SII-SWORD/CoKE huggingface dataset:
ATPase, V0 complex, subunit D (ATPase_V0-cplx_dsu)
Type: Family

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra-and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release . V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins .

The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis . The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases.
Neuroblastoma suppressor of tumourigenicity 1 (Neuroblast_suppress_tumour_1)
Type: Family

This group represents the neuroblastoma suppressor of tumorigenicity 1 protein, also known as zinc finger protein DAN. This protein is a possible candidate for a tumor suppressor of neuroblastoma and may play an important role in preventing cells from entering the final stage (G1/S) of the transformation process .
FAS-associated death domain protein (FADD)
Type: Family

This entry includes FAS-associated death domain (FADD) proteins from animals.

This entry includes the Fas-associated death domain (FADD) protein. This protein is an apoptotic adaptor molecule that recruits caspase-8 or caspase-10 to the activated Fas (CD95) or TNFR-1 receptors . The resulting aggregate, called the death-inducing signalling complex (DISC), performs caspase-8 proteolytic activation . Active caspase-8 initiates the subsequent cascade of caspases mediating apoptosis .
RNA-binding FAU-1 (RNA-bd_FAU-1)
Type: Family

This entry represents the FAU-1 protein from archaea. In Pyrococcus furiosus, FAU-1 (P. furiosus AU-binding), is highly charged, heat-stable protein from that binds specifically to the AU-rich sequence in a loop region of RNA .

FAU-1 consists of two domains, N- and C-terminal, and from a structure determined in FAU-1 from Pyrococcus furiosus, it forms a homo-trimer . The C-terminal domain forms the trimer and each N-terminal domain locates outside of the trimer core. A dinucleotide, pApUp, was bound to the N-terminal domain, indicating that it has the RNA-binding ability and resembles RNase E from Escherichia coli. FAU-1 has been shown to possess an RNase activity against precursor 5S rRNA derived from P. furiosus and T. kodakarensis in the order Thermococcales in vitro . In Haloferax volcanii, it has been described as a RNase that participates in the maturation of pre-16S rRNA and renamed to RNase W, comprising the first archaea-specific contributor to archaeal ribosome biogenesis .
Uncharacterised conserved protein UCP018649 (UCP018649)
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 UCP018688 (UCP018688)
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 UCP018747 (UCP018747)
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.
Methanogenesis marker 12 protein (Methan_mark_12)
Type: Family

This group represents uncharacterised conserved proteins. They share distant sequence similarity with members of

. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it.
Uncharacterised protein MJ1481, archaea (MJ1481_archaea)
Type: Family

This family contains uncharacterised proteins conserved in archaea. One family member (MJ1481) has been reported to be SepCysE, a translation factor, essential for the methanococcal Cys biosynthesis. SepCysE forms a bridge between Sep-tRNA:Cys-tRNA synthase (SepCysS) and O-phosphoseryl-tRNA synthetase (SepRS), forming the transsulfursome complex , enabling substrate channelling of Sep-tRNACys .
Uncharacterised conserved protein UCP018868 (UCP018868)
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.
DNA double-strand break repair nuclease NurA-like (NurA-like)
Type: Family

This entry represents NurA, an archaeal nuclease that exhibits both single-stranded endonuclease activity and 5'-3' exonuclease activity on single-stranded and double-stranded DNA from the hyperthermophilic archaeon Sulfolobus acidocaldarius . This entry also includes similar uncharacterised proteins.
Uncharacterised conserved protein UCP018933 (UCP018933)
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 UCP018938 (UCP018938)
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 UCP018953 (UCP018953)
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.
tRNA methyltransferase, archaea (tRNA_m1G_mtfrase_arc)
Type: Family

This group represents a group of tRNA (guanine-N(1)-)-methyltransferases from archaeal, including TK0422 from Thermococcus kodakaraensis and Saci_1677 from Sulfolobus acidocaldarius. TK0422 catalyzes the S-adenosyl-L-methionine-dependent formation of either N(1)-methyladenine or N(1)-methylguanine at position 9 (m1A9 or m1G9) in tRNA . Saci_1677 catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenine at position 9 (m1A9) in tRNA .
Nuclear factor interleukin-3-regulated protein (NFIL3/E4BP4)
Type: Family

Nuclear factor interleukin-3-regulated protein (NFIL3, also known as E4BP4) was first identified as a transcriptional repressor capable of binding an activating transcription factor (ATF) DNA consensus sequence site in the adenovirus E4 promoter . Later, it was independently identified as a transactivator of the IL3 promoter in human T cells .

E4BP4 is involved in a several biological processes, including transcriptional control of the circadian clock, neuron growth and survival, osteoblast function, and regulation of ovulation . It is essential for the development of NK cells and CD8alpha(+) conventional dendritic cells, and is also involved in macrophage activation, polarisation of CD4(+) T cell responses and B cell class switching to IgE .
Uncharacterised conserved protein UCP019072 (UCP019072)
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.
Archaeal GINS complex, Gins51 subunit (Gins51)
Type: Family

This protein family includes the GINS subunit Gins51 from Thermococcus kodakarensis and similar proteins from archaea. Archaeal GINS is a α2β2 type tetramer that plays a key role to move from initiation to elongation of the DNA replication. Gin51 is organised into a larger α-helical domain at the N-terminal and a smaller β-stranded domain at the C-terminal, showing the same structural domains as the other subunit of the complex, Gin23, in reverse order .
Uncharacterised conserved protein UCP019078 (UCP019078)
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.
Phosphotransbutyrylase (Phosphotransbutyrylase)
Type: Family

This entry represents a family of phosphotransbutyrylases that contain a VanZ domain.
Transcription regulator, CopG/Arc/MetJ DNA-binding domain-containing, predicted (Tscrpt_reg_CopG_prd)
Type: Family

This group represents a predicted transcriptional regulator with CopG/Arc/MetJ DNA-binding domain.
Acetophenone carboxylase beta subunit/Acetone carboxylase gamma subunit (Aceto_COase_bsu/gsu)
Type: Family

This entry represents the beta subunit of acetophenone carboxylase and the gamma subunit of acetone carboxylase. Acetophenone carboxylase catalyses the carboxylation of acetophenone to form 3-oxo-3-phenylpropanoate (benzoylacetate) in the anaerobic catabolism of ethylbenzene . Acetone carboxylase catalyses the carboxylation of acetone to form acetoacetate .
Uncharacterised conserved protein UCP019236 (UCP019236)
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 UCP019240, SpoVT/AbrB-related (UCP019240_SpoVT/AbrB-related)
Type: Family

This entry represents a small family of archaeal proteins, including SpoVT-AbrB domain-containing protein from Pyrococcus horikoshii (PHS018,

), which consists of six-stranded Greek-key barrel fold and two α-helices, with a very similar overall appearance to the double-psi and swapped-hairpin β-barrel . Members of this group are predicted regulators of stationary/sporulation gene expression with an SpoVT/AbrB like domain.
Phage portal protein PBSX family, Firmicutes (PBSX_Firmicutes)
Type: Family

This entry represents the phage-like element PBSX protein from Firmicutes. PBSX protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average molecular weight of 40-90kDa.
Connectase MJ0548-like (MJ0548-like)
Type: Family

This entry represents Connectase MJ0548 from Methanocaldococcus jannaschii and similar archaeal sequences. MJ0548 is a distant, monomeric proteasome homologue which connects proteins in a sequence-specific manner. It forms a hydrolysis-resistant amide intermediate between the Thr-1 amino group and the substrate carbonyl carbon, allowing protein ligations without side reactions .
Uncharacterised conserved protein UCP019302 (UCP019302)
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-dependent hydrolase, membrane-bound predicted (Metal-dep_Ohase_Mem-prd)
Type: Family

This group represents a small group of predicted membrane-bound metal-dependent hydrolases found in Thermococci.
Uncharacterised conserved protein UCP019322 (UCP019322)
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.
Glucose-6-phosphate isomerase, archaea/bacteria (G6P_isomerase_archaea/bacteria)
Type: Family

This entry represents a group of glucose-6-phosphate isomerases from archaea and bacteria .
HTH-type transcriptional repressor RghR (RghR)
Type: Family

RghR represses the expression of yvaM and both rapG and rapH. It binds directly to the promoter regions of yvaM, rapG and rapH .
Radical S-adenosyl methionine enzyme HcgG-like (HcgG-like)
Type: Family

This protein family includes HcgA from Methanococcus maripaludis (MMP0125,

) and similar archaeal proteins. HcgG is a radical S-adenosyl methionine enzyme involved in the biosynthesis of the iron-guanylylpyridinol (FeGP) cofactor .

Proteins annotated as HmdC, whose gene regularly occurs in the context of genes for HmdA (5,10-methenyltetrahydromethanopterin hydrogenase) and the radical SAM protein HmdB involved in biosynthesis of the HmdA cofactor, also belong to this family. Bioinformatics suggests this protein, a homologue of eukaryotic fibrillarin, may be involved in biosynthesis of the guanylyl pyridinol cofactor in HmdA .
Uncharacterised conserved protein UCP019454, CBS (UCP019454_CBS)
Type: Family

This group represents an uncharacterised protein with two CBS domains.
Methanogenesis marker 17 protein (Methan_mark_17)
Type: Family

There is currently no experimental data for members of this group or their homologues. There function is unknown but they are likely to be linked to methanogenesis or a process closely connected to it .
Vesicle-associated membrane-protein-associated protein (VAP)
Type: Family

This entry represents a family of vesicle-associated membrane-protein-associated proteins (VAPs) and plant VAP homologs (PVAPs) . VAPs (VAPA and VAPB in humans, VAPA, VAPB and VAPC in other mammals ) are endoplasmic reticulum (ER) proteins that play roles in vesicle trafficking, neurotransmitter release, microtubule organisation, lipid transport and unfolded protein response . VAP proteins contain an MSP domain in their N-terminal half, which has been shown to interact with proteins containing a FFAT motif, such as members of the oxysterol-binding protein (OSBP) family or the phosphatidylinositol transfer proteins from the PITPNM family . Yeast VAP homologues are known as Scs2 and Scs22 .
Methyltransferase Mtx subunit X (MeTrfase_MtxX_xsu)
Type: Family

This group represents a methyltransferase Mtx subunit X, also referred to as methanogenesis marker protein Mmp4/MtxX . The exact function is unknown, but likely is linked to methanogenesis or a process closely linked to it. Some members have been suggested to be a methyltransferase, based on the proximity of its gene to genes of the multi-subunit complex, N5-methyl-tetrahydromethanopterin--coenzyme M methyltransferase. That context is not conserved, however. The family shows similarity to various phosphate acyltransferases.
Metal-dependent membrane protease, predicted (M_metal-dep_Prtase_arc_prd)
Type: Family

This entry represents a predicted metal-dependent membrane protease found in archaea.
Trichothecene biosynthesis transcription regulator TRI6 (Tscrpt_reg_Tri6)
Type: Family

Tri6 is part of the core trichothecene biosynthesis cluster . It is a zinc finger DNA-binding protein that functions as a pathway-specific transcription factor and positively regulates the other Tri genes .
Uncharacterised conserved protein UCP019853 (UCP019853)
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 UCP019883, membrane (UCP019883)
Type: Family

There is currently no experimental data for members of this group or their homologues. However, these proteins are predicted to contain transmembrane segments.
Bacteriophage SP01, Orf1 (Phage_SP01_Orf1)
Type: Family

This entry is represented by Bacteriophage SP01, Orf1. 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.
Nonstructural, NS2 (Non-structural_NS2)
Type: Family

This group represents a nonstructural protein NS2.
Fe-S oxidoreductase, radical SAM domain-containing, TM0948, predicted (Fe-S_OxRdtase_rSAM_TM0948_prd)
Type: Family

This group represents a predicted Fe-S oxidoreductase with radical SAM domain, TM0948 type.
Uncharacterised conserved protein UCP020408 (UCP020408)
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.
Ferric uptake regulator, CjrA, predicted (Fe3_uptake_reg_CjrA_prd)
Type: Family

This group represents a predicted ferric uptake regulator, CjrA type.
Nodulation, NolB (Nodulation_NolB)
Type: Family

This group represents a nodulation protein, NolB type .
ApeP-like dehydratase (ApeP-like_dehydratase)
Type: Family

This entry ApeP dehydratase and its homologues. This enzyme forms a heterodimer with ApeI that carries out dehydratation in APE biosynthesis. Both subunits in this complex adopt a typical hotdog fold comprising six antiparallel β-strands and a central α-helix .
Uncharacterised conserved protein UCP020772 (UCP020772)
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.
Competence protein ComB (Competence_ComB)
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 ComB.
Radical SAM enzyme, MSMEG0568 (rSAM_MSMEG0568)
Type: Family

Members of this protein family are radical SAM proteins related to MSMEG_0568 from Mycobacterium smegmatis. Members occur within 8-gene operons in species as diverse as M. smegmatis, Rhizobium leguminosarum, Synechococcus elongatus, and Sorangium cellulosum. The function of the operon is unknown, but similarity of MSMEG_0568 to some cofactor biosynthesis radical SAM proteins suggests a similar biosynthetic function.
Uncharacterised conserved protein UCP020893 (UCP020893)
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.
Anti-sigma regulatory factor, PmgA, predicted (Anti-sigma_regulat_PmgA_prd)
Type: Family

This group represents a predicted anti-sigma regulatory factor, PmgA type.
Uncharacterised conserved protein UCP022271 (UCP022271)
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.
Biofilm formation YmcA (Biofilm_formation_YmcA)
Type: Family

Wild strains of Bacillus subtilis are capable of forming architecturally complex multicellular communities of cells known as biofilms. They display a high degree of spatiotemporal organisation . Exopolysaccharides may be responsible for binding chains of cells together in bundles .

The six genes that are involved in the formation of biofilms are yhxB (encoding a putative phosphohexomutase that may mediate exopolysaccharide synthesis), sipW (encoding a signal peptidase), ecsB (encoding an ABC transporter subunit), yqeK (encoding a putative phosphatase), ylbF (encoding a regulatory protein), and ymcA (a gene of unknown function) .
Uncharacterised protein UCP021288 with ACT domain (UCP021288_ACT)
Type: Family

This group represents an uncharacterised protein with an N-terminal ACT domain.
ComG operon protein 4 (ComGD)
Type: Family

This entry represents ComG operon protein 4 (also known as Competence protein ComGD).

The comG operon of Bacillus subtilis encodes seven membrane associated proteins, which function in binding of transforming DNA to the competent cell surface . ComGC, GD, GE and GG have N-terminal sequence motifs typical of type 4 pre-pilins and are processed by a pathway that requires the product of comC, also an essential competence gene. They form form pilin-like structures that are localised to the cytoplasmic membrane and cell wall . The comG operon also consist of ComGF, a small integral membrane protein, ComGA and ComGB, which are predicted to be a nucleotide binding protein and an integral membrane protein respectively . When strains missing each of the 7 proteins are created, they were all found to be nontransformable and failed to bind transforming DNA to the cell surface .
Uncharacterised protein YdeI, bacterial (YdeI_bac)
Type: Family

This entry specifically represents bacterial YdeI. YdeI is important for resistance to polymyxin B in broth and for bacterial survival in mice upon oral, but not intraperitoneal inoculation, suggesting a role for YdeI in the gastrointestinal tract of mice . Production of the ydeI gene is regulated by the Rcs (regulator of capsule synthesis) phospho-relay system pathway independently of RcsA, and additionally transcription of the protein is regulated by the stationary-phase sigma factor, RpoS (sigma-S) . YdeI confers protection against cationic AMPs (antimicrobial peptides) or bacteriocins in conjunction with the general porin Omp, thus justifying its name of OmdA, for OmpD-Associated protein .
Uncharacterised conserved protein UCP021328 (UCP021328)
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.
Membrane protein YqfB (YqfB)
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. This entry includes the membrane protein YqfB from Bacillus subtilis.
Uncharacterised conserved protein UCP021389 (UCP021389)
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.
Thiol ester hydratase, Rv0216, predicted (Thiol_ester_hydratase_Rv0216)
Type: Family

This group represents a predicted thiol ester hydratase, Rv0216 type.
Rubromycin-type polyketide biosynthesis protein, GrhN/RubW, predicted (Polyketide_synth_GrhN/RubW_prd)
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 within operons involved in rubromycin-family polyketides , and may be involved in their biosynthesis.
Uncharacterised conserved protein UCP021573 (UCP021573)
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.