SII-SWORD/CoKE huggingface dataset:
Cytochrome b/b6, N-terminal domain (Cyt_b/b6_N)
Type: Domain

In the mitochondrion of eukaryotes and in aerobic prokaryotes, cytochrome b is a component of respiratory chain complex III (

) - also known as the bc1 complex or ubiquinol-cytochrome c reductase. In plant chloroplasts and cyanobacteria, there is a analogous protein, cytochrome b6, a component of the plastoquinone-plastocyanin reductase (

), also known as the b6f complex.

Cytochrome b/b6 is an integral membrane protein of approximately 400 amino acid residues that probably has 8 transmembrane segments. In plants and cyanobacteria, cytochrome b6 consists of two subunits encoded by the petB and petD genes. The sequence of petB is colinear with the N-terminal part of mitochondrial cytochrome b, while petD corresponds to the C-terminal part. Cytochrome b/b6 non-covalently binds two haem groups, known as b562 and b566. Four conserved histidine residues are postulated to be the ligands of the iron atoms of these two haem groups.

Apart from regions around some of the histidine haem ligands, there are a few conserved regions in the sequence of b/b6. The best conserved of these regions includes an invariant P-E-W triplet which lies in the loop that separates the fifth and sixth transmembrane segments. It seems to be important for electron transfer at the ubiquinone redox site - called Qz or Qo (where o stands for outside) - located on the outer side of the membrane. This entry represents the N-terminal region of these proteins.
Cytochrome b/b6, C-terminal (Cyt_b/b6_C)
Type: Domain

In the mitochondrion of eukaryotes and in aerobic prokaryotes, cytochrome b is a component of respiratory chain complex III (

) - also known as the bc1 complex or ubiquinol-cytochrome c reductase. In plant chloroplasts and cyanobacteria, there is a analogous protein, cytochrome b6, a component of the plastoquinone-plastocyanin reductase (

), also known as the b6f complex.

Cytochrome b/b6 is an integral membrane protein of approximately 400 amino acid residues that probably has 8 transmembrane segments. In plants and cyanobacteria, cytochrome b6 consists of two subunits encoded by the petB and petD genes. The sequence of petB is colinear with the N-terminal part of mitochondrial cytochrome b, while petD corresponds to the C-terminal part. Cytochrome b/b6 non-covalently binds two haem groups, known as b562 and b566. Four conserved histidine residues are postulated to be the ligands of the iron atoms of these two haem groups.

Apart from regions around some of the histidine haem ligands, there are a few conserved regions in the sequence of b/b6. The best conserved of these regions includes an invariant P-E-W triplet which lies in the loop that separates the fifth and sixth transmembrane segments. It seems to be important for electron transfer at the ubiquinone redox site - called Qz or Qo (where o stands for outside) - located on the outer side of the membrane. This entry is the C terminus of these proteins.
ADC synthase (ADC_synthase)
Type: Homologous_superfamily

This domain superfamily is characteristic of ADC synthases, including:

Anthranilate synthase aminodeoxyisochorismate synthase/lyase subunit, TrpE, which catalyses the formation of anthranilate (o-aminobenzoate) and pyruvic acid from chorismate and glutamine .

P-aminobenzoate synthase component I (Aminodeoxychorismate synthase), which catalyses the two-step biosynthesis of 4-amino-4-deoxychorismate (ADC), a precursor of p-aminobenzoate and folate in microorganisms .

Menaquinone-specific isochorismate synthase MenF, which catalyses the conversion of chorismate to isochorismate .

Salicylate synthetase Irp9, which is involved in the biosynthesis of the siderophore yersiniabactin in Yersinia enterocolitica .

Salicylate synthase MbtI (Mycobactin synthetase protein I), which is involved in salicylate production .
Aminodeoxychorismate synthase, component I (ADC_synth_comp_1)
Type: Family

Aminodeoxychorismate synthase, component I (pabB) is closely related to anthranilate synthase component I (trpE). The apparent orthologs of pabB in Aquifex aeolicus and Helicobacter pylori 26695 score well below most TrpE proteins because of a different architecture, in which the less strongly conserved N-terminal domain is absent. The noise cut off is set to exclude most examples of TrpE.
Fatty acid desaturase type 2, conserved site (FADS-2_CS)
Type: Conserved_site

This conserved region is found at the C-terminal part of family 2 enzymes.

Fatty acid desaturases are enzymes that catalyse the insertion of a double bond at the delta position of fatty acids. There seem to be two distinct families of fatty acid desaturases which do not seem to be evolutionary related.

Family 1 is composed of:

Stearoyl-CoA desaturase (SCD) (

) .

Family 2 is composed of:

Bacterial fatty acid desaturases.

Plant stearoyl-acyl-carrier-protein desaturase (

) , this enzyme catalyzes the introduction of a double bond at the delta(9) position of steraoyl-ACP to produce oleoyl-ACP. This enzyme is responsible for the conversion of saturated fatty acids to unsaturated fatty acids in the synthesis of vegetable oils.

Cyanobacterial DesA , an enzyme that can introduce a second cis double bond at the delta(12) position of fatty acid bound to membranes glycerolipids. DesA is involved in chilling tolerance; the phase transition temperature of lipids of cellular membranes being dependent on the degree of unsaturation of fatty acids of the membrane lipids.

Members of this entry are endoplasmic reticulum (ER) integral membrane proteins that share the same mushroom-like shape fold consisting of four transmembrane helices (TM1-TM4) which anchor them to the membrane, capped by a cytosolic domain containing a unique 9-10 histidine-coordinating di metal (di-iron) catalytic centre . The structure of mouse stearoyl-CoA desaturase (SDC) revealed that TM2 and TM4 are longer than TM1 and TM3 and protrude into the cytosolic domain, providing three of the nine histidine residues that coordinate the two metal ions, while the other histidine residues are provided by the soluble domain in this enzyme .
Fatty acid desaturase domain (FA_desaturase_dom)
Type: Domain

Fatty acid desaturases are enzymes that catalyse the insertion of a double bond at the delta position of fatty acids. There seem to be two distinct families of fatty acid desaturases which do not seem to be evolutionary related.

Family 1 is composed of:

Stearoyl-CoA desaturase (SCD) (

) .

Family 2 is composed of:

Bacterial fatty acid desaturases.

Plant stearoyl-acyl-carrier-protein desaturase (

) , this enzyme catalyzes the introduction of a double bond at the delta(9) position of steraoyl-ACP to produce oleoyl-ACP. This enzyme is responsible for the conversion of saturated fatty acids to unsaturated fatty acids in the synthesis of vegetable oils.

Cyanobacterial DesA , an enzyme that can introduce a second cis double bond at the delta(12) position of fatty acid bound to membranes glycerolipids. DesA is involved in chilling tolerance; the phase transition temperature of lipids of cellular membranes being dependent on the degree of unsaturation of fatty acids of the membrane lipids.

Members of this entry are endoplasmic reticulum (ER) integral membrane proteins that share the same mushroom-like shape fold consisting of four transmembrane helices (TM1-TM4) which anchor them to the membrane, capped by a cytosolic domain containing a unique 9-10 histidine-coordinating di metal (di-iron) catalytic centre . The structure of mouse stearoyl-CoA desaturase (SDC) revealed that TM2 and TM4 are longer than TM1 and TM3 and protrude into the cytosolic domain, providing three of the nine histidine residues that coordinate the two metal ions, while the other histidine residues are provided by the soluble domain in this enzyme .
Rieske iron-sulphur protein, C-terminal (Rieske_Fe-S_prot_C)
Type: Domain

Ubiquinol-cytochrome c reductase (bc1 complex or complex III) is an enzyme complex of bacterial and mitochondrial oxidative phosphorylation systems It catalyses the oxidoreduction of the mobile redox components ubiquinol and cytochrome c, generating an electrochemical potential, which is linked to ATP synthesis . The complex consists of three subunits in most bacteria, and nine in mitochondria: both bacterial and mitochondrial complexes contain cytochrome b and cytochrome c1 subunits, and an iron-sulphur `Rieske' subunit, which contains a high potential 2Fe-2S cluster .The mitochondrial form also includes six other subunits that do not possess redox centres. Plastoquinone-plastocyanin reductase (b6f complex), cyanobacteria and the chloroplasts of plants, catalyses the oxidoreduction of plastoquinol and cytochrome f. This complex, which is functionally similar to ubiquinol-cytochrome c reductase, comprises cytochrome b6, cytochrome f and Rieske subunits .

The Rieske subunit acts by binding either a ubiquinol or plastoquinol anion, transferring an electron to the 2Fe-2S cluster, then releasing the electron to the cytochrome c or cytochrome f haem iron . The 2Fe-2S cluster is bound in the highly conserved C-terminal region of the Rieske subunit.
SecE subunit of protein translocation complex, bacterial-like (SecE_bac)
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.

The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) . The chaperone protein SecB is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion . SecE, part of the main SecYEG translocase complex, is ~106 residues in length, and spans the inner membrane of the Gram-negative bacterial envelope. Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains . Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices.
Succinate--CoA ligase-like, beta subunit (Succ_CoA_ligase-like_bsu)
Type: Family

This entry represents a group of different enzymes that share a similar catalytic mechanism which involves the phosphorylation by ATP (or GTP) of a specific histidine residue in the active site. These enzymes are:

Succinate--CoA ligase (GDP-forming (

) is a mitochondrial enzyme that catalyses the substrate level phosphorylation step of the tricarboxylic acid cycle: the formation of succinyl-CoA from succinate with a concomitant hydrolysis of GTP to GDP and phosphate. This enzyme is a dimer composed of an alpha and a beta subunits;

Succinate--CoA ligase (ADP-forming) (

) is a bacterial enzyme that during aerobic metabolism functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP. It can also function in the other direction for anabolic purposes. This enzyme is a tetramer composed of two alpha and two beta subunits;

Malate--CoA ligase (

) (malyl-CoA synthetase) , is a bacterial enzyme that forms malyl-CoA from malate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. Malate-CoA ligase is composed of two different subunits.

ADP-forming sulfoacetate-CoA ligase, subunit SauC and SqwK, that catalyse the CoA- and ATP-dependent conversion of sulfoacetate to sulfoacetyl-CoA and ADP .
Succinyl-CoA ligase, alpha subunit (CoA_lig_alpha)
Type: Family

This entry describes succinyl-CoA synthetase alpha subunits, but does not discriminate between GTP-specific and ATP-specific reactions. ATP citrate lyases appear to form an outgroup, and are not included in this entry.

There are four different enzymes that share a similar catalytic mechanism which involves the phosphorylation by ATP (or GTP) of a specific histidine residue in the active site. These enzymes are:

ATP citrate-lyase (

) , the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues, catalyses the formation of acetyl-CoA and oxaloacetate from citrate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. ATP-citrate lyase is a tetramer of identical subunits.

Succinyl-CoA ligase (GDP-forming) (

) is a mitochondrial enzyme that catalyses the substrate level phosphorylation step of the tricarboxylic acid cycle: the formation of succinyl-CoA from succinate with a concomitant hydrolysis of GTP to GDP and phosphate. This enzyme is a dimer composed of an alpha and a beta subunits.

Succinyl-CoA ligase (ADP-forming) (

) is a bacterial enzyme that during aerobic metabolism functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP. It can also function in the other direction for anabolic purposes. This enzyme is a tetramer composed of two alpha and two beta subunits.

Malate-CoA ligase (

) (malyl-CoA synthetase) , is a bacterial enzyme that forms malyl-CoA from malate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. Malate-CoA ligase is composed of two different subunits.
ATP-citrate synthase/succinyl-CoA ligase, C-terminal domain (SUCC_ACL_C)
Type: Domain

This entry represents a domain found in both the alpha and beta chains of succinyl-CoA synthase (

(GDP-forming) and

(ADP-forming)) . This domain can also be found in ATP citrate synthase (

, ) and malate-CoA ligase (

). Some members of the domain utilise ATP others use GTP.
Large ribosomal subunit protein bL20 (Ribosomal_bL20)
Type: Family

This entry represents the large ribosomal subunit protein family bL20 that contains members from eubacteria, as well as their mitochondrial and plastid homologs. bL20 is an assembly protein, required for the first in vitro reconstitution step of the 50S ribosomal subunit, but does not seem to be essential for ribosome activity. bL20 has been shown to partially unfold in the absence of RNA, in regions corresponding to the RNA-binding sites. bL20 represses the translation of its own mRNA via specific binding to two distinct mRNA sites, in a manner similar to the bL20 interaction with 23S ribosomal RNA .

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 .
Aminotransferase class-III (Aminotrans_3)
Type: Family

Aminotransferases share certain mechanistic features with other pyridoxalphosphate-dependent enzymes, such as the covalent binding of the pyridoxalphosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped into subfamilies . One of these, called class-III, includes:

Acetylornithine aminotransferase (

), which catalyses the transfer of an amino group from acetylornithine to alpha-ketoglutarate, yielding N-acetyl-glutamic-5-semi-aldehyde and glutamic acid ;

Ornithine aminotransferase (

), which catalyses the transfer of an amino group from ornithine to alpha-ketoglutarate, yielding glutamic-5-semi-aldehyde and glutamic acid ;

Omega-amino acid--pyruvate aminotransferase (

), which catalyses transamination between a variety of omega-amino acids, mono-and diamines, and pyruvate ;

4-aminobutyrate aminotransferase (

) (GABA transaminase), which catalyses the transfer of an amino group from GABA to alpha-ketoglutarate, yielding succinate semialdehyde and glutamic acid ;

DAPA aminotransferase (

), a bacterial enzyme (bioA), which catalyses an intermediate step in the biosynthesis of biotin, the transamination of 7-keto-8-aminopelargonic acid to form 7,8-diaminopelargonic acid ;

2,2-dialkylglycine decarboxylase (

), a Burkholderia cepacia (Pseudomonas cepacia) enzyme (dgdA) that catalyses the decarboxylating amino transfer of 2,2-dialkylglycine and pyruvate to dialkyl ketone, alanine and carbon dioxide ;

Glutamate-1-semialdehyde aminotransferase (

) (GSA) ;

Bacillus subtilis aminotransferases yhxA and yodT;

Haemophilus influenzae diaminobutyrate--2-oxoglutarate aminotransferase (HI0949) ;

Caenorhabditis elegans alanine--glyoxylate aminotransferase 2-like (T01B11.2).
Adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA (BioA)
Type: Family

BioA is an adenosylmethionine-8-amino-7-oxononanoate aminotransferase that functions in biotin synthesis. It utilises S-adenosyl-L-methionine (SAM) to transaminate the biotin precursor 7-keto-8-aminopelargonic acid and form the next intermediate in the pathway, 7, 8-diaminopelargonic acid . It is currently the only aminotransferase that is known to use SAM as an amino donor. The Bacillus subtilis enzyme, which is included in this entry, uses lysine rather than SAM as the amino donor .
Wnt (Wnt)
Type: Family

Wnt proteins constitute a large family of secreted molecules that are involved in intercellular signalling during development. The name derives from the first 2 members of the family to be discovered: int-1 (mouse) and wingless (Drosophila) . It is now recognised that Wnt signalling controls many cell fate decisions in a variety of different organisms, including mammals . Wnt signalling has been implicated in tumourigenesis, early mesodermal patterning of the embryo, morphogenesis of the brain and kidneys, regulation of mammary gland proliferation and Alzheimer's disease .

Wnt-mediated signalling is believed to proceed initially through binding to cell surface receptors of the frizzled family; the signal is subsequently transduced through several cytoplasmic components to B-catenin, which enters the nucleus and activates the transcription of several genes important in development . Several non-canonical Wnt signalling pathways have also been elucidated that act independently of B-catenin. Canonical and noncanonical Wnt signaling branches are highly interconnected, and cross-regulate each other .

Members of the Wnt gene family are defined by their sequence similarity to mouse Wnt-1 and Wingless in Drosophila. They encode proteins of ~350-400 residues in length, with orthologues identified in several, mostly vertebrate, species. Very little is known about the structure of Wnts as they are notoriously insoluble, but they share the following features characteristics of secretory proteins: a signal peptide, several potential N-glycosylation sites and 22 conserved cysteines that are probably involved in disulphide bonds. The Wnt proteins seem to adhere to the plasma membrane of the secreting cells and are therefore likely to signal over only few cell diameters. Fifteen major Wnt gene families have been identified in vertebrates, with multiple subtypes within some classes.

In humans, 19 Wnt proteins have been identified that share 27% to 83% amino-acid sequence identity and a conserved pattern of 23 or 24 cysteine residues . Wnt genes are highly conserved between vertebrate species sharing overall sequence identity and gene structure, and are slightly less conserved between vertebrates and invertebrates.