suggested that autophosphorylation is essential to activate NOD2 signaling pathway (PubMed:19473975). However, it was later shown that autophosphorylation is however not essential for NOD2 signaling (By similarity)
The article by Evans et al was retracted by the editors due to concerns over image manipulation, which raised sufficient doubts regarding the credibility of the study
Although related to the CATSPERD family, it is unclear whether the protein is part of a Catsper complex
Despite the presence of this enzyme, this enzyme may not be involved in verruculogen synthesis in vivo. In contrast to other A.fumigatus strains, strain ATCC MYA-4609 does not produce indole alkaloids such as fumitremorgins and verruculogen. While the biosynthetic pathway is complete, a variation in the O-methyltransferase FtmD (AC Q4WAW6) abolishes production of the tryprostatin A intermediate (PubMed:23649274)
Recombination phenotypes may be due to polar effects on the downstream gene mfd rather than due to loss of the anti-sigma factor (PubMed:21037003)
Could be the product of a pseudogene. MJ0821, MJ0820 and MJ0819 respectively represent the N-terminal, central and C-terminal sections of other members of this family
Does not seem to have a protease activity as it lacks one of the conserved zinc-binding sites
The oxidation form of Met-30 is subject of controversy and could be the artifactual result of sample handling
Was initially thought to be palmitoylated at Ser-239. It was later shown that it is palmitoleoylated
This sequence is an example of a full-length immunoglobulin alpha-2 heavy chain
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-8; H2BK6su = sumoylated Lys-8; H2BK7ac = acetylated Lys-9; H2BK7su = sumoylated Lys-9; H2BK11ac = acetylated Lys-15; H2BK16ac = acetylated Lys-24; H2BK16su = sumoylated Lys-24; H2BK17su = sumoylated Lys-25; H2BK123ub1 = monoubiquitinated Lys-132
Was originally (PubMed:8649854, PubMed:8971156, PubMed:9174057) thought to be much longer and included an arginine-rich region thought to be the target of cancer-causing mutations. All these mutations are in what is now thought to be the 5'-UTR of the mRNA
May be inactive since it lacks one cysteine involved the redox-active disulfide bond
The subunit composition of membrane-bound hydrogenase complex is currently unclear. It has been shown to be a heterodimer of MbhK and MbhL (PubMed:10852873). Other studies have shown it to contain MbhJ in addition to MbhK and MbhL (PubMed:11054105)
Was originally thought to be a translation initiation factor
Was termed (Ref.5) polyadenylate binding protein II
It is unclear if PMVIII is glycosylated as other members of the same enzyme family, i.e. PMI and PMII, are not
Interaction with the Ras-like GTPases failed to be confirmed in other species
Does not exhibit histone methyltransferase towards histone H3 in vitro (PubMed:18952892). The isolated catalytic SET domain lacks binding activity towards cofactor S-adenosyl-L-methionine; instead of the highly conserved XGXG, Y and NH motifs, KMT2E displays NKKI (Asn-339-Ile-342), F (Phe-381) and RR (Arg-408-Arg-409) motifs. Also lacks binding activity towards histone H3 due to a poor conservation of the key residues involved in the binding and the presence of large loop which prevents the docking of the H3 'Lys-4' side chain
Although it belongs to the protein kinase superfamily, the ATP-binding motif VAIK has an arginine instead of a lysine residue suggesting that KSR1 cannot bind ATP and therefore lacks protein kinase activity. However, KSR1 is capable of binding ATP (PubMed:29433126). Has protein kinase activity towards MAP2K1 in the presence of RAF1/c-RAF in vitro (By similarity)
PubMed:1572366 reported the formation of pyroglutamic acid by the N-terminal glutamic acid and of gamma-ethyl glutamate in peptide A. This is most probably an artifact of isolation
Hexokinase is known to act as a monomer in normal conditions (By similarity). It however homodimerizes at elevated protein concentrations used for crystallizations (PubMed:26985301, PubMed:29298880)
Could be the product of a pseudogene. This is the C-terminal part of aquaporin-2. A natural 11 bp deletion in position 109 leads to a frameshift, which disrupts the gene coding for this protein and produces two ORFs SCY_3532 and SCY_3531. A contiguous sequence for aquaporin-2 can be found in strain Sigma 1278B (AC P0CD89)
Contains only 5 Cys residues instead of the 6 residues that are usually found in the O2 superfamily
Has been shown to interact with voltage-gated potassium channels, including the KCNB1 subunit, and to be critical for current enhancement. However, in view of its mostly nuclear subcellular location and its established function as a transcriptional coregulator, promoting the sumoylation of several transcription factors, the effect on potassium channels awaits further experimental confirmation
Was originally thought to be an undecaprenol kinase
Asn-85 is present instead of the conserved Lys which is expected to bind the lipoyl cofactor
This protein is 88 amino acids long in strain Classical Ogawa 395. However, there is a putative ribosomal frameshift motif present in this strain which under special conditions might allow the full-length protein to be translated
Lacks the whole C-terminal region found in the GRF family, and therefore lacks transactivation activity
Was originally (PubMed:2693942, PubMed:2259340, PubMed:2376575, PubMed:1731992, PubMed:10874039, PubMed:18042701) thought to be a ribosomal protein
There are 2 paralogs in M.tuberculosis, in some references this gene is called nei2 (PubMed:18457574, PubMed:19496823)
Was originally thought to be a 60 kDa chain of placental scatter protein
PubMed:2247479 report a decline in expression during oogenesis, but PubMed:1729676 show expression is maintained at a high level throughout oogenesis
As a homolog of the DNA glycosidase mag1, has been identified to be an alkylbase DNA glycosidase (PubMed:18270439). However, further studies revealed that it did not have any DNA glycosylase activity for alkylated bases due to the loss of the active site 'Ser-56', and was rather involved in structural sculpting DNA to facilitate damage signaling (PubMed:23273506, PubMed:23245849)
The expected hydroxylation of Lys-33 was not identified, probably due to poor representation of the N-terminal peptide in mass fingerprinting
A report observed N-glycosylation at Asn-235 (PubMed:19139490). However, as the protein is not predicted to localize in an extracellular compartment of the cell, additional evidence is required to confirm this result
Could be the product of a pseudogene unlikely to encode a functional protein. This is a truncated version of a DUP/COS protein family member. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
Called LivF in S.typhimurium, but we renamed it to LivG for the sake of consistency with the E.coli protein
An expected iron ligand Cys residue was not found at position 29 in this sequence
Eristocophin I appears to represent degradation product of EMF10A
Although highly related to the Ras family, lacks the conserved prenylation motif at the C-terminus, which serves to target Ras proteins to membrane compartments
According to a report, mainly mediates demethylation of N(6),2'-O-dimethyladenosine cap (m6A(m)), by demethylating the N(6)-methyladenosine adjacent to mRNA cap, whereas it has low activity toward internal N(6)-methyladenosine (m6A) in mRNAs (PubMed:28002401). According to a second report, has strong activity toward internal N(6)-methyladenosine (m6A) in mRNAs and is able to demethylate different RNA species, such as tRNA, mRNA or small nuclear RNA (snRNA), depending on the context and subcellular location (PubMed:30197295)
Gstm7 is the putative homolog of human GSTM2
Was initially reported to localize in the cytoplasm and nucleus (PubMed:11374908). However, many reports in different species have shown that it is associated with the Golgi apparatus and the centrosome
It is uncertain whether Met-1, Met-13 or Met-31 is the initiator
The C-terminus of mocs1a was previously believed to be thiocarboxylated, but it is now known not to be the case
Could be the product of a pseudogene, it is missing about 50 N-terminal and up to 140 C-terminal residues compared to orthologs
There is conflicting evidence as to whether gtf2ird1 acts as a transcriptional activator or repressor when directly bound to the distal element of the gsc promoter. PubMed:11937490 shows that gtf2ird1 acts cooperatively with smads and foxh1/fast1 to activate activin/nodal-mediated gsc transcription. However, PubMed:16055724 report that in the absence of TGF-beta, gtf2ird1 represses gsc transcription. Upon TGF-beta stimulation, smad2 is translocated to the nucleus as a complex with smad4, interacts with TFII-I, and binds to the distal element to dislodge gtf2ird1 and up-regulate gsc gene transcription
Could be the product of a pseudogene. A few point mutations in the signal peptide region of the PYY2 gene and in several other regions results in destruction of the normal initiation code, generation of an alternative initiation site and an early stop codon which reduces the predicated size of the peptide to only 33 amino acids
It is uncertain whether Met-1 or Met-41 is the initiator. In human and mouse, initiation starts at a conserved non-canonical ACG threonine codon decoded as Met-1 upstream of the canonical initiation at Met-41
GTF2F2 appears to have ATP-dependent DNA-helicase activity; however this is probably an artifact that happened during the protein purification
Was initially thought to act as an atypical peptidyl-tRNA hydrolase (PubMed:29632312). However, it was later shown to act as a nuclease that cleaves off the terminal 3'-CCA nucleotides from the tRNA part of polypeptidyl-tRNAs (PubMed:31189955)
Product of a dubious CDS prediction. Translation must be initiated from a non-canonical GUG codon (PubMed:24040107). Overlaps with the ATXN8 gene but is transcribed in the opposite strand and was originally considered as non-protein coding (PubMed:10192387)
The P1 reactive site residue Lys-41 is replaced by Asn-41. The impact of this replacement on the protease inhibition has not yet been determined
According to PubMed:17258408, chimpanzee like human only express a C-terminally truncated protein compared to orthologs
The possibility that PCM2 is a pseudogene cannot be ruled out
Has been reported not to be involved in Fe(2+) uptake in strains F38001 and M129, when the strains were grown in iron-containing medium (PubMed:14735223). When the feoB deletion strain of NCTC 11168 is grown in iron-containing medium Fe(2+) uptake occurs, suggesting the prior results in strain F38001 and M129 may not be correct (PubMed:16988218)
Could be the product of a pseudogene. It does not seem to start with an initiator Met
It is uncertain whether Met-1, Leu-59 or Met-74 is the initiator
Although related to the protein phosphatase 2C family, lacks 1 of the conserved residues that bind manganese, suggesting it has no phosphatase activity
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-5; H2AK7ac = acetylated Lys-7; H2AS128ph = phosphorylated Ser-128
In contrast to mouse, human RDH11 exhibits little or no activity towards toxic lipid peroxidation products, such as nonanal or 4-hydroxy-nonenal
The human ortholog was originally thought to interact with the D1 dopamine receptor (DRD1) and to play a role in potentiating calcium ion-dependent signaling but this work was later retracted
NPY has been reported to be a ligand for GPR83 (By similarity). However, a more recent study found that radiolabeled PEN binding to GPR83 is not affected by NPY concentrations below 1 mM, only very high, non-physiological concentrations causes a partial, displacement of PEN binding (PubMed:27117253)
PubMed:7512814 shows amino acid differences at positions 317, 321, 410, 694, 738 and 866 due to incorrect translation of the nucleotide sequence
Was originally thought to be a cinnamyl-alcohol dehydrogenase
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-37; H2BK143ub1 = monoubiquitinated Lys-148
In contrast to other metacaspases of the peptidase C14B family, the catalytic histidine and cysteine residues do not appear to be conserved. Contains a serine residue at the position of the canonical catalytic cysteine which may constitute the active site
A family suffering from Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract (PHARC) was initially clinically diagnosed with Usher syndrome type 3 (PubMed:22938382). Reexamination of one affected member of this family revealed ataxia but not polyneuropathy, demonstrating the phenotypic heterogeneity in PHARC and the need for careful neurological assessments to distinguish this disease from other neuropathic disorders (PubMed:22938382)
Was originally thought to be RAD4
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-36; H2BK34ac = acetylated Lys-37; H2BK143ub1 = monoubiquitinated Lys-144
The previously assigned stop codon (TAA) of pks3 (Rv1180) is found to be a Tyr codon (TAC), and with this change, pks3 and pks4 become a single open reading frame designated msl3 (PubMed:12207710). Large scale proteomics studies identify protein sequence that extends N-terminal to the initially annotated start site of Rv1181, more evidence that a single protein is translated from this locus
Matsuda et al. identified this gene on chromosome 14. However, it is not currently present on the reference genome assembly (GRCh38/hg38)
Lacks the ATP-binding site
Lacks the conserved Cys and His active sites that are essential for the activity of deubiquitinating enzymes. Lacks ubiquitin terminal hydrolase activity
Does not function as a sesquiterpene synthase since it does not contain a functional DDXXD metal-binding motif
The disintegrin is also encoded by another precursor (AC Q90220)
Was originally thought to be a linker peptide
The substrate-binding sites for the inactive DHBP synthase activity are conserved while several cofactor-binding sites are lost
An out-of-frame translation product, PYST2SB, has been experimentally demonstrated to be formed from the alternative promoter. The expression of the in-frame product has not yet been shown
Although related to the glycosyl hydrolase 22 family, lacks the conserved Asp active site, suggesting it may not have lysozyme activity
Approximately 30% of the residue corresponding to Tyr-62 is present as Phe, suggesting there may be more than 1 gene for this protein in this organism
Although similar to deoxyhypusine synthase, lacks the active site Lys at position 344 and does not show deoxyhypusine synthase activity. Converting Leu-344 to a lysine does not restore activity
Although it belongs to the glycosyl hydrolase 18 family, Leu-138 is present instead of the conserved Glu which is an active site residue. Therefore this protein lacks chitinase activity
Was initially reported to use Cu(2+) as a cofactor (PubMed:4708670). However, cofactor composition could not be confirmed later (PubMed:9108257), and the discrepancies in the reported characteristics of the enzyme were suggested to originate from the characterization of a contaminating protein in PubMed:4708670
The RS447 megasatellite DNA is a highly polymorphic conserved tandem repetitive sequence which contains a copy of the USP17 gene. It is present with an interindividual variation in copy number, ranging from 20 to 103, and can be found in the genome both on chromosome 4 and chromosome 8. USP17 is also frequently named DUB3 in the literature. The high similarity between the UPS17-like genes makes impossible to clearly assign data to one of the genes of the family. Oligonucleotides designed in RNAi experiments are for instance not specific of a given UPS17-like gene
According to PubMed:12694617, it appears that PagP is not expressed because of disruption of the putative promoter region by insertion of an IS element
Was originally described as a cyclodextrin-binding protein, but it was shown later that it has no affinity for cyclodextrin
The cytoplasm localization is controversial. One study showed that the protein localizes predominantly to the nucleus and the food vacuole (PubMed:21659511). Two studies showed that it localizes to the cytoplasm and the food vacuole (PubMed:33536500, PubMed:12166515). The discrepancy between studies is due to the staining procedure (PubMed:21659511)
Conflicting data exist on the pro-apoptotic function of the protein. It was initially claimed that overexpression of FSP1 induces caspase-independent apoptosis, but new evidence disputes this function
Was originally (PubMed:9722542, PubMed:11872755) thought to be a lantibiotic but was later shown to be an S-linked glycopeptide
Although strongly related to the LPD1 dihydrolipoyl dehydrogenase, it lacks the redox-active disulfide bond suggesting that it has no dehydrogenase activity
A N-terminal fragment of KCTD11 isoform 2 (comprising residues 15 - 115) has been used for some KCTD11:CUL3 interaction studies
Was originally called endoglucanase EG-II
Product of a dubious CDS prediction. Encoded in an intron of the SSBP3 gene (opposite strand)
Was originally thought to be a guanine tRNA-ribosyltransferase
This protein was originally thought to have ribose 1,5-bisphosphate isomerase activity despite the fact that some recombinant ortholog proteins were not active in vitro (PubMed:15375115, PubMed:17303759). Moreover, another protein from M.acetivorans likely possesses this activity (MA_0379). Finally, a thiamine synthase activity has been shown for the ortholog protein in M.jannaschii
Product of a dubious CDS prediction. May not code for a protein although there is some proteomics data to suggest the existence of a protein
In contrast to BANF1, it does not seem to bind DNA
Reported to form a E3 ubiquitin-ligase complex and promote degradation of TOB1 (PubMed:21130766). Additional evidence is however required to confirm these data
As DLC8 is commonly used to refer to both DLC1 and DLC2 proteins, it is preferable to adopt the following nomenclature (see PubMed:11602781) where DLC8a and DLC8b corresponds respectively to DLC1 and DLC2
A predicted cleavage site is located at position Val-157-158-Lys, giving a peptide of 34 residues instead of the 30 residues found for the purified protein. The 30 residues cathelicidin-BF could result from a further processing
There is a discrepancy in nomenclature: was submitted as Lp1.8 but is named Lp1.7 in PubMed:17400270
The three residues, Asp, His and Ser forming the catalytic triad are conserved (PubMed:28559405). However, the conserved motifs HGT and GTS, which encompass His and Ser residues of subtilases, respectively, are not present in PIMMS2, suggesting that the catalytic triad may be non-functional (PubMed:28559405)
The C-terminal section of the sequence may be incorrect
Was originally thought to be the product of one gene (ARTEMIS) that in fact corresponds to two separate genes At1g24485 and At1g24490
This protein seems to consist of a CitG domain with an incomplete N-terminal CitX region. The start site is approximate as there is similarity downstream up to the C-terminal codon of the adjacent sodA gene
Could be the product of a pseudogene. Probable pseudogene which is probably not functional. However, according to PubMed:11186129, some individuals may have an allele allowing the expression of a functional protein with an extended N-terminus
The gene for this protein is either identical to or adjacent to that of ATRIP. Some of the mRNAs that encode ATRIP also encode TREX1 in another reading frame
This potential protein codes for a PSK precursor that would produce a PSK-alpha that differs in the last residue (His) from a normal PSK-alpha (Gln). Furthermore there are no ESTs or cDNAs so far for this potential gene
Could be the product of a pseudogene. There is no ortholog for HP_0451 in strain J99
Although related to peptidase S1 family, lacks the conserved active Ser residue in position 346 which is replaced by a Thr, suggesting that it has no protease activity
Its ability to complement a strain lacking the homoserine kinase thrB gene suggested that it acts as a homoserine kinase (PubMed:10220164). The ability to rescue a thrB mutant is explained by the phosphoserine:homoserine phosphotransferase activity in presence of phosphoserine, in a mechanism different from homoserine kinase, suggesting it is inappropriate to define it as a homoserine kinase (PubMed:14699121)
While it is structurally defined as a knottin it lacks the conserved Cys residue in position 89
The function in peroxisome biogenesis is dubious
Lacks part of the deaminase domain and the catalytically essential zinc-binding residues. It is therefore most likely inactive
Was termed (Ref.1) RASSF5
Was originally called endoglucanase EG-III
Although related to the peptidase M67A family, it lacks the JAMM motif that probably constitutes the catalytic center and therefore it probably does not have a protease activity
A paper describing ATG4C tissue expression and activity has been retracted, due to concerns of image duplication in some of the figures
Wang et al., 2022 propose a shorter sequence (45-61) that the one shown in this entry. Furthermore, they suggest that its C-terminal Cys is amidated, whereas it is not followed by the usual Gly that provides the amide group
Although highly similar to the deubiquitinase OTULIN, lacks both the conserved active site residue Cys at position 136 which is replaced by an Asp residue and the conserved active site residue His at residue 347 which is replaced by a Gln residue, and does not have deubiquitinase activity
This toxin is functionally similar to alpha toxins and structurally similar to beta toxins
Conflicting results are reported regarding the interaction with PABPC1. Some studies found that the interaction depends on the presence of mRNA; others found that the interaction is direct and does not depend on the presence of mRNA
Supposed to contain a SH3 domain which is not detected by PROSITE, Pfam or SMART
Has been shown to be active in cv. Columbia (AC Q9M670) due to naturally occurring sequence variation in this strain. The sequence shown is from strains cv. Ge-1
There are two almost identical copies of this gene on chromosome 5q35. One copy is frameshifted and unlikely to encode a functional protein
This fragment is 100% identical to cardiotoxin 5 (AC Q98961) and cardiotoxin A4b (AC P07525) from the same species
A paper describing the crystal structure of this protein has been retracted due to evidence of fabricated data (see also US Office of Research Integrity Notice 2018-07782)
Could be the product of a pseudogene. Encoded by a single-exon gene, absent in other mammals, including mouse, and not supported by EST data. Expression could not be detected at the mRNA level in a genomic DNA-free liver library, nor at the protein level in kidney (PubMed:15246535)
In contrast to other members of the family, lacks the conserved Glu active site in position 473, which is replaced by an Arg residue, explaining why it is inactive
Although the complete sequence is not known with certainty, sequence shown here appears to be the most probable in accordance with human sequence ortholog
The exact range of the peptide is deduced from experimental results. It as been shown that the mature peptide weight is 10 kDa and is only composed of the first ShKT domain
Was originally thought to be a receptor for angiotensin II
Was originally (Ref.1) thought to be an RNA polymerase subunit
This TrpA is highly divergent compared to other bacterial TrpA. As C.trachomatis seems to have lost part of the trp biosynthetic operon, it is possible that this protein is not active
Was wrongly named DNA polymerase eta (POLH) somne authors (Ref.4). This protein corresponds to DNA polymerase theta (POLQ) and should not be confused with DNA polymerase eta (POLH) (AC Q9Y253)
Zhu and colleagues published information on another 'Neurotoxin MeuNaTx-6' in 2012 (AC E7CZY9), whose sequence highly differs from the one presented here
Initial enzymatic assays were performed with a protein sequence containing a Gly residue instead of a Val at position 224: such protein displays lower Ca(2+)-binding affinity and reduced transglutaminase activity
According to a report, lacks histone methyltransferase activity and regulates chromatin by interacting with HDAC3 and PAF1 complex (PAF1C) complex (PubMed:30455454). According to another publication, displays histone methyltransferase activity and directly trimethylates 'Lys-36' of histone H3 (H3K36me3) (PubMed:31515109)
Due to a highly divergent N-terminal sequence, the DNA-binding zinc finger could not be predicted
Was initially identified as a genuine component of the 26S proteasome
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AXS139ph = phosphorylated Ser-134
Manganese (Mn(2+)) transport by SLC40A1 remains controversial. Some in vitro studies have suggested that SLC40A1 transports minimal amounts of Mn(2+)
Structures with a target of 12 nt or less are in a cleavage-incompatible state. As target size increases cleavage becomes possible; a 15 nt RNA target is cleavage compatible while a 15 nt DNA target is cleavage incompatible
In contrast to the related histone demethylases jhdm1d and phf8, the conserved active His in position 321 is replaced by an Asn. However, the presence of an Asn residue neither affects binding to the catalytic iron nor abolishes demethylase activity
Was not identified as subunit of the 26S proteasome complex
Could be the product of a pseudogene. Lacks two of the four zinc-binding sites, which are conserved features of the MOB1/phocein family
This protein has not been reported as being secreted in the venom
Lacks the conserved Glu residue in position 482 essential for carbopeptidase activity. The mature form lacks catalytic activity towards synthetic peptide substrates
The role of UCP2/SLC25A8 in mitochondrial proton transport is a matter of debate. It was initially suggested that it mediates proton leak that increases net proton conductance in response to ROS such as reactive alkenals generated during fatty acid oxidation in mitochondria. By lowering the proton motive force, it would provide for feedback control of mitochondrial ROS metabolism limiting extensive ROS production and protecting cells against oxidative stress. This activity and its potential regulation by ubiquinones and nucleotides was disputed by later studies, which failed to reproduce the effect on proton conductance under physiological conditions. Rather than 'uncoupling' the link between electron transfer and ATP synthesis, it may couple metabolite transport to proton re-entry to allow for proton flux switching and optimal ATP turnover
The region from 1 to 163 was deduced from the genomic sequence and ESTs by similarity to the mouse sequence
Was initially reported to be a SUMO-dependent isopeptidase (PubMed:20516210), but this activity could not be confirmed (PubMed:24998930)
PubMed:1651324 sequence was originally thought to originate from mouse
Although strongly related to the peptide:N-glycanase enzyme, it lacks the conserved active site Cys in position 246, which is replaced by a Val residue suggesting that it has no activity
Signal and propeptide sequences are imported from ArachnoServer. The sequence differences may reflect different paralogs
Lacks one of the 9 transmembrane regions, which are conserved features of the family
An inactivating mutation in MYH16 probably appeared 2.4 million years ago in a hominid ancestor (PubMed:15042088). The inactivation and its correlation with evolution of the skull and cranial capacity in hominids is not clear (PubMed:15042088, PubMed:16376411). However, the gene is transcribed and the N-terminally truncated protein shown here was detected in a human cell line (PubMed:24240322). Its biological significance remains unclear since it lacks most of the domains important for the function of myosins (PubMed:15042088)
In contrast to other members of the family, shows reduced activity toward of m7G capped or incompletely capped RNAs, probably caused by the presence of an Asn residue in position 298 instead of a Gly (PubMed:30949699). The presence of an Asn-298 does not affect the decapping activity on NAD-cap RNAs (PubMed:30949699)
Could be the product of a pseudogene. Although it is strongly related to the hemolysin E toxin from E.coli K12 strain, it lacks all the N-terminal part of the protein, and it is therefore probably not functional
Represents a conventional myosin. This protein should not be confused with the unconventional myosin-15 (MYO15)
Most probably a non-functional protein that cannot participate in the synthesis of a productive immunoglobulin chain due to a mutation at position 43, corresponding to the first cysteine from the disulfide bridge, potentially leading to uncorrect folding (PubMed:9619395)
While it is structurally defined as a knottin it lacks the conserved Cys residue in position 110
Was originally isolated as a glutamyl-tRNA reductase
Could be the product of a pseudogene. This is a truncated version of AP endonuclease 1. In strain 972 and its derivative FY527, this gene has a stop codon in position 5, which disrupts the gene coding for this protein. PubMed:21193357 shows that the truncated protein is not functional. A full sequence for apn1 can be found in strains SPK19802 (S.pombe var. kambucha), NCYC 132, NCYC 683, NCYC 936 and NCYC 2722 (PubMed:21193357)
No activity observed following immunoprecipitation from adult head (PubMed:15673286). However, it is likely that the protein has phosphodiesterase activity based on the conservation of the active site as well as nucleotide-binding and metal-binding sites
Was originally thought to originate from Chlamydia psittaci
Was originally given the gene name dsbB; however another gene encoding a dsbB more closely related to that of the characterized E.coli protein bears this gene name (DSBB_SALTY, AC Q8XG65)
Could be the product of a pseudogene. The lack of an initiation codon prevents translation of this gene, in agreement with the observation that D-Tyr-tRNA(Tyr) deacylase activity cannot be detected in some strains of B.subtilis (PubMed:4292198, PubMed:24097941, PubMed:25441601). Mutagenesis to restore the start codon (in strain NCIB 3610, the parent of the fully sequenced 168) confers resistance to D-Tyr (PubMed:24097941)
Is indicated by Ref.1 as being involved in the transcriptional regulation of alginate biosynthesis. However, there is no evidence for such function in proteins belonging to this family
It is not clear whether a synaptic vesicle protein acts as its receptor; there is evidence for and against SV2 fulfilling this function (PubMed:19650874, PubMed:21483489, PubMed:19476346)
The precise role of Rnf8 at telomeres is subject to debate. 2 publications reported recruitment of Rnf8 at uncapped telomeres followed by regulation of non-homologous end joining (NHEJ), however the 2 publications reported different data and conclusions. According to a report, Rnf8 promotes telomere end protection and inhibits NHEJ by mediating ubiquitination via 'Lys-63'-linked ubiquitin and stabilization of Tpp1 at uncapped telomeres (PubMed:22101936). According to another report, Rnf8 recruitment at uncapped telomeres leads to promote NHEJ and the joining of deprotected chromosome ends by inducing H2A ubiquitination and TP53BP1 recruitment, suggesting that Rnf8 may have a detrimental role in case of telomeric crisis and enhance cancer development by aggravating telomere-induced genome instability (PubMed:21857671)
Lacks the Asn-Xaa-Arg residues, which are typical of the ACP-binding site and are essential for the association between AcpP and FabH
This polyprotein is encoded by an endogenous retrovirus expressed in some mouse strains. Multiple sequences are present in different regions of the genome, probably reflecting the different sites of integration of the exogenous retrovirus
Contrary to isoform 2, isoform 1 contains an RNA polymerase domain and has DNA-dependent RNA polymerase function. Synteny studies in vertebrates suggest that this isoform has been created by a mammalian-specific retrotransposition event of an ancestral gene which has been lost later on in this lineage
Association with the cytoplasmic side of the thylakoid membrane proposed in PubMed:9599805 is at odds with the subcellular location of orthologs in Synechocystis PCC 6803 and the presence of a signal peptide in this protein
Although PubMed:17875669 show that irx1 is dispensable for pronephric kidney development, PubMed:18715948 show that irx1 is required for formation of the pronephros
The gene name for this protein was previously taf-4 (PubMed:11963920). The nomenclature was changed in PMID:11963920 and so readers should take care to avoid confusion (PubMed:11963920)
Was originally (PubMed:19965467) thought to be required for the first step of diphthamide biosynthesis but further studies (PubMed:22188241, PubMed:23468660) clearly suggest that it is involved in the third step of diphthamide biosynthesis
It is uncertain whether Met-1 or Met-99 is the initiator
Was originally thought to have a disulfide bond between Cys-40 and Cys-99
Has been reported to be located in the Golgi apparatus (PubMed:26805781). However, another study was unable to detect Golgi localization (PubMed:32909282). Has also been reported to be located in the mitochondrion (PubMed:32909282). However, no mitochondrial localization was detected in another study which reported that the protein is primarily cytoplasmic (PubMed:31276219)
Has no detectable retinol saturase activity
Gln-122 is present instead of the conserved Glu which is expected to act as an active site proton donor
Was originally thought to be a selenoprotein and was known as sperm mitochondrial capsule selenoprotein
Functional studies have principally been done on a short synthetic amidated peptide (AA 45-67) instead of the native peptide (AA 45-70) which is not amidated
PubMed:9915832 demonstrated interaction with TSPO but later PubMed:12435798 demonstrated in the rat ortholog that is not associated with TSPO in the brain
PubMed:21205639 reported that AMA1 may also be involved in a signaling pathway leading to replication. However, PubMed:22523242 refutes this model
Despite the presence of an intact gas vesicle operon and gvpA transcripts, there is no evidence this strain produces gas vesicles. Operon expression in E.coli allows cells to float and produces irregularly shaped gas vesicles
Not expected to have protease activity
Was originally thought to release indoles from indoxyl-beta-glucosides
The predicted cleavage site for the activation peptide of HF2 is uncertain. It could have either 2 (ER) or 7 (KRGGCER) AA
Was originally thought to be a kinetochore protein, but co-localization has not been confirmed (PubMed:16079914). A more recent study identified it as a secreted protein (PubMed:16823372)
An expected heme iron ligand His residue was not found at position 83 in this sequence
Was initially thought to be the ortholog of mouse FEM1A
Showed to form heterodimers (PubMed:26267894, PubMed:31525467). However in a later study, showed to exist predominantly as a monomer (PubMed:32343703)
Lacks the conserved glutamate residue in position 469 that binds magnesium; it is replaced by a serine residue
Could be the product of a pseudogene. This protein lacks the central 330 residues found in AKIII, including a number of amino acids known to be important for function in E.coli
Could be the product of a pseudogene. The original protein is truncated by an IS3C element
Although strongly related to the membrane-bound acyltransferase family, it lacks the conserved His active site which is replaced by an Asn-415 residue
Exons 1a and 1b of the sequence reported in PubMed:17180578 are of human origin, however exon 2 shows strong similarity to the rat sequence
Native TIIIA is not detected in crude venom
Initially it was postulated to be an endoplasmic reticulum membrane protein, but later it was proved by combined proteomic analysis, APEX fingerprinting and confocal and electron microscopy to be localized to the mitochondrion instead
Lacks the typical His active site around position 277, suggesting it has no methyltransferase activity
Was originally suggested to be an RNase
Ser-854 is present instead of the conserved Asp which is expected to be an active site residue
Initially proposed to function as agmatinase but this activity was not proved when using the purified enzyme. A recent study showed that it rather functions as a guanidino acid hydrolase
Annotated as gyrB by PubMed:9797224 but is probably parE
The conserved active site Cys (or selenocysteine) residue in position 49 is replaced by an Arg and therefore lacks selenide-dependent monoselenophosphate synthetase activity
Weng et al. identified this gene on chromosome 14. However, it is not currently present on the reference genome assembly (GRCh38/hg38)
Compared to PRMT7 orthologs in other metazoans, it is shorter and lacks the C-terminal part
Has sometimes been attributed to correspond to FcR-IIC
There are several genes encoding the J region in the immunoglobulin lambda locus. The peptide described in this entry is a representative for all the peptides encoded by these genes. For an example of a full-length immunoglobulin lambda light chain see AC P0DOX8
In contrast to other serine-repeat antigen proteins (SERA) of the peptidase C1 family, contains a serine residue at the position of the canonical catalytic cysteine and has been shown to lack protease activity. However, other studies show that it has protease activity towards synthetic peptides in vitro (PubMed:13679369, PubMed:24769454, PubMed:29716996)
Was originally erroneously assigned as an alpha subunit
This sequence is an example of a full-length TR alpha chain. M/matrix protein 1-specific TRAV27*01J42*01C*01 TR alpha chain is generated by somatic recombination of variable TRAV27 (AC A0A087WT01) and joining TRAJ42 (AC A0A075B6Y9) gene segments spliced to constant TRAC (AC P01848) gene segment
Despite a certain similarity to SelA, PubMed:16201757 reported that this protein does not harbor SelA activity, i.e. it fails to bind to Ser-tRNA(Sec) and is not able to convert this substrate to selenocysteinyl-tRNA(Sec). It also does not convert O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec)
Ser-186 is present instead of the conserved Val which is part of the DDVD box
Lacks the conserved ATP binding sites, the conserved active site tyrosine at position 404, the conserved isoleucine at position 455 important for DNA bending, and the conserved magnesium binding site at position 143, and therefore probably lacks topoisomerase activity
In psbV2 it is not clear which residue serves as the second axial ligand for the heme group. Tyr-133 has been suggested (PubMed:12881497) but this seems unlikely as it is not conserved
SopE is not present in the complete genome strain LT2
A 10-residue longer version of this protein (starting with the sequence MLSGYIAGAI) has been identified in strain W3110 (PubMed:9740056). Other evidence, including ribosomal profiling and comparison with other bacterial genera, suggests this protein actually starts on the indicated Met codon (PubMed:25078267)
Lacks the conserved threonine residue in position 50, which is part of the carbamoylphosphate binding site; it is replaced by a leucine residue
The sequence displayed is a non-functional allele found in cv. Columbia. The protein in cv. Landsberg erecta (AC A0SWL0) only differ by two residues in positions 132 and 401 (Pro to Ala and Gln to Leu changes, respectively); these variations leading to activate the protein in cv. Landsberg erecta
Could be the product of a pseudogene. Similar to the N-terminal section of E.coli YidK, but does not seem to be complete and thus may not be functional as a transporter
Differs from other ScpB proteins because it has a much longer N-terminus
It is uncertain whether Met-1 or Met-53 is the initiator. Met-53 is probably the physiologically relevant initiator methionine, as Met-1 is dispensable for the expression of functional STE23, whereas Met-53 is not
The proteins described here are encoded by the gene CDKN2A, but are completely unrelated in terms of sequence and function to cyclin-dependent kinase inhibitor 2A (AC O77617) which is encoded by the same gene
Originally described as a 2-lysophosphatidate/LPA phosphatase (PubMed:12730698). However, following studies suggested it does not have such activity or only a residual one (PubMed:19766573). This is further supported by the fact that the phosphatase sequence motifs as well as the His residue acting as a nucleophile in active phosphatases of the PA-phosphatase related phosphoesterase family are not conserved (PubMed:19766573)
Was initially thought (PubMed:7750566, PubMed:1451776) to be a protease inhibitor
Gly-125 is present instead of the conserved His which is expected to be an active site residue
Defects in RASGRP2 were initially thought (PubMed:17576779) to be the cause of leukocyte adhesion deficiency type 3 (LAD3), a syndrome characterized by recurrent bacterial infections and major bleeding disorders. However, it was later shown (PubMed:19064721, PubMed:19234463, PubMed:19234460) that it is not the case and that LAD3 is caused by defects in FERMT3 gene
A number of papers have reported some protein lysine acetyltransferase activity in vitro (PubMed:14592445, PubMed:17631499, PubMed:19303003, PubMed:26882543, PubMed:27993683, PubMed:30165671). However, most experiments have been performed in vitro using a protein construct lacking the RNA-binding region at the terminus (PubMed:14592445, PubMed:17631499, PubMed:19303003). Recent evidence suggests that NAT10 mainly acts as a RNA cytidine acetyltransferase in vivo (PubMed:30449621)
It is uncertain whether Met-1, Met-5 or Met-17 is the initiator
Most probably a non-functional protein that cannot participate in the synthesis of a productive immunoglobulin chain due to a mutation at position 110, corresponding to the second cysteine from the disulfide bridge, potentially leading to uncorrect folding (PubMed:9619395)
Was initially named FOXK1a by some reports (PubMed:12402362, PubMed:16624804). It should not be confused with FOXK1 (AC P85037) paralog
Was originally (PubMed:2792375) thought to be a thiol protease inhibitor. The inhibitory activity was due to the presence of leukocyte cysteine proteinase inhibitor and not to cathelin itself
Substoichiometric amounts of non-heme iron (about 1 iron atom per ammonia monooxygenase complex) have been found, however it does not seem to function as a cofactor
In contrast to other members of the histone H2A family, this protein is much longer and has a highly divergent N-terminus. It is therefore unclear whether it is a real histone
Was wrongly referred as Gly dehydrogenase subunit P2 in PubMed:20089767
Was originally erroneously termed IAA26 and IAA30 (Ref.5)
Was originally thought to originate from Synechocystis PCC6803
It is unclear whether AAC39431 and AAC39432 represent different alleles or different products derived from two germacrene C synthase loci
Lacks the conserved threonine and arginine residues in positions 60 and 61, which are part of the carbamoylphosphate binding site; the threonine residue is replaced by a glycine residue
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BA1me1/2/3 = mono-, di- and trimethylated Ala-2; H2BK3me1 = monomethylated Lys-4; H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-39; H2BK34ac = acetylated Lys-40; H2BK143ub1 = monoubiquitinated Lys-146
Could be the product of a pseudogene, it is missing both the N- the C-terminus compared to orthologs
Palmitoylation of either Cys-308 or Cys-311 was reported to be sufficient to maintain functional coupling to G(s) proteins and signaling (PubMed:12488443). However, this publication was retracted due to figure duplication
According to PubMed:18060440, it is predicted to be a non-inhibitory serpin due to Val-384 and Thr-385 which differ from the conserved residues in the reactive center loop (RCL) that is involved after cleavage in covalent linking and inhibition of the target proteinase
Could be the product of a pseudogene. Encoded by an expressed retrotransposed copy of the SYT14 locus into an intron of TMPRSS11F
Could be the product of a pseudogene. Almost identical to BUD5 N-terminal
Was originally thought to be involved in the biosynthesis of a rhizopine, catalyzing the conversion of scyllo-inosamine to 3-O-methyl-scyllo-inosamine (PubMed:8349559). However, does not show methyltransferase activity in the presence of scyllo-inosamine and S-adenosylmethionine (SAM), and does not interact with rhizopines and SAM (PubMed:18536061)
Was thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB
According to a report, has no detectable intrinsic GTPase activity
Was originally assigned as At3g16230, which is now a completely different protein not related to aquaporins
Was originally (Ref.1) thought to originate from Leptospira interrogans serovar copenhageni, but is most probably from a Bacillus species
A palmitoylation site was proposed at Cys-77, but it was later shown that this cysteine is engaged in a disulfide bond (PubMed:24292069)
Was initially reported to localize in the endoplasmic reticulum (PubMed:12886954). However, it was later shown that it localizes to mitochondrion (PubMed:20038677)
The initiator methionine may be further upstream making the sequence a precursor
Was originally thought to belong to the DNA polymerase type-B family based on conserved motifs (PubMed:12093911). Has later been shown to be unrelated to B class DNA polymerases. The observation of a low level of polymerase activity in vitro, which is not required for its essential cellular function, may require further validation (PubMed:12695662)
Like its mammalian and yeast counterparts, PEX19-2 might be farnesylated and interacting transiently with the peroxisome membrane. However, this post-translational modification has not been demonstrated and only a trace of PEX19 was found associated with the peroxisome (PubMed:16923726)
Was termed importin alpha-3
While it is structurally defined as a knottin it lacks the conserved Cys residue in position 4
Was originally (Ref.1) thought to be a malate dehydrogenase
Was originally (PubMed:10192768) thought to correspond to a new class of synuclein. In fact, it is ortholog of the human gamma-synuclein
Contains a predicted homeobox domain which is degenerated and lacks residues that are important for DNA-binding. The protein localizes in the endoplasmic reticulum and not in the nucleus, which also argues against homeobox function (PubMed:15823095)
Human ortholog was initially reported to have ornithine decarboxylase or arginine decarboxylase activities, but it was later found that the mouse ortholog does not possess either of them
The sequence shown in this entry differs from the translation of the reference genome assembly (GRCh38/hg38) due to a variant (dbSNP:rs905709) in the reference genome which abolishes the intron 1 donor splice site leading to loss of CD300H transcripts
Was originally (PubMed:11278849) thought to modulate amyloid-beta toxicity by coupling to G protein. However, PubMed:12836168 showed that this effect is not direct
Could be the product of a pseudogene. Three frameshifts produce three separate ORFs
Product of a dubious gene prediction. Identified as a novel protein related to chemokines on the basis of a 3D profile-based proteome-wide analysis (PubMed:22586462)
Lacks the conserved Cys that is essential for lipidation
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me1/2/3 = mono-, di- and trimethylated Lys-10; H3S10ph = phosphorylated Ser-11; H3T11ph = phosphorylated Thr-12; H3K14ac = acetylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me = methylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me = methylated Lys-24; H3K27me1/2/3 = mono-, di- and trimethylated Lys-28; H3S28ph = phosphorylated Ser-29; H3K36me = methylated Lys-37
Was originally thought to be the IK factor, a cytokine involved in the negative regulatory pathway of constitutive MHC class II antigens expression
Strain CBS 513.88 / FGSC A1513 contains only one gene encoding for an extracellular endo-inulinase (inuA), contrary to other strains containing two genes (inuA and inuB)
Lacks the conserved Tyr residue in position 211 in the active site triad of Ser-Tyr-Lys necessary for dehydrogenase activity, suggesting that it has no oxidoreductase activity
The proteins described here are encoded by the gene CDKN2A, but are completely unrelated in terms of sequence and function to tumor suppressor ARF (AC Q8QZZ9) which is encoded by the same gene
Originally thought to dephosphorylate RET. However this paper was retracted due to manipulation of immunoblot data
Was originally (PubMed:1623198) reported to be isolated from an A.thaliana cDNA library. PubMed:9426607 authors have assigned that the sequence has been amplified from an other contaminating organism
Was originally thought to be a carotenoid-binding protein
Was initially thought (PubMed:1995329, PubMed:7705336, PubMed:9715910) to be a protease inhibitor
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC Q2PMM3
PubMed:15631621 shows two different sequences with Tyr-5 and with Glu-5 (see fig.2 and 4, respectively). The sequence of fig.2 is probably the erroneous one, since table 2 shows a Glu at position 5 and authors mention in the text the lack of aromatic residue on the first helix
HSN2 was originally thought to be an intronless gene lying within a WNK1 gene intron. It has been shown to be an alternative exon of the WNK1 gene in other mammalian species, including human and mouse. Isoforms bearing this exon (isoform 2 and isoform 3 in this entry) are specifically expressed in the nervous system in these species. system
Encoded in an intron of the ZNF512B gene (opposite strand)
Was originally called NPY5-R
This protein was originally thought to be a DNA-binding protein with a helix-loop-helix domain
Throughout PMID:11566890, the gene name taf-10 is used instead of taf-9, based on an earlier nomenclature; readers should be aware to avoid confusion
Was originally thought to be an ACP phosphodiesterase, but ACP phosphodiesterase activity was not detected in vivo or in vitro in further analysis
It is uncertain whether Met-1 or Met-88 is the initiator
Was termed (Ref.2) DEFB133
Was originally reported to be highly similar to the mammalian chorionicgonadotropic hormone receptor, but is not significantly related
Has been shown to be mono-ADP-ribosylated at Glu-657 and Glu-705 by PARP14 which prevents phosphorylation at Tyr-701 (By similarity). However, the role of ADP-ribosylation in the prevention of phosphorylation has been called into question (By similarity). It has been suggested that the lack of phosphorylation may be due to sumoylation of Lys-703 (By similarity)
The Dom34-Hbs1 complex was initially thought to mediate endonucleolytic cleavage of the mRNA to release non-functional ribosomes and degrade damaged mRNAs. DOM34 was reported to have endoribonuclease activity (PubMed:16554824, PubMed:17889667). However, it was later shown that it is not the case (PubMed:19420139)
Was originally (PubMed:17766251) thought to have endonuclease activity, but it could not be confirmed with orthologs purified from M.jannaschii (PubMed:18951093) and S.cerevisiae (PubMed:21183954)
The role of the N-terminal domain is controversial. A recent paper (PubMed:21864539) found it had no effect on enzyme activity, while another (PubMed:20826344) reported that it had an inhibitory role and had to be cleaved off for full enzyme activity
Was originally thought to be a killing factor. PubMed:8602138 showed that it is not involved in killing system
Lacks the conserved Glu active site in position 166, which is replaced by an Ala residue, explaining why it is inactive
It is uncertain if Met-1 or Met-4 is the initiator
The species of origin is incorrect in one of the citations where it was originally thought to be rice (PubMed:2143016). However, the sequence from that paper was later shown to originate from Petunia and the paper was retracted (PubMed:2235528)
Lacks the conserved cysteine (here Ser-49), present in the redox-active center, which is one of the conserved features of the thioredoxin family
Has low similarity to mammalian endoglins and lacks the canonical ZP (zona pellucida) domain typically found in these proteins
There are conflicting results concerning the role of ABCA7 in lipid transport. ABCA7 was described to play a role in apolipoprotein-mediated phospholipid and cholesterol efflux when expressed in HEK293 cells (By similarity). However, another report shows that ABCA7 deficiency does not influence cholesterol and phospholipid efflux in mouse primary macrophages, but leads to lower serum HDL cholesterol levels and a reduction in fat mass in female mice (By similarity)
Was originally thought (PubMed:7921236, PubMed:9353933) to be a high affinity ribose transport protein
May be the product of a pseudogene
Was initially thought to mediate to mediate poly-ADP-ribosylation of proteins (PubMed:10477748). However, it was later shown to act as a mono-ADP-ribosyltransferase (PubMed:25043379)
Conotoxins Lt1.1 and Lt1.2 are the same protein. They possess a different name due to their different precursors
This protein lacks the Tyr in position 450 required for a tyrosination/detyrosination cycle, the cyclic removal and re-addition of a C-terminal tyrosine residue; it is replaced by a Phe
Although it is highly related to enolase enzyme family, lacks the conserved Glu active site
Gene disruption gives rise to contradictory results (PubMed:24908487, PubMed:27457814, PubMed:28469074, PubMed:28346477, PubMed:30840898). The majority of studies report normal body weight, normal startle responses to noise and relatively minor behavorial defects (PubMed:24908487, PubMed:27457814, PubMed:28469074, PubMed:30840898). Another publication finds that gene disruption gives rise to mice with strongly reduced body weight and profound deafness. Gene disruption was due to random insertion of a Cre construct under the control of the TEK promoter. Analysis of the genomic DNA showed that in 21 cases the Cre construct had inserted in an Ig kappa locus, and in 13 cases the construct had inserted into the first intron of the SORCS2 gene, leading to strongly reduced SORCS2 expression (PubMed:28346477). The reasons for these discrepancies are not clear, but may be due to the way the experiments were done. The fact that an identical phenotype was found when the Cre construct under the control of the TEK promoter had inserted in an Ig kappa locus suggests that there are additional, unidentified causes that play a role in the observed defects
GMPPA is a close homolog of GMPPB, that has been shown to catalyze the formation of GDP-mannose, an essential precursor of glycan moieties of glycoproteins and glycolipids. It has been hypothesized that GMPPA might serve as a regulatory subunit and allow allosteric feedback inhibition of GMPPB by GDP-mannose. Alignment of GMPPAs and GMPPBs from various species shows that GMPPAs are characterized by a 2 amino acid-insertion (residues 11-12) in a highly conserved motif that borders the catalytic pocket and binds the nucleotide substrate in homologous enzymes. This insertion might inactivate the ancestral catalytic site, converting it to an allosteric site
The disulfide bond observed in the structure does not exist in vivo (PubMed:15907468). The enzyme reaction was initially thought to act via a redox-active disulfide bond mechanism; however the disulfide bond only takes place with inactive enzyme that lacks the copper cofactor (PubMed:25931126). The catalytic copper is required to activate oxygen and catalyze oxidative C-H activation (PubMed:25931126)
Lacks the conserved Glu active site which is replaced by Gly. Its enzyme activity is therefore unsure
Product of an intronless, probably retrotransposed, copy of AMD1. mRNA levels are 10-40 times lower than AMD1 (PubMed:9620866)
Was originally thought to be a steroid receptor on the basis of non-significant sequence similarities
Was originally (PubMed:9332376, PubMed:7860751) thought to constitute the ATP pyrophosphatase enzyme (NTPPH). However, it was later shown that it is probably not the case
A protein kinase activity has been reported kinase activity however PROSITE, Pfam do not detect a protein kinase domain. Its enzyme activity is therefore unsure
Was initially thought to act as a negative regulator of reactive oxygen species (ROS) that limits ROS production by phagocytes during inflammatory response, thereby playing a role during host defense (PubMed:24739962). However, these results were based on indirect evidences and could not be confirmed by another group (PubMed:29909984). It was later shown to act as a key regulator of transforming growth factor beta-1 (TGFB1) (PubMed:29909984)
The conserved zinc-binding site Asp residue in position 368 is replaced by an Asn
Lacks the phospho-accepting Asp (here Glu-71), present in the receiver domain, which is one of the conserved features of the two-component response regulators (ARRs) family
According to PubMed:27825305, lack of this gene leads to loss of glycopeptidolipids (GPLs) of the cell wall, but according to PubMed:27028886, this protein is not involved in the biosynthesis of GPLs
Studies in clathrin-mediated endocytosis of ITGB1 and TFR used a siRNA mixture of EPS15 and EPS15L1, and a Dab2 mutant with impaired binding to EH domain-containing proteins EPS15 and ITSN1 suggesting a partially overlapping role of the EH domain-containing proteins
Strain CLIB 122 / E 150 has a defective URA3 sequence (ura3-302) which is disrupted (positions 8 to 249) by S.cerevisiae SUC2
Was originally (PubMed:9851025) thought to originate from Pseudomonas sp. Then it was changed to Enterobacter cloacae, then to P.putida
Has been shown to be inactive in cv. Columbia (AC Q67Z93), cv. Landsberg Erecta and cv. Wassilewskija due to loss-of-function mutations. The sequence shown is from strain cv. H51
The N-terminus was initially (PubMed:2758468) thought to be fused with glucose-6-phosphate-dehydrogenase (G6PD) protein in vivo. However, PubMed:2570640 showed that it encodes a GMP reductase, and PubMed:1694726 showed that the chimeric protein is an artifact
Was originally thought to be a bifunctional enzyme with transglycosylase and transpeptidase activities
It was initially reported to be a ligand for some putative receptor present on T-, B-, natural killer (NK) cells and various human cell lines. However, PubMed:12672804 showed that it does not bind any receptor
In contrast to other members of the family, it is not lipidated
Knockout experiments to inactivate Spata6 were first attempted but were unsuccessful, because chimeras did not transmit the targeted allele to their progeny, generating high-percentage of lethality for chimeric embryos (PubMed:12771232). This suggests that genes other than Spata6 may have been targeted or affected in this study (PubMed:25605924)
It has been reported that many phenotypes associated with the Bristol N2 reference allele of the receptor npr-1 may reflect a neomorphic gain-of-function sensitivity of the receptor to flp-18 in addition to sensitivity to flp-21
Was originally identified in the small subunit (28S) of mitochondrial ribosomes that were purified on sucrose gradients (By similarity). This observation has been challenged by experiments showing MRPS36 copurification with the oxoglutarate dehydrogenase complex (OGDC), also called alpha-ketoglutarate dehydrogenase complex (KGDH). Both mitochondrial ribosome 28S subunit and OGDC have a similar size and OGDC is highly abundant, therefore OGDC has been found to contaminate ribosomal preparations performed by sequential centrifugation steps (PubMed:25165143). In addition, MRPS36 could not be located in the structure of the human mitochondrial ribosome, supporting the hypothesis that it is not a mitoribosomal protein (By similarity)
Has been described as heme-binding protein (PubMed:15518569) in mouse, but the human protein does not bind hemin. His-42, a residue essential for heme binding in mouse, is not conserved in all orthologs, or in the heme-binding family member HEBP1
Was initially characterized as a beta-1,3-N-acetylglucosaminyltransferase involved in the synthesis of poly-N-acetyllactosamine, able to initiate the synthesis or the elongation of the linear poly-N-acetyllactosaminoglycans (PubMed:9405606). However, it was later shown that it acts as a beta-1,4-glucuronyltransferase (PubMed:25279699, PubMed:25279697)
In contrast to other xyloglucan endotransglucosylase proteins, the catalytic motif is atypical and lacks the proton donor site. It therefore may not be functional in vivo
Product of a dubious CDS prediction. This protein is encoded in a genomic region overlapping with the 3'-UTR of GNAI2
Despite significant sequence similarity to lipoamide dehydrogenases this protein cannot catalyze the reduction of lipoyl substrates. It lacks one of two cysteine residues involved in dithiol-disulfide interchange with lipoyl substrates and a His-Glu pair involved in general acid catalysis
Originally thought to be a histone deacetylase and shown in vitro to have this activity (By similarity). Has also been shown to be involved in MSH2 deacetylation (By similarity). However, protein deacetylase activity is a matter of debate, as 3D structure analysis shows that a glutamate gatekeeper and a sterically constricted active site confer specificity for N(8)-acetylspermidine hydrolysis and disfavour acetyllysine hydrolysis. Supporting this observation, has been shown to exhibit only very low activity, if any, towards acetyl-lysine peptide substrates (By similarity)
This bacteria is missing genes associated with the botulinum neurotoxin cluster in Clostridia (botR, hemagglutinin genes and ORF-X proteins), so it is not clear if it is actually a toxin. The in situ target might not be animal as this bacteria was isolated from fermented rice grains
X-ray structure in 1YIZ has been refined and redeposited in 5VEH
The humanin peptide described here has been shown to be biologically active but is the product of a mitochondrial gene, MT-RNR2 (PubMed:12009529). If translation of the mRNA occurs in the mitochondrion rather than in the cytoplasm, then the usage of the mitochondrial genetic code would lead to the production of a shorter peptide lacking the last three C-terminal residues. The mechanisms allowing the production and the secretion of humanin remain unclear. The possibility exists that the physiologically active humanin peptide is encoded by one of the related genes present in the nuclear genome (PubMed:19477263)
Although strongly related to acetylglycerophosphocholine esterase enzymes, it lacks the active site and has no lipase activity
It is not known if this is Pep A-2 or Pep A-3
There are 3 copies of the NOMO gene on chromosome 16p12-p13: NOMO1 (AC Q5JPE7), NOMO2 (AC Q5JPE7) and NOMO3. All 3 are extremely similar, which makes their individual characterization difficult. Thus, most experiments probably do not discriminate between the different members. The results reported in other entries may therefore apply for this protein
Could be the product of a pseudogene. It is encoded in the reverse strand of the region coding for rpoK
In cv. Columbia, could be the product of a pseudogene (AC P0DKH2) due to a frameshift in position 140. The resulting shorter protein lacks the conserved features of the family
There is a disagreement about sodium-independent transport of cationic amino acids, such as L-arginine and L-lysine (By similarity). While Padmanabhan et al (PubMed:23451088) shown that SLC38A4 may mediate sodium-independent transport of cationic amino acids, such as L-arginine (PubMed:23451088). Recent studies by Fairweather et al., using quantitative LC-MS analysis, shown any transport activity of cationic amino acids, such as L-arginine and L-lysine (By similarity)
Although it belongs to the tubulin--tyrosine ligase family, the TTL domain lacks some of the ATP binding sites predicted to be essential for TTL activity (PubMed:23251473). Lacks tyrosine ligase activity in vitro (PubMed:23251473). Lacks glutamylation activity in vitro (By similarity). Although TTLL12 contains a potential SET-like domain in the N-terminus, it does not have lysine methyltransferase activity towards histone in vitro (PubMed:23251473)
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC A0A398
Lacks the second part of the protein and the active site Asp and His residues which is a conserved feature of peptidase S10 family
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 392 in the dsPTPase catalytic loop and does not have phosphatase activity
Ref.2, PubMed:1924265 and PubMed:10409823 N-terminal modification was incorrect. X-ray structure has cyclic pyroglutamic acid
Has been classified as a the potassium channel toxin alpha-KTx 22.3 in PubMed:22230549. Since the subfamily 22 has already been attributed, this peptide should be reclassified as alpha-KTx 23.3
Has been shown to interact (via PDZ domain) with atad-3 (via C-terminus) (PubMed:22245785). The physiological significance of this interaction is uncertain; the atad-3 C-terminus is expected to be within the mitochondrial matrix
Although it belongs to the tubulin--tyrosine ligase family, the TTL domain lacks some of the ATP binding sites predicted to be essential for TTL activity (By similarity). Lacks tyrosine ligase activity in vitro (By similarity). Lacks glutamylation activity in vitro (PubMed:17499049). Although TTLL12 contains a potential SET-like domain in the N-terminus, it does not have lysine methyltransferase activity towards histone in vitro (By similarity)
Seems to be truncated compared to other members of this subfamily
Was originally thought to be located in the peroxisome (By similarity). However, was later shown to be cytosolic (PubMed:12736493)
Was originally (PubMed:3562437, PubMed:2502543) thought to be the pancreatic lipase, but has been shown to lack lipase activity
This sequence containing mHag HB-1 may not represent the full-length protein, because functional domains are absent in this short gene product
PubMed:9892612 postulated that the initiator methionine is coded by a non-canonical CTG leucine codon
Protein/histone deacetylase activity in vivo is uncertain. The 3D structure analysis of the zebrafish ortholog shows that a glutamate gatekeeper and a sterically constricted active site confer specificity for N(8)-acetylspermidine hydrolysis and disfavour acetyllysine hydrolysis. Supporting this observation, has been shown to exhibit only very low activity, if any, towards acetyl-lysine peptide substrates. However, histone deacetylase activity has been observed in vitro and HDAC10 has also been shown to be involved in MSH2 deacetylation
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-26; H2BK143ub1 = monoubiquitinated Lys-132
Has been termed C11orf2, but is not the official C11orf2 as defined by HGNC
This protein has been proposed to undergo autophosphorylation on tyrosine residues which is induced in response to cell adhesion (PubMed:1371458). However, as mammalian orthologs of this protein seem to lack kinase activity this protein may associate with, and be phosphorylated by, an unknown active tyrosine kinase
Was originally proposed to code for two separate adjacent ORFs, HI_1182 and HI_1183
PubMed:16857010 reports that adult expression is restricted to the intestine and absent from the liver, whereas PubMed:19953126 detects expression in the liver, intestine, heart, testis, ovary, and gills
It was originally thought that there are multiple subunits in the exosome that have exonuclease activity but it was later shown (PubMed:17173052, PubMed:17174896) that only this DIS3/RRP44 subunit of the exosome core has this activity
This protein is predicted to be unusually long in N.olivacea
Was originally thought to originate from A.sobria
Could be the product of a pseudogene. According to PubMed:12388767, it is not clear whether this transcript encodes a protein
Was originally identified as a repressor of the glycerol-3-phosphate regulon
Lacks one conserved zinc binding site
It is uncertain whether Met-1 or Met-55 is the initiator. However, for the rat ortholog it has been shown that the equivalent alternative isoform is produced by alternative initiation at a conserved initiator methionine at position 55
A report observed N-glycosylation at Asn-89 (PubMed:19139490). However, as the protein is not predicted to localize in an extracellular compartment of the cell, additional evidence is required to confirm this result
Was shown to be an inhibitor of protein-phosphatase 1, to promote cell growth and cell cycle progress at the G1/S transition and to interact with PPP1CB (PubMed:18310074). The article has later been withdrawn by the authors
An article reported an interaction with LPA2; however, this paper was later retracted. An article reported an interaction with LPA3; however, this paper was later retracted
Could be the product of a pseudogene. Lacks the C-terminal part of the protein containing the NADP-binding domain, which is a conserved feature of the family
Could be the product of a pseudogene. This sequence is shorter than orthologs and lacks the conserved active site Tyr residue
There is a confusion with this peptide name. In the original refence Chen et al., 2006, authors attribute this sequence to Phylloseptin-9. This sequence is erroneously reproduced as 'Phylloseptin-11' in Amiche et al. 2008, in the nucleotide entry, and in the antimicrobial peptide database
This sequence does not have the Cys-Cys motif at the C-terminal as do homologous sequences from yeast species. It may be either geranylgeranylated at an alternative motif or it may be subject to farnesylation on Cys-215
Lacks catalytic activity, even though the active site residues are conserved
This ORF was incorrectly assigned as MEI4
Has been suggested to be a pseudogene, RNA seq evidence shows this is transcribed
Human ortholog was initially reported to have ornithine decarboxylase or arginine decarboxylase activities, but it was later found that the mouse ortholog does not possess neither of them
Could be the product of a pseudogene. This is the C-terminal part of aquaporin-2. A natural 11 bp deletion in position 109 leads to a frameshift, which disrupts the gene coding for this protein and produces two ORFs SCRG_04941 and SCRG_04940. A contiguous sequence for aquaporin-2 can be found in strain Sigma 1278B (AC P0CD89)
According to some authors (PubMed:12165468) it is involved in axon guidance by promoting ubiquitination of comm and subsequent endocytosis of the comm/robo complex. However, according to others (PubMed:15657595), it is not the case
Non-collagenous domain 1 seems to be the predominant tissue form from which endostatin is cleaved. However, the proteolytic cleavage site to generate non-collagenous domain 1 is not known. Soluble recombinant non-collagenous domain 1 amenable to biochemical studies has been used instead
Was originally thought to be involved in hexaheme nitrite reductase (cytochrome c552) expression
Although it is unknown whether it is a serine/threonine or a tyrosine protein kinase, it is strongly related to the serine/threonine-protein kinase family
Was reported to trimethylate H3 'Lys-9' and H4 'Lys-20' (PubMed:12397363). Was also reported to bind non-coding RNAs of trithorax response element (TRE) (PubMed:16497925). However, both papers were retracted because some data, results and conclusions are not reliable
Could be the product of a pseudogene. This is a truncated version of an allantoate permease subfamily member protein. Strain S288c has a stop codon in position 170, which disrupts the gene coding for this protein and produces two ORFs YOL163W and YOL162W
Was originally thought to confer resistance to staurosporine
It is unclear if hemoglobin Beckman (Hb Beckman) is defined by p.Ala136Glu or p.Ala136Asp. Hb Beckman has been originally identified by reverse phase-HPLC and tandem mass spectrometry, and has been reported as variant p.Ala136Glu (Ref.140). Subsequently, variant p.Ala136Asp has been reported based on HBB gene complete sequencing results (PubMed:19453576). Variant p.Ala136Asp has also been detected by mass spectrometry (PubMed:26209877). Although the name Hb Beckman is currently used for variant p.Ala136Asp, it cannot be ruled out that Hb Beckman is indeed variant p.Ala136Glu (PubMed:19453576)
Lacks the conserved His heme iron ligand in position 81. There is a Gln in this position
Was originally (PubMed:8195160) thought to be a nuclear protein involved in transcriptional regulation of genes required for the functional assembly of mitochondrial respiratory proteins. This was later proven not to be the case (PubMed:11509667)
The C-terminal part of the kinase domain is truncated
The sequence shown in this entry differs from the translation of the reference genome assembly (GRCh38/hg38) due to a nonsense variant creating stop codon at position 205 in the reference genome
Mutagenesis results from PubMed:8858103 should be interpreted carefully, since the authors found waglerin-2 (AC P58930) as inactive, despite the finding of other groups that found this peptide equipotent in lethality to waglerin-1
The molecular function of NOTUM has remained unclear for many years. It was initially thought to hydrolyze glycosaminoglycan (GAG) chains of glypicans, thereby affecting glypicans ability to interact with Wnt ligands (PubMed:12015973, PubMed:12000788). It was later reported to trigger glypican shedding, by mediating cleavage of their GPI-anchor (PubMed:15469839). However, while NOTUM specifically inhibit the Wnt signaling pathway, more pleiotropic effects would be expected from an enzyme affecting glypicans. It was finally shown that it requires glypicans to suppress Wnt signaling, but does not cleave their GPI-anchor (PubMed:25731175). It acts by mediating depalmitoleoylation of WNT proteins, impairing WNT binding to frizzled receptors (PubMed:25731175)
Mao et al suggest that CLN3 has five transmembranes with a long lumenal N-terminus because their antibody does not immunoprecipitate the N-terminus in the presence of microsomes
According to a report, it is incorporated into stress granules upon arsenite-induced stress and associates with heme-regulated kinase and eIF-2-alpha (EIF2S1) in regulating eIF-2-alpha phosphorylation (PubMed:20154146). However, no effect in eIF-2-alpha phosphorylation have been observed by another study (PubMed:24550447)
PubMed:12740394 has shown that the protein is cleaved at Lys-122 but PubMed:15355958 has shown that the cleavage site is at Gly-120 as in other mammalian orthologs
Was originally identified as 39S ribosomal protein L56 (MRP-L56)
PubMed:12633865 reports expression in the ventral endoderm at 36 hpf, whereas PubMed:16857010 does not detect expression this early. The different timings may reflect strain-specific differences
In contrast with human ortholog, not able to transport steroid sulfate conjugates estrone 3-sulfate (E1S), dehydroepiandrosterone sulfate (DHEA-S) and pregnenolone sulfate (PregS)
It is uncertain whether Met-1, Met-8 or Met-23 is the initiator
This protein has also been shown to act as an inducible nitric oxide synthase (iNOS) (PubMed:12757708), but the paper has been retracted (PubMed:15599984)
The gene name MAGI1, shown in this entry as a synonym, is an obsolete human gene nomenclature committee-approved name. It should be noted that MAGI1 currently is the official name for the unrelated membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
Highly similar to the L-lysine 2,3-aminomutase. However lacks lysyl-binding Asp residues at positions 332 and 369, that are replaced by Lys and Asn residues, respectively (PubMed:17222594)
The kinesin motor domain is truncated at the C-terminus in comparison with other members of the gene family
Was originally thought to have DNA binding activity (PubMed:12192004). However, more recent studies show that CDT1 binds DNA indirectly via ORC
In contrast to other HIT domain proteins, lacks the conserved histidine triad motif (HXHXH), suggesting it has no hydrolase activity
Although it contains a Lon N-terminal domain also found in proteases of the peptidase S16 family, it does not contain the ATP-binding and catalytic domains, suggesting that it has no protease activity
In contrast to the rodent orthologous protein, it is longer in N-terminus and no signal sequence is detected by any prediction method
The active site Cys-600 is replaced by a Asp residue suggesting that egg-4 may lack catalytic activity. Despite the lack of catalytic activity, egg-4 may retain the capacity to bind to phosphorylated substrates. Does not dephosphorylate mbk-2 (PubMed:19879842)
The deduced amino acid sequence of the orf11 gene lacks a DNA-binding domain and contains only the conserved domain (termed 'middle homology region') that is commonly found in Zn(II)2Cys6-type transcription factors
Was originally thought to be (S)-tetrahydro-berberine oxidase (EC 1.3.3.8)
Highly divergent compared to other bacterial HisD
Recombination protein U, a short form proposed to initiate from Met-33, which is equivalent to RecU-delta1-32, is not detected in vivo, and would not be functional. The name is misleading and should no longer be used
Was originally named prfA (Penicillin-binding protein-related factor A, PBP-related factor A) due to its proximity to the ponA gene; this name is misleading and should no longer be used
Was originally termed SOX-9
In contrast to the ortholog protein in primates, human KIF25 protein is shorter at the N-terminus. While the kinesin motor domain is intact, it is unknown whether the absence of the N-terminus affects the microtubule-dependent motor activity
Was originally (PubMed:8493092) identified as a gene coding for an antisense RNA to thymidylate synthase, and was proposed to down-regulate TYMS activity (PubMed:8869746), possibly by promoting the degradation of TYMS mRNA via an antisense RNA-based mechanism (PubMed:12084460)
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-5; H2AK7ac = acetylated Lys-9; H2AS128ph = phosphorylated Ser-130
There are conflicting results concerning the role of ABCA7 in lipid transport. ABCA7 was described to play a role in apolipoprotein-mediated phospholipid and cholesterol efflux when expressed in HEK293 cells (PubMed:12917409, PubMed:27472885). However, another report shows that ABCA7 deficiency does not influence cholesterol and phospholipid efflux in mouse primary macrophages, but leads to lower serum HDL cholesterol levels and a reduction in fat mass in female mice (By similarity)
Although assigned as two separate genes (PPP1R12C and LENG3), it is probable that LENG3 does not exist by itself and is a part of the PPP1R12C gene
Was originally thought to be a mitochondrial ribosomal protein (PubMed:9151978), but has not been identified in the structure of the yeast mitoribosome (PubMed:28154081)
Asn-56 is present instead of the conserved His which is expected to be an active site residue. Asn-102 is present instead of the conserved Asp which is expected to be an active site residue. Thr-196 is present instead of the conserved Ser which is expected to be an active site residue. It is therefore expected that this protein has lost its catalytic activity
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 391 in the dsPTPase catalytic loop, suggesting that it has no phosphatase activity
It was shown by two studies that dimerization of DEFA5 is crucial for antimicrobial activity (By similarity). Another study, however, states that dimer formation is not indispensable for antimicrobial activity of DEFA5 (By similarity)
CD68 is a commonly used marker for macrophages. However, a number of studies (PubMed:15194571, PubMed:15647451, PubMed:18405323) have shown that CD68 antibodies react with other hematopoietic and non-hematopoietic cell types, suggesting that CD68 may not be a macrophage-specific antigen
This sequence has been copied from a figure, and no information except the name are available for it. The species, and the sequence origin are only deduced to be C.ferrugineus and nucleotide sequence
May have little or no activity due to the lack of several residues essential for manganese binding and catalytic activity
In contrast to other cytidine and deoxycytidylate deaminase, lacks to conserved Glu active site in position 218 which is replaced by a Val residue, suggesting that it acts as a regulatory subunit
The protein name 'Bcl2 antagonist of cell death' may be misleading. The protein antagonises Bcl2-mediated repression of cell death, hence it promotes apoptosis
Has a EGEVF motif instead of the conserved GG[D/E]EF motif characteristic of active diguanylate cyclases, suggesting that CdgI may be inactive. However, site-directed mutagenesis shows that it is probably a functional diguanylate cyclase
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-8; H2BK33ac = acetylated Lys-29; H2BK34ac = acetylated Lys-30; H2BK143ub1 = monoubiquitinated Lys-135
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-9; H2BK33ac = acetylated Lys-35; H2BK34ac = acetylated Lys-36; H2BK143ub1 = monoubiquitinated Lys-141
It is unclear if SLC25A4/ANT1 constitutes a pore-forming component of mitochondrial permeability transition pore (mPTP) (PubMed:14749836, PubMed:31489369). Initial reports, based on deletion of Slc25a4/Ant1 and Slc25a5/Ant2, suggested that ADP/ATP translocase rather acts as a regulator of mPTP (PubMed:14749836). However, deletion of all ADP/ATP translocase components (Slc25a4/Ant1, Slc25a5/Ant2 and Slc25a31/Ant4) completely inhibits mPTP, suggesting that ADP/ATP translocase constitutes a pore-forming component of mPTP (PubMed:31489369). Discrepancy between reports may be caused by overexpression of Slc25a31/Ant4 in mice lacking Slc25a4/Ant1 and Slc25a5/Ant2, which compensates for the loss of Slc25a4/Ant1 and Slc25a5/Ant2 (PubMed:31489369)
Reported to be glycosylated with sialylated N-glycans and in its sialylated form to interact with MYH9 (PubMed:12944413). However, this publication was retracted due to image duplication in the figures
Ile-16 is present instead of the conserved His which is expected to be an active site residue. Substrate-binding sites are also not conserved. Thus, this enzyme may not display fae activity
Was initially thought to be the ortholog of mouse KRT71
An article that concluded that AURKA-mediated phosphorylation of BRCA1 Ser-308 plays a role in the normal cell cycle G2/M transition was withdrawn due to data manipulation of flow cytometry data
It is not sure if the variants are due to different alleles or to the existence of at least two genes
Ref.1 indicates that this sequence represents the C-terminal part of a protein produced after trans-splicing. No experimental data confirms this assertion
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4me = methylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me = methylated Lys-10; H3S10ph = phosphorylated Ser-11; H3T11ph = phosphorylated Thr-12; H3K14ac = acetylated Lys-15; H3K14me = methylated Lys-14; H3K18ac = acetylated Lys-19; H3K18me = methylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me = methylated Lys-24; H3K27me = methylated Lys-28; H3S28ph = phosphorylated Ser-29; H3K36me = methylated Lys-37
Was originally (Ref.1) thought to be a receptor for neuropeptide Y type 3 (NPY3R) (NPY3-R)
In contrast to other phospholipases, it lacks the typical His active site (His->Gln in position 63)
Has distant sequence similarity to aminopeptidases that belong to the MEROPS peptidase family M28, but binds only one zinc ion, contrary to the metallopeptidases of the MEROPS family M28 that bind two catalytic zinc ions. Lacks the active site Asp and Glu residues that are conserved in family members with aminopeptidase activity
Two articles reported an interaction with LPA2; however, these papers were later retracted
The sequence shown here has been extracted from PDB entry 1B70
Although strongly related to polypeptide N-acetylgalactosaminyltransferase proteins, it lacks the conserved Asp-Xaa-His motif in positions 199-201 and the conserved His residue in position 330 which are involved in the binding to the cofactor Mn(2+). This suggests that it may have lost its activity
Interaction with BANP was reported to enhance phosphorylation on Ser-15 upon ultraviolet irradiation (PubMed:15701641). However, the publication has been retracted due to image duplication and manipulation. Interaction with BANP has been confirmed in mouse studies (By similarity). Phosphorylation at Ser-15 has been confirmed by other studies (PubMed:10570149, PubMed:11554766, PubMed:16219768, PubMed:15866171, PubMed:17317671, PubMed:17954561, PubMed:20959462, PubMed:25772236). Its nuclear and cytoplasmic localization has been confirmed by other studies (PubMed:15340061, PubMed:17170702, PubMed:19011621, PubMed:21597459, PubMed:22726440, PubMed:17591690, PubMed:18206965)
Was originally (Ref.1) incorrectly stated to be similar to the S14P family of ribosomal proteins
Conflicting results are reported regarding the interaction with PABPC1. Some studies found that the interaction depends on the presence of mRNA (PubMed:23711370, PubMed:28650797). Others found that the interaction is direct and does not depend on the presence of mRNA (PubMed:20430826, PubMed:24532714, PubMed:25940091)
PubMed:12174087 and PubMed:12193612 report that SpiC is not translocated into the infected cell, and is localized in the bacterial cytoplasm. They show it is required for secretion of SseB and SseC virulence proteins into infected cells
Could be the product of a pseudogene. The N-terminus is much shorter than in related proteins
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 375 in the dsPTPase catalytic loop, suggesting that it has no phosphatase activity
It is not sure if the metal-binding site is on position 81 or 82
The proteins described here are encoded by the gene CDKN2A, but are completely unrelated in terms of sequence and function to cyclin-dependent kinase inhibitor 2A (AC Q9R0Z3) which is encoded by the same gene
Was erroneously thought to be a glycosyltransferase
Was originally assigned to be BF-2 (FOXG1)
Was originally (PubMed:1551905, PubMed:8252639) identified in genetic screens for bona fide RNA splicing factors, but it has later been shown that not the MRS2 protein per se but certain magnesium concentrations are essential for group II intron splicing
In contrast to other members of the family, it lacks the conserved active sites, suggesting that it has no phospholipase activity
Protein kinase activity is reported (PubMed:24735981). However, no protein kinase domain is detected by any prediction method (PROSITE, Pfam). Its enzyme activity is therefore unsure
Product of a dubious gene prediction. Encoded in intron of the PATZ1 gene
Could be the product of a pseudogene. Lacks the N-terminal half of the protein found in other members of this family
Lacks the conserved sequence motif DxxDxDxE that is essential for the catalytic activity of chitinases of the glycosyl hydrolase 18 family, and therefore has no chitinase activity
Reported to be a member of the bZIP family but does not match diagnostic signatures for this family and has low similarity to other family members
Ser-67 is present instead of the conserved His which is one of the active site residues. It is therefore expected that this protein lacks catalytic activity
The N-terminal region is predicted based on cross-species conservation and limited EST data. Exact gene structure in this region is unclear
This sequence lacks the conserved His that serves as a ligand for the 7Fe-Mo-9S-C-homocitryl cluster
To obtain a protein of the same size as its counterpart in other Mycobacteria, it would be necessary to introduce a frameshift. As both independent DNA sequences are identical, this seems to be a natural frameshift and the M.leprae sequence is therefore N-terminally truncated by about 30 residues
Subsequent steps in cytosine demethylation are subject to discussion. According to a first model cytosine demethylation occurs through deamination of 5hmC into 5-hydroxymethyluracil (5hmU) and subsequent replacement by unmethylated cytosine by the base excision repair system. According to another model, cytosine demethylation is rather mediated via conversion of 5hmC into 5fC and 5caC, followed by excision by TDG
Was initially characterized as an N-monooxygenase proposed to hydroxylate rifampicin at the N2' atom to produce 2'-N-hydroxyrifampicin. Later structural studies showed that RIFMO catalyzes a different reaction involving monooxygenation of position 2 of the naphthyl group, followed by linearization of the antibiotic (PubMed:29578336)
There is some conflicting nomenclature, as some groups still name this protein B3gnt1 (PubMed:18008318). The correct and official nomenclature is however B3gnt2
This protein lacks the required Tyr in position 450; it is replaced by a Phe
Experiments with human recombinant protein (in mouse system by intracerebroventricular treatment) are reported for BMP8B but the protein is corresponding to BMP8A according sequence data provided by the supplier; related experiments with Bmp8b-/- mice show similar results
Due to its high GC content it turned out to be difficult to sequence the 5' end of the gene encoding the N-terminal proline-rich region of the protein and to unambiguously determine which sequence is correct. We display the sequence described in PubMed:16159594. This sequence fits better with orthologous sequences but is not consistent with the human reference genome sequence
Has been classified as a the potassium channel toxin alpha-KTx 22.6 in PubMed:22230549. Since the subfamily 22 has already been attributed, this peptide should be reclassified as alpha-KTx 23.6
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC Q0G9F5
The mechanism by which the SCF(FBXL21) complex stabilizes CRY proteins (CRY1 and CRY2) is still unclear: according to a report, the SCF(FBXL21) complex does not catalyze 'Lys-48'-linked polyubiquitin chains, but catalyzes a different type of ubiquitin chains that do not lead to degradation (PubMed:23452856). According to a second report, FBXL21 has a higher affinity for CRY proteins compared to FBXL3, while the SCF(FBXL21) complex has weaker ubiquitin-ligase activity compared to the SCF(FBXL3) complex: as a consequence, the SCF(FBXL21) complex protects CRY proteins from SCF(FBXL3) activity and degradation in the nucleus, while it promotes slow degradation of CRY proteins in the cytosol (PubMed:23452855)
Lacks the phospho-accepting Asp (here Glu-66), present in the receiver domain, which is one of the conserved features of two-component response regulators (ARRs) family
This is an X-ray determined sequence, alanine is indicated in position where no side chain could be observed
Lacks the conserved active site residues critical for glyoxalase activity. Its enzyme activity is therefore unsure
The N-terminal peptide may increase IL1B secretion by peripheral blood monocytes; however as this region is probably in the cytosol, the in vivo relevance of this observation needs to be confirmed
The 192-residue sequence submitted as AAS45276 has been confirmed by the authors of PubMed:22128173 to be incorrect as translation starts from a downstream methionine
Was originally called RBOHA
Bioinformatics prediction programs detect only 9 instead of 10 transmembrane regions
Was originally (PubMed:1937036, PubMed:1718870) thought to originate from Chlamydia trachomatis
Could be the product of a pseudogene. NIT1/YIL164C seems to be the N-terminal part of a putative nitrilase-like protein formed of NIT1/YIL164C and YIL165C
In contrast to other members of the family, lacks the C-terminal ricin B-type lectin domain, which contributes to the glycopeptide specificity. The precise function of the enzyme is therefore unsure
Was originally (Ref.6) erroneously named IAA31
Although a transcript has been detected, this protein has no catalase activity. Comparison with orthologs shows that the last 50 C-terminal amino acids, which seem to be essential for activity, are missing due to a natural frameshift in position 446. The sequence also contains six missense mutations, including the replacement of Pro-317 with Ser, which could modify the structure of the protein. Both alterations seem to contribute to the lack of catalase activity
The conserved active site Tyr residue in position 221 is replaced by a Phe
The molecular function of NOTUM has remained unclear for many years. It was initially thought to hydrolyze glycosaminoglycan (GAG) chains of glypicans, thereby affecting glypicans ability to interact with Wnt ligands. It was later reported to trigger glypican shedding, by mediating cleavage of their GPI-anchor. However, while NOTUM specifically inhibit the Wnt signaling pathway, more pleiotropic effects would be expected from an enzyme affecting glypicans. It was finally shown that it requires glypicans to suppress Wnt signaling, but does not cleave their GPI-anchor. It acts by mediating depalmitoleoylation of WNT proteins, impairing WNT binding to frizzled receptors (PubMed:25731175)
This ORF is coded on the other strand of an ORF which has been called modD (by PubMed:7665460 and PubMed:8564363), but which seems to be wrong
The original rnc-105 mutation is described as G44->D but the nucleotide sequence given indicates G44->S (PubMed:3903434). A later paper calls the same mutation G45->K (PubMed:9632264), which alters the residue and mutation
It is uncertain whether Met-1 or Met-56 is the initiator
Could be the product of a pseudogene unlikely to encode a functional protein. Strain S288c has a stop codon in position 67, which disrupts the gene coding for this protein and produces two ORFs. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
Lacks the conserved His residue in position 67 essential for protease activity
According to PubMed:9512348, it is a component of the 26S proteasome
This protein has lost two of the potential magnesium binding sites found in 5-phosphoribose 1-diphosphate synthases. It is also divergent from other prokaryotic member of the family. It may therefore have acquired another function
There are conflicting results concerning the role of LETM1 as a mitochondrial proton/calcium exchanger. According to (PubMed:19797662, PubMed:24344246, PubMed:29123128) LETM1 has been shown to function as a proton/calcium exchanger. However (PubMed:36321428) demonstrates the absence of this function in LETM1
There seems to be a sequencing error that fuses together porC and porD. We have cut the ORF into its two constituents
Despite its name, this protein may not be the one-to-one ortholog of TMEM184B
It is uncertain whether Met-1 or Met-2 is the initiator. Some orthologous sequences cannot be extended
The same name has been given to a lectin from Bothropoides pauloensis (AC P86970)
The disintegrin is also encoded by another precursor (AC Q14FJ4)
Many publications have reported a critical role of Fto in regulating fat mass, adipogenesis and total body weight (PubMed:19234441, PubMed:19680540, PubMed:21076408, PubMed:23817550, PubMed:23300482). However, some reports suggest that some effects are indirect and caused by impaired expression of adjacent genes such as Irx3 and Rpgrip1l (PubMed:24807221, PubMed:24646999)
The oxidation form of Trp-543 is subject of controversy and could be the artifactual result of sample handling
Tyr-13 is present instead of the conserved Cys which is expected to be the active site residue of peptidase C39. Thus they are presumed to be without peptidase activity
The conserved pyridoxal-binding site Lys at position 216 is replaced by a Glu
It is uncertain whether Met-1, Met-2 or Met-5 is the initiator
Was previously reported to interact with KDM1A, CBX1, CBX3 and CBX5. However, this publication has been retracted
Although this protein is said to have a reductase activity, it clearly belongs to the thioesterase (hydrolase) family
Lacks the typical Glu active site in position 113 that is replaced by an Asn residue. Some catalytic activity was found but in a fraction that contained both Hyaluronidase A and Hyaluronidase B
This gene is probably a pseudogene. In contrast to other members of the family, Y.pestis PagP is truncated by a deletion of the last three amino acid residues which contribute to key hydrogen bonds in the inner leaflet exposed region. Consequently, it seems highly unlikely that the truncated PagP is capable of folding into a beta-barrel in the outer membrane (OM)
Could be the product of a pseudogene. In strain cv. Columbia, a naturally occurring variation results in the deletion of 35 amino acids in the middle part of the protein. Lacks part of the extracellular leucine-rich repeats that are required for the specificity of the elicitor protein recognition
Was originally thought to be involved in the expression of the phosphatidylserine synthetase pssA
Was originally thought to originate from Mycobacterium bovis (PubMed:8880935, PubMed:9012664, PubMed:9671504, PubMed:11910040). However, there is now convincing evidence that this is incorrect (PubMed:19394346). The source is unknown, but the sequence similarity suggests the protein is of enterobacterial origin
Was originally thought to use biuret as substrate (PubMed:11544232). But new evidence has shown that 1-carboxybiuret is the real substrate. The error occurred since 1-carboxybiuret hydrolyzes spontaneously to biuret (PubMed:29523689)
PubMed:12612062 has shown that it is not involved in Wolf-Hirschhorn syndrome
Was reported to be required for the abcission step in cytokinesis, possibly regulating the ESCRT-III complex via its interaction with CHMP4B (PubMed:20208530). According to the same authors, localizes to the centrosome during all stages of the cell cycle and is recruited to the midbody during cytokinesis (PubMed:20208530). However, the midbody localization could not be confirmed by others (PubMed:21278747)
This is very poor signal peptide prediction
A paper describing the function, enzyme activity and expression patterns of this protein has been retracted due to concerns of image manipulation
Was termed importin alpha-4
Was originally thought to be the catalytic subunit (PubMed:3061797). The low processing activity which was previously observed with alpha-MPP which has been purified from a mitochondrial extract is most likely due to contamination by the beta-subunit. Does not seem to have protease activity as it lacks the zinc-binding site (PubMed:9299349)
The enzyme that would modify Asp-102 to 3-methylthioaspartic acid has not been found in the proteome of this organism, and that modification does not occur
The O-glycosylation on Ser-269 is identified in PubMed:8747463 as D-xylose based on weak electron density. Such a modification has not been reported in the fungi, and the saccharide is probably D-mannose as at the other positions
Despite the gene name, this is not the ortholog of vertebrate PAK2
The role of PARP14-mediated ADP-ribosylation of STAT1 in the prevention of STAT1 phosphorylation has been called into question and it has been suggested that the inhibition of phosphorylation may be the result of sumoylation of STAT1 'Lys-703'
According to PubMed:29239122 Asn-525 is not glycosylated in contrast to PubMed:17509134, which reports that all predicted N-glycosylation sequences are glycosylated
Product of a dubious CDS prediction. May be a non-coding RNA. According to PubMed:22108211, silencing of that gene results in altered transcription of cAMP-responsive genes. However, PubMed:22108211 does not provide evidence that it is due to the absence of the putative protein
PUBMED:19940129 has been retracted because the same data were used to represent different experimental conditions
The interacting region with TESC is conflicting: In human, it has been reported that SLC9A1 interacts with TESC via the juxtamembrane region of the cytoplasmic C-terminal domain, including residues 503-545. However, another publication has reported interaction with TESC via residues 633-816, the region of the cytoplasmic C-terminus more distal to the membrane
The DNA coding for this protein is not found in the complete genome of strain 98/2. Sequence in PubMed:10383958 could have originated from another strain
The sequence corresponding to this entry was originally entered in Swiss-Prot as AC Q57704 in November 1997 and was deleted in July 1999 because TIGR removed the CDS for that ORF. We have recreated it because of the evidence (PubMed:10940029) that it really exists
Could be the precursor of pseudonajatoxin b. But there are three amino-acid differences that could be strain variations or due to a multigene family
Was originally derived from a readthrough transcript including ASB14 and DNAH12
Has been classified as a the potassium channel toxin alpha-KTx 22.7 in PubMed:22230549. Since the subfamily 22 has already been attributed, this peptide should be reclassified as alpha-KTx 23.7
The phosphatase activity appears to be controversial (PubMed:20070315, PubMed:22387043). The active site residues are not conserved (PubMed:22387043). One study shows that there is no phosphatase activity towards synthetic substrate pNPP (PubMed:22387043). However, another study shows a broad specificity towards organic phosphoester substrates (PubMed:20070315)
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7
Lacks almost all of the known catalytic and substrate-binding residues for this enzyme; hence it is annotated as putative
Was originally thought to be located in the peroxisome (PubMed:10191291). However, was later shown to be cytosolic (PubMed:14729858, PubMed:27052676)
Initially the conserved reside Thr-90 was thought to be a nucleophile; mutagenesis in this organism and E.coli indicates it is not
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-8; H2BK6su = sumoylated Lys-8; H2BK7ac = acetylated Lys-9; H2BK7su = sumoylated Lys-9; H2BK11ac = acetylated Lys-24; H2BK123ub1 = monoubiquitinated Lys-137
Although it belongs to the protein kinase superfamily, lacks the active site residue Asp at position 227 and the Asp residue at position 245 involved in Mg(2+) chelation, suggesting that it has no protein kinase activity
Could be the product of a pseudogene, it is missing the C-terminus compared to orthologs. A full-length version has several ankyrin repeats (see for example AC A0A0H3JEK5)
The sequence derived in PubMed:2402492 was probably derived from a mutant gene and shows poor transcriptional activation and DNA-binding activity, but is still able to efficiently form heterodimers with retinoic acid receptors
Was originally thought to originate from chick
The crystal structure article has been retracted because submission was made without agreement from the last author. The protein was predicted in that paper to be a Baeyer-Villiger monooxygenase, but such activity was never experimentally shown. However, the protein binds to FAD in the crystal structure, and is probably an oxidoreductase
Was originally (Ref.4) thought to originate from Proteus vulgaris, but was shown to originate from E.coli
Could be the product of a pseudogene unlikely to encode a functional protein. Strain S288c has two stop codons in position 132 and 432, which disrupt the gene coding for this protein and produce three ORFs. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
Original thought to be dephosphorylated by PTPRJ on Tyr-905, Tyr-1015 and Tyr-1062. However this paper was retracted due to manipulation of immunoblot data
The presence of U-box domain is not predicted by SMART and SWISS-MODEL tools
Its topology is subject to discussion. According to some groups, it has a single-pass type II membrane protein in normal conditions and is retrotranslocated into a single-pass type III membrane protein in response to stress. According to other reports, it is integrated into the endoplasmic reticulum membrane via multiple membrane-spanning alpha-helices (PubMed:20629635, PubMed:26268886)
Was initially thought to be either inactive as transcription factor or to repress transcriptional activation mediated by other isoforms (PubMed:9580677). The presence of the transmembrane region at the N-terminus may explain the inability to observe transcription factor activity
The mature peptide could also result from natural deamidation of the Asn residue of CnIK (AC P56973)
Could be the product of a pseudogene. The N-terminus is much shorter than in related proteins and lacks the active sites and the heme-binding sites. Moreover, the 71 first amino acids of this sequence are not homologous to other KatG sequences
Authors of PubMed:21329715 cite the nucleotide sequence HQ262493 as coding for Css8 (AC P0DL83), but the sequence corresponds to Css4. For this reason, the corresponding cross-reference is indicated in this entry
Was originally thought to act as an activator for the mntABCD operon
Gly-60 is present instead of the conserved His which is expected to be zinc-binding residue. There is therefore some uncertainty concerning the enzymatic activity of this protein
Was originally (PubMed:1701261) proposed to code for three separate adjacent ORFs, ORF2, ORF3 and ORFE. This has been reconstructed to match proteins in other enterobacteria
At protein level, the N-terminus was determined to be Leu-118 but it is uncertain whether this is the true N-terminus of the mature protein or not
It is uncertain whether Met-1, Met-2 or Met-4 is the initiator
Was initially thought (Ref.2) to be a protease inhibitor
Was originally named veg by similarity to the D.melanogaster ortholog. However, it was later shown that the veg phenotype does not map to this protein. It is still not known which gene corresponds to the veg phenotype
In contrast to other members of the family that display ribonuclease activity, lacks the conserved catalytic sites that bind the divalent metal cations. Ribonuclease activity is therefore unsure
Could be the product of a pseudogene. Probably inactive as a ubiquitin-conjugating enzyme since it lacks the essential active site cysteine
Was originally (PubMed:2973057) thought to be a protease. However, removal of residues '165-200' of complex member HflC (a ClpP-protease-like motif) does not alter the lysogenization process, and in vitro studies show no evidence of a protease activity for the isolated HflKC complex
The sequence shown here has been extracted from the Sulfobacillus thermosulfidooxidans DSM 9293 genome sequencing BioProject (Accession PRJNA61271, JGI sequencing center)
This gene has been duplicated in rat. This copy on chromosome 9 corresponds to the active gene while the copy on chromosome 5 is a pseudogene
Lacks the conserved threonine residue in position 53, which is part of the carbamoylphosphate binding site; it is replaced by a leucine residue
Received originally the C6orf50 official gene symbol but the corresponding HGNC record was withdrawn
Could be the product of a pseudogene. Corresponds to residues 290 to 407 of the R.prowazekii RP603, whereas RC0924 corresponds to residues 18 to 104 of RP603. To reconstruct a sequence that would be similar to R.prowazekii RP603, it would be necessary to correct 4 frameshifts and to bypass a stop codon
This gene is not currently present in the reference genome assembly (GRCh38/hg38) and is probably the result of a gene duplication of MUC3A
Was originally called CpsD
Two L-amino-acid oxidase isoforms from C.cerastes venom have been described: Cc-LAAOI and Cc-LAAOII. Both isoforms show very similar activities on different substrates tested, as well as for activity regulation by metal ions. It is unknown which isoform is presented here
In contrast to other members of the family, it is shorter and lacks the C-terminal part that contains the conserved Glu and His active sites
The several steps and mechanisms that permit controlled Shh dispersion and gradient formation remain controversial. The Shh C-terminal domain displays an autoproteolysis activity and a cholesterol transferase activity resulting in the cleavage and covalent attachment of a cholesterol moiety to the C-terminal of the newly generated N-terminal fragment (ShhN). The protein is further modified by covalent addition of palmitate at the N-terminal of ShhN, resulting to the dual-lipidated Shh (ShhNp). ShhNp is firmly tethered to the cell membrane where it forms multimers. Further solubilization and release from the cell surface seem to be achieved through different mechanisms, including the interaction with DISP1 and SCUBE2, movement by lipoprotein particles, transport by cellular extensions called cytonemes or by proteolytic removal of both terminal lipidated peptides. Once released, the fully processed Shh can signal within embryonic tissues both at short and long-range
Most probably a non-functional protein that cannot participate to the synthesis of a productive T cell receptor (TR) chain due to a mutation at position 111, corresponding to the second cysteine from the disulfide bridge, potentially leading to uncorrect folding (PubMed:9619395)
It is uncertain whether Met-1, Met-10 or Met-21 is the initiator
Lacks the typical Cys at position 1000 required for the thioester bond formation
The protein was previously thought to dimethylate histone 3 'Lys-36', but this is now known not to take place in vivo
According to PubMed:20884799, this protein should not be regarded as a classical SR protein although it could complement an animal in vitro splicing extract deficient in SR proteins
Could be the product of a pseudogene. Gene encoding ANP32CP is intronless suggesting that is pseudogene generated by retrotransposition. There is no evidence for transcription
E.coli has 2 glycerate kinases, GK1 and GK2; it is not clear which gene encodes which enzyme
In contrast to human, not able to transport immunoreactive cyclic dinucleotides, such as cyclic GMP-AMP (2'-3'-cGAMP), an immune messenger produced in response to DNA virus in the cytosol
It was initially reported to localize to the Golgi apparatus, but this was later found to be artifactual mislocalization due to C-terminal tagging interfering with the ER retention signal
PubMed:11245572 has not been able to detect expression of this protein
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC Q0G9H8
Could be the product of a pseudogene, it is missing up to 240 N-terminal residues compared to orthologs
In contrast to other members of the family, ASAH2B has no predicted transmembrane domain, and lacks the active site, suggesting that it may be catalytically inactive
It is not known if C.botulinum or C.tetani infect this organism
The precise function of this protein in melanin biosynthesis is still under debate. DHICA oxidase activity is controversial. The mouse protein has been shown to have DHICA oxidase activity (PubMed:7813420). In contrast, the human protein was shown lack DHICA oxidase activity, or to have DHICA oxidase activity only in the presence of Cu(2+), but not with Zn(2+) (By similarity)
Variants MKMS 743-Trp--Phe-1231 DEL and HPE13 1033-Arg--Phe-1231 DEL were previously described; however, the corresponding paper has been retracted as Case 1's sex was incorrectly reported invalidating the conclusions
Defined as a polymorphic pseudogene by MGI. In strain C57BL/6, a polymorphism creates a premature stop codon at position 161. PubMed:9300695 shows that the truncated protein is not functional
Was initially thought to act as a glucose transporter (PubMed:10970791). However, later studies demonstrated that it does not transport glucose (PubMed:30431159)
Was named GLUT9 by a report, but this gene name has already been used for SLC2A9
In C.vinosum two similar set of genes code for RuBisCO large and small chains: the RbcL-RbcS (this entry) and the RbcA-RbcB pair. Under standard photoautotrophic culture conditions only the latter pair seems active, the former probably being cryptic
TAF12B in cv. Columbia (AC Q940A7) is 2 amino acids longer
Was reported to be activated by androgen receptor agonist dihydrotestosterone (DHT) in hepatic cancer cells (HCC), resulting in HCC growth and apoptotic resistance. However, this study was later retracted
According to PubMed:12361482, the human TDH gene is an expressed pseudogene encoding non-functional truncated proteins that are unable to make appropriate contacts with the substrates, L-threonine and NAD(+). Although all exons expected to encode a functional L-threonine 3-dehydrogenase of 369 residues are present in the human genome, all transcripts described encode truncated proteins that result from mutations within the gene causing the loss of acceptor splice site preceding exon 4 and exon 6
Could be the product of a pseudogene. In strain cv. Columbia, a naturally frameshift at position 65 results in a truncated TPS02 protein. Lacks the conserved active sites, suggesting that it has no terpenoid synthase activity. A complete sequence for TPS02 can be found in strain cv. Wassilewskija (AC P0CJ43)
Lacks the conserved His and Cys residues that are essential for the activity of de-ubiquitinating enzymes. Lacks ubiquitin C-terminal hydrolase activity
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 399 in the dsPTPase catalytic loop, suggesting that it has no phosphatase activity
The sequence shown here is a temptative reconstruction from the four submitted CDS; the exact positions of the frameshifts are unsure
Could be the product of a pseudogene. This is the C-terminal part of aquaporin-2. In strain S288c and many laboratory strains, a natural 11 bp deletion in position 109 leads to a frameshift, which disrupts the gene coding for this protein and produces two ORFs YLL052C and YLL053C. A contiguous sequence for aquaporin-2 can be found in strain Sigma 1278B (AC P0CD89)
The interaction between DSCAM, PAK1 and RAC1 has beend described. This article has been withdrawn by the authors
There are data describing interaction and regulation by the product of CRIPAK, a putative single exon gene (PubMed:16278681). However, considering all available data there is no sufficient supporting evidence for the existence of such protein
According to PubMed:15995190, this enzyme is not functional in M.kansasii, due to mutations outside this fragment, possibly in the ribosome-binding site or promoter/regulatory regions
Previously identified as the mitochondrial deoxyribonucleotide carrier (By similarity). However other experiments later demonstrated that SLC25A19 is a thiamine diphosphate transporter and not a mitochondrial deoxyribonucleotide carrier (By similarity)
The role of this protein complex as a component of a magnetic biocompass is controversial and further experiments are required to verify how migrating birds and other animals make use of the Earth's magnetic field to navigate or orient themselves. Only about half of the rod-shaped protein complexes align with magnetic fields of 1 mT at room temperature. It is not certain that this is sufficient to mediate responses to the Earth's magnetic field (about 0.03-0.065 mT) in vivo, but the complex may give rise to technical applications
Was originally thought to be an iron-sulfur cluster assembly scaffold protein (PubMed:20097860, PubMed:21236255). It is now thought to be a zinc-dependent sulfur transfer protein (PubMed:24321018)
The inhibition of SufS activity by the Cys-41 mutation in this protein has been described as competitive and non-competitive inhibition (PubMed:21236255, PubMed:24321018)
Ser-314 is present instead of the conserved Cys which is expected to be a zinc-binding residue
Most probably a non-functional protein that cannot participate to the synthesis of a productive immunoglobulin chain due to an altered splicing site (PubMed:9619395). Watson et al (PubMed:23541343) identified this gene on chromosome 14. However, it is not currently present on the reference genome assembly (GRCh38/hg38)
Was originally thought to be a phosphodiesterase on the basis of spurious sequence similarities
Could be the product of a pseudogene. Lacks the C-terminal half of the catalytic domain found in other members of this family. This truncated polypeptide does not display phospho-alpha- or phospho-beta-glucosidase activity (PubMed:9209025)
Has sometimes been attributed to correspond to FcR-IIB
FCGR2C is both a gene and a pseudogene in the human population, the reference genome corresponding currently to the non-functional allele with a stop codon at position 57. The sequence shown here with a Gln at that position is the one of the functional protein
Was originally thought to be the receptor for fMet-Leu-Phe (N-formyl peptide receptor)
Lacks the conserved Glu residue in position 458 essential for carbopeptidase activity. The mature form lacks catalytic activity towards synthetic peptide substrates
Was originally thought to catalyze the entire reaction from (6E)-8-oxogeranial to nepetalactol including a cyclase step (PubMed:23172143). New results have shown that the cyclase is a different enzyme and this enzyme exclusively catalyzes a reduction step (PubMed:30531909)
Clone A1 form may be a splice variant or an artifact
It is uncertain whether Met-1, Met-46 or Met-60 is the initiator
Could be the product of a pseudogene. This sequence is shorter than orthologs in other Buchnera species
Was proposed to be mitochondrial, based on experiments with an N-terminal GFP-tag (PubMed:10781606). The in vivo localization to the mitochondrion could not be confirmed (PubMed:15845354). However, it has been observed for the mouse (AC Q9JHE3) and rat (AC Q91XT9) orthologs
Was originally thought to be a major constituent of the S-layer. However, structural and deletion mutant studies showed that SlpA is an outer membrane protein and is not an integral part of the S-layer (PubMed:35943982)
The authors of PubMed:12016226 consistently use the word ferrodoxin instead of ferredoxin
PubMed:3936839 sequence does not report residues in positions 30 and 39 probably due to their modification, and reports a cyclic permutation of the peptide sequence
Partial protein sequence was obtained following expression in E.coli, not P.aeruginosa
First thought to play a role in the regulation of apoptosis, mediating mitochondria-induced cell death in vascular smooth muscle cells through the release of cytochrome c (COX) from mitochondria and the activation of the caspase cascade. However, recent studies show that it is not directly involved in apoptosis regulation but in the protection of COX from oxidatively induced degradation
It is unlikely that this protein binds calcium as none of the 2 EF-hand domains seem to contain a canonical calcium-binding site
This sequence was first thought to be an alternatively spliced isoform of Pla2g4b. It is derived from Jmjd7 which is located upstream of Pla2g4b. Most tissues also express read-through transcripts from Jmjd7 into the downstream Pla2g4b gene, some of which may encode fusion proteins combining the N-terminus of this protein with PLA2G4B protein
Expression of endA requires a ribosomal frameshift to allow contiguous translation of a 453 amino acid protein; this is suggested to take place at position 127 but could in fact occur anywhere between positions 82 and 127
On the basis of sequence similarities the C-terminal part of this sequence seems to be incorrect
Lacks the conserved glutamate residue in position 462 that binds magnesium; it is replaced by a glycine residue
Tyr-9 is present instead of the conserved Cys which is expected to be the active site residue of peptidase C39. Thus this protein is presumed to be without peptidase activity
PubMed:18461140 reports that IrtA is a siderophore exporter, however this activity could be due to functional differences of IrtA in the molecular context of M.smegmatis and M.tuberculosis
Was originally thought to be involved in the regulation of molybdate metabolism, which gave rise to the name molR, however the locus in PubMed:2156810 was mapped at 65 centisomes (minutes) on the E.coli chromosome, while this locus maps to 47.3 centisomes (PubMed:2156810). This locus gives rise to a transcript that could encode the 'interrupted' N-terminal 274 amino acid gene product of yehF. The protein it encodes (shown here) is missing the C-terminus compared to orthologs
It is uncertain whether a Met upstream of this sequence or Met-14 is the initiator
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC A6MMG4
The conserved putative phosphorylation site is a Glu instead of an Asp
In strain 301 it seems to be a pseudogene. It is interrupted by a frameshift in position 119. The sequence has been verified by the authors and is believed to be correct
Despite the presence of a PPIase cyclophilin-type domain, it has probably no peptidyl-prolyl cis-trans isomerase activity
Lacks three conserved histidine residues that bind copper and zinc
Could be the product of a pseudogene. According to PubMed:16911775, it could constitute the ancestral killer immunoglobulin-like receptor gene in primates
Was briefly thought to be FRE2
Could be the product of a pseudogene; in this organism the endonuclease subunit carries 2 frameshift mutations (resulting in 3 short ORFs) and is probably not expressed
In strain W3110, the sequence is interrupted by the insertion of an IS5 element between positions 69 and 70
The protein might be post-translationally truncated or the gene model could be wrong, because experimentally the protein migrates like a 56 kDa protein whereas it should migrate around 117 kDa
While this subunit has weak helicase activity in vitro (PubMed:8433990), it does not act as one in vivo but rather as an ATP-dependent pump that drives DNA passage through the RuvA-RuvB complex to promote Holliday junction branch migration
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-10; H2BK34ac = acetylated Lys-11; H2BK143ub1 = monoubiquitinated Lys-115
In PubMed:2902184 it is said that 50% of the peptides have N-methyl-Phe and 50% begin with Thr-8. N-terminal methylation produces preview during Edman degradation, which makes this appear to happen when the peptide is completely N-terminally methylated
SHISA7 has been reported to interact with AMPAR subunit GRIA1 in heterologous conditions and in the brain (PubMed:26623514, PubMed:29199957). However, it was later demonstrated that SHISA7 does not colocalize neither interact with AMPAR, but with GABA(A)R (PubMed:31601770). Therefore additional experiments are needed to understand the discrepancy for SHISA7 function
Transfer of a plasmid encoding this gene has been detected between bacteria within a patient (between K.pneumoniae and E.coli). Additionally the gene may be encoded within a transposon
Predicted to contain a signal peptide and to be secreted. However, this is not consistent with an interaction with DOCK7 and MYO6 and the suggested function in cytoskeleton organization
Lacks the conserved signal peptide, which is one of the features of the BURP domain-containing proteins
Was originally thought to be the overgrown hematopoietic organs-31 protein (OHO-31)
Was originally thought to originate from Leptospira biflexa; taxonomy has been changed based on information in PubMed:11751822
Although strongly related to the abraxas1 protein, lacks the C-terminal pSXXF that constitutes a specific recognition motif for the BRCT domain of brca1
Could be the product of a pseudogene, according to PubMed:15233988
Exists an other tandem duplicated gene (NANOG) and 10 other NANOG-related nucleotide sequences located on different chromosomes, all of which are processed pseudogenes lacking introns (NANOGP2 to NANOGP11); except NANOGP8 which is a retrogene
Two phospholipase A2 inhibitor gamma subunit A that have only 75% identities have been described by the group of Huang. They are shown in UniProt as subunit A1 (AC I6PG79) and subunit A2 (AC P0DQX3)
Lacks the conserved tripeptide Ser/Thr-Asn-Pro in position 205 necessary for the ACS activity
A publication reported that a complex is formed with TGFB1 (PubMed:7798248). According to another report, there is no association with TGFB1 (PubMed:10930463)
Was originally thought to be involved in phosphonate metabolism
Was originally proposed to be fused with GmhA
Phe-89 is present instead of the conserved Cys which is expected to be an active site residue suggesting that this protein has lost its catalytic activity
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC A4GYN8
No expression of this protein has been seen during autotrophic and mixotrophic growth, however the protein is probably expressed under other conditions. In a related bacteria (T.neapolitanus) expression has been seen when the form I enzyme has been knocked out
Related to oxidoreductases, but misses the conserved Thr active site. Therefore it may not have any oxidoreductase activity
It is uncertain whether Met-1, Met-494, Met-539, Met-544 or Met-553 is the initiator
Gurskaya et al., 2001 describe 2 different proteins coming from C.gigantea (cgCP) and C.passiflora (cpCP). Since both C.passiflora and C.passiflora species are synonym, the 2 proteins are merged and some conflicts are reported
PubMed:16284174 reports obestatin as ligand of GPR39. However, PubMed:17289961 and others are unable to reproduce these results. It also seems to be unclear whether obestatin has opposite effects on food intake compared with ghrelin
Could be the product of a pseudogene. However, some data suggest that it could be a protein-coding gene (PubMed:15313892)
Could be the product of a pseudogene. The FKBP domain is truncated
This protein should not be confused with Fbxo11 (AC Q7TPD1) that was initially erroneously named Prmt9
Able to autophosphorylate in cis in vitro. This activity may not be relevant in vivo and only reflects in vitro conditions. Probably does not act as a protein kinase as it is unable to act in trans (PubMed:27499294)
Was originally (PubMed:1648478) isolated as a multicopy suppressor of a yeast strain harboring a mutation in a cytochrome b translational activator (cbs2-223). But more recently it has been shown (PubMed:15063807) that a tRNA(Trp) gene located downstream of COQ8 mediates suppression of the cbs2-223 mutation. The inability of COQ8 to suppress the cbs2-223 allele in multicopy indicates it may not be a chaperone as previously reported
A report has suggested that the protein is expressed at the cell surface, associated with the cell membrane via its N-terminus. However, there is no direct evidence for that localization and the properties of the protein argue against it
Could be the product of a pseudogene unlikely to encode a functional protein. This is the C-terminal part of guanine nucleotide exchange factor SDC25. Strain S288c has a frameshift in position 92, which disrupts the gene coding for this protein and produces two ORFs YLL016W and YLL017W. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. A contiguous sequence for SDC25 can be found in strain W303 (AC P0CF32)
Was initially proposed to transport palmitoylcarnitine, based on complementation experiments in yeast mutants lacking CRC1 and CIT2 and release of radiolabeled carnitine from mitochondria incubated with radiolabeled palmitoylcarnithine (By similarity). Later experiments done primarily with human indicate the protein functions instead as transporter of basic amino acids (PubMed:24652292)
Lacks the stop codon recognition motif 'SPF' and the catalytic center 'GGQ' for peptidyl-tRNA hydrolysis, which are two conserved features of the family
The function of the TMEM150C complex is debated. One study confirms that naive cells expressing TMEM150C is activated by mechanically stimuli but this response is absent in CRISPR-Cas9 PIEZO1 knockout cell lines suggesting that TMEM150C is not sufficient to function as mechanically activated channels but is a modulatory protein of PIEZO1 (PubMed:28426961). In another study, based on coexpression of TMEM150C and PEIZO1 and mutant variants of TMEM150C supports that TMEM150C is a pore-forming unit, and not an amplifying adapter for PIEZO1 activity (PubMed:28426962)
Was originally believed to be a metal-dependent phosphatase but shown to lack catalytic activity; can bind metals (Zn(2+) and Mn(2+)) with very low affinity suggesting that metal binding is not required for its function
Could be the product of a pseudogene unlikely to encode a functional protein. This is the C-terminal part of a second copy of formate dehydrogenase in the yeast genome. Strains BY4741, S288c and W303 have a stop codon in position 146, which disrupts the gene coding for this protein and produces two ORFs YPL275W and YPL276W. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. A contiguous sequence for formate dehydrogenase 2 can be found in strain CEN.PK113-7D (AC P0CT22)
This sequence is encoded by a gene on chromosome 15 and is unlikely to be the med13 ortholog because it shows similarity but not synteny with human MED13. The chromosome 10 med13 gene identified by PubMed:17208216 is distinct from this entry
Lacks the typical His and Asp active sites in position 65 and 112, which are replaced by an Asn and Thr residues, preventing the protease activity. The sequence corresponding to the activity described in PubMed:20184912 may be slightly different from the sequence shown
By homology with the human sequence, it is uncertain whether Met-1 or Met-5 is the initiator
Thought to be palmitoylated by ZDHHC17 (PubMed:22496366). This work was later retracted due to image manipulation (PubMed:29475958)
There is a significant difference between sequences of PubMed:20631207 and PubMed:8408054. The sequence of PubMed:8408054 may contain multiple errors since its last cysteine is absent from all other lizard toxin sequences and an insertion of 6 amino acids is present that is missing in other varanid lizard kallikrein toxins
Contains Thr-228 instead of the expected predicted active site Lys
Although strongly related to peptidase C1 family, it lacks the conserved active Cys in position 210, which is replaced by a Ser residue, suggesting that it has no protease activity
The fusion between the ATP-binding domain and LysR substrate binding domain is unusual. It could be due to a sequencing error
Unlike for B.subtilis, the PyrR protein of L.lactis was shown not to encode UPRTase activity
Although it contains a Rho-GAP domains, does not have GTPase activator activity (PubMed:25721503, PubMed:27957544). The absence of GTPase activator activity is required to promote amplification of basal progenitors (PubMed:27957544). Restoring this activity abolishes ability to promote amplification of basal progenitors during neocortex development (PubMed:27957544)
Could be the product of a pseudogene. There are 3 rpoA-like genes in this organism (found in the inverted repeat). None of them are convincing as rpoA, and it may be that the functional gene is in the nucleus. This gene however is found in the correct operon context
An initial knockout experiment in mouse reported only minor phenotype with no development of spontaneous disease, arguing against a significant role in controlling T-cell activation (PubMed:8602528). However, subsequent analysis showed that knockout mice develop autoimmune diseases caused by T-cell activation (PubMed:21873518)
PubMed:10531037 wrongly lists the species as human
Was initially thought to be a pseudogene
Initial characterization studies with purified Atp8a1 enzyme demonstrated similar but distinct properties compared to the cell membrane aminophospholipid flippase; however, the flippase complex accessory beta subunit was not included in the assays
According to a report, recognizes and binds histone H3 succinylated at 'Lys-122' (H3K122succ) (PubMed:29463709). However, another report only observed poor binding with succinylated histone H3 (PubMed:30071723)
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me1/2/3 = mono-, di- and trimethylated Lys-10; H3S10ph = phosphorylated Ser-11; H3T11ph = phosphorylated Thr-12; H3K14ac = acetylated Lys-15; H3K14me3 = trimethylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me3 = trimethylated Lys-19; H3K23ac = acetylated Lys-24; H3K27me1/2/3 = mono-, di- and trimethylated Lys-28; H3S28ph = phosphorylated Ser-29; H3K36 = Lys-37; H3K37 = Lys-38
Bothrops jararaca venom seems to contain 2 isoforms with different hydrophobic properties (PubMed:18346051). These isoforms may reflect different glycosylation of the protein or they may have been synthesized from different genes
Unlike the case in Archaeoglobus fulgidus and some of the free-standing tRNA(Ala) AlaX editing proteins, His-721 does not bind zinc but forms a hydrogen bond with Cys-717 instead
Unlike Ref.2, PubMed:17056008 doesn't detect maternal expression
In contrast to other members of the family, lacks the conserved Arg and Glu active sites at positions 417 and 446 respectively, suggesting that it lacks dehydrogenase activity
Some studies have failed to detect adenylate kinase activity (PubMed:11485571, PubMed:19130895). However, kinase activity has been demonstrated in a number of other studies (PubMed:19766732, PubMed:23416111)
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-18; H2BK34ac = acetylated Lys-19; H2BK143ub1 = monoubiquitinated Lys-122
Was originally (PubMed:7721096, PubMed:8568274) thought to originate from human but is most probably the result of a cDNA library contamination by L.lactis
Was originally named bile acid 7-dehydroxylase (PubMed:3549693). In fact, the 7-dehydroxylation process is catalyzed by multiple enzymes
Was originally thought to be a DNA-binding transcriptional repressor (By similarity). However, later work showed that the original sequence was a chimera and that the DNA-binding activity was derived from the incorrect N-terminal sequence (By similarity)
Encoded by an alternative reading frame in the POLG gene. Translation initiation occurs at a non-canonical CUG codon
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC A4GYT5
The active channel complex is an obligate tetramer (PubMed:25820328, PubMed:30004384). In contrast, the isolated cytoplasmic C-terminal domain forms homotrimers in vitro (PubMed:20408813, PubMed:25820328, PubMed:23212381). Likewise, photobleaching experiments suggest formation of homotrimers in the membrane (PubMed:23212381)
Has also been detected in the endoplasmic reticulum but appears to be a lysosomal protein in vivo
Zebrafish has two genes coding for six1 orthologs. This gene is called six1b by ZFIN and in PubMed:23444384, but has also been described as six1 (PubMed:17035528) and as six1a (PubMed:15254912, PubMed:18789916, PubMed:19409884)
The protein is 98% identical to atrase B (AC D6PXE8), a metalloproteinase secreted by a Chinese cobra from the Hunan Province of China. Surprisingly, mature proteins released from the two similar precursors are not the same size
It is uncertain whether Met-1 or Met-48 is the initiator
UGT2B4 has been previously described as an enzyme named UGT2B11. However the name UGT2B11 has now been reused for another human protein (see AC O75310)
Was originally thought to be the product of two separate ORFs, baiC and baiD
Although strongly related to the nudix NUDT16 protein, lacks the Nudix box and is therefore not related to the rest of the family (PubMed:18820299, PubMed:21070968). Gene organization and evolutionary distribution suggest that syndesmos NUDT16L1 probably originated as a gene duplication event of the more ancient U8 snoRNA-decapping enzyme NUDT16 (PubMed:18820299). Although similar to U8 snoRNA-decapping enzyme NUDT16, lacks a number of residues which are necessary for hydrolase activity and does not play a role in U8 snoRNA decapping activity (PubMed:21070968)
The oxidation form of Trp-365 is subject of controversy and could be the artifactual result of sample handling
Was originally called HPr kinase/phosphatase (PubMed:12368461, PubMed:12589763). But P-Ser-HPr dephosphorylation was shown in several bacteria to follow a quite unique mechanism, in which Pi instead of H(2)O is used for the nucleophilic attack on the phosphoryl group. P-Ser-HPr dephosphorylation is therefore not a phosphohydrolysis but a phospho-phosphorolysis reaction, and the bifunctional enzyme was dubbed HPr kinase/phosphorylase
In contrast with human ortholog, not able to transport urate and orotate (PubMed:35144162)
Although this protein belongs to the G-alpha family, its Walker A GTP-binding motif is defective and therefore both its GTP-binding activity and function are dubious
Although defined as a pseudogene by HGNC, it is clearly expressed
Possibly identical to gltE
An article reported S-acylation of Cys residues that regulates localization to membranes; however, this paper was later retracted
This toxin precursor is identical to three other precursors (AC B1NWR6, AC P0CH46 and AC B1NWR7). AC B1NWR6 shows 8 variants that could also be associated with this gene
Defined as a pseudogene by MGI. Compared to other members of the family it contains a frameshift in position 20. However, proteomics data suggest the existence of the protein
Although related to histone H2AB1 in mouse (AC Q9CQ70), it is unclear whether human and mouse H2AB1 proteins are involved in similar processes. In mouse, histone H2AB1 is specifically required to direct the transformation of dissociating nucleosomes to protamine in male germ cells during spermatogenesis. It is however unclear whether human protein, which participates in mRNA processing and is associated with active transcription, is also involved in nucleosomes to protamine replacement (PubMed:22795134)
This enzyme was also named ureidoglycolate hydrolase in the literature. However, this is the recommended name of another enzyme (EC 3.5.1.116) acting on ureidoglycolate. To make the distinction between ammonia- or urea-releasing activities from ureidoglycolate, the use of this ambiguous name is deprecated
Isoform 6: Controversial data exists concerning the repressor activity of isoform 6. In human, a study showed that human isoform 3 exhibits weak repressor activity of a NRSE motif-containing reporter construct (By similarity). Another report, however, does not observe any isoform 3 repressor activity of a NRSE motif-containing reporter construct (By similarity). Isoform 6: Controversial data also exists regarding the function of isoform 6 on the negative regulation of isoform 1. In mouse, it was shown that isoform 2 negatively regulates the repressor activity of isoform 1 by binding to isoform 1, thereby preventing its binding to NRSE and leading to derepression of target genes (By similarity). Another study in human, however, did not observe any inhibitory activity of human isoform 3 on the isoform 1 transcriptional repressor activity (By similarity)
Was originally thought to be a membrane protein kinase involved in phosphorylation of the AO and LAO periplasmic-binding proteins (PubMed:9733684). However, its role needs to be reexamined
Although its N-terminus is strongly related to pyridoxal 5'-phosphate synthase PDX1 subunits (PDX1), it is much shorter and probably not functional
The sequence shown in this entry differs from the translation of the reference genome assembly (GRCh38/hg38) due to a nonsense variant creating stop codon at position 140 in the reference genome
Lacks the conserved Asp active site
Mistakenly referred to as AT2G04070 in PubMed:11739388
The sequence shown in this entry differs from the translation of the reference genome assembly (GRCh38/hg38) due to a nonsense variant creating stop codon at position 456 in the reference genome
Sequence (AAA73925.1) highly divergent from genome sequence. It could originate from another bacterial species
Has been sometimes referred to as a collectin receptor
PubMed:11994479 reported that C1q is not a ligand for C1QR1
Was originally thought to be a spore coat protein
COR2 seems not to have codeinone reductase activity
The physiological significance of this enzyme is not known since D.mccartyi is cobalamin auxotroph
It was reported that dephosphorylation on tyrosine residues by PTPN2 would negatively regulate prolactin signaling pathway (PubMed:11773439). However, the corresponding article has been retracted (PubMed:24319783)
In strains CO-92 and KIM5 it could be the product of a pseudogene
This sequence is an example of a full-length immunoglobulin mu heavy chain
According to PubMed:18483174 Ddr2 is required for male and female fertility, since smallie mice with a 150 kb deletion that extends into the Ddr2 gene are sterile. Smallie males have defects in spermatogenesis (PubMed:19681157). On the other hand, the fertility status of mice with a targeted disruption of the Ddr2 gene has not been mentioned (PubMed:11375938). Thus, the infertility of smallie mice may be due to some additional, not yet identified defect
PubMed:9557703 sequence originates from strain Jacp of pestivirus type 1 which seems to contain a cellular insertion of part of the bovine host MAP1LC3 gene
Was originally thought to contain a [6Fe-6S] cluster as indicated
Lacks the conserved glutamate residue in position 464 that binds magnesium; it is replaced by a glycine residue
The DNA coding for this protein is not found in the complete genome of strain ATCC 27872 / DSM 7271 / JCM 12966 / VPI 2845
Has no demonstrable enzymatic activity. This may be due to several critical changes in its sequence, relative to those of related proteases
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC P18663
The sequence aligns with alpha-KTx but has the CSalpha/alpha scaffold of a kappa-KTx due to the unusual pattern of disulfide bonds. As is the method of choice in UniProtKB, the assignment to the alpha-KTx 20 subfamily is based purely on the primary structure
Has been shown to be a pseudogene in cv. Columbia (AC P0CZ22) due to a naturally occurring frameshift at position 277 in this strain. The sequence shown is from strain cv. Landsberg erecta
Was originally called Pim-1 but seems to represent the protein pim3
Human MYDGF has been reported to be secreted into blood plasma and localized to the endoplasmic reticulum-Golgi intermediate compartment. However, another report shows resident localization to the endoplasmic reticulum and Golgi apparatus and secretion when the two most C-terminal residues of the RTEL motif are abolished
It is uncertain whether Met-1, Met-7 or Met-11 is the initiator
Was originally suggested to be a tRNA synthase, however its lack of an anticodon-binding domain made this highly unlikely
Was originally thought to be an outer membrane protein with porin-like properties
Was named BEX1 by some authors
Was originally thought to originate from pea
Lacks the starch-binding CBM20 domain and has no starch-active lytic polysaccharide monooxygenase activity
This protein lacks the conserved Cys in position 39; it is replaced by Arg. Thus this protein is probably unable to bind the 4Fe-4S cluster and may be non-functional
This toxin was originally named EVIA. As another delta-conotoxin was named EVIA in 2004 for which structural studies were carried out, the present toxin was renamed here EVIB
Reported to be associated with components of the peptide-loading complex, TAPBP, CALR, CANX and PDIA3 (PubMed:23457030, PubMed:12794138). This association in primary cells and its functional relevance is disputable, given that antigen presentation and MAIT cell activation is shown to be TAP1-TAP2 and proteasome-independent
Was originally thought to have inorganic pyrophosphatase activity
Unlike the glycerol-1-phosphate phosphohydrolases, this enzyme cannot hydrolyze L-glycerol 3-phosphate (sn-glycerol 3-phosphate) and is therefore not associated with EC 3.1.3.21 / RHEA:11476
Lacks the conserved His residue in position 64 essential for protease activity
In contrast to other members of the histone H3 family, this protein is much longer and has a highly divergent N-terminus. It is therefore unclear whether it is a real histone
There is a known reversal of the Pgm1 and Pgm2 nomenclature applied to mouse versus other vertebrates. The official name of this gene in mouse is Pgm1 but it is the ortholog of other vertebrate PGM2 genes
Lacks the RING-type zinc finger domain that is essential for ubiquitin ligase activity. May not possess E3 ubiquitin-protein ligase activity by itself
Was originally thought to originate from a rabbit cDNA library and was known as protein phosphatase 2Bw (PP2Bw)
Structural and functional studies of the ASAP complex have been conducted with a chimeric complex involving a conserved fragment of Drosophila melanogaster Acinus/hkl
In contrast to the mouse ortholog, it does not interact with Ras
Ser-376 is present instead of the conserved Asp which is expected to be an active site residue
In contrast to other members of the histone H3 family, this protein is shorter and has a highly divergent N-terminus. It is therefore unclear whether it is a real histones
Although related to peptidase S1 family, lacks the conserved active Ser residue in position 345 which is replaced by a Thr, suggesting that it has no protease activity
Gln-187 is present instead of the conserved His which is expected to be an active site residue
The C-terminal Ser/Thr kinase domain was reported to phosphorylate histone H2B at 'Ser-34'. However, the paper was retracted because some data, results and conclusions in the paper are not reliable
There is a putative pseudogene of CIA30 on chromosome 19 (19p12)
Was originally thought (PubMed:9603997) to be involved in the early steps of isoprenoid biosynthesis
Both Met-1 and Met-3 seem to be able to act as initiation codons
The venom of this snake was originally thought to be that of N.nigricollis while it is really from N.pallida
While different publications agree on the role of N6-methyladenosine (m6A) on RNA stability and its role in embryonic stem cells (ESCs) pluripotency, the precise function of Mettl3 in ESCs self-renewal is unclear. A first paper reported that Mettl3 promotes self-renewal of ESCs by maintaining the groung state of ESCs (PubMed:24394384). However, opposite conclusions were drawn by publications from other groups (PubMed:25456834, PubMed:25569111). The differences may be explained by different experimental conditions (such as cell types or RNAi off-target effects)
PubMed:10419956 reported that this protein is not expressed and that the protein that transfers sn-1 phosphoglycerol substituents to the cyclic beta-1,2-glucan backbone is CgmB. CgmB is encoded on the opposite strand from cgmA and completely overlaps it
It is uncertain whether Met-1 or Val-52 is the initiator
GRS1, which appears to be a duplication of GRS2, is necessary and sufficient for both mitochondrial and cytoplasmic glycyl-tRNA synthetase activities, suggesting that GRS2 may not be essential
Was originally thought to cleave the C-terminal dipeptide from the first intermediate product formed by the action of MftC on MftA, i.e. MftA modified with a C-terminal glycyl-L-valyl-decarboxylated L-tyrosine (PubMed:28077628). However, it was later shown that the terminal product formed by the action of MftC on MftA is the true substrate of MftE, i.e. MftA modified with a C-terminal glycyl-3-amino-5-[(4-hydroxyphenyl)methyl]-4,4-dimethylpyrrolidin-2-one (PubMed:30183269)
All experiments concerning the proteolytic cleavage are done with isoform 1
Could be the product of a pseudogene. Despite its name, it does not contain a canonical C2H2-type zinc-finger
Possesses an Asp at position 69 instead of a conseved Cys
Probably inactive enzyme; missing the second Asp of the DXDD motif that has been reported to be essential in forming hydrogen-bonded 'proton wires' during catalysis
In contrast to other members of the family, lacks the conserved His active site in position 75, suggesting it is inactive
Was originally thought to be comB, a competence gene
Could be the product of a pseudogene; is missing 186 N-terminal amino acids compared to its orthologs
The oxidation form of Trp-24 is subject of controversy and could be the artifactual result of sample handling
The gene coding for this protein seems to be defective in strain Ames ancestor where it is interrupted by an insertion sequence
Was originally isolated as a proteoglycan protein. Although not excluded, such secreted function is not clear
In PubMed:3042385 the location of any palmitoylation was not determined. Mutagenesis of either Cys-205 or Cys-206 would disrupt normal geranylgeranylation, and there would be no primary membrane association for secondary S-palmitoylation to occur at some other position, for example Cys-23. Mutagenesis of both Cys-205 and Cys-206 is lethal, so protein production could not have been observed
It is uncertain whether Met-1, Met-18 or Met-20 is the initiator
It is uncertain whether Met-1 or Met-34 is the initiator. Orthologous sequences start at a downstream Met
Functional studies (PubMed:10050851, PubMed:10950960, PubMed:12665568) have used a C-terminal fragment of isoform 1 which has been described originally as isoform MBD2b but cannot however be proven by supporting cDNA sequences
This toxin has been called Lt1.3 b, since the name Lt1.3 is already attributed to AC Q2I2R6
This sequence is an example of a full-length TR beta chain. M/matrix protein 1-specific TRBV19*01J2S7*01C*02 TCR beta chain is generated by somatic recombination of variable TRBV19 (AC A0A075B6N1), diversity (AC P0DPI4) and joining TRBJ2-7 (AC A0A0A0MT78) gene segments spliced to constant TRBC2 (AC A0A5B9) gene segment (PubMed:1833769, PubMed:7807026, PubMed:29997621, PubMed:27036003). CDR3-beta clonotype identifier: sIRSSy.1456B19S1B27L11 (PubMed:19568742)
Although related to peptidase S1 family vitamin K-dependent clotting factors, it has lost two of the essential catalytic residues and therefore lacks protease activity
Part of the btuCED operon, and was originally thought to participate in the transport of vitamin B12, but it was shown later that it plays no essential role in vitamin B12 transport
The proteins described here are encoded by the gene CDKN2A, but are completely unrelated in terms of sequence and function to cyclin-dependent kinase inhibitor 2A (AC P42771) which is encoded by the same gene
Was prevsiouly characterized as an enzyme that possesses uracil phosphoribosyltransferase (UPRT) activity (PubMed:17143579). Further publications show a lack of such activity (PubMed:19563437, PubMed:21828290)
Could be the product of a pseudogene. Promoterless gene that is a remnant of an ancestral flagellar gene cluster, Flag-2. The N-terminus is shorter than in orthologs
Was originally thought to originate from rat
The protein might be 25 residues longer at the N-terminus
Was originally thought to have epimerase activity
Was originally thought to be a receptor for neuropeptide Y type 3 (NPY3R) (NPY3-R) (PubMed:8329116, PubMed:8234909). Later reports showed that it acts as a receptor for the C-X-C chemokine CXCL12/SDF-1 (PubMed:9427609, PubMed:10825158, PubMed:12034737)
Pkd1l3 and Pkd2l1 have been identified as sour taste receptor in gustatory cells based on a number of indirect evidences: Pkd2l1 is expressed in circumvallate papillae cells on the posterior part of the tongue distinct from those responsible for sweet, bitter and unami taste and genetic elimination of cells expressing Pkd2l1 reduces gustatory nerve responses to sour taste stimuli (PubMed:16891422, PubMed:16929298). However, a number of experiments have recently shown that the sour taste receptor activity is probably indirect: mice lacking Pkd1l3 do not show defects in sour taste perception (PubMed:20605874, PubMed:21625513). Moreover, the Pkd1l3-Pkd2l1 heteromer, when expressed in cells does not respond to acid stimuli used to evoke proton currents in taste cells (PubMed:21098668)
Lacks the conserved Asn residue of the catalytic triad in position 292, which is replaced by an Asp residue
In contrast to other members of the family, does not contain a R-G-D cell attachment site motif that mediates binding to integrins and promotes release of Latency-associated peptide (LAP) chain from TGF-beta-2
Was originally thought to be an ortholog of KDR, but PubMed:18516225 has shown that it represents a fourth vertebrate vascular endothelial growth factor receptor (VEGFR) that is not present in eutherian mammals (marsupials and placental mammals)
Thiostrepton is produced by Streptomyces azureus ATCC 14921, S.hawaiiensis ATCC 12236, and by S.laurentii ATCC 31255. The species used as a thiostrepton producer in all studies is uncertain
Acidification of the cytosol strongly increases channel permeability to glycerol (PubMed:30420639). Initial experiments showed that isoform 2 is permeable to water, but not to glycerol, but these results were obtained without lowering the cytosolic pH (PubMed:11573934)
CD68 is a commonly used marker for macrophages. However, a number of studies in human have shown that CD68 antibodies react with other hematopoietic and non-hematopoietic cell types, suggesting that CD68 may not be a macrophage-specific antigen
Was thought to be a ubiquitin ligase ubiquitinated by UBE2D1, but was confirmed by numerous studies that it's main function is as E3 ISG15 ligase
Was initially reported to be secreted (PubMed:15340161). However, it was later shown to be localized in the inner mitochondrial membrane (PubMed:25008109, PubMed:25605331)
The role of cdc-48.1 in the regulation of kinase air-2, a component of the chromosomal passenger complex (CPC), is controversial. One study suggests that cdc-48.1 inactivates air-2 at the end of mitosis whereas a second study shows that cdc-48.1 is not implicated in the regulation of air-2
In contrast to other members of the peptidase S8 family, contains Gly and Glu residues at the position of the canonical catalytic Asp and His, respectively, suggesting that the protein lacks protease activity
Several genes are coding for this toxin, it is therefore also shown in entry AC Q9U655
Was originally (PubMed:9482853, PubMed:10698937) thought to be a transcriptional coregulator with protein kinase activity. However, crystal structure reveals a short chain dehydrogenase/reductase fold binding NADPH rather than ATP
Truncated; frameshift leads to premature stop codon
Could be the product of a pseudogene, it is missing up to 230 N-terminal residues compared to orthologs
It is uncertain whether Met-1 or Met-6 is the initiator. If Met-1 is the initiator, MymT would undergo a first cleavage after Arg-5 followed by processing of the N-terminal methionine
Although the active site residues are conserved, it lacks the conserved His residue which is normally found 9 residues before the catalytic His
Could be the product of a pseudogene. In contrast to other H2B histones, it does not contain the conserved residue in C-terminus that is the target of monoubiquitination
According to PubMed:9349714, does not have levansucrase activity, despite a very strong similarity to SacB from B.subtilis
Ser-356 and Gln-363 are present instead of the conserved Phe and positively charged residue Lys/His/Arg, respectively, which could be important for activity. These point mutations might explain the inactivity of the enzyme
Was named (PubMed:18196551) 'Kallikrein-related in prostate protein 1' because this protein is encoded by a transcript from the KLKP1 gene region. It is encoded in an exon which is similar to the intronic region between exons 1 and 2 of KLK1, KLK2 and KLK3
Gln-626 is present instead of the conserved Asp which is expected to act as an active site proton acceptor therefore suggesting that it has no protein kinase activity
Gly-652 is present instead of the conserved Ser which is expected to be an active site residue suggesting that this protein has no peptidase activity
It is not obvious if the APS kinase domain is functional; the conserved active site serine (position 546) is replaced by an alanine. Furthermore P.aeruginosa seems to harbor a bona fide single domain APS kinase (CysC)
Was originally thought to be the small subunit of hydrogenase 2
In contrast to the related histone demethylases JHDM1D and PHF8, the conserved active His in position 321 is replaced by a Tyr. However, the presence of a Tyr residue neither affects binding to the catalytic iron nor abolishes demethylase activity
It is uncertain whether Met-1 or Met-79 is the initiator
It is uncertain whether Met-1 or Met-16 is the initiator methionine
Was originally thought to be a glutaminyl-tRNA synthetase
This peptide is linear as it lacks the C-terminal Asp/Asn residue required for cyclization
A paper showing an interaction with TBP and phosphorylation at Tyr-86 and Tyr-654 has been retracted due to panel duplication in several figures
Differs from other ScpB proteins because it has a longer N-terminus
Encoded in the 3'-UTR of AAK1 but there is evidence for the existence of the protein from a number of proteomics studies
According to PubMed:14660436 interacts with human BMP2, BMP4, BMP5, BMP6, BMP7 but not human INHBA. According to PubMed:15094188 interacts with human INHBA but not human BMP2, BMP4 and BMP6
Was originally thought to be a transport protein
Was originally (PubMed:10368157) thought to have a role in the purine repressor-mediated regulation of purA or the pur operon. The effect of yabJ (now ridA) on regulation of purA was due to the orientation of the marker gene downstream of purR in the yabJ mutant strain used in PubMed:10368157
Could be the product of a pseudogene unlikely to encode a functional protein. This is the N-terminal part of an aryl-alcohol dehydrogenase homolog of the AAD family. In strain S288c, a -1 frameshift disrupts the gene coding for this protein and produces two ORFs YFL056C and YFL057C. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
Although demonstrated for the human ortholog, involvement in osteoclastogenesis failed to be demonstrated in mouse cells
Although the DWD box motif has been suggested to mediate interaction of DDB2 with DDB1A, mutagenesis experiments have to date failed to demonstrate a role for this motif
Pro proteins of ERVK-6 tandem proviruses have been initially reported as being identical (AAF88166 and AAD21096). However, the same Pro proteins sequences, when translated from the human genome draft (AC072054), show one conflict with respect to each other
Does not bind calcium as one of the calcium-binding ligands is lost (Asp->Lys in position 64, which corresponds to 'Lys-49' in the current nomenclature)
Strain 3010/96 exhibits a partial deletion of the gene
The conserved zinc-binding site Asp residue in position 367 is replaced by an Asn
This protein lacks the conserved Cys in positions 48 and 292; they are replaced by a Ser and a Glu, respectively. It is therefore possible that the C- and D-clusters are either altered or missing in this protein, which may not form homodimers
In contrast to other members of the family, lacks the C-terminal ricin B-type lectin domain, which contributes to the glycopeptide specificity. No glycosyltransferase activity has been detected in an in vitro assay (PubMed:24398516)
PubMed:18461140 reports that IrtB forms a siderophore importer with Rv2895c, however this activity could be due to functional differences of IrtB in the molecular context of M.smegmatis and M.tuberculosis
A peptide arising from positions 165 to 173 was originally termed neurotensin-related peptide (NRP) and was thought to regulate fat digestion, lipid absorption, and blood flow
Although related to the protein phosphatase 2C family, lacks the conserved residues that bind manganese, suggesting it has no phosphatase activity
Was shown to interact with ZDHHC19, leading to recruitment of STAT3. However, this study was later retracted
Could be the product of a pseudogene. The original sequence is interrupted between codons 21 and 22 by a IS5K insertion element
No UPRTase activity has been detected in vitro and the uracil binding region known from UPRTases is missing
Was originally proposed to be a subunit from an L-xylulose uptake system, but PubMed:16385129 shows that YiaO does not bind L- or D-xylulose
Was initially reported to specifically bind 5-hydroxymethylcytosine (5hmC)-containing DNA in stem cells (By similarity). It was later suggested to act as an endonuclease that specifically cleaves 5hmC-containing DNA (By similarity). However, the endonuclease activity on 5hmC-containing DNA could not be confirmed by another report (PubMed:30554877)
The role of N(6),2'-O-dimethyladenosine cap (m6A(m)) on transcripts is unclear and subject to discussion. According to a report, m6A(m) promotes the translation of capped mRNAs (PubMed:30467178). However, another study did not observe a clear effect on mRNA translation, but reported an increased stability of a subset of m6A(m) transcripts (By similarity). According to a third report, m6A(m) inhibits mRNA translation without affecting mRNA stability (By similarity)
Was termed (Ref.2) DEFB135
Was originally (PubMed:12220620) thought to be a receptor for sphingosine 1-phosphate. It has been demonstrated that it is not the case in human (PubMed:19286662)
Although the active site residues are conserved, lacks the conserved Asp/Asn residue which is normally found 7-9 residues after the catalytic His
Although strongly related to the DcpS enzyme, it has apparently no scavenger mRNA-decapping activity
Was originally purified as a heterodimer of the N- and C-terminal end of the DAT gene product, but the cleavage of DAT protein appears to be a purification artifact
Lacks the conserved cysteine and histidine residues potentially involved in the active site of the GAT domain
PubMed:2690001 sequence revises that published in Ref.2
Was originally thought to be an amino-acid permease
In cv. Landsberg erecta, FRL1 (AC P0DKC9) is not functional due to a naturally occurring premature stop codon at position 279
Could be the product of a pseudogene. Corresponds to the N-terminal of members of this family
Although the active site Cys-452 is conserved, another important catalytic site, 'Arg-458', is replaced by a Lys residue suggesting that egg-3 may lack catalytic activity. Despite the lack of catalytic activity, egg-3 may retain the capacity to bind to phosphorylated substrates
Was originally thought to be myoblast cell surface antigen 24.1D5 and a possible membrane-bound protein ectokinase
Ser-225 is present instead of the conserved Cys which is expected to be an active site residue suggesting that this protein has lost its phosphatase activity
It is possible that in some cases Met-40 is the initiator in this case the expressed enzyme would remain cytoplasmic
In contrast to other members of the family, has no phosphoglycerate mutase activity
Product of a dubious CDS prediction. May be a non-coding RNA (PubMed:22302877)
SCN9A has been originally reported to be involved in generalized epilepsy with febrile seizures plus (GEFS+)(PubMed:19763161). However, it has later been shown that SCN9A variants are not a likely cause of autosomal dominant febrile seizures/febrile seizures plus and other monogenic seizure phenotypes (PubMed:33216760)
The molecular function of NOTUM has remained unclear for many years. It was initially thought to hydrolyze glycosaminoglycan (GAG) chains of glypicans, thereby affecting glypicans ability to interact with Wnt ligands. It was later reported to trigger glypican shedding, by mediating cleavage of their GPI-anchor (PubMed:17967162). However, while NOTUM specifically inhibit the Wnt signaling pathway, more pleiotropic effects would be expected from an enzyme affecting glypicans. It was finally shown that it requires glypicans to suppress Wnt signaling, but does not cleave their GPI-anchor. It acts by mediating depalmitoleoylation of WNT proteins, impairing WNT binding to frizzled receptors
Was originally termed Galnt15/pp-GaNTase 15
Could be the product of a pseudogene. C-terminally truncated compared to other bacterial TruB
Was originally reported to be located in the mitochondrion, but the evidence seems to be weak and contradictory with the presence of a cleaved signal sequence
Was reported that reduction/oxidation of cysteine residues Cys-23, Cys-45 and Cys-106 and a possible intramolecular disulfide bond involving Cys-23 and Cys-45 give rise to different redox forms with specific functional activities. However, this work was later retracted, although the roles of different redox forms in some functional activities is supported by other papers
Although it belongs to the adenosylhomocysteinase family, recombinant mouse homolog AHCYL1 expressed in bacteria shows no hydrolase activity, suggesting that Drosophila AhcyL1 may also lack this activity
Was originally (PubMed:12220620) thought to be a receptor for sphingosine 1-phosphate. PubMed:19286662 demonstrated that it is not the case
According to a report based on bioinformatics studies, this protein is not related to serine proteases but is homologous to mitochondrial SLC25 carrier proteins. Additional experimental evidences are needed to confirm this prediction
Ser-94 is present instead of the conserved Lys which is expected to bind the lipoyl cofactor
Lacks the conserved N-terminal cytochrome b5 heme-binding domain. Its enzyme activity is therefore unsure
Was initially characterized with a propeptide of 20 residues; this is now thought to be the result of in vitro proteolysis when the protein is overexpressed (PubMed:12220175, PubMed:14973029)
Was originally termed ARFGAP1
The publication has been retracted as they falsified western blot data
Was initially identified as a bi-functional protein that has an N-terminal domain with O-GlcNAcase activity and a C-terminal domain with histone acetyltransferase activity (PubMed:16356930). The histone acetyltransferase activity was detected only when the protein was expressed in mammalian cells, but not when expressed in bacterial cells, suggesting that the histone acetyltransferase activity might be due to the presence of a contaminant. Characterization of the human protein shows that this protein does not bind acetyl-CoA and therefore cannot have acetyltransferase activity
Does not show squalene synthase activity
Was initially shown to have low deadenylase activity that was lost when the metal-binding Glu was mutated (PubMed:17400819). Later studies showed that the purified protein lacked deadenylase activity (PubMed:29860338). Was subsequently shown to act as a phosphatase (By similarity)
Could be the product of a pseudogene. However an antibody which recognizes both Nat8 and Nat8B detects a product of approximately 27 kDa in brain extracts, which provides some evidence for existence of this protein (PubMed:22267734)
Could be the product of a pseudogene. Sequence is interrupted by the insertion of an IS1004 element
PubMed:2153657 sequence was originally thought to originate from Pseudomonas aeruginosa
This protein lacks the conserved Cys in position 45; it is replaced by a Tyr. It is therefore possible that the D-cluster is either altered or missing in this protein, which may not form homodimers
The catalytic activity is unsure despite catalytic sites being conserved (PubMed:23525007, PubMed:27836991). One report shows that LDAH has low cholesterol esterase activity when overexpressed in RAW 264.7 macrophages (PubMed:24357060). However, in another study, LDAH lacks cholesterol esterase activity when overexpressed in Hela cells (PubMed:27836991). Lack lipolytic activity towards trioleoylglycerol, dioleoylglycerol or monooleoylglycerol when overexpressed in COS-7 cells or Hela cells (PubMed:23525007, PubMed:27836991)
The disintegrin is also encoded by another precursor (AC Q3BER1)
Does not bind calcium as one of the calcium-binding sites is lost (Asp->Gln in position 48, which corresponds to 'Gln-49' in the current nomenclature)
PubMed:16484612 decribes a naa35/zEgap-containing complex as evolutionary conserved NatC complex; however, the zMak3 protein investigated in this context corresponds to mammalian NAA50 and not NAA30 and its interaction with NAA35 is ambiguous
May represent an artifactually modified form of ascaphin-7 arising from hydrolysis during the purification procedure
The C-terminus of this sequence has an annotated frameshift; it can be made to better match orthologs upon shifting at position 874
Was originally defined as a RNase HII; but belongs to the RNase HIII subfamily
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK33ac = acetylated Lys-40; H2BK34ac = acetylated Lys-41; H2BK143ub1 = monoubiquitinated Lys-152
A paper describing the expression patterns of this protein has been retracted due to concerns of image manipulation
Partial ORF that appears to be frameshifted continuation of Rv1088 (PE9). Sequence has been checked and appears correct. PE9 and PE10 are expressed independently of each other (PubMed:26031846)
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9me1/2/3 = mono-, di- and trimethylated Lys-10; H3K9ac = acetylated Lys-10; H3S10ph = phosphorylated Ser-11; H3T11ph = phosphorylated Thr-12; H3K14ac = acetylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me1 = monomethylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me1 = monomethylated Lys-24; H3K27me1/2/3 = mono-, di- and trimethylated Lys-28; H3S28ph = phosphorylated Ser-29; H3K36me1/2/3 = mono-, di- and trimethylated Lys-37
Most tissues also express read-through transcripts from this gene into the upstream gene (JMJD7), some of which may encode fusion proteins
Was originally thought to be the sequence of Arhgap8 but is actually the sequence of Prr5
The role of the nuclear export signal (NES) motif in XPO1-mediated DDX3X export is controversial (By similarity). In one study, NES has been found dispensable for DDX3X export while the helicase domain mediates the interaction with XPO1 (By similarity). However, in two other studies, DDX3X nuclear export is dependent on both NES and Ran in its GTP-bound form while the helicase domain is not required (By similarity)
According to PubMed:16322216, another protein (SRG) is encoded on the 3'-UTR of the CASZ1 gene. The existence of this protein that may play a role in apoptosis is extremely dubious despite the fact it was localized in the cytoplasm with the help of a polyclonal antibody
Was initially thought to be an arylsulfatase, given its similarity with the AtsA family. PubMed:12029081 however showed that it is a zinc phosphodiesterase
The subcellular localization of a truncated sequence of DGAT3, lacking AA 1-75, has been shown to be cytosolic (PubMed:22760209). However, the N-terminus of the full-length protein is predicted to contain a transit peptide for chloroplast targeting. Therefore, the localization of DGAT3 is unsure
PubMed:11584023 reported a cytosolic, as well as nuclear subcellular location. This result was obtained using an N-terminally GFP-tagged construct which most probably affected signal peptide-driven targeting to the ER. As a consequence, the in vivo revelance of the observed interaction with APOBEC1, a nuclear protein, is dubious
The kinase may be catalytically inactive
Could be the product of a pseudogene. The protein is truncated and lacks two of the residues of the predicted catalytic triad, suggesting that it does not have this enzymatic activity
The measured mass obtained by MALDI is higher than the calculated mass
Most probably a non-functional protein that cannot participate in the synthesis of a productive immunoglobulin chain due to an altered splice site and a mutation at position 105, corresponding to the second cysteine from the disulfide bridge, potentially leading to uncorrect folding (PubMed:9619395)
There are several genes encoding the J region in the T cell receptor delta locus. The peptide described in this entry is a representative for all the peptides encoded by these genes
Possibly identical to GltE
The substrate of the reaction was originally identified as L-erythrulose 4-phosphate (PubMed:26560079). It was then corrected to L-erythrulose 1-phosphate by the same group (PubMed:26978037)
Interacts with serine peptidase inhibitor SRPN2 in vitro; however, SRPN2 does not inhibit CLIPB8 activity suggesting that CLIPB8 may not be a physiological target of SRPN2 in vivo
Could be the product of a pseudogene. It corresponds to positions 1 to 91 of the complete orthologous and probably active protein in R.felis (RF_0890)
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-8; H2BK6su = sumoylated Lys-8; H2BK7ac = acetylated Lys-9; H2BK7su = sumoylated Lys-9; H2BK11ac = acetylated Lys-13; H2BK16ac = acetylated Lys-24; H2BK16su = sumoylated Lys-24; H2BK17su = sumoylated Lys-25; H2BK123ub1 = monoubiquitinated Lys-131
Has been shown to be a pseudogene in cv. Columbia (AC P0CJ42) due to a naturally occurring frameshift at position 65 in this strain. The sequence shown is from strain cv. Wassilewskija
The POM-ZP3 transcript appears to have arisen from a partial duplication and fusion of a 5' portion of a POM121 homolog and exons 5-8 of ZP3
The name Vt3.2 given by the authors is incorrect, since the first number indicates a cysteine framework III which does not correspond to this cysteine framework
According to a report, does not bind chromate (PubMed:8576221). According to another report, binds chromate with high affinity and is able to remove it from an aqueous solution in vitro (PubMed:28150901)
The mod operon containing this protein has previously been called the chlD locus
It is uncertain whether Met-1 is the initiator. An alternative upstream Met is found in primates, but not in other mammals
Could be the product of a pseudogene. Lyz1 has been shown to be expressed, but not Lyz2
A stretch of the chloroplast genome is duplicated within chromosome 10 resulting in the duplication of the gene. The expression of these duplicated genes (Os10g0355100, Os10g0527100) has not been demonstrated
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me1 = monomethylated Lys-10; H3K14ac = acetylated Lys-15; H3K14me2 = dimethylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me1 = monomethylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me1 = monomethylated Lys-24; H3K27ac = acetylated Lys-28; H3K27me1/2/3 = mono-, di- and trimethylated Lys-28; H3K36ac = acetylated Lys-39; H3K36me1/2/3 = mono-, di- and trimethylated Lys-39; H3K56ac = acetylated Lys-58
Was originally thought to be a DNA-binding transcriptional repressor. However, later work showed that the original sequence was a chimera and that the DNA-binding activity was derived from the incorrect N-terminal sequence
Alternative splicing has been shown to occur but the shorter forms are believed to be non-functional
Has also been found in a preparation of mitochondrial small ribosomal subunits. Was erroneously (PubMed:11279123, PubMed:11551941) assigned to be MRP-S32
The authors initially published the new framework as framework XVI which was already attributed to another cysteine pattern (AC Q2I2P8). In order to be consistent with the current nomenclature rules and with the new reassignment proposed by ConoServer, we now designate this cysteine pattern as XVII. We also follow ConoServer for assigning this toxin to the conotoxin Y superfamily
Was originally termed FMO2
Could be the product of a pseudogene. Similar to the C-terminus of ZBED6, but lacks BED domains, and therefore is probably not involved in transcriptional regulation. Encoded by a DNA transposon located in the 5'-untranslated region (5'-UTR) of LRRC61
Has been classified as a the potassium channel toxin alpha-KTx 22.4 in PubMed:22230549. Since the subfamily 22 has already been attributed, this peptide should be reclassified as alpha-KTx 23.4
Identified as having similarity to the core DENN family and referred to as DENN6A. Prediction methods do not indicate a DENN domain for this sequence and, the exact role of the DENN or the DENN-like domain in GEF activity needs to be clarified
Was originally thought to be a negative regulator of sigma-E function and to act directly on sigma-E and RpoH; this may not be physiologically relevant
The cGAS-STING pathway promotes a limited inflammatory response in bats (PubMed:29478775). This may be caused by the absence of the phosphorylation site at position 357, which is required to production of type-I interferons and other cytokines in other species (PubMed:29478775). The dampened cGAS-STING pathway may explain why bats show an increased tolerance to highly pathogenic viruses, such as coronaviruses, and serve as a virus reservoir (PubMed:29478775)
Although related to the lipase family, lacks the conserved His active site at position 344 which is replaced by a Gln residue, suggesting it is inactive
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-5; H2AK7ac = acetylated Lys-10; H2AS128ph = phosphorylated Ser-133
A stretch of the chloroplast genome is duplicated within chromosomes 7 and 9 resulting in the duplication of the gene. The expression of these duplicated genes has not been demonstrated
Does not have phosphatidylinositol 5-phosphatase activity
The mechanism of inactivation of the BCR(KEAP1) complex by covalent modifications of reactive cysteines is unclear. Covalent modifications were initially thought to disrupt interaction between KEAP1 and NFE2L2/NRF2 (By similarity). Recent publications suggest that cysteine modifications disrupt the interaction between KEAP1 and CUL3 without affecting the interaction between KEAP1 and NFE2L2/NRF2 (PubMed:16006525, PubMed:17127771, PubMed:18251510, PubMed:24896564)
An article reported a role in essential for photosystem II assembly; however, this paper was later retracted
The gene is not associated with corresponding maltase and maltose permease genes on chromosome 16 as it is the case for the other functional maltose fermentation loci, so its transcription regulation activity is speculative
AAL61996 is a fragment and was originally reported as a spliced variant of AAL61995
Although CCL17 was shown to bind to CCR8, additional studies demonstrated that CCR4, not CCR8, was the bona fide CCL17 receptor
LolA2 has similarity only to the C-terminal domain of aspartate kinases, excluding the kinase active site (PubMed:15654104)
Was originally thought to constitute the ATP pyrophosphatase enzyme (NTPPH). However, it was later shown (PubMed:12746903, PubMed:15864306) that it is not the case
Rats and mice do not produce appreciable cortisol, because they do not express the 17-alpha hydroxylase (Cyp17a1) enzyme in the adrenals
Was initially shown to catalyze the removal of carboxy-terminus tyrosine from alpha-tubulin (By similarity). However, later studies did not identified any detyrosinase or deglycylase activities from the carboxy-terminus of tubulin (PubMed:25103237)
Mutations in GPSM2 have been identified in people with profound congenital non-syndromic deafness designated as DFNB82 (PubMed:20602914). Subsequent brain imaging of these individuals has revealed frontal polymicrogyria, abnormal corpus callosum, and gray matter heterotopia, consistent with a diagnosis of Chudley-McCullough syndrome (PubMed:22578326)
Could be the product of a pseudogene. It corresponds to positions 278 to 323 of the complete orthologous and probably active protein in R.felis (RF_0890)
Product of a dubious gene prediction. Overlaps in opposite strand with PYCARD
Unlike in strain 927/4 GUTat10.1, there is a Glu instead of a Lys residue at position 55. Lys-55 is predicted to be conserved between strains as the enzyme undergoes auto-processing at this site. It is not clear if the presence of a Glu residue is due to a sequencing error
Was initially thought to play a role in the spindle checkpoint (PubMed:17417629). However, it was later shown that it is not the case and that phenotypes initially observed are the cause of the siRNA used that has an off-target effect resulting in MAD2L1 inhibition (PubMed:19904549, PubMed:20162290)
While it is structurally defined as a knottin it lacks the conserved Cys residue in position 82
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK6su = sumoylated Lys-7; H2BK7ac = acetylated Lys-8; H2BK7su = sumoylated Lys-8; H2BS10ph = phosphorylated Ser-11; H2BK11ac = acetylated Lys-12; H2BK123ub1 = monoubiquitinated Lys-120
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BA1me1/2/3 = mono-, di- and trimethylated Ala-2; H2BK6ac = acetylated Lys-7; H2BK11ac = acetylated Lys-12; H2BK22ac = acetylated Lys-28; H2BK27ac = acetylated Lys-33; H2BK33ac = acetylated Lys-39; H2BK34ac = acetylated Lys-40; H2BK143ub1 = monoubiquitinated Lys-146
In contrast with other SMARC proteins, there is currently no evidence that it associates with actin or actin-related proteins. It may rather act as a sequence-specific DNA binding ATPase, whose precise function remains to be fully characterized
PubMed:19174511 reported that MCA1 may have a prion form, dubbed [MCA]. However, the same authors have later not been able to reproduce these results and retracted the paper
While it is structurally defined as a knottin it lacks the conserved Cys residue in position 77
The catalytic mechanisms is still under debate. Cys-304 was proposed to function as a nucleophile that forms a covalent intermediate with acetyl-CoA during the reaction (PubMed:12368900), and indeed the residue can be acetylated (in vitro) (PubMed:12368900, PubMed:17223684). Depending on the assay system, mutation of Cys-304 leads to reduced or undetectable activity, indicating that is plays an important role. Still, mutation of Cys-304 has only a minor effect on the catalytic activity of the NuA4 histone acetyltransferase (HAT) complex (PubMed:17223684), making it unlikely that this residue functions as the catalytic nucleophile
No monoterpene, sesquiterpene or diterpene synthase activity detected in the heterologous expression system tested
According to PubMed:18060440, it is predicted to be a non-inhibitory serpin due to Gln-387 and Ile-390 which differ from the conserved residues in the reactive center loop (RCL) that is involved after cleavage in covalent linking and inhibition of the target proteinase
Could be the product of a pseudogene, it is missing about 90 N-terminal residues compared to some paralogs
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC A4QKZ7
Reported to be testis-specific (PubMed:20180869). However the transcript is found in many tissues, suggesting that the protein is present in many tissues
PubMed:3533140 originally reported Cys-117 to be the active site. PubMed:8314784 has shown this to be wrong
Was originally (Ref.1) thought to be a dehydrin
This protein-coding gene has been repurposed in primates, with the presence of a new enhancer sequence that drives expression in brain in response to sensory experience (PubMed:27830782)
Despite the presence of a JmjC domain, lacks the conserved residues that bind the iron cofactor, explaining the absence of histone methyltransferase activity
Pro-13, Tyr-17 and His-20 are present instead of the conserved Cys which are required to bind a 4Fe-4S-S-AdoMet cluster, as occurs with other proteins of this family. This protein may be an inactive homolog
In contrast to most nucleotidases that need divalent cations as cofactor, this enzyme does not require ions for activity
Lacks the conserved Ser residue in position 384 that is modified to a GPI-anchor amidated serine in homolog proteins
Although strongly related to the phospholipase A2 family, it lacks the conserved active Asp in position 129, which is replaced by a Val residue, suggesting that it has no activity
Was initially classified as a member of the small heat shock family protein. However, it was later shown that it is not the case (PubMed:21505417)
SPAC17G8.03c was previously identified as the homolog of budding yeast DBP3 in fission yeast (PubMed:15388803). However, it was further demonstrated that SPCC16C4.22 is the true ortholog of DBP3 (PubMed:29109278)
Previous studies suggested the 3 different paralogs (YTHDF1, YTHDF2 and YTHDF3) have unique functions with limited redundancy (By similarity). However, later studies showed that YTHDF1, YTHDF2 and YTHDF3 paralogs have redundant functions to a profound extent and directly promote degradation of m6A-containing mRNAs (PubMed:32943573)
According to PubMed:18060440, it is predicted to be a non-inhibitory serpin due to Val-328 and Glu-329 which differ from the conserved residues in the reactive center loop (RCL) that is involved after cleavage in covalent linking and inhibition of the target proteinase
Its precise role in the regulation of RAC1 activity is under debate. Was originally proposed to function as a guanine nucleotide exchange factor for RAC1, but later publications indicate it attenuates RAC1 activation by guanine nucleotide exchange factors and prevents accumulation of active, GTP-bound RAC1 (PubMed:12919680, PubMed:25074804, PubMed:28869598). Conflicting results have also been reported regarding its preferential interaction with nucleotide-free RAC1, as opposed to GPD or GTP-bound RAC1 (PubMed:12919680, PubMed:25074804)
Has been reported to act as a receptor for prosaposin (PSAP) (PubMed:23690594). However, it has also been shown that prosaposin does not increase activity (PubMed:27072655, PubMed:28688853). It has been suggested that GPR37L1 is a constitutively active receptor (PubMed:27072655)
Was suggested to bind pyrroloquinoline quinone (PQQ) based on prediction tools and indirect results (PubMed:12712191). However, this has not been confirmed in other publications (PubMed:15689995, PubMed:15689994)
In invertebrates, the aminoadipate-semialdehyde dehydrogenase reaction is a key step of the L-lysine biosynthesis pathway which is not fully conserved in vertebrates and it has been suggested that this protein participates in the reverse reaction i.e. in lysine catabolism (PubMed:12712191). However, this is unlikely to be the case as no dehydrogenase activity has been detected and the authentic mammalian 2-aminoadipate semialdehyde dehydrogenase has been identified as ALDH7A1 (PubMed:24467666)
Has similarity to alpha 1,2-mannosidases, but the catalytic activity of this protein is controversial (PubMed:15537790, PubMed:25092655). One study shows that it is important for a specific oligosaccharide trimming step from Man9GlcNAc2 to Man8GlcNAc2, suggesting activity as a mannosidase (PubMed:25092655). However, another study reports that this protein has no mannosidase activity (PubMed:15537790)
The N-terminal sequence shown here has been extracted from PDB entry 1L1Y
Represents a conventional myosin. This protein should not be confused with the unconventional myosin-XVI (MYO16)
Despite its name, the human homolog of this protein appears to lack measurable glycerol-3-phosphate acyltransferase activity under some conditions (PMID:19318427)
This peptide does not correspond to any sequence of the cDNA library
Initially the conserved reside Thr-80 was thought to be a nucleophile; mutagenesis in this organism and P.falciparum indicates it is not
Was originally thought to have uracil-DNA glycosylase activity, but further protein analysis show that it does not exhibit DNA uracil glycosylase activity when produced in an Ung-deficient Escherichia coli host
Lacks the lysine residue within the HhH motif critical for AP lyase activity
Was originally thought to play a role in adaptive immunity through control of dendritic cell-mediated antigen transport to lymph nodes from peripheral sites. However, this was later shown to be dependent on DOCK8
The N-terminal region is not conserved, preventing the detection of a bZIP domain
Was originally (PubMed:2531072) thought to originate from the sponge Geodia cydonium, but, on the basis of phylogenetic studies (Ref.2) it seems very probable that the DNA sequence coding for this protein comes from a rodent as agreed by the original authors (Ref.3). It is also doubtful that this is a real active insulin
Could be the product of a pseudogene. This gene encodes a non-functional protein due to an extra G nucleotide which gives rise to a truncated protein. This reverts with a frequency of 10 -4 to 10 -5 on urea containing agar. This reversion does not effect virulence in mice in any detectable fashion, suggesting urease is not important in the virulence of Y.pestis (PubMed:11119503)
Lacks the VHIID motif which is one of the conserved features of the GRAS family
The sequence has been determined from a mixture of all the subunits and so the exact sequence as well as the relevance of the variants described is unknown for each subunit
Prl2c3 and Prl2c4 have previously been regarded as different proteins, but they seem to be products of the same gene
This is a truncated version of a putative glutamine--fructose-6-phosphate aminotransferase. Strain S288c has a frameshift in position 258, which disrupts the gene coding for this protein and produces two ORFs YMR084W and YMR085W. A contiguous sequence for this protein can be found in strain YJM789 (AC A6ZME2)
It is uncertain whether Met-1 or Met-38 is the initiator. PCR experiments indicate the protein is probably shorter than indicated here, but the transcription start site was not precisely identified
This protein was previously referred to as T2R26 or T2R12 but is now considered to be the ortholog of human TAS2R41
It is not known if heme and GST are required for prostaglandin synthase activity. The protein copurifies with heme and GST when DTT is omitted during the purification procedure. The GSH-heme complex-bound enzyme has been proposed to act as a lyase and catalyze the degradation of prostaglandin E2 H2 (PGH2) to 12(S)-hydroxy-5(Z),8(E),10(E)-heptadecatrienoic acid (HHT) and malondialdehyde (MDA) (By similarity). Boiling the enzyme leads to loss of prostaglandin synthase activity, but does not eliminate the lyase activity. Besides, free heme can catalyze the formation of 12L-hydroxy-5,8,10-heptadecatrienoic acid (HHT) (By similarity). A more recent study demonstrates the GSH-dependent property of PTGES2, DTT dissociates the bound heme to produce active PGE2 synthase in vitro (PubMed:23426368). PTGES2 can only catalyzes PGE2 synthesis in the free state as an enzyme, while in vivo it forms a complex with heme and does not participate in PGE2 synthesis (PubMed:23426368). In agreement with this study, the in vivo evidence from PTGES2 deficient mice do not show that this protein is responsible for the PGE2 production under basal or pathophysiological conditions (By similarity)
Asp-165 is present instead of the conserved Glu which is expected to be a substrate-binding residue
Ala-369 is present instead of the conserved His which is expected to be part of the substrate-binding region
All strains have an amber mutation in position 215
It was previously reported that PEBP4 is a lysosomal protein which is highly expressed in tumor cells, and may promote cellular resistance to TNF-induced apoptosis. However the paper has since been retracted by the journal due to concerns of image manipulation
According to PubMed:11278534, this enzyme is unable to transfer GalNAc onto serine or threonine residue on the protein receptor, but instead requires the prior addition of a GalNAc on a peptide before adding additional GalNAc moieties, thereby acting as a glycopeptide transferase
Was originally termed Galnt9/pp-GaNTase 9
Compared to other bacterial ArnF, it has a divergent C-terminal domain. The upstream arnE gene has a premature stop codon and an internal deletion; as the 2 proteins form a heterodimer, ArnF probably does not accumulate to high levels
Could be the product of a pseudogene. The kinesin motor domain is truncated at the N-terminus and lacks the ATP-binding site which is one of the conserved features of the KIN7 family
The N-terminus of isoform 4 has been derived from EST and genomic sequences
In an older version of the nucleotide entry, this gene was in two parts, called hupH and hupI respectively
Neb-colloostatin may be proteolytically cleaved from collagen IV
The sequence shown here has been extracted from PDB entry 1IW7
Can promote osteogenic differentiation in vitro (PubMed:25751889). This is probably not physiologically relevant
When highly overexpressed there can be substoichiometric amounts of TPQ in the enzyme; this may be due to imperfect conversion of tyrosine to TPQ (see PubMed:8647101)
Lacks the 2 conserved His residues involved in iron binding and essential for dioxygenase activity. Its enzyme activity is therefore unsure
Overlaps in opposite strand with ZNF428
Has been shown to be a pseudogene in cv. Columbia (AC O04093) due to a stop codon at position 117 and a naturally occurring frameshift at position 846 in this strain. The sequence shown is from strain cv. Cl-0
In contrast to PubMed:17074753, PubMed:9851867 show a strictly maternal expression that decreases progressively during oocyte maturation and early cleavage stages. This is more similar to the expression pattern of lsm14b/rap55b
The sequence is interrupted by the insertion of an IS4 element between positions 304 and 305
NALCN was also originally reported to be a voltage-independent, cation-nonselective channel which is permeable to sodium, potassium and calcium ions (PubMed:17448995). However, NALCN is recently reported to be selective only for monovalent cations and to be blocked by extracellular divalent cations (PubMed:32494638). Futhemore, coexpression of NALCN, UNC79, UNC80, and NALF1 results in voltage-dependent NALCN currents (PubMed:32494638, PubMed:31409833)
A paper describes Frenatin 2.3S as a non-amidated peptide of 17 amino acids (PubMed:27049440). In contrast, another report describes it as a non-amidated peptide of 16 amino acids (PubMed:24704757). Since the absence of a C-terminal Gly is generally explained by the activity of Gly as an amide donor, it is possible that Frenatin 2.3S described by PubMed:24704757 comes from another gene, and should be presented in another entry
Was originally thought to be the ultraviolet sensitive opsin
The sequence shown here has been extracted from PDB entry 1CLC
Could be the product of a pseudogene. A frameshift in position 87 produces two separate ORFs
Was originally termed SIR-T8/SIRT8 (PubMed:11953824). This was later retracted (PubMed:12454780, PubMed:12454781)
A report observed N-glycosylation at Asn-354 (PubMed:19139490). However, as the protein is not predicted to localize in an extracellular compartment of the cell, additional evidence is required to confirm this result
Authors of PubMed:21329715 describe the nucleotide sequencing of this toxin. Unfortunately, the nucleotide sequence submitted (accession number HQ262493) corresponds to Css4 (AC P60266). As a consequence, we choose to show the mature sequence of Css8, since it has been partially directly sequenced. As the authors propose that Css4 and Css8 differ by only two residues (table 2 and 3), the missing residues in Css8 are propagated from Css4 and indicated as 'unsure' in the feature table
Several peptides are generated during UQCRFS1 insertion (PubMed:28673544). According to some authors, the identification of the transit peptide as the subunit 9, does not necessary imply that it must be considered as a structural subunit of the complex III dimer as additional fragments from UQCRFS1 are also present (PubMed:28673544)
In the PI-PLC X-box Thr-487 is present instead of the conserved His which is one of the active site residues. It is therefore expected that this protein lacks catalytic activity
May be inactive since it lacks many features found in other glutaredoxins such as the cysteines forming the redox-active disulfide bond
The active site cannot be determined by similarity to the viral poxins
Controversial data exist concerning the topology of PRSS55. One study in mouse shows that PRS55 is a GPI-anchored protein (By similarity). An other study does not confirm the GPI-anchor status of PRSS55 (PubMed:18844450). However as a GPI-anchor motif is detected, the possibility of a GPI-anchor instead of a single-pass type I membrane protein is probable
Could be the product of a pseudogene. Lacks the 4 disulfide bonds, which are conserved features of the family
Lacks the conserved threonine and leucine residues in positions 66 and 276, respectively, which are part of the carbamoylphosphate and ornithine binding sites; they are replaced by a leucine and a methionine residue, respectively
According to the crystallographic study residue 40 could be Gln
The initiator methionine is coded by a non-canonical CTG leucine codon
Originally thought to be a component of PSII; based on experiments in this organism, Synechocystis and N.tabacum, and its absence from PSII in T.elongatus and T.vulcanus, this is probably not true
It is uncertain whether the sequence from 46 to 76 is encoded by an intron as for PLDGAMMA2
The c-terminal sequence diverges from classical ADRM1 family proteins
The active channel complex is an obligate tetramer (PubMed:29567962). In contrast, the isolated cytoplasmic C-terminal domain forms homotrimers in vitro (PubMed:25820328). Likewise, photobleaching experiments suggest formation of homotrimers in the membrane (By similarity)
Pkd1l3 and Pkd2l1 have been defined as sour taste receptor in gustatory cells based on a number of indirect evidences: Pkd2l1 is expressed in a subset of taste receptor cells distinct from those responsible for sweet, bitter and unami taste and genetic elimination of cells expressing Pkd2l1 reduces gustatory nerve responses to sour taste stimuli (PubMed:16891422, PubMed:16929298). However, a number of experiments have recently shown that the sour taste receptor activity is probably indirect: mice lacking Pkd2l1 only show partial defects in sour taste perception (PubMed:21625513). Moreover, the PKD1L3-PKD2L1 heteromer, when expressed in cells does not respond to acid stimuli used to evoke proton currents in taste cells (PubMed:21098668)
Although it belongs to the glycosyl hydrolase 22 family, Thr-70 and Asn-87 are present instead of the conserved Glu and Asp which are active site residues. It is therefore expected that this protein lacks hydrolase activity
PubMed:9390441 shows a high affinity for lysine while PubMed:16816136 and PubMed:17293438 found no significant transport of this amino acid
Was originally thought to have phospholipase A2 activity
The Cys-43 indicated here is taken from the partial sequence in amino acid, and not from the translation of the transcript in which a Ser is found
Upon comparison to genes from other strains this is probably a fragment, and may have a number of sequencing errors
An isoform of Znf263 lacking residues 1-288 was described, however this paper was retracted due to concerns about the validity of figures published in the paper
This sequence is an example of a full-length immunoglobulin lambda-1 light chain
See also the NCBI entry AAB23201 which has been created from PubMed:1515064
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-9; H2AK7ac = acetylated Lys-13; H2AS128ph = phosphorylated Ser-136
Exhibits protein kinase activity according to PubMed:22730405, but in contradiction, described as an inactive pseudokinase by PubMed:30361234
The DNA N6-methyl adenine demethylase activity is subject to discussion. According to a report, biochemical assays do not reveal clear DNA N6-methyl adenine demethylase activity in vivo (PubMed:27745969). According to another study, has clear DNA N6-methyl adenine demethylase activity (PubMed:30017583)
Was originally thought to be a heme protein, but this was later shown to be an artifact
A peptide corresponding to residues 278 to 289 was isolated as part of plant proteomics studies and was originally thought to be of plant origin (PubMed:18602030, PubMed:19412582, PubMed:16529377). However, it was later shown that it is likely to be human type II keratin, a common contaminant in proteomic analyzes (PubMed:23895828)
GMPPA is a close homolog of GMPPB, that has been shown to catalyze the formation of GDP-mannose, an essential precursor of glycan moieties of glycoproteins and glycolipids. However, lymphocytes from AAMR patients, that exhibit very low GMPPA protein levels, have unchanged GDP-mannose pyrophosphorylase activity and higher GDP-mannose levels than those from healthy controls. Affected individuals and control subjects show similar N-glycosylation profiles, both for transferrin glycosylation and for N-glycans derived from either total serum protein or immunoglobulin G. These observations led to the hypothesis that GMPPA might serve as a regulatory subunit and allow allosteric feedback inhibition of GMPPB by GDP-mannose. Alignment of GMPPAs and GMPPBs from various species shows that GMPPAs are characterized by a 2 amino acid-insertion (residues 11-12) in a highly conserved motif that borders the catalytic pocket and binds the nucleotide substrate in homologous enzymes. This insertion might inactivate the ancestral catalytic site, converting it to an allosteric site (PubMed:24035193)
According to PubMed:12959640, T.stejnegeri was formerly named T.gramineus, supposing that this protein is the same as PLA-III from T.gramineus. They have been kept separated, because T.gramineus and T.stejnegeri are considered as being two different species (see http://reptile-database.org)
Could be the product of a pseudogene. Highly similar to the N-terminus of RNF216, but may encode a non-functional truncated protein
Was originally (Ref.1) thought to be a glyoxalase I
The enzyme reaction was initially thought to act via a redox-active disulfide bond mechanism; however the disulfide bond only takes place with inactive enzyme that lacks the copper cofactor. The catalytic copper is required to activate oxygen and catalyze oxidative C-H activation
Based on its structure and in vitro assays, was initially thought to have guanine nucleotide exchange factor (GEF) activity (PubMed:22977732). However, subsequent studies showed that it does not act as GEF in vivo (PubMed:24095279)
The guanine nucleotide exchange factor (GEF) activity is controversial. One study showed GEF activity towards RALA, RAP1A and RRAS (By similarity). However, in another study, a construct containing only the Ras-GEF domain lacks GEF activity towards RAP1 (PubMed:22081014)
Unlike other Plasmodium adenosine deaminases, lacks S-methyl-5'-thioadenosine deaminase activity due to the presence of a Glu residue at position 171 instead of an Asp residue
Was initially thought to be a thionin (PubMed:2226781, PubMed:8380707)
Was originally thought to be a fimbrial subunit
Was named interferon alpha-E (embryonic) based on peptide sequencing (PubMed:9244179). The differences found may be sequencing erros and have not been confirmed by other studies
The sequence of the protein was deduced from the genomic sequence and ESTs by similarity to the mouse and rat sequence
Could be the product of a pseudogene. According to PubMed:12825070, no evidence has been tendered concerning the existence of this protein
Due to a premature stop codon, the human protein is truncated and lacks the DNAJB3 canonical C-terminal domain. However, expression studies suggest the existence of the mRNA and protein in human
According to a report, AIM2 is autoinhibited in absence of double-stranded DNA (dsDNA) due to an interaction between the pyrin and HIN-200 domains that induce a closed conformation (PubMed:22483801). However, it was later shown that AIM2 is not autoinhibited and that dsDNA acts as a molecular ruler to promote its homooligomerization (PubMed:26197926)
Has been reported as being enzymatically active and calcium-dependently inducing platelet aggregation (PubMed:8921006). This activity appears to be unlikely in light of the lack of activity of both recombinant AtnL (S49) and bothropstoxin-1 (K49), especially keeping in mind the possibility of contamination of the purified protein with catalytically active sPLA2s. The fact that the high level of enzymatic activity reported was determined on PC substrates and that it was in the range of the human group IIA enzyme, which in fact displays a very low activity on PC-rich substrates, casts further doubt on the reported activity of ecarpholin S (PubMed:17927217)
This sequence was originally thought to derive from Bos taurus (PubMed:16305752). In fact it derives from Sus scrofa (PubMed:15679890, PubMed:17145712)
A palmitoylation site was proposed at Cys-91, but it was later shown that this cysteine is engaged in a disulfide bond
The human ortholog was initially reported to have ornithine or arginine decarboxylase activities, but it was later found to possess neither of them
Previously reported to be localized in the mitochondrion (PubMed:16916800). However, it was not confirmed by later reports (PubMed:18062773)
Was originally (PubMed:10714994, PubMed:11904409) called HPr kinase/phosphatase, but P-Ser-HPr dephosphorylation was shown (PubMed:12359880) to follow a quite unique mechanism, in which Pi instead of H(2)O is used for the nucleophilic attack on the phosphoryl group. P-Ser-HPr dephosphorylation is therefore not a phosphohydrolysis but a phospho-phosphorolysis reaction, and the bifunctional enzyme was dubbed HPr kinase/phosphorylase
It is unclear whether it transports carnitine in vivo
While some reports have shown that E1S transport exhibited single-saturation kinetics (PubMed:11932330, PubMed:14610227), other studies demonstrated a biphasic saturation kinetics (PubMed:22201122, Ref.24, PubMed:11932330, PubMed:14610227). Despite a previous report that demonstrated a pH-dependent substrate uptake and a transport stimulation at low pH (PubMed:14610227), another study did not observe any pH-dependent E1S and taurocholate transport (PubMed:23531488, PubMed:14610227). Was shown to mediate bile acid taurocholate transport at low pH in some studies (PubMed:14610227, PubMed:29871943), but not others (PubMed:23531488, PubMed:11159893, PubMed:29871943). The enterocyte localization of SLCO2B1/OATP2B1 remains uncertain. While some authors found it in the apical membrane (PubMed:12724351), consistent with a function as uptake carrier contributing to the intestinal absorption of drugs, other studies demonstrated a basolateral membrane expression, supporting a physiological role in substrate uptake from the blood flow and intestinal clearance (PubMed:28408210, PubMed:12724351)
The publication has been retracted as they duplicated images
The elongator complex was originally thought to play a role in transcription elongation. Was reported to display histone acetyltransferase activity and to acetylate histone H3 preferentially at 'Lys-14', and H4 preferentially at 'Lys-8' (PubMed:10445034, PubMed:11904415, PubMed:15138274). However, it was later shown that the effect on histone acetylation and chromatin regulation is indirect and that the elongator complex is primarily involved in tRNA modification (PubMed:17018299, PubMed:18986986, PubMed:21912530)
PubMed:10760570 reported that UBE2L1, UBE2L2 and UBE2L4 are most likely pseudogenes and the only expressed member of this subfamily seems to be UBE2L3
It was initially thought that PDL3 has phospholipase D activity due to its HKD motifs. The second HKD motif contains Glu instead of the canonical Asp. Its enzyme activity is therefore unsure. Catalytic phospholipase D activity is still controversial (PubMed:30312375, PubMed:9813063) (By similarity). Its closest homolog PLD4, exhibits no phospholipase activity (By similarity)
Does not encode the amino acids known to be needed in E.coli for autocatalytic cleavage, probably acts differently from E.coli LexA
DNA from strain B / AC2514 has genes in the order ribosyltransferase-ncRNA-RT (PubMed:2466573, PubMed:1722556). The data presented in Millman et al., says genes are encoded in the order ncRNA-ribosyltransferase-RT
Lacks the conserved leucine residue in position 272, which is part of the ornithine binding site; it is replaced by a methionine residue
Arg-61 is present instead of the conserved Lys which is expected to be an active site residue. The same site-directed mutant in B.cereus has no activity; therefore this protein is probably inactive
Was previously thought to be expressed in L5
CDK5RAP1 was proposed to act on both nuclear and mitochondrial RNA (PubMed:22422838). However, another study shows that ms2i6A is a mitochondrial tRNA specific modification and is absent from nuclear encoded RNA species, implying that there is no methylthiotransferase activity on nuclear RNA (PubMed:28981754)
Was originally thought to associate with TER1, the RNA molecule of the telomerase complex that provides a template for telomeric DNA synthesis (PubMed:21164032). The authentic RNA subunit of the telomerase that associates with POT1A has been recently shown to be TR and not TER1 (PubMed:31392988, PubMed:31754031). The original publication has been retracted
According to PubMed:18474358, it is autophosphorylated. However, it is not related with protein kinases, suggesting it is phosphorylated by another protein
Was thought to be recruited to promoters via its interaction with BAZ1B/WSTF, but this work has later been retracted
A pseudogene in strain MG1655 / ATCC 700926 due to a recent laboratory-derived single nucleotide insertion, but not its parent MG1655 / ATCC 47076
Could be the product of a pseudogene, it is missing the C-terminus compared to orthologs
The existence of N(3)-methylcytidine on mRNA is unclear (PubMed:34774131, PubMed:33313824). A report was unable to detect N(3)-methylcytidine formation in mammalian mRNAs using a nucleotide-resolution sequencing approach (PubMed:33313824). According to another publication, METTL8 has no activity on mRNAs and specifically methylates mitochondrial tRNAs (PubMed:34774131)
A publication reported some nucleolar localization (PubMed:32199293). However, the protein used in this publication used a N-terminal tag, which possibly interferes with the mitochondrial targeting (PubMed:34774131)
Ser-489 is missing in the human genome assembly but is present in all available mRNAs and ESTs
Product of a dubious gene prediction. Encoded in intron of TSPEAR
Has been shown in one report to not be localized to centrosomes or nuclei, and based on RNAi-mediated knockdown studies, has been shown to play a role in cytokinesis (PubMed:12213836). However, has also been reported to localize to centrosomes and nuclei and to have no role in cytokinesis, based on results obtained using the cdc-14 he118 mutant and RNAi-mediated knockdown (PubMed:15247923)
Although this is said to be a human protein, it is not encoded in the human genome. It is highly similar to microbial proteins and belongs to a family of microbial proteins
This sequence can initiate at a non-canonical CTG leucine codon. This non-AUG initiator start codon is located 21-bp upstream of the initiator methionine codon (PubMed:16169894)
It is not obvious if the APS kinase domain is functional; the conserved active site serine (position 527) is replaced by an alanine
P450-254C was originally listed as a separate gene (CYP2C17). Resequencing demonstrated that it is not a separate gene, but a chimera. The 5'-portion corresponds to a partial 2C18 clone, and the 3'-portion corresponds to a partial 2C19 clone
This protein has been named UBC13 according to the nomenclature proposed in PubMed:16339806, but it is not the same as the UBC13 described in several publications that correspond to the protein named UBC35 in our nomenclature
A unique gene in the tomato genome is described to encode for a protein with either a lycopene beta-cyclase activity or an exclusive neoxanthin synthase activity with no apparent lycopene beta-cyclase activity. According to a report, has lycopene beta-cyclase activity (PubMed:10995464). According to another report, displays exclusive neoxanthin synthase activity with no apparent lycopene beta-cyclase activity (PubMed:11029576). This discrepancy might be due to the differences in the cultivars used for the gene cloning and/or in the methods used to determine the enzymatic activities, in vitro assay or molecular analysis of mutants
In contrast with human ortholog, not able to transport urate (PubMed:35144162)
Lacks the phospho-accepting Asp (here Glu-130), present in the receiver domain, which is one of the conserved features of two-component response regulators (ARRs) family
In strain W3110, the sequence is interrupted by the insertion of an IS5 element between positions 291 and 292
The allelic variation Ile-149 designated as NAT1*17 is part of the NAT1*11 allelic variation as reported by the nomenclature committee
Was originally thought to be Heymann nephritis antigen gp330
Was originally erroneously termed BP80D
It is uncertain whether Met-1 or Val-41 is the initiator
Was originally thought to be an adenine receptor but PubMed:12397184 found no activation by adenine of the mouse ortholog
PubMed:3619442 incorrectly terms this protein to be beta-actin
Can promote osteogenic differentiation in vitro (PubMed:25237187, PubMed:25751889). This is probably not physiologically relevant
The crystal structure contains zinc ions that may be due to the crystallization medium
The light chain lacks the CLIP domain which is different from other CLIP protease family members. This is due to a cleavage at position 83 which is seen in vitro but whose physiological relevance is unclear
The gene for this protein is part of the operon phzABCDEFG which is duplicated in P.aeruginosa. Cristallographic study (PubMed:12741825) has been arbitrarily placed in PhzD2 (AC P0DPC1), because it is impossible to differentiate between the duplicate which has been chosen for the study, and because PhzD2 (AC P0DPC1) displays an important role in phenazine production and host infection
This protein was first identified as a Trichophyton rubrum transporter and called TruMDR1, but it was further realized that the isolate used for the identification was a Trichophyton interdigitale isolate
It was initially thought that PDL3 has phospholipase D activity due to its HKD motifs. The second HKD motif contains Glu instead of the canonical Asp. Its enzyme activity is therefore unsure. Catalytic phospholipase D activity is still controversial (PubMed:29053796, PubMed:30312375). Its closest homolog PLD4, exhibits no phospholipase activity (By similarity)
The potassium channel activity in endosomes and lysosomes is unclear in vivo (PubMed:35750034). Potassium transport was initially measured with a luminal side pH above 7.0, which is non-physiological for lysosomal channels (PubMed:26317472, PubMed:28723891, PubMed:32228865, PubMed:32267231, PubMed:33505021). Under the normal lysosomal pH (4.5- 5.0), TMEM175 is much more permeable to protons than to potassium or sodium (PubMed:35750034)
Lacks the conserved signal peptide, which is one of the features of the pectinesterase family
It is uncertain whether Met-1 or Met-154 is the initiator
Pro-263 is present instead of the conserved His which is expected to act as the active site proton acceptor
Originally called wnt2 by PubMed:1408135 but it is considered to be a wnt2b paralog by Xenbase
Back et al. found that TthNfo also catalyzes the excision of uracil from DNA, but further protein analysis by Schomacher et al. show that it does not exhibit DNA uracil glycosylase activity or DNA uridine endonuclease activity
Could be the product of a pseudogene. The TDGF3 locus has characteristics of a retrotransposon, including lack of introns and a poly(A) sequence
The relevance of the protein lysine acetyltransferase activity is unclear (PubMed:29415125). The publication reporting acetylation of GJA1 does not provide direct evidence of lysine acetyltransferase activity of ELP3 (By similarity)
Has been classified as a gamma-KTx toxin due to its molecular target (Kv11/ERG), but may be classified as an alpha-KTx since it shares a high level of homology in both primary and 3D structures with other alpha-KTx scorpion toxins. However, it is noteworthy that surface by which BeKm-1 interacts with ERG1 is formed by residues located in the alpha-helix and the following loop, while the traditional functional site of other alpha-KTxs is formed by residues on the beta-sheet
The isopeptide linked residue 8 is shown as Asn rather than Asp as mentioned in PubMed:1826288, because it is not known whether Asp or Asn is encoded and the isopeptide bonds are almost always formed between the amides Asn or Gln and N6-lysine or alpha amino groups, with the liberation of an ammonia that makes the reaction essentially irreversible
It is uncertain whether Met-1 or Met-38 is the initiator. Orthologous sequences cannot be extended
While it is structurally defined as a knottin it lacks the conserved Cys residue in position 64
PubMed:7715640 reported a mutation Pro-364 linked to congenital heart diseases. PubMed:8873667 later shown that it is an artifact
PubMed:11741837 reported 2 mutations (Phe-11 and Ala-24) linked to non-syndromic autosomal recessive deafness (DFNBG). These mutations have subsequently been shown (PubMed:12457340) to involve the pseudogene of connexin-43 located on chromosome 5
Although strongly related to RuBisCO family, it lacks the conserved Lys active site in position 327, which is replaced by an Arg residue, suggesting that it may catalyze enolization but not carboxylation
PubMed:9013898 sequence is supposed to originate from rat but, based on sequence similarity, it seems that this is a case of bacterial contamination from E.coli
In contrast with human ortholog, adenosine transport may be not pH-dependent
Although this enzyme participates in the selenocysteinyl-tRNA(Sec) biosynthesis pathway in many taxa, this pathway has been shown in PubMed:32220326 to be lost in embryophyta
An article reported an auxin transcription module controlling cell division plane rotation through CLASP; however, this paper was later retracted
PubMed:9015313 originally reported this protein to be a proteoglycan (thus explaining its name). Although not excluded, such secreted function is not clear
In C.vinosum two similar set of genes code for RuBisCO large and small chains: the RbcL-RbcS and the RbcA-RbcB pair (this entry). Under standard photoautotrophic culture conditions only the latter pair seems active, the former probably being cryptic
Lacks the Trp (here Arg-220), a conserved feature of the aromatic cage required for the interaction with histone H3K4me3/2
There seems to be a problem in the assembly of the Mouse genome in the region covered by contigs AC125051 and AC131674
The mature peptide AKH-1 is also encoded by another precursor (AC C0HL92)
The functional assignment is controversial
Could be the product of a pseudogene. Encodes aberrant truncated proteins
Was originally termed Galnt6/pp-GaNTase 6
Was originally (Ref.1) thought to be an inhibitor of alpha-amylase
PubMed:4934841 authors considered 'C.tartarivorum' as a separate species
PubMed:6540370 shows this sequence in their paper, but the reference for the origin of the sequence is not given
This protein should not be confused with FBXO11 (AC Q86XK2) that was initially erroneously named PRMT9
The PHTF domain was initially defined as an atypical homeodomain, suggesting that this protein could act as a transcription regulator (By similarity). However, the protein is not found in the nucleus and mainly localizes in the endoplasmic reticulum membrane, suggesting that it does not act as a transcription factor (PubMed:12604659)
Was originally thought to contain a F-box domain and LRR repeats, but it lacks both types of domains
Product of a dubious CDS prediction. Found in the 3'-UTR of PDPK1. No homolog
Asn-333 is present instead of the conserved Asp which is expected to be an active site residue
Strain S288c has a frameshift in position 403, which disrupts the gene coding for this protein and produces the non-functional allele sal1-1. A full-length functional allele can be found in strain CG379 (AC P0CI40)
Despite of the presence of a putative ATP-binding motif, this protein does not bind ATP, suggesting that it has no protein kinase activity (PubMed:29503074)
Lacks the conserved active histidine at position 115 that mediates the phosphotransfer. Shows a conserved HPt domain that may have some alternative degenerated phosphorelay role in cell signaling
Pc22g22850 has first been identified as a mannose-ethanolamine phosphotransferase-like protein. However, resequencing of the region showed that it correspond actually to a non-reducing polyketide synthase
Depending on the experimental set up and substrate used, NSD2 has been shown to mono-, di- or tri-methylate 'Lys-27', 'Lys-36' or 'Lys-79' of histone H3 and 'Lys-20' or 'Lys-44' of histone H4 (By similarity). However, dimethylation of nucleosomal histone H3 at 'Lys-36' (H3K36me2) is likely to be the physiological reaction catalyzed by NSD2 (By similarity)
Likely derived from retrogene insertion of an NLRP2/NLRP7-like gene, it was originally considered a pseudogene. However, it turns out to be functional and under purifying selection
Was initially reported to have ornithine decarboxylase (PubMed:11587527) or arginine decarboxylase (PubMed:14738999) activities, but it was later found that the mouse ortholog does not possess either of them
The active site contains a CRVC motif wich differs from the conserved CGPC motif
Based on current literature, utilization of para-aminobenzoic acid (pABA) involving C4-deamination seems not to occur in bacteria, plants and mammals where only C5 hydroxylation of HHB has been shown, even if human COQ6 is able to perform the deamination reaction in the absence of COQ9
Lacks the conserved Lys residue in position 228 required for covalent retinal binding
Neither a protein sequence nor a nucleotide sequence had been determined for this protein when the crystallographic structure was reported. The sequence of a model fit to electron density plots at 2.2 Angstroms resolution was used. When a nucleotide sequence became available, it replaced the model sequence. There are 14 differences between the model and the nucleotide sequences
Was originally thought to play a role along with PilA in the transcription regulation of PilE
The gene encoding this protein shares one overlapping exon with TMEM113
Deletion HUR1 has been reported to cause increased sensitivity to hydroxyurea (PubMed:12615994). However, HUR1 partially overlaps with PMR1 and a later analysis revealed that deletion of PMR1 but not HUR1 affected resistance to hydroxyurea (PubMed:18069899)
This protein lacks several conserved Cys residues that bind [4Fe-4S] clusters in other CODHs. Therefore, it is not clear whether this protein is active. However, the protein would be able to bind a [Ni-4Fe-4S] cluster, which is the active site of CO oxidation
Product of a dubious CDS prediction. Encoded in an intron of the CELF2/CUGBP2 gene (opposite strand)
Sequence submitted to GenBank under accession ACW82491.1 does not completely correspond to the one described in the related article, which is the correct one
Several genes are coding for this toxin for which the structure by NMR has been determined. The cross-references to PDB and additional information can be found in entry AC P86405
Phosphorylated at very low, substoichiometric levels when isolated from skeletal muscle sarcoplasmic reticulum (PubMed:1985907). Can be phosphorylated by CK2 at Thr-381 (in vitro), albeit with low efficiency, suggesting this is not a physiological CK2 substrate (PubMed:1985907). Not phosphorylated at Thr-381 (PubMed:22170046)
This protein is shorter compared to other members of the family and lacks the C-terminal part that binds zinc
The purified enzyme was shown to contain 0.5 zinc atoms per subunit, and sequence analysis was used to predict the zinc binding site (PubMed:11508704). The crystal structure indicates a lack of bound zinc ions, and shows that the residues that were predicted to bind zinc are too far apart in space to form a zinc binding site (PubMed:29976570)
Product of a dubious gene prediction. The corresponding gene is on a region of chromosome 21 that is known to be an artifactual duplication of another chromosome 21 region in the GRCh38 assembly. This entry may represent an artifactual copy of AC P57059
The metalloprotease is also encoded by another precursor (AC Q698K8)
Could be the product of a pseudogene. In contrast to other members of the family, it is shorter at the C-terminus and lacks the last 2 transmembrane regions
Lacks the distal histidine (here Ser-77), present in the active site, which is one of the conserved features of the classical plant (class III) peroxidase family
There is no sequence for the expressed copy of a2 in strain S288c, because this strain is of mating type alpha. A sequence for the expressed copy of a2 can be found in other strains (AC P0CY12)
The sequence probably misses the N-terminal part since the N-terminal acylcarrier protein transacylase domain (SAT) is absent. The correct gene model with the complete protein sequence could not be recovered from the submitted genomic sequence
In PubMed:22511981, this sequence erroneously refers to SjKTx51
Is identical to AC P86116 in mass and elution time, but not in sequence (2 amino acids are different)
The protein sequence for 83-95 might be that for residues 148-160; the 2 sequences are identical
Lacks three Cys residues in the RING-type zinc finger domain 1 and two Cys residues in the RING-type zinc finger domain 2 that are conserved features of the family
It is uncertain whether Met-1 or Met-35 is the initiator. In many S.cerevisiae strains, it is not possible to extend the sequence at the N-terminus beyond Met-35 because of a frameshift in the upstream sequence when compared to strain S288c. However, experimental evidence indicates that the longer protein is made in S288c
Studies in clathrin-mediated endocytosis of ITGB1 and TFR used a siRNA mixture of ISTN1 and ISTN2, and a Dab2 mutant with impaired binding to EH domain-containing proteins EPS15 and ITSN1 suggesting a partially overlapping role of the EH domain-containing proteins
Could be the product of a pseudogene. Possesses a truncated Fe2OG dioxygenase domain which lacks 1 iron binding site
Was initially classified as a member of the small heat shock family protein. However, it was later shown that it is not the case (PubMed:19921466)
Was originally (Ref.9) thought to be D-beta-hydroxybutyrate dehydrogenase
Was originally thought to be a dihydrofolate reductase
This is a truncated version of aquaporin-2. A natural 11 bp deletion in position 109 leads to a frameshift, which disrupts the gene coding for this protein and produces two ORFs SCRG_04941 and SCRG_04940. A contiguous sequence for aquaporin-2 can be found in strain Sigma 1278B (AC P0CD89)
Lacks the conserved Glu active site in position 117, which is replaced by an Ala residue, explaining why it is inactive
Absent in strains cv. Heinz 1706 and cv. Ailsa Craig
The conserved active site Cys (or selenocysteine) residue in position 29 is replaced by a Thr. However, as function in selenoprotein synthesis is proven, it is possible Cys-31 is the active site
Was initially thought to contain a F-box domain (PubMed:15147268). However, such a domain is not detectable by any prediction tool
Was originally thought to be from mouse but, on the basis of subsequent work (PubMed:8654948, PubMed:8877732) has been shown to be of rat origin
The complete sequence of this protein comes from PubMed:17046438, but no sequencing method is described
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BA1me1/2/3 = mono-, di- and trimethylated Ala-2; H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-39; H2BK34ac = acetylated Lys-40; H2BK143ub1 = monoubiquitinated Lys-144
Was wrongly assigned as myoneurin (Ref.2)
TAF12B in cv. Lansberg erecta (AC B2C6R6) is 2 amino acids shorter and has been shown to be involved in the negative regulation of cytokinin sensitivity
Despite the nomenclature given by PubMed:11077244, FBW2 does not contain any WD-40 repeat
PubMed:2684782 sequence was incorrect and retracted in PubMed:2227448
There is conflicting evidence for Zn(2+) acting as an active metal ion. According to one report, it inhibits the phosphonate ester hydrolase activity (PubMed:8824203). According to another report, it acts as a cofactor (PubMed:20133613)
Was originally thought to be the ortholog of mammalian DLG3
Was reported to promote CD8+ T cell immunity through effects on mitochondrial respiration. However, the corresponding article has been retracted
Human SLC47A2/MATE2 and rodent SLC47A2/MATE2 exhibit only low mutual sequence identity (38.1%) and different expression patterns. In fact, the counterparts of human SLC47A2/MATE2 have not been identified in rats and mice, and the counterpart of rodent SLC47A2/MATE2 has not been found in humans. The phylogenetic tree of mammalian MATE-type transporters clearly suggested that rodent SLC47A2/MATE2 would be classified into an new subgroup:SLC47A3/MATE3 family but not SLC47A2/MATE2 family. As the nomenclature and classification are confusing, PubMed:17715386 suggested to rename mouse and rat SLC47A2/MATE2 to SLC47A3/MATE3
Despite its name, the rat TOMT protein does not contain a transmembrane region in contrast to primate orthologs
Although related to the peptidase M28 family, it lacks some conserved zinc-binding and active site residues and therefore has probably lost hydrolase activity
This is a truncated version of a putative glutamine--fructose-6-phosphate aminotransferase. Strain Lalvin EC1118 has a frameshift in position 258, which disrupts the gene coding for this protein and produces two ORFs. A contiguous sequence for this protein can be found in strain YJM789 (AC A6ZME2)
Was originally called CpsA
The proteins described here are encoded by the gene CDKN2A, but are completely unrelated in terms of sequence and function to tumor suppressor ARF (AC Q64364) which is encoded by the same gene
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC A0A377
According to a report, ubiquitin-binding is dispensable for function (PubMed:22396592). However, such data are not confirmed by PubMed:22705371
Was first identified as a peroxisomal ATP transporter (PubMed:12445829). However, later experiments showed that it acts as a peroxisomal transporter for multiple cofactors (PubMed:22185573)
Most probably a non-functional protein that cannot participate to the synthesis of a productive T cell receptor (TR) chain due to both an altered splicing site and a mutation at position 39, corresponding to the first cysteine from the disulfide bridge, potentially leading to uncorrect folding (PubMed:9619395)
KSR2 binds ATP and has very low in vitro protein kinase activity; the physiological relevance of this activity is unknown. KSR2 is proposed to be in an inactive conformation by itself or in complex with MAP2K1. Interaction with BRAF is proposed to induce a conformation change that increases the low intrinsic kinase activity (PubMed:21441910)
In contrast to other phospholipases, it lacks the typical Asp active site (Asp->Gln in position 114)
The ubiquitin-like domain 2 was thought to interact with the catalytic domain competing with the ubiquitin substrate and thus partially inhibiting USP4 activity (PubMed:21415856). As the results could not be reproduced this work was later retracted (PubMed:24398133). The cristal structure in the paper was correct and was republished later (PubMed:25404403)
No enzymatic activity has been detected when expressed in yeast, suggesting it may be inactive
Could be the product of a pseudogene. Contains only the N-ter part of the functional aspartic proteinases
The sequence of 1-36 of PubMed:12359730 has not been submitted
Was originally (PubMed:9639683) thought to be the ortholog of chicken CHST3 and therefore named C6ST. However, it has no strong chondroitin 6-sulfotransferase activity
PubMed:17335148, examines the translation products of theses four XAGE1A transcripts, and finds that the XAGE-1c transcript is possibly translated to 9- and 17-aa polypeptides and not to a protein consisting of 160 amino acids as shown in PubMed:11992404
Lacks the zinc-binding sites found in mammalian orthologs
A stretch of the chloroplast genome is duplicated within chromosome 9 resulting in the duplication of the gene. The expression of this duplicated gene has not been demonstrated
Additional homology to the integrase family exists upstream of the current start codon
According to PubMed:12959640, T.stejnegeri was formerly named T.gramineus, supposing that this protein is the same as PLA-V from T.gramineus. They have been kept separated, because T.gramineus and T.stejnegeri are considered as being two different species (see http://reptile-database.org)
Was originally thought to be a non protein-coding gene
IL17D nucleotide sequence has been submitted under the name IL27 in INSDC AY078238 (Ref.2). However, the protein shown in this entry should not be confused with the actual IL27 protein, which forms a heterodimeric cytokine by interaction with EBI3. In order to avoid any ambiguity, we strongly recommend using the official HGNC nomenclature
It is unsure whether this protein is glycosylated or not. PubMed:5147 has shown that a preparation of aminopeptidase 1 contains about 12% of conjugated carbohydrate, while PubMed:1400574 could not identify any glycosylation, which is in agreement with the fact that aminopeptidase 1 does not transit through the secretory pathway
Ser-370 is present instead of the conserved Asp which is expected to be an active site residue
Prakash et al. cloned a partial cDNA corresponding to the 3'UTR of the last exon of the gene (PubMed:7892239). They have shown that a synthetic peptide derived from this sequence could stimulate fibroblasts growth in vitro, and that this protein could be a fibrogenic lymphokine, that could stimulate several biological activities related to scarring. It would be expressed several cell types including CD4+ lymphocytes and fibroblasts. However, it was not confirmed by in vivo data
It has been reported that many phenotypes associated with the Bristol N2 reference allele of npr-1 may reflect a neomorphic gain-of-function sensitivity of the receptor to flp-18 in addition to sensitivity to flp-21
It is uncertain whether Met-1 or Met-57 is the initiator methionine. However, according to PubMed:8021504, the initiator methionine is coded by a non-canonical CTG leucine codon; This leucine codon is in an excellent Kozak consensus located 39 bp upstream of the corresponding first mouse ATG
Lacks the conserved Tyr/Phe in position 29 necessary for binding heme
Was originally thought to be a longer ORF that encodes what is now known to be mtlA and mtlF
Lacks the conserved tripeptide Ser-Pro-Cys in position 672 necessary for the methyltransferase activity in DRM protein (AC Q9M548)
Fei et al (PMID:10823827) shows that the transport process is electrogenic with a Na(+):L-glutamine stoichiometry of 2:1, contrary to the conclusions of Chaudhry et al (PMID:10619430) who finds that the transport is electroneutral with a Na(+):L-glutamine stoichiometry of 1:1. Chaudhry et al (PMID=11742981) shows that this electrogenic transport describes by Fei et al (PMID=10823827) would correspond to an amino acid-gated H(+) conductance that is not stoichiometrically coupled to the amino acid transport but which influences the ionic gradients that drive the amino acid transport
There seem to be two proteins that can be transcribed from FAM127A, one with a C-terminal CAAX box (AC O15255) and a smaller protein (the sequence shown here) that seems to be encoded by a multicopy gene originating from a retrotransposon
A protein kinase activity has been reported however PROSITE, Pfam do not detect a protein kinase domain. Its enzyme activity is therefore unsure
Lacks the typical Glu active site in position 165 that is replaced by a Gln residue, exhibits no chitinolytic activity towards either polymeric and oligomeric substrates. Its precise function remains unclear
Some authors (PubMed:9560439, PubMed:10821186) called this protein rpl5, however rpl5 is a completely different protein and stands for 60S ribosomal protein L5
Could be the product of a pseudogene. This is the C-terminal part of a putative glutamine--fructose-6-phosphate aminotransferase. Strain Lalvin EC1118 has a frameshift in position 258, which disrupts the gene coding for this protein and produces two ORFs. A contiguous sequence for this protein can be found in strain YJM789 (AC A6ZME2)
Was reported to homodimerize in presence of double-stranded DNA (dsDNA) (PubMed:24332030). However, this result was based on a structure lacking the N-terminal part (1-146), which caused homodimerization in presence of dsDNA (PubMed:28214358)
Was originally (PubMed:11554733) identified as an isoamylase despite of its little activity on glycogen, but was renamed as glycogen debranching enzyme due to the characterization of the flanking gene coding for the glycogen branching enzyme (PubMed:12480526)
Was originally (PubMed:10642548, PubMed:10869184, PubMed:11141055) thought to have both prolyl- and cysteinyl-tRNA synthetase activities (ProCysRS). However, recent biochemical and structural studies show that ProRS misaminoacylates tRNA(Pro) with cysteine but is unable to aminoacylate tRNA(Cys). These conflicting results may be due to the fact that much of the previous work was done with unfractionated tRNA
According to PubMed:12130658, ProRS is unable to edit the misacylated Cys-tRNA(Pro) and Ala-tRNA(Pro), whereas according to PubMed:11408489, it hydrolyzes Ala-AMP and Ala-tRNA(Pro) by 'pretransfer' and 'posttransfer' editing activities, respectively
Was originally thought to be an ascorbate peroxidase (PubMed:12068123, PubMed:16034597). PubMed:19828564 fails to show any peroxidase activity associated with TL29 and demonstrates that TL29 could bind neither heme nor ascorbate. TL29 lacks the heme-binding site, the proton acceptor and the transition state stabilizer, which are conserved features of the ascorbate peroxidase
Lacks the conserved Glu residue in position 504 essential for carbopeptidase activity. The mature form lacks catalytic activity towards synthetic peptide substrates
Has been reported to be located in the outer membrane
Gene overlaps with the mbiA open reading frame on the opposite strand. Disruptions of one gene are also usually disruptions in the other
Could be the product of a pseudogene. Several pseudogenes of POU5F1 have been described on chromosomes 1, 3, 8, 10 and 12. Two of them, localized on chromosomes 8 and 10 have been shown to be preferentially transcribed in cancer tissues and may be involved in the regulation of POU5F1 gene activity in carcinogenesis
Was originally (Ref.1) thought to be involved in molybdate transport
PDLPs were initially named Cysteine-rich secretory proteins based on a classification work that failed to predict the transmembrane region at the C-terminus (PubMed:11402176). However, it was later shown that PDLPs are membrane proteins (PubMed:18215111, PubMed:20886105)
Was suggested to be a central component of a quality control system that is linked to the Tat translocation system (PubMed:19343049). However, it was shown later that malfolded Tat substrates are Tat-independently degraded and that TatD is not involved in quality control of the Tat substrates (PubMed:20659466)
Although strongly related to the peptidase M1 family, it lacks the conserved active metal binding Glu and His in positions 496 and 499, which are replaced by a Arg and Ala residues respectively, suggesting that it has no activity
Was reported to be activated by DDX5. However, this study has been retracted due to concerns of image manipulation
Was initially characterized as an endodeoxyribonuclease involved in DNA repair (PubMed:22664237). While it shows some weak endodeoxyribonuclease activity in vitro, such activity probably does not exist in vivo
Contains a predicted homeobox domain which is degenerated, lacking residues important for DNA-binding. Moreover, the protein localizes in the endoplasmic reticulum and not in the nucleus, which also argues against homeobox function (PubMed:22038835)
The sequence probably misses the N-terminus part since the N-terminal FAD-binding PCMH-type is absent. The correct gene model with the complete protein sequence could not be recovered from the submitted genomic sequence
According to a report, deletion of Cers5 protects from obesity: knockout mice are associated with reduced weight gain and improved systemic health after high fat diet challenge (PubMed:26853464). This result was however not confirmed by another study, which did not observe any protection from diet-induced obesity in knockout mice (PubMed:31150623). Effects observed in the first study might be indirect and caused by a large deletion that affects neighboring genes and/or deletes non-coding RNAs (PubMed:26853464, PubMed:31150623)
Was originally thought to be involved in the oxidation of protoporphyrinogen into protoporphyrin IX
Toxicity tests have been done on recombinant non-amidated toxin. The sequence shown in supplementary table 3 is longer than the sequence shown here
Could be the product of a pseudogene. It lacks the N-terminal part of the replication protein P
Was originally thought to be a phosphatidyl-inositol 4,5-bisphosphate phosphodiesterase type I (phospholipase C-alpha) then was thought (PubMed:1321829, PubMed:1330685) to be a thiol protease
Was found to lack a conserved putative promoter and, therefore, may not be transcribed
The active site contains a CGVC motif wich differs from the conserved CGPC motif
Was originally thought to be the product of two separate ORFs, eccCa5 and eccCb5
Was originally believed to be a subunit of the 2-deoxy-scyllo-inosose synthase
Is possibly a hybrid of Cvv-E6a and Cvv-E6f. The hybrid-like PLAs have never been expressed or purified in the venoms for all the cases so far studied. Therefore regulation mechanisms must exist to halt translation or secretion of the proteins in the venom glands (PubMed:12623078)
PubMed:8905232 and PubMed:16738553 sequences differ from that shown due to the presence of an IS5 insertion element between codons 327 and 328. Strain W3110A but not W3110B harbors this IS5 insertion
A paper showing involvement in Hermansky-Pudlak syndrome 9 was retracted due to image duplication
The fusion between the ATP-binding domains and one of the transmembrane domain is unusual. It could be due to a sequencing error
Despite its name, it is unclear whether the protein is part of some Catsper complex: in contrast to Catsperg2, it has not been identified in the Catsper complex and its expression is not restricted to testis tissues
The Rab-GAP TBC domain is short and lacks the C-terminal part. It is therefore unclear whether the protein has GTPase-activating activity
The N-terminus of the protein was constructed in analogy to that of the mouse ortholog using the sequence of chromosome 4
Contains a tyrosine at position 27 instead of the conserved histidine found in mammalian homologs that is involved in copper binding
According to mail exchange with L.D. Possani, the recommended name of this toxin has been updated to alpha-KTx 2.19, since alpha-KTx 2.15 is already used for Toxin II.10.5 (AC C0HJW1)
Was termed (Ref.2) DEFB134
It was previously proposed that SLC39A2 operates as a Zn2(+)/HCO3(-) symport mechanism (PubMed:10681536). However in more recent studies, SLC39A2-mediated transport is independent of both HCO3(-) and H(+)-driving forces, but modulated by extracellular pH and voltage (PubMed:29791142, PubMed:30914478)
Was originally thought (PubMed:10710312) to be a putative gustatory receptor named Gr65a but further analysis (PubMed:14608037) suggested that this is not the case
PubMed:6177696 sequence was originally thought to originate from rat
Lacks the conserved Tyr residue in position 127 in the active site triad of Ser-Tyr-Lys that is necessary for dehydrogenase activity, suggesting that it has no oxidoreductase activity
Could be the product of a pseudogene. This protein may not be the 'real' hobH because it is on the opposite frame of an ORF (aphA) which has been shown, by microsequencing, to exist. Furthermore the real hobH is probably seqA
The sequence of the wild-type (streptomycin sensitive) protein is shown
Although in PubMed:9792440 a cytidine deaminase activity has been shown in vitro, it would be the first time that a member of this family that contains a fibrinogen C-terminal domain signature shows an enzymatic activity. And it is surprising that this protein that shows an in vitro cytidine deaminase activity does not have the cytidine and deoxycytidylate deaminases domain signature
According to (Ref.2, PubMed:22665786, PubMed:23413188, PubMed:25006873) there are no direct protein ligands to pheophytin D2, whereas (PubMed:14764885, PubMed:16355230, PubMed:19219048, PubMed:20558739, PubMed:21367867, PubMed:25043005) show 1 or 2 direct ligands
Was initially reported (PubMed:9592142) as a 3'-5' exonuclease due to contamination of samples. This protein possesses no such activity (PubMed:17567612, PubMed:19000038)
Isoform 2 was reported to be located in the nucleus and to interact with HDAC1 and HDAC2 (PubMed:21285511). However, this work was later retracted (PubMed:30882370)
Although it belongs to the DHHC palmitoyltransferase family, lacks the conserved active site cysteine residue at position 479 and may lack catalytic activity
The mouse and rat orthologs were initially identified as bi-functional proteins containing an N-terminal domain with O-GlcNAcase activity and a C-terminal domain with histone acetyltransferase activity. The histone acetyltransferase activity was detected only when the protein was expressed in mammalian cells, but not when expressed in bacterial cells, suggesting that the histone acetyltransferase activity might be due to the presence of a contaminant. Comparison of the human protein with a bacterial putative acetyltransferase (AC Q2CEE2) shows that the residues important for acetyl-CoA binding are not conserved, and that the residues proposed to be important for histone acetyltransferase activity are not in a position where they could participate in catalysis. Characterization of the human protein shows that it does not bind acetyl-CoA and therefore cannot have acetyltransferase activity
In cv. Columbia (AC P0CW77), a naturally occurring frameshift at position 543 results in a shortened C-terminus. The sequence shown is from strain cv. Wassilewskija
Was initially thought to be considered to be a low affinity lactate transporter with negligible affinity for pyruvate (PubMed:11101640). However, it was later shown that SLC16A3 is a high affinity lactate transporter with physiologically relevant affinity for pyruvate (PubMed:31719150)
Was initially assigned as monocarboxylate transporter 3 (MCT3) (PubMed:9425115). However, it was later shown that it corresponds to monocarboxylate transporter 4 (MCT4)
Could be the product of a pseudogene. In strain cv. Columbia, a stop codon at position 117 and a naturally occurring frameshift at position 846 result in a truncated LOV1 protein. A complete sequence for LOV1 can be found in strain cv. Cl-0 (AC A7XGN8)
Usually PreT interacts with PreA to form the active dehydrogenase. In S.typhi PreA is a pseudogene which does not possess the conserved 4Fe-4S ferredoxin-type domains
According to some authors RANBP9 is located in centrosomes and involved in microtubule assembly. Other authors infirmed these results
Was originally thought to be involved in mitochondrial protein import
Was originally thought to be a lyase and was therefore termed prenylcysteine lyase
PubMed:8154186 misquoted the gene name as 'MPL1'
Was identified as a CAHS family protein, an intrinsically unstructured protein that shows heat-dependent glass transition, which contributes to the vitrification of cells, and this further leads to desiccation tolerance (PubMed:28306513). However, it actually belongs to the LEA type 4 family of proteins and there was no evidence supporting glass transition itself to be contributing to the glass transition of the whole tardigrade (PubMed:33545053)
Fei et al (PMID:10823827) shows that the transport process is electrogenic with a Na(+):L-glutamine stoichiometry of 2:1, contrary to the conclusions of Chaudhry et al (PMID:10619430) who finds that the transport is electroneutral with a Na(+):L-glutamine stoichiometry of 1:1 (By similarity). Chaudhry et al (PMID:11742981) shows that this electrogenic transport describes by Fei et al (PMID:10823827) would correspond to an amino acid-gated H(+) conductance that is not stoichiometrically coupled to the amino acid transport but which influences the ionic gradients that drive the amino acid transport (By similarity)
Lacks the conserved histidine residue in position 89 which is potentially part of the active site; it is replaced by a tyrosine residue
Was initially identified as a negative regulator of the TSC1-TSC2 complex (PubMed:17658474). However, it was later shown that TBC1D7 is part of the TSC-TBC complex and participates in GTPase-activating protein activity, leading to inhibition of the TOR signaling cascade (PubMed:22795129). The differences between 2 reports might be explained by experimental conditions in the initial report, in which they overexpressed the TBC1D7 subunit, possibly leading to disrupt the stoichiometric complex and its downstream functions
An Alu-mediated mutation of this gene occured in a common ancestor of Homo sapiens and Homo sapiens neanderthalis, approximately 2.1-2.2 million years ago, before brain expansion. It is generally accepted that the product of this gene, if any, is catalytically inactive as suggested by the absence of CMP-Neu5Gc sialic acid in human, while it is abundantly expressed at the surface of many cells in other vertebrates. The gene is however, significantly transcribed and the product described here might be expressed in vivo (PubMed:19890979). The putative protein is N-terminally truncated compared to orthologs and lacks a region probably essential to the CMP-N-acetylneuraminate monooxygenase activity
Does not bind calcium as one of the calcium-binding sites is lost (Asp->Arg in position 48, which corresponds to 'Arg-49' in the current nomenclature)
Originally thought to be a component of PSII; based on experiments in Synechocystis, N.tabacum and barley, and its absence from PSII in this organism and T.vulcanus, this is probably not true
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 1433 in the dsPTPase catalytic loop, suggesting that it has no phosphatase activity
MTMR2 protein levels are decreased in sciatic nerves but not in the brain (PubMed:18349142, PubMed:23297362). However, MTMR2 protein levels have also been shown not to be affected in sciatic nerves (PubMed:17855448)
The positions of the amino acids 89-93 were arranged by homology with other cytochrome c sequences. This order differs from that submitted to PIR by Chan et al. The presence of Lys-105 is not certain
Absence of tyrosine and threonine phosphorylation is demonstrated in PubMed:17376771. However, tyrosine and threonine phosphorylation may still occur in different experimental conditions
It is uncertain whether Met-1 or Met-39 is the initiator. Met-1 does not seem to exist in orthologs
Although strongly related to DNA helicases, it lacks the helicase C-terminal domain, suggesting that it has no helicase activity
Zebrafish has two genes coding for six1 orthologs. This gene is called six1a by ZFIN, but has also been described as six1b (PubMed:18789916)
Most probably a non-functional protein that cannot participate to the synthesis of a productive T cell receptor (TR) chain due to a mutation at position 42, corresponding to the first cysteine from the disulfide bridge, potentially leading to uncorrect folding (PubMed:9619395)
This sequence is an example of a full-length immunoglobulin epsilon heavy chain
This gene is interrupted by a stop codon in strain 301 / Serotype 2a
A stretch of the chloroplast genome is duplicated within chromosome 8 resulting in the duplication of the gene. The expression of this duplicated gene (Os08g0252000) has not been demonstrated
Was originally believed to be a metal-dependent phosphatase but shown to lack catalytic activity; can bind metals with very low affinity suggesting that metal binding is not required for its function
This is a truncated version of the ABC transporter NFT1. S288c has a stop codon in position 1219, which disrupts the gene coding for this protein and produces two ORFs YKR103W and YKR104W. A contiguous sequence for ABC transporter NFT1 can be found in strains Sigma 1278B, EG123 and SK1 (AC P0CE70)
Truncated; premature stop codon upstream of the fusion peptide on TM
It is uncertain whether Met-1 or Met-100 is the initiator
Although this protein contains the conserved Asp-252 that functions as an active site, this protein does not have proteolytic activity, and may therefore be catalytically inactive
Was initially identified as protein involved in the translocation of transit peptide-containing proteins across the mitochondrial inner membrane by its role in maintaining the integrity and stability of the inner membrane translocase TIM23 complex (PubMed:16943180, PubMed:16790493). It has later been shown that this phenotype can be attributed to the pleiotropic effects of mitochondria lacking cardiolipin (PubMed:19114592)
EBF4 is expressed in human NK cells and CD8(+) T-cells (PubMed:35939714). It has been suggested, therefore, that the functions of EBF4 differ between humans and mice (PubMed:35939714)
The name Vt3.1 given by the authors is incorrect, since the first number indicates a cysteine framework III which does not correspond to this cysteine framework
Encoded in intron of the LRCH2 gene
Was named CARP for 'CARD domain-containing protein' by PubMed:12054670. However, no CARD domain is detected by any prediction tool
Upon expression in E.coli, Rv1955 has been shown to function as an antitoxin against Rv1956 (PubMed:19016878). It is not clear if these conflicting results are due to expression in a heterologous system. The gene names higA and higB have been assigned to both Rv1955 and Rv1956; we have chosen to call Rv1955 higB1 after consulting the authors
Protein/histone deacetylase activity in vivo is uncertain. The 3D structure analysis of the zebrafish ortholog shows that a glutamate gatekeeper and a sterically constricted active site confer specificity for N(8)-acetylspermidine hydrolysis and disfavour acetyllysine hydrolysis. Supporting this observation, has been shown to exhibit only very low activity, if any, towards acetyl-lysine peptide substrates (PubMed:28516954). However, histone deacetylase activity has been observed in vitro (PubMed:28516954, PubMed:11861901, PubMed:11726666, PubMed:11677242, PubMed:11739383). Has also been shown to be involved in MSH2 deacetylation (PubMed:26221039)
The role of the NLRP6 inflammasome in the regulation of the gut microbiota composition is unclear (PubMed:21565393, PubMed:22763455, PubMed:26638072, PubMed:29281815, PubMed:29281837, PubMed:28801232). Some studies suggest that NLRP6 shapes the commensal gut microbiota composition (PubMed:21565393, PubMed:22763455, PubMed:26638072). However, other groups do not observe any difference in microbiota composition between wild-type and knockout mice (PubMed:29281815, PubMed:29281837, PubMed:28801232). Differences observed were attributed to mother and cage covariates rather than Nlrp6 deficiency (PubMed:29281815, PubMed:29281837, PubMed:28801232)
Was originally thought to be Fut2
Contrary to earlier results, does not contain a pyrroloquinoline quinone (PQQ) cofactor
Protein characterization data are from PubMed:19379691. Due to a number of errors in the figure panels, the article has been retracted but the authors stand by the validity of the main results and conclusions (PubMed:20873370)
While it is structurally defined as a knottin it lacks the conserved Cys residue in position 62
This protein lacks the N-terminal domain found in other NifA proteins
Glu-51 is present instead of the conserved Ser which is expected to be the active site residue
There are two other putative pseudogenes, FDH2 and FDH3
The foxi1-C gene is not pseudo-allelic to foxi1-A and foxi1-B
Tyr-195 is present instead of the conserved Cys which is expected to be a metal-binding residue
Was initially reported to mediate activation of SUMO2 in addition to UFM1 (PubMed:18442052). However, it was later shown that it is specific for UFM1 (By similarity)
Lacks a Cys at position 158 preventing the formation of a third disulfide bond
MalC lacks the characteristic Tyr and Lys catalytic amino acids, and also the essential Asn and Ser residues of typical SDR family proteins, suggesting that the active site is reconfigured to fit its unique catalytic roles
In contrast to the human ortholog, does not seem to interact with FYN
Was originally (Ref.2) erroneously thought to be a nitrilase associated protein NAP16kDa
HSN2 was originally thought to be an intronless gene lying within a WNK1 gene intron. However, it is most probably an alternative exon which has been also described in alternative splicing products of the human and mouse WNK1 genes. Isoforms bearing this exon are specifically expressed in the nervous system in these species
Four isoforms exist; 6.01 (without 4 N-ter AA and 2 extra C-ter AA), 6.02 (without 4 N-ter AA but with 2 extra C-ter AA), 6.03 (with 4 N-ter AA but without 2 extra C-ter AA) and 6.04 (with 4 N-ter AA and with 2 extra C-ter AA) (PubMed:17069633, PubMed:11344362). The sequence displayed corresponds to isoform 6.03. It is unknown if the variants api m 6.01 and api m 6.02 (without 4 N-ter AA) are the result of different transcript, an alternative splicing, or an enzymatic cleavage
Despite its name, it does not contain a zinc-finger domain
Was originally thought to bind to the palindromic consensus sequence 5'-TCCCAGCACTTTGGGA-3' and to regulate the transcription of numerous genes in the lung
Was originally thought to be an RNase; when the C-terminus (residues 379-531) is expressed in E.coli it has RNase, not DNase activity, and inhibits growth upon expression in E.coli. In vitro RNase activity and in vivo growth inhibition are neutralized by cognate immunity protein YobK, but not by immunity proteins specific to other LXG toxins
Strain B4107 was originally classified as being from Bacillus pumilus, hence protein name pumilarin
Was initially assigned as wee1 (PubMed:9486797). However, it corresponds to the meiosis-specific protein WEE2 in mammals
The article describing the function and the phosphodiesterase activity has been retracted due to duplications and irregularities in some figures, but repeated experiments using the original strains support the findings
(Microbial infection) Was initially reported to enhance infectivity of retroviruses, such as HIV-1, by stabilizing the capsid of retroviruses (PubMed:20573829, PubMed:24554657). However, it was later shown that PDZD8 is not absolutely required for HIV-1 infection, suggesting that its role in retroviral infection is probably indirect (PubMed:25771112)
Despite its name, this protein may not be the one-to-one ortholog of TMEM184A
Lacks the conserved Glu residue that is essential for catalytic activity, suggesting it lacks enzyme activity
Dictyopterin was not identified in one of the enzymatic assays [PubMed:10987137]
Due to the probable chloroplastic localization, the interactions with ROPs are questionable
Was initially thought to constitute the phosphatidylserine receptor, a receptor that mediates recognition of phosphatidylserine, a specific marker only present at the surface of apoptotic cells. Phosphatidylserine receptor probably participates in apoptotic cell phagocytosis. This protein was identified using phage display expressing mAb 217, an antibody that specifically recognizes phosphatidylserine receptor. However, its nuclear localization and the fact that mAb 217 antibody still recognizes the phosphatidylserine receptor in mice lacking JMJD6, strongly suggest that it does not constitute the receptor for phosphatidylserine and is not involved in apoptotic cell removal
Could be the product of a pseudogene. Product of a degenerated gene that is homologous to the 5'-portion of the X-linked TXLNG gene
Gene overlaps with the mbiA open reading frame on the opposite strand (PubMed:18226237). Disruptions of one gene are also usually disruptions in the other
Lacks the signal peptide, which is a conserved feature of the gene family
The role of this protein in Akt activation has been demonstrated by Du et al (PubMed:12791994) for the mouse ortholog but Iynedjian (PubMed:15469416) has not been able to reproduce the result in rat hepatocytes
Contains a predicted homeobox domain which is degenerated and lacks residues that are important for DNA-binding. The protein localizes in the endoplasmic reticulum and not in the nucleus, which also argues against homeobox function (By similarity)
Was thought be the product of a pseudogene due to the substitution or deletion of many conserved amino acids in the motor domain. However it has been observed with several high-quality proteotypic peptides in several independent proteomic studies
Represents an unconventional myosin. This protein should not be confused with the conventional myosin-15 (MYH15)
Was originally thought to have lysophosphatidic acid acyltransferase activity, but has since been experimentally shown not to have this activity
Non-functional in strain Madrid E
There is some controversy as to whether this protein preferentially binds Fe(2+) or Fe(3+)
Although assigned as two separate genes (DIS3L2 and FAM6A), it is quite clear that the gene FAM6A described by PubMed:11352565 is a fragmentary prediction of DIS3L2
According to a well-established model, RNF168 cannot initiate H2A 'Lys-63'-linked ubiquitination and is recruited following RNF8-dependent histone ubiquitination to amplify H2A 'Lys-63'-linked ubiquitination (PubMed:19500350, PubMed:19203578, PubMed:19203579). However, other data suggest that RNF168 is the priming ubiquitin ligase by mediating monoubiquitination of 'Lys-13' and 'Lys-15' of nucleosomal histone H2A (H2AK13Ub and H2AK15Ub respectively) (PubMed:22980979). These data suggest that RNF168 might be recruited to DSBs sites in a RNF8-dependent manner by binding to non-histone proteins ubiquitinated via 'Lys-63'-linked and initiates monoubiquitination of H2A, which is then amplified by RNF8 (PubMed:22980979). Additional evidence is however required to confirm these data
Was originally thought to be an arachidonate 8-lipoxygenase and was called LOX8
The several steps and mechanisms that permit controlled tiggy-winkle hedgehog dispersion and gradient formation remain controversial. The C-terminal part of the tiggy-winkle hedgehog protein precursor displays an autoproteolysis activity and a cholesterol transferase activity resulting in the cleavage and covalent attachment of a cholesterol moiety to the C-terminal of the newly generated N-terminal fragment (N-product). The protein is further modified by covalent addition of palmitate at the N-terminal of N-product, resulting to the dual-lipidated N-product. The latter is firmly tethered to the cell membrane where it forms multimers. Further solubilization and release from the cell surface seem to be achieved through different mechanisms, including the interaction with DISP1 and SCUBE2, movement by lipoprotein particles, transport by cellular extensions called cytonemes or by proteolytic removal of both terminal lipidated peptides. Once released, the fully processed TWHHN can signal within embryonic tissues both at short and long-range
Lacks the last conserved histidine that binds copper
Was originally thought to originate from L.plantarum (PubMed:1840590, PubMed:1425707)
Was originally (PubMed:8955422) thought to be the tRNA-processing ribonuclease BN (rbn). This was later proven not to be the case (PubMed:15764599)
Cellular localization of OCT1 in the intestine and the kidney remains to be finally defined. While most authors have deduced a localization at the basolateral side of enterocytes consistent with a physiological role in organic anions uptake from the blood flow and intestinal excretion (PubMed:16263091), other studies demonstrated an apical localization (PubMed:23680637), supporting a function in intestinal absorption of organic anions and drugs (PubMed:16263091, PubMed:23680637). Similarly, contradictory results localized the transporter to the basolateral side (By similarity) or to the apical side (PubMed:19536068) of proximal tubules (By similarity) (PubMed:19536068). Although initially reported to transport carnitine across the hepatocyte membrane (PubMed:28942964), another study was unable to verify this finding (PubMed:34040533, PubMed:28942964). Affinity and capacity of the transporter for endogenous substrates vary among orthologs (PubMed:16581093, PubMed:34040533, PubMed:35469921). For endogenous compounds such as dopamine, histamine, serotonin and thiamine, mouse ortholog display higher affinity and capacity compared with human OCT1 (PubMed:35469921). In contrast with mouse ortholog, not able to transport carnitine, noradrenaline and choline (PubMed:34040533)
In strain CO-92 it seems to be a pseudogene which is encoded in two separate ORFs on the plasmid
SKL2 does not possess shikimate kinase activity in vitro probably because it lacks the conserved active sites and substrate binding sites of the shikimate kinase family
This protein is shorter than the other members of the BRX family and is missing the second DZC domain. Some internal exons might be missing in this gene model prediction
The subcellular location of endogenous eipr-1 could not be identified; diffuse expression of a eipr-1 construct in the cytoplasm may be an artifact due to over-expression of the construct
Was originally thought to interact with the D1 dopamine receptor (DRD1) and to play a role in potentiating calcium ion-dependent signaling but this work was later retracted
In cerebrospinal fluid (CSF), found to be O-glycosylated in the predicted intracellular region at Thr-180 and Thr-189 (PubMed:19838169). This glycosylation has been confirmed by a separate mass spectrometry (MS) method (PubMed:23234360). Glycosylation in this region of the protein is unexplained as yet
Contrary to other family members, does not interact with CMV glycoprotein UL16
The potential active site Asp residue in position 14 is replaced by a Val
In spite of its official gene name, this protein may not be the functional ortholog of human MRGPRX2
Could be the product of a pseudogene. Corresponds to the truncated C-ter of membrane transporter
While genetic evidence suggests this enzyme is involved in leucine and isoleucine catabolism (PubMed:9341119, PubMed:10753893), no decarboxylase enzymatic activity could be detected in cell extracts of S.cerevisiae strains expressing the individual gene (PubMed:22904058)
Although this protein is stated to be a nicotinate phosphoribosyltransferase, it has not been functionally characterized, and it might be a quinolinate phosphoribosyltransferase (QPRTase)
Despite the fact that this protein belongs to a subfamily proposed to have ribose 1,5-bisphosphate isomerase activity (PubMed:15375115), the recombinant protein does not possess this activity (PubMed:17303759). In contrast, another protein from P.kodakaraensis has been shown to display this activity (TK0185)
Was originally termed luxG
The sequence shown here has been extracted from PDB entry 1UVH
Was shown to inhibit expression of hypoxia-inducible factor 1alpha and ERK1/2 and p38 MAPK activation, and to function as a ligand for alpha1/beta1 integrin. However, this study was later retracted
Was initially thought to act as a major regulator of cardiac hypertrophy in myocytes and muscle and investigations have been made on selective PDE5A inhibitors that could protect against cardiovascular disease. However, while PDE5A regulates nitric-oxide-generated cGMP, nitric oxide signaling is often depressed by heart disease, limiting its effect. Moreover, clinical trial using PDE5A inhibitors were disappointing
Was originally thought to be PhrA, involved in photoreactivation. The protein was thought to be the C-terminus of what is now accepted to be a longer reading frame called ModF; overexpression from a plasmid yields an approximately 50 kDa protein, which is too long to be PhrA (PubMed:8564363)
Has been reportedly associated with a protein carboxyl methyltransferase activity, but whether this protein indeed has such an activity remains to be determined (PubMed:25732820). It has been later shown to belong to a family of metal-dependent phosphatases implicated in metabolite damage-control (PubMed:27322068)
There are 3 copies of the NOMO gene on chromosome 16p12-p13: NOMO1 (AC Q15155), NOMO2 and NOMO3 (AC P69849). All 3 are extremely similar, which makes their individual characterization difficult. Thus, most experiments probably do not discriminate between the different members. The results reported in other entries may therefore apply for this protein
Was originally (PubMed:8407955) thought to be a protein that could have played a role as a potentially important mediator of cellular proliferative responses to various growth factors and other environmental signals. Capable of specific binding to a cAMP response element in DNA
Was originally thought to be the receptor for VIP
Renamed LptH in P.aeruginosa to avoid acronym homonymy with the lysophosphatidic acid acyltransferase protein LptA
In cv. Columbia (AC Q84M91), a naturally occurring frameshift at position 444 results in a shortened C-terminus. The sequence shown is from strain cv. Landsberg erecta
The cDNA sequence of this peptide has been submitted (EMBL entry JF460791) and described in PubMed:22781954 under the name Mr1.8
Was originally thought to regulate bop expression (PubMed:6093059). However, this seems to result from a polar effect on the downstream gene bat, which forms a transcription unit with brp
Was originally thought to be part of the complex AP-2
Was called CYP710A7 in EMBL:BAE93156. According to the cytochrome P450 homepage, CYP710A7 is a rice cytochrome
This gene is encoded entirely within the yaaW gene on the opposite strand (PubMed:18226237). Disruptions of one gene are also usually disruptions in the other
Was originally characterized as part of a cryptic cel operon for a cellobiose degradation system (PubMed:8121401, PubMed:2179047). The Cel+ phenotype is due to mutations making expression chitobiose-independent and altering the substrate specificity
PubMed:1849680 sequence is supposed to originate from Cercopithecus aethiops, but this is clearly a case of bacterial contamination from E.coli
This protein probably does not originate from A.thaliana, rather it resembles fungal cytochrome c
Lacks the conserved Asp residue in position 252 essential for pectinase activity. Likewise, most of the residues involved in substrate binding are not conserved. Was originally (PubMed:15808744) thought to have palmitoyl-CoA thioesterase activity, but PubMed:19452549 were unable to detect any pectinase or palmitoyl-CoA thioesterase activity. Its enzyme activity is therefore unsure
The function in telomere maintenance is inferred from experiments in cells displaying alternative lengthening of telomeres/ALT a process specific of cancer cells
In contrast to other members of the MINDY family, lacks the conserved active sites required for deubiquitination
Was originally (PubMed:10762262) called HPr kinase/phosphatase, but P-Ser-HPr dephosphorylation was shown (PubMed:12359880) to follow a quite unique mechanism, in which Pi instead of H(2)O is used for the nucleophilic attack on the phosphoryl group. P-Ser-HPr dephosphorylation is therefore not a phosphohydrolysis but a phospho-phosphorolysis reaction, and the bifunctional enzyme was dubbed HPr kinase/phosphorylase
The role of N(6),2'-O-dimethyladenosine cap (m6A(m)) on transcripts is unclear and subject to discussion (PubMed:31279658, PubMed:31279659, PubMed:30467178). According to a report, m6A(m) promotes translation of capped mRNAs (PubMed:30467178). In contrast, another study did not observe a clear effect on mRNA translation, but reported an increased stability of a subset of m6A(m) transcripts (PubMed:31279658). According to a third report, m6A(m) inhibits mRNA translation without affecting mRNA stability (PubMed:31279659)
Could be the product of a pseudogene. A frameshift in position 399 produces two separate ORFs
Could be the product of a pseudogene. This peptide sequence originates from a processed pseudogene derived from a retro-transcript of the mRNA coding for VENTX. The protein sequence is translated from a region that corresponds to the 3'-UTR of the original gene
The relevance of the protein lysine acetyltransferase activity is unclear (By similarity). The publication reporting acetylation of GJA1 does not provide direct evidence of lysine acetyltransferase activity of ELP3 (By similarity)
Was originally thought to have an essential function in lipopolysaccharide biosynthesis
This protein was previously referred to as T2R7 but is now considered to be the ortholog of human TAS2R13
Does not belong to the cutinase family. We doubt this is really a cutinase
In the PMID:15151999, a typographical error has been introduced leading to L-cysteine spelling instead of L-cystine
This sequence does not have the Cys-Cys motif at the C-terminal as do homologous sequences from yeast species. It may be either geranylgeranylated at an alternative motif or it may be subject to farnesylation on Cys-205
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BA1me1/2/3 = mono-, di- and trimethylated Ala-2; H2BK3me1 = monomethylated Lys-4; H2BK6ac = acetylated Lys-7; H2BK11ac = acetylated Lys-12; H2BK22ac = acetylated Lys-23; H2BK27ac = acetylated Lys-28; H2BK33ac = acetylated Lys-34; H2BK34ac = acetylated Lys-35; H2BK143ub1 = monoubiquitinated Lys-141
Although TylM3 shows significant similarity to cytochrome P450 family, it lacks the heme-binding sites. The conservation of amino acid sequence is confined primarily to the C-terminal half of the protein
A paper describing an additional role for this protein in a base excision repair pathway that is not coupled to transcription has been retracted, because some of the experimental data were incorrect
Could be the product of a pseudogene unlikely to encode a functional protein. Strain S288c has a stop codon in position 9, which disrupts the gene coding for this protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
Genetic studies provided compelling evidence implicating ivoA in the biosynthesis of N-acetyl-hydroxytryptophan (Ref.3, PubMed:28108400). The proposed acetyltransferase activity of ivoA is however an unlikely fit for a single-module NRPS and further studies showed that ivoA actually catalyzes ATP-dependent unidirectional stereo-inversion of L-tryptophan to D-tryptophan (PubMed:31573806)
This entry should not be confused with kdrl (AC Q8AXB3), which used to be called kdr
Was originally thought to be involved in multiple antibiotic resistance
It is uncertain whether Met-1 or Val-20 is the initiator
PubMed:12610726 presented the dephosphorylation reaction catalyzed by HPrK/P as a phosphatase activity, but it is most likely a phosphorylase activity as shown in B.subtilis
Was originally thought to function in mRNA expression
Was initially thought to be WNT13
Was originally identified as a potential transcription factor, because of the presence of a potential basic motif and leucine-zipper domain, and because isoform 1 is detected in the nucleus upon heterologous expression. However, homology at several typical position for basic or hydrophobic residues is missing. Besides, another publication showed it is important for normal Golgi apparatus structure and function
Could be the product of a pseudogene. This is the product of related genes or pseudogenes located in a region of chromosome 10q which contains a segmental duplication resulting in three nearly identical regions
The article describing the function has been retracted due to duplications and irregularities in some figures, but repeated experiments using the original strains support the findings
Incorrectly identified as MBL2 by PubMed:11063327
Although MAGT1 has been reported to be involved in intellectual disability (PubMed:18455129), its pathological role is questionable (PubMed:23871722)
It is uncertain whether Met-1 or Met-143 is the initiator
Several N-terminally and/or C-terminally extended versions of the predicted orcokinin-1 sequence can be detected; it is unclear which one is the active form. Orcokinin-2 is only predicted
The gene model consists of only one exon and does not include an expected signal sequence
Although ZNF41 has been reported to be involved in X-linked intellectual disability (PubMed:14628291), its pathological role is questionable (PubMed:23871722)
N-terminal sequencing (PubMed:9422751) indicates the presence of a signal peptide but an unprocessed form where the signal sequence is not cleaved has also been detected (PubMed:8529649). It is unclear if this exists in vivo
PubMed:1426985 has published some partial sequence, these sequences do not originate from T.acidophilum, rather they seem to be contaminated with human samples
MROH5 may be both a gene and a pseudogene in the human population, the reference genome corresponding currently to the non-functional allele with a stop codon at position 925. The sequence shown here with a Gln at that position is the one of the functional protein
The several steps and mechanisms that permit controlled Shh dispersion and gradient formation remain controversial. The ShhNC C-terminal domain displays an autoproteolysis activity and a cholesterol transferase activity resulting in the cleavage and covalent attachment of a cholesterol moiety to the C-terminal of the newly generated N-terminal fragment (ShhN). The protein is further modified by covalent addition of palmitate at the N-terminal of ShhN, resulting to the dual-lipidated Shh (ShhNp). ShhNp is firmly tethered to the cell membrane where it forms multimers. Further solubilization and release from the cell surface seem to be achieved through different mechanisms, including the interaction with DISP1 and SCUBE2, movement by lipoprotein particles, transport by cellular extensions called cytonemes or by proteolytic removal of both terminal lipidated peptides (PubMed:26875496). Once released, the fully processed Shh can signal within embryonic tissues both at short and long-range
The isolated nudix hydrolase domain was shown to have low catalytic activity with ADP-ribose upon heterologous expression (PubMed:11385575). However, a more recent publication demonstrates that the nudix hydrolase domain lacks enzyme activity and suggests that spontaneous degradation of the substrate underlies the previously reported low activity (PubMed:27383051)
There was previous evidence showing expression across a broad range of tissues. However this paper was retracted as immunoblot data was viewed as unreliable
While it is structurally defined as a knottin it lacks the conserved Cys residue in position 66
The formation of disulfide-linked oligomers may be an artifact that occurs upon heterologous expression in vitro (PubMed:25771893, PubMed:26902720). Formation of disulfide-linked oligomers is not observed when the protein is coexpressed with AFM (PubMed:26902720)
Although related to peptidase S1 family, lacks the conserved active Ser residue in position 667 which is replaced by a Thr, suggesting that it has no protease activity
The role of p38 MAPK kinases is unclear in phosphorylation and activation of Mapkapk5. According to some reports, it interacts and is phosphorylated by p38-alpha/MAPK14 and p38-beta/MAPK11 (PubMed:9480836). According to other reports, it is not activated by p38-alpha/MAPK14 and p38-beta/MAPK11 (PubMed:14560018). An explanation for these discrepancies, might be that the interaction with p38 MAPK kinases is weak and occurs only under specific conditions
A previous study found the localization of TMEM174 in the endoplasmic reticulum (PubMed:20331980). A more recent study detected TMEM174 in cell membrane (PubMed:35459732). The difference between these two studies could be due to the use of different cell lines
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK33ac = acetylated Lys-27; H2BK34ac = acetylated Lys-28; H2BK143ub1 = monoubiquitinated Lys-133
Unlike other plasmepsins, one of the two catalytic aspartates, Asp-157, is replaced with histidine; however, the protein is catalytic active (PubMed:16624575). Unlikely to act as a serine protease (PubMed:18312598). His-157 may stabilizes the catalysis and Asp-337 may act as both an acid and a base during catalysis
The RS447 megasatellite DNA is a highly polymorphic conserved tandem repetitive sequence which contains a copy of USP17. It is present with an interindividual variation in copy number and between 20 to 103 copies can be found on chromosome 4 and chromosome 8
Was originally annotated as an arginase by the genome sequencing project
Although it belongs to the adenylate kinase family, lacks several residues involved in ATP and AMP binding and has no adenylate kinase activity
Was reported to act as a transcriptional coactivator for estrogen receptor ESR1 (PubMed:11250900). Although this publication was retracted because of aberrations in some figures, this function was also described in other publications by different groups and may be real (PubMed:24275493, PubMed:20406972, PubMed:20663877, PubMed:19995069)
Was originally thought to interact with CCNA1 and found in a complex with CCNA1 and CDK2 (PubMed:15159402). However the amino acid sequence described in this paper contains several frameshifts and a wrong choice of frame, so results from this paper need to be validated
This gene differs from CFC1B by only one residue at position 78:R -> W. R78W is also thought to be a CFC1 polymorphism which has been shown to lead to a different cell surface distribution and activity (PubMed:11799476, PubMed:11062482)
It is unclear if Met-1 or Met-26 is the start codon
Although the enzyme shows affinity to L-glycerol 3-phosphate (sn-glycerol 3-phosphate), it hydrolyzes the substrate with poor efficacy and is therefore not associated with EC 3.1.3.21 / RHEA:11476
Although it belongs to the non-receptor class myotubularin subfamily, lacks the conserved active site cysteine residue at position 380 in the dsPTPase catalytic loop, suggesting that it has no phosphatase activity
It is uncertain whether Met-1 or Met-41 is the initiator
Was originally thought to be a methyltransferase
The Berkeley strain used in the genome project has an 8 bp deletion relative to the Canton-S strain, which disrupts the open reading frame. The Berkeley strain may carry a null allele of the AttC gene
When expressed in bacteria, recombinant OTUD4 specifically hydrolyzes 'Lys-48'-linked diubiquitin. The physiological relevance of this activity remains unknown (PubMed:23827681, PubMed:25944111, PubMed:29395066). In vivo deubiquitinates 'Lys-63'-linked ubiquitin chains (PubMed:29395066)
A study showed that INSIG2 is not ubiquitinated by AMFR/gp78 (PubMed:17043353). However, another paper showed that it is ubiquitinated on Cys-215, and that ubiquitination takes place in some tissues only and depends on the differentiation state (PubMed:31953408)
PubMed:9097040, PubMed:9278503 and PubMed:16738553 sequences differ from that shown due to the presence of an IS5I insertion element between codons 148 and 149
Lacks the phospho-accepting Asp (here Asn-65), present in the receiver domain, which is one of the conserved features of the two-component response regulators (ARRs) family
The protein is inactive for transport, probably due to the presence of a Leu instead of a Pro at position 100
Has been termed C11orf5, but is not the official C11orf5 as defined by HGNC
In PubMed:1369024 Figure 2, this sequence is erroneously labeled xyn1, but in the remainder of the paper and all subsequent publications, this protein is referred to as xylanase 2 (xyn2)
Was originally (Ref.1) thought to be a lysine decarboxylase and was consequently named cad
Could be the product of a pseudogene. The C-terminus is shorter than in related proteins. In addition, LsrC and LsrD permeases are missing, this ABC transporter is therefore probably not functional in strain E24377A
According to a report, Asn-217 is not glycosylated (PubMed:17591618). Another study observed glycosylation at this position (PubMed:19139490)
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-4; H2AK7ac = acetylated Lys-7; H2AS128ph = phosphorylated Ser-127
There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC A4QJV5
Was originally thought that the N- and C-termini were extracellular (PubMed:16847258). However, more recent data suggests that the N- and C-termini are cytoplasmic (PubMed:28346351)
Manganese Mn(2+) transport by SLC40A1 remains controversial. Some in vitro studies have suggested that SLC40A1 transports minimal amounts of Mn(2+) (PubMed:22178646, PubMed:30247984). Other groups have suggested that it does not (PubMed:24304836, PubMed:29792530). The affinity of SLC40A1 for Mn(2+) is extremely low compared with iron, implying that any SLC40A1-mediated Mn(2+) transport in vivo would likely be trivial (PubMed:24304836). A recent study examined the role of SLC40A1 in Mn(2+) homeostasis by using Tmprss6-O mice, which express high levels of hepcidin/HAMP and therefore have very low SLC40A1 levels in their tissues. These mice show frank iron deficiency and reduced iron levels in most tissues, but manganese levels are largely unaffected (By similarity). These studies suggest that manganese is propably not the physiological substrate of SLC40A1
Although PubMed:15905132 report high expression throughout oocyte development and throughout embryogenesis, PubMed:16574097 detect no maternal expression, with zygotic expression beginning at stage 20 (end of neurulation)
Could be the product of a pseudogene. It is N-terminaly truncated compared to othologs
Manganese (Mn) transport by SLC40A1 remains controversial. Some in vitro studies have suggested that SLC40A1 transports minimal amounts of Mn(2+) (By similarity). Other groups have suggested that it does not (By similarity). The predicted apparent affinity of SLC40A1 for manganese is extremely low compared with iron, implying that any SLC40A1-mediated Mn transport in vivo would likely be trivial (By similarity). A recent study examined the role of SLC40A1 in Mn homeostasis by using Tmprss6-O mice, which express high levels of hepcidin/HAMP and therefore have very low SLC40A1 levels in their tissues. These mice show frank iron deficiency and reduced iron levels in most tissues, but manganese levels are largely unaffected (PubMed:30888356). These studies suggest that manganese is propably not the physiological substrate of SLC40A1
Subcellular location is subject to discussion. Different publications report a mitochondrial localization (PubMed:29335528, PubMed:29599527, PubMed:31127291). According to some reports, tranlocates to the nucleus in response of DNA damage (PubMed:26807646, PubMed:31255466). However, according to another publication, DNA damage does not result in nuclear translocation (PubMed:31127291). Its precise localization in mitochondrion is also controversial (PubMed:29335528, PubMed:29599527, PubMed:31127291). Two different groups report a localization to the mitochondrial outer membrane, which is consistent with the presence of a N-terminal transmembrane region (PubMed:29599527, PubMed:31127291). In contrast, a publication reports localization to the mitochondrial matrix; protease accessibility used in this assay can however lead to misinterpretation if the target protein is unexpectedly resistant to proteases (PubMed:29335528). Mechanisms that explain its dual role in mitochondrion and nuclear DNA repair are unknown and additional evidences are needed to reconciliate these two apparently incompatible functions
Was initially thought to form a homodimer (PubMed:19712682). However, it was later shown to act as a monomer (PubMed:22645124)
Although ZNF674 has been reported to be involved in X-linked intellectual disability (PubMed:16385466), its pathological role is questionable (PubMed:23871722)
Was originally thought to have uracil-DNA glycosylase (UDG) activity and wrongly named UNG2 and UDG2 (PubMed:2001396). It was later shown that it is a member of the cyclin family (PubMed:8419333). UNG2 corresponds to the isoform 2 of UNG gene
Crystallographic structure revealed that QueF enzyme forms an asymmetric tunnel-fold homodecamer (PubMed:22787148) and not a homododecamer as originally proposed (PubMed:15767583)
Was originally described as a plasma membrane G-protein coupled receptor (GPCR) that binds ABA. Binding of ABA to GCR2 results in the release of G protein and dissociation of the heterotrimeric complex to activate downstream ABA effectors and to trigger the ABA responses (PubMed:17347412). However, GCR2 has been controversial with respect to the reproducibility of the results (PubMed:17894782, PubMed:18714360, PubMed:19286934). Moreover, GCR2 lacks the prototypical seven transmembrane domains of GPCRs, and is homologous to mammalian lanthionine synthetase C-like (LANCL) proteins (PubMed:17991845). Intriguingly, it was shown that human granulocytes and insulin-producing rat insulinoma cells release ABA, and that LANCL2 is necessary for ABA binding and signaling in these cells (PubMed:19667068)
Does not appear to be a subunit of the clathrin-associated adaptor protein complex 1 (AP-1)
Authors numbered this protein framework XXVII. Since this number is already attributed to another Cys arrangment (C-C-C-CCC-C-C), it is not indicated here to define the cysteine framework of this toxin
A longer peptide than exendin-2 has been described in the venom (PubMed:10880980). It has been indicated here as exendin-2-long
Could be the product of a pseudogene. This is the C-terminal part of the ABC transporter NFT1. S288c has a stop codon in position 1219, which disrupts the gene coding for this protein and produces two ORFs YKR103W and YKR104W. A contiguous sequence for ABC transporter NFT1 can be found in strains Sigma 1278B, EG123 and SK1 (AC P0CE70)
The fusion of AML1 with EAP in T-MDS induces a change of reading frame in the latter resulting in 17 AA unrelated to those of EAP
Glu-170 and Asp-172 are present instead of the conserved His and Glu which are expected to be active site residues
The role of Thr-34 and Ile-37 variants in deafness was unclear (PubMed:9139825, PubMed:9422505, PubMed:14694360, PubMed:17935238, PubMed:16849369). However, their pathogenicity has been definitely confirmed (PubMed:31160754)
This protein is more closely related to beta-type parvalbumins then to alpha-type
Could be the product of a pseudogene. There is no mRNA or EST support for this sequence, and GJE1 is a pseudogene in most other primate species
Was originally thought to be a heterodimer. However, methods used then would have missed the Aalpha chain
Based on similarity to other family members, it is assumed that all three chains derive from a single precursor but the genomic DNA sequence to support this is not yet available
Ref.3 sequence was originally thought to originate from Mycobacterium phlei
Although PubMed:17053005 refers to the biosynthesis of dTDP-6-deoxy-beta-D-allose, it seems it is the alpha anomer which is produced by GerKI and involved in dihydrochalcomycin biosynthesis, as shown by the NMR analysis of this compound made in the same article
Was originally thought to be a transferase that mediates the conversion of mo5U(34) to cmo5U(34) in tRNAs
The conserved active site Asp residue in position 402 is replaced by a Gly
Has sometimes been referred to as ADAM-12
Disulfide bonds have been reported but this may not be physiologically relevant
We are unable to find this protein in the translation of the genome of strain H37Rv
According to PubMed:9200603, it contains a transmembrane domain and may be responsible to anchor the complex into membranes, however, PubMed:12925762 showed that it is peripherically associated with membranes, and is probably not a transmembrane protein
Was originally thought to be a P-type ATPase
Although it belongs to the glycosyl hydrolase 22 family, Thr-128 and Asn-145 are present instead of the conserved Glu and Asp which are active site residues. It is therefore expected that this protein lacks hydrolase activity
Was originally thought to be the catalytic subunit (PubMed:2967109). The low processing activity which was previously observed with alpha-MPP which has been immunoprecipitated from a mitochondrial extract is most likely due to contamination by the beta-subunit (PubMed:8106471). Does not seem to have protease activity as it lacks the zinc-binding site
Was originally thought to be a PPi-dependent phosphofructokinase (PubMed:8645233), but it has later been shown that the enzyme does not possess PPi-dependent activity and instead is an ATP-dependent phosphofructokinase (PubMed:11262402)
Was originally (PubMed:9465101) called P-Ser-HPr phosphatase as it has been shown to stimulate P-Ser-HPr dephosphorylation, but actually (PubMed:12359880) it has pyrophosphatase activity
Lacks the N-terminal tyrosine-protein phosphatase domain of the family. It is therefore most likely inactive
In vitro shows no activity towards glutathione. Lacks 16 amino acids at the N-terminus including a glutathione binding site known to be important for catalysis
Was initially thought to play a role in the spindle checkpoint. However, it was later shown that phenotypes initially observed are due to off-target effects of the siRNA used which results in MAD2L1 down-regulation and mis-localization
Was first identified as a pseudogene since it seemed to be altered polyketide synthase with only the dehydratase (DH) and ketoreductase (KR) domains remaining (PubMed:23488861). Further study showed it encoded indeed for a functional keto-reductase involved in fumagillin biosynthesis (PubMed:24568283)
Was originally (Ref.1) annotated as coding for a sorbitol/mannitol-binding protein based solely on its position in the genome close to the smo operon encoding known sorbitol/mannitol catabolic genes
The role of chn-1 in ufd-2-mediated unc-45 ubiquitination is controversial. While two studies showed that unc-45 ubiquitination by ufd-2 requires ubiquitin-protein ligase chn-1, one study showed that ufd-2 ubiquitinates unc-45 independently of chn-1
Although this resembles mtnW of B.subtilis, its genomic context is different, it is too short and it is missing a Mg-binding residue. Thus it may not be a functional ortholog
The purified protein lacks deadenylase activity
Was reported to participate in the protection of telomeres against non-homologous end-joining (NHEJ)-mediated repair in the absence of TERF2 (PubMed:19763083). However, this probably does not corresponds to its primary function and experiments in mouse showed that it is dispensible for such process and is required for repression of homology-directed repair (HDR)
Most probably a non-functional protein that cannot participate to the synthesis of a productive T cell receptor (TR) chain due to an unusual recombination signal (RS) sequence altering V-(D)-J recombination (PubMed:9619395)
Could be the product of a pseudogene. The reference genome assembly (GRCh38/hg38) corresponds to a non-functional allele with a stop codon at position 56 suggesting that this gene may be a pseudogene, at least in some part of the population. The existence of a functional transcript at this locus is supported by only one sequence submission
Although it belongs to the alpha-carbonic anhydrase family, Arg-117 is present instead of the conserved His which is a zinc-binding residue. It is therefore expected that this protein lacks carbonic anhydrase activity
The protein in cv. Landsberg erecta and cv. Columbia (AC Q9C6S2) only differ by two residues in positions 132 and 401 (Ala to Pro and Leu to Gln changes, respectively); these variations leading to inactivate the protein in cv. Columbia
The regions from 407 to 653 were deduced from the genomic sequence and ESTs by similarity to the human sequence
Was originally thought to be involved in glycogen synthesis, but it was shown later that its effect on glycogen metabolism is probably indirect
Was originally thought to be UBE2R1/CDC34
It is uncertain whether Met-1 or Val-100 is the initiator
Product of a dubious gene prediction. Pizzuti et al (PubMed:8644734) identified this gene on chromosome 22, however it is not currently present in the reference genome assembly (GRCh37/hg19)
It is uncertain whether Ser-139 or Glu-142 is the start of the chain
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-39; H2BK143ub1 = monoubiquitinated Lys-150
Although PubMed:12724401 reports that it contains a PHD-type zinc finger, it contains a RING-type zinc finger. Moreover, PHD-type zinc fingers do not have any ubiquitin ligase activity
This sequence is 71 amino acid shorter than orthologs and therefore lacks two conserved residues involved in calcium binding and active site activity. The two other residues involved in calcium binding are present but it is not known if they still bind calcium
Although this protein contains the conserved Asp-247 that functions as an active site, this protein does not have proteolytic activity, and may therefore be catalytically inactive
Ref.2 sequence was originally submitted as from rat origin
There is a discrepancy in nomenclature: was submitted as Lp1.7 but is named Lp1.8 in PubMed:17400270
This protein was previously thought to be a phosphatidylinositol 4-phosphate 5-kinase
This open reading frame is annotated as an authentic frameshift in the genome
In PubMed:1369024 Figure 3, this sequence is erroneously labeled xyn2, but in the remainder of the paper and all subsequent publications, this protein is referred to as xylanase 1 (xyn1)
Contains a Gln instead of a Glu in position 176 and a Phe residue instead of a Tyr in position 209; these residues being essential in substrate recognition by ACS enzymes
GMPPA is a close homolog of GMPPB, that has been shown to catalyze the formation of GDP-mannose, an essential precursor of glycan moieties of glycoproteins and glycolipids. It has been hypothesized that GMPPA might serve as a regulatory subunit and allow allosteric feedback inhibition of GMPPB by GDP-mannose. Alignment of GMPPAs and GMPPBs from various species shows that GMPPAs are characterized by a 2 amino acid-insertion (residues 11-12) in a highly conserved motif that borders the catalytic pocket and binds the nucleotide substrate in homologous enzymes. This insertion might inactivate the ancestral catalytic site, converting it to an allosteric site (PubMed:24035193)
Lacks the conserved Glu residue in position 222 essential activity and has thereforelost enzyme activity
Lacks the C-terminal domain, which is a conserved feature of the family
A pseudogene in strain MG1655 / ATCC 700926, but not its parent MG1655 / ATCC 47076. In ATCC 700926 IS1I has recently inserted into the gene (PubMed:22081388)
The KIR2DL5B gene is not directly represented on the GRCh38 primary reference genome assembly but on alternate loci of that assembly
Could be the product of a pseudogene unlikely to encode a functional protein. Transposon Ty2-GR1 (YGRCTy2-1) has a stop codon at position 28, which disrupts the gene coding for this protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set
PubMed:11586360 sequence differs from that shown due to the presence of an IS100 insertion element between positions 182 and 183. This gene in strain CO-92 may, therefore, be a pseudogene
Was originally (PubMed:1315051) thought to be a kappa-type opioid receptor and to originate from human. PubMed:8947459 showed that it is a tachikinin receptor and was termed NK-4R. PubMed:11864635 shows that it is from guinea pig and is NK-3R
Lacks the conserved zinc finger domain, which is one of the features of the CESA family
Another delta-conotoxin was named EVIA in 2001, but this toxin was renamed EVIB (AC P69752)
Has some similarity to hydrolases, but lacks the conserved Ser-His-Asp catalytic triad. Has no hydrolase activity towards p-nitrophenylbutyrate (in vitro)
Leu-235 is present instead of the conserved His which is expected to bind ATP
In contrast to other members of the family, lacks the conserved His active site in position 60, which is replaced by an Thr residue, suggesting a different reaction mechanism
In contrast to other metacaspases (MCA) of the peptidase C14B family, contains a serine residue at the position of the canonical catalytic cysteine and has been shown to lack protease activity
Was originally thought (PubMed:641056) to be a translation initiation factor but further analysis (PubMed:19424157, PubMed:19338753) clearly suggests that it is involved in translation elongation and not translation initiation. subclass
Could be the product of a pseudogene. This is the C-terminal part of aquaporin-2. A natural 11 bp deletion in position 109 leads to a frameshift, which disrupts the gene coding for this protein and produces two ORFs EC1118_1L10_0111g and EC1118_1L10_0100g. A contiguous sequence for aquaporin-2 can be found in strain Sigma 1278B (AC P0CD89)
Was originally identified as a putative plastidic SufS-like protein and thus called CpNifS2
Residue 20 is assigned as E by similarity to other bombin sequences instead of Z (Glutamic acid or Gutamine) given in the original sequence by the authors
There is conflicting N-terminal sequencing data for this protein. The mature protein may start from Ser-2 (PubMed:10852873) or Lys-3 (PubMed:11054105)
Has been proposed to be involved in c-di-GMP turnover (PubMed:15882417), but also not be involved in its turnover (PubMed:19376870). Mutagenesis of Glu-29 in the EAL domain suggests if this protein has c-di-GMP phosphdiesterase activity it is not involved in motility regulation (PubMed:21278297). Note that (PubMed:21278297) experiments were done in strain LT2, which is not a 14028 derivative
According to PubMed:11120760 it is not detectable in blood plasma
The potential active site Asp residue in position 11 is replaced by a Gln
The submitted nucleotide sequence (AAB59335) does not agree with that shown in (Ref.1) Fig.4 or with that determined in (PubMed:9407103); as amino acid 269 should be H to act as a ligand for the non-heme iron, the sequence shown has been corrected to correspond to that shown in the figure
Phosphorylated D2 was searched for but not found in (PubMed:9407103)
Could be the product of a pseudogene. Appears to have arisen by retrotransposition of ZRSR2. Its uncertain if ZRSR2P1 is the ortholog of mouse ZRSR1, synteny is not conserved
The sequence shown has an N-terminus according to mammalian orthologs. The original sequence from PubMed:14684875 gives a longer N-terminus and suggests a signal sequence of 97 AA
Although assigned as a calmodulin family member by Ref.9, it only contains EF-hand domains
In contrast to human protein, does not interact with KLHL12 and is not ubiquitinated by the BCR(KLHL12) complex
The nuclear speckles location of SDCBP2 is under debate. One study shows that in paraformaldehyde fixed cells, SDCBP2 is highly enriched in nuclear speckles (PubMed:15961997). The same authors investigate subcellular location in living cells and fail to detect SDCBP2 in nuclear speckles, and propose that enrichment in nuclear speckles is fixation-dependent (PubMed:23300061)
The function in endocytosis may depend on the cell type. Plays a role in EGFR endocytosis via clathrin-coated pits in cancer cells, but apparently not in normal cells (PubMed:30249660). A later study used both HeLa cells and BSC1 cells (a C.aethiops kidney cell line), and did not mention any cell-type specific effects (PubMed:29887380)
It has been reported that this enzyme possesses no measurable activity against L-kynurenine and is subject to inhibition by both L-kynurenine and D-kynurenine at pH 7.9
Has lost all three of the essential catalytic residues and so probably has no enzymatic activity
Could be the product of a pseudogene. Although it is strongly related to the hemolysin E toxin from E.coli K12 strain, it lacks all the C-terminal part of the protein, due to a deletion that creates a frameshift, and it is therefore not functional
Product of a dubious CDS prediction. The TIAF1 protein is coded in the 3'-UTR region of MYO18A. Does not seem to exist in orthologs
Contains a Phe residue instead of a Tyr in position 151, the Tyr residue being essential in substrate recognition by ACS enzymes
Two variants of the PRC2 complex have been described, termed PRC3 and PRC4. Each of the three complexes may include a different complement of EED isoforms, although the precise sequences of the isoforms in each complex have not been determined. The PRC2 and PRC4 complexes may also methylate 'Lys-26' of histone H1 in addition to 'Lys-27' of histone H3 (PubMed:15099518, PubMed:15684044). In contrast, other studies have demonstrated no methylation of 'Lys-26' of histone H1 by PRC2 (PubMed:16431907)
Was initially described as nuclear
There seem to be two proteins encoded by the FAM127A gene, one with a C-terminal CAAX box (the sequence shown here) and a smaller protein (AC A6ZKI3)
Was originally thought to be myosin IB
To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-13
Genetic disruption of the protein-coding gene was initially reported to cause early embryonic lethality (PubMed:10727859). However, only a partial deletion of the coding region was performed, leading to dominant-negative effects (PubMed:10727859). A complete deletion of the coding region later showed that mice are viable and display deficits in several forms of long-term memory formation (PubMed:17088210)
It is probable that CSTX-14 A and B chains originate from the same gene. Both chains may be separated by some amino acids
May be a cleavage product of CSTX-12
Formerly thought to be the product of a pseudogene, although could be a bona fide protein. However, scarce EST evidence confirms only the C-terminal sequence
In cv. Columbia, FRL1 (AC Q9FFF1) is full-length and functional
Was originally thought to originate from Bos taurus
Firstly described as not catalyzing the monomethylation of unmethylated H3 peptide (PubMed:16292313). However other in vitro experiments described that can also methylate unmodified 'Lys-4' of histone H3 (PubMed:24095733, PubMed:24785241, PubMed:27362481)
There is no mitochondrial-type translation initiation codon present in frame in the sequence. In PubMed:19533212, the authors suggest the presence of a novel start codon coding for either Pro or Ser in Drosophila CoI transcripts. In PubMed:19540318, further evidence for the presence of the same start codon coding for Ser in D.melanogaster CoI transcript is presented
PubMed:18058037 has crystallized PPM1K in the presence of magnesium ions. However, PubMed:17336929 reported that no activity toward p-nitrophenylphosphate was seen in the absence of manganese ions and magnesium could not substitute for manganese
This protein may be non-functional as it lacks the cysteine active site residue which is replaced by Gly-132