SII-SWORD/CoKE huggingface dataset:
Decahaem cytochrome, c-type, OmcA/MtrC (Decahaem_cyt-c_OmcA/MtrC)
Type: Family

The protein MtrC (SO_1778) of Shewanella oneidensis MR-1, its homologue MtrF and its paralog OmcA (SO_1779), with which it interacts, are large decahaem proteins, about 900 amino acids in length, involved in the use of manganese [Mn(III/IV)] and iron [Fe(III)] as terminal electron acceptors . This entry represents these and similar decahaem proteins, which are also found in Rhodoferax ferrireducens DSM 15236, Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / NCIB 9240), and a few other bacterial species.
Decaheme cytochrome, c-type, DmsE (Decahaem_cyt-c_DmsE)
Type: Family

Members of this family are small, decahaem c-type cytochromes that are related to DmsE of Shewanella oneidensis MR-1, which has been shown to be part of an anaerobic dimethyl sulphoxide reductase .
Decahaem-associated outer membrane protein, MtrB/PioB (Decahaem-assoc_OM_MtrB/PioB)
Type: Family

Members of this protein family are integral proteins of the bacterial outer membrane, associated with multi-haem c-type cytochromes involved in electron transfer . The MtrB protein of Shewanella oneidensis MR-1 (SO1776) has been shown to form a complex with 1:1:1 stochiometry with the small, periplasmic decahaem cytochrome MtrA and large, surface-exposed decahaem cytochrome MtrC.
XapX domain (XapX_domain)
Type: Domain

This entry describes an uncharacterised small, hydrophobic protein of about 50 amino acids, known as XapX found between the xapB and xapR genes of the Escherichia coli xanthosine utilization system. It is also found in a number of other small proteins, such as the N-terminal region of proteins modeled by

.
Gliding motility-associated lipoprotein, GldH (Motility-assoc_lipoprot_GldH)
Type: Family

Members of this protein family are predicted lipoproteins, exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). Members include GldH, a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Cytophaga johnsonae (Flavobacterium johnsoniae) and Cytophaga hutchinsonii . Gliding motility appears closely linked to chitin utilization in the model species C. johnsonae. Not all Bacteroidetes with members of this protein family may have gliding motility.
Acyltransferase PglD-like (AcTrfase_PglD-like)
Type: Family

This entry represents a family of characterised and putative acyltransferases mainly found in bacteria, including UDP-N-acetylbacillosamine N-acetyltransferase from Campylobacter jejuni (PglD) and UDP-N-acetylbacillosamine N-acetyltransferase from Bacillus subtilis (EpsM). These enzymes catalyse the formation of UDP-N,N'-diacetylbacillosamine (UDP-2,4,6-trideoxy-2,4-diacetamido glucose) in the N-linked protein glycosylation pathway .

This group is composed of mostly uncharacterised proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV].-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity .

Some members of this group are identified as NeuD, a sialic acid (Sia) O-acetyltransferase that is required for Sia synthesis and surface polysaccharide sialylation. The neuD gene is often observed in close proximity to the neuABC genes for the biosynthesis of CMP-N-acetylneuraminic acid (CMP-sialic acid) .
Luciferase-type oxidoreductase (Luciferase-type_oxidoreductase)
Type: Family

This entry represents a distinct subgroup among members of the luciferase monooxygenase domain family. The larger family contains both FMN-binding enzymes (luciferase, alkane monooxygenase) and F420-binding enzymes (methylenetetrahydromethanopterin reductase, secondary alcohol dehydrogenase, glucose-6-phosphate dehydrogenase). Although some members of the domain family bind coenzyme F420 rather than FMN, members of this family are from species that lack the genes for F420 biosynthesis.
Glycosyl amidation-associated protein, WbuZ (Glycosyl_amidation-assoc_WbuZ)
Type: Family

This entry represents a protein highly similar to the HisF protein, but generally represents the second HisF homologue in the genome where the other is an authentic HisF observed in the context of a complete histidine biosynthesis operon. The similarity between these WbuZ sequences and true HisFs is such that often the closest match by BLAST of a WbuZ is a HisF. Only by making a multiple sequence alignment is the homology relationship among the WbuZ sequences made apparent. WbuZ genes are invariably observed in the presence of a homologue of the HisH protein (designated WbuY) and a proposed N-acetyl sugar amidotransferase designated in WbuX in Escherichia coli , IfnA in Pseudomonas aeruginosa and PseA in Campylobacter jejuni . Similarly, this trio of genes is invariably found in the context of saccharide biosynthesis loci.
N-acetyl sugar amidotransferase (N-acetyl_sugar_amidoTrfase)
Type: Family

This entry represents an enzyme that has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In Escherichia coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid . In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation . In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterised by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an invariable contextual association with homologues of the HisH and HisF proteins known as WbuY and WbuZ, respectively. These two proteins are believed to supply the enzyme with ammonium by hydrolysis of glutamine and delivery through an ammonium conduit .
UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose hydrolase (PseG)
Type: Family

This protein is found in association with enzymes involved in the biosynthesis of pseudaminic acid, a component of polysaccharide in certain Pseudomonas strains as well as a modification of flagellin in Campylobacter and Helicobacter .
L-seryl-tRNA(Sec) kinase, archaea (L-seryl-tRNA_Sec_kinase_arc)
Type: Family

This entry represents L-seryl-tRNA(Sec) kinase, which is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity .
UDP-N-acetylglucosamine 4,6-dehydratase (inverting) (PseB)
Type: Family

This enzyme catalyses the first step in the biosynthesis of pseudaminic acid, the conversion of UDP-N-acetylglucosamine to UDP-4-keto-6-deoxy-N-acetylglucosamine .
UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine transaminase (PseC)
Type: Family

This entry represents a family of aminotransferases involved in the biosynthesis of pseudaminic acid . They convert UDP-4-keto-6-deoxy-N-acetylglucosamine into UDP-4-amino-4,6-dideoxy-N-acetylgalactose. Pseudaminic acid has a role in surface polysaccharide in Pseudomonas as well as in the modification of flagellin in Campylobacter and Helicobacter species .
Pseudaminic acid biosynthesis-associated methyltransferase (Pseudamin_synth-assoc_MeTrfase)
Type: Family

This entry represents a group of methyltransferases that are encoded within operons for the biosynthesis of pseudaminic acid, a component of exopolysaccharide and flagellin glycosyl modifications . These enzymes may convert one of the two hydroxyl groups of pseudaminic acid to a methoxy group.
L-seryl-tRNA(Sec)kinase, eukaryote (L-seryl-tRNA_Sec_kinase_euk)
Type: Family

This entry represents L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity .
CRISPR-associated protein Csp2 (CRISPR-assoc_Csp2)
Type: Family

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.

Members of this protein family are cas, or CRISPR-associated, proteins. They are found within cas gene clusters that are adjacent to CRISPR DNA repeats in two members of the order Bacteroidales, Porphyromonas gingivalis W83 and Bacteroides forsythus ATCC 43037.
Pseudaminic acid biosynthesis, PseI (Pseudaminic_synth_PseI)
Type: Family

The PseI protein catalyses the final step of pseudaminic acid biosynthesis, the condensation of PEP with 6-deoxy-beta-L-AltNAc4NAc to generate pseudaminic acid . PseI is part of a broader family of synthases that includes the NeuB protein involved in the PEP-dependent biosynthesis of neuraminic acid.
CRISPR-associated protein Cas5p (CRISPR-assoc_Cas5p)
Type: Family

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.

Members of this protein family are cas, or CRISPR-associated, proteins. The two sequences in the alignment seed are found within cas gene clusters that are adjacent to CRISPR DNA repeats in two members of the order Bacteroidales, Porphyromonas gingivalis W83 and Bacteroides forsythus ATCC 43037. This cas protein family is unique to the Pging (Porphyromonas gingivalis) subtype, but shows some sequence similarity to genes of the Cas5 type (see

).
CRISPR-associated protein Csp1 (CRISPR-assoc_Csp1)
Type: Family

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.

Members of this protein family are Csp1, also known as Cas7, a CRISPR-associated (cas) gene marker for the Pging subtype of CRISPR/cas system, as found in Porphyromonas gingivalis W83 and Bacteroides forsythus ATCC 43037. This protein belongs to the family of DevR (

), a regulator of development in Myxococcus xanthus located in a cas gene region. A different branch of the DevR family, Cst2 (

), is a marker for the Tneap subtype of CRISPR/cas system.
Pyridoxal phosphate-dependent transferase, archaea (PyrdxlP-dep_transferase_arc)
Type: Family

Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). Pyridoxal 5'-phosphate (PLP) is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy .

PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the ε-amino group of an active site lysine residue on the enzyme. The α-amino group of the substrate displaces the lysine ε-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalysed reactions, enzymatic and non-enzymatic .

This entry represents pyridoxal phosphate enzymes of unknown function found in archaea. Sequence similarity to SelA, a bacterial enzyme of selenocysteine biosynthesis, has led to some members being misannotated as functionally equivalent, but selenocysteine is made on tRNA in Archaea by a two-step process that does not involve a SelA homologue.
Conserved hypothetical protein CHP03577, EF0830/AHA3911 (CHP03577_EF0830/AHA3911)
Type: Family

This entry represents small (about 120 amino acid) proteins found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown.
UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase (PseH)
Type: Family

This entry represents a family of N-acetyltransferases that are proposed to perform an N-acetylation step in the process of pseudaminic acid biosynthesis in Campylobacter species . They are commonly encoded in apparent operons with other genes involved in the biosynthesis of pseudaminic acid, and are components of flagellar and exopolysaccharide biosynthesis loci. Significantly, many genomes containing other components of this pathway lack this gene, indicating that some other N-acetyl transferases may be involved and/or the step is optional, resulting in a non-acetylated pseudaminic acid variant sugar.
Protein of unknown function DUF4312 (DUF4312)
Type: Family

The proteins in this family are functionally uncharacterised.
Circular bacteriocin (Circ_bacteriocin)
Type: Family

Circular bacteriocins are antimicrobial peptides produced by a variety of Gram-positive bacteria. They are part of a growing family of ribosomally synthesized peptides with a head-to-tail cyclization of their backbone that are found in mammals, plants, fungi and bacteria and are exceptionally stable . These circular bacteriocins arise after the cleavage of a leader peptide and the formation of a peptide bond between the N and C termini. They contain a saposin-fold, which is similar to the structure of leaderless bacteriocins . Enterocin AS-48 was the first bacteriocin identified with a head-to-tail cyclized backbone that was shown to be ribosomally synthesized . This entry includes AS-48 from Enterococcus, pumilarin from Bacillus safensis , carnocyclin-A from Carnobacterium maltaromaticum , and bacteriocin uberolysin from Streptococcus uberis .
Pseudaminic acid cytidylyltransferase (PseF)
Type: Family

This entry represents PseF, a Acylneuraminate cytidylyltransferase domain-containing protein which is homologous to the NeuA protein responsible for the transfer of CMP to neuraminic acid. PseF is responsible for the transfer of CMP to the structurally related sugar, pseudaminic acid, which is observed as a component of sugar modifications of flagellin in Campylobacter species . It is commonly encoded in flagellar and exopolysaccharide biosynthesis loci, generally located in apparent operons with other genes responsible for the biosynthesis of pseudaminic acid.
Large ribosomal subunit protein uL6, alpha-beta domain (Ribosomal_uL6_a/b-dom)
Type: Domain

This entry represents the α-β domain found duplicated in ribosomal uL6 proteins. This domain consists of two β-sheets and one α-helix packed around single core .

Large ribosomal subunit protein uL6 was previously known as L6. In Escherichia coli, it is located in the aminoacyl-tRNA binding site of the peptidyltransferase centre, and is known to bind directly to 23S rRNA. It belongs to a family of ribosomal proteins, including L6 from bacteria, cyanelles (structures that perform similar functions to chloroplasts, but have structural and biochemical characteristics of Cyanobacteria) and mitochondria; and L9 from mammals, Drosophila, plants and yeast. L6 contains two domains with almost identical folds, suggesting that is was derived by the duplication of an ancient RNA-binding protein gene. Analysis reveals several sites on the protein surface where interactions with other ribosome components may occur, the N terminus being involved in protein-protein interactions and the C terminus containing possible RNA-binding sites .

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Protein of unknown function DUF4311 (DUF4311)
Type: Family

The proteins in this family are functionally uncharacterised.
Deacetylase Atu3266-like (Deacetylase_Atu3266-like)
Type: Family

Atu3266 from Agrobacterium tumefaciens and Oant2987 from Ochrobactrum anthropi catalyze the hydrolysis of acetyl-(R)-mandelate and similar esters . These enzymes were previously misannotated as either dihydroorotases or adenine deaminases.
PRD domain protein, EF0829/AHA3910 (PRD_EF0829/AHA3910)
Type: Family

Members of this family of relatively uncommon proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The proteins contain a PRD domain (see

). Their function is unknown.
DNA polymerase I-like, H3TH domain (DNA_polI_H3TH)
Type: Domain

This entry represents the H3TH (helix-3-turn-helix) domain of the 5'-3' exonuclease (53EXO) of mutli-domain DNA polymerase I and single domain protein homologues. Taq (Thermus aquaticus) DNA polymerase I contains a polymerase domain for synthesizing a new DNA strand and a 53EXO domain for cleaving RNA primers or damaged DNA strands . Taq's 53EXO recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp .
5'-3' exonuclease, alpha-helical arch, N-terminal (5-3_exonucl_a-hlix_arch_N)
Type: Domain

The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (

) are never found outside the '53EXO' domains. The latter are found in more diverse proteins . The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families.

In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (

) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures.

This entry represents the N-terminal resolvase-like domain, which has a 3-layer α/β/α core structure and contains an α-helical arch .
NADPH-dependent FMN reductase, SsuE (NADPH-dep_FMN_reduc_SsuE)
Type: Family

This entry represents a protein family that uses NAD(P)H to reduce FMN and regenerate FMNH2. Members include the homodimeric, NAD(P)H-dependent enzyme SsuE from Escherichia coli, which serves as a partner to an FMNH2-dependent alkanesulphonate monooxygenase. It is induced by sulphate starvation.
Major capsid protein-like (Major_capsid-like)
Type: Family

This entry represents a group of proteins from tailed bacteriophages, bacterial prophages and some lower eukaryotes, including Major capsid protein from Pseudomonas phage KPP22 . This family was previously known as DUF2184.
FO synthase, subunit 2 (FO_synthase_su2)
Type: Family

FO synthase catalyzes the radical-mediated transfer of the hydroxybenzyl group from 4-hydroxyphenylpyruvate (HPP) to 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione to form 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) . This entry represents CofH/subunit 2 of FO synthase, it binds 1 4Fe-4S cluster, which is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Although this entry contains CofH/subunit2 of coenzyme F(420) biosynthesis it appears to hit genomes more broadly than just the subset that make coenzyme F(420), so that narrower group is being built as a separate family (

).
SagB-type dehydrogenase domain (SagB-type_dehydrogenase)
Type: Domain

SagB of Streptococcus pyogenes participates in the maturation of streptolysin S from a ribosomally produced precursor polypeptide . Chemically similar systems operate on highly diverse sets of bacteriocin precursors in numerous other bacteria. This entry represents a domain found within SgaB and other proteins, many of which appear to be involved in biosynthesis of secondary metabolites. While some substrates may be intermediates in non-ribosomal peptide syntheses, others are involved in heterocycle-containing bacteriocin biosynthesis, and can be found near SgaC-like (see

, cyclodehydratase) and SgaD-like (see

) "docking" proteins. In many cases a partial second copy of the domain is present, though it is not always detected by this entry.