SII-SWORD/CoKE huggingface dataset:
Transglutaminase-like cysteine peptidase, predicted (Transglutaminase-like_Cys_pept)
Type: Family

Structural analysis predicts that this family of proteins are bacterial transglutaminase-like cysteine peptidases (BTLCPs) with an invariant Cys-His-Asp catalytic triad and an N-terminal signal sequence. They are predicted to possess the papain-like cysteine proteinase fold and catalyse post-translational protein modification through transamidase, acetylase or hydrolase activity. Inspection of neighbouring genes suggests a link between this predicted activity and a type-I secretion system resembling ATP-binding cassette exporters of toxins and proteases involved in bacterial pathogenicity .
Protein of unknown function DUF922 (DUF922)
Type: Family

This entry consists of several hypothetical bacterial proteins of unknown function.
Protein of unknown function DUF924 (DUF924)
Type: Family

This entry consists of several hypothetical bacterial proteins of unknown function.
Dam-replacing (DRP)
Type: Family

Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis .
Rhamnogalacturonate lyase (Rhamnogal_lyase)
Type: Family

Rhamnogalacturonate lyase degrades the rhamnogalacturonan I (RG-I) backbone of pectin . This family contains mainly members from plants, but also contains the plant pathogen Erwinia chrysanthemi.
Exocyst complex component EXOC3/Sec6 (EXOC3/Sec6)
Type: Family

Sec6 is a component of the multiprotein exocyst complex. Sec6 interacts with Sec8, Sec10 and Exo70. These exocyst proteins localise to regions of active exocytosis-at the growing ends of interphase cells and in the medial region of cells undergoing cytokinesis-in an F-actin-dependent and exocytosis-independent manner .
FldB/FldC dehydratase alpha/beta subunit (FldB/FldC_alpha/beta)
Type: Family

This entry includes HgdA/B from Acidaminococcus fermentans, FldB/C from Clostridium sporogenes and BcrB/C from Thauera aromatica. Acidaminococcus fermentans 2-hydroxyglutaryl-CoA dehydratase consists of two components: A (for activator or initiator) and D (for dehydratase). HgdA and B form a heterodimeric enzyme designated as component D, which contains an oxidized [4Fe-4S]2+ cluster and reduced riboflavin-5'-phosphate.
Protein of unknown function DUF928 (DUF928)
Type: Family

This is a family of uncharacterised bacterial proteins.
3-hydroxyanthranilic acid dioxygenase (3hydroanth_dOase)
Type: Family

Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase (

). It is part of the kynurenine pathway for the degradation of tryptophan and the biosynthesis of nicotinic acid .The prokaryotic homologue is involved in the 2-nitrobenzoate degradation pathway .

The enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Competence protein CoiA, nuclease-like domain (CoiA_nuc)
Type: Domain

This entry represents a domain found in the Competence protein CoiA from Bacillus subtilis and related proteins. This domain has a detectable similarity to PD-(D/E)XK nuclease superfamily and is predicted to adopt a similar structure.

CoiA falls within a competence-specific operon in Streptococcus. It is required for optimal transformation .

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 .
Exopolysaccharide synthesis, ExoD (ExoD)
Type: Family

Among the bacterial genes required for nodule invasion are the exo genes. These genes are involved in the production of an extracellular polysaccharide. Mutations in the exoD result in altered exopolysaccharide production and defects in nodule invasion .
Terminase, ATPase subunit, N-terminal domain (ATPase_terminase-su_N)
Type: Domain

This entry represents the N-terminal domain of Terminase, ATPase subunit from Escherichia phage P2 and similar proteins from tailed bacteriophages and bacterial prophages. Terminases are viral proteins that are involved in packaging viral DNA into the capsid .
Bacterial virulence (VirJ)
Type: Domain

This entry contains several bacterial VirJ virulence proteins. VirJ is thought to be involved in the type IV secretion system. It is thought that the substrate proteins localised to the periplasm may associate with the pilus in a manner that is mediated by VirJ, and suggest a two-step process for type IV secretion in Agrobacterium .
mRNA-decapping enzyme subunit 1 (Dcp1)
Type: Family

An essential step in mRNA turnover is decapping. In yeast, two proteins have been identified that are essential for decapping, Dcp1 (this family) and Dcp2. Dcp1 is a coactivator that binds to the decapping enzyme Dcp2 and forms a decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation . Yeast Dcp1 interact directly with Dcp2, however, the Dcp1-Dcp2 interaction is promoted by an additional factor, EDC4 . In the nervous system, it promotes neurons' lifespan through the negative regulation of the insulin-like peptide ins-7 expression .
Mesothelin (Mesothelin)
Type: Family

This family consists of several mammalian pre-pro-megakaryocyte potentiating factor precursor (MPF) or mesothelin proteins. Mesothelin is a glycosylphosphatidylinositol-linked glycoprotein highly expressed in mesothelial cells, mesotheliomas, and ovarian cancer, which participates in cell adhesion, tumour progression, metastasis, and drug resistance . This protein is predicted have superhelical structures with ARM-type repeats which suggests that it may act as superhelical lectins to bind the carbohydrate moieties of extracellular glycoproteins . Due to its overexpression in various tumours, it constitutes a diagnostic and therapy target .
Baculoviridae ME53 (Baculo_ME53)
Type: Family

ME53 is one of the major early-transcribed genes. The ME53 protein is reported to contain a putative zinc finger motif .
TIP49, P-loop domain (TIP49_P-loop)
Type: Domain

This entry represents the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the AAA ATPase, central region

domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway . TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases .
Herpesvirus UL11/UL32 (Herpes_UL11/UL32)
Type: Family

The large phosphorylated protein (UL32-like) of herpes viruses is the polypeptide most frequently reactive in immuno-blotting analyses with antisera when compared with other viral proteins .
Protein of unknown function DUF936, plants (DUF936_pln)
Type: Family

This family consists of several hypothetical proteins from plants. The function of this family is unknown.
Protein of unknown function DUF938 (DUF938)
Type: Family

This family consists of several hypothetical proteins from both prokaryotes and eukaryotes. Chordate members are known as 'methyltransferase-like 26'. The function of this family is unknown.
Aromatic acid exporter family member 1 (ArAE_1)
Type: Family

This family consists of bacterial proteins with three transmembrane regions that are purported to be aromatic acid exporters.
Exopolysaccharide biosynthesis protein YbjH (YbjH)
Type: Family

YjbH is a family of Gram-negative β-barrel outer-membrane lipoproteins that act as putative porins. YbjH is one of four gene-products expressed from an operon, yjbEFGH, which is regulated by the Rcs phosphorelay in a RcsA-dependent manner, similar to that of other exopolysaccharide biosynthetic pathways. It is highly possible that the yjbEFGH operon encodes a system involved in EPS secretion since none of the products is predicted to have enzymic activity, the products are all secreted and YbjH and F are predicted to be β-barrel lipoproteins similar to porins. It may be that the operon products play some role in biofilm formation and/or matrix production .
Interleukin-17 family (IL-17_fam)
Type: Family

Interleukins (IL) are a group of cytokines that play an important role in the immune system. They modulate inflammation and immunity by regulating growth, mobility and differentiation of lymphoid and other cells.

Interleukin-17 (IL-17) is a potent proinflammatory cytokine produced by activated memory T cells . The IL-17 family (of which there are 6 known members, termed IL-17A to IL-17F) is thought to represent a distinct signalling system that appears to have been highly conserved across vertebrate evolution . Family members play an active role in inflammatory diseases, autoimmune diseases and cancer .

This entry represents interleukin-17 family IL-17A to IL-17F. Interleukin-17E has been renamed as interleukin-25 (IL-25). The orthologue from the nematode Caenorhabditis elegans, known as interleukin cytokine-related protein 17.1, is a neuromodulator of sensory responses, and the ligand for the receptor complex composed of ilcr-1 and ilcr-2 .
Spanin, outer membrane subunit (O-spanin)
Type: Family

The lysis of Gram-negative hosts by double-strand DNA bacteriophages requires, in addition to the actions of a holin and endolysin, a third step involving the spanin complex. This complex consists of a small outer membrane lipoprotein and an integral cytoplasmic membrane protein, designated as o-spanins and i-spanins, respectively. The spanin complex is involved in the disruption of the outer membrane. Without the spanin function, lysis is blocked and progeny virions are trapped in dead spherical cells .

The first spanins to be characterised were phage lambda Rz and Rz1 . Rz corresponds to the inner membrane or i-spanin, whereas Rz1 represents the outer membrane or o-spanin. Rz and Rz1 (

) represent a unique example of two genes located in different reading frames in the same nucleotide sequence, which encode different proteins that are both required in the same physiological pathway . Rz and Rz1 form a disulfide-linked complex that spans the host inner and outer membranes .

This family consists of the outer membrane subunit from Lambdalikevirus and other phages and prophages.
Tyrosyl-DNA phosphodiesterase I (Tdp1)
Type: Family

Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 3'-phosphodiester bond, giving rise to DNA with a free 3' phosphate .
L-asparaginase II (Asparaginase_II)
Type: Family

This family consists of several bacterial L-asparaginase II proteins. L-asparaginase (

) catalyses the hydrolysis of L-asparagine to L-aspartate and ammonium. Rhizobium etli possesses two asparaginases: asparaginase I, which is thermostable and constitutive, and asparaginase II, which is thermolabile, induced by asparagine and repressed by the carbon source .
Thioredoxin-like ferredoxin, bacteria (Aim32/Apd1-like_bac)
Type: Family

This entry include a group of bacteria proteins that contain a ferredoxin-like fold and show protein sequence similarity to yeast Aim32/Apd1.
Protein of unknown function DUF943 (DUF943)
Type: Family

This family consists of several hypothetical membrane proteins mainly from Enterobacteria. Recently, it was proposed that members of this family along with members of [

] should be recognised as a putative toxin-antitoxin pair in which [

] is a homologue of Colicin M and [

] acts as its cognate immunity protein .
Protein of unknown function DUF945 (DUF945)
Type: Family

This entry consists of several hypothetical bacterial proteins of unknown function.
Phenol 2-monooxygenase, auxiliary component DmpK (DmpK)
Type: Family

This family consists of several bacterial phenol hydroxylase subunit proteins, which are part of a multicomponent phenol hydroxylase, including Phenol 2-monooxygenase, auxiliary component DmpK from Pseudomonas sp. DmpK may be involved in the post-translational incorporation of iron into the oxygenase component of the phenol hydroxylase .
Oleate hydratase (Oleate_hydratase)
Type: Family

Oleate hydratase catalyses the hydration of oleate at its cis-9-double bond to yield 10-hydroxyoctadecanoate. The hydration of unsaturated fatty acids is suggested to be a detoxification mechanism and a survival strategy for living in fatty acid-rich environments . It also appears to play a role in bacterial virulence .
Thioredoxin domain-containing protein 17-like domain (TXNDC17_dom)
Type: Domain

This domain can be found in thioredoxin domain-containing protein 17 (also known as TRP14), which is a highly conserved and ubiquitously expressed oxidoreductase involved in controlling of cellular redox signalling pathways. TXNDC17 has been shown to efficiently reduce l-cystine and can directly reactivate oxidized protein-tyrosine phosphatase PTP1B .
BRCA1-A complex subunit BRE (BRE)
Type: Family

Brain and reproductive organ-expressed (BRE, also known as BRCC45) is a component of the BRCA1-A complex, a complex that specifically recognises 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesions sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at double-strand breaks (DSBs) . It acts as an adapter that bridges the interaction between BABAM1/NBA1 and the rest of the complex, thereby being required for the complex integrity and modulating the E3 ubiquitin ligase activity of the BRCA1-BARD1 heterodimer . It is also part of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys-63'-linked ubiquitin in various substrates . Within the BRISC complex, it acts as an adapter that bridges the interaction between BABAM1/NBA1 and the rest of the complex, thereby being required for the complex integrity .
IrrE N-terminal-like domain (IrrE_HExxH)
Type: Domain

This entry includes the catalytic domain of the protein ImmA (MEROPS identifier M78.001), which is a metallopeptidase containing an HEXXH zinc-binding motif. ImmA is encoded on a conjugative transposon. Conjugating bacteria are able to transfer conjugative transposons that can, for example, confer resistance to antibiotics. The transposon is integrated into the chromosome, but during conjugation excises itself and then moves to the recipient bacterium and re-integrate into its chromosome. Typically a conjugative tranposon enodes only the proteins required for this activity and the proteins that regulate it. During exponential growth, the ICEBs1 transposon of Bacillus subtilis is inactivated by the immunity repressor protein ImmR, which is encoded by the transposon and represses the genes for excision and transfer. Cleavage of ImmR relaxes repression and allows transfer of the transposon. ImmA has been shown to be essential for the cleavage of ImmR .

This domain is also found in in metalloprotease IrrE, a central regulator of DNA damage repair in Deinococcaceae , HTH-type transcriptional regulators RamB and PrpC .
Protein of unknown function DUF956 (DUF956)
Type: Family

This is a family of bacterial sequences with undetermined function.
Domain of unknown function DUF959, collagen XVIII, N-terminal (DUF959_COL18_N)
Type: Domain

The function of this collagen XVIII N-terminal domain has not been characterised. It is not expressed in the 'short' isoform of collagen XVIII .
Uncharacterised protein family, inner membrane CreD (Uncharacterised_IM_CreD)
Type: Family

This family consists of several bacterial CreD or Cet inner membrane proteins. Dominant mutations of the cet gene of Escherichia coli result in tolerance to colicin E2 and increased amounts of an inner membrane protein with a Mr of 42,000. The cet gene is shown to be in the same operon as the phoM gene, which is required in a phoR background for expression of the structural gene for alkaline phosphatase, phoA. Although the Cet protein is not required for phoA expression, it has been suggested that the Cet protein has an enhancing effect on the transcription of phoA .
Protein of unknown function DUF961 (DUF961)
Type: Family

This entry consists of several hypothetical bacterial proteins of unknown function.
Arginine ADP-riboxanase OspC1-4 (OspC1-4)
Type: Family

This family represents Arginine ADP-riboxanase OspC1-4, found in Proteobacteria. OspC1-4 are ADP-riboxanase effectors that inhibit host cell pyroptosis .
Poxvirus G3 (Poxvirus_G3)
Type: Family

This entry represents G3 from Vaccinia virus, also called Entry-fusion complex protein OPG086, and similar proteins from poxvirus. G3 is a component of the entry fusion complex (EFC), which consists of 11 proteins. During cell infection, this complex mediates entry of the virion core into the host cytoplasm by a two-step mechanism consisting of lipid mixing of the viral and cellular membranes and subsequent pore formation .
Control of competence regulator ComK, YlbF/YmcA (Com_YlbF)
Type: Family

This entry consists of several relatively short bacterial and archaeal hypothetical sequences. It also includes YlbF and YmcA proteins which are involved in the formation of biofilms .

YlbF Is a family of short Gram-positive and archaeal proteins that includes both YlbF and YmcA which may interact synergistically. The family is necessary for correct biofilm formation, as null mutants of ymcA and ylbF fail to form pellicles at air-liquid interfaces and grow on solid media as smooth, undifferentiated colonies. During development, YmcA, YlbF and YaaT, family PSPI (

), interact directly with one another forming a stable ternary complex, in vitro. All three proteins are required for competence, sporulation and the formation of biofilms. The YmcA-YlbF-YaaT complex affects the phosphotransfer between Spo0F and Spo0B, thus accelerating the production of Spo0A~P. The three processes of biofilm formation, mature spore formation and competence all require the active, phosphorylated form of Spo0A, as Spo0A-P .
Protein SOSEKI (SOK)
Type: Family

This entry represents a group of plant-specific proteins, including protein SOSEKI 1-5 from Arabidopsis thaliana and Physcomitrium patens. SOSEKI proteins (SOK1-5) integrate apical-basal and radial organismal axes to localize to polar cell edges and contain a DIX oligomerization domain that resembles that in the animal Dishevelled polarity regulator .
YBR137W-like (YBR137W-like)
Type: Family

This entry represents a family of proteins from bacteria and some fungal species, including YBR137W from Saccharomyces cerevisiae (

). This protein may play a role in the regulation of tail-anchored (TA) protein targeting. It shows an antiparallel β-sheet made of four β-strands surrounded by seven α-helices .
DNA polymerase III delta, N-terminal (DNA_pol3_delta_N)
Type: Domain

This entry represents the N-terminal domain of the DNA polymerase III, delta subunit (

), which is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction . The delta subunit is also known as HolA.
Protein of unknown function DUF968 (DUF968)
Type: Family

This is a family of uncharacterised prophage proteins that are also found in bacteria. They have been predicted to have the His-Me finger nuclease domain and may act as a recombinase that participates in DNA repair and replication .
Protein of unknown function DUF969 (DUF969)
Type: Family

This is a family of uncharacterised bacterial membrane proteins.
Cyclic-di-AMP receptor (CdAMP_rec)
Type: Family

CdAMP is a family of bacterial cyclic-di-AMP receptor proteins. Cyclic-di-AMP (c-di-AMP) is a bacterial secondary messenger involved in various processes, including sensing of DNA-integrity, cell wall metabolism and potassium transport. CdAMP_rec has a ferredoxin-like fold and is structurally related to Pii-signal transduction proteins .
Gamma-butyrobetaine hydroxylase-like, N-terminal (GBBH-like_N)
Type: Domain

Gamma-butyrobetaine hydroxylase (GBBH/BBOX) is an alpha-ketoglutarate-dependent dioxygenase that catalyses the biosynthesis of L-carnitine by hydroxylation of gamma-butyrobetaine (GBB). GBBH is a dimeric enzyme. The monomer consists of a catalytic double-stranded β-helix domain and a smaller N-terminal domain. The N-terminal domain has a bound Zn ion, which is coordinated by three cysteines and one histidine. The N-terminal domain facilitates the assembly of a symmetric head-to-tail dimer formation through the interface with the C-terminal domain of the other monomer .

This is the N-terminal dimerisation domain found in gamma-butyrobetaine dioxygenases, Fe-S cluster assembly factor HCF101, TMAEP hydroxylase (TmpA) and trimethyllysine dioxygenase proteins. The N-terminal domains of TmpA and BBOX are structurally homologous, despite sharing less than 20% sequence identity. TmpA lacks the CxCxxCxxxH sequence motif required for metal binding, and a divalent cation is not observed in its N-terminal domain .
Replication initiation control protein YabA (YabA)
Type: Family

YabA is involved in initiation control of chromosome replication . It interacts with both DnaA and DnaN, acting as a bridge between these two proteins .
Trafficking protein particle complex subunit 13 (TRAPPC13)
Type: Family

Three transport protein particle (TRAPP) complexes exist in yeast (TRAPPI-TRAPPIII), which share a common core in addition to unique subunits. TRAPPI-TRAPPIII regulate endoplasmic reticulum (ER)-to-Golgi transport, intra-Golgi transport and autophagy, respectively. TRAPPC composition seems to be more complex in higher eukaryotes than in yeast, and its roles are less clear.

Mammalian TRAPPC13 is involved in regulating autophagy and survival in response to small molecule compound-induced Golgi stress . The overall architecture of TRAPPC is not disrupted upon TRAPPC13 depletion. This is also the case for yeast TRAPP II Trs65 subunit, which was previously reported to be specific to yeast. However, Trs65 has been shown to have homology to TRAPPC13 and they are now thought to be orthologues . This entry consists of high eukaryotes TRAPPC13 and some related yeast proteins, but it does not include S. cerevisiae Trs65 (see

).
Septation ring formation regulator EzrA (EzrA)
Type: Family

During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation .
Protein of unknown function DUF975 (DUF975)
Type: Family

This is a family of uncharacterised bacterial proteins.
Putative pyroglutamyl peptidase 1 (PgaPase_1)
Type: Family

This is a family of functionally diverse Caenorhabditis proteins. The family is homologous to the cysteine-peptidases, but lack of a strictly conserved Glu-Cys-His catalytic triad or pGlu binding site implies that it has other functions that could have resulted in a change in reaction-specificity or even of catalytic activity .