SII-SWORD/CoKE huggingface dataset:
PEP-CTERM-box response regulator transcription factor (PEP-CTERM_resp_reg)
Type: Family

This entry represents a protein family that shares full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC (see

). These proteins have a Fis family DNA binding sequence, a response regulator receiver domain, and sigma-54 interaction domain. They are found strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria, where members of

and

also occur.

Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions . Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk . These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more . Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) . The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK.

A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response .
PEP-CTERM system TPR-repeat protein PrsT (PEP-CTERM_TPR_PrsT)
Type: Family

This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system , analogous to the LPXTG/sortase system common in Gram-positive bacteria. The proteins in this entry occur in a species if, and only if, a transmembrane histidine kinase (

) and a DNA-binding response regulator (

) also occur. The present of tetratricopeptide repeats (TPR) suggests they may be involved in protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
Glycosyltransferase GtfA (GtfA)
Type: Family

Glycosyltransferase GtfA is an N-acetylglucosaminyl transferase that is part of the accessory SecA2/SecY2 system specifically required to export serine-rich repeat cell wall proteins usually encoded upstream in the same operon .
Glycosyltransferase-stabilising protein GtfB (GtfB)
Type: Family

Glycosyltransferase-stabilising protein GtfB, together with GtfA, forms a two-protein enzyme complex that is involved in glycosylation. GtfB stabilises the glycosylation activity of GtfA, causing it to partially localise to the cellular membrane where it is more protease resistant .
Accessory Sec system protein translocase subunit SecY2 (SecY2)
Type: Family

Members of this family are restricted to the Firmicutes lineage (low-GC Gram-positive bacteria) and appear to be paralogous to, and much more divergent than, the preprotein translocase SecY. Members include the SecY2 protein of the accessory Sec system in Streptococcus gordonii, involved in export of the highly glycosylated platelet-binding protein GspB .
PEP-CTERM integral membrane protein (PEP-CTERM_IMP)
Type: Family

This family includes a group of uncharacterised proteins found mainly in cyanobacteria. Some members have a PEP-CTERM sequence at the C-terminal (

), but are unusual among PEP-CTERM proteins in having multiple predicted transmembrane segments. The function is unknown. It is proposed that a member of the EpsH family, to be designated exosortase (see

), recognises and cleaves PEP-CTERM proteins in a manner analogous to the cleavage of LPXTG proteins by sortase .
Conserved hypothetical protein CHP02922 (CHP02922)
Type: Family

Two members of this family are found in Colwellia psychrerythraea (strain 34H / ATCC BAA-681) and one each in various other species of Colwellia and Shewanella. One member from C. psychrerythraea is of special interest because it is preceded by the same cis-regulatory site as a number of genes that have the PEP-CTERM domain described by

.
ATPase, V0 complex, C subunit (ATPase_V0-cplx_csu)
Type: Family

This entry represents the subunit C of the V0 complex.

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra-and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release . V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins .

A-type ATPases (archaeal-type ATPases) and V-ATPases, all included in this entry, are thought to have evolved from common ancestral genes .
Isocitrate dehydrogenase, bacteria-type (Isocitrate_DH_bac-typ)
Type: Family

This entry represents a group of isocitrate dehydrogenases found mainly in bacteria, including Isocitrate dehydrogenase [NADP] from Rickettsia typhi. Many of the species containing these proteins appear to have a TCA cycle lacking only a determined isocitrate dehydrogenase.
Peptidyl-prolyl cis-trans isomerase, EpsD-type (PPIase_EpsD)
Type: Family

Proteins in this entry include EpsD from Methylobacillus sp. 12S and belong to the peptidyl-prolyl cis-trans isomerase family. They are located at loci associated with exopolysaccharide biosynthesis and are encoded near a homologue of EpsH (

).
ATPase, A1A0, subunit H (ATPase_A1A0-cplx_hsu)
Type: Family

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

A-ATPases (or A1A0-ATPase) (

) are found exclusively in Archaea and display a close resemblance in structure and subunit composition with V-ATPases, although their function in both ATP synthesis and ATP hydrolysis is closer to that of F-ATPases . A-ATPases are composed of two linked complexes: the A1 complex consisting of seven subunits contains the catalytic core that synthesizes/hydrolyses ATP, while the A0 complex consisting of at least two subunits forms the membrane-spanning pore . The rotary motor in A-ATPases is composed of only two subunits, the stator subunit I and the rotor subunit C . A-ATPases may have arisen as an adaptation to the different cellular needs and the more extreme environmental conditions faced by Archaeal species.

A-ATPases (or A1A0-ATPase) (

) are found exclusively in Archaea and display a close resemblance in structure and subunit composition to V-ATPases, although their function in both ATP synthesis and ATP hydrolysis is closer to that of F-ATPases . A-ATPases are composed of two linked complexes: the A1 complex, consisting of seven subunits, contains the catalytic core that synthesizes/hydrolyses ATP, while the A0 complex, consisting of at least two subunits, forms the membrane-spanning pore . The rotary motor in A-ATPases is composed of only two subunits, the stator subunit I and the rotor subunit C . A-ATPases may have arisen as an adaptation to the different cellular needs and the more extreme environmental conditions faced by Archaeal species.

This entry represents subunit H of the archaeal A-ATPase; it is unclear precisely where subunit H fits into the complex.
2-oxoglutarate dehydrogenase, E2 component (2-oxoglutarate_DH_E2)
Type: Family

This entry represents the mainly actinobacterial clade of the E2 component of the 2-oxoglutarate dehydrogenase complex involved in the TCA cycle. These proteins have multiple domains including the catalytic domain (

), one or two biotin domains (

) and an E3-component binding domain (

).
Orc1/Cdc6-type DNA replication protein, archaea (Orc1/Cdc6_arc)
Type: Family

This set of DNA binding proteins are found exclusively in the archaea and show homology to the origin recognition complex subunit 1/cell division control protein 6 (Orc1/Cdc6) family in eukaryotes. Several members may be found in a genome and interact with each other. The Cdc6/Orc1 protein from the archaeon Pyrococcus furiosus specifically binds to the oriC region .
Nitrogenase iron-iron, delta subunit (Nase_Fe-Fe_dsu)
Type: Family

Nitrogenase, also called dinitrogenase, is the enzyme which catalyses the conversion of molecular nitrogen to ammonia (biological nitrogen fixation). The most widespread and most efficient nitrogenase contains a molybdenum cofactor. This entry, also known as the AnfG family, represents the delta subunit of the iron-only alternative nitrogenase. It is homologous to VnfG, the delta subunit of the vanadium-containing V nitrogenase.
Nitrogenase vanadium-iron, delta subunit (Nase_V-Fe_dsu)
Type: Family

Nitrogenase, also called dinitrogenase, is the enzyme which catalyses the conversion of molecular nitrogen to ammonia (biological nitrogen fixation). The most widespread and most efficient nitrogenase contains a molybdenum cofactor. This entry, also known as the VnfG family, represents the delta subunit of the vanadium-containing V nitrogenase. It is homologous to AnfG, the delta subunit of the iron-only nitrogenase.
Nitrogenase iron-iron, beta subunit (Nase_Fe-Fe_bsu)
Type: Family

NNitrogenase, also called dinitrogenase, is the enzyme which catalyses the conversion of molecular nitrogen to ammonia (biological nitrogen fixation). The most widespread and most efficient nitrogenase contains a molybdenum cofactor. This entry, also known as the AnfK family, represents the beta subunit of the iron-only alternative nitrogenase . It is homologous to NifK and VnfK, of the molybdenum-containing and the vanadium-containing nitrogenases, respectively.
Nitrogenase vanadium-iron protein beta chain (Nase_VnfK)
Type: Family

Nitrogenase, also called dinitrogenase, is the enzyme which catalyses the conversion of molecular nitrogen to ammonia (biological nitrogen fixation) . The most widespread and most efficient nitrogenase contains a molybdenum cofactor. This protein family, VnfK, represents the beta subunit of the vanadium-containing V nitrogenase. It is homologous to NifK and AnfK, of the molybdenum-containing and the iron-only types, respectively.
Nitrogen fixation protein NifM (Nitrogen_fix_NifM)
Type: Family

Members of this entry are found in a subset of nitrogen-fixing bacteria and are annotated as nitrogen fixation protein NifM. NifM is homologous to peptidyl-prolyl cis-trans isomerases and appears to be an accessory protein for NifH, the Fe protein, also called component II or dinitrogenase reductase, of nitrogenase .
Ferredoxin III 4[4Fe-4S], nif-specific (FdIII_4_nif)
Type: Family

This entry consists of ferredoxins which are encoded in the nitrogen fixation regions of many nitrogen-fixing bacteria. The charcterised protein from Rhodobacter capsulatus (Rhodopseudomonas capsulata) is homodimeric and contains two [4Fe-4S] clusters bound per monomer. Although nif-specific, these prtoeins are not universal in nitrogen-fixers as other nitrogenase systems may substitute flavodoxins, or different types of ferredoxin.
RNA polymerase sigma-70-like domain (RNA_pol_sigma-70_dom)
Type: Domain

This entry is found in all varieties of the sigma-70 type sigma factors, including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (

) are included within this entry.

The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.

With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors .

The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. All plastid sigma factors belong to the superfamily of sigmaA/sigma70 and have sequences homologous to the conserved regions 1.2, 2, 3, and 4 of bacterial sigma factors .
Nitrogen fixation negative regulator NifL (N_fixation_neg-reg_NifL)
Type: Family

NifL from Azotobacter vinelandii senses both the redox and fixed nitrogen status to regulate nitrogen fixation. NifL acts by modulating the activity of the nitrogen fixation positive regulator protein NifA; NifL inhibits NifA in response to oxygen and low level of fixed nitrogen. NifA and NifL are encoded by adjacent genes. NifL is FAD-containing, and has a domain architecture similar to that of the cytoplasmic histidine protein kinases, containing two N-terminal PAS domains and a C-terminal transmitter region containing a conserved histidine residue (H domain) and a nucleotide binding GHKL domain corresponding to the catalytic core of the histidine kinases . However, NifL does not exhibit kinase activity and regulates its partner NifA by direct protein-protein interactions rather than phosphorylation.
RNA polymerase sigma-70 RpoE type (RNA_pol_sigma70_RpoE)
Type: Family

The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.

With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors .

The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. All plastid sigma factors belong to the superfamily of sigmaA/sigma70 and have sequences homologous to the conserved regions 1.2, 2, 3, and 4 of bacterial sigma factors .

This entry represents the clade of sigma factors called RpoE. These proteins are variously annotated as sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Nitrogenase iron-iron, accessory protein AnfO (Nase_Fe-Fe_AnfO)
Type: Family

Proteins in this entry include Anf1 from Rhodobacter capsulatus (Rhodopseudomonas capsulata) and AnfO from Azotobacter vinelandii. They are found exclusively in species which contain the iron-only nitrogenase, and are encoded immediately downstream of the structural genes for the nitrogenase enzyme in these species.
RNA polymerase sigma-B factor (RNA_pol_sigma-B)
Type: Family

The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.

With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors .

The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. All plastid sigma factors belong to the superfamily of sigmaA/sigma70 and have sequences homologous to the conserved regions 1.2, 2, 3, and 4 of bacterial sigma factors .

This entry represents the sigma factor, sigmaB. It is restricted to certain species within the order Bacillales including Staphylococcus aureus , Listeria monocytogenes and Bacillus cereus (strain ATCC 14579 / DSM 31) .
RNA polymerase sigma-24-related (RNA_pol_sigma-24-rel)
Type: Family

The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.

With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors .

The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. All plastid sigma factors belong to the superfamily of sigmaA/sigma70 and have sequences homologous to the conserved regions 1.2, 2, 3, and 4 of bacterial sigma factors .

This group of sigma factors are part of the larger sigma-70 family. From homology, tree building, bidirectional best hits and their one-to-a-genome distribution, they appear to represent a conserved family.
Acyltransferase, WS/DGAT/MGAT (Acyl_transf_WS/DGAT)
Type: Family

This bacteria-specific protein family includes a characterised, homodimeric, broad specificity acyltransferase from Acinetobacter sp. (strain ADP1). It has been shown to function as a wax ester synthase, acyl coenzyme A:diacylglycerol acyltransferase, and as a acyl-CoA:monoacylglycerol acyltransferase . This enzyme has been widely studies due to its potential for the production of different compounds, from wax to biofuels .

In the actinobacterial genus Rhodococcus, the homologue of this enzyme plays an essential role in the acumulation of triacylglycerols (TAG), which can reach more than 20% of its cellular dry weight .