SII-SWORD/CoKE huggingface dataset:
Ion-translocating oxidoreductase complex, subunit RnfG/RsxG (Ion_transpt_RnfG/RsxG)
Type: Family

The six-subunit complex RnfABCDGE in Rhodobacter capsulatus (Rhodopseudomonas capsulata) encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation . A closely related complex in Escherichia coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized . Although this family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR family, a Na(+)-translocating NADH-quinone reductase (

), RnfABCDGE is distinct.
2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase (ADH_synthase)
Type: Family

This entry represents a family of enzymes related to fructose-bisphosphate aldolase. This enzyme catalyses a transaldol reaction between 6-deoxy-5-ketofructose 1-phosphate (DKFP) and L-aspartate semialdehyde (ASA) with an elimination of hydroxypyruvaldehyde phosphate to yield 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonic acid (ADH). It plays a key role in an alternative pathway of the biosynthesis of 3-dehydroquinate (DHQ), which is involved in the canonical pathway for the biosynthesis of aromatic amino acids. It can also catalyse the cleavage of fructose-1,6-bisphosphate (FBP) to glyceraldehyde-3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP) .
Redox-sensitive transcriptional activator SoxR (Redox-sen_tscrpt-act_SoxR)
Type: Family

SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulphur cluster activates SoxR. The physiological role in Escherichia coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species .
Probable transcription termination protein NusA, archaeal (NusA_arc)
Type: Family

This entry represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains and is most closely related to the central region bacterial NusA, a transcription termination factor named for its interaction with phage lambda protein N in Escherichia coli. The proteins required for antitermination by N include NusA, NusB, NusE (ribosomal protein S10), and NusG. This system, on the whole, appears not to be present in the archaea.
Transcription termination factor NusA (Tscrpt_termination_fac_NusA)
Type: Domain

This entry describes NusA, or N utilisation substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in Escherichia coli of
Bacteriophage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry represents a region of NusA shared by all bacterial forms, and includes the S1 (

) and KH RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this entry, with two repeats of 50-residue domain rich in acidic amino acids.
Transcription termination factor NusA, C-terminal duplication (Tscrpt_termin_fac_NusA_C_rpt)
Type: Repeat

NusA, or N utilisation substance protein A, is a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in Escherichia coli of Bacteriophage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry represents an acidic 50-residue region found in two copies toward the C terminus of most proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic
Transcription antitermination protein RfaH (Transcription_antiterm_RfaH)
Type: Family

This entry represents the transcription antitermination protein, RfaH . This protein is most closely related to the transcriptional termination/antitermination protein NusG (

) and contains the KOW motif (

) . This protein appears to be limited to the proteobacteria.

In Escherichia coli, it enhances distal genes transcription elongation in a specialised subset of operons that encode extracytoplasmic components . RfaH is recruited into a multi-component RNA polymerase complex by the ops element, which is a short conserved DNA sequence located downstream of the main promoter of these operons. Once bound, RfaH suppresses pausing and inhibits Rho-dependent and intrinsic termination at a subset of sites. Termination signals are bypassed, which allows complete synthesis of long RNA chains. Enhances expression of several operons involved in synthesis of lipopolysaccharides, exopolysaccharides, hemolysin, and sex factor. Also negatively controls expression and surface presentation of AG43 and possibly another AG43-independent factor that mediates cell-cell interactions and biofilm formation .
Transcription antitermination protein, NusG, mycoplasma-related (Transcrpt_antiterm_NusG_myco)
Type: Family

This entry represents a family proteins orthologous to the bacterial transcription termination/antitermination factor NusG from Mycoplasmas and related species. These sequences from Mycoplasma are notably diverged from those in bacterial species, and although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system, which includes this family as a member.
NAD(P)H-quinone oxidoreductase subunit 5, organellar chromatophore 2 (NU5C2)
Type: Family

This family represents NAD(P)H-quinone oxidoreductase subunit 5, organellar chromatophore 2 (NU5C2 or NdhF2). Proteins in this entry are mainly found in Cyanobacteria. These enzymes are responsible for the following reaction:

plastoquinone + H
+
+ NADPH = plastoquinol + H
+
+ NADP+

It is restricted to two paralogs in each completed cyanobacterial genome, in which several subtypes of ndhF are found. Included in this family is NdhF3, shown to play a role in high-affinity CO2 uptake in Synechococcus sp. (strain PCC 7002) (Agmenellum quadruplicatum). In all cases, neighbouring genes include a paralog of ndhD but do include other NAD(P)H dehydrogenase subunits. Instead, genes related to C02 uptake tend to be found nearby .

In the amoeba Paulinella chromatophora, which carries an endosymbiotic cyanobacterium, more than 30 cyanobacterial genes have moved to its cell nucleus .
NADH dehydrogenase, subunit C (NADH_DH_suC)
Type: Family

This entry describes the C subunit of the NADH dehydrogenase complex I in bacteria, as well as many instances of the corresponding mitochondrial subunit (NADH dehydrogenase subunit 9) and of the F420H2 dehydrogenase in Methanosarcina. Complex I contains subunits designated A-N. This C subunit often occurs as a fusion protein with the D subunit. This entry excludes the NAD(P)H and plastoquinone-dependent form of chloroplasts and Synechocystis.
CO2 hydration (CO2_hydration)
Type: Family

This small family of proteins includes paralogs ChpX and ChpY in Synechococcus sp. (strain PCC 7942) (Anacystis nidulans R2) and other cyanobacteria, associated with distinct NAD(P)H dehydrogenase complexes. These proteins collectively enable light-dependent CO2 hydration and CO2 uptake; loss of both blocks growth at low CO2 concentrations.
VCBS domain (VCBS_dom)
Type: Domain

This domain of about 100 residues is found multiple (up to 35) copies in long proteins from several species of Vibrio, Colwellia, Bradyrhizobium, and Shewanella (hence the name VCBS) and in smaller copy numbers in proteins from several other bacteria. The large protein size and repeat copy numbers, species distribution, and suggested activities of several member proteins suggests a role for this domain in adhesion.
RNA helicase HrpA (RNA_helicase_HrpA)
Type: Family

This entry represents HrpA, one of two related but uncharacterised DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterised, is about 800 amino acids long. Related characterised eukarotic proteins are RNA helicases associated with pre-mRNA processing. The HrpA/B homologue from Borrelia is 500 amino acids shorter but appears to be derived from HrpA rather than HrpB .
ATP binding protein MinD (MinD)
Type: Family

This entry describes MinD, a multifunctional cell division protein that guides correct placement of the septum. In Escherichia coli, the cell division site is determined by the cooperative activity of min operon products MinC, MinD, and MinE . MinD is a membrane-associated ATPase and is a septum site-determining factor through the activation and regulation of MinC and MinE. MinD is also known to undergo a rapid pole-to-pole oscillation movement in vivo as observed by fluorescent microscopy. In plants, chloroplast division requires the dimerisation of stromal MinD . The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate entry.
ATP binding protein MinD, archaea (MinD_archaea)
Type: Family

This entry represents the archaeal MinD family. The exact roles of the various archaeal MinD homologues are unknown.
ATP-dependent helicase HrpB (HrpB)
Type: Family

This entry represents HrpB, one of two related predicted DEAH-box ATP-dependent helicases of unknown function found in many proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti (Sinorhizobium meliloti), designated HelO, has been studied but is not essential for growth and mutants have no obvious phenotype . HrpB is typically about 800 residues in length, while its paralog HrpA (

), also uncharacterised, is about 1300 amino acids long. Related characterised eukaryotic proteins are RNA helicases associated with pre-mRNA processing .
NADH-quinone oxidoreductase, chain I (NADH_quinone_OxRdtase_chainI)
Type: Family

This entry represents the I subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I (

) which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain 'I' subunits from the closely related F420H2 dehydrogenase and formate hydrogenlyase complexes.
NADH-quinone oxidoreductase, chain M/4 (NADH_Q_OxRdtase_chainM/4)
Type: Family

This entry contains members of the complex I subunit 4 family. Members of this family include the 13th structural gene, M, of bacterial NADH dehydrogenase I (based on Escherichia coli), as well as chain 4 of the corresponding mitochondrial complex I and of the chloroplast NAD(P)H dehydrogenase complex.
NADH:ubiquinone oxidoreductase, subunit G (NADH_UbQ_OxRdtase_Gsu)
Type: Family

This entry describes the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain related subunits from formate dehydrogenase complexes.
Peptidase M38, beta-aspartyl dipeptidase (Pept_M38_dipep)
Type: Family

Over 70 metallopeptidase families have been identified to date. In these enzymes a divalent cation, which is usually zinc but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys. At least one other residue is required for catalysis, which may play an electrophilic role.

Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .

This group of proteins include metallopeptidases belonging to the MEROPS peptidase family M38 (clan MJ, beta-aspartyl dipeptidase family). This entry includes the beta-aspartyl dipeptidase from Escherichia coli, (

, IadA; MEROPS identifier M38.001), which degrades isoaspartyl dipeptides and may unblock degradation of proteins that cannot be repaired. This entry also describes closely related proteins from other species (e.g. Clostridium perfringens, Thermoanaerobacter tengcongensis) that may have an equivalent in function. This family shows homology to dihydroorotases. The L-isoaspartyl derivative of Asp arises non-enzymatically over time as a form of protein damage. In this isomerisation, the connectivity of the polypeptide changes to pass through the β-carboxyl of the side chain. Much but not all of this damage can be repaired by protein-L-isoaspartate (D-aspartate) O-methyltransferase.
SUF system FeS cluster assembly, SufB (SUF_FeS_clus_asmbl_SufB)
Type: Family

This entry represents SufB, which is part of the SUF system and forms a complex with SufBCD.

Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far in bacteria, three FeS assembly machineries have been identified that are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.

The ISC system is conserved in eubacteria and eukaryotes (mitochondria) and has broad specificity, targeting general FeS proteins . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transferring them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .

The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoprotein targets.

In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .
Probable protein kinase UbiB (UbiB)
Type: Family

This entry represents the probable protein kinase UbiB (also known as as AarF), which is required for ubiquinone biosynthesis . It may function in regulating Q8 biosynthesis via its putative kinase activity .
Ubiquinone biosynthesis O-methyltransferase (UbiG_MeTrfase)
Type: Family

This entry represents an O-methyltransferase, which is believed to act at two points in the ubiquinone biosynthetic pathway in bacteria (UbiG) and mitochondria (COQ3) . A separate methylase (MenG/UbiE) catalyses the single C-methylation step. The most commonly used names for genes in this family do not indicate whether this gene is an O-methyl, or C-methyl transferase.
Phasin, subfamily 2 (Phasin_subfam-2)
Type: Family

Phasins (or granule-associate proteins) are surface proteins found covering Polyhydroxyalkanoate (PHA) storage granules in bacteria. Polyhydroxyalkanoates are linear polyesters produced by bacterial fermentation of sugar or lipids for the purpose of storing carbon and energy, and are accumulated as intracellular granules by many bacteria under unfavorable conditions, enhancing their fitness and stress resistance . The layer of phasins stabilises the granules and prevents coalescence of separated granules in the cytoplasm and nonspecific binding of other proteins to the hydrophobic surfaces of the granules. For example, in Ralstonia eutropha (strain ATCC 17699/H16/DSM 428/Stanier 337) (Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337)), the major surface protein of polyhydroxybutyrate (PHB) granules is phasin PhaP1(Reu), which occurs along with three homologues (PhaP2, PhaP3, and PhaP4) that have the capacity to bind to PHB granules but are present at minor levels . These four phasins lack a highly conserved domain but share homologous hydrophobic regions.

This entry represents a family of phasins that are part of the polyhydroxyalkanoate synthesis machinery . Members of this family are related to

.
Probable ribonuclease HepT (HepT)
Type: Family

The member of this family from Haemophilus influenzae, Probable ribonuclease HepT (also known as HI0074), is an homologue of the mRNA nuclease HepT (SO_3166) from Shewanella oneidensis, being probably the toxic component of a type VII toxin-antitoxin (TA) system. It contains a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain containing a RX4-6H motif whose conformations are remarkably different form SO_3166, indicating that they have different substrate-binding specificities . It forms a complex with HI0073 (

), encoded by the adjacent gene, which contains a nucleotidyltransferase nucleotide binding domain (

) .
Pyrimidine 5-nucleotidase (Pyr-5-nucltdase)
Type: Family

This family of proteins includes the SDT1/SSM1 gene from yeast, which has been shown to code for a pyrimidine (UMP/CMP) 5'nucleotidase . The family spans plants, fungi and bacteria. These enzymes are members of the haloacid dehalogenase (HAD) superfamily of hydrolases, specifically the IA subfamily.
NIF system FeS cluster assembly, NifU (NIF_FeS_clus_asmbl_NifU)
Type: Family

This entry represents the NifU protein from the NIF system that is involved in nitrogenase maturation.

Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far in bacteria, three FeS assembly machineries have been identified that are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.

The ISC system is conserved in eubacteria and eukaryotes (mitochondria) and has broad specificity, targeting general FeS proteins . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transferring them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .

The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoprotein targets.

In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .
Conserved hypothetical protein CHP02001 (CHP02001)
Type: Family

This entry represents a conserved hypothetical protein about 240 residues in length found so far in Proteobacteria including Shewanella oneidensis and Ralstonia solanacearum, usually as part of a paralogous family. The function is unknown.
Cysteine desulfurase IscS (Cys_deSase_IscS)
Type: Family

This entry represents cysteine deusulfurase (IscS), one of several cysteine desulfurases from a larger protein family designated (misleadingly, in this case) class V aminotransferases. IscS is one of at least 6 enzymes characteristic of the IscSUA-hscAB-fsx system of iron-sulphur cluster assembly . In M. tuberculosis this enzyme is associated with oxidative stress defence .