SII-SWORD/CoKE huggingface dataset:
3-5 exoribonuclease, actinobacteria (3_5_Exoribonuc_actinobac)
Type: Family

This entry represents 3'-5' exoribonucleases found in Mycobacterium tuberculosis and other Actinobacteria. This exonuclease cleaves single-stranded 3' overhangs of double-stranded RNA, but has no activity with 5' overhangs and negligible endonuclease activity .

Structurally, these enzymes are similar to DEDD family of nucleases. They form stable homodimers and each monomer in these dimers adopts a compact α/β fold in which a central four-stranded β-sheet is surrounded by α-helices .
Ribonuclease J, bacteria (RNase_J_bac)
Type: Family

This entry represents bacterial ribonuclease J. There are two paralogues in Bacillus subtilis, RNase J1 and J2 (RnjA and RnjB). J1 forms a complex with J2, and this complex has both endonuclease and 5'-3' exonuclease activity, playing a role in both rRNA and mRNA stability and degradation. Both J1 and the J1/J2 complex have robust 5'-to-3' exoribonuclease activity in vitro, however, J2 has at least two orders of magnitude weaker exonuclease activity .
Bifunctional ligase/repressor BirA (Bifunct_BirA)
Type: Family

BirA acts both as a biotin ligase and a biotin-operon repressor. In the presence of ATP, BirA activates biotin to form the BirA-biotinyl-5'-adenylate (BirA-bio-5'-AMP) or holoBirA complex. HoloBirA can either transfer the biotinyl moiety to the biotin carboxyl carrier protein (BCCP) subunit of acetyl-CoA carboxylase, or bind to the biotin operator site and inhibit transcription of the operon . The switch between the enzymatic activity and the repressor activity of BirA is regulated by cellular demand for biotin. In conditions of high biotin demand, holoBirA associates with apoBCCP and transfers biotin from bio-5'-AMP to apoBCCP. In conditions of low biotin demand, holoBirA dimerises and binds the biotin operator .
Sensor histidine kinase RcsC (RcsC)
Type: Family

Sensor histidine kinase RcsC forms part of a phosphorelay signal transduction pathway with RcsD and RcsB. RcsC functions as a membrane-associated protein kinase that phosphorylates RcsD in response to environmental signals . The phosphoryl group is then transferred to the response regulator RcsB. The system controls transcription of numerous genes. It was first identified by its role in the regulation of capsular polysaccharide or colanic acid synthesis . Pathways regulated by the Rcs system include maintenance of cell wall integrity, cell division,motility, and virulence . A novel signaling pathway that depends on RcsC, but independent of RcsD and RcsB, has also been described .
Lipid A biosynthesis palmitoleoyltransferase, LpxP (Lipid_A_LpxP)
Type: Family

LpxP catalyses the transfer of palmitoleate from palmitoleoyl-acyl carrier protein (ACP) to Kdo(2)-lipid IV(A) to form Kdo(2)-(palmitoleoyl)-lipid IV(A) . It is required for the biosynthesis of a distinct molecular species of lipid A, which is present only in cells grown at low temperatures .
Mid-cell-anchored protein Z (MapZ)
Type: Family

In Streptococcus pneumoniae, mid-cell-anchored protein Z (MapZ) forms ring structures at the cell equator and moves apart as the cell elongates, therefore behaving as a permanent beacon of division sites. During cell division, a new MapZ ring marks the future cell division site and positions tubulin-like protein FtsZ rings through direct interactions . MapZ is conserved amongst Streptococcaceae and most other Lactobacillales .
Phosphotransferase RcsD (Ptransferase_RcsD)
Type: Family

Phosphotransferase RcsD is a component of the Rcs signaling system. RcsD is a phosphotransfer intermediate between the sensor kinase RcsC and the response regulator RcsB . The system controls transcription of numerous genes. It was first identified by its role in the regulation of capsular polysaccharide or colanic acid synthesis . Pathways regulated by the Rcs system include maintenance of cell wall integrity, cell division,motility, and virulence .
L-2-hydroxyglutarate dehydrogenase, bacteria (L2HG_DH_bact)
Type: Family

This family of L-2-hydroxyglutarate dehydrogenase includes lhgD from E. coli, which catalyzes the dehydrogenation of L-2-hydroxyglutarate (L2HG) to alpha-ketoglutarate and couples to the respiratory chain by feeding electrons from the reaction into the membrane quinone pool .
1,4-dihydroxy-2-naphthoyl-CoA hydrolase, MenI (MenI)
Type: Family

MenI (also known as ydiI) is a thioesterase catalysing the hydrolysis of 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) to 1,4-dihydroxy-2-naphthoate (DHNA). It also shows significant activity toward a wide range of acyl-CoA thioesters, and minimal activity toward benzoyl-holoEntB .
Transcriptional regulatory protein RcsB (RcsB)
Type: Family

RcsB, together with RcsC and RcsD, is a component of the Rcs signaling system. RcsC functions as a membrane-associated protein kinase that phosphorylates RcsD in response to environmental signals. The phosphoryl group is then transferred to the response regulator RcsB, which binds to regulatory DNA regions. RcsB can function as a homodimer or form a heterodimer with the auxiliary activator RcsA . The system regulates expression of numerous genes, including genes involved in colanic acid capsule synthesis, biofilm formation, and growth . It is also involved, with GadE, in controlling glutamate-dependent acid resistance and, with BglJ, in derepression of the cryptic bgl operon .
Lipopolysaccharide assembly protein B (LapB)
Type: Family

Lipopolysaccharide assembly protein B (LapB), together with LapA, is involved in assembling lipopolysaccharide . E. coli LapB, also known as YciM, has been shown to act by altering LpxC, an enzyme that catalyses the first committed step of lipid A biosynthesis .
Transcriptional regulatory protein RcsA (RcsA)
Type: Family

RcsA is a component of the Rcs phosphorelay signaling system. Pathways regulated by the Rcs system include maintenance of cell wall integrity, cell division, motility, and virulence. The pathway involves a histidine kinase (RcsC), a response regulator (RcsB), a phospho-transfer protein (RcsD), a signal transductor (RcsF) and the auxiliary activator protein (RcsA) . The response regulator RcsB associates with an unstable protein RcsA to bind to an RcsAB box in the promoter region of several genes, though not all genes require RcsA . RcsA and RcsB regulate the polysialic and colanic acids metabolism in Escherichia coli .
tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase (TYW2_archaea)
Type: Family

This entry represents tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase TYW2 from archaea. It is a s-adenosyl-L-methionine-dependent transferase that acts as a component of the wyosine derivatives biosynthesis pathway. It catalyses the transfer of the alpha-amino-alpha-carboxypropyl (acp) group from S-adenosyl-L-methionine to 4-demethylwyosine (imG-14), forming 7-aminocarboxypropyl-demethylwyosine (wybutosine-86) at position 37 of tRNA(Phe) .
Chorismate dehydratase (MqnA)
Type: Family

Chorismate dehydratase, also known as menaquinone biosynthetic enzyme MqnA, catalyses the dehydration of chorismate into 3-[(1-carboxyvinyl)oxy]benzoate, a step in an alternative pathway for the biosynthesis of menaquinone (MK, vitamin K2) . In prokaryotes, menaquinone is an obligatory component of the electron-transfer pathway.
1,4-dihydroxy-6-naphtoate synthase (MqnD)
Type: Family

1,4-dihydroxy-6-naphtoate synthase, also known as menaquinone biosynthetic enzyme MqnD, catalyses the conversion of cyclic dehypoxanthine futalosine (cyclic DHFL) into 1,4-dihydroxy-6-naphthoate, a step in the biosynthesis of menaquinone (MK, vitamin K2) through an alternative pathway operating in some bacteria, such as Streptomyces and the pathogenic species Helicobacter pylori and Campylobacter jejuni . In prokaryotes, menaquinone is an obligatory component of the electron-transfer pathway.
Cell division protein ZapE (ZapE)
Type: Family

ZapE is a cell division protein found in Gram-negative bacteria. The bacterial cell division process relies on the assembly, positioning, and constriction of FtsZ ring (the so-called Z-ring), a ring-like network that marks the future site of the septum of bacterial cell division [

,

. ZapE is a Z-ring associated protein required for cell division under low-oxygen conditions suggesting that ZapE is a stress-regulated cell division protein . It is an ATPase that appears at the constricting Z-ring late in cell division. It reduces the stability of FtsZ polymers in the presence of ATP in vitro .
Cardiolipin synthase C (Cardiolipin_synth_ClsC)
Type: Family

Cardiolipin (CL) synthases catalyse the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (diphosphatidylglycerol) and glycerol . In E. coli, three genes encoding CLs have been identified as clsA/B/C. This entry includes ClsC protein (also known as ymdC) from E. coli and other Enterobacteriaceae .
Cardiolipin synthase B (Cardiolipin_synth_ClsB)
Type: Family

Cardiolipin (CL) synthases catalyse the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (diphosphatidylglycerol) and glycerol . In E. coli, three genes encoding CLs have been identified as clsA/B/C. This entry includes ClsB (also known as ybhO) from E. coli and other Proteobacteria .
Beta-barrel assembly-enhancing protease (Protease_BepA)
Type: Family

Beta-barrel assembly-enhancing protease (BepA) functions both as a chaperone and a metalloprotease. BepA enhances biogenesis of LptD, an essential outer membrane protein (OMP) involved in OM transport and assembly of lipopolysaccharide, and is responsible for the degradation of incorrectly folded LptD. It also interacts with components of the β-barrel assembly machinery (BAM) complex. These observations indicate that BepA maintains the integrity of the outer membrane both by promoting assembly of OMPs and by proteolytically eliminating misfolded OMPs .
Cardiolipin synthase, Firmicutes-type (Cardiolipin_synth_Firmi)
Type: Family

This entry represents cardiolipin synthases (Cls) mostly from Firmicutes. Cardiolipin (CL) synthases catalyse the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (diphosphatidylglycerol) and glycerol . Bacillus subtilis has three genes (clsA, ywjE and ywiE) for CL synthase; the main role in CL synthesis being played by clsA . This entry includes ClsA and YwiE proteins from Bacillus subtilis .
Sulfoquinovose isomerase (SQ_isomerase)
Type: Family

Escherichia coli and other Enterobacteria can perform sulphoglycolysis in addition to standard glycolysis. In this pathway, sulphoquinovose (SQ) -a sulfonic acid derivative of glucose- is used as source of carbon and energy .

Sulfoquinovose isomerase is an enzyme of the sulfoquinovose (SQ) degradative pathway. It catalyses the isomerisation of SQ to 6-deoxy-6-sulfo-D-fructose (SF) .
3-sulfolactaldehyde reductase (SLA_reductase)
Type: Family

This entry represents 3-sulfolactaldehyde (SLA) reductase from Enterobacteriaceae. It reduces 3-sulfolactaldehyde to 2,3-dihydroxypropane 1-sulfonate (DHPS) . It is one of the core enzymes involved in the sulphoquinovose (SQ) metabolic process .
Sulfofructose kinase (SF_kinase)
Type: Family

Escherichia coli and other Enterobacteria can perform sulphoglycolysis in addition to standard glycolysis. In this pathway, sulphoquinovose (SQ) -a sulfonic acid derivative of glucose- is used as source of carbon and energy .

Sulfofructose kinase phosphorylates 6-deoxy-6-sulfo-D-fructose (SF) to 6-deoxy-6-sulfo-D-fructose 1-phosphate (SFP). It is part of the sulphoquinovose degradative pathway .
Large ribosomal subunit protein uL15 (Ribosomal_uL15)
Type: Family

This entry represents the large ribosomal subunit protein family uL15. Previously, these proteins were known as L15 from bacteria, L28 from yeast, and L27A from eukaryotes.

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 .
Ribonuclease J, archaea (RNase_J_arc)
Type: Family

Archaeal ribonuclease J shares protein sequence similarity with bacterial RNase J. In Pyrococcus abyssi, ribonuclease J is an exoribonuclease with a 5' end dependence and a 5' to 3' directionality. It may be involved in RNA degradation. It also degrades ssNDA but not dsDNA .
DEAD-box ATP-dependent RNA helicase CshA (DEAD_helicase_CshA)
Type: Family

DEAD-box ATP-dependent RNA helicase CshA is an enzyme that unwinds dsRNA in both 5'- and 3'-directions. It also has RNA-dependent ATPase activity and plays a role in ribosomal 50S subunit assembly .
DEAD-box ATP-dependent RNA helicase CshB (CshB)
Type: Family

DEAD-box RNA helicases play important roles in remodelling RNA molecules and in facilitating a variety of RNA-protein interactions . CshB is a DEAD-box RNA helicase involved in cold tolerance, motility, and tolerance to heat, alkali and oxidative stress . It may work in conjunction with the cold shock proteins to ensure proper initiation of transcription at low and optimal temperatures .
Putative DNA helicase Rad25, archaea (Helicase_Rad25_arc)
Type: Family

This entry represents a family of putative helicases from archaea with homology to DNA repair helicase RAD25.
D-allose kinase (AlsK)
Type: Family

D-allose kinase AlsK catalyses the phosphorylation of D-allose to D-allose 6-phosphate . It also possesses weak phosphoryl transfer activity toward the alternate substrate d-glucose in vitro .
Uncharacterised protein family CHP04551 (CHP04551)
Type: Family

Members of this family are proteins of unknown function, about 620 amino acids in length, and universal in but restricted to the Myxococcales, an order within the Deltaproteobacteria.
Putative large structural protein (Lepto_longest)
Type: Family

Members of this family are restricted so far to the lineage Leptospira, where they may be the longest protein encoded by the genome. Two or three paralogues are often found. Sequences have significant length variability, with an intein feature most full-length members of this family share. Oddly, members closely related in sequence up to the start of the intein (

) usually show very little sequence similarity C-terminal to the end of the intein (

).
Lipoprotein, tandem type (Lepto_lipo)
Type: Family

Members of this family are lipoproteins restricted (so far) to the genus Leptospira, sometimes with several paralogues clustered with each other, such as four in a row (out of six) in Leptospira interrogans str. UI 13372. The tandem set may be co-clustered with a putative structural protein that is usually the longest encoded by the leptospiral genome (and that often is an intein-containing protein).
YaiO, beta-barrel domain (Beta-barrel_YaiO)
Type: Domain

Proteins in this entry share a domain of bacterial outer membrane β-barrel, up to the protein C-terminal residue (usually Phe or Trp). The member YaiO was experimentally shown to be localised to the outer membrane .
Putative ccm operon protein (Put_ccm)
Type: Family

Members of this protein family are small (typically less than 50 amino acids in length), with the first half highly hydrophobic like transmembrane α helices and containing a nearly invariant tyrosine residue. Members from the Desulfovibrionales appear in the position of ccmD of system I c-type cytochrome biogenesis operons (

). This family and ccmD appear very similar in sequence properties, but the very low level of actual sequence identify makes it unclear that the similarity reflects homology per se .
Three transmembrane helix protein (3TM_Mycoplasma)
Type: Family

Members of this rare family are small, highly hydrophobic, and restricted so far to the genus Mycoplasma, where it appears not to be essential. All members have three hydrophobic transmembrane helical segments.
Substrate import-associated zinc metallohydrolase lipoprotein (LP_HExxH_w_TonB)
Type: Family

Members of this family are lipoproteins with the typical zinc metallohydrolase HExxH motif and additional similarities to a better-documented zinc peptidase family, MtfA (

). Up to five members of this protein family occur per genome, in the context of certain gene pairs related to RagA and RagB, or to SusC and SusD. Those gene pairs, like the present family, are restricted to the Bacteriodetes, may number up to 100 pairs per genome, and are linked to TonB-dependent uptake of biopolymer-derived nutrients such as glycans. A possible function for this lipoprotein is to hydrolyse larger molecules to prepare substrates for import and utilisation.
HaoA-associated protein HaoB (HaoB_nitrify)
Type: Family

Members of this family occur as the HaoB protein, encoded next to the homotrimeric HaoA, a hydroxylamine oxidoreductase protein with eight heme groups. The haoB gene is cotranscribed with haoA, but its function is unknown . It appears all species with this enzyme are nitrifying bacteria .
DnaD family protein (DnaD_Mollicutes)
Type: Family

This entry represents a group of Mollicutes proteins homologous to the N-terminal region of the Bacillus subtilis DnaD protein. Their function is not clear.
MOLPALP family lipoprotein (Mollicu_LP)
Type: Family

Members of this family are surface lipoproteins, about 900 amino acids in length, found only in the Mollicutes; hence the name MOLPALP (Mollicutes Paralogous Lipoprotein).
Fe-coproporphyrin III synthase AhbC, Proteobacteria type (Ahb_Proteobacteria)
Type: Family

This entry represents one of a pair of radical SAM enzymes involved in the alternative heme biosynthesis (ahb) pathway for heme b biosynthesis from siroheme. This anaerobic pathway occurs in sulfate-reducing bacteria and methanogens. A very similar pair of radical SAM enzymes, NirJ1 and NirJ2 (

,

) is involved in heme d1 biosynthesis in species such as Heliobacillus mobilis and Heliophilum fasciatum.
T5SS/PEP-CTERM-associated repeat (T5SS_PEPC_rpt)
Type: Repeat

This entry describes a repeat about 50 amino acids in length. Most proteins with this repeat have a C-terminal autotransporter domain (

) and/or an N-terminal type V secretion system signal peptide (

), while others instead have a C-terminal PEP-CTERM domain (

).
AdoMet-dependent heme synthase AhbD (rSAM_AhbD_hemeb)
Type: Family

Members of this family are AhbD (alternative heme biosynthetic protein D), a radical SAM enzyme in sulfate-reducing bacteria and methanogens that performs the last decarboxylations to synthesise heme b from Fe-coproporphyrin III. This entry includes DVU_0855 from Desulfovibrio vulgaris, which may be involved in heme d1 biosynthesis .
Choline trimethylamine-lyase (Choline_CutC)
Type: Family

Members of this family, homologues to pyruvate formate-lyases and benzylsuccinate synthases, are glycine radical enzymes that appear to act as choline TMA-lyase, that is, to perform a C-N bond cleavage turning choline into trimethylamine (TMA) plus acetaldehyde. The gene symbol is cutC, for choline utilisation. The activase, CutD, is a radical SAM enzyme .
Beta-methylarginine biosynthesis bifunctional aminotransferase (3metArgNH2trans)
Type: Family

This entry represents a bifunctional aminotransferase that catalyses the first and third steps in the three-step conversion of arginine to beta-methylarginine. It first converts arginine to 2-ketoarginine, then converts 3-methyl-2-ketoarginine to 3-methylarginine. Genes that encode proteins in this family are found to be next to a 2-ketoarginine methyltransferase (

) .
2-ketoarginine methyltransferase (MrsA)
Type: Family

This entry represents MrsA, a S-adenosylmethionine (SAM)-dependent methyltransferase that can convert 5-guanidino-2-oxo-pentanoic acid into 5-guanidino-3-methyl-2-oxo-pentanoic acid . It is involved in the biosynthesis of MeArg (3-methylarginine), a potent antibiotic produced by Pseudomonas syringae pv. syringae against the closely related soybean pathogen P.syringae pv. glycinea .
GMC family mycofactocin-associated oxidreductase (GMC_mycofac_OxRdtase)
Type: Family

This entry represents a group of dehydrogenases belonging to the glucose-methanol-choline oxidoreductase (GMC oxidoreductase) family. Proteins in this entry are restricted to Gordoniaceae and seem to replace the related glucose-methanol-choline oxidoreductase family (

) from other Actinobacteria. Members of both families are associated with the mycofactocin biosynthesis operon in Actinobacteria .
Thiaminase-1 (Thiaminase_BcmE)
Type: Family

This entry represents thiamine pyridinylase (

), also known as thiaminase I, which is a secreted, thiamine-degrading enzyme. The gene encoding this protein, BcmE, is located in most cases in the bacimethrin biosynthetic gene cluster .
Conserved hypothetical protein (CLB_0814_fam)
Type: Family

This entry represents a group of conserved hypothetical proteins from a narrow range of species. In Clostridium botulinum A ATCC 19397, the gene occurs immediately after a five gene operon for biosynthesis of the natural product bacimethrin, a thiamin antivitamin antibiotic.
Cyclodipeptide synthase (CDPS)
Type: Family

Cyclodipeptide synthase (CDPS) is a tRNA-dependent peptide bond-forming enzyme that uses aminoacyl-tRNAs (aa-tRNAs) as substrates to synthesise the two peptide bonds of various cyclodipeptides, which are the precursors of many natural products with biological activities . This entry includes the cyclodityrosine synthase from Mycobacterium tuberculosis (an essential gene), the cyclo(L-Phe-L-Leu) synthase from Streptomyces noursei and cyclodileucine synthase YvmC from Bacillus licheniformis. Many cyclodipeptide synthases are found next to a cytochrome P450 that further modifies the product .
Cytochrome P450, CypX (CypX)
Type: Family

This entry represents a group of cytochrome P450 enzymes, including pulcherriminic acid synthase CypX (CYP134A1) from Bacillus subtilis. CypX is involved in the biosynthesis of pulcherrimin, a red extracellular pigment. It catalyses the oxidation of cyclo(L-Leu-L-Leu) (cLL) to yield pulcherriminic acid, which forms pulcherrimin via a nonenzymic reaction with Fe3+ . This entry does not include CYP121 (Rv2275) from Mycobacterium tuberculosis, adjacent to the cyclodityrosine synthetase Rv2276.