SII-SWORD/CoKE huggingface dataset:
Ferredoxin [2Fe-2S], plant (Fd_pln)
Type: Family

This entry represents single domain 2Fe-2S (also called plant type) ferredoxins. In general, these occur as a single domain proteins or with a chloroplast transit peptide. In higher plants, ferredoxin is the unique soluble electron carrier protein located in the stroma, and a wide variety of essential metabolic and signalling processes depend upon the reduction by ferredoxin. Species tend to be photosynthetic, but several forms may occur in one species and individually may not be associated with photosynthesis. For instance, in Arabidopsis two ferredoxins are leaf-type that support high photosynthetic activity, while one is a root-type that is more efficiently reduced under non-photosynthetic conditions and supporting a higher activity of sulphite reduction .
DNA-directed RNA polymerase beta subunit, bacterial-type (RNA_pol_bsu_bac)
Type: Family

DNA-directed RNA polymerases

(also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.

RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.

Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:

RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.

RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.

RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.

Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.

This entry describes orthologues of the beta subunit of bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.
Chlorophyllide reductase subunit Z (BchZ)
Type: Family

This entry represents the Z subunit of the three-subunit enzyme, bacteriochlorophyllide reductase . This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase.
Chlorophyllide reductase subunit Y (BchY)
Type: Family

This entry represents the Y subunit of the three-subunit enzyme, (bacterio)chlorophyllide reductase . This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase.
Chlorophyllide reductase iron protein subunit X (BchX)
Type: Family

This entry represents the X subunit of the three-subunit enzyme, (bacterio)chlorophyllide reductase . This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase. This subunit is homologous to the nitrogenase component II, or 'iron' protein.
N-formylglutamate deformylase (HutG_amidohyd)
Type: Family

In some species, histidine is converted to via urocanate and then formimino-L-glutamate to glutamate in four steps, where the fourth step is conversion of N-formimino-L-glutamate to L-glutamate and formamide. In others, that pathway from formimino-L-glutamate may differ, with the next enzyme being formiminoglutamate hydrolase (HutF) yielding N-formyl-L-glutamate. This entry represents the enzyme N-formylglutamate deformylase, also called N-formylglutamate amidohydrolase, which then produces glutamate .
Histidine utilization repressor (His_ut_repres)
Type: Family

This entry represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Bacteriochlorophyll 4-vinyl reductase (BchJ)
Type: Family

This entry represents the component of bacteriochlorophyll synthetase responsible for reduction of the B-ring pendant ethylene (4-vinyl) group. It appears that this step must precede the reduction of ring D, at least by the 'dark' protochlorophyllide reductase enzymes BchN, BchB and BchL . This family appears to be present in photosynthetic bacteria except for the cyanobacterial clade. Cyanobacteria must use a non-orthologous gene to carry out this required step for the biosynthesis of both bacteriochlorophyll and chlorophyll.
Magnesium-protoporphyrin IX methyltransferase (Mg_prot_MeTrfase)
Type: Family

This entry represents magnesium-protoporphyrin IX methyltransferase (

). This converts magnesium-protoporphyrin IX to magnesium-protoporphyrin IX metylester using S-adenosyl-L-methionine as a cofactor , which represents the second committed step in the biosynthesis of chlorophyll and bacteriochlorophyll from protoporphyrin IX .
Formimidoylglutamate deiminase (HutF)
Type: Family

In some species, histidine utilisation goes via urocanate to glutamate in four step, the last being removal of formamide. This entry describes an alternate fourth step, formimidoylglutamate deiminase which leads to N-formyl-L-glutamate . This product may be acted on by formylglutamate amidohydrolase (

) and bypass glutamate as a product during its degradation. Alternatively, removal of formate (by

) would yield glutamate.
Geranylgeranyl reductase, plant/prokaryotic (BchP_ChlP_pln/prok)
Type: Family

This entry represents a group of geranylgeranyl reductases specific for the biosyntheses of bacteriochlorophyll and chlorophyll . It is unclear whether the processes of isoprenoid ligation to the chlorin ring and reduction of the geranylgeranyl chain to a phytyl chain are necessarily ordered the same way in all species (see introduction to ).
B12-dependent dehydratases, beta subunit (B12-dep_deHydtase_bsu)
Type: Homologous_superfamily

This superfamily includes the beta (or middle) subunit of the oligomeric (alpha2beta2gamma2) diol dehydratases (DDH) and glycerol dehydratases (GDH), which are enzymes produced by some enterobacteria, as well as the beta subunit of the tetrameric (alpha2beta2) glycerol dehydratase reactivase, which removes damaged coenzyme B12 from GDH that has suffered mechanism-based inactivation . The beta subunit of GDH reactivase resembles that of GDH and DDH, displaying a three-layer α/β/α fold, except that the reactivase subunit lacks some B12-binding elements.
Haem peroxidase superfamily (Haem_peroxidase_sf)
Type: Homologous_superfamily

Peroxidases are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions. Most haem peroxidases follow the reaction scheme:

Fe
3+
+ H
2
O
2
-->[Fe
4+
=O]R' (Compound I) + H
2
O

[Fe
4+
=O]R' + substrate -->[Fe
4+
=O]R (Compound II) + oxidised substrate

[Fe
4+
=O]R + substrate -->Fe
3+
+ H
2
O + oxidised substrate

In this mechanism, the enzyme reacts with one equivalent of H
2
O
2
to give [Fe
4+
=O]R' (compound I). This is a two-electron oxidation/reduction reaction where H
2
O
2
is reduced to water and the enzyme is oxidised. One oxidising equivalent resides on iron, giving the oxyferryl intermediate, while in many peroxidases the porphyrin (R) is oxidised to the porphyrin pi-cation radical (R'). Compound I then oxidises an organic substrate to give a substrate radical .

Haem peroxidases include two superfamilies: one found in bacteria, fungi, plants and the second found in animals. The animal peroxidases comprise a group of homologous proteins that differ markedly from the plant/fungal/bacterial peroxidases in primary, secondary and tertiary structure, but which share with them a common function. Animal peroxidases probably arose independently of the plant/fungal/bacterial peroxidase superfamily and most likely belong to a different gene family. The crystal structures of a number of these proteins show that the active sites of animal peroxidase and plant/fungal/bacterial peroxidases are remarkably similar .
Conjugal transfer, TrbG/VirB9/CagX (Conjugal_tfr_TrbG/VirB9/CagX)
Type: Family

Several bacterial pathogens utilise conjugation machines to export effector molecules during infection. Such systems are members of the type IV or 'adapted conjugation' secretion family. The prototypical type IV system is the Agrobacterium tumefaciens T-DNA transfer machine, which delivers oncogenic nucleoprotein particles to plant cells. Other pathogens, including Bordetella pertussis, Legionella pneumophila, Brucella spp. and Helicobacter pylori (Campylobacter pylori), use type IV machines to export effector proteins to the extracellular milieu or the mammalian cell cytosol.

Conjugation machines of Gram-negative bacteria consist of two surface structures, the mating channel through which the DNA transfer intermediate and proteins are translocated and the conjugal pilus for contacting recipient cells. Various conjugative pili have been visualised, but to date there is no ultrastructural information about the mating channel. Recent work on the A. tumefaciens T-DNA transfer system has focused on identifying interactions among the VirB protein subunits and defining steps in the transporter assembly pathway. There are three functional groups of VirB proteins: proteins localised exocellularly forming the T-pilus or other adhesive structures; mating-channel components; and cytoplasmic membrane ATPases. Although all of these proteins probably assemble as a supramolecular complex, as yet there is no direct evidence for a physical association between the conjugative pilus and the mating channel.

Several lines of evidence suggest that VirB6-VirB10 are probable channel subunits. VirB6, a highly hydrophobic protein, is thought to span the cytoplasmic membrane several times and presently is the best candidate for a channel-forming protein. VirB7, an outer membrane lipoprotein, interacts with itself and with VirB9 via disulphide bonds between unique reactive cysteines present in each protein. The VirB7-VirB9 heterodimer localises at the outer membrane and plays a critical role in stabilising other VirB proteins during assembly of the transfer machine. VirB9 is also required for formation of chemically crosslinked VirB10 oligomers probably corresponding to homotrimers .
Peptidase S8 propeptide/proteinase inhibitor I9 (S8pro/Inhibitor_I9)
Type: Domain

Proteinase propeptide inhibitors (sometimes refered to as activation peptides) are responsible for the modulation of folding and activity of the pro-enzyme or zymogen. The pro-segment docks into the enzyme moiety shielding the substrate binding site, thereby promoting inhibition of the enzyme. Several such propeptides share a similar topology , despite often low sequence identities . The propeptide region has an open-sandwich antiparallel-α/antiparallel-β fold, with two α-helices and four β-strands with a (β/α/β)x2 topology.

This entry represents the propeptide domain at the N terminus of peptidases belonging to MEROPS family S8A, subtilisins. The subtilisin propeptides are known to function as molecular chaperones, assisting in the folding of the mature peptidase . The propeptide is removed by proteolytic cleavage; removal activating the enzyme. This domain is also found in members of MEROPS proteinase inhibitor family I9.
DNA-binding transcriptional activator AlpA (AlpA)
Type: Family

This family consists of several short bacterial and phage proteins which are related to the E. coli protein AlpA. AlpA suppresses two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light. AlpA acts as a transcriptional regulator of the slpA gene; activation of slpA transcription is necessary to suppress these phenotypes . Several of the sequences in this family are thought to be DNA-binding proteins.
Tir chaperone protein (CesT) family (Tir_chaperone)
Type: Family

This family consists of a number of sequences which are highly similar to the Tir chaperone protein in Escherichia coli. In many Gram-negative bacteria, a key indicator of pathogenic potential is the possession of a specialised type III secretion system, which is utilised to deliver virulence effector proteins directly into the host cell cytosol. Many of the proteins secreted from such systems require small cytosolic chaperones to maintain the secreted substrates in a secretion-competent state. CesT serves a chaperone function for the enteropathogenic Escherichia coli (EPEC) translocated intimin receptor (Tir) protein, which confers upon EPEC the ability to alter host cell morphology following intimate bacterial attachment .

This family also contains the chaperone protein sicP and several DspF and related sequences from several plant pathogenic bacteria. The "disease-specific" (dsp) region next to the hrp gene cluster of Erwinia amylovora is required for pathogenicity but not for elicitation of the hypersensitive reaction. DspF and AvrF are small (16kDa and 14kDa) and acidic with predicted amphipathic α helices in their C termini; they resemble chaperones for virulence factors secreted by type III secretion systems of animal pathogens .

This entry also includes Pseudomonas aeruginosa ExsC, which functions as a chaperone for ExsE. It is also part of the regulatory cascade that plays a role in the transcriptional regulation of the type III secretion system (T3SS) .

The family also contains a number of proteins from eukaryotic parasites.
Arylsulfotransferase, bacteria (Arylsulfotransferase_bact)
Type: Family

This entry represents a group of arylsulphotransferase (ASST) mostly from bacteria. It transfers a sulphate group from phenolic sulphate esters to a phenolic acceptor substrate .
Type VI secretion system TssK (T6SS_TssK)
Type: Family

TssK is an essential baseplate component of the type VI secretion system, which connects the membrane complex, the baseplate and the tail components .

The structure of TssK was solved revealing the proteins organise into a tightly packed trimer . Each TssK monomer comprises three domains: an N-terminal β-sandwich domain, a linker and a four-helix-bundle middle domain, and a C-terminal domain. The N-terminal domain of TssK is structurally homologous to the shoulder domain of phage receptor-binding proteins, and the C-terminal domain binds the T6SS membrane complex .

This family includes TssK proteins and TssK homologues ImpJ and vasE.

The type VI secretion system (T6SS), also known as CIS contractile injection system , is a supra-molecular bacterial complex that resembles phage tails. It is a toxin delivery systems which fires toxins into target cells upon contraction of its TssBC sheath . Thirteen essential core proteins are conserved in all T6SSs: the membrane associated complex TssJ-TssL-TssM, the baseplate proteins TssE, TssF, TssG, and TssK, the bacteriophage-related puncturing complex composed of the tube (Hcp), the tip/puncturing device VgrG, and the contractile sheath structure (TssB and TssC). Finally, the starfish-shaped dodecameric protein, TssA, limits contractile sheath polymerization at its distal part when TagA captures TssA .
Plant self-incompatibility S1 (Self-incomp_S1)
Type: Family

This family consists of a series of plant proteins which are related to the Papaver rhoeas S1 self-incompatibility protein. Self-incompatibility (SI) is the single most important outbreeding device found in angiosperms and is a mechanism that regulates the acceptance or rejection of pollen. S1 is known to exhibit specific pollen-inhibitory properties .
Bacteriophage lambda, Tail tip protein M (Phage_lambda_TipM)
Type: Family

This entry represents Tail tip protein M from Escherichia phage lambda (Bacteriophage lambda). Members of this protein family are found in tailed bacteriophages (Caudovirales) and in bacterial prophages mostly among Proteobacteria.

TipM is part of the distal tail tip which plays a role in DNA ejection during entry, and in tail assembly initiation during exit. It may bind tail tip complex associated with tape measure protein and allow tail tube protein polymerization on top of tail tip .
NnrS (NnrS)
Type: Family

This family consists of several bacterial NnrS like proteins. NnrS is a haem-Cu protein (NnrS) and a member of the short-chain dehydrogenase family . Expression of nnrS is dependent on the transcriptional regulator NnrR, which also regulates expression of genes required for the reduction of nitrite to nitrous oxide, including nirK and nor. NnrS is a haem- and copper-containing membrane protein. Genes encoding putative orthologues of NnrS are sometimes but not always found in bacteria encoding nitrite and/or nitric oxide reductase . NnrS contributes to nitrosative-stress tolerance in V. cholerae and protects the cellular iron pool from the formation of dinitrosyl iron complexes (DNICs), thus protecting critical metabolic pathways from inhibition .
Chordopoxvirus A20R (Chordopox_A20R)
Type: Family

This family consists of several Chordopoxvirus A20R proteins. The A20R protein, also known as DNA polymerase processivity factor component OPG148, plays an essential role in viral DNA replication by acting as the polymerase processivity factor together with protein OPG116 . It serves as a bridge which links the DNA polymerase OPG071 and the uracil DNA glycosylase . A20R may contribute to the assembly or stability of the multiprotein DNA replication complex .
Archaeal PaREP1 (PaREP1)
Type: Family

This family consists of several archaeal PaREP1 proteins, the function of the family is unknown.
Type VI secretion system TssC-like (T6SS_TssC-like)
Type: Family

The long cytoplasmic tubular structure of the T6SS system is wrapped by a sheath structure composed of two proteins, TssB and TssC. Contraction of the sheath causes the internal tube of the T6SS with associated effectors to be propelled out of the effector cell and across the membranes of bacterial or eukaryotic target cells .

TssB and TssC assemble into tubular structures with cogwheel patterns resembling the bacteriophage contractile sheath . Several structures of T6SS sheath assemblies have been solved displaying a helical assembly . Interactions between TssB and TssC occur between the N-terminal region of TssC and the conserved a-helix of TssB . The two proteins of the F. novicida T6SS outer sheath, IglA (TssB) and IglB (TssC), are interdigitated into a single fold similar to that of the phage sheath. The F. novicida T6SS outer sheath has a highly interlaced two-dimensional array architecture with augmented β sheets that is essential to secretory function .

Three distinct T6SS subtypes exist, T6SSi, in which most proteobacterial T6SSs are found, including V. cholerae and P. aeruginosa; T6SSii for the Francisella T6SS; and T6SSiii for Bacteroidetes systems .

TssB/TssC are also known as IglA/IglB and VipA/VipB.

The type VI secretion system (T6SS), also known as CIS contractile injection system , is a supra-molecular bacterial complex that resembles phage tails. It is a toxin delivery systems which fires toxins into target cells upon contraction of its TssBC sheath . Thirteen essential core proteins are conserved in all T6SSs: the membrane associated complex TssJ-TssL-TssM, the baseplate proteins TssE, TssF, TssG, and TssK, the bacteriophage-related puncturing complex composed of the tube (Hcp), the tip/puncturing device VgrG, and the contractile sheath structure (TssB and TssC). Finally, the starfish-shaped dodecameric protein, TssA, limits contractile sheath polymerization at its distal part when TagA captures TssA .
Bacteriophage P2, GpM (Phage_P2_GpM)
Type: Family

This entry is represented by Bacteriophage P2, GpM. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

This family consists of several phage small terminase subunit proteins as well as some related bacterial sequences . M protein is probably an endonuclease which directs cos cleavage. The Q, P and M proteins are needed to package DNA into proheads and for the conversion of proheads to capsids.
Toxin-coregulated pilus subunit TcpA (TcpA)
Type: Family

This family consists of toxin-coregulated pilus subunit (TcpA) proteins from Vibrio cholerae and related sequences. The major virulence factors of toxigenic V. cholerae are cholera toxin (CT), which is encoded by a lysogenic bacteriophage (CTXPhi), and toxin-coregulated pilus (TCP), an essential colonisation factor which is also the receptor for CTXPhi. The genes for the biosynthesis of TCP are part of a larger genetic element known as the TCP pathogenicity island .
Type VI secretion system TssF (T6SS_TssF)
Type: Family

This entry represents a group of Gram-negative bacterial proteins that form part of the type VI pathogenicity secretion system (T6SS), including TssF . TssF is an essential baseplate component of the type VI secretion system. TssF is a homologue of phage tail proteins and is required for proper assembly of the Hcp tube (the T6SS inner tube) in bacteria .

The cryoEM structure of a TssK-TssF-TssG complex revealed that TssF comprises 3 domains; an α-helical N-terminal domain, a central domain made up of three β-barrels and a C-terminal four-stranded mixed β-sheet packed against α-helices via a hydrophobic core . TssF and TssG assembled into a heterotrimer with 2:1 stoichiometry .

The type VI secretion system (T6SS), also known as CIS contractile injection system , is a supra-molecular bacterial complex that resembles phage tails. It is a toxin delivery systems which fires toxins into target cells upon contraction of its TssBC sheath . Thirteen essential core proteins are conserved in all T6SSs: the membrane associated complex TssJ-TssL-TssM, the baseplate proteins TssE, TssF, TssG, and TssK, the bacteriophage-related puncturing complex composed of the tube (Hcp), the tip/puncturing device VgrG, and the contractile sheath structure (TssB and TssC). Finally, the starfish-shaped dodecameric protein, TssA, limits contractile sheath polymerization at its distal part when TagA captures TssA .
Protein of unknown function DUF881 (DUF881)
Type: Family

This family consists of a series of hypothetical bacterial proteins. One of the family members

from Bacillus subtilis is thought to be involved in cell division and sporulation .
Orthopoxvirus A36R (Orthopox_A36R)
Type: Family

This entry represents A36R from Vaccinia virus, also called Protein OPG164, and similar proteins predominantly found in orthopoxvirus. A36R is involved in the intracellular transport and egress of virions to the host cell surface with help of protein OPG056 . It also participates in the formation of actin tails at the plasma membrane to allow efficient actin-based motility and thus cell to cell transmission of viral particles .