SII-SWORD/CoKE huggingface dataset:
Cell division protein CrgA (CrgA)
Type: Family

CrgA is a transmembrane (TM) protein, first described in Streptomyces as being required for sporulation through the coordination of several aspects of reproductive growth. In Mycobacterium tuberculosis, CrgA is a central component of the divisome, and consists of 93 residues with two predicted TM helices (TM1: residues 29-51 and TM2: residues 66-88). CrgA facilitates the recruitment of the proteins essential for peptidoglycan synthesis to the divisome and also stabilizes the divisome. Reduced production of CrgA results in elongated cells and reduced growth rate, and loss of CrgA impairs peptidoglycan synthesis. CrgA has homologs in other actinomycetes .
Uncharacterised protein family UPF0236 (UPF0236)
Type: Family

This entry represents a family of bacterial proteins of unknown function. Some family members are thought to be transposases .
Uncharacterised protein family UPF0239 (UPF0239)
Type: Family

This is a group of transmembrane proteins of unknown function.
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 4 (NDUFAF4)
Type: Family

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 4 (NDUFAF4, also known as HRPAP20) is involved in the assembly of mitochondrial NADH:ubiquinone oxidoreductase complex (complex I) . It may be involved in cell proliferation and survival of hormone-dependent tumor cells .
UPF0242, N-terminal (UPF0242_N)
Type: Domain

This region includes an N-terminal transmembrane region and a C-terminal coiled-coil.
Uncharacterised protein family UPF0253 (UPF0253)
Type: Family

This is a group of proteins of unknown function.
FeGP cofactor biosynthesis protein HcgF (HcgF)
Type: Family

This archaeal family includes the iron guanylylpyridinol (FeGP) cofactor biosynthesis protein HcgF which catalyses the transesterification of AMP-GP to afford a Cys (HcgF)-S-GP thioester .
Major intrinsically disordered Notch2-binding receptor 1-like, C-terminal (MINAR1-like_C)
Type: Domain

MINAR1 is a Notch2-binding protein that has been shown to inhibit angiogenesis and breast cancer growth . This entry represents the C terminus of the MINAR1 protein.
Uncharacterised protein family UPF0259 (UPF0259)
Type: Family

This is a group of membrane proteins of unknown function.
Bacteriophage tail tape measure, N-terminal (Phage_tape_measure_N)
Type: Domain

This entry represents a conserved region located towards the N-terminal end of prophage tail length tape measure protein (TMP). TMP is important for assembly of phage tails and involved in tail length determination. Mutated forms TMP cause tail fibres to be shortened . The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

This entry includes a domain near the N terminus of the bacteriophage lambda tail tape measure protein, GpH.
Erythrovirus X (Erythrovirus_X)
Type: Family

This family consists of several Erythrovirus X proteins, which seem to be found exclusively in human parvovirus and human erythrovirus. The function of this family is unknown.
Protein of unknown function DUF1229 (DUF1229)
Type: Family

This family consists of several hypothetical proteins of around 415 residues in length which seem to be specific to the bacterium Leptospira.
CGLD27-like (CGLD27-like)
Type: Family

This family consist of proteins found in plants and algal chloroplasts, and in cyanobacteria. It includes CGLD27 (CONSERVED IN THE GREEN LINEAGE AND DIATOMS 27), which has been described as one out of 14 Fe-responsive orthologues in Chlamydomonas and Arabidopsis, indicating that it is an important component of the iron deficiency response of the plant lineage .
Vaccinia virus, B17 (Vaccinia_virus_B17)
Type: Family

This family consists of several Orthopoxvirus specific proteins predominantly of around 340 residues in length. This family contains the Vaccinia virus, B17 protein, the function of which is unknown.
Putative excisionase (Put_exci)
Type: Family

This family consists of several putative phage and prophage excisionase proteins of around 80 residues in length.
Neural proliferation differentiation control-1 (NPDC1)
Type: Family

This family consists of several neural proliferation differentiation control-1 (NPDC1) proteins. NPDC1 plays a role in the control of neural cell proliferation and differentiation. It has been suggested that NPDC1 may be involved in the development of several secretion glands. This family also contains the C-terminal region of the Caenorhabditis elegans protein CAB-1 (

) which is known to interact with AEX-3 .
Capsid assembly scaffolding protein (SCAF)
Type: Family

This entry consists of several phage scaffolding proteins involved in the icosahedric procapsid assembly . They co-assemble with the capsid proteins to form the procapsid, in which the scaffolding protein is found within the external shell of icosahedrally arranged capsid protein subunits. In a subsequent step the scaffolding protein molecules are released from the procapsid .
Transmembrane protein GPR107/GPR108-like (GPR107/GPR108-like)
Type: Family

This entry represents a group of transmembrane proteins, including mammalian GPR107, GPR108, TMEM87A and TMEM87B which have been collectively termed lung seven transmembrane receptor or LUSTR and are evolutionary related. Together with GPR180, TMEM145, TMEM181, and WLS, they have been described as GOST proteins (for GOLD domain seven-transmembrane helix proteins) given they share the same domain architecture consisting of a GOLD domain atop of a membrane-spanning seven-transmembrane helix domain .

GPR107 and GPR108 localize to the Golgi and have suggested roles in protein trafficking . GPR107 is implicated in the transport of Pseudomonas aeruginosa Exotoxin A, Campylobacter jejuni cytolethal distending toxin (CDT), and ricin, while GPR107 knockout cells display deficits in receptor-mediated endocytosis and recycling . GPR108 is critical for the transduction of a majority of AAV serotypes . It may play a potential role in the regulation of Toll-like receptor-mediated signaling .

This entry also includes proteins from fungi and plants . The plant proteins in this entry, including CAND6 and CAND7, are predicted to be G-protein coupled receptors .
Peptidase A24A-predicted, C-terminal archaea (Pept_A24A_C_arc)
Type: Domain

This region is of unknown function found at the C terminus of some archeal proteins that have multiple transmembrane domains and are predicted to be aspartic peptidases belonging to the MEROPS peptidase subfamily A24A (type 4 prepilin peptidase 1. This entry includes EppA, which is a prepilin-peptidase that can cleave proteins with class III signal peptides (

) .
Bacteriophage 933W, L0121, tail fibre, C-terminal (Phage_933W_L0121_C)
Type: Domain

This entry represents the C terminus of phage 933W tail fibre protein. This domain is found together with conserved RLGP motif. The characteristics of the protein distribution suggest prophage matches.
Vaccinia virus, A37 (Vaccinia_virus_A37)
Type: Family

This family contains a number of poxviral proteins, which include Vaccinia virus A37, also known as Protein OPG165, the function of which is unknown.
Protein of unknown function DUF1236 (DUF1236)
Type: Family

This family contains a number of hypothetical bacterial proteins of unknown function. Some family members contain more than one copy of the region represented by this family.
Heat shock factor binding 1 (HS1-bd)
Type: Family

Heat shock factor binding protein 1 (HSBP1) interacts with the oligomerization domain of heat shock factor 1 (Hsf1), suppressing Hsf1's transcriptional activity following stress. It plays an essential role during early mouse and zebrafish embryonic development . In the plant Arabidopsis, heat shock factor-binding protein (HSBP) is required for acquired thermotolerance but not basal thermotolerance and for seed development .
FKTN/MNN4/W02B3.4-1/T07A5.1 (FKTN/MNN4/W02B3.4-1)
Type: Family

This entry covers FKTN protein in mammals and its orthologues in C.elegans (W02B3.4, W02B3.1 and T07A5.1) and yeast (MNN4).

Ribitol-5-phosphate transferase (FKTN) is a eukaryotic protein necessary for the maintenance of muscle integrity, cortical histiogenesis, and normal ocular development. Mutations in the fukutin gene have been shown to result in Fukuyama-type congenital muscular dystrophy characterised by brain malformation - one of the most common autosomal-recessive disorders in Japan . FKTN participates in glycosylation of alpha-dystroglycan/DAG1 . MNN4 from budding yeast may function as a positive regulator for mannosylphosphate transferase .
Uncharacterised conserved protein GguC (GguC)
Type: Family

There is currently no experimental data for members of this family or their homologues. Agrobacterium tumefaciens GguC is encoded by the same operon as ChvE (periplasmic sugar-binding protein that transmits the signal to the VirA/VirG signalling system), GguA and GguB (putative ABC-type sugar transporter components) . However, the function of GguC is not known yet.
Root cap (Root_cap)
Type: Family

The cells at the periphery of the root cap are continuously sloughed off from the root into the mucilage, and are thought to be programmed to die .This family represents a conserved region approximately 60 residues in length within plant root cap proteins, which may be involved in the process.
Penicillin-binding, C-terminal (PBP_C)
Type: Domain

This conserved region of approximately 90 residues is found in a sub-group of bacterial Penicillin-Binding Proteins (PBPs). A variable length loop region separates this region from the transpeptidase unit (

). It is predicted to be a β fold.
Biotin-dependent malonate decarboxylase, gamma subunit (Malonate_gamma)
Type: Family

This family consists of several bacterial malonate decarboxylase gamma subunit proteins. Malonate decarboxylase of Klebsiella pneumoniae consists of four different subunits and catalyses the conversion of malonate plus H
+
to acetate and CO2. The catalysis proceeds via acetyl and malonyl thioester residues with the phosphribosyl-dephospho-CoA prosthetic group of the acyl carrier protein (ACP) subunit. MdcD and E together probably function as malonyl-S-ACP decarboxylase .

Malonate decarboxylase may be a soluble enzyme, or linked to membrane subunits and active as a sodium pump. In the malonate decarboxylase complex, the beta subunit appears to act as a malonyl-CoA decarboxylase, while the gamma subunit appears either to mediate subunit interaction or to act as a co-decarboxylase with the beta subunit. The beta and gamma subunits exhibit some local sequence similarity .
TraU (TraU)
Type: Family

This family consists of several bacterial TraU proteins. TraU appears to be more essential to conjugal DNA transfer than to assembly of pilus filaments .
Fijivirus P9-2 (Fijivirus_P9-2)
Type: Family

This family consists of several Fijivirus specific P9-2 proteins from Rice black streaked dwarf virus (RBSDV) and Fiji disease virus. The function of this family is unknown.
Putative methionine gamma-lyase (Met_g_lyase_put)
Type: Family

This is a putative pyridoxal 5'-phosphate-dependent methionine gamma-lyase enzyme involved in methionine catabolism .
Programmed cell death protein 10 (PDCD10)
Type: Family

Programmed cell death 10 protein (PDCD10/CCM3) is part of the CCM complex and is required for neuronal migration . It also has roles outside of this complex , it is crucial in vascularization and in angiogenesis as it functions in vessel permeability and stability . PDCD10/CCM3 was originally discovered to be upregulated during granulocyte apoptosis and is thought to play a role in cell death . However, a specific role for PDCD10 in cell survival is not clear as both pro-survival and pro-apoptotic effects have been reported . PDCD10/CCM3 contains an N-terminal dimerisation domain and a C-terminal focal adhesion targeting-homology (FAT-H) domain .

There are three CCM proteins: CCM1 (also known as KRIT1), CCM2 (also known as OSM and malcavernin) and CCM3 (also known as PDCD10). Mutations in the genes encoding CCM proteins cause cerebral cavernous malformations (CCMs), a disease characterised by dilated leaky blood vessels, especially in the neurovasculature, that result in increased risk of stroke, focal neurological defects and seizures. The CCM proteins can form a trimeric complex. They can also interact with a range of signaling, cytoskeletal and adaptor proteins that may account for their roles in a range of basic cellular processes including cell adhesion, migration, polarity and apoptosis .
Protein kish (Ksh1)
Type: Family

Protein kish is involved in the early part of the secretory pathway .
Preflagellin peptidase, C-terminal (Preflagellin_peptidase_C)
Type: Domain

This region is of unknown function, which is found at the C terminus of archaeal preflagellin peptidase . The preflagellin peptidase is a membrane-bound enzyme topologically similar to its counterpart in the type IV pilus system (prepilin peptidase); the two enzymes utilizing the same catalytic mechanism . The preflagellin peptidase is required for the removal of the leader peptide from archaeal flagellin .
PHB de-polymerase, C-terminal (PHB_depo_C)
Type: Domain

This entry represents the C terminus of bacterial poly(3-hydroxybutyrate) (PHB) de-polymerase. This degrades PHB granules to oligomers and monomers of 3-hydroxy-butyric acid.
Protein Ac34 (Protein_Ac34)
Type: Family

Protein Ac34 from Autographa californica nuclear polyhedrosis virus (AcMNPV) induces translocation subunits of the actin nucleator actin-related protein complex Arp2/3 to the nucleus during AcMNPV infection. The Arp2/3 complex regulates actin polymerization and plays a variety of roles during infection, including nuclear actin polymerization to assist in virus replication .
Domain of unknown function DUF1248 (DUF1248)
Type: Domain

This entry represents a conserved region within a number of proteins of unknown function that seem to be specific to Caenorhabditis elegans. Note that some proteins in the entry contain more than one copy of this region. Structurally related to Gcn5-related N-acetyltransferase (GNAT) family.
Protein of unknown function DUF1249 (DUF1249)
Type: Family

This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Bacteriophage A500, Gp15 (Phage_A500_Gp15)
Type: Family

This entry describes Gp15 from Bacteriophage A500 (Listeria phage A500), related proteins in other bacteriophage, and prophage regions of bacterial genomes. The function is unknown.
Autographa californica nuclear polyhedrosis virus, Da18 (AcMNPV_Da18)
Type: Family

This entry is represented by Da18 from Autographa californica nuclear polyhedrosis virus (AcMNPV), also known as Early 18.5 kDa protein. It is a family of uncharacterised viral proteins.
Malonate decarboxylase delta subunit (Malonate_deCO2ase_dsu)
Type: Family

This family consists of the acyl carrier protein, also called the delta subunit, of malonate decarboxylase. This subunit has the same covalently bound prosthetic group, derived from and similar to coenzyme A, as does citrate lyase, although this protein and the acyl carrier protein of citrate lyase do not show significant sequence similarity. Both malonyl and acetyl groups are transferred to the prosthetic group for catalysis.

This entry represents the malonate decarboxylate delta subunit. Malonate decarboxylase of Klebsiella pneumoniae consists of four different subunits and catalyses the conversion of malonate plus H
+
to acetate and CO2. The catalysis proceeds via acetyl and malonyl thioester residues with the phosphribosyl-dephospho-CoA prosthetic group of the acyl carrier protein (ACP) subunit. MdcC is the (apo) ACP subunit .
Pilin accessory predicted (PAP_PilO)
Type: Family

This family consists of several enterobacterial PilO proteins. The function of PilO is unknown although it has been suggested that it is a cytoplasmic protein in the absence of other Pil proteins, but PilO protein is translocated to the outer membrane in the presence of other Pil proteins. Alternatively, PilO protein may form a complex with other Pil protein(s). PilO has been predicted to function as a component of the pilin transport apparatus and thin-pilus basal body . This family does not seem to be related to

.
Pyrimidine/purine nucleoside phosphorylase (Ppnp)
Type: Family

This family consist of YaiE and related proteins. YaiE from E. coli catalyses phosphorolysis of diverse nucleosides, yielding D-ribose 1-phosphate and free bases .
Spore protease-like YyaC (YyaC)
Type: Family

This family consists of a number of proteins conserved among the endospore-forming subset of the firmicutes, which are largely uncharacterised. A member of this entry, called YyaC, shows many similarities to the germination protease GPR, which is found in exactly the same set of organisms and has a known role in the sporulation/germination process.
Uncharacterised protein family Ycf35 (Uncharacterised_Ycf35)
Type: Family

This family represents Ycf35, which is encoded in algal chloroplast and in cyanobacteria. The function of these proteins are unknown. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
Protein of unknown function DUF1258 (DUF1258)
Type: Family

This family represents a conserved region approximately 260 residues long within a number of hypothetical proteins of unknown function that seem to be specific to rotifers, nematodes and arthropods. Note that this family contains a number of conserved cysteine and histidine residues.
RNA polymerase I associated factor, A49-like (RNA_pol-assoc_fac_A49-like)
Type: Family

Saccharomyces cerevisiae A49 is a specific subunit associated with RNA polymerase I (Pol I) in eukaryotes. Pol I maintains transcription activities in A49 deletion mutants. However, such mutants are deficient in transcription activity at low temperatures. Deletion analysis of the fusion yeast homologue indicates that only the C-terminal two thirds are required for function. Transcript analysis has demonstrated that A49 is maximising transcription of ribosomal DNA .
Cysteine protease, VirA/EspG (Cys_protease_VirA/EspG)
Type: Family

This entry represents a family of bacterial virulence proteins, including EspG from Citrobacter rodentium and Escherichia coli and VirA from Shigella flexneri. Both EspG and VirA are delivered into infected host epithelial cells by a type III secretory system . These proteins function through the disruption of the host cell microtubule network . VirA acts as a cysteine protease (

) on alpha-tubulin, a major component of microtubules, in order to destabilise surrounding microtubules and invade the cytoplasm of their target host cells . VirA also promotes the formation of membrane ruffles through the activation of host rac1, which is associated with the destruction of microtubule networks . In this way, VirA creates a tunnel inside the host cell cytoplasm by breaking down the microtubule infrastructure, which facilitates the bacterium's movement through the cytoplasm and also helps other bacteria move faster during the invasion of the eukaryotic cell.
Cell surface immobilisation antigen SerH (SerH)
Type: Family

This entry consists of several cell surface immobilisation antigen SerH proteins which seem to be specific to Tetrahymena thermophila. The SerH locus of T. thermophila is one of several paralogous loci with genes encoding variants of the major cell surface protein known as the immobilisation antigen (i-ag) .
Regulator of ribonuclease activity B domain (RraB_dom)
Type: Domain

This entry represents a domain found in regulator of ribonuclease activity B (RraB) protein. RraB regulates mRNA abundance by binding to RNaseE and inhibiting its endonucleolytic activity . A subset of these proteins are predicted to function as immunity proteins .
Pkip-1 (Pkip-1)
Type: Family

Pkip-1 is a baculoviral gene encoding a protein kinase-interacting protein. It interacts with and stimulates the activity of virus-encoded protein kinase PK-1 . Pkip-1 is not essential for virus replication .
DNA-directed RNA polymerase I subunit RPA2, domain 4 (Rpa2_dom_4)
Type: Domain

This domain is found between domain 3 and domain 5, but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability .
TPX2 (TPX2_fam)
Type: Family

This family represents the eukaryotic targeting protein for Xklp2 (TPX2). TPX2 is a microtubule-associated protein that targets a plus end-directed motor (Xklp2) to the minus ends of microtubules in the mitotic spindle. In Xenopus, it has been shown that Xklp2 protein is required for centrosome separation and maintenance of spindle bi-polarity . It is phosphorylated during mitosis in a microtubule-dependent way . TPX2 activates Aurora A kinase by promoting its autophosphorylation and protects the phosphorylated residue against dephosphorylation .
Protein of unknown function DUF1265 (DUF1265)
Type: Family

This family represents a conserved region approximately 50 residues long within a number of proteins of unknown function that seem to be restricted to Caenorhabditis elegans.
Protein of unknown function DUF1266 (DUF1266)
Type: Family

This family consists of several hypothetical bacterial proteins of unknown function.
Bacteriophage tail completion protein R (Phage_tail_completion_R)
Type: Family

Bacteriophage tail completion R is thought to be essential for stable head joining .
Bacteriophage 186, CII-like (Phage_186_CII-like)
Type: Family

This entry represents Regulatory protein CII from Escherichia phage 186 (Bacteriophage 186) and similar proteins from tailed bacteriophages (Caudovirales) and prophages from Proteobacteria. CII (also known as CP76) is a transcriptional activator essential for the establishment of lysogeny . The expression of this protein increases gradually with lysogenisation, which frequency increases with multiple infections .
Phage tail assembly chaperone protein, Siphoviridae (Phage_TAC_Siphoviridae)
Type: Family

This is a family of phage tail tube assembly chaperone proteins from some Siphoviridae viruses .
Protein of unknown function DUF1270 (DUF1270)
Type: Family

This entry includes Bacteriophage 92, Orf86. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

This family consists of several hypothetical Staphylococcus aureus and phage proteins of 53 residues in length. The function of this family is unknown.
Extensin-like, C-terminal (Extensin-like_C)
Type: Domain

This entry represents the C terminus (approx. 120 residues) of a number of bacterial extensin-like proteins. Extensins are cell wall glycoproteins normally associated with plants, where they strengthen the cell wall in response to mechanical stress .
Latexin (Latexin)
Type: Family

This family consists of several animal specific latexin and proteins related to latexin that belong to MEROPS proteinase inhibitor family I47, clan I- .
Male enhanced antigen 1 (MEA1)
Type: Family

This family consists of several mammalian male enhanced antigen 1 (MEA1) proteins. The Mea-1 gene is found to be localised in primary and secondary spermatocytes and spermatids, but the protein products are detected only in spermatids. Intensive transcription of Mea-1 gene and specific localisation of the gene product suggest that Mea-1 may play a important role in the late stage of spermatogenesis .