SII-SWORD/CoKE huggingface dataset:
Modified peptide precursor CbpA (Mod_peptide_prec_CbpA)
Type: Family

Members of this family are short peptides predicted to reach mature form after modification by a radical SAM enzyme (

).
VPEID-CTERM protein sorting domain (VPEID-CTERM)
Type: Domain

Proteins with this domain are small, 80 to 120 residues, and include a signal peptide, a central low-complexity region, and this roughly 31-amino acid extreme C-terminal region. Members occur paired with a variant form of exosortase. Species include Ruegeria sp., Phaeobacter gallaeciensis, Roseovarius nubinhibens ISM, and two in Methylobacter tundripaludum .
Peptide-modifying radical SAM enzyme CbpB (rSAM_cobopep)
Type: Family

Members of this family are radical SAM enzymes that modify a short peptide encoded by an upstream gene. A role in metal chelation is suggested.
Modification target Cys-rich peptide, AC3_0185 family (Cxxx_AC3_0185)
Type: Family

Radical SAM enzyme family

is paired with a number of short peptides with multiple tandem repeats of Cys-Xaa-Xaa-Xaa (see

). This entry represents a peptide family with a TIGR04114-like region, although the repeat region is relatively short in this group of proteins .
Cys-rich radical SAM target, FibroRumin family (FibroRuminTarg)
Type: Family

Members of this protein family are cysteine-rich small peptides, about 52 amino acids long, that are proposed targets for modification by a radical SAM enzyme. Known occurrences as tandem gene pairs can be found in Fibrobacter succinogenes subsp. succinogenes S85 and in Ruminococcus albus 8 .
Radical SAM peptide maturase, FibroRumin system (rSAM_FibroRumin)
Type: Family

Members of this protein family are radical SAM enzymes proposed to act on small, Cys-rich peptides encoded by tandem gene pairs. Members occur in enzymes Fibrobacter succinogenes subsp. succinogenes S85 (genes for their target peptides missed) and in Ruminococcus albus 8. This enzyme family is similar in sequence to the SCIFF (Six Cysteines in Forty-Five) system maturase

.
Putative peptidyl-prolyl cis-trans isomerase, LIC12922 family (Put_pepPro_cis-trans_isomerase)
Type: Family

Members of this protein family have a known crystal structure showing similarity to the peptidyl-prolyl cis-trans isomerase SurA . Members are found in Leptospira species next to an uncharacterised radical SAM enzyme and a cytidylyltransferase family protein.
VPXXXP-CTERM protein-sorting domain (VPxxxP_CTERM)
Type: Domain

This C-terminal protein sorting domain has been detected in Methanohalophilus mahii DSM 5219 (five members) and Methanohalobium evestigatum Z-7303 (nine members). This domain resembles the PEP-CTERM, PEF-CTERM, and PGF-CTERM domains of other exosortase/archaeosortase systems. Member proteins co-cluster with a variant member of the exosortase/archaeosortase protein family, and represent a boutique second sorting system in these species .
3-methyl-2-indolic acid synthase (MIA_synthase)
Type: Family

Members of this family are a radical SAM enzyme that converts L-Trp to 3-methyl-2-indolic acid (MIA) .
Archaeosortase B (Archaeosortase_B)
Type: Family

Members of this protein family are found so far in Methanohalophilus mahii DSM 5219 and Methanohalobium evestigatum Z-7303, along with five and nine proteins, respectively, with the VPXXXP-CTERM protein sorting signal. In these species, this boutique system represents a second exosortase/archaeosortase-type system .
Methanobactin biosynthesis cassette protein MbnB (Methbact_MbnB)
Type: Family

The first characterised methanobactin is made from a ribosomal precursor in Methylosinus trichosporium OB3b. Two additional species with homologous precursor peptides are Azospirillum sp. B510 and Gluconacetobacter sp. SXCC-1. This entry describes a clique of related sequences that occur always and only next to a methanobactin precursor .
Archaeosortase D (Archaeo_ArtD)
Type: Family

This entry describes archaeosortase D, one of several strictly archaeal subfamilies related to exosortase, the bacterial protein-sorting putative transpeptidase. ArtD is found in the genus Methanocaldococcus. Its predicted target, encoded by an adjacent gene, has a C-terminal VPIP motif-containing region

likely to be its recognition site .
EPS-associated transcriptional regulator, MarR family (MarR_EPS)
Type: Family

Members of this family of MarR-family transcriptional regulators are associated with long genomic loci consisting of genes encoding enzymes for the biosynthesis of exopolysaccharides. These genes include glycosyl transferases, sugar modifying enzymes (epimerases, isomerases, methyltransferases, aminotransferases, etc.), and exopolysaccharide polymerases (wzx, wzy). In Leptospira interrogans, borgpeterenii and biflexa, this gene is observed first in unidirectional EPS biosynthesis loci as long as 90 genes. MarR genes are known to bind to DNA regions with palindromic or pseudopalindromic sequences as homodimers, and to bind small molecules as triggers for conformational changes controlling on/off states .
Cys-rich repeat, Myxococcales-type (Myxo_Cys_rpt)
Type: Repeat

This repeat is restricted to the Myxococcales, a division of the deltaproteobacteria. It occurs in several surface proteins, and may form a stalk region. The repeat averages about 21 amino acids in length with four or five Cys, three of which are nearly invariant.
Conserved hypothetical protein CHP04206 (CHP04206)
Type: Family

Members of this integral membrane protein family are found exclusively in halophilic archaea. In at least three species (Haloarcula marismortui, Haloquadratum walsbyi, and Haloferax volcanii), members are found in the gene neighbourhood of archaeosortase A, suggesting a role in protein sorting.
Putative peptide modification target (CxxCx5CxxC_targ)
Type: Family

This entry represents a rare family of small putative polypeptides, including three encoded in tandem in Sphingobacterium spiritivorum ATCC 33300, in the vicinity of a

protein. This pairing is conserved in Chryseobacterium gleum ATCC 35910, Kordia algicida OT-1, and other species. TIGR04085 describes a C-terminal additional 4Fe4S-binding domain in PqqE and other radical SAM enzymes that seems to be a marker for peptide modification, and the family here is a candidate modified peptide precursor.
Geranylgeranylglyceryl phosphate synthase, archaea (GGGP_synthase_archaea)
Type: Family

This enzyme, known also as GGGP synthase and GGGPS, is a prenyltransferase that catalyses the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). It catalyses the stereospecific first step in the biosynthesis of the characteristic membrane diether lipids of archaea. To a much lesser extent, is also able to use heptaprenyl pyrophosphate (HepPP; 35 carbon atoms) as the prenyl donor. Interestingly, the closest homologues outside this family are not the functionally equivalent enzymes of other archaea, but rather functionally distinct bacterial enzymes .
ATP-grasp ribosomal peptide maturase, MvdD family (ATP_grasp_rbs_pep_matu_MvdD)
Type: Family

The ATP-grasp proteins MvdD and MvdC (microviridin D and C) are part of the microviridin (mvd) biosynthetic gene cluster responsible for the production of microviridin K. Microviridin K is an example of a RiPP (ribosomally synthesized and posttranslationally modified peptide), with four post-translational modifications required to convert the linear prepeptide MvdE into microviridin K . Microviridins are peptidase inhibitors.
DNA phosphorothioation-associated DGQHR protein 1 (DNA_PRithio_assoc_DGOHR_pro_1)
Type: Family

The DND (DNA degradation) system produces an phosphorothioation modification to DNA, replacing a non-bridging oxygen of a phosphate group with sulfur. The modification causes DNA degradation during electrophoresis in Tris buffer. This protein, like DndB , contains a DGQHR domain, which also occurs in several contexts that suggest lateral transfer rather than DNA phosphorothioation-dependent restriction .
Exosortase H, IPTLxxWG-CTERM-specific (Exosort_XrtH)
Type: Family

This entry represents exosortase subfamily H, for which most cognate recognition sequences are found by the IPTLxxWG-CTERM model

. Species with this exosortase and multiple (up to 15) copies of the target domain include Acidovorax citrulli, Acidovorax delafieldii 2AN, Delftia acidovorans SPH-1, and gamma proteobacterium NOR5-3 .
IPTL-CTERM protein sorting domain (IPTL_CTERM)
Type: Domain

This entry represents a variant form of the PEP-CTERM C-terminal protein-sorting domain, with a consensus motif IPTL replacing the more typical VPEP. A majority of these sequences have a WG (Trp-Gly) motif at positions 7-8 of the domain. Species with multiple (up to 15) copies of this domain include Acidovorax citrulli, Acidovorax delafieldii 2AN, Delftia acidovorans SPH-1, and gammaproteobacterium NOR5-3 .
Rhombotail lipoprotein (Rhombo_lipo)
Type: Family

Members of this protein family are probable lipoproteins. Nearly every member ends with a C-terminal region consisting of a glycine-rich probable cleavage site, a hydrophobic probable transmembrane helix. Furthermore, members tend to be encoded next to a rhomboid family protease, called rhombosortase

predicted to perform a C-terminal cleavage.
Secretion system C-terminal sorting domain (Secre_tail)
Type: Domain

Species that include Porphyromonas gingivalis, Fibrobacter succinogenes, Flavobacterium johnsoniae, Cytophaga hutchinsonii, Gramella forsetii, Prevotella intermedia, and Salinibacter ruber have on average twenty or more copies of this C-terminal domain, associated with sorting to the outer membrane and covalent modification. This domain targets proteins to type IX secretion systems and is secreted then cleaved off by a C-terminal signal peptidase . This domain adopts a typical Ig-like fold.
Alkylhydroperoxidase/carboxymuconolactone decarboxylase family (AlkhydPrxdase/COmuclacdeCOase)
Type: Family

Members of this family are usually annotated as putative carboxymuconolactone decarboxylases, are related also to alkylhydroperoxidase AhpD, and contain a peroxidase-like Cys-X-X-Cys putative redox-active disulfide. All members occur in genomes with a radical SAM protein of family

, which occasionally are selenoproteins.
ATP-grasp ribosomal peptide maturase, MvdC family (ATP_grasp_MvdC)
Type: Family

The ATP-grasp proteins MvdD and MvdC (microviridin D and C) are part of the microviridin (mvd) biosynthetic gene cluster responsible for the production of microviridin K. Microviridin K is an example of a RiPP (ribosomally synthesized and posttranslationally modified peptide), with four post-translational modifications required to convert the linear prepeptide MvdE into microviridin K . Microviridins are peptidase inhibitors.

This family includes MvdC and corresponding members of similar cassettes.
B12-binding domain/radical SAM domain protein, Ta0216 family (B12_SAM_Ta0216)
Type: Family

Members of this family are enzymes with an N-terminal B12-binding domain and central radical SAM domain.
Methyltransferase, ATP-grasp peptide maturase system (Methyltr_grasp)
Type: Family

Members of this protein family are predicted SAM-dependent methyltransferases that regularly occur in the context of a putative peptide modification ATP-grasp enzyme(

, related to enzymes of microviridin maturation) and a putative ribosomal peptide modification target (

).
ATP-grasp ribosomal peptide maturase, SAV-5884 family (GRASP_SAV_5884)
Type: Family

Members of this protein family are ATP-grasp ligase family enzymes that regularly occur in a contexts with a methyltransferase and a putative ribosomally translated post-translationally modified peptide precursor. Because of this conserved gene neighbourhood and close sequence similarity to ATP-grasp enzymes from microviridin/marinostatin biosynthesis cassettes, this enzyme is suggested also to serve as a peptide maturase.
MAST domain (MAST_dom)
Type: Domain

This entry describes a domain (or in most cases the full length) of archaeal surface proteins that are putative targets for C-terminal processing by archaeosortase A (

). Most members of this family belong to proteins encoded by tandem genes in the genus Methanosarcina. The putative processing signal, PGF-CTERM (

), included within the domain definition, takes a variant form, with consensus motif PAF instead of PGF. We suggest the name MAST domain: Methanosarcina Archaeosortase-Sorted Tandem gene family domain.
Class III signal peptide protein, archaeosortase D/PIP-CTERM system (ClassIII_w_PIP)
Type: Family

Members of this protein family are short proteins that consist largely of the archaeal class III signal peptide. Members are encoded in a gene cassette between archaeosortase D and its PIP-CTERM target protein .
Surface glycoprotein signal peptide (Surf_glycop_sig_pep)
Type: Domain

This N-terminal homology domain appears to be a specialised class of signal peptide. It occurs mostly in the halophilic archaea, primarily on proteins with the C-terminal PGF-CTERM domain, including the S-layer-forming major surface glycoprotein of several species. The PGF-CTERM domain is the putative archaeosortase A recognition sequence. However, this N-terminal domain occurs also in several archaeal proteins that lack PGF-CTERM, and occurs in bacteria on a protein from Clostridium leptum DSM 753.
PGF-pre-PGF domain (PGF_pre_PGF)
Type: Domain

This domain occurs in archaeal species. Most domains in this family end with a motif PGF, after which the member sequences change in character to low-complexity sequence (usually Thr-rich) for about 40 residues. The low complexity region usually is followed by a PGF-CTERM domain, which we suggest is the recognition sequence for archaeosortase A, a putative protein-sorting transpeptidase. The similarity between the PGF motif in this domain and in the PGF-CTERM domain is highly suggestive.
Rhombotarget A (Rhombotarget_A)
Type: Family

Members of this protein family are found, so far, exclusively in the genus Acinetobacter. Members average just over 600 amino acids in length, including a 22-amino acid C-terminal putative protein sorting recognition sequence, GlyGly-CTERM. The GlyGly-CTERM signal always co-occurs with a subfamily of the rhomboid family intramembrane serine proteases called rhombosortase. Members occur paired with a second rhombosortase target, with which it also shares an N-terminal motif CSLREA. This protein is designated Acinetobacter rhombotarget A (rbtA).
ATP-GRASP peptide maturase, grasp-with-spasm system (GRASP_w_spasm)
Type: Family

Members of this protein family are ATP-GRASP proteins that occur in a peptide maturation cassette with a SPASM domain protein. SPASM usually occurs as a C-terminal extension to radical SAM enzymes that act as peptide maturases, although it can occur independently.
Glycosyltransferase AglJ (GCTrfase_AglJ)
Type: Family

Members of this family are glycosyltransferases restricted to archaea.
Most members are from species with the PGF-CTERM/archaeosortase A system, a proposed maturation system for exported, glycosylated proteins as are found often in S-layers .
CSLREA domain (CSLREA_Nterm)
Type: Domain

This entry represents an N-terminal region, with a motif CSLREA, shared by tandem genes in Acinetobacter that both have the GlyGly-CTERM putative protein-sorting domain. Many proteins with this domain are putative outer membrane proteins (OMPs) with predicted β-strand-forming repeats.
Cell surface glycoprotein, halobacteria (Csg_halobact)
Type: Family

This family includes Cell surface glycoprotein from Haloferax volcanii (Csg) and other S-layer-forming halobacterial major cell surface glycoproteins. Modifications include an N-linked and O-linked glycosylation, a C-terminal diphytanylglyceryl modification, and probable cleavage of the PGF-CTERM tail and a C-terminal diphytanylglyceryl modification that depends on that cleavage .
Ribonucleotide reductase, class 1b, subunit NrdE (RNR_1b_NrdE)
Type: Family

Ribonucleotide reductase (also known as ribonucleoside-diphosphate reductase) catalyses the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides providing the precursors necessary for DNA synthesis. Three main classes of ribonucleotide reductases (RNR) have been discovered that depend on different metal cofactors for the catalytic activity: class I enzymes contain a diiron-oxygen cluster, class II a cobalt containing cobalamin cofactor (vitamin B12), and class III an 4Fe-4S iron-sulfur cluster coupled to S-adenosylmethionine (SAM) .

Class I RNRs can be further divided into two subclasses, Ia and Ib. Class Ia exists in eukaryotes, prokaryotes, viruses, and bacteriophages, while Ib has only been found in prokaryotes. Class I RNRs are tetrameric enzymes (alpha2beta2). The substrate binding active site is located in the large alpha2-homodimer which is called R1 in class Ia, encoded by nrdA, and R1E in class Ib, encoded by nrdE .

Members of this family are NrdE, the alpha subunit of class 1b ribonucleotide reductase. This form of ribonucleotide reductase uses a dimanganese moiety associated with a tyrosine radical to reduce the cellular requirement for iron .
Aldehyde dehydrogenase, Rv0768 family (Aldehyde_dehydrogenase_Rv0768)
Type: Family

This family describes a branch of the aldehyde dehydrogenase (NAD) family that includes Rv0768 from Mycobacterium tuberculosis. All members of this family belong to species predicted to synthesise mycofactocin, suggesting that this enzyme or another upstream or downstream in the same pathway might be mycofactocin-dependent. However, the taxonomic range of this family is not nearly broad enough to make that relationship conclusive.
Transferase 2, rSAM/selenodomain-associated (Trfase_2_rSAM/seldom_assoc)
Type: Family

This entry includes diverse glycosyltransferases with a common GT-A type structural fold, having two tightly associated β/α/β domains that tend to form a continuous central sheet of at least eight β-strands. These are enzymes that catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds . Other members of the entry include are proposed to be a nucleotide transferase and a phosphoesterase. These enzymes co-occur with a radical SAM enzyme characterised as an enzyme of arsenosugar biosynthesis whose C-terminal domain frequently contains a selenocysteine.
Chitooligosaccharide synthase NodC (Chitooligosach_Synthase_NodC)
Type: Family

Members of this family are NodC, an N-acetylglucosaminyltransferase involved in the production of nodulation factors through which rhizobia establish symbioses with leguminous plants.
Nitrous oxide reductase family maturation protein NosD (NosD_copper_fam)
Type: Family

Members of this family include NosD, a repetitive periplasmic protein required for the maturation of the copper-containing enzyme nitrous-oxide reductase. NosD appears to be part of a complex with NosF (an ABC transporter family ATP-binding protein) and NosY (a six-helix transmembrane protein in the ABC-2 permease family). However, NosDFY-like complexes appear to occur also in species whose copper requiring enzymes are something other than nitrous-oxide reductase .
Serine-rich repeat adhesion glycoprotein, N-terminal domain (Ser_adhes_glycop_N)
Type: Domain

This entry represents a conserved N-terminal domain shared by highly repetitive Streptococcal serine-rich adhesion glycoproteins that may exceed 4000 amino acids in length, consisting largely of long regions in which every second amino acid is Ser. Members of this family normally begin with a KxYKxGKxW motif region (

) and end with an LPXTG motif region. Members are exported by the accessory secretory system (SecA2 and SecY2). They are highly variable among the Streptococci and may help determine host ranges for pathogenesis .

Some of the proteins belonging to this entry are: Platelet binding protein GspB from Streptococcus gordonii, which plays a role in virulence, biofilm formation and host-pathogen interactions ; Streptococcal hemagglutinin from Streptococcus gordonii (Hsa), a cell wall protein involved with PadA in host cell interactions required for colonization and pathogensis (Probable) ; and Fap1 adhesin from Streptococcus parasanguinis, the major structural element of fimbriae, required for adherence to saliva-coated hydroxyapatite beads (SHA), an in vitro tooth model .
Fimbrial isopeptide formation D2 domain (Fim_isopep_form_D2_dom)
Type: Domain

This entry represents the middle domain of Fimbrial subunit type 1 from Actinomyces viscosus (FimA), the Streptococcus Pneumoniae pilus backbone protein RrgB, and similar bacterial proteins. This domain contain one autocatalysed intramolecular isopeptide bond, which is used by Gram-positive bacteria for stabilisation of surface proteins. In FimA, it folds into an IgG-like domain of the CnaA-type, showing a a β-sandwich of two five-stranded anti-parallel sheets and an helix wedged in between the upper part of the sandwich . This domain was initially known as the D2 domain in RrgB .

Platelet adherence protein A from Streptococcus gordonii (PadA), a much longer protein, contains 17 copies of this domain. This central region may serve as a flexible extension that holds the N terminus away from the bacterial surface. PadA is a cell wall protein involved with Hsa in host cell interactions required for colonization and pathogenesis .

Three of every four members of this group have the typical Gram-positive C-terminal motif, LPXTG, although in many cases this motif may be involved in pilin subunit cross-linking rather than cell wall attachment. Proteins with this domain include fimbrial proteins with lectin-like adhesion functions, and the majority of characterised members are involved in surface adhesion to host structures .
Ser/Gly rich, Cys interspersed, C-terminal domain (Ser/Gly_Cys_C_dom)
Type: Domain

This entry represents a domain of extremely low-complexity sequence, rich in Ser or in Gly interspersed with Cys found in the extreme C-terminal region of a number of proteins.
Nitrous-oxide reductase, Sec-dependent (Nitrous_oxide_Rdtase_Sec-dep)
Type: Family

This entry represents the nitrous-oxide reductase protein NosZ as characterised in Geobacillus thermodenitrificans. In contrast to the related form in Pseudomonas stutzeri, this version lacks a recognisable twin-arginine translocation (TAT) signal at the N terminus. Consequently, its accessory protein may differ. Some members of this family have an additional cytochrome c-like domain at the C terminus .
Putative ABC transporter PGF-CTERM-modified substrate-binding protein (Peripla_PGF_1)
Type: Family

Members of this archaeal protein family resemble periplasmic substrate-binding proteins of ABC transporters and appear in gene neighbourhoods with permease and ATP-binding cassette proteins. Studies suggest that one family member (

) is part of the ABC transporter complex BtuCDF involved in cobalamin (vitamin B12) import . Notably, essentially all members also have the PGF-CTERM putative protein-sorting domain at the C terminus, while more distant homologues instead have what appear to be lipoprotein signal peptides at the N terminus.
Flavivirus envelope glycoprotein E, Stem/Anchor domain (Flavi_E_Stem/Anchor_dom)
Type: Domain

This entry describes the C-terminal domain, containing a stem region followed by two transmembrane anchor domains, of the envelope protein E. This protein is cleaved from the large flavivirus polyprotein, which yields three structural and seven nonstructural proteins .
Zinc metalloproteinase 18-residue repeat (Zmp_18_rpt)
Type: Repeat

This entry represents a short (18-amino acid) tandem repeat that occurs variable numbers of times in zinc metalloproteinase C (zmpC) homologues in various species of Streptococcus. This repeat occurs, oddly, as an interruption in a region of tandem repeats of another type.
Membrane glycoprotein E3 CR1-alpha-1 (E3_CR1-alpha-1)
Type: Domain

This domain occurs only in the adenovirus E3 region CR1-alpha-1 protein. It may occur once, twice, or three times .