SII-SWORD/CoKE huggingface dataset:
Photosynthetic NDH subunit of subcomplex B 4, chloroplastic (PNSB4)
Type: Family

The chloroplast NADH dehydrogenase-like complex (NDH) was first discovered based on its similarity to complex I in respiratory electron transport. However, it seems to be a ferredoxin-dependent plastoquinone reductase rather than an NAD(P)H dehydrogenase. Furthermore, it also comprises a subcomplex on the stromal side of the thylakoid membrane and a lumenal subcomplex . The chloroplast NDH complex has been divided into four categories: membrane, lumen, A, and B subcomplexes. The subcomplex A and membrane subcomplex are conserved in cyanobacteria, but the subcomplex B and lumen subcomplex are specific to chloroplasts. PNSB4/NDF6 is a subunit of subcomplex B .
Protein APEM9 (APEM9)
Type: Family

Several peroxisome biogenesis factors, termed peroxins (PEXs), are involved in the transport of peroxisomal proteins from the cytosol to peroxisomes. ABERRANT PEROXISOME MORPHOLOGY9 (APEM9) is involved in peroxisomal protein transport through its recruitment of the AAA ATPase complex PEX1-PEX6 to peroxisomal membranes via protein-protein interactions with PEX6 . APEM9 has a similar function in plants to mammalian Pex26 and yeast Pex15p, although the amino acid conservation among them is very low. APEM9 plays critical roles in peroxisome biogenesis and function, which is essential for jasmonic acid production and pollen maturation and germination .
Protein MULTIPLE CHLOROPLAST DIVISION SITE 1 (MCD1)
Type: Family

Chloroplast division requires the formation of an FtsZ division ring, its positioning being regulated by the proteins MinD and MinE. MCD1 is a plant-specific protein that directly interacts with MinD and is required for MinD localization to regulate FtsZ ring formation .
Succinate dehydrogenase subunit 7, mitochondrial (SDH7)
Type: Family

The succinate dehydrogenase complex (complex II) is a highly conserved protein complex composed of the SDH1-SDH4 subunits in bacteria and in the mitochondria of animals and fungi, with up to four additional subunits in complex II of plants, termed SDH5-SDH8. SDH6 and SDH7 contribute to anchoring succinate dehydrogenase to the inner mitochondrial membrane .

This entry represents SDH7.
Succinate dehydrogenase subunit 6, mitochondrial (SDH6)
Type: Family

This entry represents SDH6.

The succinate dehydrogenase complex (complex II) is a highly conserved protein complex composed of the SDH1-SDH4 subunits in bacteria and in the mitochondria of animals and fungi, with up to four additional subunits in complex II of plants, termed SDH5-SDH8. SDH6 and SDH7 contribute to anchoring succinate dehydrogenase to the inner mitochondrial membrane .
Outer envelope pore protein 21 (OEP21)
Type: Family

Oep21 has been identified in plants as an ATP-regulated anion-selective solute channel from the outer chloroplast membrane . Members of this family are also found in green algae.
Protein NIM1-INTERACTING 2 (NIMIN-2)
Type: Family

NIMIN-2 is a member of a novel family of proteins from Arabidopsis (also consisting of NIMIN-1 and NIMIN-3) that interact with NPR1/NIM1, a key regulator of systemic acquired resistance in plants .
Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12 (PTAC12)
Type: Family

PTAC12, also known as HEMERA (HMR), has been shown in both rice and Arabidopsis to be involved in chloroplast development . Furthermore, PTAC12/HMR has a function in the nucleus, where it acts specifically in phytochrome signalling . It is essential for both phytochrome B localization to photobodies and PIF (phytochrome-interacting factor) degradation. Photoactivated phytochromes directly interact with HMR and promote HMR accumulation, which in turn mediates the formation of photobodies and the degradation of PIF transcription factors to trigger photomorphogenesis .
Protein EMBRYONIC FLOWER 1 (EMF1)
Type: Family

EMBRYONIC FLOWER1 (EMF1) is a plant-specific protein that encodes a transcriptional regulator. It is involved in plant Polycomb-mediated gene repression and also targets flower homeotic genes directly . EMF1 regulates developmental phase transitions, as well as specifies cell fates, during vegetative development . It also regulates additional gene programs, including photosynthesis, seed development, hormone, stress, and cold signalling .
Sperm microtubule inner protein 8 (SPMIP8)
Type: Family

This family represents homologues of Sperm microtubule inner protein 8 (SPMIP8, also known as Testis, prostate and placenta-expressed protein TEPP). SPMIP8 is an axonemal microtubule inner protein (MIP) part of the doublet microtubules (DMTs) in flagellum axoneme . SPMIP8 is specifically expressed in testis, prostate, and placenta, and might have a role in reproductive biology .
Retinitis pigmentosa 9 protein (PAP-1)
Type: Family

PAP-1 (for Pim-1-associated protein) is thought to be a target for Pim-1 kinase . It has been implicated as the defective gene in RP9, one type of autosomal dominant retinitis pigmentosa . PAP-1 has a role in pre-mRNA splicing and this activity is dependent on its phosphorylation state . PAP-1 interacts with Prp3p; both were found to be components of the U4/U6.U5-tri-snRNP complex, one form of the spliceosome .
GTPase activating protein complex, subunit Bfa1/Byr4 (Bfa1/Byr4)
Type: Family

Bfa1 is required for the spindle assembly checkpoint in budding yeast. It functions in the same pathway with Bub2 in one of the branches of the spindle assembly checkpoint which prevents cytokinesis before the completion of chromosome segregation . Bub2 and Bfa1 are also required for the maintenance of G2/M arrest in response to DNA damage and to spindle misorientation . The homologue of Bfa1 in fission yeast is Byr4, which together with Cdc16 (homologue of Bub2) forms a two-component GTPase-activating protein for Spg1 GTPase . Spg1 GTPase positively regulates septation and constriction of the actomyosin ring for cell division.

Bfa1 and Bub2 may function as a universal checkpoint in response to various checkpoint signals to avoid improper mitotic exit .
D-mannonate dehydratase (MAND)
Type: Family

Characterised enzymes in the mannonate dehydratase family catalyse the dehydration of mannonate to 2-dehydro-3-deoxy-D-gluconate, as part of the catabolism of D-glucuronate . Generally, genomes that encode a member of the mannonate dehydratase family do not have a UxuA homologue. Though UxuA also has the TIM barrel fold, it is not a member of the enolase superfamily. Thus, the enolase superfamily mannonate dehydratase family and the UxuAs are an example of convergent evolution of function .
RBM12B, RNA recognition motif 2 (RBM12B_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of RNA-binding protein 12B (RBM12B), which contains five distinct RNA binding motifs (RRMs). Its biological role remains unclear.
D-mannonate dehydratase-like (D-mannonate_dehydratase-like)
Type: Family

The mannonate dehydratase (manD) group consists of the subset of enolase superfamily enzymes with a conserved tyrosine, presumably acting as an active site base, at the position of Y159 in the experimentally characterised manD from
Novosphingobium aromaticivorans
. An additional conserved arginine controls the p
K
a
of this tyrosine (R147 in
N. aromaticivorans
manD). At the present time, mannan dehydratase is the only characterised family within this group. Other enzymes within the group have been shown to catalyze the low efficiency dehydration of D-gluconate and/or D-mannonate, but the biologically relevant function of these enzymes is unclear .
POLYCHOME/GIGAS CELL1 (POLYCHOME/GIG1)
Type: Family

This family of plant proteins includes POLYCHOME (UVI4, UV-B-INSENSITIVE 4) and its paralogue GIGAS CELL1 (GIG1 , UV-B-INSENSITIVE 4-like). GIG1 and UVI4 negatively regulate activities of anaphase-promoting complex/cyclosome (APC/C) ubiquitin ligase. GIG1 and UVI4 may regulate endomitosis and endoreplication, preventing an unscheduled increase in cellular ploidy, by inhibiting APC/C in different ways . They preferentially inhibit APC/C(CDC20) and APC/C(FZR), respectively .
RBM12, RNA recognition motif 1 (RBM12_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of RNA-binding protein 12 (RBM12).

RBM12 is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), two proline-rich regions, and several putative transmembrane domains. The biological role of RBM12 remains unclear .
Coiled-coil domain-containing protein 91 (CCDC91)
Type: Family

Coiled-coil domain-containing protein 91 (also known as GGA-binding partner or accessory protein p56) colocalizes and interacts with GGA proteins, which are adaptors involved in clathrin-mediated transport between the trans-Golgi network and endosomal system . p56 cooperates with the GGAs and clathrin in the sorting of cathepsin D to lysosomes .
D-galactonate dehydratase DgoD-like (DgoD-like)
Type: Family

This entry includes a subgroup of mandelate racemases, including D-galactonate dehydratase (DgoD) and related proteins.

The mandelate racemase group consists of the subset of enolase superfamily enzymes with a conserved histidine, presumably acting as an active site base, at the position of H297 in
Pseudomonas putida
mandelate racemase (

). An additional conserved aspartic acid controls the p
K
a
of this histidine (D270 in Pseudomonas putida mandelate racemase). Families contained within this group include mandelate racemase, D-galactonate dehydratase (dgoD), gluconate dehydratase, L-fuconate dehydratase, D-tartrate dehydratase, and L-talarate/galactarate dehydratase .
RBM12, RNA recognition motif 2 (RBM12_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of RNA-binding protein 12 (RBM12).

RBM12 is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), two proline-rich regions, and several putative transmembrane domains. The biological role of RBM12 remains unclear .
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 8 (NDUFAF8)
Type: Family

NDUFAF8 (previously C17orf89) is a mitochondrial complex I assembly factor . It is likely a member of the coiled-coil-helix-coiled-coil-helix (CHCH) domain family of proteins .
Large ribosomal subunit protein mL52 (Ribosomal_mL52)
Type: Family

Mitochondria contain 55S ribosomes, with a 28S subunit and a 39S subunit. These ribosomes resemble bacterial ribosomes and eukaryotic-cytoplasmic ribosomes in their main functional properties, but they differ in structure and physical chemical properties. Many of the mitochondrial ribosomal proteins (MRPs) are distinctive, having no closely related homologues in bacterial or eukaryotic-cytoplasmic ribosomes. This entry includes the large ribosomal subunit protein mL52 (also known as MRPL52) .
D-Glucarate dehydratase-like (GlucD-like)
Type: Family

D-Glucarate dehydratase (GlucD) catalyses the dehydration of both D-glucarate and L-idarate to form 5-keto-4-deoxy-D-glucarate (5-KDG), the initial reaction of the catabolic pathway for (D)-glucarate. GlucD belongs to the enolase superfamily of enzymes, characterised by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and that is stabilised by coordination to the essential Mg2+ ion .

The glucarate dehydratase family has a similar constellation of active site residues to the mandelate racemase family, including a conserved histidine, presumably acting as an active site base (H339 in
E. coli
glucarate dehydratase) and a conserved aspartic acid that controls the p
K
a
of this histidine (D313 in
E. coli
glucarate dehydratase). However, in the glucarate dehydratase family, the third metal ligand is an Asn rather than an Asp/Glu, as in the mandelate racemase family. Furthermore, structural alignments show that the third metal-binding ligand of the glucarate dehydratase family is offset by one position from that of the mandelate racemase family. Currently, the only characterised enzyme is glucarate dehydratase, though other enzymes in the family have also been shown to catalyse the glucarate dehydratase reaction, but only at very low levels. It is unclear what the biologically relevant reaction for these sequences is .
Gluconate dehydratase (Gluconate_dehydratase)
Type: Family

Enzymes in the gluconate dehydratase family catalyse the dehydration of gluconate to 2-dehydro-3-deoxy-d-gluconate as part of the Entner-Doudoroff pathway. The experimentally characterised enzyme from
Sulfolobus solfataricus
also catalyses the dehydration of galactonate, while the experimentally characterised enzyme from
Thermoproteus tenax
does not .
Large ribosomal subunit protein bL31m (Ribosomal_bL31m)
Type: Family

Mitochondria contain 55S ribosomes, with a 28S subunit and a 39S subunit. These ribosomes resemble bacterial ribosomes and eukaryotic-cytoplasmic ribosomes in their main functional properties, but they differ in structure and physical chemical properties. Many of the mitochondrial ribosomal proteins (MRPs) are distinctive, having no closely related homologues in bacterial or eukaryotic-cytoplasmic ribosomes .

This entry represents the large ribosomal subunit protein bL31m (also known as MRPL36) from fungi which is a highly diverged eubacterial ribosomal protein bL31 homologue with derived domains functioning in mRNA selection in yeast mitochondria .
Ragulator complex protein LAMTOR4 (LAMTOR4)
Type: Family

Lamtor4 is a component of the Ragulator complex, a complex that functions as a guanine nucleotide exchange factor for the Rag GTPases that signal amino acid levels to mTORC1. The mTOR Complex 1 (mTORC1) pathway regulates cell growth in response to numerous cues. Lamtor4 is required for mTORC1 activation by amino acids . The Rag-Ragulator complex also has functions independent of mTOR signaling; RagA and Lamtor4 are essential regulators of lysosomes in microglia .
Dipeptide epimerase (Dipeptide_epimerase)
Type: Family

Enzymes in the dipeptide epimerase family catalyze the epimerization of dipeptides, with the preferred substrate often L-Ala-D/L-Glu. Based on genomic context and substrate specificity, these enzymes may be involved in metabolism of the murein peptide, of which L-Ala-D-Glu is a component .
Serine/Arginine-related protein 53 (SRRP53)
Type: Family

The SR (serine- and arginine-rich) family proteins and SR-related proteins are important regulators of pre-mRNA splicing. SRRP53 (for SR-related protein of 53kDa) is required in the second step of pre-mRNA splicing and also regulates alternative splicing in a concentration-dependent manner . SRRP53, also known as RSRC1, may also be required for regulation of PIAS1-mediated estrogen receptor beta SUMOylation .
PGC-1 (PGC-1)
Type: Family

The PGC-1 family members, including PGC-1alpha, PGC-1beta and PRC, are transcriptional coactivators that regulate cell metabolic processes ranging from mitochondrial biogenesis to oxidative respiration . They target NRF-1, a transcription factor that binds to a palindromic sequence in the cytochrome c promoter and associate with the expression of many genes required for expression and function of the respiratory chain. They also bind to CREB (cAMP response element-binding protein) and ERRalpha (estrogen-related receptor alpha). However, knockout of individual components in the PGC-1 family can result in diverse phenotypes ranging from early embryonic lethality to complete viability with very mild effects on global mitochondrial content and function. They contain an N-terminal region with a nuclear receptor coactivator signature-LXXLL and a C-terminal region with a RS domain and a RNA recognition motif .
Coiled-coil domain-containing protein 127 (CCDC127)
Type: Family

CCDC127 has been identified as a suppressor of Hsp70 gene expression . The major heat shock protein Hsp70 functions as a molecular chaperone.
Coiled-coil domain-containing protein 125 (CCDC125)
Type: Family

Kenae/CCDC125 may act as a regulator of cell motility through RhoA, Rac1 and cdc42 .
Synaptonemal complex central element protein 2 (Syce2)
Type: Family

The synaptonemal complex (SC) is a tripartite structure that physically links homologous chromosomes during prophase I. The SC has a zipper-like structure composed of two lateral elements (LEs) and a central element (CE). Transverse filaments, composed of SYCP1 molecules, bridge the gap between one LE and the CE.

Syce2/CESC1 localises to the CE and interacts with the transverse filament protein SYCP1. Its localization to the CE is dependent on recruitment by SYCP1 . Syce2/ CESC1 is required for synaptonemal complex assembly and also for double strand break repair and homologous recombination .
L-fuconate dehydratase (L-fuconate_dehydratase)
Type: Family

Enzymes in the L-fuconate dehydratase family catalyze the dehydration of L-fuconate to 2-keto-3-deoxy-L-fuconate, as part of the L-fucose catabolic pathway .
D-tartrate dehydratase (D-tartrate_dehydratase)
Type: Family

Enzymes in the D-tartrate dehydratase family catalyze the dehydration of D-tartrate to the enol tautomer of oxaloacetate .
Muconate cycloisomerase (anti) (Muconate_cycloisomerase_anti)
Type: Family

Enzymes in the muconate cycloisomerase (anti) family catalyze the conversion of cis,cis-muconate to muconolactone, in the beta-ketoadipate pathway. Although the enzymes in this family catalyze the same reaction as those in the muconate cycloisomerase (syn) family, the two families use stereochemically distinct mechanisms, and may have evolved independently within the superfamily .
D-galactarolactone cycloisomerase (GLI)
Type: Family

This entry includes D-galactarolactone cycloisomerase (GLI) from Agrobacterium tumefaciens strain C58. It catalyzes the isomerizaton of D-galactaro-1,5-lactone to D-galactaro-1,4-lactone .
L-lyxonate dehydratase (L-lyxonate_dehydratase)
Type: Family

Characterised enzymes in the L-lyxonate dehydratase family catalyse the dehydration of L-lyxonate as part of a pathway for degradation of L-lyxonate .
cis-3-Hydroxy-L-proline dehydratase (Cis-3-h-L-Pro_dehydratase)
Type: Family

Characterised enzymes in the cis-3-hydroxy-L-proline dehydratase family catalyze the dehydration of cis-3-hydroxy-L-proline to form delta1-pyrroline-2-carboxylate as part of a metabolic pathway allowing usage of several isomeric 3- and 4-hydroxyprolines as sole carbon sources .
4R-hydroxyproline betaine 2-epimerase (4R-hPro_betaine_2-epimerase)
Type: Family

Characterised enzymes in the 4R-hydroxyproline betaine 2-epimerase family catalyse the 2-epimerization of trans-4-hydroxy-L-proline betaine to cis-4-hydroxy-D-proline betaine as part of a pathway by which trans-4-hydroxy-L-proline betaine is converted to alpha-ketoglutarate .
Galactarate dehydratase 3 (Galactarate_dehydratase_3)
Type: Family

This entry includes galactarate dehydratase III (

) from Agrobacterium tumefaciens C58. It catalyzes the dehydration of m-galactarate to 2-keto-3-deoxy-galactarate, as part of the synthesis of alpha-ketoglutarate. It has also been shown to convert D-galacturonate to 3-deoxy-D-xylo-hexarate or 3-deoxy-D-lyxo-hexarate, an unexpected reaction for an enolase superfamily member, because it involves abstraction of a proton alpha to an aldehyde group rather than a proton alpha to a carboxylate group .
Xylonate dehydratase 2 (Xylonate_dehydratase_2)
Type: Family

The experimentally characterised member of the xylonate dehydratase 2 family from
Haloferax volcanii
has been shown to catalyse the dehydration of D-xylonate to 2-dehydro-3-deoxy-D-xylonate as part of the D-xylose degradation pathway. The enzyme also turns over D-gluconate. Though this enzyme catalyses the same overall reaction as those in the xylonate dehydratase 1 family, it is more closely related to other characterised enzymes in the mandelate racemase subgroup, and thus has been categorised as a separate family .
Outer envelope pore protein 24 (OEP24)
Type: Family

The chloroplastic outer envelope protein OEP24 is a voltage-dependent channel that can function as a general solute channel in plants. OEP24 is present in chloroplasts, etioplasts, and non-green root plastids .
Increased recombination centres protein 6 (Irc6)
Type: Family

Yeast Irc6 is a clathrin accessory protein. It functions in clathrin-mediated traffic between the trans-Golgi network and endosomes, linking clathrin adaptor complex AP-1 and the Rab GTPase Ypt31p .
Maltose excess protein 1 (MEX1/MEX1-like)
Type: Family

MEX1 is a plastid envelope maltose transporter. Together with pGlcT, it contributes significantly to the export of starch degradation products from chloroplasts .

This plant family also includes Maltose excess protein 1-like, of unknown function.
Pentatricopeptide repeat-containing protein 2, mitochondrial (PTCD2)
Type: Family

Pentatricopeptide repeat (PPR) proteins constitute a large family of RNA-binding proteins that contain a canonical 35 residue repeat motif. Seven examples have been identified in human mitochondria, and are known to affect mitochondrial translation . One of these is PTCD2, a pentatricopeptide domain (PTCD)-containing protein that affects mitochondrial translation. PTCD2 appears to have a role in processing RNA transcripts involving cytochrome b encoded by mitochondrial DNA . Disruption in PTCD2 resulted in elevated levels of the unprocessed precursor encoding cytochrome b. PTCD2 has been identified as a target for autoantibodies in neurodegenerative disease and is used as a biomarker for Alzheimer disease .
MEF-2, RNA recognition motif 1 (MYEF2_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of MEF-2 (also known as MyEF-2), a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene . MEF-2 contains three RNA recognition motifs (RRMs).
MEF-2, RNA recognition motif 3 (MYEF2_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of MEF-2 (also known as MyEF-2), a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene . MEF-2 contains three RNA recognition motifs (RRMs).
Ribonucleoprotein PTB-binding 1, RNA recognition motif 1 (RAVER1_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of RAVER1.

Ribonucleoprotein PTB-binding 1 (RAVER1) interacts with the polypyrimidine tract-binding protein (PTB), which is an important regulator of alternative splicing. It has four PTB-Raver1 interacting motifs (PRIs) that bind to the helical face of the second RNA recognition motif (RRM2) in PTB . It contains three N-terminal RRMs and an extended Pro-rich C terminus that contains four conserved PTB-Raver1 interacting motifs (PRIs) with the consensus sequence [S/G][I/L]LGxxP . It also contains a long proline rich region, two nuclear localization sequences (NLS), and a putative nuclear export sequence (NES). RAVER1 also binds to cytoskeletal components like alpha-actinin and vinculin/metavinculin . It may play an important role for the regulation of neuronal synaptic plasticity .
Ribonucleoprotein PTB-binding 1, RNA recognition motif 3 (RAVER1_RRM3)
Type: Domain

Ribonucleoprotein PTB-binding 1 (RAVER1) interacts with the polypyrimidine tract-binding protein (PTB), which is an important regulator of alternative splicing. It has four PTB-Raver1 interacting motifs (PRIs) that bind to the helical face of the second RNA recognition motif (RRM2) in PTB . It contains three N-terminal RRMs and an extended Pro-rich C terminus that contains four conserved PTB-Raver1 interacting motifs (PRIs) with the consensus sequence [S/G][I/L]LGxxP . It also contains a long proline rich region, two nuclear localization sequences (NLS), and a putative nuclear export sequence (NES). RAVER1 also binds to cytoskeletal components like alpha-actinin and vinculin/metavinculin . It may play an important role for the regulation of neuronal synaptic plasticity .

This entry represents the RNA recognition motif 3 (RRM3) of RAVER1.