SII-SWORD/CoKE huggingface dataset:
Guanosine monophosphate reductase, type2 (GuaC_type_2)
Type: Family

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 is found in a variety of bacterial lineages. The other type (

) is found in eukaryotic and some proteobacterial lineages.
Phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent (Pgm_bpd_ind)
Type: Family

This 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGAM) is a metalloenzyme found particularly in eubacteria and higher plants. It is distantly related to archaeal iPGAM (

) and distinct from the unrelated cofactor-dependent PGAM. Activity has been demonstrated for proteins from a variety of organisms, including Pseudomonas syringae pv. tomato , Bacillus subtilis , Bacillus stearothermophilus , maize , castor bean , and Trypanosoma brucei . The structure of the B. stearothermophilus enzyme has two domains . Residues 1-76 and 311-511 form the phosphatase domain, containing the active site residue and two metal-binding sites. This domain is similar to alkaline phosphatase and arylsulphatase, which are members of the SCOP alkaline phosphatase-like superfamily, but there is meagre sequence similarity outside of the metal-binding segments. Residues 77-310 form the phosphotransferase domain, which is poorly conserved (or perhaps unrelated) in the archaeal enzymes.
Large ribosomal subunit protein uL30, bacterial-type (Ribosomal_uL30_bac-type)
Type: Family

Ribosomal protein uL30 is one of the proteins from the large ribosomal subunit. uL30 belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacteria and archaea uL30, yeast mitochondrial uL33m, and Drosophila, slime mould, fungal and mammalian L7 ribosomal proteins . uL30 from bacteria are small proteins of about 60 residues.

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Large ribosomal subunit protein uL30, archaeal (Ribosomal_uL30_arc)
Type: Family

Ribosomal protein uL30 is one of the proteins from the large ribosomal subunit. This model describes archaeal 50S ribosomal protein uL30. These proteins share similarity to the longer eukaryotic 60S ribosomal protein, previously known as L7, and to the much shorter (~60 residue) bacterial 50S ribosomal protein uL30.

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Large ribosomal subunit protein uL30, eukaryotic (Ribosomal_uL30_euk)
Type: Family

This entry represents the large ribosomal subunit protein uL30 found in eukaryotes that was previously know as L7. The eukaryotic ribosomal protein uL30 contains an N-terminal bZIP DNA binding domain and a second, DNA-binding domain has been mapped to the 50 C-terminal amino acids of the protein . In addition to its role in translation, uL30 has also been shown to be involved in nuclear-receptor mediated transcriptional control.

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Glycerol kinase (Glycerol_kin)
Type: Family

Glycerol kinase (

) is a bacterial sugar kinase which catalyses the Mg-ATP-dependent phosphorylation of glycerol to yield glycerol 3-phosphate. The enzyme from Escherichia coli is an allosteric regulatory enzyme whose activity is inhibited by fructose 1,6-bisphosphate (FBP) and the glucose-specific phosphocarrier of the phosphoenolpyruvate:glycose phosphotransferase system, IIA(Glc), structural studies suggest a nucleophilic in-line transfer mechanism for the ATP-dependent phosphorylation of glycerol by glycerol kinase .
Xylulokinase (Xylulokinase)
Type: Family

The ability to metabolise xylose, one of the most abundant sugars in nature, is dependent on its conversion to xylulose-5-phosphate, which then enters the non-oxidative pentose phosphate pathway . Xylulose-5-phosphate is produced from xylose by the sequential action of two enzymes; xylose isomerase, which converts xylose to xylulose, and xylulokinase, which subsequently phosphorylates xylulose.

This entry represents bacterial xylulokinase. In addition to its role in xylose metabolism this enzyme may also have a biosynthetic role. 1-deoxy-D-xylulose 5-phosphate serves as a precursor for the biosynthesis of the vitamins thiamine and pyridoxal and for the formation of isopentenyl pyrophosphate and dimethylallyl pyrophosphate via the nonmevalonate pathway of terpenoid biosynthesis. Xylulokinase catalyses the phosphorylation of 1-deoxy-D-xylulose at the hydroxy group of C-5 . This reaction therefore constitutes a potential salvage pathway for the generation of 1-deoxy-D-xylulose 5-phosphate from exogenous or endogenous 1-deoxy-D-xylulose as starting material for the biosynthesis of terpenoids, thiamine and pyridoxal.
Carbohydrate kinase, thermoresistant glucokinase (Therm_gnt_kin)
Type: Family

This family of proteins includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases. The structure of the E. coli thermoresistant gluconate kinase GntK has been revealed . GntK catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits .
Gluconate kinase (Gluconate_kinase)
Type: Family

Gluconate kinase (

) has an α/β structure consisting of a twisted parallel β-sheet surrounded by α-helices with overall topology similar to nucleoside monophosphate (NMP) kinases, such as adenylate kinase. Significant conformational changes are induced upon binding of ATP to the enzyme. The largest changes involve a hinge-bending motion of the NMP(bind) part and a motion of the LID with adjacent helices, which opens the cavity to the second substrate, gluconate. The opening of the active site cleft upon ATP binding is the opposite of what has been observed in the NMP kinase family so far, which usually close their active site to prevent fortuitous hydrolysis of ATP. The beta and gamma-phosphate groups of ATP bind in the predicted P-loop. A conserved lysine side-chain interacts with the gamma-phosphate group, and might promote phosphoryl transfer.
ATP + D-gluconate = ADP + 6-phospho-D-gluconate.
Gluconate-6-phosphate binds with its phosphate group in a similar position as the gamma-phosphate of ATP, consistent with inline phosphoryl transfer .
FGGY carbohydrate kinase, pentulose kinase (FGGY_RbtK-like)
Type: Family

This entry represents a subfamily of the FGGY family of carbohydrate kinases, including FGGY carbohydrate kinase domain-containing proteins from mammals and D-ribulokinase YDR109C from S. cerevisiae, which catalyse ATP-dependent phosphorylation of D-ribulose at C-5 to form D-ribulose 5-phosphate . These proteins may function in a metabolite repair mechanism by preventing toxic accumulation of free D-ribulose formed by non-specific phosphatase activities, and may also play a role in regulating D-ribulose 5-phosphate recycling in the pentose phosphate pathway.

This subfamily is closely related to a set of ribulose kinases, and many members are designated ribitol kinase. However, the member from Klebsiella pneumoniae, rbtK, from a ribitol catabolism operon, accepts D-ribulose and to a lesser extent D-arabinitol and ribitol .
Sulfide dehydrogenase subunit alpha-like (SudA-like)
Type: Family

This entry represents a group of prokaryotic dehydrogenases with a FAD/NAD(P)-binding domain, including Sulfide dehydrogenase subunit alpha (SudA) and Oxidoreductase (

) from Pyrococcus furiosus. SudA is a bifunctional enzyme with four iron-sulfur centers that catalyses the reduction of elemental sulfur or polysulfide to hydrogen sulfide with NADPH as electron donor . It also functions as a reduced ferredoxin:NADP oxidoreductase with a very high affinity for reduced ferredoxin .

, also a bifunctional enzyme, plays an important role in maintaining redox homeostasis .
Glutamate synthase, NADH/NADPH, small subunit 1 (Glut_synth_ssu1)
Type: Family

This family includes glutamate synthases from all cellular organisms. This enzyme, involved in the assimilation of ammonia and glutamate biosynthesis, transfers the amide group of glutamine to 2-oxoglutarate to yield two molecules of glutamate.

2 L-glutamate + NADP
+
= L-glutamine + 2-oxoglutarate + NADPH + H
+

Several archaeal and deeply branched bacterial lineages of a homotetrameric show several forms of the small subunit of this enzyme: the NADPH-dependent or NADH-dependent glutamate synthase (

and

respectively).

Members from fungi and plants are also included in this entry.
Glutamate synthase NADPH small chain-like (GltD-like)
Type: Family

This entry represents the glutamate synthase [NADPH] small chain (GltD) and closely related proteins from a number of gamma and alpha subdivision Proteobacteria, including the putative oxidoreductases AegA and ucaF from E.coli. Proteins in this entry have an N-terminal 4Fe-4S dicluster domain, and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain. GltD catalyzes the conversion of L-glutamine and 2-oxoglutarate into two molecules of L-glutamate . AegA and ucaF are involved in formate-dependent uric acid degradation under microaerobic and anaerobic conditions.The C-terminal domain of AegA contains NADPH-binding sites, which are essential for the urate-degrading activity .
Inorganic carbon transporter (Inorganic_carbon_transpt)
Type: Family

Many photosynthetic organisms including cyanobacteria can concentrate CO2/HCO3- against a greater than ten-fold concentration gradient. This is the difference observed for dissolved CO2 at equilibrium in air and the Km for CO2 of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco). In cyanobacteria, the CO2 concentrating mechanism involves:

CO2 conversion to HCO3-,

energy-dependent HCO3- transport,

and carbonic anhydrase-catalysed formation of CO2 from HCO3- in close proximity to Rubisco in the carboxysomes.

This entry contains IctB (

), which is believed to be a Na+:HCO3- symporter in Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2) . The protein is 467 amino acids long and possesses 10-12 putative transmembrane regions. PSI-BLAST searches of the databases revealed homology with members of the O-antigen ligase family.
Inner membrane-spanning protein YciB (YciB)
Type: Family

Inner membrane-spanning protein YciB (also known as intracellular septation protein A) is a family of proteins which are essential for both normal cell division and bacterial virulence and are believed to play a role in the septation process . These proteins play a role in cell envelope biogenesis, maintenance of cell envelope integrity and membrane homeostasis .
N-acetylglucosaminyltransferase, MurG (GlcNAc_MurG)
Type: Family

The murG gene of Escherichia coli encodes the N-acetylglucosaminyltransferase, UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase, responsible for the final step in the formation of the lipid-linked disaccharide-pentapeptide subunit of peptidoglycan . It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide (NAM). The resulting disaccharide is then transported across the cell membrane, where it is polymerized into NAG-NAM cell-wall repeat structure. The enzyme is peripherally associated with the inner face of the cytoplasmic membrane. Therefore, the peptidoglycan subunit is completely assembled before it traverses the cytoplasmic membrane .

MurG belongs to the GT-B structural superfamily of glycoslytransferases, which have characteristic N-and C-terminal domains, each containing a typical Rossmann fold . The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic centre and permits a high degree of flexibility.
Syntaxin, N-terminal domain (Syntaxin_N)
Type: Domain

Syntaxins are the prototype family of SNARE proteins. They usually consist of three main regions - a C-terminal transmembrane region, a central SNARE domain which is characteristic of and conserved in all syntaxins

, and an N-terminal domain that is featured in this entry. This domain varies between syntaxin isoforms; in syntaxin 1A (

) it is found as three α-helices with a left-handed twist. It may fold back on the SNARE domain to allow the molecule to adopt a 'closed' configuration that prevents formation of the core fusion complex - it thus has an auto-inhibitory role.

The function of syntaxins is determined by their localisation. They are involved in neuronal exocytosis, ER-Golgi transport and Golgi-endosome transport, for example. They also interact with other proteins as well as those involved in SNARE complexes. These include vesicle coat proteins, Rab GTPases, and tethering factors .
Syntaxin/epimorphin, conserved site (Syntaxin/epimorphin_CS)
Type: Conserved_site

Syntaxins A and B are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane. Syntaxins are a family of receptors for intracellular transport vesicles. Each target membrane may be identified by a specific member of the syntaxin family .

Members of the syntaxin family have a size ranging from 30 Kd to 40 Kd; a C-terminal extremity which is highly hydrophobic and anchors the protein on the cytoplasmic surface of cellular membranes; a central, well conserved region SNARE motif, which seems to be in a coiled-coil conformation. SNARE motifs assemble into parallel four helix bundles stabilised by the burial of these hydrophobic helix faces in the bundle core . Monomeric SNARE motifs are disordered so this assembly reaction is accompanied by a dramatic increase in α-helical secondary structure. The parallel arrangement of SNARE motifs within complexes bring the transmembrane anchors, and the two membranes, into close proximity.
Antifreeze, type III (Antifreeze_III)
Type: Family

Marine teleosts from polar oceans can be protected from freezing in icy sea-water by serum antifreeze proteins (AFPs) or glycoproteins (AFGPs) : these function by binding to, and preventing the growth of, ice crystals within the fish. Despite functional similarity, the proteins are structurally diverse and include glycosylated and at least 3 non-glycosylated forms: the AFGP of notothenioids and cods are polymers of a tripeptide repeat, Ala-Ala-Thr, with a disaccharide attached to the threonine residue; type I AFPs are Ala-rich, α-helical peptides found in flounder and sculpin; type II AFPs of sea-raven, smelt and herring are Cys-rich proteins; and type III AFPs, found in eelpouts, are rich in β-structure . As well as antifreeze proteins, entry also includes N-acetylneuraminate-9-phosphate synthase from human and mouse (NANS/SIAS, formerly known sialic acid synthase) covering the C-terminal region. The function of this domain in SIAS is not known, but it may be involved in sugar binding . NANS/SIAS catalyses the condensation of phosphoenolpyruvate (PEP) and N-acetylmannosamine 6-phosphate (ManNAc-6-P) to synthesize N-acetylneuraminate-9-phosphate (Neu5Ac-9-P) . It is required for brain and skeletal development .
Universal stress protein A family (Universal_stress_UspA)
Type: Family

Transcriptional induction of the uspA gene of Escherichia coli occurs when conditions cause growth arrest; cells deficient in UspA survive poorly in stationary phase . The product of uspA has been shown to be a cytoplasmic serine and threonine phosphoprotein. Members of the Usp family are predicted to be related to the MADS-box proteins and bind to DNA . Some members of the family contain 2 copies of the domain.

This entry includes five E. coli Usp paralogues: uspA, uspC, uspD, uspF and uspG .
UspA (UspA)
Type: Domain

This entry represents a domain found in the universal stress protein UspA , which is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA reveals
an α/β fold similar to that of the Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0577 protein, which binds ATP , though UspA lacks ATP-binding activity.

Proteins containing this domain include the TeaD protein from Halomonas elongata. TeaD regulates the ectoine uptake by the transporter TeaABC.
TeaD shows an ATP-dependent oligomerisation .
Caldesmon/lymphocyte specific protein (Caldesmon_LSP)
Type: Family

This group of proteins includes two protein families: caldesmon and lymphocyte specific protein.

Caldesmon (CDM) is an actin-and myosin-binding protein implicated in the regulation of actomyosin interactions in smooth muscle and non-muscle cells, possibly acting as a bridge between myosin and actin filaments . CDM is believed to be an elongated molecule, with an N-terminal myosin/calmodulin-binding domain and a C-terminal tropomyosin/actin/calmodulin-binding domain, separated by a 40nm-long central helix .

A high-molecular-weight form of CDM is predominantly expressed in smooth muscles, while a low-molecular-weight form is widely distributed in non-muscle tissues and cells (the protein is not expressed in skeletal muscle or heart).