SII-SWORD/CoKE huggingface dataset:
Large ribosomal subunit protein eL19, domain 2 (Ribosomal_eL19_dom2)
Type: Homologous_superfamily

Ribosomal protein eL19 from eukaryotes and eL19 (known as L19e) from archaea form part of the large ribosomal subunit, whose structure has been determined in a number of eukaryotic and archaeal species . eL19 is a multi-helical protein consisting of two different 3-helical domains connected by a long, partly helical linker. This superfamily represents an α-helical linker domain that assumes an up-and-down bundle topology from archaeal ribosomal protein L19e.

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 eL19, domain 3 (Ribosomal_eL19_dom3)
Type: Homologous_superfamily

Ribosomal protein eL19 from eukaryotes and eL19 (known as L19e) from archaea form part of the large ribosomal subunit, whose structure has been determined in a number of eukaryotic and archaeal species . eL19 is a multi-helical protein consisting of two different 3-helical domains connected by a long, partly helical linker. This superfamily represents an α-helical domain that assumes an orthogonal bundle topology from ribosomal protein eL19 from archaea.

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 .
Bacteriophage T4, Gp11, C-terminal finger domain (Phage_T4_Gp11_C)
Type: Homologous_superfamily

The bacteriophage baseplate controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. The baseplate is a multi-subunit assembly at the distal end of the tail, which is composed of long and short tail fibres . The tail region is responsible for attachment to the host bacteria during infection: long tail fibres enable host receptor recognition, while irreversible attachment is via short tail fibres. Recognition and attachment induce a conformational transition of the baseplate from a hexagonal to a star-shaped structure. In viruses such as Bacteriophage T4, Gp11 acts as a structural protein to connect the short tail fibres to the baseplate, while Gp9 connects the baseplate with the long tail fibres. Both Gp9 and Gp11 are trimers. Each Gp11 monomer consists of three domains, which are entwined together in the trimer: the N-terminal domains of the three monomers form a central, trimeric, parallel coiled coil surrounded by the entwined middle finger domains; the C-terminal domains appear to be responsible for trimerisation .

This superfamily includes the middle finger domain, which is a seven-stranded, antiparallel, skewed β-roll with one α-helix .
Baseplate structural protein Gp11, N-terminal domain superfamily (Baseplate_struct_Gp11_N_sf)
Type: Homologous_superfamily

The bacteriophage baseplate controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. The baseplate is a multi-subunit assembly at the distal end of the tail, which is composed of long and short tail fibres . The tail region is responsible for attachment to the host bacteria during infection: long tail fibres enable host receptor recognition, while irreversible attachment is via short tail fibres. Recognition and attachment induce a conformational transition of the baseplate from a hexagonal to a star-shaped structure. In viruses such as Bacteriophage T4, Gp11 acts as a structural protein to connect the short tail fibres to the baseplate, while Gp9 connects the baseplate with the long tail fibres. Both Gp9 and Gp11 are trimers. Each Gp11 monomer consists of three domains, which are entwined together in the trimer: the N-terminal domains of the three monomers form a central, trimeric, parallel coiled coil surrounded by the entwined middle finger domains; the C-terminal domains appear to be responsible for trimerisation .

This superfamily represents the N-terminal domain of Gp11, which has an α-helical structure that assumes an orthogonal bundle topology.
Cytochrome c prime, subgroup (Cyt_c_prime_subgr)
Type: Family

Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler recognised four classes of cytC.
Tellurite resistance methyltransferase TehB-like domain (TehB-like_dom)
Type: Domain

Tellurite resistance protein TehB is part of a tellurite-reducing operon tehA and tehB. When present in high copy number, TehB is responsible for potassium tellurite resistance, probably by increasing the reduction rate of tellurite to metallic tellurium within the bacterium. TehB is a cytoplasmic protein which possesses three conserved motifs (I, II, and III) found in S-adenosyl-L-methionine (SAM)-dependent non-nucleic acid methyltransferases . Conformational changes in TehB are observed upon binding of both tellurite and SAM, suggesting that TehB utilises a methyltransferase activity in the detoxification of tellurite.

This entry represents the methyltransferase domain found in all TehB proteins.
Sortase B, Firmicutes (SrtB_Firmicute)
Type: Family

Members of this transpeptidase family are, in most cases, designated sortase B, product of the srtB gene. This protein shows only distant similarity to the sortase A family, for which there may be several members in a single bacterial genome. Typical SrtB substrate motifs include NAKTN, NPKSS, etc, and otherwise resemble the LPXTG sorting signals recognised by sortase A proteins.

This entry represents the Firmicute sortase B proteins.
Uncharacterised conserved protein UCP022704 (UCP022704)
Type: Family

This family consists of several hypothetical bacterial proteins but contains one sequence Ree1 (

) from Saccharomyces cerevisiae . Members of this family are typically around 200 residues in length. The function of this family is unknown.
ADP-specific phosphofructokinase/glucokinase, archaeal (ADP_PFK/GK_arc)
Type: Family

Proteins in this entry show high ADP-dependent activities for both glucokinase and /or phosphofructokinase . They act in a modified Embden-Meyerhof sugar metabolism pathway that is present in some archaea .
Hydrolase TatD/YcfH-like (TatD/YcfH-like)
Type: Family

This entry includes a group of enzymes, including the putative 3'-5' ssDNA/RNA exonuclease TatD from Enterobacter sp., the uncharacterised metal-dependent hydrolase YcfH from Escherichia coli, the D-aminoacyl-tRNA deacylase Dtd3 from Synechocystis sp. and some uncharacterised proteins. YchF has D-tyrosyl-tRNA deacylase activity in vitro . Dtd3 may catalyse the hydrolysis of D-tyrosyl-tRNA(Tyr) .
CDP-diacylglycerol pyrophosphatase, proteobacterial (CDP-diacylglyc_Pase_proteobac)
Type: Family

The CDP-diacylglycerol pyrophosphatases

play a role in the regulation of phospholipid metabolism by inositol, as well as regulating the cellular levels of phosphatidylinositol . This entry is specific for the proteobacterial enzymes.
Phosphoenolpyruvate carboxykinase (ATP), conserved site (PEPCK_ATP_CS)
Type: Conserved_site

Phosphoenolpyruvate carboxykinase (ATP) (

) (PEPCK) catalyses the formation of phosphoenolpyruvate by decarboxylation of oxaloacetate while hydrolysing ATP, a rate limiting step in gluconeogenesis (the biosynthesis of glucose).
Microcystin LR degradation protein MlrC, N-terminal (MlrC_N)
Type: Domain

Proteins in this entry are involved in degradation of the cyanobacterial heptapeptide hepatotoxin microcystin LR, and are encoded in the mlr gene cluster . MlrC from Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273) is believed to mediate the last step of peptidolytic degradation of the tetrapeptide. It is suspected to be a metallopeptidase based on homology to known peptidases and its inhibition by metal chelators. The proteins encoded by the mlr cluster may be involved in cell wall peptidoglycan cycling and subsequently act fortuitously in hydrolysis of microcystin LR.

This entry represents the N-terminal region of these proteins.
Uncharacterised conserved protein UCP028451 (UCP028451)
Type: Family

Members of this family are widely (though sparsely) distributed bacterial proteins, about 230 residues in length. All members have a motif RxxRDxRFxxx[DN]KxxY. The function of this protein family is unknown.
Succinate dehydrogenase cytochrome b558 subunit, Firmicute (Succ_DH_cyt_b558_Firmicute)
Type: Family

This family contains succinate dehydrogenase (also known as succinate:quinone oxidoreductase, SQR) subunit C of Bacillus subtilis, designated cytochrome b-558, and related sequences that include a fumarate reductase subunit C. This family is only weakly similar to the main group of succinate dehydrogenase cytochrome b subunits described by

, so that some members score above the gathering threshold and some do not .

SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Bacillus subtilis SQR reduces low potential quinones such as menaquinone . SQR is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this entry are classified as Type B as they contain one transmembrane subunit and two heme groups . The heme and quinone binding sites reside on the cytochrome b558 subunit . The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centres, and the transmembrane subunit containing the electron acceptor (quinone). The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes .
Photosystem II extrinsic protein V, cytochrome c-550 precursor-like (PsbV_cyt_c550-like)
Type: Family

This entry represents a family of cytochrome c550 proteins mainly found in cyanobacteria and red algae.

Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes.

Ambler recognised four classes of cytC. Class 1 cytochromes have the haem-attachment site towards the N terminus, and can be further subdivided into five groups (1A to 1E) based on sequence similarity. Cytochrome C550 (CytC550) is a class 1A cytochrome. CytC550 (also known as Photosystem II extrinsic protein V, PsbV) is an extrinsic membrane protein that forms part of the oxygen-evolving complex in photosystem II, this complex being responsible for the splitting of water into O(2) and 4H+, the latter being used to reduce CO2 to glucose. CytC550 is only found in cyanobacteria and red algae , this protein having been lost during the evolution of green plants . Other Class 1A cytochrome C proteins include mitochondrial cytochrome C, which acts as an electron carrier between cytochrome reductase and the cytochrome oxidase complex, the final electron carrier in the mitochondrial electron transport chain; and cytochrome C6, which acts as an electron carrier between cytochrome b6f and photosystem I in cyanobacteria .
Phosphomevalonate kinase Erg8 (Erg8)
Type: Family

This entry includes phosphomevalonate kinase Erg8 from fungi and plants. Budding yeast Erg8 is involved in step 2 of the subpathway that synthesizes isopentenyl diphosphate from (R)-mevalonate . Arabidopsis Erg8 (AT1G31910, also known as PMK) is involved in the mevalonic acid pathway .
Alpha-L-rhamnosidase (Alpha_rhamnosid)
Type: Family

This family consists of alpha-L-rhamnosidase enzymes which are primarily involved in the degradation of complex polysaccharides. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are important bioactive compounds. For example, terpenyl glycosides, the glycosidic precursor of aromatic terpenoids, act as important flavouring substances in grapes. Other rhamnosides act as cytotoxic rhamnosylated terpenoids, as signal substances in plants or play a role in the antigenicity of pathogenic bacteria . Some members of this family are also capable of releasing L-rhamnose from a variety of plant-derived compounds, including citrus flavonoids and arabinogalactan-proteins. The presence of a carbohydrate-binding module (CBM67) in some family members suggests a specialized domain for L-rhamnose recognition, which is calcium-dependent for its ligand binding.

This entry also includes the Bifunctional sulfatase/alpha-L-rhamnosidase from Formosa agariphila, which is involved in ulvan degradation .
Amine dehydrogenase light chain (Amine_DH_Ltc)
Type: Family

This entry represents a group of bacterial amine dehydrogenase light chains. They include methylamine and arylamine dehydrogenase light chains, which form heterotetramers with their respective heavy chains, and catalyse the oxidative deamination of amines to their corresponding aldehydes.

RCH2NH2 + H2O + acceptor = RCHO + NH3 + reduced acceptor
tRNA methyltransferase TRMD/TRM10-type domain (tRNA_MeTrfase_TRMD/TRM10)
Type: Domain

This domain is found in tRNA methyltransferases including tRNA (guanine-N(1)-)-methyltransferases (TRMD) and mitochondrial ribonuclease P protein 1. Proteins containing this domain also include tRNA (guanine(9)-N1)-methyltransferase (Trm10) from yeasts and Trmt10A from fruit flies.
Binary exotoxin A, clostridial type (Binary_toxinA_clost-typ)
Type: Family

A large group of bacterial exotoxins are referred to as "A/B toxins", essentially because they are formed from two subunits. The "A" subunit possesses enzyme activity, and is transferred to the host cell following a conformational change in the membrane-bound transport "B" subunit .

Clostridial species are one of the major causes of food poisoning/gastro-intestinal illnesses. They are Gram-positive, spore-forming rods that occur naturally in the soil . Included in the family are: Clostridium botulinum, which produces one of the most potent toxins in existence; Clostridium tetani, causative agent of tetanus; and Clostridium perfringens, commonly found in wound infections and diarrhoea cases.
Clusterin, N-terminal (Clusterin_N)
Type: Domain

Clusterin is a vertebrate glycoprotein , the exact function of which is not yet clear. Clusterin expression is complex, appearing as different forms in different cell compartments. One set of proteins is directed for secretion, and other clusterin species are expressed in the cytoplasm and nucleus. The secretory form of the clusterin protein (sCLU) is targeted to the ER by an initial leader peptide. This ~60kDa pre-sCLU protein is further glycosylated and proteolytically cleaved into alpha- and beta-subunits, held together by disulphide bonds. External sCLU is an 80kDa protein and may act as a molecular chaperone, scavenging denatured proteins outside cells following specific stress-induced injury such as heat shock. sCLU possesses nonspecific binding activity to hydrophobic domains of various proteins
in vitro
.

A specific nuclear form of CLU (nCLU) acts as a pro-death signal, inhibiting cell growth and survival. The nCLU protein has two coiled-coil domains, one at its N terminus that is unable to bind Ku70, and a C-terminal coiled-coil domain that is uniquely able to associate with Ku70 and is minimally required for cell death.

Clusterin is synthesized as a precursor polypeptide of about 400 amino acids which is post-translationally cleaved to form two subunits of about 200 amino acids each. The two subunits are linked by five disulphide bonds to form an antiparallel ladder-like structure . In each of the mature subunits the five cysteines that are involved in disulphide bonds are clustered in domains of about 30 amino acids located in the central part of the subunits.

This entry represents the N-terminal domain of the clusterin precursor.
Clusterin, C-terminal (Clusterin_C)
Type: Domain

Clusterin is a vertebrate glycoprotein , the exact function of which is not yet clear. Clusterin expression is complex, appearing as different forms in different cell compartments. One set of proteins is directed for secretion, and other clusterin species are expressed in the cytoplasm and nucleus. The secretory form of the clusterin protein (sCLU) is targeted to the ER by an initial leader peptide. This ~60kDa pre-sCLU protein is further glycosylated and proteolytically cleaved into alpha- and beta-subunits, held together by disulphide bonds. External sCLU is an 80kDa protein and may act as a molecular chaperone, scavenging denatured proteins outside cells following specific stress-induced injury such as heat shock. sCLU possesses nonspecific binding activity to hydrophobic domains of various proteins
in vitro
.

A specific nuclear form of CLU (nCLU) acts as a pro-death signal, inhibiting cell growth and survival. The nCLU protein has two coiled-coil domains, one at its N terminus that is unable to bind Ku70, and a C-terminal coiled-coil domain that is uniquely able to associate with Ku70 and is minimally required for cell death.

Clusterin is synthesized as a precursor polypeptide of about 400 amino acids which is post-translationally cleaved to form two subunits of about 200 amino acids each. The two subunits are linked by five disulphide bonds to form an antiparallel ladder-like structure . In each of the mature subunits the five cysteines that are involved in disulphide bonds are clustered in domains of about 30 amino acids located in the central part of the subunits.

This entry represents the C-terminal domain of the custerin precursor.
Clusterin (Clusterin)
Type: Family

Clusterin (Clu), also known as apolipoprotein J, is a vertebrate glycoprotein . Clusterin expression is complex, appearing as different forms in different cell compartments. One set of proteins is directed for secretion, and other clusterin species are expressed in the cytoplasm and nucleus. The secretory form of the clusterin protein (sCLU) is targeted to the ER by an initial leader peptide. This ~60kDa pre-sCLU protein is proteolytically cleaved into alpha- and beta-subunits and further glycosylated to form mature disulfide-linked heterodimeric secretory CLU (sCLU). sCLU is an 80kDa protein and acts as a molecular chaperone, scavenging denatured proteins outside cells . sCLU possesses nonspecific binding activity to hydrophobic domains of various non-native proteins , binds to some bacteria and bacterial proteins , and interacts with different immune molecules .

A specific nuclear form of CLU (nCLU) acts as a pro-death signal, inhibiting cell growth and survival. The nCLU protein has two coiled-coil domains, one at its N terminus that is unable to bind Ku70, and a C-terminal coiled-coil domain that is uniquely able to associate with Ku70 and is minimally required for cell death. The sCLU protein is cytoprotective and anti-apoptotic, whereas the nCLU protein is pro-apoptotic .
GDNF/GAS1 (GDNF/GAS1)
Type: Domain

This cysteine rich domain is found in multiple copies in GNDF and GAS1 proteins. GDNF and neurturin (NTN) receptors are potent survival factors for sympathetic, sensory and central nervous system neurons . GDNF and neurturin promote neuronal survival by signalling through similar multicomponent receptors that consist of a common receptor tyrosine kinase and a member of a GPI-linked family of receptors that determines ligand specificity .