SII-SWORD/CoKE huggingface dataset:
GTPase, MTG1 (GTPase_MTG1)
Type: Family

This group represents GTPases that belong to MMR1/HSR1 GTP-binding protein family, MTG1 subfamily. This entry includes Mitochondrial GTPase MTG1 which is required for mitochondrial translation. It is probably involved in assembly of the large ribosomal subunit . This family also includes Ribosome biogenesis GTPase A, an essential protein for a late step of 50S ribosomal subunit assembly .
tRNA/rRNA methyltransferase, YfiF, predicted (YfiF_prd)
Type: Family

This group represents a predicted tRNA/rRNA methyltransferase, YfiF type.
Glucose translocase, bactoprenol-linked (Glc_translocase_bactprenl-link)
Type: Family

This group represents a group of bactoprenol-linked glucose translocases. GtrA and GtrB are responsible for O-antigen glucosylation in Shigella flexneri .
Transcription factor TFE, archaea (TF_E_archaea)
Type: Family

Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (

) and the small beta (

). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE .

The TFIIE β-central core DNA-binding domain consists of three helices with a β-hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow .

Archaea contain a TFIIE homologue, called TFE, which corresponds to the N-terminal half of TFIIEalpha. It appears that archaeal TFE corresponds to the minimal essential region of eukaryotic TFIIEalpha. In archaea TFE contains an N-terminal, weakly conserved, helix-turn-helix (HTH) motif within a leucine-rich region and a C-terminal zinc ribbon . It has been proposed that the TFE/IIEalpha-type HTH domain acts as a bridging factor or adapter between the TATA box-binding protein, the polymerase, and possibly promoter DNA .

This entry represents archaeal TFE.
Protein transport protein SecG/Sec61-beta/Sbh (SecG/Sec61-beta/Sbh)
Type: Family

This family includes preprotein translocase subunit SecG, protein transport protein Sec61 subunit beta and Sbh1.

A conserved heterotrimeric integral membrane protein complex--the Sec61 complex (eukaryotes) or SecY complex (prokaryotes)--forms a protein-conducting channel that allows polypeptides to be transferred across (or integrated into) the endoplasmic reticulum (eukaryotes) or across the cytoplasmic membrane (prokaryotes) . This complex is itself a part of a larger translocase complex.

The alpha subunits (

), called Sec61alpha in mammals, Sec61p in Saccharomyces cerevisiae (Baker's yeast), and SecY in prokaryotes, and the gamma subunits, called Sec61gamma in mammals, Sss1p in S. cerevisiae, and SecE in prokaryotes, show significant sequence conservation. Both subunits are required for cell viability in S. cerevisiae and Escherichia coli.
The beta subunits, called Sec61beta in mammals, Sbh in S. cerevisiae, and SecG in archaea, are not essential for cell viability. They are similar in eukaryotes and archaea, but show no obvious homology to the corresponding SecG subunits in bacteria.
Uncharacterised conserved protein UCP006404, peptidase M50/CBS (UCP006404_Pept_M50_CBS)
Type: Family

This group represents an uncharacterised protein with peptidase M50 and CBS domains.
GTPase Der (GTPase_Der)
Type: Family

This group represents GTPase Der, also known as GTP-binding protein EngA. In Escherichia coli, EngA is involved in ribosome stability and/or biogenesis, as well as cell viability . In Salmonella typhimurium however, EngA binds with higher affinity to GDP than GTP .
Uncharacterised conserved protein UCP006591, MJ1004 type (UCP006591_CBS)
Type: Family

This group represents an uncharacterised protein with CBS domain pair, MJ1004 type.
Sm-like protein Lsm6/SmF (Lsm6/sSmF)
Type: Family

Small nuclear ribonucleoproteins (snRNPs) are components of major and minor spliceosomes that play an important role in the splicing of cellular pre-mRNAs. snRNPs contain a common core, composed of seven Sm proteins bound to snRNA. Five small snRNPs (U1, U2, U4 and U5) share the Sm heptamer ring composed of SmB/B', SmD1/2/3, SmE, SmF, and SmG (also known as snRNP-G), while U6 snRNP has a heptamer ring consist of seven Sm-like (Lsm) proteins: Lsm2, Lsm3, Lsm4, Lsm5, Lsm6, Lsm7 and Lsm8 .

This entry includes the snRNP heptamer ring components SmF (small nuclear ribonucleoprotein F), Lsm6 and LSM36B from
Arabidopsis
.
NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 (NADH_Ub_cplx-1_asu_su-6)
Type: Family

This group represents the NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 (NDUFA6). This is a non-catalytic subunit .
BAPKO_0422-like (BAPKO_0422-like)
Type: Family

This entry represents a group of proteins mainly found in Spirochaetota, including the outer member β-barrel protein BAPKO_0422 from Borrelia afzelii (

), which was shown to bind human factor H, a regulator of complement activation .
Transcriptional regulator, HTH, AF0396-type (Tscrpt_reg_HTH_AF0396-typ3)
Type: Family

This group represents a predicted HTH transcriptional regulator, AF0396 type.
Septin (Septin)
Type: Family

This entry represents various septin proteins. These proteins were initially described in yeast, where a cross wall (septum) is produced during cytokinesis and then splits in certain organisms to allow the daughter cells to separate . However, the septin family is now recognised to extend to mammals and is associated with a variety of events. Septins are GTPases that form filaments used during cytokinesis in fungi and animals. Septins at the bud site serve as a structural scaffold that recruits different components involved in diverse processes at specific stages during the cell cycle. The septin assembly is regulated by protein kinases Gin4 and/or Cla4, and may act by recruiting Myo1 and Hof1 (involved in septation) to the site of cleavage. In addition to their original role in cell division, septins are also involved in cell morphogenesis, bud site selection, chitin deposition, cell cycle regulation, cell compartmentalisation, membrane trafficking, spore wall formation and organisation of the cytoskeleton. The localisation of a septin reflects its function :

Septins localising to projections help shape and compartmentalise emerging growth.

Septins localising to partitions help compartmentalise pre-existing cellular material.

Septins localising to the whole cell are involved in membrane trafficking and organising the cytoskeleton (usually in animals).

In yeast, septins encoded by Cdc3, Cdc10, Cdc11, Cdc12 and probably Shs1, form a septin complex localised at the cytoplasmic face of the plasma membrane in the mother-bud neck, where it rearranges to a cortical collar of highly ordered filaments . This complex can form long filaments through end-to-end polymerisation of Cdc3-Cdc12-Cdc11 complexes with Cdc10 serving as a bridge to bundle the polymers into paired filaments.

In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments .

In Drosophila, protein peanut is involved in cytokinesis, and is an enhancer of the sina gene, which has a role in photoreceptor development .
Spore coat protein CotF (Spore_coat_CotF)
Type: Family

The Coat F proteins contribute to the Bacillales spore coat. They occur multiple times in the genomes in which they are found. Bacillus subtilis endospore protein coats protect them and may play a role in their germination . Spore coat protein F, on the outer surface of the endospore, is one of a suite of proteins that could be used to differentiate between members of the Bacillus genus .

This group represents a spore coat protein F, CotF type.
5'-3' exoribonuclease 1 (5_3_exoribonuclease_1)
Type: Family

5'-3'-exoribonucleases are enzymes that degrade RNA by removing terminal nucleotides from the 5' end. 5'-3'exoribonuclease type 1 (Xrn1, also known as kem1) occurs in animal and fungal lineages. In Saccharomyces cerevisiae, Xrn1 can be activated by Dcs1, a non-essential hydrolase that involved in mRNA decapping. The activation of Xrn1 by Dcs1 is important for respiration .
p53 negative regulator Mdm2/Mdm4 (p53_neg-reg_MDM_2/4)
Type: Family

This group represents a p53 negative regulator Mdm2/Mdm4.

MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription . In addition, MDM2 acts as an E3 ubiquitin ligase responsible for the ubiquitination and subsequent degradation of p53 . P53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. MDM2 is also known to have p53-independent functions.

The core of MDM2 folds into an open bundle of four helices which is capped by two small 3-stranded β-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 α-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. In addition to its N-terminal p53 binding domain, MDM2 contains a central acidic domain, zinc finger domain and a C-terminal RING-finger domain.

MDM4, also known as MDMX, is a MDM2-related protein that has also been shown to inhibit p53, although not as well as MDM2. Most studies have not been able to ascribe E3 ligase function to MDM4.
GTPase HflX (GTPase_HflX)
Type: Family

This protein family is one of a number of homologous small, well-conserved GTP-binding proteins with pleiotropic effects. Bacterial family members are designated HflX, following the naming convention in Escherichia coli, where HflX is encoded immediately downstream of the RNA chaperone Hfq, and immediately upstream of HflKC, a membrane-associated protease pair with an important housekeeping function .
Herpesvirus UL5 (Herpes_UL5)
Type: Family

This group represents an uncharacterised conserved protein UL5.
Protein YzcX (YzcX)
Type: Family

The function of YzcX (also known as CyaX) is not clear .
Nucleic acid binding protein, Rv2694c, predicted (NucleicA-bd_Rv2694c_prd)
Type: Family

This group represents a predicted nucleic acid binding protein, Rv2694c type.
Uncharacterised conserved protein UCP006993 (UCP006993)
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.
Uncharacterised conserved protein UCP007004 (UCP007004)
Type: Family

This group represents an uncharacterised conserved protein.
Type II secretion system (T2SS) pilotin, S protein (T2SSS_2)
Type: Family

This entry represents pilotin AspS from Vibrio and some E.coli and Shigella. This entry also includes YghG from E. coli. AspS is part of the Vibrio-type T2SS secretin system that drives the secretion of fully-folded protein substrates across the bacterial outer membrane. The structure of AspS has been revealed .

The type II secretion system (T2SS) is one of several extracellular secretion systems in gram-negative bacteria. It delivers toxins and a range of hydrolytic enzymes including proteases, lipases and carbohydrate-active enzymes to the cell surface or extracellular space . T2SS systems are composed of 11 to 15 different proteins, which are generally called GspA to GspO and GspS. The T2SS spans the two bacterial membranes and ensures secretion of folded proteins across the outer membrane pore formed by GspD. The inner membrane complex contains GspC, GspL, GspM, and GspF. The cytoplasmic domains of GspL and GspF interact with an ATPase, GspE. GspE is thought to energize the formation of a short pseudopilus by several pilin-like proteins, GspG to GspK . GspD has been shown to interact with the inner membrane component GspC .
Outer membrane protein YaiO (YaiO)
Type: Family

This entry represents a group of proteins including the outer membrane protein YaiO from E. coli .
Protein YopQ (YopQ)
Type: Family

Salmonella, and related proteobacteria, secrete large amounts of proteins into the culture media. The major secreted proteins are either flagellar proteins or virulence factors , secreted through the flagellar or virulence export structures respectively. Both secretion systems penetrate the inner and outer membranes and their components bear substantial sequence similarity. Both the flagellar and needle like pilus look fairly similar to each other .

This entry represents Protein YopQ from Yersinia enterocolitica, a protein secreted by the type III secretion system under low-calcium conditions. YopQ may function as a virulence determinant . Members of this protein family are specific to Yersinia.
Competence protein D, Pasteurellaceae (ComD_Pasteurellaceae)
Type: Family

Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions .

This group represents a competence protein D (also known as DNA transformation protein ComD) from Pasteurellaceae.
Uncharacterised conserved protein UCP007061 (UCP007061)
Type: Family

This group represents an uncharacterised conserved protein.
Uncharacterised conserved protein UCP007103 (UCP007103)
Type: Family

This group represents an uncharacterised conserved protein.
Factor-induced gene 1 protein (Fig1)
Type: Family

Fig1 is a integral membrane protein that facilitates Ca2+ influx and cell fusion during mating of Saccharomyces cerevisiae . It is required for yeast mating differentiation .
Uncharacterised conserved protein UCP007248 (UCP007248)
Type: Family

This group represents an uncharacterised conserved protein.
Uncharacterised protein family, inner membrane YidI (Uncharacterised_IM_YidI)
Type: Family

This group represents an inner membrane protein, YidI type.
Uncharacterised conserved protein UCP007319 (UCP007319)
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.
Fimbrial protein EcpA (EcpA)
Type: Family

This group represents the fimbrillin protein MatB . It is also known as EcpA, and is part of the ecpRABCDE operon, which encodes the E.coli common pilus (ECP), an adhesive structure produced by all E. coli pathogroups and plays a dual role in early-stage biofilm development and host cell recognition .
Uncharacterised conserved protein UCP007407, Abi protease-like (UCP007407_Abi-like)
Type: Family

This group represents an uncharacterised protein with Abi protease domain.
Uncharacterised conserved protein UCP07580 (UCP07580)
Type: Family

This entry represents a group of uncharacterised bacterial proteins. Many members of this family are predicted to be metal-dependent hydrolases.
Peptidase M11, autolysin (Peptidase_M11_autolysin)
Type: Family

Over 70 metallopeptidase families have been identified to date. In these enzymes a divalent cation, which is usually zinc but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys. At least one other residue is required for catalysis, which may play an electrophilic role.

Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .

This group of autolysin matrix metallopeptidases belongs to the MEROPS peptidase family M11 (gametolysin family, clan MA(M)).
Alpha-L-fucosidase (Alpha-L-fucosidase)
Type: Family

This entry represents alpha-L-fucosidase, which converts a fucoside to fucose and an alcohol .
Uncharacterised conserved protein UCP007778 (UCP007778)
Type: Family

This group represents an uncharacterised conserved protein.
RNA-processing, Lsm12 (RNA-processing_Lsm12)
Type: Family

Sm and Sm-like proteins of the Lsm (like Sm) domain family are generally involved in essential RNA-processing tasks . All the LSM proteins are evolutionarily conserved in eukaryotes with an N-terminal Lsm domain to bind nucleic acids followed by as yet uncharacterised C-terminal region, some of which have a C-terminal methyltransferase domain.

This family includes fungal Sm-like protein 12 (LSM12), which is possibly involved in mRNA degradation or tRNA splicing .
Ribosome assembly protein RSM22, mitochondrial, budding yeast (RSM22_mit_bud)
Type: Family

This group represents Ribosome assembly protein RSM22 from Saccharomyces cerevisiae and similar sequences predominantly found in Saccharomycetales (budding yeasts). RSM22 is a mitochondrial ribosome (mitoribosome) assembly factor that binds at the interface of the head and body domains of the mitochondrial small ribosomal subunit (mt-SSU), occluding the mRNA channel and preventing compaction of the head domain towards the body .
Calcipressin-like protein (Rcn1_fungi)
Type: Family

This entry represents calcipressin-like protein Rcn1 from fungi. Rcn1 is involved in calcineurin regulation during calcium signalling .
Ubiquitin-like-conjugating enzyme Atg10 (Atg10)
Type: Family

Atg10 is an E2-like enzyme required for the cytoplasm to vacuole transport (Cvt), autophagy and nucleophagy. It catalyses the conjugation of Atg12 to Atg5, which is required for proper localisation of Atg8 to the preautophagosomal structure (PAS) .
Origin recognition complex subunit 4 (ORC4)
Type: Family

The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded by ORC1-6 . ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle . ORC directs DNA replication throughout the genome and is required for its initiation . ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex . Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase . Cell cycle-regulated phosphorylation of ORC2, ORC6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase .

In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) . ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers .

This group represents an origin recognition complex, subunit 4.
Vacuolar protein sorting-associated protein 11 (VPS11)
Type: Family

This entry includes E3 ubiquitin-protein ligase Pep5 (also known as Vacuolar biogenesis protein END1 and vacuolar protein sorting-associated protein 11, Vps11) from fungi, and its homologues from plants and animals. Pep5 is a peripheral vacuolar membrane protein required for protein trafficking and vacuole biogenesis . It is also identified as an E3 ubiquitin ligase that regulates histone protein levels in Saccharomyces cerevisiae . Human Vps11 may play a role in vesicle-mediated protein trafficking .

S.cerevisiae END1 mutants described as four vacuolar protein sorting mutants (class C vps) were found to lack a morphologically distinguishable and functional vacuole. These mutants internalise but do not degrade alpha-factor . They were also partly defective for mating. These response defects of END1 mutants were attributed to partial defects in signal transduction . The effects of these mutant defects were linked to the importance of a functional vacuole for optimal response to pheromone.
Mediator of RNA polymerase II transcription subunit 22, Saccharomycetes (Med22_Saccharomyce)
Type: Family

This entry represents the Med22 subunit of the Mediator complex in Saccharomycetaceae.

The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.

The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11.
RNA polymerase I-specific transcription initiation factor Rrn6 (Rrn6)
Type: Family

Rrn6 is a component of the core factor (CF) rDNA transcription factor complex (consists of Rrn6, Rrn7 and Rrn11), which is required for transcription of 35S rRNA genes by RNA polymerase I .