SII-SWORD/CoKE huggingface dataset:
D-cysteine desulfhydrase (D-Cys_desShydrase)
Type: Family

This entry represents a family of pyridoxal phosphate-dependent enzymes closely related to (and often designated as putative examples of) 1-aminocyclopropane-1-carboxylate deaminase. Members of this family include D-cysteine desulfhydrase (

) , 1-aminocyclopropane-1-carboxylate deaminase (

), and L-cysteate sulfo-lyase (

).

1-aminocyclopropane-1-carboxylate deaminase (

) catalyses a cyclopropane ring-opening reaction, the irreversible conversion of 1-aminocyclopropane-1-carboxylate (ACC) to ammonia and alpha-ketobutyrate . Some plant growth-promoting rhizobacteria can produce 1-aminocyclopropane-1-carboxylate deaminase to enhance plant growth .

D-cysteine desulfhydrase (d-CDes) (

) catalyses the alpha, beta-elimination reaction of D-cysteine and of several D-cysteine derivatives. The Escherichia coli d-CDes catalyses D-cysteine into pyruvate, H2S, and NH3 . The physiological function of bacterial d-CDes is not clear.
Thiamin/thiamin pyrophosphate ABC transporter, substrate-binding protein, Proteobacteria (ThiB)
Type: Family

This entry represents thiB, which is a thiamine-binding protein and part of the ABC transporter complex ThiBPQ involved in thiamine import. ThiBPQ is required for transport of thiamine and thiamine pyrophosphate in Salmonella typhimurium .

Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. Most of the bacterial ABC (ATP-binding cassette) importers are composed of one or two transmembrane permease proteins, one or two nucleotide-binding proteins and a highly specific periplasmic solute-binding protein. In Gram-negative bacteria the solute-binding proteins are dissolved in the periplasm, while in archaea and Gram-positive bacteria, their solute-binding proteins are membrane-anchored lipoproteins .
Thiamine ABC transporter, ATP-binding protein ThiQ (Thiamine_ABC_ThiQ)
Type: Family

This entry represents the energy-transducing ATPase subunit ThiQ of the ThiBPQ thiamine (and thiamine pyrophosphate) ABC transporter in several proteobacteria. This protein is found so far only in proteobacteria, and is found in complete genomes only if the ThiB and ThiP subunits are also found.
Light-independent protochlorophyllide reductase, B subunit (Protochl_reductB)
Type: Family

Synonym: dark protochlorophyllide reductase

Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. The light-independent (dark) form of protochlorophyllide reductase plays a key role in the ability of gymnosperms, algae, and photosynthetic bacteria to form chlorophyll in the dark. Genetic and sequence analyses have indicated that dark protochlorophyllide reductase consists of three protein subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the reductive formation of ammonia from dinitrogen. Dark protochlorophyllide reductase activity was shown to be dependent on the presence of all three subunits, ATP, and the reductant dithionite .
Light-independent protochlorophyllide reductase, N subunit (Protochl_reductN)
Type: Family

Synonym: dark protochlorophyllide reductase

Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. The light-independent (dark) form of protochlorophyllide reductase plays a key role in the ability of gymnosperms, algae, and photosynthetic bacteria to form chlorophyll in the dark. Genetic and sequence analyses have indicated that dark protochlorophyllide reductase consists of three protein subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the reductive formation of ammonia from dinitrogen. Dark protochlorophyllide reductase activity was shown to be dependent on the presence of all three subunits, ATP, and the reductant dithionite.

This enzyme describes the N subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme .
Light-independent protochlorophyllide reductase, iron-sulphur ATP-binding protein (Protochlorophyllide_ATP-bd)
Type: Family

Synonym: dark protochlorophyllide reductase

Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. Three genes, bchL, bchN and bchB, are involved in light-independent protochlorophyllide reduction in bacteriochlorophyll biosynthesis. In cyanobacteria, algae, and gymnosperms, three similar genes, chlL, chlN and chlB are involved in protochlorophyllide reduction during chlorophylls biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB exhibit significant sequence similarity to the nifH, nifD and nifK subunits of nitrogenase, respectively. Nitrogenase catalyzes the reductive formation of ammonia from dinitrogen . The light-independent (dark) form of protochlorophyllide reductase plays a key role in the ability of gymnosperms, algae, and photosynthetic bacteria to form chlorophyll in the dark. Genetic and sequence analyses have indicated that dark protochlorophyllide reductase consists of three protein subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the reductive formation of ammonia from dinitrogen. Dark protochlorophyllide reductase activity was shown to be dependent on the presence of all three subunits, ATP, and the reductant dithionite.

The BchL peptide (ChlL in chloroplast and cyanobacteria) is an ATP-binding iron-sulphur protein of the dark form protochlorophyllide reductase, an enzyme similar to nitrogenase .
Nitrogenase molybdenum-iron protein alpha chain (Nase_Mo-Fe_asu)
Type: Family

The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene which has an Fe4S4 cluster bound between the subunits and two ATP-binding domains. The Fe protein supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia . Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of the nifNE operon and of some other nif genes . It has been proposed that nifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I .

This entry refers to the alpha subunit of the MoFe protein (component I) of molybdenum (Mo-) nitrogenase, which is encoded by the nifD gene.
Nitrogenase MoFe cofactor biosynthesis protein NifE (NifE)
Type: Family

This entry refers to the nitrogenase MoFe cofactor biosynthesis protein encoded by the gene nifE.

The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene which has an Fe4S4 cluster bound between the subunits and two ATP-binding domains. The Fe protein supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia . Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of the nifNE operon and of some other nif genes . It has been proposed that nifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I .
Nitrogenase alpha chain (Nase_asu)
Type: Family

The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene. Two operons, nifDK and nifEN, encode a tetrameric (alpha2beta2 and N2E2) enzymatic complex. Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of nifNE and of some other nif genes. It has been proposed that NifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I.

This model represents the alpha chains of various forms of the nitrogen-fixing enzyme nitrogenase: vanadium-iron, iron-iron, and molybdenum-iron. Most examples of NifD, the molybdenum-iron type nitrogenase alpha chain, are excluded from this model and described instead by equivalog model

.
Nitrogenase molybdenum-iron cofactor biosynthesis protein (Nase_Mo-Fe_CF)
Type: Family

The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene which has an Fe4S4 cluster bound between the subunits and two ATP-binding domains. The Fe protein supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia . Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of the nifNE operon and of some other nif genes . It has been proposed that nifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I .

This entry refers to the nitrogenase iron-molybdenum cofactor biosynthesis protein NifN, which forms an alpha2beta2 tetramer with NifE. NifN and NifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively . NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The nifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron-and sulfur-containing analog of FeMoco. It has been suggested that this nifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco) .
Nitrogenase molybdenum-iron protein beta chain (Nase_Mo-Fe_CF_bsu)
Type: Family

The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene which has an Fe4S4 cluster bound between the subunits and two ATP-binding domains. The Fe protein supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia . Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of the nifNE operon and of some other nif genes . It has been proposed that nifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I .

This entry represents the molybdenum-iron protein beta chain, encoded by nifK.
Nitrogenase iron protein NifH (Nitrogenase_Fe_NifH)
Type: Family

The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene which has an Fe4S4 cluster bound between the subunits and two ATP-binding domains. The Fe protein supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia . Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of the nifNE operon and of some other nif genes . It has been proposed that nifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I .

This entry represents the nitrogenase iron protein (component II), which is encoded by nifH.
Nodulation ABC transporter, NodI (ABC_transptNodI)
Type: Family

Nodulation ABC transporter, NodI is required for normal nodulation by nitrogen-fixing root nodule bacteria such as Rhizobium loti (Mesorhizobium loti). It is a member of the family of ABC transporter ATP binding proteins and works with NodJ

to export a variety of modified carbohydrate molecules as signals to plant hosts to establish root nodules.

This entry does not include the highly divergent NodI from Azorhizobium caulinodans.
Protochlorophyllide reductase (Prochl_reduct)
Type: Family

Protochlorophyllide (Pchlide) reductases act in chlorophyll biosynthesis. There are distinct enzymes that catalyze Pchlide reduction in light or dark conditions . This family contains the light-dependent, NADPH-dependent form of protochlorophyllide reductase (

) which catalyses the reaction
chlorophyllide A + NADP+ = protochlorophyllide + NADPH.
The enzyme belongs to the short chain alcohol dehydrogenase family (SDR).
Nitrogenase cofactor biosynthesis protein NifB (Nase_CF_NifB)
Type: Family

NifB is a protein required for the biosynthesis of the iron-molybdenum
(or iron-vanadium) cofactor used by the nitrogen-fixing enzyme nitrogenase. NifB belongs to the radical SAM family, and the FeMo cluster biosynthesis process requires S-adenosylmethionine .
ABC-2 type transporter, NodJ (ABC_transptNodJ)
Type: Family

ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.

This entry consists of nodulation protein J (Nod J). Nod J together with NodI (

), forms a membrane transport complex involved in the nodulation process . It exports lipo-chitin oligosaccharides that induce nodule formation in the host plant . The substrates transported by the non-rhizobial proteins are not currently known.
Thioredoxin reductase (Thioredox_Rdtase)
Type: Family

Reactive oxygen species (ROS) are known mediators of intracellular signalling cascades. Excessive production of ROS may, however, lead to oxidative stress, loss of cell function, and ultimately apoptosis or necrosis. A balance between oxidant and antioxidant intracellular systems is hence vital for cell function, regulation, and adaptation to diverse growth conditions. Thioredoxin reductase in conjunction with thioredoxin is a ubiquitous oxidoreductase system with antioxidant and redox regulatory roles. Thioredoxin reductase (

) reduces oxidised thioredoxin in the presence of NADPH. Reduced thioredoxin serves as an electron donor for thioredoxin peroxidase which consequently reduces H
2
O
2
to H
2
O. In mammals, extracellular forms of Trx also have cytokine-like effects. Mammalian TrxR has a highly reactive active site selenocysteine residue resulting in a profound reductive capacity, reducing several substrates in addition to Trx .
Phospholamban (PLB)
Type: Family

Phospholamban (PLB) is a small protein (52 amino acids) that regulates the affinity of the cardiac sarcoplasmic reticulum Ca2+-ATPase (SERCA2a) for calcium. PLB is present in cardiac myocytes, in slow-twitch and smooth muscle and is expressed also in aorta endothelial cells in which it could play a role in tissue relaxation. The phosphorylation/dephosphorylation of phospholamban removes and restores, respectively, its inhibitory activity on SERCA2a. It has in fact been shown that phospholamban, in its non-phosphorylated form, binds to SERCA2a and inhibits this pump by lowering its affinity for Ca
2+
, whereas the phosphorylated form does not exert the inhibition. PLB is phosphorylated at two sites, namely at Ser-16 for a
cAMP-dependent phosphokinase and at Thr-17 for a Ca
2+
/calmodulin-dependent phosphokinase, phosphorylation at Ser-16 being a prerequisite for the phosphorylation at Thr-17.
Pediocin PA-1 biosynthesis protein PedC (PedC_BrcD)
Type: Family

Class II bacteriocins are small are ribosomally-synthesized, non-lantibiotic peptide antibiotics produced by many bacteria . This entry represents a protein encoded within a number of operons responsible for class II bacteriocin production . It is generally the third protein in the operon and, together with the fourth protein, is responsible for transport to the extracellular environment . Members of this entry are found in operons for pediocin PA-1 from Pediococcus acidilactici (PedC) and brochocin-C from Brochothrix campestris (BrcD) .
Aspartate-semialdehyde dehydrogenase, beta-type (Asp_semialdehyde_DH_beta)
Type: Family

Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids -lysine, threonine, methionine and isoleucine -in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see .

Aspartate-semialdehyde dehydrogenase (

), the second enzyme in the aspartate pathway, converts aspartyl phosphate to aspartate-semialdehyde, the branch point intermediate between the lysine and threonine/methionine pathways. Based on sequence alignments, the aspartate-semialdehyde dehydrogenase family appears to have at least three distinct subfamilies. Most studies have been performed on enzymes isolated from Gram-negative bacteria . The N-terminal domain forms the active site and NADP-binding pocket, while C-terminal domain is primarily involved in hydrophobic intersubunit contacts. The catalytic mechanism involves the formation of a covalent thioester acyl-enzyme intermediate mediated through nucleophilic attack by an active site cysteine residue on the substrate aspartyl phosphate. Release of inorganic phosphate is followed by hydride transfer from NADPH to yield the product. The recently described archaeal structure suggests that the two subgroups of aspartate semi-aldehyde dehydrogenase share similar structures and have an identical catalytic mechanism, despite their relatively low sequence identity . Unlike the bacterial enzymes, the archaeal enzyme utilised both NAD and NADP as cofactor.

This entry represents the most widely distributed subfamily of asparate semialdehyde dehydrogenases, found in diverse groups of bacteria and some eukaryotes.
Ribonuclease T (RNase_T)
Type: Family

Ribonuclease T (

) is an enzyme found so far only in gamma-subdivision proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a UV-repair defect caused by deletion of three other single-stranded DNA exonucleases .
Sucrose/H+ symporter, plant (Suc_symporter_pln)
Type: Family

These sucrose/proton symporters, found in plants, are from the Glycoside-Pentoside-Hexuronide (GPH)/cation symporter family. These proteins are predicted to have 12 transmembrane domains. Members may export sucrose (e.g. SUT1, SUT4) from green parts to the phloem for long-distance transport or import sucrose (e.g SUT2) to sucrose sinks such as the tap root of the carrot .
Inosine-5'-monophosphate dehydrogenase (IMP_DH)
Type: Family

This entry includes inosine-5'-monophosphate dehydrogenases and guanosine 5'-monophosphate (GMP) reductase. Inosine-5'-monophosphate dehydrogenase catalyses the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP), the first committed and rate-limiting step in the de novo synthesis of guanine nucleotides, and therefore plays an important role in the regulation of cell growth . GMP catalyses the irreversible NADPH-dependent deamination of GMP to IMP .
GMP reductase GuaB1 (GUAB1)
Type: Family

This family of proteins restricted to the high GC Gram-positive bacteria includes GMP reductase from Mycobacterium smegmatis (GUAB1), which is involved in the purine-salvage pathway. This protein is composed of two domains: a catalytic domain with a TIM barrel structure and another that folds as a typical Bateman domain composed of two CBS domains (cystathionine-beta-synthase domain, CBS,

), which are essential for the NADPH-dependent conversion of GMP to IMP .
IMP dehydrogenase-related 2 (IMP_DH-rel2)
Type: Family

This family of proteins, often annotated as a putative IMP dehydrogenase, are related to IMP dehydrogenase and GMP reductase. Most species with a member of this family belong to the high GC Gram-positive bacteria.
GMP reductase (GMPR)
Type: Family

GMP (guanosine monophosphate) reductase catalyses the irreversible and NADPH-dependent reductive deamination of GMP into IMP.
NADPH + guanosine 5-phosphate = NADP+ + inosine 5-phosphate + NH3

It converts nucleobase, nucleoside and nucleotide derivatives of G to A nucleotides, and maintains intracellular balance of A and G nucleotides. A deep split separates two families of GMP reductase. This family includes both eukaryotic and some proteobacterial sequences.