SII-SWORD/CoKE huggingface dataset:
Plasmid partitioning protein, RepA (Plasmid_partition_RepA)
Type: Family

The RepA (or ParA) protein is involved in replicon partitioning . All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Repa belongS to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase,.
Plasmid partitioning protein, RepB (Plasmid_partition_RepB)
Type: Family

RepABC plasmids are generally very low copy-number and therefore depend on an efficient system of plasmid partitioning to enure their stability and replication . The partioning system in these plasmids involves two proteins, RepA and RepB, and centromere-like sequences known as parS. Mutations in RepA, RepB or parS can dramatically lower plasmid stability and affect plasmid incompatibility. RepB is related to the plasmid partitoning protein ParB and is thought to function in a similar way by binding to segregation filaments formed by RepA and also to parS sites, thus recruiting the plasmid to the segregation machinery.
Sulphoacetaldehyde acetyltransferase (Sulphoacetald_Actrfrase)
Type: Family

Sulphoacetaldehyde acetyltransferase is a thiamine pyrophosphate-dependent enzyme involved in taurine utilization . Taurine, or 2-aminoethanesulphonate, can be used by bacteria as a source of carbon, nitrogen, and sulphur.
Succinate CoA transferase (Succinate_CoA_transferase)
Type: Family

These CoA transferases include enzyme catalyzing at least two related, but distinct, activities. The Escherichia coli YgfH protein has been characterised as a propionyl-CoA:succinate CoA transferase where it appears to be involved in a pathway for the decarboxylation of succinate to propionate . The Clostridium kluyveri CAT1 protein has been characterised as a acetyl-CoA:succinate CoA transferase and is believed to be involved in anaerobic succinate degradation . Succinyl-CoA:acetate CoA-transferase (

)from Acetobacter aceti utilizes succinyl-CoA to convert toxic acetate to acetyl-CoA and succinate and it is required for growth on acetic acid .
Alpha-(1->6)-mannopyranosyltransferase A-like (MptA-like)
Type: Family

This entry represents a family of hydrophobic presumed membrane proteins found in actinobacteria, including Alpha-(1->6)-mannopyranosyltransferase A from Mycobacterium tuberculosis (MptA). MptA is involved in the latter stages of the biosynthesis of the alpha-(1->6) mannan core of lipomannan (LM) and catalyses the addition of alpha-(1->6)-mannose residue . The genes encoding these proteins are syntenically associated with (found proximal to) genes involved in carotene biosynthesis, usually including phytoene synthase (crtB), phytoene dehydrogenase (crtI) and geranylgeranyl pyrophosphate synthase (ispA).
Bisanhydrobacterioruberin hydratase CruF (CruF)
Type: Family

This entry represents a family of hydrophobic presumed membrane proteins, mainly from Halobacteria. The representative member is CruF, a C50 carotenoid 2',3'-hydratase involved in the synthesis of the C50 carotenoid bacterioruberin in the halophilic archaeon Haloarcula japonica. CruF catalyses the reaction that introduces hydroxyl groups to C3'' and C3''' of bisanhydrobacterioruberin (BABR) to generate BR .
Aminodeoxychorismate lyase, class IV (Aminodeoxychorismate_lyase_IV)
Type: Family

Aminodeoxychorismate lyase (ADC lyase) converts aminodeoxychorismate to para-aminobenzoate during the process of tetrahydrofolate biosynthesis . Tetrahydrofolate is an essential precursor for de novo purine biosynthesis. ADC lyase is a pyridoxal-phosphate-binding protein belonging to the class IV aminotransferase family. This entry also includes Bifunctional aminodeoxychorismate lyase / D-amino acid transaminase from Mycobacterium tuberculosis, which catalyses two enzymatic reactions in biochemically unrelated pathways: this protein acts as an aminodeoxychorismate (ADC) lyase (ADCL) in folate biosynthesis, converting 4-amino-4-deoxychorismate (ADC) to 4-aminobenzoate (PABA), and as a D-amino acid transaminase (DAAT) in peptidoglycan (PG) biosynthesis .
Lycopene cyclase domain (Lycopene_cyclase_dom)
Type: Domain

This domain is often repeated twice within the same polypeptide, as is observed in Archaea, Thermus, Sphingobacteria and Fungi. In the fungal sequences, this tandem domain pair is observed as the N-terminal half of a bifunctional protein , where it has been characterised as a lycopene beta-cyclase and the C-terminal half is a phytoene synthetase. In Myxococcus and Actinobacterial genomes this domain appears as a single polypeptide, tandemly repeated and usually in a genomic context consistent with a role in carotenoid biosynthesis. One member of this family has been annotated as a lycopene beta-cyclase . The domain is generally hydrophobic with a number of predicted membrane spanning segments and contains a distinctive motif (hPhEEhhhhhh). In certain sequences one of either the proline or glutamates may vary, but always one of the tandem pair appear to match this canonical sequence exactly.
2,3-oxidosqualene cyclase (2-3-oxidosqualene_cyclase)
Type: Family

2,3-oxidosqualene cyclases are found in Stigmatella aurantiaca producing cycloartenol, and Gemmata obscuriglobus and Methylococcus capsulatus producing the closely related sterol, lanosterol .
Hydroxysqualene synthase HpnC (HSQ_synthase_HpnC)
Type: Family

In bacteria, squalene (SQ) is an intermediate in the biosynthesis of hopanoids. The genes for hopanoid biosynthesis are typically located on clusters that consist of four highly conserved genes -hpnC, hpnD, hpnE, and hpnF- for conversion of farnesyl diphosphate (FPP) to hopene or related pentacyclic metabolites .

HpnC has been characterised as a hydroxysqualene synthase. HpnC catalyzes the second step in the biosynthesis of SQ from FPP, converting presqualene diphosphate (PSPP) to hydroxysqualene (HSQ) .
Squalene synthase HpnD-like (SQ_synth_HpnD-like)
Type: Family

In bacteria, squalene (SQ) is an intermediate in the biosynthesis of hopanoids.
The genes for hopanoid biosynthesis are typically located on clusters that consist of four highly conserved genes -hpnC, hpnD, hpnE, and hpnF- for conversion of farnesyl diphosphate (FPP) to hopene or related pentacyclic metabolites .

HpnD catalyzes formation of presqualene diphosphate (PSPP) from two molecules of FPP, the first step in the synthesis of SQ .
Hopanoid-associated sugar epimerase (Hopanoid-assoc_sugar_epimerase)
Type: Family

The sequences in this entry belong to the superfamily of NAD-dependent epimerases and dehydratases which typically act on nucleotide-sugar substrates. The genes encoding proteins in this entry are generally in the same locus as genes involved in the biosynthesis and elaboration of hopene, the cyclization product of the polyisoprenoid squalene. This gene and its association with hopene biosynthesis in Zymomonas mobilis has been noted in the literature where the gene symbol hpnA was assigned . Hopanoids are known to be components of the plasma membrane and to have polar sugar head groups in Z. mobilis and other species.
Hydroxysqualene dehydroxylase HpnE (SQase_HpnE)
Type: Family

In bacteria, squalene (SQ) is an intermediate in the biosynthesis of hopanoids.
The genes for hopanoid biosynthesis are typically located on clusters that consist of four highly conserved genes -hpnC, hpnD, hpnE, and hpnF- for conversion of farnesyl diphosphate (FPP) to hopene or related pentacyclic metabolites.

HpnE is a member of the amine oxidoreductase family, and catalyzes the third and last step in the synthesis of SQ, consisting in the reduction of hydroxysqualene (HSQ) to SQ .
Hopanoid-associated phosphorylase HpnG (Hopanoid-assoc_phosphoryl_HpnG)
Type: Family

These proteins are part of the wider family of phosphorylases that typically act on nucleotide-sugar substrates. The proteins in this entry are generally encoded in the same locus as genes involved in the biosynthesis and elaboration of hopene, the cyclization product of the polyisoprenoid squalene. The gene from Zymomonas mobilis is adjacent to the genes for PhnA-E and squalene-hopene cyclase (which would be HpnF) and its association with hopene biosynthesis has been noted in the literature . Extending the gene symbol sequence, suggests the symbol HpnG for the product of this gene. Hopanoids are known to be components of the plasma membrane and to have polar sugar head groups in Z. mobilis and other species.
Glycosyl transferase, family 2, hopene-associated, HpnB (Glyco_trans_2_hopen-assoc_HpnB)
Type: Family

The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates ([ec:2.4.1.-]) and related proteins into distinct sequence based families has been described . This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'.

Proteins in this entry contain glycosyl transferase family 2 domains which are responsible, generally, for the transfer of nucleotide-diphosphate sugars to substrates such as polysaccharides and lipids. These proteins are often encoded in the same genetic locus as squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. Indeed, proteins in this entry appear to never be encoded in a genome lacking squalene-hopene cyclase (SHC), although not all genomes encoding SHC have this glycosyl transferase. In the organism Zymomonas mobilis the linkage of this protein to hopanoid biosynthesis has been noted and it was named HpnB . Hopanoids are known to feature polar glycosyl head groups in many organisms.
Hopanoid biosynthesis associated radical SAM protein HpnH (Hopanoid_synth-assoc_rSAM_HpnH)
Type: Family

Proteins in this entry are members of the radical SAM superfamily of enzymes that utilise an iron-sulphur redox cluster and S-adenosylmethionine to carry out diverse radical mediated reactions . This group of proteins are frequently encoded in the same locus as squalene-hopene cyclase (SHC,

) and other proteins associated with the biosynthesis of hopanoid natural products. The linkage between SHC and this radical SAM enzyme is strong; one is nearly always observed in the same genome where the other is found. A hopanoid biosynthesis locus was described in Zymomonas mobilis consisting of the genes for HpnA-E and SHC (HpnF) . Continuing past SHC are the genes for a phosphorylase enzyme (ZMO0873, i.e. HpnG,

) and this radical SAM enzyme (ZMO0874) which we name here HpnH. Granted, in Z. mobilis, HpnH is in a convergent orientation with respect to HpnA-G, but one gene beyond HpnH and running in the same convergent direction is IspH (ZM0875, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase), an essential enzyme of IPP biosynthesis and therefore essential for the biosynthesis of hopanoids. One of the well-described hopanoid intermediates is bacteriohopanetetrol. In the conversion from hopene several reactions must occur in the side chain for which a radical mechanism might be reasonable. These include the four (presumably anaerobic) hydroxylations and a methyl shift.
Hopanoid biosynthesis associated radical SAM protein HpnJ (Hopanoid_synth-assoc_rSAM_HpnJ)
Type: Family

These proteins are members of the wider radical SAM superfamily of enzymes that enzymes utilise an iron-sulphur redox cluster and S-adenosylmethionine to carry out diverse radical mediated reactions . The Acidithiobacillus ferrooxidans ATCC 23270 protein (AFE_0975) is encoded in the same locus as the genes for squalene-hopene cyclase (SHC,

) and other proteins associated with the biosynthesis of hopanoid natural products. Similarly, in Ralstonia eutropha (strain JMP134) (Alcaligenes eutrophus) (Reut_B4901) this protein is encoded adjacent to the genes for HpnAB, IspH and HpnH (

), although SHC itself is elsewhere in the genome. Notably, this protein (here named HpnJ) and three others form a conserved set (HpnIJKL) which occur in a subset of all genomes containing the SHC enzyme. This relationship was discerned using the method of partial phylogenetic profiling . This group includes Zymomonas mobilis the organism where the initial hopanoid biosynthesis locus was described consisting of the genes HpnA-E and SHC (HpnF) . Continuing past SHC are genes encoding a phosphorylase enzyme (ZMO0873, i.e. HpnG,

) and another radical SAM enzyme (ZMO0874), HpnH. Although discontinuous in Z. mobilis, we continue the gene symbol sequence with HpnIJKL. One of the well-described hopanoid intermediates is bacteriohopanetetrol. In the conversion from hopene several reactions must occur in the side chain for which a radical mechanism might be reasonable. These include the four (presumably anaerobic) hydroxylations and a methyl shift.
Hopanoid biosynthesis associated glycosyltransferase, HpnI (Hopen-assoc_HpnI)
Type: Family

Proteins in this entry contain glycosyl transferase family 2 domains which are responsible, generally, for the transfer of nucleotide-diphosphate sugars to substrates such as polysaccharides and lipids. The Acidithiobacillus ferrooxidans ATCC 23270 protein (AFE_0974) is encoded in the same locus as the genes for squalene-hopene cyclase (SHC,

) and other proteins associated with the biosynthesis of hopanoid natural products. Similarly, in Ralstonia eutropha (strain JMP134) (Alcaligenes eutrophus) this protein (Reut_B4902) is encoded adjacent to the genes for HpnAB, IspH and HpnH (

), although SHC itself is encoded elsewhere in the genome. Notably, this protein (here named HpnI) and three others form a conserved set (HpnIJKL) which occurs in a subset of all genomes containing the SHC enzyme. This relationship was discerned using the method of partial phylogenetic profiling . This group includes Zymomonas mobilis, the organism where the initial hopanoid biosynthesis locus was described consisting of the genes HpnA-E and SHC (HpnF) . Continuing past SHC are found genes for a phosphorylase enzyme (ZMO0873, i.e. HpnG,

) and another radical SAM enzyme (ZMO0874), HpnH. Although discontinuous in Z. mobilis, we continue the gene symbol sequence with HpnIJKL. Hopanoids are known to feature polar glycosyl head groups in many organisms.
Hopanoid biosynthesis associated protein HpnK (Hopanoid_biosynth-assoc_HpnK)
Type: Family

This entry represents a subset of the YdjC-like family of uncharacterised proteins. The Acidithiobacillus ferrooxidans ATCC 23270 protein (AFE_0976) is encoded in the same locus as the genes for squalene-hopene cyclase (SHC,

) and other proteins associated with the biosynthesis of hopanoid natural products. Similarly, in Ralstonia eutropha (strain JMP134) (Alcaligenes eutrophus) this protein (Reut_B4902) is encoded adjacent to the genes for HpnAB, IspH and HpnH (

), although SHC itself is encoded elsewhere in the genome. Notably, this protein (here named HpnK) and three others form a conserved set (HpnIJKL) which occurs in a subset of all genomes containing the SHC enzyme. This relationship was discerned using the method of partial phylogenetic profiling . This group includes Zymomonas mobilis, the organism where the initial hopanoid biosynthesis locus was described consisting of the genes for HpnA-E and SHC (HpnF) . Continuing past SHC are found genes encoding a phosphorylase enzyme (ZMO0873, i.e. HpnG,

) and a radical SAM enzyme (ZMO0874), HpnH. Although discontinuous in Z. mobilis, we continue the gene symbol sequence with HpnIJKL.
Plasmid replication initiator, RepA, IncFII type (Plasmid_rep_init_RepA_IncFII)
Type: Family

This entry represents plasmid replication initiator RepA from the incFII (plasmid incompatibility group F-II) plasmids. This group of plasmids includes R1 and R100. Immediately upstream of repA is found tap, which encodes a leader peptide of about 24 amino acids, often not assigned as a gene in annotated plasmid sequences. Note that other, non-homologous plasmid replication proteins share the gene symbol (repA) and similar names (eg plasmid replication protein RepA).
DMSO reductase family, type II, haem b-binding subunit (DMSO_Rdtase_II_haem_b-bd_su)
Type: Family

The DMSO reductase family is a large and rapidly expanding group of enzymes found in bacteria and archaea that share a common form of molybdenum cofactor known as bis(molybdopterin guanine dinucleotide)Mo . This entry represents a haem b-binding subunit, typically called the gamma subunit, found in various type II DMSO reductase family enzymes that, in addition to the molybdopterin subunit also contain an iron-sulphur subunit. These include two distinct but very closely related periplasmic proteins of anaerobic respiration: selenate reductase and chlorate reductase . Other proteins containing this subunit include dimethyl sulphide dehydrogenase and ethylbenzene dehydrogenase .
DMSO reductase family, type II, iron-sulphur subunit (DMSO_Rdtase_II_Fe-S_su)
Type: Family

The DMSO reductase family is a large and rapidly expanding group of enzymes found in bacteria and archaea that share a common form of molybdenum cofactor known as bis(molybdopterin guanine dinucleotide)Mo . This entry represents the iron-sulphur subunit, typically called the beta subunit, found in various type II DMSO reductase family enzymes. These include two distinct but very closely related periplasmic proteins of anaerobic respiration; selenate reductase and chlorate reductase . Other proteins containing this subunit include dimethyl sulphide dehydrogenase and ethylbenzene dehydrogenase .
DMSO reductase family, type II, molybdopterin subunit (DMSO_Rdtase_II_Mopterin_su)
Type: Family

The DMSO reductase family is a large and rapidly expanding group of enzymes found in bacteria and archaea that share a common form of molybdenum cofactor known as bis(molybdopterin guanine dinucleotide)Mo . This entry represents the molybdopterin subunit, typically called the alpha subunit, found in various type II DMSO reductase family enzymes. These include two distinct but very closely related periplasmic proteins of anaerobic respiration; selenate reductase and chlorate reductase . Other proteins containing this subunit include dimethyl sulphide dehydrogenase and ethylbenzene dehydrogenase . This alpha subunit has a twin-arginine translocation (TAT) signal for Sec-independent translocation across the plasma membrane.
Hopanoid transporter HpnN (Hopanoid_biosynth_HpnN)
Type: Family

This family includes Hopanoid transporter HpnN which is essential for hopanoid transport from the cytoplasmic to the outer membrane . It is capable of shuttling hopanoid lipids from the inner membrane to the periplasm, where they probably spontaneously insert to the inner leaflet of the outer membrane, strengthening the cell envelope . In Burkholderia, it is critical for multidrug resistance and cell wall remodeling .
Hopanoid biosynthesis-associated membrane protein HpnM (Hopanoid_biosyn-assoc_HpnM)
Type: Family

The genes encoding the proteins in this entry are all found in bacteria containing the machinery necessary for biosynthesis of hopanoid lipids. Furthermore, these genes are usually located proximal to other components of this biological process. The proteins are members of a family of putative transporters known as "toluene tolerance protein Ttg2D", although it is unlikely that the proteins in this entry have anything to do with toluene per-se.
DMSO reductase family, type II, chaperone (DMSO_Rdtase_II_chaperone)
Type: Family

The DMSO reductase family is a large and rapidly expanding group of enzymes found in bacteria and archaea that share a common form of molybdenum cofactor known as bis(molybdopterin guanine dinucleotide)Mo . Type II members of the DMSO reductase family are heterotrimeric proteins with bis(molybdopterin guanine dinucleotide)Mo, iron-sulphur, and haem B prosthetic groups bound by the alpha, beta, and gamma subunits respectively . This entry represents polypeptides that are not part of the mature protein, although they are the product of a fourth clustered gene, and are thought to function as chaperones, analogous to NarJ of nitrate reductases.
Cell division protein FtsZ, C-terminal extension (Cell_div_FtsZ_C)
Type: Domain

This entry describes a domain found as a C-terminal extension to the cell division protein FtsZ in many, but not all, members of the alphaproteobacteria.
Chlorosome envelope protein H, CsmH (Chlorosome_envelope_CsmH)
Type: Repeat

This entry contains proteins with a repeated sequence element that is restricted to species of the Chlorobiaceae.
Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, bacterial type (Nict_dMeBzImd_PRibTrfase_bact)
Type: Family

This entry represents bacterial-type nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase enzymes involved in dimethylbenzimidazole synthesis . This enzyme catalyses the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB). This function is essential to
de novo
cobalamin (vitamin B12) production in bacteria.

Nicotinate mononucleotide (NaMN):5,6-dimethylbenzimidazole (DMB) phosphoribosyltransferase (CobT) plays a central role in the synthesis of alpha-ribazole-5'-phosphate, an intermediate for the lower ligand of cobalamin . It is one of the enzymes of the anaerobic pathway of cobalamin biosynthesis, and one of the four proteins (CobU, CobT, CobC, and CobS) involved in the synthesis of the lower ligand and the assembly of the nucleotide loop .

Vitamin B
12
(cobalamin) is used as a cofactor in a number of enzyme-catalysed reactions in bacteria, archaea and eukaryotes . The biosynthetic pathway to adenosylcobalamin from its five-carbon precursor, 5-aminolaevulinic acid, can be divided into three sections: (1) the biosynthesis of uroporphyrinogen III from 5-aminolaevulinic acid; (2) the conversion of uroporphyrinogen III into the ring-contracted, deacylated intermediate precorrin 6 or cobalt-precorrin 6; and (3) the transformation of this intermediate to form adenosylcobalamin . Cobalamin is synthesised by bacteria and archaea via two alternative routes that differ primarily in the steps of section 2 that lead to the contraction of the macrocycle and excision of the extruded carbon molecule (and its attached methyl group) . One pathway (exemplified by Pseudomonas denitrificans) incorporates molecular oxygen into the macrocycle as a prerequisite to ring contraction, and has consequently been termed the aerobic pathway. The alternative, anaerobic, route (exemplified by Salmonella typhimurium) takes advantage of a chelated cobalt ion, in the absence of oxygen, to set the stage for ring contraction .
Type VI secretion system, RhsGE-associated Vgr family subset (T6SS_RhsGE_Vgr_subset)
Type: Family

This entry represents a subset of the RhsGE element associated Vgr protein family (

) found only in genomes with type VI secretion loci. However, members of this entry, although recognisably correlated to type VI secretion according the partial phylogenetic profiling algorithm, are often encoded far from the type VI secretion locus.

Proteins in this entry include the actin cross-linking toxin VgrG1 from Vibrio cholerae. VgrG1 catalyses the covalent cross-linking of host cytoplasmic monomeric actin. It mediates the cross-link between 'Lys-50' of one monomer and 'Glu-270' of another actin monomer, resulting in formation of highly toxic actin oligomers that cause cell rounding .