SII-SWORD/CoKE huggingface dataset:
Phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein (PhnD)
Type: Family

This family includes the periplasmic binding protein component of ABC transporters for phosphonates as well as other related binding components for closely related substances such as phosphate and phosphite . A number of members of this family are found in genomic contexts with components of selenium metabolic processes, suggestive of a role in selenate or other selenium-compound transport.

Phosphonates are a varied class of phosphorus-containing organic compound in which a direct C-P bond is found, rather than a C-O-P linkage of the phosphorus through an oxygen atom. They may be toxic but also may be used as sources of phosphorus and energy by various bacteria. Phosphonate utilization systems typically are encoded in 14 or more genes, including a three gene ABC transporter. This family includes the periplasmic binding protein component of ABC transporters for phosphonates as well as other, related binding components for closely related substances such as phosphate and phosphite. A subset of this entry in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system (GenProp0232, ) is shown in (

). Nevertheless, there are members of this subfamily which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates.
UTP--glucose-1-phosphate uridylyltransferase, bacterial/archaeal-type (GalU_uridylyltTrfase_bac/arc)
Type: Family

Uridine 5'-triphosphate:glucose-1-phosphate uridylyltransferase (uridine diphosphoglucose pyrophosphorylase,

) is responsible for the synthesis of UDP-glucose, a key compound in the biosynthesis of polysaccharides. Glucose is fermented through the glycolysis step to pyruvate, which in turn is converted to lactate. The glycolytic intermediate glucose 6-phosphate is converted to glucose 1-phosphate by phosphoglucomutase activity, and this metabolite is subsequently converted to UDP-glucose by UDP-glucose pyrophosphorylase (GalU) activity.
ATPase, V1 complex, subunit F, eukaryotic (ATPase_V1-cplx_fsu_euk)
Type: Family

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

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

This entry represents subunit F found in the V1 complex of V-ATPases in eukaryotes. Subunit F is a 16kDa protein that is required for the assembly and activity of V-ATPase, and has a potential role in the differential targeting and regulation of the enzyme for specific organelles. This subunit is not necessary for the rotation of the ATPase V1 rotor, but it does promote catalysis .
Type III secretion system, Yop virulence translocation protein R-like (T3SS_YscR-like)
Type: Family

This entry represents a group of virulence translocation proteins mainly found in the type III secretion system in proteobacteria, including Yop proteins translocation protein R from Yersinia pestis (YscR) and Surface presentation of antigens protein SpaP from Salmonella typhimurium.
YscR is a component of the yop secretion machinery. It may have a role in the negative pathway regulation of yop expression controlled by calcium. SpaP is involved in a secretory pathway responsible for the surface presentation of determinants needed for the entry of Salmonella species into mammalian cells .
UTP-glucose pyrophosphorylase, regulatory subunit (GalF)
Type: Family

This family of proteins, GalF, represents a non-catalytic subunit of the UTP-glucose pyrophosphorylase modulating the enzyme activity to increase the formation of UDP-glucose .
P-type ATPase subfamily IIC, subunit alpha (P-type_ATPase_IIC)
Type: Family

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

P-ATPases (also known as E1-E2 ATPases) (

) are found in bacteria and in a number of eukaryotic plasma membranes and organelles . P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, which transport specific types of ion: H
+
, Na
+
, K
+
, Mg
2+
, Ca
2+
, Ag
+
and Ag
2+
, Zn
2+
, Co
2+
, Pb
2+
, Ni
2+
, Cd
2+
, Cu
+
and Cu
2+
. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2.

This entry represents the alpha subunit found in the P-type cation exchange ATPases located in the plasma membranes of animal cells. These P-ATPases include both H
+
/K
+
-ATPases (

) and Na
+
/K
+
-ATPases (

), which belong to the IIC subfamily of ATPases . These ATPases catalyse the hydrolysis of ATP coupled with the exchange of cations, pumping one cation out of the cell (H
+
or Na
+
) in exchange for K
+
. These ATPases contain an alpha subunit that is the catalytic component, and a regulatory beta subunit (

) that stabilises the alpha/beta assembly . Different alpha and beta isoforms exist, permitting greater regulatory control.

An example of a H
+
/K
+
-ATPase is the gastric pump responsible for acid secretion in the stomach, transporting protons from the cytoplasm of parietal cells to create a large pH gradient in exchange for the internalisation of potassium ions, using ATP hydrolysis to drive the pump .
Oxaloacetate decarboxylase, alpha subunit (OadA)
Type: Family

This family describes the bacterial oxaloacetate decarboxylase alpha subunit and its equivalents in archaea . The oxaloacetate decarboxylase Na+ pump is the paradigm of the family of Na+ transport decarboxylases that present in bacteria and archaea. It a multi subunit enzyme consisting of a peripheral alpha-subunit and integral membrane subunits beta and gamma. The energy released by the decarboxylation reaction of oxaloacetate is coupled to Na+ ion pumping across the membrane.
Acetyl-S-ACP:malonate ACP transferase (MadA)
Type: Family

MadA is an alpha subunit of the biotin-dependent and biotin-independent malonate decarboxylase multienzyme complex ((

) and (

)). It acts as an acyl-carrier protein (ACP) transferase component. This first step in malonate decarboxylation involves the exchange of an acetyl thioester residue bound to the activated ACP subunit for a malonyl thioester residue. It has a weak activity with acetyl-CoA as substrate .
Tetrahydromethanopterin S-methyltransferase subunit A, MtrA (MtrA)
Type: Family

Tetrahydromethanopterin S-methyltransferase is a complex that catalyses the formation of methyl-coenzyme M and tetrahydromethanopterin from coenzyme M and methyl-tetrahydromethanopterin in methanogenic archaea . It is a membrane-associated enzyme complex that uses the methyl-transfer reaction to drive a sodium-ion pump .

The complex is composed of eight different subunits, MtrA-H. This entry describes subunit A (MtrA), which harbours a corrinoid as prosthetic group .
Tetrahydromethanopterin S-methyltransferase, subunit D (MeTrfase_D)
Type: Family

This model describes N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit D in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump.
5-methyl-5,6,7,8-tetrahydromethanopterin + 2-mercaptoethanesulphonate = 5,6,7,8-tetrahydromethanopterin + 2-(methylthio)ethanesulphonate.
Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase (encoded by subunit A) is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase.
Tetrahydromethanopterin S-methyltransferase, subunit E (MeTrfase_E)
Type: Family

This model describes N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit E in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump.

5-methyl-5,6,7,8-tetrahydromethanopterin + 2-mercaptoethanesulphonate = 5,6,7,8-tetrahydromethanopterin + 2-(methylthio)ethanesulphonate.

Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase (encoded by subunit A) is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase.
Photosynthetic reaction centre, M subunit (Photo_RC_M)
Type: Family

This entry describes the photosynthetic reaction centre M subunit.

The L and M subunits are arranged around an axis of 2-fold rotational symmetry perpendicular to the membrane, forming a scaffold that maintains the cofactors in a precise configuration. The L and M subunits have both sequence and structural similarity, suggesting a common evolutionary origin. The L and M subunits bind noncovalently to the nine cofactors in 2-fold symmetric branches: four bacteriochlorophylls, two bacteriopheophytins, two ubiquinone molecules (QA and QB), and a non-heme iron.

The photosynthetic apparatus in non-oxygenic bacteria consists of light-harvesting (LH) protein-pigment complexes LH1 and LH2, which use carotenoid and bacteriochlorophyll as primary donors . LH1 acts as the energy collection hub, temporarily storing it before its transfer to the photosynthetic reaction centre (RC) . Electrons are transferred from the primary donor via an intermediate acceptor (bacteriopheophytin) to the primary acceptor (quinine Qa), and finally to the secondary acceptor (quinone Qb), resulting in the formation of ubiquinol QbH2. RC uses the excitation energy to shuffle electrons across the membrane, transferring them via ubiquinol to the cytochrome bc1 complex in order to establish a proton gradient across the membrane, which is used by ATP synthetase to form ATP .

The core complex is anchored in the cell membrane, consisting of one unit of RC surrounded by LH1; in some species there may be additional subunits . RC consists of three subunits: L (light), M (medium), and H (heavy). Subunits L and M provide the scaffolding for the chromophore, while subunit H contains a cytoplasmic domain . In Rhodopseudomonas viridis, there is also a non-membranous tetrahaem cytochrome (4Hcyt) subunit on the periplasmic surface.
P-type ATPase, subfamily IIA, SERCA-type (P-type_ATPase_IIA)
Type: Family

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

P-ATPases (also known as E1-E2 ATPases) (

) are found in bacteria and in a number of eukaryotic plasma membranes and organelles . P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, which transport specific types of ion: H
+
, Na
+
, K
+
, Mg
2+
, Ca
2+
, Ag
+
and Ag
2+
, Zn
2+
, Co
2+
, Pb
2+
, Ni
2+
, Cd
2+
, Cu
+
and Cu
2+
. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2.

This entry represent the P-type ATPase responsible for translocating calcium ions across the endoplasmic reticulum membrane of eukaryotes , and is of particular importance in the sarcoplasmic reticulum of skeletal and cardiac muscle in vertebrates . These pumps transfer Ca2+ from the cytoplasm to the lumen of the endoplasmic reticulum. In humans and mice, at least, there are multiple isoforms of the SERCA pump with overlapping but not redundant functions. Defects in SERCA isoforms are associated with diseases in humans . The calcium P-type ATPases have been characterised as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump described in

. A separate analysis divides Type IIA into sub-types, SERCA and PMR1 the latter of which is described in

.
Methylmalonyl-CoA decarboxylase, alpha subunit (MemalonylCoA_decase_suA)
Type: Family

This family describes methymalonyl-CoA decarboxylase alpha subunit (

) in archaea and bacteria. Metylmalonyl-CoA decarboxylase Na+ pump is a representative of a class of Na transport decarboxylases that couples the energy derived by decarboxylation of carboxylic acid substrates to drive the extrusion of Na+ ion across the membrane, thereby creating a sodium ion motive force that is used for ATP synthesis . This subunit may catalyse the Na-independent carboxyl transfer from methylmalonyl-CoA to the prosthetic biotin group located on the gamma subunit.
D-amino acid aminotransferase (D_amino_transT)
Type: Family

D-amino acid aminotransferase (

) catalyzes transamination between various D-amino acids and alpha-keto acids. This enzyme is a homodimer. The pyridoxal phosphate attachment site is a Lys in the motif Cys-Asp-Ile-Lys-Ser-Leu-Asn. Specificity is broad for various D-amino acids, and differs among members of the family .
Branched-chain amino acid aminotransferase I (B_amino_transI)
Type: Family

Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped into subfamilies.

One of these, called class-IV, currently consists of proteins of about 270 to 415 amino-acid residues that share a few regions of sequence similarity. Surprisingly, the best conserved region does not include the lysine residue to which the pyridoxal-phosphate group is known to be attached, in ilvE, but is located some 40 residues at the C terminus side of the PlP-lysine.

Among the class IV aminotransferases are two phylogenetically separable groups of branched-chain amino acid aminotransferase (IlvE) (

). The last common ancestor of the two lineages appears also to have given rise to a family of D-amino acid aminotransferases (DAAT). This model represents the IlvE family more strongly similar to the DAAT family.
Branched-chain amino acid aminotransferase II (B_amino_transII)
Type: Family

Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped into subfamilies.

One of these, called class-IV, currently consists of proteins of about 270 to 415 amino-acid residues that share a few regions of sequence similarity. Surprisingly, the best conserved region does not include the lysine residue to which the pyridoxal-phosphate group is known to be attached, in ilvE, but is located some 40 residues at the C terminus side of the PlP-lysine.

Among the class IV aminotransferases are two phylogenetically separable groups of branched-chain amino acid aminotransferase (IlvE) (

). The last common ancestor of the two lineages appears also to have given rise to a family of D-amino acid aminotransferases (DAAT). This model represents the IlvE family less similar to the DAAT family.

Also included in this group is branched-chain amino acid aminotransferase gloG from the yeast
Glarea lozoyensis
, which is required for biosynthesis of the mycotoxin pneumocandin, a lipohexapeptide of the echinocandin family . Transaminase AMT5 from the Alternaria rot fungus is one of many enzymes required for the non-ribosomal biosynthesis of the cyclic depsipeptides known as AM-toxins . The aminotransferase FGSG_00049 from Fusarium graminearum is part of the gene cluster that mediates the biosynthesis of gramillins A and B, bicyclic lipopeptides that induce cell death in maize leaves but not in wheat, suggesting host-specific adaptation .
Threonine dehydratase, biosynthetic (Thr_deHydtase_biosynth)
Type: Family

Threonine dehydratase (

) (TDH) catalyzes the dehydratation of threonine into alpha-ketobutarate and ammonia. In Escherichia coli and other microorganisms, two classes of TDH are known to exist. One is involved in the biosynthesis of isoleucine, the other in hydroxamino acid catabolism.

This entry describes a form of threonine dehydratase with two copies of the threonine dehydratase C-terminal domain (

_. Members with known function participate in isoleucine biosynthesis and are inhibited by isoleucine.
Protein disulfide-isomerase, thioredoxin-like domain (PDI_thioredoxin-like_dom)
Type: Domain

This entry represents a domain found in eukaryotic protein disulphide isomerases (PDI), multifunctional proteins that catalyse the formation, breakage and rearrangement of disulfide bonds . PDI generally shows four thioredoxin-like domains. This entry represents the two redox active domains, which are located at the N-and C-terminal ends .
Threonine dehydratase, catabolic (Thr_deHydtase_catblc)
Type: Family

Threonine dehydratase (

) (TDH) catalyzes the dehydratation of threonine into alpha-ketobutarate and ammonia. In Escherichia coli and other microorganisms, two classes of TDH are known to exist. One is involved in the biosynthesis of isoleucine, the other in hydroxamino acid catabolism.

A form of TDH with two copies of the C-terminal domain

is described by

. This entry describes a phylogenetically distinct form, which includes the catabolic threonine dehydratase of E. coli; many members are designated as catabolic for this reason. The catabolic form appears to lack a

domain. Many members of this family are found in species with other isoleucine biosynthetic enzymes.
DNA polymerase III, delta subunit (DNA_polIII_delta)
Type: Family

This family of proteins includes subunits of DNA polymerase III, specifically the delta subunit, which plays a crucial role in bacterial DNA replication. The delta subunit is involved in the assembly of the DNA polymerase III holoenzyme by interacting with other subunits to facilitate the loading of the beta sliding clamp onto the DNA. This process is essential for the replication machinery to achieve high processivity during DNA synthesis. The delta subunit's interaction with the gamma subunit is particularly important for transferring the beta subunit onto the DNA . Additionally, these proteins may exhibit 3' to 5' exonuclease activity, contributing to the proofreading function of the polymerase.

DNA polymerase III delta (holA,

) and delta prime (holB) subunits are distinct proteins encoded by separate genes. The delta prime subunit (holB) exhibits sequence homology to the tau and gamma subunits (dnaX), but the delta subunit (holA) does not demonstrate this same homology with dnaX. The delta, delta prime, gamma, chi and psi subunits form the gamma complex sub-assembly of DNA polymerase III holoenzyme, which couples ATP to assemble the ring-shaped beta subunit around DNA forming a DNA sliding clamp. Both delta and delta prime are monomeric in their native state, and they bind each other tightly to form a 1:1 complex. Neither delta nor delta prime alone binds tightly to the gamma subunit .
Protein translocase subunit SecD (SecD)
Type: Family

Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component . From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.
Protein disulphide isomerase (Prot_disulphide_isomerase)
Type: Family

This family represents eukaryotic protein disulphide isomerases retained in the endoplasmic reticulum (ER) and other closely related forms . Some members have been assigned alternative or additional functions such as prolyl 4-hydroxylase . Members of this family have at least two protein-disulphide domains, each similar to thioredoxin but with the redox-active disulphide in the motif PWCGHCK, and an ER retention signal at the extreme C terminus (KDEL, HDEL, and similar motifs).
Formyl transferase, C-terminal (Formyl_trans_C)
Type: Domain

Methionyl-tRNA formyltransferase (

) transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA. The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and by impairing its binding to EFTU-GTP. This family also includes formyltetrahydrofolate dehydrogenases, which produce formate from formyl-tetrahydrofolate. These enzymes contain an N-terminal domain in common with other formyl transferase enzymes (

). The C-terminal domain has an open β-barrel fold .
Methionyl-tRNA formyltransferase (Fmt)
Type: Family

Methionyl-tRNA formyltransferase (

) transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA. The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and by impairing its binding to EFTU-GTP.
Major pollen allergen Lol pI (LolPI)
Type: Family

Grass pollens are a major cause of type I allergy. Lol pI, the major rye grass (Lolium perenne) allergen, is a 240-amino acid protein . Analysis of the amino acid sequence has revealed a determinant within the Lol pI molecule that is recognised by human leukocyte antigen class II-restricted T cells obtained from patients allergic to rye grass pollen .