SII-SWORD/CoKE huggingface dataset:
MasK-like C-terminal domain (MasK-like_C)
Type: Domain

This entry represents a C-terminal domain identified in the Tyrosine-protein kinase MasK (

) and related bacterial proteins. Proteins containing this domain also include the adventurous gliding motility proteins AgmX (GltJ) and PglI in M. xanthus. This domain spans approximately 92 amino acids and contains a pair of Cys residues frequently separated by about 45 amino acids .
DpdD-like (DpdD-like)
Type: Family

This entry represents DpdD protein (

) from Salmonella montevideo and related bacterial proteins. The 7-deazapurine derivatives, 2'-deoxy-7-cyano-7-deazaguanosine (dPreQ0) and 2'-deoxy-7-amido-7-deazaguanosine (dADG) are recently-discovered DNA modifications encoded by the dpd cluster found in a diverse set of bacteria . Amongst the genes in this gene cluster, dpdD and possibly dpdJ appear to be involved in a restriction-like phenotype. The dpdD gene is present alongside the helicase-like genes and putative DNA-binding genes and therefore DpdD could be involved in the restriction system .
CONSTANS-like, B-box-type 1 zinc finger (CONSTANS-like_Bbox1)
Type: Domain

This entry includes a group of plant sequences which belong to the BBX family, a group of zinc finger transcription factors that contain one or two B-box motifs, and sometimes also feature a CCT (CONSTANS, CO-like, and TOC1) domain. They play important roles in plant growth and development, including seedling photomorphogenesis, photoperiodic regulation of flowering, shade avoidance, and responses to biotic and abiotic stresses . Their B-box motifs show high sequence similarity with B-Box-type 1 zinc finger found in tripartite motif-containing proteins (TRIMs) and are involved in mediating transcriptional regulation and protein-protein interaction in plant signaling .

The type 1 B-box (Bbox1) zinc finger is characterised by a C6H2 zinc-binding consensus sequence motif. This family adopts a canonical B-box fold and coordinates two zinc atoms

but contains a modified motif, C3XC2H2, where X can be D, E, C or H .
YehF/YfeS-like, WGR domain (YehF/YfeS-like_WGR)
Type: Domain

This entry represents the WGR domain found in Escherichia coli YehF and YfeS, and related uncharacterised bacterial proteins. YehF was first described as a putative molybdate metabolism regulator , however, this role hasn't been confirmed. YehF has been implicated in selenate reduction .

This domain appears to occur in single-domain proteins and in a variety of domain architectures, together with ATP-dependent DNA ligase domains, WD40 repeats, leucine-rich repeats, and other domains. It has been proposed to function as a nucleic acid-binding domain.
Pyocin S6 toxin immunity protein-like (S6_alt_immun-like)
Type: Family

This entry represents Pyocin S6 toxin immunity protein from Pseudomonas aeruginosa and related proteins mainly from Pseudomonas species. The S6 toxin immunity gene is always found adjacent or close to genes encoding proteins containing ribonuclease domain (

) of 16S rRNA-cleaving colicin E3 and pyocin S6 family toxins. High basal expression of the immunity gene protects the pyocin-producing cell against invading pyocins, and in addition, ensures that it can rapidly respond to changing conditions .
MJ1673-like domain (MJ1673-like_dom)
Type: Domain

This entry represents a domain found in uncharacterised protein MJ1673 (

) from Methanocaldococcus jannaschii and related prokaryotic proteins. This domain is found mainly standalone. In a number of bacterial CRISPR-associated proteins, it is also found in combination with CRISPR system endoribonuclease Csx1, HEPN domain (

).
DpdG-like (DpdG-like)
Type: Family

This entry represents DpdG protein (

) from Salmonella montevideo and related bacterial proteins. The 7-deazapurine derivatives, 2'-deoxy-7-cyano-7-deazaguanosine (dPreQ0) and 2'-deoxy-7-amido-7-deazaguanosine (dADG) are recently-discovered DNA modifications encoded by the dpd cluster found in a diverse set of bacteria . Amongst the genes in this gene cluster, dpdG appear to be involved in a restriction-like phenotype .
Echinoderm microtubule-associated protein-like elp-1, trimerization domain (Elp-1-like_TD)
Type: Domain

This entry corresponds to a conserved trimerization domain located at the N-terminal of Elp-1 and similar sequences.

This entry includes the echinoderm microtubule-associated protein-like elp-1 from C.elegans and related sequences mainly from nematodes and arthropods. Elp-1 belongs to the echinoderm microtubule-associated protein (EMAP)-like (EML) family which is involved in the modulation of the assembly and organization of the microtubule cytoskeleton, probably playing a role regulating the orientation of the mitotic spindle and the orientation of the plane of cell division. It is required for normal proliferation of neuronal progenitor cells in the developing brain and for normal brain development .
Response regulator WalK (Resp_reg_WalK)
Type: Family

This entry represents transcriptional regulatory protein WalK from Bacillus subtilis (also known as YycG) (

) and similar proteins predominantly found in firmicutes.

The WalK protein, alongside its response regulator WalR, is a member of the two-component regulatory system WalK/WalR, involved in the regulation of the ftsAZ operon, the yocH, ykvT, cwlO, lytE, ydjM, yjeA, yoeB genes and the tagAB and tagDEF operons. It is essential for cell wall metabolism, virulence regulation, and biofilm production, among many other cellular processes .
MgtR-like (MgtR-like)
Type: Family

This entry represents MgtR protein from Salmonella enterica and related proteins from Enterobacterales. MgtR is a hydrophobic peptide, which is encoded by the mgtCB operon. It was shown to interact with the MgtC virulence protein and to promote the MgtC degradation by the FtsH protease . Overexpression of the MgtR peptide leads to a decrease of the replication rate of Salmonella. The MgtA Mg2 transporter is another protein under the direct control of the MgtR peptide and lack of MgtR enhances Salmonella growth in low Mg2 .
Maintenance of carboxysome distribution protein B (McdB)
Type: Family

This entry contains the maintenance of carboxysome distribution (Mcd) protein B (McdB), also called maintenance of carboxysome positioning B protein (McsB). It is found in cyanobacteria, where carboxysome maintenance is mediated by a DNA partition-like ParA-ParB system called the McdA-McdB. In order to actively position carboxysomes, McdB binds directly to McdA, a putative Walker-box ParA-like protein. McdB harbors a unique α-helical fold and it enables McdA dimer formation

.
Encapsulin nanocompartment shell protein 2B (Encap_f2b)
Type: Family

This entry represents a family of capsid-like encapsulin nanocompartment shell proteins (type 2B) commonly found in bacteria. Encapsulin nanocompartments, which are assembled from shell proteins, encapsulate various cargo proteins, typically peroxidases or ferritin-like proteins, to protect cells from oxidative stress caused by peroxide .
Expansin EXLX1-like (Expansin_EXLX1-like)
Type: Family

This entry represents the EXLX1 family as it is found in Bacillus subtilis (expansin YoaJ) (

) and related proteins. Expansins are cellulose-binding proteins capable of facilitating bacterial colonisation of plant roots . YoaJ structure consists of 2 tightly packed domains (D1, D2). Domain D1 has a double-psi β-barrel fold with partial conservation of the catalytic site found in family 45 glycosyl hydrolases and in the MltA family of lytic transglycosylases. Domain D2 has an Ig-like fold similar to group 2/3 grass pollen allergens, with structural features similar to a type A carbohydrate-binding domain

. YoaJ binds ligands through hydrophobic interactions of three linearly arranged aromatic residues in domain D2

.
SP_0009-like (SP_0009-like)
Type: Family

This entry represents the SP_0009 protein (

) from Streptococcus pneumoniae and related proteins found in Streptococcus species. The function of these proteins is unknown.
Transporter small subunit-like (Trnsprt_adja_ssu-like)
Type: Family

Members of this family are very small, highly hydrophobic proteins regularly encoded adjacent to transporters. They are likely to be previously overlooked small subunits of transporters. Members of this family are found in actino- and proteobacteria. Their function is unknown.
DnaE1-like, PHP domain (PolIIIA_DnaE1_PHP)
Type: Domain

DNA polymerase III alpha subunits (PolIIIAs) that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, standalone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterised protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. PolIIIA core enzyme catalyses the reaction for polymerising both DNA strands. DnaE1 is the longest compared to DnaE2 and DnaE3. A unique motif was also identified in dnaE1 and dnaE3 genes .

This entry represents the PHP domain of DnaE1 type of the DNA polymerase III alpha subunit.
Encapsulin nanocompartment shell protein 2A (Encap_f2a)
Type: Family

This entry represents a family of capsid-like encapsulin nanocompartment shell proteins (type 2A) found in bacteria. Encapsulin nanocompartments, which are assembled from shell proteins, encapsulate various cargo proteins, typically peroxidases or ferritin-like proteins, to protect cells from oxidative stress caused by peroxide .
Exosortase H-associated membrane protein (XrtH_assoc)
Type: Family

This entry represents a family of uncharacterised proteins frequently encoded adjacent to exosortase H (XrtH). Members of this family are found mainly in proteobacteria. Their function is unknown.
RtxA toxin-like, peptidase C80 cysteine binding domain (RtxA-like_C80)
Type: Domain

This entry represents the autoproteolytic cysteine protease domain (CPD) of Vibrio cholerae multifunctional autoprocessing repeats-in-toxin (MARTX) toxin (

), a member of the peptidase C80 family that causes disassembly of the actin cytoskeleton and enhances V. cholerae colonization of the small intestine, possibly by facilitating evasion of phagocytic cells. The central region of this toxin is composed of several domains, including the actin cross-linking domain (ACD) that introduces lysine-glutamate cross-links between actin protomers, the Rho-inactivating domain (RID) that disables small Rho GTPases, and an autoprocessing cysteine protease domain (CPD). Within the cell, the CPD is activated by the binding of inositol hexakisphosphate to release individual effector domains of the toxin into the cytosol. The CPD contains the characteristic Cys/His residues in the active site .
Lasso peptide paeninodin-like (Lasso_PadeA-like)
Type: Family

This entry represents the homologues of lasso peptide paeninodin from Paenibacillus dendritiformis (

). Members of this family are found mainly in Bacillales species. Within the paeninodin biosynthetic cluster is a gene encoding a class of lasso peptide-tailoring kinases . This kinase specifically phosphorylates the C-terminal serine residue of paeninodin.

Lasso peptides are a class of ribosomally synthesised and post-translationally modified peptides (RiPPs) . Up to date, they have been only isolated from proteo- and actinobacterial sources. Typically, lasso peptide biosynthetic gene clusters encode enzymes for biosynthesis and export but not for tailoring. A wide range of interesting biological activities are known for these RiPPs, including antimicrobial, enzyme inhibitory, and receptor antagonistic activities. Generally, all known lasso peptides carry a Gly, Ala, Cys, or Ser residue at position 1 and a ring-forming Glu or Asp residue at positions 7-9. Their respective processing enzymes are highly specific for the nature and location of these residues .
Ig-like Ice domain (Ig-like_ice)
Type: Domain

This entry represents an immunoglobulin-like domain found mainly in Gammaproteobacteria. Thig Ig-like domain occurs as a repeat in a number of large adhesins, including a 1.5-MDa ice-binding adhesin, the Marinomonas primoryensis antifreeze protein .
N-acetylneuraminate anomerase NanQ (NanQ)
Type: Family

This entry represents N-acetylneuraminate anomerase NanQ (previously known as YhcH) family mainly found in Gammaproteobacteria (

). NanQ plays a role in sialic acid catabolism by opening both the α- and β-forms of N-acetylneuraminate (sialic acid; Neu5Ac) to provide aceneuramate, the preferred substrate for the sialic acid aldolase (NanA) . It has a preferential activity on the β-anomer rather than the α-anomer.
Diguanylate cyclase DgcJ (DgcJ_diguan)
Type: Family

This entry represents the diguanylate cyclase (DgcJ,

) found in Escherichia coli and related proteins from Enterobacterales species. DgcJ protein is involved in the pathway 3',5'-cyclic di-GMP biosynthesis, which is part of Purine metabolism .
Alpha-(1->6)-mannopyranosyltransferase A/B-like (MptA/B-like)
Type: Family

This entry represents the homologues of alpha-(1->6)-mannopyranosyltransferases A (MptA) and B (MptB). Proteins of this family are found mainly in Actinomycetes. Members of this family are involved in the initiation of core alpha-(1,6) mannan biosynthesis of lipomannan (LM-A) and multi-mannosylated polymer (LM-B), extending triacylatedphosphatidyl-myo-inositol dimannoside (Ac1PIM2) and mannosylated glycolipid, 1,2-di-O-C16/C18:1-(alpha-D-mannopyranosyl)-(1->4)-(alpha-D-glucopyranosyluronic acid)-(1->3)-glycerol (Man1GlcAGroAc2), respectively.
NADP-reducing hydrogenase subunit HndD (HndD)
Type: Family

This entry represents NADP-reducing hydrogenase subunit HndD from Solidesulfovibrio fructosivorans and similar sequences mainly found in bacteria. HndD is a component of a heterotetramer consisting of HndA, HndB, HndC, and HndD subunits, with HndD likely serving as the hydrogenase subunit .
UGSC-motif contining selenoprotein (UGSC_seleno)
Type: Family

This family includes selenoproteins containing a UGSC motif, and non-selenoproteins with a CGSC motif. Selenocysteine (Sec or U) is encoded by UGA, a stop codon reassigned by a Sec-specific elongation factor and a distinctive RNA structure . The function of these UGSC/CGSC-motif containing proteins is unclear.
BREX system serine/threonine kinase PglW (BREX_PglW)
Type: Family

This entry includes the probably kinase PglW from Streptomyces coelicolor (

) and related sequences mainly from actinomycetes. PglW is a predicted serine/threonine kinase of the Pgl (phage growth limitation) system (now called BREX type 2) and the BREX type 3 system .
Small membrane protein KPN01023-like (KPN01023-like)
Type: Family

Members of this family, including paralogues KPN_01023 (

) and KPN_01923 (

) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578, are small proteins, typically about 40 amino acid residues in length. They contain a highly hydrophobic region with a composition typical of transmembrane segments, followed by a highly basic region. Analogous proteins of similar size, with apparently similar hydrophobic regions, have been described as membrane-associated proteins expressed in response to various types of cell envelope stress. The function of these proteins is unknown.
D-ornithine 4,5-aminomutase subunit beta-like (OraE-like)
Type: Family

This entry represents D-ornithine 4,5-aminomutase subunit beta from Acetoanaerobium sticklandii (OraE) and similar bacterial sequences. OraE is component of a complex that catalyses the reversible migration of the omega amino group of D-ornithine to C-4 to form (2R,4S)-2,4-diaminopentanoic acid. OraE may be the catalytic subunit. Active only on D-ornithine and 2,4-diaminopentanoic acid but not active on L-ornithine, L-beta-lysine, L-alpha-lysine or D-alpha-lysine .
Sensor histidine kinase RppB (RppB)
Type: Family

This entry represents Sensor histidine kinase RppB from Synechocystis sp. (

) and similar proteins from cyanobacterial species. RppB is member of two-component regulatory system RppA/RppB, involved in the establishment of the appropriate stoichiometry between the 2 photosystems. It senses changes in the plastoquinone (PQ) redox poise . It has also been reported that the RppA/RppB two-component pair (also known as NrsR/NrsS) regulates the nickel-dependent expression of the nrsBACD operon . It has been suggested that the photosystem-related activities are a result of the expression of NrsS (formerly RppB) in the absence of its natural substrate NrsR (formerly RppA) .
Peptidoglycan endopeptidase RipA (RipA)
Type: Family

This entry represents the Peptidoglycan endopeptidase RipA found exclusively in Mycobacteriales. RipA is a peptidoglycan endopeptidase that cleaves the bond between D-glutamate and meso-diaminopimelate . It binds and degrades high-molecular weight peptidoglycan from a number of Actinobacteria and its activity is increased in the presence of RpfB and inhibited by PBP1A (ponA1). RipA is required for normal separation of daughter cells after cell division and for cell wall integrity. RipA is also required for host cell invasion and intracellular survival in host macrophages .
Transposon-encoded protein TnpC-like (TnpC_reg-like)
Type: Family

This entry represents the transposon-encoded protein TnpC from Pseudomonas putida and related proteins found in beta- and gammaproteobacteria. TnpC downregulates the expression of transposase TnpA and interferes with its regulation at the post-transcriptional level .
D-xylose 1-dehydrogenase XacA-like (XacA-like)
Type: Family

This entry represents the XacA family found in Haloferax volcanii (

) and related species. XacA is a NADP-dependent D-xylose dehydrogenase involved in the degradation of D-xylose (major component of hemicelluloses such as xylan) . This family also includes the Gfo6 protein from Haloarcula marismortui (

) which catalyses the initial reaction in the xylose utilisation pathway by oxidising D-xylose into D-xylonolactone .
Lmo0850-like (Lmo0850-like)
Type: Family

This entry represents the uncharacterised protein Lmo0850 (

) from Listeria monocytogenes and related proteins found in bacillales. The function of these proteins is unknown, but the sRNA LhrA sRNA regulates expression of Lmo0850 in L. monocytogenes by negatively regulating the stability of its mRNA. The regulation depends on Hfq and involves an antisense interaction .
FlgM-associated protein DVU0524-like (DVU0524-like)
Type: Family

This entry represents the uncharacterised protein DVU0524 (

) from Desulfovibrio vulgaris and related proteins found mainly in thermodesulfobacteria. Members of this family are frequently found adjacent to the flagellar biosynthesis anti-sigma factor FlgM, which is a much more broadly distributed family (

). The nature of the relationship between these two proteins, other than their co-operonic co-occurrence, is unknown.
VPA1267-like (VPA1267-like)
Type: Family

This entry represents the uncharacterised protein VPA1267 (

) from Vibrio parahaemolyticus and related proteins found in proteobacteria. Members of this family occur in mobile elements, as for VPA1267 found in pathogenicity island 6 of Vibrio parahaemolyticus RIMD2210633 .
3-dehydro-scyllo-inosose hydrolase IolN (Diketo_inos_hlase_IolN)
Type: Family

This entry represents the 3-dehydro-scyllo-inosose hydrolase (IolN,

) from Thermotoga maritima and related prokaryotic proteins. IolN catalyses the ring-opening hydrolysis of 3-dehydro-scyllo-inosose (diketo-inositol) to 5-dehydro-L-gluconate, and thus probably functions in a myo-inositol degradation pathway together with IolG, IolM and IolO .
Zinc piracy TonB-dependent receptor ZnuD (ZnuD)
Type: Family

This entry represents a family of proteins from Acinetobacter, including the Zinc piracy TonB-dependent receptor ZnuD from Acinetobacter baumannii. ZnuD collaborates with the zinc uptake transporter ZnuABC to counteract the host's sequestration of zinc. ZnuD acquires zinc by intercepting it from the host protein calprotectin .
RsaX20-like (RsaX20-like)
Type: Family

Members of this family average just 38 amino acids in length, but are widely conserved among species of Gram-positive firmicutes. Expression of an RNA designated RsaX20, which encodes a member of this family, was studied in a Staphylococcus aureus of possible structural RNAs, and shown to be controlled by Fur-like transcription factor Zur. The broad conservation of the coding region across multiple species and protein-like pattern of amino acid substitutions in multiple sequence alignments strongly suggests that that members of this family are indeed translated into functional proteins .
Conjugative relaxosome accessory protein SAG1252-like (Tn5252_Orf10-like)
Type: Family

This entry represents SAG1252 protein (also known as Tn5252, Orf 10 protein,

) from Streptococcus agalactiae and related proteins from lactobacillales. SAG1252 is a member of the Tn5252 ORF10 family which occurs in mobile elements from a class associated with the movement of bacteriocins and antibiotic resistance proteins in Streptococcus .
NF038105-like (NF038105-like)
Type: Family

This family of small proteins, about 66 amino acid residues long, appears to be restricted to Acinetobacter. The function of these proteins is unknown.
CrpP-related (CrpP-rel)
Type: Family

This entry represents a family of uncharacterised proteins found in alpha- and betaproteobacteria. Members of this protein family show sequence similarity, and apparently homology, to a family of integrative and conjugative element (ICE) proteins that has the founding member CrpP. Although CrpP, a protein about 65 aminos in length, was originally described as ciprofloxacin-inactivating enzyme that works by phosphorylation, that assertion has since been challenged .
Type IVa secretion system protein TapY2-like (TapY2-like)
Type: Family

Members of this family, found exclusively in gammaproteobacteria, are about 100 amino acid residues in length and include two invariant Cys residues. The family is named for TapY2 (Type IV Aeromonas Pilus Y2), which has been described as the counterpart to PilY2 from the type IVa pilus system Pil in Pseudomonas aeruginosa . However, sequence similarity between TapY2 and PilY2 is very low, and is not certain to represent a true homology.
LPFR-motif containing-like (LPFR_strepto)
Type: Family

This entry describes a family of uncharacterised small, hydrophobic proteins that are widespread in Streptomyces. Multiple sequence alignment shows a well-conserved sequence motif VTLPFRxxARLF. The function of these proteins is unknown.
Holdfast attachment protein HfaA (Holdfast_HfaA)
Type: Family

This entry represents the Holdfast attachment protein A (HfaA,

) from Caulobacter vibrioides and related proteins from alphaproteobacteria. HfaA is involved in attachment of the holdfast to the cell. The holdfast is a structure that allows the bacteria to firmly adheres to surfaces. The holdfast biosynthesis and secretion machinery are encoded by two major loci, hfsEFGH and hfsDABC. The hfsDAB genes encode a secretion protein complex believed to span the inner and outer membrane of the cell envelope. Deletion of any of the components of this complex results in holdfast shedding and decreased adherence and biofilm formation .
YpfM-like (YpfM-like)
Type: Family

Members of this family average just 19 amino acids in length, but are widely conserved among species of Enterobacterales, including the uncharacterised protein YpfM from Escherichia coli (

). The broad conservation of the coding region across multiple species and protein-like pattern of amino acid substitutions in multiple sequence alignments strongly suggests that that members of this family are indeed translated into functional proteins .