SII-SWORD/CoKE huggingface dataset:
Large ribosomal subunit protein eL8, archaea (Ribosomal_eL8_arc)
Type: Family

This entry specifically identifies the archaeal version of the large ribosomal complex eL8 protein, previously designated L7Ae. These are multifunctional RNA-binding proteins that recognises the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs . It interacts with protein L15e.

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 .
Proteasome ATPase (Proteasome_ATPase)
Type: Family

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an ε-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.
Proteasome subunit beta, actinobacteria (PSB_actinobac)
Type: Family

Threonine peptidases are characterised by a threonine nucleophile at the N terminus of the mature enzyme. The threonine peptidases belong to clan PB or are unassigned, clan T-. The type example for this clan is the archaean proteasome beta component of Thermoplasma acidophilum.

This entry represents Proteasome subunit beta from Streptomyces coelicolor and similar proteins of found predominantly in Actinobacteria . PSB is a component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. In Mycobacterium tuberculosis, the proteasome is able to cleave oligopeptides not only after hydrophobic but also after basic, acidic and small neutral residues . In complex with the ATPase Mpa, it degrades protein targets conjugated to a prokaryotic ubiquitin-like protein (Pup) . It is essential for persistence of the pathogen during the chronic phase of infection in the host and may also function to recycle amino acids under nutrient starvation, thereby enabling the cell to maintain basal metabolic activities . It has been related to the resistance of this bacteria to antimicrobial antifolates via regulating both folate reduction and cytokinin production .

Members of this protein family are threonine peptidases belonging to MEROPS peptidase family T1 (clan PB(T)), subfamily T1A.
PEP-CTERM/exosortase system-associated acyltransferase, predicted (PEP-CTERM/exosrtase_acylTfrase)
Type: Family

Members of this protein family are restricted to bacterial species with the PEP-CTERM/exosortase system predicted to act in exopolysaccharide-associated protein targeting . Different sequence analysis methodologies reveal relationships to the acyltransferase family that includes N-acyl-L-homoserine lactone synthetase. Several members of this family may be found in a single genome. These proteins likely contribute to chemical modifications in exopolysaccharide and biofilm structural material production.
2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (SHCHC_synthase_MenH)
Type: Family

This protein catalyzes the formation of SHCHC, or (1 R,6 R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate, by elmination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) . Note that SHCHC synthase activity previously was attributed to MenD, which in fact is SEPHCHC synthase.
Polyphosphate kinase 2, PA0141 (PPK2_PA0141)
Type: Family

Members of this protein family are designated polyphosphate kinase 2 (PPK2) after the characterised protein in Pseudomonas aeruginosa . This family comprises one of three well-separated clades in the larger family described by Pfam model

. GDP-polyphosphate phosphotransferase, also known as Polyphosphate kinase PPK2 1 (gene PA0141) (

) from this family has been shown capable of operating in reverse, with GDP preferred (over ADP) as a substrate, producing GTP (or ATP) by transfer of a phosphate residue from polyphosphate . Most species with a member of this family also encode a polyphosphate kinase 1 (PPK1).
L-aspartate dehydrogenase, archaeal (Asp_DH_arc)
Type: Family

This entry represents L-aspartate dehydrogenase, as shown for the NADP-dependent enzyme TM_1643 of Thermotoga maritima. Members lack homology to NadB, the aspartate oxidase (

) of most mesophilic bacteria (described by

), which this enzyme replaces in the generation of oxaloacetate from aspartate for the NAD biosynthetic pathway. All members of the seed alignment are found adjacent to other genes of NAD biosynthesis, although other uses of L-aspartate dehydrogenase may occur.
Polyphosphate kinase-2-related (PPK2-related)
Type: Domain

Inorganic polyphosphate (polyP) plays a role in metabolism and regulation and has been proposed to serve as a energy source in a pre-ATP world. In prokaryotes, the synthesis and utilisation of polyP are catalysed by PPK1, PPK2 and polyphosphatases. PPK2s can be subdivided into three classes: class I preferentially phosphorylates nucleoside diphosphates, class II converts nucleoside monophosphates into diphosphates and class III can phosphorylate either nucleoside mono- or diphosphates . This domain can be found in one or two copies; in class I proteins there is a single copy of this domain (which preferentially catalyse polyP-dependent phosphorylation of ADP to ATP), whereas in class II proteins (which phosphorylate AMP to ADP) there are 2 fused PPK2 domains. The structure of PPK2 from Pseudomonas aeruginosa has revealed a 3-layer α/β/α-sandwich fold with an α-helical lid similar to the structures of microbial thymidylate kinases .
Polyphosphate:AMP phosphotransferase (PolyP_AMP_Tfrase)
Type: Family

Members of this protein family contain a domain duplication. The characterised member from Acinetobacter johnsonii is polyphosphate:AMP phosphotransferase (PAP), which can transfer the terminal phosphate from poly(P) to AMP, yielding ADP. In the opposite direction, this enzyme can synthesise poly(P). Each domain of this protein family is homologous to polyphosphate kinase, an enzyme that can run in the forward direction to extend a polyphosphate chain with a new terminal phosphate from ATP, or in reverse to make ATP (or GTP) from ADP (or GDP).
Protein translocase subunit SecA2 (SecA2)
Type: Family

Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii .
Phosphomutase MSMEG4193, putative (Phosphomutase_MSMEG4193_put)
Type: Family

This entry represents a three-gene system broadly conserved among the Actinobacteria which includes MSMEG_4193 and homologues. Another member of the trio is a probable kinase, related to phosphatidylinositol kinases; that context supports the hypothesis that this protein acts as a phosphomutase.
Integral membrane YkoY (CHP03716_TM_YkoY)
Type: Family

This entry represents a group of proteins that are commonly preceded by a structured RNA element called the yybP-ykoY leader, or SraF, which may precede one or several genes in a genome. Members of this highly hydrophobic protein family often are preceded by a yybP-ykoY leader, which may serve as a riboswitch. From the larger group of TerC homologues, this subfamily contains proteins YceF and YkoY from Bacillus subtilis. A transport function is proposed .
Sulfopyruvate decarboxylase, beta subunit (Sulfopyruvate_deCO2ase_bsu)
Type: Domain

Nearly every member of this entry is the beta subunit, or else the C-terminal region, of sulfopyruvate decarboxylase, in an archaeal species capable of coenzyme M biosynthesis. However, the enzyme also occurs in Roseovarius nubinhibens ISM in a degradative pathway, where the resulting sulfoacetaldehyde is desulfonated to acetyl phosphate, then converted to acetyl-CoA .
Serine/threonine-protein kinase Bud32 (Bud32)
Type: Family

Serine/threonine-protein kinase Bud32 is conserved from Archaea to human. In many Archaeal genomes, Kae1 and Bud32 are fused . The complex is homologous to the Kae1 and Bud32 subunits of the eukaryotic KEOPS complex (composed of Bud32, Kae1, Cgi121, Pcc1 and Gon7), an apparently ancient protein kinase-containing molecular machine that is essential for t6A tRNA modification .
tRNA threonylcarbamoyl adenosine modification protein TsaB (T6A_TsaB)
Type: Family

TsaB, previously known as YeaZ, has been shown to be involved in N6-threonylcarbamoyladenonsine (t(6)A) biosynthesis, together with YgjD (TsaD), YrdC (TsaC), and YjeE (TsaE) .
ABC transporter, urea permease, UrtC (ABC_trnspt_urea_permease_UrtC)
Type: Family

Members of this protein family are ABC transporter permease subunits restricted to the Archaea. Several lines of evidence suggest this protein is functionally analogous, as well as homologous, to the UrtC subunit of the Corynebacterium glutamicum urea transporter. All members of the operon show sequence similarity to urea transport subunits, the gene is located near the urease structural subunits in two of three species, and partial phylogenetic profiling identifies this permease subunit as closely matching the profile of urea utilisation.
Tungstate ABC transporter, substrate-binding protein WtpA (ABC_trnspt_W-bd_WtpA)
Type: Family

Members of this protein family are tungstate (and, more weakly, molybdate) binding proteins of tungstate(/molybdate) ABC transporters, as first characterised in Pyrococcus furiosus. Note that this family is homologous to molybdate transporters, and that at least one other family of tungstate transporter binding protein, TupA, also exists.

Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. Most of the bacterial ABC (ATP-binding cassette) importers are composed of one or two transmembrane permease proteins, one or two nucleotide-binding proteins and a highly specific periplasmic solute-binding protein. In Gram-negative bacteria the solute-binding proteins are dissolved in the periplasm, while in archaea and Gram-positive bacteria, their solute-binding proteins are membrane-anchored lipoproteins .
ParB-related, ThiF-related cassette, protein A (PRTRC_protein-A)
Type: Family

A novel genetic system characterised by six major proteins, included a ParB homologue and a ThiF homologue, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated protein A.
ParB-related, ThiF-related cassette, ThiF (PRTRC_ThiF)
Type: Family

A novel genetic system characterised by six major proteins, included a ParB homologue and a ThiF homologue, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. This family is the PRTRC system ThiF family protein.
Gallidermin ABC transporter, ATP-binding subunit (ABC_Gallidermin_ATP-bd)
Type: Family

Entry

represents the family of all lantibiotics related to gallidermin, including epidermin, mutatin, and nisin. This protein family describes the ATP-binding subunit of a gallidermin/epidermin class lantibiotic protection transporter. It is largely restricted to gallidermin-family lantibiotic biosynthesis and export cassettes, but also occurs in orphan transporter cassettes in species that lack candidate lantibiotic precursor and synthetase genes.
Sulfopyruvate decarboxylase, alpha subunit (Sulfopyruvate_deCO2ase_alpha)
Type: Domain

This entry represents the alpha subunit, or the N-terminal region, of sulfopyruvate decarboxylase, an enzyme of coenzyme M biosynthesis. Coenzyme M is found almost exclusively in the methanogenic archaea. However, the enzyme also occurs in Roseovarius nubinhibens ISM in a degradative pathway, where the resulting sulfoacetaldehyde is desulfonated to acetyl phosphate, then converted to acetyl-CoA .
Conjugative coupling factor TraG/TraD, PFGI-1 (Conj_coupling_TraG/TraD_PFGI-1)
Type: Family

Members of this family are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion.
Exosortase, archaea (Exosortase_arc)
Type: Family

Members of this family are archaeal homologues to bacterial PEP-CTERM-sorting protein exosortase (

) . Members of this family are found in species with an archaeal variant sorting motif, PEF-CTE (

). They are found in the thermoacidophilic Aciduliprofundum boonei, the mesophilic psychromethanogens Methanosarcina mazei and Methanococcoides burtonii, and in Ferroglobus placidus DSM 10642.
Exosortase, cyanobacteria (Exosortase_cyanobac)
Type: Family

The predicted protein-sorting transpeptidase that we call exosortase (see

) has distinct subclasses that associated with different types of exopolysaccharide production loci and/or different taxonomic lineages. We designate this relatively divergent cyanobacterial type to be type 3. We propose the gene symbol xrtC. This type coexists with a

-recognised form in Nostoc sp PCC 7120.
Metallophosphoesterase, PPA1498 (Metallophosphoesterase_PPA1498)
Type: Family

This entry describes a small collection of probable metallophosphoresterases, related to

but with long inserts separating some of the shared motifs such that the homology is apparent only through multiple sequence alignment. Members of this protein family, in general, have a Sec-independent TAT (twin-arginine translocation) signal sequence, N-terminal to the region modeled by this HMM. Members include YP_056203.1 from Propionibacterium acnes KPA171202.
Metallophosphoesterase, RPA4764 (Metallophosphoesterase_RPA4764)
Type: Family

This entry describes a small collection of probable metallophosphoresterases, related to

. Members of this protein family usually have a Sec-independent TAT (twin-arginine translocation) signal sequence, N-terminal to the region modeled by this HMM. This model and

divide a narrow clade of

-related enzymes.
ABC transporter, anchored repeat-type, ATP-binding subunit (ABC_trspt_anch-rpt_ATP-bd)
Type: Family

This protein family is the ATP-binding cassette subunit of binding protein-dependent ABC transporter complex that strictly co-occurs with

. TIGRFAMs model

describes a protein domain that occurs singly or as one of up to three repeats in proteins of a number of Actinobacteria, including Propionibacterium acnes KPA171202. The

domain occurs both in an adjacent gene for the substrate-binding protein and in additional (often nearby) proteins, often with LPXTG-like sortase recognition signals. Homologous ATP-binding subunits outside the scope of this family include manganese transporter MntA in Synechocystis sp PCC 6803 and chelated iron transporter subunits. The function of this transporter complex is unknown.
Conjugation system ATPase, TraG (Conjugation_ATPase_TraG)
Type: Family

Members of this family include the predicted ATPase, TraG, encoded by transfer region genes of conjugative transposons of Bacteroides, such as CTnDOT, found on the main chromosome. Members also include TraG homologues residing on plasmids in Bacteroides. The protein family is related to the conjugative transfer system ATPase VirB4.
Sortase system, histidine kinase (Sortase_His-kinase)
Type: Family

This histidine kinase protein is paired with an adjacent response regulator (

) gene. It co-occurs with a variant sortase enzyme (

), usually in the same gene neighbourhood, in proteobacterial species most of which are marine, and with an LPXTG motif-containing sortase target conserved protein (

). Sortases and LPXTG proteins are far more common in Gram-positive bacteria, where sortase systems mediate attachment to the cell wall or cross-linking of pilin structures. We give this predicted sensor histidine kinase the gene symbol psdS, for Proteobacterial Dedicated Sortase system Sensor histidine kinase.
Proteobacterial sortase system peptidoglycan-associated protein (PdsO)
Type: Family

A newly defined histidine kinase (

) and response regulator (

) gene pair occurs exclusively in Proteobacteria, mostly of marine origin, nearly all of which contain a subfamily 6 sortase (

) and its single dedicated target protein (

) adjacent to to the sortase. This protein family shows up in only in those species with the histidine kinase/response regulator gene pair, and often adjacent to that pair. It belongs to the OmpA protein family (

). Its function is unknown. We assign the gene symbol pdsO, for Proteobacterial Dedicated Sortase system OmpA family protein.
Conserved hypothetical protein CHP03792 (CHP03792)
Type: Family

Members of this family are found predominantly in Cyanobacteria. These proteins are small, with around 100-150 amino acids. The function is unknown.
NHLP leader peptide domain (TOMM_pelo)
Type: Domain

This entry represents a domain that is conserved among a large number of putative thiazole/oxazole-modified microcins (TOMM), including PoyA from Bacterium symbiont subsp. Theonella swinhoei. As a leader peptide domain, it is likely to be removed from the mature product. This domain is unusual in several ways. First, it is longer than most previously described RNP leader peptides. Second, most of the domain is homologous to nitrile hydratase alpha subunits . Finally, it appears that this domain correlates with a specific family of cleavage/export proteins while members undergo modifications by different classes of peptide maturase, including cyclodehydratases, lantibiotic synthases, radical SAM peptide maturases. This family is expanded especially in Pelotomaculum thermopropionicum SI .
NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein (NHPM_micro_ABC1)
Type: Family

This protein describes an multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N terminus.

describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHPM, Nitrile Hydratase Propeptide Microcin.
NHPM bacteriocin system ABC transporter, ATP-binding protein (NHPM_micro_ABC2)
Type: Family

Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (

), which has an N-terminal propeptide cleavage domain, and an HlyD homologue (

). In a number of genomes, a conserved propeptide sequence with a classic Gly-Gly motif
Nif11-like leader peptide (CHP03798_Ocin)
Type: Domain

This entry describes a conserved, fairly long (about 65 residue) leader peptide region for a family of putative ribosomal natural products (RNP) of small size. Members of the seed alignment (most sequences scoring better than 54 bits to the HMMER 2 model) tend to have the Gly-Gly motif as the last two residues of the matched region. This is a cleavage site for a combination processing/export ABC transporter with a peptidase domain. Members include the prochlorosins, lantipeptides from Prochlorococcus .
Aspartate 1-decarboxylase, pyridoxal-dependent (Asp_decarboxylase_pyridox)
Type: Family

This enzyme is proposed here to be a form of aspartate 1-decarboxylase, pyridoxal-dependent, that represents a non-orthologous displacement to the more widely distributed pyruvoyl-dependent form (

). Aspartate 1-decarboxylase makes beta-alanine, used usually in pathothenate biosynthesis, by decarboxylation from asparatate. A number of species with the PanB and PanC enzymes, however, lack PanD. This protein family occurs in a number of Proteobacteria that lack PanD. This enzyme family appears to be a pyridoxal-dependent enzyme (see

). The family was identified by Partial Phylogenetic Profiling; members in Geobacter sulfurreducens, Geobacter metallireducens, and Pseudoalteromonas atlantica are clustered with the genes for PanB and PanC. We suggest the gene symbol panP (panthothenate biosynthesis enzyme, Pyridoxal-dependent).
Aspartate 4-decarboxylase (Aspartate_4-decarboxylase)
Type: Family

This enzyme, aspartate 4-decarboxylase (

), removes the side-chain carboxylate from L-aspartate, converting it to L-alanine plus carbon dioxide. It is a PLP-dependent enzyme, homologous to aspartate aminotransferase (

).
Gloeobacter/Verrucomicrobia repeat (Gloeo/Verruco_rpt)
Type: Repeat

This entry describes a repeat originally found in proteins from two species of Verrucomicrobia (Chthoniobacter flavus and Verrucomicrobium spinosum) and in four different proteins of Gloeobacter violaceus PCC7421. In the Verrucomicrobial species, the repeat region is followed by a PEP-CTE protein-sorting signal, suggesting an extracellular location. Members of this group of proteins are found in different bacterial taxa.
Putative glutamate/gamma-aminobutyrate antiporter (Glu/GABA_antiporter_put)
Type: Family

Members of this protein family (GadC) are antiporters thought to import glutamine and export gamma-aminobutyrate as part of an acid resistance system, although glutamate might also be transported. Some members are found adjacent to a glutamate decarboxylase (GadB), which converts glutamate (Glu) to gamma-aminobutyrate (GABA). However, the majority belong to genome contexts with a glutaminase (converts Gln to Glu) as well as the decarboxylase that converts Glu to GABA. The exact specificity of the transporter remains uncertain. Note that the gene symbol gadC is used both for this antiporter and for known glutamate/gamma-aminobutyrate antiporters such as in Escherichia coli.