SII-SWORD/CoKE huggingface dataset:
Histone acetyltransferase Rtt109 (Rtt109)
Type: Family

Rtt109, also known as KAT11, is fungal-specific histone acetyltransferase (HAT) that modifies histone H3 lysine 56 (H3K56) to promote genome stability and resistance to a variety of DNA-damaging agents. Rtt109 does not show sequence conservation with other known HATs and depends on association with either of two histone chaperones, Asf1 or Vps75, for HAT activity .

Rtt109-type HAT domain consists of a core HAT subdomain, which binds the acetyl-CoA cofactor. A second subdomain, the activation subdomain, is tightly associated with the HAT subdomain. Autoacetylation of a lysine within the activation subdomain is required for stabilising the interaction between the two subdomains and is essential for catalysis. The Rtt109-type HAT domain contains eight β strands and nine α helices and displays mixed three-layered α/β architecture with eight β strands sandwiched by five α helices (α1-α5) from one side, and four α helices (α6-α9) from the other side .
Transcription initiation factor Rrn11, budding yeast (TIF_Rrn11_budding_yeast)
Type: Family

The RNA polymerase I specific transcription initiation factor Rrn11 is a member of a multiprotein complex essential for the initiation of transcription by RNA polymerase I, together with Rrn6 and Rrn7 subunits . Binding to the DNA template is dependent on the initial binding of other factors . Rrn11 contains a tetratricopeptide repeats (TPRs) and interacts with Rrn6 and Rrn7 to form the core factor (CF), which resembles a right hand holding the DNA molecule between the fingers and the palm. The palm is composed of the N-terminal regions of both Rrn11 and Rrn6, the thumb is composed of the C-terminal of Rrn11, and the fingers and knuckles are composed of Rrn7 and the C-terminal half of Rrn6, respectively .
Kinetochore-associated protein Nnf1 (Nnf1)
Type: Family

Nnf1 is an essential component of the MIND kinetochore complex required for accurate chromosome segregation .
SET domain methyltransferase (SET_MeTrfase)
Type: Family

The ribosomal protein L12ab (Rpl12ab) in Saccharomyces cerevisiae is modified by methylation at both arginine and lysine residues. Rkm2 (ribosomal lysine methyltransferase 2) is responsible for the predominant epsilon-trimethylation at lysine 10 of Rpl12ab .

This entry includes Rkm2 and other SET domain proteins that may also be lysine methyltransferases.
S-adenosyl-L-methionine binding protein, YMR209C, predicted (S-AdoMet-bd_YMR209C_prd)
Type: Family

This entry represents proteins predicted to function as S-adenosyl-L-methionine binding proteins, such as the uncharacterised protein YMR209C from Saccharomyces cerevisiae (Baker's yeast).
Cell death protein 4 (Ced-4)
Type: Family

Ced-4 is a family of apoptosis proteins from nematodes. Caenorhabditis elegans has three genes, ced-3, ced-4 and ced-9, which code for the components of an induction pathway of apoptosis that is conserved in the nematode and mammals. Homologues in have also been found in Drosophila . Egl-1 binds to and directly inhibits the activity of ced-9, releasing the cell death activator ced-4 from a ced-9/ced-4 containing protein complex. This allows ced-4 to activate the cell-killing caspase ced-3 . It regulates CEP neuron apoptosis in response to high Al3+ levels . It may regulate germline apoptosis in response to DNA damage, probably downstream of let-60/ras and mpk-1 pathway . During larval development, Ced-4 is required for the elimination of transient presynaptic components downstream of egl-1 and ced-9 and upstream of ced-3 apoptotic pathway . It has also been described that, together with ain-1, it is a component of the miRNA-induced-silencing complex (miRISC), and probably upstream of ced-3, regulates temporal cell fate patterning during larval development .

Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans . In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death.
Endoplasmic reticulum resident protein 29 (ERp29)
Type: Family

ERp29 (also known as ERp28 and ERp31) is a ubiquitously expressed endoplasmic reticulum protein found in mammals . This protein has an N-terminal thioredoxin-like domain, which is homologous to the domain of human protein disulphide isomerase (PDI). ERp29 may help mediate the chaperone function of PDI. The C-terminal Erp29 domain has a 5-helical bundle fold. ERp29 is thought to form part of the thyroglobulin folding complex .
NADPH-dependent 7-cyano-7-deazaguanine reductase, QueF type 1 (QueF_type1)
Type: Family

Members of this group are involved in the biosynthesis of queuosine, a 7-deazaguanine-modified nucleoside found in tRNA(GUN) of Bacteria and Eukarya. QueF (YkvM) from Bacillus subtilis has been shown to catalyse the NADPH-dependent reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine, a late step in the biosynthesis of queuosine .

Queuosine is located in the anticodon wobble position 34 of tRNAs specific for Tyr, His, Asp, and Asn. With few exceptions (such as yeast and mycoplasma), it is widely distributed in most prokaryotes and eukaryotes . Queuosine is based on a very unusual 7-deazaguanosine core, which is further modified by addition of a cyclopentendiol ring .

This group of proteins belongs to the T fold structural superfamily and is related to GTP cyclohydrolase (GTP-CH-I) FolE. Two major features differentiate the QueF and FolE groups. First, the strictly conserved QueF motif E-78(S/L)K(S/A)hK(L/Y)(Y/F/W)-85 (residue numbers are those of B. subtilis YkvM, h is hydrophobic amino acid) is characteristic of the QueF family, but is not found in the FolE family. Second, four catalytically important residues in FolE , His-112, 113, and 179 and Cys-181 (Escherichia coli FolE numbering), are absent in the QueF group.

QueF-like proteins form two groups, type I proteins exemplified by Bacillus subtilis YkvM (

) and type II proteins exemplified by Escherichia coli YqcD (

). The type I proteins are comparable in size with bacterial and mammalian FolE, whereas the type II proteins are larger and are predicted to be comprised of two domains, similar to plant FolE .

The discovery of oxidoreductase activity within the FolE scaffold is an intriguing example of structural and functional evolution, particularly in light of the need to bind a second organic substrate, the cofactor NADPH. The specificity of the QueF motif to the QueF family suggests that these residues might be involved in NADPH binding . Additionally, the binding of a modified base to QueF, instead of the nucleotide to FolE, in principle leaves vacant in QueF the binding site occupied by the ribosyl portion of GTP. This putative "empty" ribosyl pocket might also contribute to NADPH binding .
Uncharacterised conserved protein UCP027682, CUB, vWA (UCP027682_CUB_vWA)
Type: Family

This group represents an uncharacterised conserved protein with CUB and vWA domain from nematodes.
N-lysine methyltransferase KMT5A-like (KMT5A-like)
Type: Family

This entry includes a group of animal proteins that belong to the class V-like SAM-binding methyltransferase superfamily and contain the SET domain usually flanked by other domains forming the so-called pre- and post-SET regions. The enzymes belonging to this class all N-methylate lysine in proteins. Most of them are histone methyltransferases (

), including human N-lysine methyltransferase KMT5A (also known as PR-Set7), which is a nucleosomal histone-lysine N-methyltransferase that specifically monomethylates 'Lys-20' of histone H4 (H4K20me1). It plays a central role in the silencing of euchromatic genes .

Methyltransferases ([ec:2.1.1.-]) constitute an important class of enzymes present in every life form. They transfer a methyl group most frequently from S-adenosyl L-methionine (SAM or AdoMet) to a nucleophilic acceptor such as nitrogen, oxygen, sulfur or carbon leading to S-adenosyl-L-homocysteine (AdoHcy) and a methylated molecule. The substrates that are methylated by these enzymes cover virtually every kind of biomolecules ranging from small molecules, to lipids, proteins and nucleic acids. Methyltransferases are therefore involved in many essential cellular processes including biosynthesis, signal transduction, protein repair, chromatin regulation and gene silencing . More than 230 different enzymatic reactions of methyltransferases have been described so far, of which more than 220 use SAM as the methyl donor [E1]. A review published in 2003 divides all methyltransferases into 5 classes based on the structure of their catalytic domain (fold):

class I: Rossmann-like α/β

class II: TIM β/α-barrel

class III: tetrapyrrole methylase α/β

class IV: SPOUT α/β

class V: SET domain all-β

A more recent paper based on a study of the Saccharomyces cerevisiae methyltransferome argues for four more folds:

class VI: transmembrane all-α

class VII: DNA/RNA-binding 3-helical bundle all-α

class VIII: SSo0622-like α+β

class IX: thymidylate synthetase α+β
Uncharacterised conserved protein UCP207779 (UCP207779)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Cerberus (Cerberus)
Type: Family

This entry represents the cerberus family of proteins. Cerberus is a cytokine that may play a role in anterior neural induction and somite formation during embryogenesis, in part through a BMP-inhibitory mechanism . It can regulate Nodal signalling during gastrulation as well as the formation and patterning of the primitive streak.
Uncharacterised conserved protein UCP027936 (UCP027936)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
dTDP-4-amino-4,6-dideoxy-D-glucose ammonia-lyase (DesII)
Type: Family

DesII is a member of the radical S-adenosyl-L-methionine (SAM) enzyme superfamily involved in the biosynthesis of TDP-D-desosamine. D-Desosamine is found in a number of macrolide antibiotics produced by Streptomyces venezuelae . DesII catalyses the deamination of TDP-4-amino-4,6-dideoxy-d-glucose to form TDP-3-keto-4,6-dideoxy-d-glucose . It can act as a deaminase or a dehydrogenase depending on the nature of its TDP-sugar substrate .
Uncharacterised conserved protein UCP028035 (UCP028035)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Inner membrane protein RclC (RclC)
Type: Family

This entry includes inner membrane protein RclC which is a reactive chlorine-specific transcription factor in
Escherichia coli
. Oxidation of cysteine residues leads to activation of genes required for the response to reactive chlorine species .
Uncharacterised conserved protein UCP028069 (UCP028069)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 , and are predicted to be localized to the periplasmic space.

Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Glycine cleavage system transcriptional repressor (GcvR)
Type: Family

Glycine cleavage system transcriptional repressor
GcvR acts as a negative transcriptional regulator of the glycine cleavage system operon (GCV) .
Bacteriophage B3, Orf5 (Phage_B3_Orf5)
Type: Family

This entry is represented by Bacteriophage B3, Orf5. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP028135, HipA-like (UCP028135_HipA-like)
Type: Family

This group represents an uncharacterised protein with HipA-like domain.
Uncharacterised conserved protein UCP028137, membrane (UCP028137)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are predicted to be integral membrane proteins (with several transmembrane segments).
MSHA biogenesis protein, MshI (MSHA_biogenesis_MshI)
Type: Family

This group represents a MSHA biogenesis protein, MshI type.
Uncharacterised conserved protein UCP028160 (UCP028160)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they possess a predicted signal peptide.
Capsular polysaccharide biosynthesis protein, BcbE, predicted (Caps_polysacc_synth_BcbE_prd)
Type: Family

This group represents a predicted capsular polysaccharide biosynthesis protein known as BcbE.
Methyltransferase TcmP-like (TcmP-like)
Type: Family

This entry represents the enzyme tetracenomycin polyketide synthesis O-methyltransferase TcmP and related proteins. TcmP catalyses the methylation of the C-9 carboxy group of tetracenomycin E (TCM E) to yield TCM A2, which is then further processed to produce the antibiotic TCM C .

This entry also includes DpfgK from Gibberella zeae. DpfgK is a S-adenosyl-L-methionine-dependent methyltransferase involved in the biosynthesis of diterpenoid pyrones .
Uncharacterised conserved protein UCP028200 (UCP028200)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, several members are predicted to have a membrane lipoprotein lipid attachment site. In addition, there are several stringently conserved glutamine residues.
Uncharacterised conserved protein UCP028234 (UCP028234)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP028235 (UCP028235)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Metal-independent carbonic anhydrase-like (MICAH-like)
Type: Family

This entry represents Metal-independent carbonic anhydrase from Nostoc sp. (MICAH, also known as all2909) and similar prokaryotic proteins. all2909 catalyses the hydration of carbon dioxide (CO2) to bicarbonate (HCO3-). It may function even in metal-poor environments .
Uncharacterised conserved protein UCP028299 (UCP028299)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
ABC-type oligopeptide transport system, solute-binding component, Mycoplasmataceae, predicted (ABC_oligopep_solut-bd_myco_prd)
Type: Family

This group represents a predicted ABC-type oligopeptide transport system, solute-binding component, Mycoplasmataceae type.
Uncharacterised conserved protein UCP028340 (UCP028340)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. They are closely related to the N-terminal portion of a KpnI-like type III restriction-modification system methyltransferase in Mycoplasmas (

). However, they lack the conserved catalytic motifs .
Nucleoside triphosphate/diphosphate phosphatase (SA1684)
Type: Family

This entry represents Nucleoside triphosphate/diphosphate phosphatase from Staphylococcus aureus (SA1684,

) and similar sequences predominantly found in firmicutes. This protein, which shows nucleoside phosphatase activity towards nucleoside triphosphates and nucleoside diphosphates, has a significant effect on the proliferation of S. aureus colonies and the killing ability of the host . Members of this family contain the domain (

).
Uncharacterised conserved protein UCP028431 (UCP028431)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.

This entry represents a family of proteins from bacteria whose function is unknown. Most members contain the domain

, conserved in glycoamylases.
Uncharacterised conserved protein UCP028438 (UCP028438)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP028445 (UCP028445)
Type: Family

This group represents an uncharacterised conserved protein.
Predicted glycerophosphotransferase UCP028458 (UCP028458_glyceroPtfrase)
Type: Family

This group represents an uncharacterised protein with glycerophosphotransferase domain.
Uncharacterised conserved protein UCP028470, steroid isomerase-related (UCP028470_steroid_isom-rel)
Type: Family

There is currently no experimental data for members of this family or their homologues. However they appear to be related to steroid isomerases.
Uncharacterised conserved protein UCP028498 (UCP028498)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP028503 (UCP028503)
Type: Family

This entry represents a group of uncharacterised proteins. There is currently no experimental data for any of the members of this group.
Uncharacterised conserved protein UCP028520 (UCP028520)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Protein of unknown function DUF2321 (DUF2321)
Type: Family

Members of this family of hypothetical proteins have no known function.
Uncharacterised conserved protein UCP028583 (UCP028583)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Protein of unknown function UCP028589 (UCP028589)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP028609 (UCP028609)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP028680 (UCP028680)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Protein of unknown function DUF2860 (DUF2860)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
S-phase kinase-associated protein 1 (SKP1)
Type: Family

This entry includes SKP1 from yeasts, animals and plants.
Polyphosphate phosphotransferase (Polyphosphate_phosphotransfera)
Type: Family

This family represents NDP-polyphosphate phosphotransferases (

), which use inorganic polyphosphate (polyP) as a donor to convert NDP to NTP and are key enzymes for polyP metabolism in bacteria . In M. tuberculosis, it is important for its survival in macrophages . Members of this protein family were first designated polyphosphate kinase 2 (PPK2) after the characterised protein in Pseudomonas aeruginosa .
mRNA cap guanine-N7 methyltransferase, eukaryotes (mRNA_G-N7_MeTrfase_euk)
Type: Family

This entry includes mRNA (guanine-N(7))-methyltransferase, which methylates the N7 position of the added guanosine to the 5'-cap structure of mRNAs. It binds RNA containing 5'-terminal GpppC . This family of enzymes is found in nucleus .
Alpha-2-glucosyltransferase Alg10 (Alg10)
Type: Family

Alg10 (asparagine-linked glycosylation) (

) is a dolichyl-phosphoglucose-dependent glucosyltransferase which adds the terminal alpha-1,2 glucose to the lipid-linked Glc2Man9GlcNAc2 oligosaccharide. The terminal alpha-1,2-linked glucose residue is important for substrate recognition by the oligosaccharyltransferase . In Saccharomyces cerevisiae, Alg10 has a role in regulation of the expression of a myo-inositol transporter, Itr1 (hence the name Die2, standing for derepression of Itr1 expression) . It also regulates the expression of Ino1, which is an inositol-3-phosphate synthase . Alg10 is homologous to human and rat potassium channel regulatory protein KCR1, which diminishes the cardiac repolarising current I(Kr) drug response .
Anaphase-promoting complex subunit APC10/Doc1 (APC10/Doc1)
Type: Family

The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis, such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome .

One of the subunits of the APC that is required for its ubiquitination activity is Doc1/Apc10, a protein composed of a Doc1 homology domain that has been identified in a number of diverse putative E3 ubiquitin ligases . The Doc1 homology domain forms a β-sandwich structure that is related in architecture to the galactose-binding domain of galactose oxidase, the coagulation factor C2 domain and a domain of XRCC1. This group represents a subgroup of subunit 10.
Vacuolar protein sorting-associated protein 41 (Vps41)
Type: Family

This entry represents the eukaryotic Vacuolar protein sorting-associated protein 41 (Vps41).

Vsp41 is a subunit of the homotypic vacuole fusion and vacuole protein sorting (HOPS) complex, which is essential for membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of protein transport . This protein interacts with Caspase-8, which plays a key role in apoptosis and development . Vsp41 consists of a β-propeller at the N-terminal (

), represented in this entry, followed by an α-solenoid (TPR-like) domain, a CHCR domain and a RING zinc finger (

).
Nucleolar complex-associated protein 3 (Nucleolar_cplx-assoc_3)
Type: Family

Budding yeast nucleolar complex-associated protein 3 (Noc3) is required for initiation of DNA replication and for synthesis of 60S ribosomal subunits and the transport of pre-ribosomes from the nucleoplasm to the cytoplasm . This entry also includes Noc3 homologues from animals and plants. The mammalian Noc3 is a positive regulator in adipocyte differentiation .
Glycyl radical enzyme YjjI-like (Glycyl_radical_YjjI-like)
Type: Family

Members of this family are homologues to enzymes known to undergo activation by a radical SAM protein to create an active site glycyl radical. This family appears to be activated by the YjjW radical SAM protein, usually encoded by an adjacent gene.