SII-SWORD/CoKE huggingface dataset:
Type-F conjugative transfer system pilin assembly protein TraF (TraF)
Type: Family

This entry includes TraF; a protein that is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically in the F-type system. TraF has been predicted to contain a thioredoxin fold and has been shown to be localized to the periplasm . Unlike the related protein TrbB (

), TraF does not contain a conserved pair of cysteines and has been shown not to function as a thiol disulphide isomerase by complementation of an Escherichia coli DsbA defect . The protein is believed to be involved in pilin assembly . Even more closely related than TrbB is a clade of genes (

), which do contain the CXXC motif, but it is unclear whether these are involved in type-F conjugation systems per se.
Type IV conjugative transfer system protein TraF-like (T4SS_TraF-like)
Type: Family

This entry contains TraF-like proteins that are related to the F-type conjugation system pilus assembly proteins TraF (

)and TrbB (

) both of which exhibit a thioredoxin fold . The proteins in this entry have the same length and architecture as TraF, but lack the CXXC-motif found in TrbB that is believed to be responsible for the disulphide isomerase activity.
Type-F conjugative transfer system pilin chaperone TraQ, proteobacteria (TraQ_proteobacteria)
Type: Family

This entry represents TraQ, a protein that makes a specific interaction with pilin (TraA) to aid its transfer through the inner membrane during the process of F-type conjugative pilus assembly .
Type-F conjugative transfer system pilin assembly protein TrbC, subgroup (T4SS_TrbC_subgr)
Type: Family

This entry represents TrbC, a protein that is an essential component of the F-type conjugative pilus assembly system (aka type 4 secretion system) for the transfer of plasmid DNA . The N-terminal portion of these proteins is heterogeneous.
Type-F conjugative transfer system protein TraW (TraW)
Type: Family

This entry represents TraW, an essential component of the F-type conjugative transfer system for plasmid DNA transfer that has been shown to be localized to the periplasm .
Type-F conjugative transfer system protein TrbI (TrbI_Ftype)
Type: Family

This entry represents TrbI, an essential component of the F-type conjugative transfer system for plasmid DNA transfer that has been shown to be localized to the periplasm .
Cytochrome c oxidase cbb3 type, accessory protein FixG (Cyt_c_oxidase_cbb3_FixG)
Type: Family

Member of this ferredoxin-like protein family, include FixG, CcoG and RdxA,. They are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else; it is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are also nitrogen-fixing, hence the gene symbol fixG. FixG was shown essential for functional cco-cbb3 expression in Bradyrhizobium japonicum .
Type-IV secretion system protein TraC (TraC-F-type)
Type: Family

The proteins in this entry are found in the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The proteins contain the Walker A and B motifs and so are putative nucleotide triphosphatases .
Type IV conjugative transfer system protein TraV (T4SS_TraV)
Type: Family

This entry represents TraV, a component of a conjugative type IV secretion system. TraV is an outer membrane lipoprotein that is believed to interact with the secretin TraK . This protein contains three conserved cysteines in the N-terminal half.
Heptaprenyl diphosphate synthase component II (GerC3_HepT)
Type: Family

The proteins in this entry are component II of the heterodimeric heptaprenyl diphosphate synthase. They are found proximate to the gene for component I (

). This enzyme acts in menaquinone-7 isoprenoid side chain biosynthesis.
Type-F conjugative transfer system mating-pair stabilisation protein TraN (TraN_Ftype)
Type: Family

TraN is a large cysteine-rich outer membrane protein involved in the mating-pair stabilisation (adhesin) component of the F-type conjugative plasmid transfer system. TraN is believed to interact with the core type IV secretion system apparatus through the TraV protein .
Demethylmenaquinone methyltransferase (MenG_heptapren)
Type: Family

MenG is a generic term for a methyltransferase that catalyses the last step in menaquinone biosynthesis; the exact enzymatic activity differs for different MenG because the menaquinone differ in their prenoid side chains in different species. Members of this MenG protein family are 2-heptaprenyl-1,4-naphthoquinone methyltransferase, and are found together in operons with the two subunits of the heptaprenyl diphosphate synthase in Bacillus subtilis and related species.
Superoxide dismutase, Nickel-type (Superoxide_dismutase_Ni-type)
Type: Family

This entry represents nickel-dependent superoxide dismutase (NiSOD) (

), a SOD enzyme that uses nickel, rather than iron, manganese, copper, or zinc. All SOD enzymes catalyse the dismutation of toxic superoxide radical anions to oxygen and hydrogen peroxide in order to protect cells from oxidative damage. The catalytic cycle of NiSOD consists of two half-reactions, each initiated by the successive approach of substrate to the metal centre. The first (reductive) phase involves Ni(III) reduction to Ni(II), and the second (oxidative) phase involves the metal reoxidation back to its resting state . NiSOD has a novel SOD fold and assembly, consisting of a hexameric assembly of 4-helix bundles of up-and-down topology, which contains a 9-residue nickel-hook structural motif that is critical for metal binding and catalysis . A gene for a required protease (NiSOD maturation protease;

) is adjacent to the NiSOD gene.
Peptidase S26A, superoxide dismutase maturation protease, nickel-type (Pept_S26A_Sod_Ni_maturase)
Type: Family

Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .

Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) .

Members of this protein family are predicted proteases that are encoded adjacent to the genes for a nickel-type superoxide dismutase (

). This family of predicted peptidases belong to MEROPS peptidase subfamily S26A (signal peptidase I), which have a Ser/Lys catalytic dyad.
Type-F conjugative transfer system pilin acetylase TraX (TraX_Ftype)
Type: Family

TraX is responsible for the acetylation of the F-pilin TraA during conjugative plasmid transfer. The purpose of this acetylation is unclear, but the reported transcriptional regulation of TraX may indicate that it is involved in the process of pilu extension/retraction .
Type-F conjugative transfer system secretin TraK (TraK_Ftype)
Type: Family

The TraK protein is predicted to interact with the TraV and TraB proteins as part of the scaffold, which extends from the inner membrane, through the periplasm to the cell envelope and through which the F-type conjugative pilus passes. TraK is homologous to the P-type IV secretion system protein TrbG, the Ti-type protein VirB9 and the I-type TraN protein. The protein is related to the secretin family especially the HrcC subgroup of the type III secretion system. The protein is hypothesized to oligomerize to form a ring structure akin to other secretins .
Conserved hypothetical protein CHP02757 (CHP02757)
Type: Family

Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.
Type IV conjugative transfer system, coupling protein TraD (T4SS_TraD)
Type: Family

The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM) .
Conjugative transfer relaxase protein TraI (Conjug_relaxase_TraI)
Type: Family

This entry represents TraI, which is a component of the relaxosome complex. In the process of conjugative plasmid transfer the relaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein . TraI contains four domains: a trans-esterase (relaxase) domain that executes the nicking and covalent attachment of the T-strand to the relaxase, a vestigial helicase domain (carrying the 2B/2B-like sub-domain) that operates as an ssDNA-binding domain, an active 5' to 3' helicase domain, and a C-terminal domain that functions as a recruitment platform for relaxosome components.
Chlamydia phage, Vp3, scaffold (Chlamydia_phage_Vp3)
Type: Family

This entry represents homologues of the Internal scaffolding protein VP3 found mainly in Microviridae.

Some members of this entry are encoded by genes in chlamydiaphage such as Vp3. These viruses have around eight genes and infect obligately intracellular bacterial pathogens of the genus Chlamydia. This protein is annotated as VP3 or structural protein (as if a protein of mature viral particles), however, it is displaced from procapsids as DNA is packaged, and therefore is more correctly described as a scaffolding protein.
Sporulation polysaccharide deacetylase PdaB-like (PdaB-like)
Type: Family

This entry describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reduced sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy . Members of this family are homologous to a characterised polysaccharide deacetylase.

This entry also includes BC_3618 from Bacillus cereus. It is a peptidoglycan-N-acetylglucosamine deacetylase that catalyzes the deacetylation of N-acetylglucosamine (GlcNAc) residues in peptidoglycan. It acts on cell wall peptidoglycan from the Gram-positive bacteria B.cereus and B.subtilis and the Gram-negative bacterium H.pylori, but not on acetylated xylan .
Cryptochrome DASH (Cry_DASH)
Type: Family

The cryptochrome and photolyase families consist of structurally related flavin adenine dinucleotide (FAD) proteins that use the absorption of blue light to accomplish different tasks. The photolyasess use the blue light for light-driven electron transfer to repair UV-damaged DNA, while the cryptochromes are blue-light photoreceptors involved in the circadian clock for plants and animals .

This entry represents a branch of the photolyase/cryptochrome family that is known as the cryptochrome-DASH family (Cry-DASH). The Cry-DASH family members have been shown to act as photolyases with high degree of specificity for cyclobutane pyrimidine dimers in ssDNA .
Cryptochrome, plant (Cryptochrome_pln)
Type: Family

The cryptochrome and photolyase families consist of structurally related flavin adenine dinucleotide (FAD) proteins that use the absorption of blue light to accomplish different tasks. The photolyasess use the blue light for light-driven electron transfer to repair UV-damaged DNA, while the cryptochromes are blue-light photoreceptors involved in the circadian clock for plants and animals .

Members of this subfamily are from plants; they appear mostly to be regulatory proteins that respond to blue light. For instance, Arabidopsis cryptochromes Cry1 and Cry2 antagonistically regulate primary root elongation . Cry2 is also reported to interact with CIB1 and regulate transcription and floral initiation .
Conjugal transfer protein TraG-like (Ti-typ_conjug_TS_TraG-like)
Type: Family

This entry contains the Agrobacterium tumefaciens Ti-plasmid TraG, it is responsible for conjugative transfer of the entire plasmid among Agrobacterium strains . The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems.

Also in this entry is the type IV secretion system-coupling protein VirD4 from Bartonella henselae. Substrates for VirD4 include the effector proteins BepA-G, which when injected into the human host epithelial cells (HEC) brings about rearrangement of the HEC cytoskeleton, inhibition of apoptosis, and proinflammatory activation by nuclear factor NF-kappa-B .
Ti-type conjugative transfer relaxase TraA (TraA_Ti)
Type: Family

This entry represents the Ti-type conjugative transfer relaxase TraA. TraA contains domains distinctive of a single strand exonuclease (N terminus, MobA/MobL,

) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI,

). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer .
Peptidase S26C, conjugative transfer signal peptidase TraF (Peptidase_S26C_TraF)
Type: Family

This entry contains the conjugative transfer signal peptidase (TraF), which belongs to MEROPS peptidase family S26, subfamily S26C (TraF signal peptidase, clan SF). It is found in operons that encode elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as LepB. This family is present in both Ti-type and I-type conjugative systems .
DNA helicase subunit AddB (DNA_helicase_suAddB)
Type: Family

DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RexAB) in others. AddA is conserved between the firmicutes and the alphaproteobacteria, while its partner protein (RexB) is not. This entry describes the ATP-dependent nuclease subunit B (AddB/RexB) protein as found Bacillus subtilis and related species. Although the RexB protein of Streptococcus and Lactococcus is considered to be orthologous and functionally equivalent, merely named differently, all members of this protein family have a P-loop nucleotide binding motif GxxGxGK[ST] at the N terminus, unlike RexB proteins, and a CxxCxxxxxC motif at the C terminus, both of which may be relevant to function.

The AddA/AddB heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent, dual-direction single-stranded exonuclease. It recognises the chi site generating a DNA molecule suitable for the initiation of homologous recombination. The AddB nuclease domain is not required for chi fragment generation; this subunit has 5' -> 3' nuclease activity.
DNA helicase subunit RexB (DNA_helicase_suRexB)
Type: Family

DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RexAB) in other. The AddA is conserved between the firmicutes and the alphaproteobacteria, while its partner protein (RexB) is not. The partner may be designated AddB, as in Bacillus and in alphaproteobacteria, or RexB as in Streptococcus and Lactococcus. Note, however, that RexB proteins lack an N-terminal GxxGxGK[ST] ATP-binding motif found in Bacillus subtilis and related species, and this difference may be important. This entry represents RexB proteins as found in Streptococcus and Lactococcus.
P-type conjugative transfer protein TrbG (TrbG_Ti)
Type: Family

The TrbG protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer . TrbG is a homologue of the F-type TraK protein (which is believed to be an outer membrane pore-forming secretin,

) as well as the vir system VirB9 protein .
DNA ligase D (NHEJ_ligase_prk)
Type: Domain

Members of this entry are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NheJ). The system of the bacterial Ku protein (

) plus this DNA ligase is seen in about 20% of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This entry describes a central and C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs. An additional N-terminal 3 -phosphoesterase (PE) domain (

) is present in some members of this ligase. Most examples of genes for this ligase are adjacent to the gene for Ku.
DNA ligase D, 3'-phosphoesterase domain (LigD_PE_domain)
Type: Domain

This entry represents a 3'-phosphoesterase domain of a multidomain, multifunctional DNA ligase, LigD, which is involved along with bacterial Ku protein in non-homologous end joining - the less common of two general mechanisms of repairing double-stranded breaks in DNA sequences.

LigD is variable in architecture, as it lacks this domain in Bacillus subtilis, is permuted in Mycobacterium tuberculosis, and occasionally is encoded by tandem ORFs rather than a multifunctional protein. In a few species (Dehalococcoides ethenogenes and the archaeal genus Methanosarcina), sequences corresponding to the ligase and polymerase domains of LigD are not found, and the role of this protein is unclear.
DNA ligase D, polymerase domain (LigD_pol_dom)
Type: Domain

DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see

), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria . This region represents the polymerase domain.
DNA ligase D, ligase domain (LigD_ligase_dom)
Type: Domain

DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see

), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This region represents the ligase domain .
Type IV conjugative transfer protein TrbJ (T4SS_TrbJ)
Type: Family

The TrbJ protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer . TrbJ is a homologue of the F-type TraE protein (which is believed to be an inner membrane pore-forming protein (

), as well as the vir system VirB5 protein .
P-type conjugative transfer protein VirB9 (VirB9)
Type: Family

The VirB9 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in a type IV secretion system . VirB9 is a homologue of the F-type conjugative transfer system TraK protein (which is believed to be an outer membrane pore-forming secretin,

) as well as the Ti system TrbG protein .
Conjugative transfer, TrbB (Conjug-transfer_TrbB)
Type: Family

This entry represents TrbB, a protein, which is encoded in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer . TrbB is a homologue of the vir system VirB11 ATPase , and the Flp pilus system ATPase TadA .
Conjugal transfer, TrbL (Conjugal_tfr_TrbL)
Type: Family

This entry represents TrbL, a protein, which is encoded in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer . TrbL is a homologue of the F-type TraG protein (which is believed to be a mating pair stabilisation pore-forming protein,

) as well as the vir system VirB6 protein .
DNA helicase, AddA type (DNA_helicase_AddA)
Type: Family

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination . The term AddAB is used broadly, with AddA homologues between the alphaproteobacteria and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.
ATP-dependent helicase/nuclease subunit A (AddA)
Type: Family

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologues between the firmicutes and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.

The AddA/AddB heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent, dual-direction single-stranded exonuclease. It recognises the chi site generating a DNA molecule suitable for the initiation of homologous recombination.

This entry represents the ATP-dependent helicase/nuclease subunit A (AddA) which is required for chi fragment generation; this subunit has the helicase and 3' -> 5' nuclease activities .
Double-strand break repair protein AddB (Ds_break_AddB)
Type: Family

AddAB is a system well described in the Firmicutes as a replacement for RecBCD in many prokaryotes for the repair of double stranded break DNA damage . More recently, a distantly related gene pair conserved in many alphaproteobacteria was shown also to function in double-stranded break repair in Rhizobium etli. This family consists of AddB proteins of alphaproteobacterial types.
Global transcriptional regulator CodY (CodY)
Type: Family

This entry represents pleiotropic repressors in Bacillus subtilis, CodY, and other Firmicutes (low-GC Gram-positive bacteria) that respond to intracellular levels of GTP and branched chain amino acids. CodY is a DNA-binding protein that represses the expression of many genes that are induced as cells make the transition from rapid exponential growth to stationary phase and sporulation. It is a GTP-binding protein that senses the intracellular GTP concentration as an indicator of nutritional limitations. At low GTP concentration it no longer binds GTP and stops to act as a transcriptional repressor .
Type IV secretion system protein VirB11 (VirB11)
Type: Family

This entry contains VirB11, a protein that is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer . VirB11 is believed to be an ATPase and is a homologue of the P-like conjugation system TrbB protein and the Flp pilus system protein TadA .