SII-SWORD/CoKE huggingface dataset:
Large ribosomal subunit protein uL10, bacterial type (Ribosomal_uL10_bac_type)
Type: Family

This entry represents the large ribosomal subunit protein uL10 family found in bacteria and in eukaryotic organelles such as mitochondria and chloroplast.

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 .
Small ribosomal subunit protein uS5, archaea (Ribosomal_uS5_arc)
Type: Family

This entry includes small ribosomal subunit protein uS5 found in 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 .
Large ribosomal subunit protein uL22, bacterial/organelle-type (Ribosomal_uL22_bac/org-type)
Type: Family

This entry represents large ribosomal subunit protein uL22 found in bacteria and eukaryotic organelles such as chloroplast and mitochondria.

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 eL34, archaeal-type (Ribosomal_L34e_arc-type)
Type: Family

This entry represents the large ribosomal subunit protein eL34 family found in archaea and eukaryotes, predominantly in arthropods.

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 .
2-oxoadipate dioxygenase/decarboxylase, bacterial-type (YdcJ_bac-like)
Type: Family

This entry represents a group of bacterial and fungal sequences, including 2-oxoadipate dioxygenase/decarboxylase (YdcJ, also known as HGLS) from Escherichia coli. YdcJ, which is involved in D-lysine metabolism, catalyses a successive decarboxylation and intramolecular hydroxylation of 2-oxoadipate forming 2-hydroxyglutarate in a Fe(II) and oxygen-dependent manner. Members of this protein family are thought to belong to the the vicinal oxygen chelate (VOC) superfamily . The structure has been solved (

,

).
Gas vesicle protein GvpA (Gas_vesicle_GvpA)
Type: Family

This entry is specific for GvpA, which forms the protein shell of the gas vesicles wall . GvpA is highly conserved but the small differences in amino acid composition that do occur might contribute to the differences in gas vesicle morphology .

Gas vesicles (GVs) are small, hollow, gas filled protein structures found in several cyanobacterial and archaebacterial microorganisms . They allow the positioning of the bacteria at the favourable depth for growth. Gas vesicles are hollow cylindrical tubes, closed by a hollow, conical cap at each end. Both the conical end caps and central cylinder are made up of 4-5 nm wide ribs that run at right angles to the long axis of the structure. Gas vesicles seem to be constituted of two different protein components, GvpA and GvpC. GvpA, a small protein of about 70 amino acid residues, is the main constituent of gas vesicles and form the essential core of the structure, while GvpC binds the exterior of the GV and provides additional structural reinforcement . The sequence of GVPa is extremely well conserved. GvpJ and GvpM, two proteins encoded in the cluster of genes required for gas vesicle synthesis in the archaebacteria Halobacterium salinarum and Halobacterium mediterranei (Haloferax mediterranei), have been found to be evolutionary related to GVPa. The exact function of these two proteins is not known, although they could be important for determining the shape determination gas vesicles. The N-terminal domain of Aphanizomenon flos-aquae protein GvpA/J is also related to GvpA.
Elongation factor G, domain IV (EFG_IV)
Type: Domain

This entry includes domain IV of Elongation factor G family found mainly in bacteria and eukaryotic mitochondria.

Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position . This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome.

Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome . EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution.
Large ribosomal subunit protein uL16 (Ribosomal_uL16)
Type: Family

This entry represents the large ribosomal subunit protein uL16 family, which is widespread among all cellular organisms. Members of this entry contain a single structural domain with an α/β-hammerhead fold (

).

uL16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack uL16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. uL16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in uL16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for uL16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of uL16. Bacterial, archaeal, and eukaryotic uL16 proteins exhibit structural differences at the N terminus .

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 .
D-galactarolactone isomerase/2-pyrone-4,6-dicarbaxylate hydrolase (GLI/LigI)
Type: Family

This entry represents the GLI/LigI family. GLI and LigI are both members of the functionally diverse amidohydrolase superfamily .

GLI (also known as D-galactarolactone isomerase) catalyses the isomerisation of D-galactaro-1,5-lactone to D-galactaro-1,4-lactone

]. This is a step in the oxidative degradation pathway of D-galacturonate .

LigI (also known as 2-pyrone-4,6-dicarboxylic acid (PDC) hydrolase) hydrolyses PDC to yield 4-oxalomesaconic acid (OMA) or its tautomer, 4-carboxy-2-hydroxymuconic acid (CHM)

. This reaction is part of the protocatechuate (PCA) 4,5-cleavage pathway. PCA is one of the most important intermediate metabolites in the bacterial pathways for various phenolic compounds, including lignin, which is the most abundant aromatic material in nature .

The ability of GLI to catalyse lactone isomerisation instead of hydrolysis can be explained by the absence of the general basic catalysis used by LigI .
SHKBP1/KCTD3 (SHKBP1/KCTD3)
Type: Family

This entry includes two closely related human proteins SHKBP1 (also known as SETA-binding protein 1) and Potassium Channel Tetramerization Domain Containing protein 3 (KCTD3), which correspond to group D of KCTD family . The complete biological role of SHKBP1 has not yet been characterised, however, it has been associated with tumorigenesis. It interacts with cathepsin B and participates in tumor necrosis factor (TNF)-induced apoptosis in ovarian cancer cells . It binds to SH3 domains of the SETA adapter protein, whose overexpression is related to brain tumours . KCTD3 has been associated with neurogenetic and neurodevelopmental disorders. It is an accessory subunit of potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3 (HCN3) as it interacts and increases its stability and cell surface expression .
Ubiquitin-like protein 7, ubiquitin-like domain (UBL7_Ubl)
Type: Domain

This entry represents the ubiquitin-like (UBL) domain of UBL7 and similar sequences from vertebrates.

UBL7, also termed bone marrow stromal cell ubiquitin-like (Ubl) protein (BMSC-UbP), or ubiquitin-like protein SB132, is a novel Ubl protein that may play roles in regulation of bone marrow stromal cell (BMSC) function or cell differentiation via an evocator-associated and cell-specific pattern. UBL7 contains an N-terminal Ubl domain with a β-grasp Ubl fold, and a C-terminal ubiquitin-associated (UBA) domain. The Ubl domain interacts with 26S proteasome-dependent degradation, and the UBA domain links cellular processes and the ubiquitin system .
Ubiquitin-like protein 7, UBA domain (UBL7_UBA)
Type: Domain

This entry represents the ubiquitin associated (UBA) domain of UBL7 and similar sequences from animals.

UBL7, also termed bone marrow stromal cell ubiquitin-like (Ubl) protein (BMSC-UbP), or ubiquitin-like protein SB132, is a novel Ubl protein that may play roles in regulation of bone marrow stromal cell (BMSC) function or cell differentiation via an evocator-associated and cell-specific pattern. UBL7 contains an N-terminal Ubl domain with a β-grasp Ubl fold, and a C-terminal ubiquitin-associated (UBA) domain. The Ubl domain interacts with 26S proteasome-dependent degradation, and the UBA domain links cellular processes and the ubiquitin system .
YjiT-like (YjiT)
Type: Family

This family includes bacterial proteins mainly found in proteobacteria that are about 1100 amino acid residues long. The family also includes the half-length uncharacterised protein YjiT from Escherichia coli

. The function of these proteins is unknown.
Immunity protein MafI-like (MafI-like)
Type: Family

This entry represents the MafI family of bacterial immunity proteins found broadly, primarily in Proteobacteria. They are part of a functional toxin-immunity system where they neutralise MafB toxin . It was shown that a bacterial strain can harbor several MafB/MafI modules with distinct toxic activities.
LktA-like tandem repeat (LktA_repeat)
Type: Repeat

This entry represents a repeat, about 53 amino acid residues in length, found in tandem copies in a number of bacterial proteins. In some of them, these tandem repeats may comprise most of the entire protein length. The best characterised protein containing this repeat is the leukotoxin LktA of Fusobacterium necrophorum. Leukotoxin (Lkt) is a secreted protein encoded by a tricistronic operon (lktBAC) and it is the major virulence factor of F. necrophorum causing apoptosis and necrosis of bovine leukocytes in a dose-dependent manner . The leukotoxin operon consists of three genes, lktB, lktA, and lktC, of which lktA is the toxin structural gene .
RPRD1B, CID domain (RPRD1B_CID)
Type: Domain

Regulation of nuclear pre-mRNA domain-containing protein 1B (RPRD1B, also called CREPT for cell cycle-related and expression-elevated protein in tumor) is a CID containing protein that co-purifies with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD . RPRD1B form homodimers and heterodimers with RPRD1A through their coiled-coil domains. Both RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2 . RPRD1B is highly expressed during tumorigenesis and in endometrial cancer; it has been shown to promote tumor growth by accelerating the cell cycle .

This entry represents the CID domain of RPRD1B.
Regulator of Ty1 transposition protein 103-like, CID domain (Rtt103-like_CID)
Type: Domain

Yeast Rtt103 is a 3'-end RNA-processing and transcription termination factor that functions in DNA damage response. It associates with sites of DNA breaks and is essential for recovery from DNA double strand breaks in the chromosome . It forms homodimers through its C-terminal coiled-coil domain and, via the CID domain, it binds tightly to the repetitive sequence of the phosphorylated carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II) . Rtt103 CID can bind CTD phosphorylated at Thr4 and Ser2 which facilitates transcription termination at protein-coding genes. It may preferentially interacts with CTD phosphorylated at Ser2 . During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD .

This entry represents the CID domain of Rtt103 and its homologues from yeast.
RPRD1A, CID domain (RPRD1A_CID)
Type: Domain

Regulation of nuclear pre-mRNA domain-containing protein 1A (RPRD1A, also known as cyclin-dependent kinase inhibitor 2B-related protein or p15INK4B-related protein (P15RS)) is a CID (CTD-Interacting Domain) containing protein that co-purifies with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD . RPRD1A forms homodimers and heterodimers with RPRD1B through their coiled-coil domains. Both RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2 . RPRD1A regulates cell cycle genes and attenuates Wnt signaling . It has been proposed that RPRD1A may act as an intrinsic transcriptional repressor for Wnt/beta-catenin-mediated gene transcription through the recruiting of histone deacetylase 2 (HDAC2) to maintain deacetylated histone H3 in the promoter region of Wnt-targeted genes .

This entry represents the CID domain of RPRD1A.
RPRD2, CID domain (RPRD2_CID)
Type: Domain

Regulation of nuclear pre-mRNA domain-containing protein 2 (RPRD2) is a CID (CTD-Interacting Domain) domain containing protein that co-purifies with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. The function of this proteins is not yet clear. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II . During transcription, RNAP II synthesises eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD .

This entry represents the CID domain of RPRD2.