SII-SWORD/CoKE huggingface dataset:
Extracellular matrix-binding protein Ebh domain (Ebh_dom)
Type: Domain

Staphylococcal protein Ebh (extracellular matrix-binding protein homolog) is a giant protein, sometimes over 10,000 amino acids long . Ebh from Staphylococcus aureus promotes bacterial attachment to both soluble and immobilised forms of fibronectin (Fn), in a dose-dependent and saturable manner . This entry represents a non-repetitive amino-terminal domain of about 2400 amino acids found in Ebh proteins.
DEXH box helicase, DNA ligase-associated (DEXH_lig_assoc)
Type: Family

Members of this protein family are DEAD/DEAH box helicases found associated with a bacterial ATP-dependent DNA ligase, part of a four-gene system that occurs in about 12 % of prokaryotic reference genomes. These proteins have the motif DE[VILW]H.
CxxC-x17-CxxC domain (CxxC-x17-CxxC_dom)
Type: Domain

This domain, with a pair of CXXC motifs separated by 17 amino acids, is a candidate zinc finger domain based on these motifs. Some proteins have two copies of the domain, while others are fused to another probable zinc-binding domain.
Ax21 family (Ax21)
Type: Family

This family consists of proteins closely related to Ax21. Ax21 was thought to be secreted by a type I-secretion system and to activate XA21-mediated immunity. Later, it was found that Ax21 secretion does not depend on the predicted type I secretion system and that it is processed by the general secretion (Sec) system. In fact, Ax21 is an outer membrane protein, secreted in association with outer membrane vesicles . It does not trigger plant XA21-mediated immune response, as previously thought . This role is performed by RaxX .
Phage-associated protein, BcepMu gp16 family (BcepMu_gp16)
Type: Family

Members of this protein family occur in Burkholderia phage BcepMu, Pseudomonas phage B3, and Burkholderia phage KS10, and many bacterial putative prophage regions. The member from Burkholderia phage BcepMu is named gp16. Homology suggests DNA-binding activity.
Putative selenium metabolism protein, YedE family (Seleno_YedE)
Type: Family

This entry represents YedE putative selenium metabolism proteins. This family is less widespread than YedF, which is also involved in selenium metabolism . Most proteins belonging to this group carry a Sulphur transport domain (

)
FxsC, C-terminal domain (FxsC_C)
Type: Domain

This entry represents a region found regularly as the C-terminal domain of some FxsC proteins from actinomycetes (where the N-terminal domain resembles a TIR domain - see

). FxsC proteins occur in the vicinity of a proposed peptide-modifying radical SAM/SPASM domain protein, FxsB (

). The first characterised member of the FxsB family was shown to cyclise Phe to Ser in the C-terminal motif FxSxx-COOH of FxsA family RiPP precursors. FxSxx-COOH modification systems appear to be involved in cell-cell interactions such as biological conflict systems .
SWIM/SEC-C metal-binding motif protein, PBPRA1643 (SWIM_PBPRA1643)
Type: Family

Members of this protein family have a SWIM, or SEC-C, motif (

, a 21-amino acid putative Zn-binding domain that is shared with SecA, plant MuDR transposases, etc. This small protein family of unknown function occurs primarily in marine bacteria .
CxxC-20-CxxC putative zinc finger (CxxC_20_CxxC)
Type: Family

This small, uncommon, poorly conserved protein is found primarily in the Firmicutes. It features are pair of CxxC motifs separated by about 20 amino acids, followed by a highly hydrophobic region of about 45 amino acids. It has no conserved gene neighbourhood, and its function is unknown.
Squalene-tetrahymanol cyclase THC1 (Tetrahymanol_synth_THC1)
Type: Family

This entry includes squalene-tetrahymanol cyclase THC1 from a small number of eukaryotes, some of them anaerobic. The pathway can occur under anaerobic conditions, and the product is thought to replace sterols, letting organisms with this compound build membrane suitable for performing phagocytosis. It catalyses the oxygen-independent cyclization of squalene into tetrahymanol, a triterpenoid sterol with five cyclohexyl rings that is involved in membrane integrity, permeability and fluidity ,

].
PGF-CTERM archaeal protein-sorting signal (PGF_CTERM)
Type: Domain

This entry represents a strictly archaeal putative protein-sorting motif, PGF-CTERM. It is the (predicted) recognition sequence for an exosortase homologue, archaeosortase. In some archaea, up to fifty proteins have this domain as their C-terminal region, usually preceded by a Thr-rich region that typically is heavily glycosylated. The sorting signal removal depends on ArtA, a cysteine peptidase, in a process shown to be required for a C-terminal prenyl group attachment in the halobacterial major cell surface glycoprotein, an S-layer protein. However, it remains unclear if ArtA acts as a transpeptidase, like the analogous though unrelated sortase enzyme SrtA, or if lipid attachment is mediated by a separate protein .
S-adenosylmethionine-dependent nucleotide dehydratase RSAD2 (RSAD2)
Type: Family

S-adenosylmethionine-dependent nucleotide dehydratase RSAD2, also known as viperin (Virus Inhibitory Protein, ER-associated, Iterferon-inducible) is a radical SAM enzyme found in human and other vertebrates. It is both induced by interferon and demonstrably active in blocking replication by several types of virus, apparently by modifying lipid chemistries in lipid droplets and membrane rafts .

Human viperin is involved in antiviral defense, playing a major role in the cell antiviral state induced by type I and type II interferon . It catalyses the conversion of cytidine triphosphate (CTP) to 3'-deoxy-3',4'-didehydro-CTP (ddhCTP) via a SAM-dependent radical mechanism [

, . The resulting ddhCTP acts as a chain terminator for the RNA-dependent RNA polymerases from multiple viruses and directly inhibits viral replication . It displays antiviral effect against a wide range of DNA and RNA viruses, such as HIV-1 virus, hepatitis C virus, human cytomegalovirus, and alphaviruses, but not vesiculovirus .
Seadornavirus VP5/VP6 protein (VP5/VP6)
Type: Family

This protein family occurs in the seadornavirus virus group, with designations VP5 in Banna virus, and VP6 in Kadipiro virus and Liao ning virus. The function is unassigned .
PEP-CTERM protein sorting domain, cyanobacterial subclass (Cyano_PEP)
Type: Domain

This entry represents the PEP-CTERM protein sorting signals associated with bacterial exosortases. This entry is restricted to Cyanobacteria, including the genera Cyanothece, Nostoc, Trichodesmium, Lyngbya, Arthospira, etc. Cyanobacteria PEP-CTERM features strongly conserved residues within the transmembrane region, including a Gx4GxG motif. The corresponding cyanobacterial form of exosortase found in most species with this domain is described in

.
Putative radical SAM-modified peptide (rSAM_modified_put)
Type: Family

This family of short peptides occurs near radical SAM/SPASM domain proteins and is proposed to be modified by that enzyme.
Cell surface SprA (Cell_surface_SprA)
Type: Family

SprA is a cell surface protein widely distributed in the Bacteroidetes lineage. In Flavobacterium johnsoniae, a species that shows gliding motility, mutation disrupts gliding .
Seadornavirus VP11 protein (Seadorna_VP11)
Type: Family

This protein family occurs in the seadornavirus virus group, with designations VP11 in Banna virus, and VP12 in Kadipiro virus and Liao ning virus . The function has not been assigned.
Seadornavirus VP3 protein (Seadorna_VP3)
Type: Family

Members of this protein family are VP3 proteins in the seadornavirus group . They display sequence similarity to methyltransferases. Viral guanylyltransferase VP3 from Banna virus is an outer capsid protein involved in mRNA capping, catalysing the final three activities (RNA guanylyltransferase, RNA-7N-methyltransferase and RNA-2'O-methyltransferase) required for the formation of 5' cap structure .
Seadornavirus VP8 protein (Seadorna_VP8)
Type: Family

This protein family occurs in the seadornavirus virus group, with designations VP8 in Banna virus, and VP9 in Kadipiro virus and Liao ning virus . VP8 from Banna virus is part of the inner core, within the outer coat of the virus. The inner core contains VP1, VP2, VP3, VP8 and VP10, with VP8 forming the core-surface layer, an icosahedral capsid with a T=13 symmetry, consisting of 230 trimers .
RNA-directed RNA polymerase (Seadorna_RNAP)
Type: Family

Members of this protein family include the seadornavirus VP1 protein, the RNA-directed RNA polymerase.
RNA endonuclease, cap-snatching, arenaviral (CapSnatch_arenavir)
Type: Domain

This entry represents a domain from an RNA endonuclease region associated with cap-snatching for mRNA production by RNA viruses . This domain usually is part of a multifunctional protein, the L protein responsible for RNA-dependent RNA polymerase activity. Cap-snatching is a viral alternative to synthesizing a eukaryotic-like mRNA cap itself . This group of proteins is specific to arenavirales.
Seadornavirus VP4 protein (Seadorna_VP4)
Type: Family

This protein family occurs in the seadornavirus virus group, with designation VP4 in Banna virus, Kadipiro virus, and Liao ning virus . Although this family has been suggested to resemble methyltransferases, members show apparent N-terminal sequence similarity to the outer capsid protein VP5 of the orbivirus group, such as bluetongue virus, which also belong to the Reoviridae.
Seadornavirus VP2 protein (Seadorna_VP2)
Type: Family

This protein family occurs in the seadornavirus virus group, with the designation VP2 in Banna virus, Kadipiro virus, and Liao ning virus .
Aminotransferase LegC-like (LegC-like)
Type: Family

This entry represents LegC from Campylobacter jejuni and similar bacterial sequences. LegC is an enzyme in the biosynthesis pathway for CMP-legionaminic acid, the activated form of a 9-carbon sugar related to sialic acid and pseudominic acid .
Outer membrane protein (OMP_w_GlyGly)
Type: Family

Members of this protein family are outer membrane proteins (OMP), as can be seen by their homology to YfaZ protein and by the OMP targeting region at the C terminus, including a C-terminal Phe residue. Members of this protein family are found in the great majority of genomes with the GlyGly-CTERM protein sorting signal and the rhombosortase putative sorting enzyme, although the relationship may be fortuitous.
Seadornavirus double-stranded RNA-binding protein (Seadorna_dsRNA-bnd)
Type: Family

This protein family occurs in the seadornavirus virus group. Family members have an N-terminal domain for binding double-stranded RNA and are designated VP12 in Banna virus, VP8 in Kadipiro virus, and VP11 in Liao ning virus .
Protein translocase subunit SecA, Actinobacteria-type (SecA_Actinobact-type)
Type: Family

Members of this family are the SecA subunit of the Mycobacterial type of accessory secretory system. This family is quite different to SecA of the Staph/Strep type .
NAD-dependent 4,6-dehydratase LegB-like (LegB-like)
Type: Family

This entry is characterised by inclusion of its members within a cassette of seven distinctive enzymes. These include four genes homologous to the elements of the neuraminic (sialic) acid biosynthesis cluster (NeuABCD), an aminotransferase and a nucleotidyltransferase in addition to the epimerase/dehydratase. Together it is very likely that these enzymes direct the biosynthesis of a nine-carbon sugar analogue to CMP-neuraminic acid. Family member LegB (BFO_1074) from Tannerella forsythia was shown to act on GDP-GlcNAc at the start of a legionaminic acid biosynthesis pathway .
CRISPR-associated protein GSU0052/csb3, Dpsyc system (Cas_GSU0052)
Type: Family

This entry represents a CRISPR-associated (cas) protein unique to the Dpsyc subtype (named for Desulfotalea psychrophila), although not universal to the that subtype. Members of this family occur in CRISPR loci of Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, Rhodospirillum centenum SW, Planctomyces limnophilus DSM 3776, and Methylosinus trichosporium OB3b.
Exosortase/Archaeosortase domain (Exo/Archaeosortase_dom)
Type: Domain

This entry represents the most conserved region of the multitransmembrane protein family of exosortases and archaeosortases. The region includes nearly invariant motifs at the ends of three predicted transmembrane helices on the extracytoplasmic face: a Cys (often Cys-Xaa-Gly), Asn-Xaa-Xaa-Arg, and His .
Modification target Cys-rich repeat (tSAM_targ_Cxxx_rpt)
Type: Repeat

This entry represents a cysteine-rich repeat found in a number of bacterial putative radical-SAM modified natural product precursors .
Streptococcal surface-anchored protein repeat (RPT_S_cricet)
Type: Repeat

This entry represents a repeat sequence that occurs primarily in LPXTG-anchored Streptococcus surface proteins, although it does occur elsewhere. It can comprise a major fraction of the length of repeat proteins that exceed 2000 amino acids in length. This repeat is flanked by collagen-like CXX motifs.
CshA domain (CshA_fibril)
Type: Domain

This entry represents a domain that is found in a variety of bacterial cell surface proteins. Many proteins with this domain have a C-terminal LPXTG anchor. The best studied protein containing this domain is the CshA adhesin protein from Streptococcus gordonii that contains 17 tandem copies of the domain . The S. gordonii fibrillar adhesin CshA plays an important role in host colonization. The structure of the CshA domain shows a variant of the immunoglobulin fold lacking the typical A and B strands .
Bunyavirus nonstructural protein NSm (Bunya_nonstruc_pro_NSm)
Type: Domain

This entry represents a protein region that is cleaved from a bunyavirus polyprotein to become the nonstructural protein NSm (encoded by the M segment). This region is flanked by glycoprotein Gn (also known as GP2) and glycoprotein Gc (also known as GP1), which plays a role in virion budding at Golgi tubes and in the subcellular location of Gc protein .
CXXX repeat peptide maturase (CXXX_matur)
Type: Domain

This entry describes a peptide maturase that works with, usually fused to, a radical SAM enzyme in a system that modifies peptides with multiple tandem repeats of CXXX sequences. Some family members have an iron-sulphur cluster binding region associated with peptide modification (

).
Chitooligosaccharide deacetylase NodB (Nodulat_NodB)
Type: Family

Nodulation factors are lipooligosaccharide signalling molecules produced by rhizobia, the symbiotic nitrogen-fixing bacteria that form nodules in plants. These Nod factor sustems have the NodABC genes in common but differ subtly in what they produce, which affects host range. NodB is a chitooligosaccharide deacetylase .
Putative lipoprotein, rSAM/lipoprotein system (Lipo_with_rSAM)
Type: Family

Members of this family are Bacteroidetes lineage putative lipoproteins that always occur in pairs with a radical SAM enzyme,

, from a branch of the radical SAM superfamily in which many members perform peptide or protein modifications. In some members, the region distal to the Cys of the putative lipoprotein cleavage motif is duplicated.
Radical SAM enzyme, rSAM/lipoprotein system (rSAM_w_lipo)
Type: Family

Members of this protein family are radical SAM enzymes with an additional 4Fe4S cluster-binding C-terminal domain shared with PqqE and many other peptide and protein-modifying radical SAM enzymes. All members occur in the context of a predicted lipoprotein that usually is encoded by an adjacent gene.
Chlamydiae/Verrucomicrobia/Planctomycetes small basic protein (Chlam/Ver/Plancto_rRNA)
Type: Family

Members of this protein family are commonly found next to markers of rRNA processing such as YbeY. They are extremely lineage-restricted, in the Planctomycetes and Chlamydiae/Verrucomicrobia group. Since classification is based on rRNA molecular phylogeny, this provides additional support for a role in rRNA metabolism. This small protein, about 50 amino acids in length, is rich in basic residues, a third line of support for rRNA interaction.
Verrucomicrobia /Planctomycetes-restricted protein (Ver/Plancto_CHP)
Type: Family

Members of this protein family are extremely lineage-restricted, occurring exclusively in the Planctomycetes and Chlamydiae/Verrucomicrobia group, although not in Chlamydia itself. The function is unknown; the lack of invariant residues other than a single Phe suggests an ancient, conserved, non-enzymatic role.
Radical SAM peptide maturase, GG-Bacteroidales family (SAM_GG-Bacter)
Type: Family

Members of this protein family are radical SAM enzymes with the additional C-terminal region that is frequently a marker of peptide modification. Many members of this family are found in the vicinity of one or several ORFs encoding short polypeptides with a Gly-Gly motif (common for bacteriocin leader peptide cleavage), followed by a Cys-rich patch and then poorly conserved sequences .
Natural product precursor, GG-Bacteroidales (GG_sam_targ_CFB)
Type: Domain

Sequences in this domain include a leader peptide region, up to and including a Gly-Gly cleavage motif, and about 15 additional residues, usually Cys-rich, from a family of predicted ribosomal natural product precursors. Many of these are associated with peptide-modifying radical SAM enzymes .
Firmicu-CTERM protein-sorting domain (Firmicu_CTERM)
Type: Domain

Proteins with this domain are most conserved in the C-terminal region, where the pattern of ending with a transmembrane domain resembles both the LPXTG (sortase target) and PEP-CTERM (exosortase target) domain structures. This C-terminal domain is found only in the Firmicutes, where its presence is sporadically distributed. However, members are found exclusively in the presence of an exosortase-like protein XrtG (

), a putative glycosyltransferase (

), and a 6-pyruvoyl tetrahydropterin synthase-related protein (

) .
Oligosaccharyl transferase, archaeal (OlisacTrfase_arch)
Type: Family

This entry represents the archaeal oligosaccharyl transferases. Members of this protein family are found, one to three members per genome, in the same species of Euryarchaeota that contain the predicted protein-sorting enzyme archaeosortase and its cognate protein-sorting signal PGF-CTERM . Oligosaccharyl transferase AglB (STT3) is responsible for transferring a pentasaccharide moiety to at least two S-layer glycoprotein sites in Haloferax volcanii . Dolichyl-phosphooligosaccharide-protein glycotransferase 3 (aglB3) from Archaeoglobus fulgidus is required for the first step in attaching an N-linked-carbohydrate to a newly-synthesized protein, by transfering a glycan from the lipid carrier dolichol-monophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif .
Cyanosortase A-associated protein (Cyanosort_A_assoc)
Type: Family

Members of this protein family are found exclusively in the Cyanobacteria, usually usually encoded next to and in at least one case fused to a gene encoding cyanoexosortase A.
Radical SAM peptide maturase, CXXX-repeat target (rSAM_Cxxx_rpt)
Type: Family

These radical SAM domain proteins are predicted peptide maturases, similar to PqqE, AlbA, the mycofactocin radical SAM maturase, and many others that share the peptide modification radical SAM protein C-terminal additional 4Fe4S-binding domain. Members co-occur with a protein of unknown function that may be a chaperone or immunity protein and with a peptide that may have twelve or more cysteines occurring regularly spaced every fourth residue. These Cys residues tend to be flanked by residues with small side chains that provide minimal steric hindrance to crosslink formation by the radical SAM enzyme as in the subtilosin A system .
CXXX repeat peptide modification system protein (CXXX_rpt_assoc)
Type: Family

Members of this protein family occur strictly in the presence of a peptide modification radical SAM enzyme and some small peptide in which, for a stretch, every fourth amino acid is Cys. Cysteine residues usually are flanked by residues with sterically small side chains, as with many radical SAM-modified peptides .
Exosortase F-associated membrane protein (ExosoTase_F-assoc_memb)
Type: Family

Members of this protein family are always found next to an exosortase/archaeosortase-like protein XrtF, and occur so far only in the flavobacteria, within the Bacteroidetes . Members do not have an obvious PEP-CTERM-like C-terminal protein sorting domain. Instead, members of this family have strongly hydrophobic nature that suggests a possible role in letting other proteins, targeted by XrtF, transit the outer membrane. This protein and its neighbour XrtF have been shown to play a role in surface attachment by Flavobacterium johnsoniae, a species that, notably, also has a type IX secretion system (T9SS) relevant to surface attachment .
UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase (FnlA)
Type: Family

The FnlA enzyme is the first step in the biosynthesis of UDP-N-acetyl-L-fucosamine (UDP-FucNAc) from UDP-GlcNAc in Escherichia coli (along with FnlB and FnlC). Proteins in this entry includes FnlA homologues in the O-antigen clusters of O4, O25, O26, O29 (Shigella D11), O118, O145 and O172 serotype strains, all of which produce O-antigens containing FucNAc (or the further modified FucNAm). A homologue from Pseudomonas aerugiosa serotype O11, WbjB, also involved in the biosynthesis of UDP-FucNAc, has been characterised and is now believed to carry out both the initial 4,6-dehydratase reaction and the subsequent epimerisation of the resulting methyl group at C-5 . A phylogenetic tree of related sequences shows a distinct clade of enzymes involved in the biosynthesis of UDP-QuiNAc (Qui=quinovosamine). This clade appears to be descendant from the common ancestor of the Pseudomonas and E. coli fucose-biosynthesis enzymes. It has been hypothesised that the first step in the biosynthesis of these two compounds may be the same, and thus that these enzymes all have the same function.
Putative folate metabolism gamma-glutamate ligase (Fol_metab_g-glu_lig)
Type: Family

This protein family is related to CofE, a gamma-glutamyl ligase of coenzyme F420 biosynthesis. However, it occurs in a different gamma-glutamyl ligase context, polyglutamylated tetrahydrofolate biosynthesis-like regions in two widely separated lineages that both occur as intracellular bacteria - Chlamydia and Wolbachia.
Geranylgeranylglyceryl phosphate synthase, halobacteria (GGGPS_halobacteria)
Type: Family

In most archaea, geranylgeranylglyceryl phosphate synthase (

), also known as GGGP synthase and GGGPS, catalyses the stereospecific first step in the biosynthesis of their characteristic membrane diether lipids. However, some groups of archaeal GGGPS homologues are more closely related to certain bacterial proteins (see

) than to each other. This family represents the GGGPS family found in the Halobacteria.
Pseudo-rSAM protein, GG-Bacteroidales system (Pseudo_rSAM)
Type: Family

Many peptide-modifying radical SAM enzymes have two 4Fe4S-binding regions, an N-terminal one recognised by

and a C-terminal one recognised by

. Members of this protein family occur in cassettes with such a radical SAM family

and with a peptide modification target

. Surprisingly, members of this family show full-length homology to each other, with several scoring at least borderline hits to both

and

, and yet differ in the presence/absence of a signature CX(3)CX(2)CX(9)C motif. Instead, members are best-conserved in the

-like C-terminal region. Therefore, this protein family is designated a quasi-radical-SAM protein, which likely works in partnership with a

family protein .
Glycosyltransferase, GG-Bacteroidales peptide system (Glyco_rSAM_CFB)
Type: Family

Members of this protein family are predicted glycosyltransferases that occur in conserved gene neighbourhoods in various members of the Bacteroidales. These neighbourhoods feature a radical SAM enzyme predicted to act in peptide modification (see

), peptides from

with a characteristic GG cleavage motif, and several other proteins .
Exosortase E/protease, VPEID-CTERM system (Exo_VPEID)
Type: Family

Members of this protein family are fusion proteins of exosortase (N-terminal) and a CAAX prenyl protease domain (C-terminal). Members are restricted to the alpha Proteobacteria. The variant C-terminal protein sequence VPEID-CTERM occurs only in these species, often adjacent .