SII-SWORD/CoKE huggingface dataset:
Mitochondrial inner membrane translocase complex, subunit Tim17 (Tim17)
Type: Family

The mitochondrial protein translocase (MPT) family, which brings nuclearly encoded preproteins into mitochondria, is very complex with 19 currently identified protein constituents. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. The inner membrane translocase is formed of a complex with a number of proteins, including the Tim17, Tim23 and Tim44 subunits. Tim17 and Tim23 are thought to form the translocation channel of the inner membrane .
Ribosomal protein uS12, bacterial-type (Ribosomal_uS12_bac)
Type: Family

Ribosomal protein uS12 is located at the interface of the large and small ribosomal subunits, where it plays an important role in both tRNA and ribosomal subunit interactions. uS12 is essential for maintenance of a pretranslocation state and, together with uS13, functions as a control element for the rRNA- and tRNA-driven movements of translocation . Antibiotics such as streptomycin bind uS12 and cause the ribosome to misread the genetic code .

This family consists of ribosomal protein uS12 from bacteria, mitochondria, and chloroplasts.

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 .
Mitochondrial inner membrane translocase complex, subunit Tim23 (Tim23)
Type: Family

The mitochondrial protein translocase (MPT) family, which brings nuclearly encoded preproteins into mitochondria, is very complex with 19 currently identified protein constituents. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. The inner membrane translocase is formed of a complex with a number of proteins, including the Tim17, Tim23 and Tim44 subunits. Tim17 and Tim23 are thought to form the translocation channel of the inner membrane .

The TIM23 complex forms a dynamic multisubunit machinery that recognises preproteins and can transport them into the inner membrane or into the matrix. It is composed of three subunits, Tim50, Tim23, and Tim17, that expose the domains to the intermembrane space. This entry includes the mitochondrial import inner membrane translocase subunit Tim23, consisting of an N-terminal intermembrane space domain that interacts with Tim50, and a C-terminal membrane-embedded domain that, together with Tim17, forms a protein-conducting channel across the inner membrane. Tim50 helps keeping the Tim23 channel in a closed state in the absence of presequence proteins, regulating the gating through the TIM channel .
Mitochondrial import receptor subunit Tom22 (Tom22)
Type: Family

The mitochondrial protein translocase family, which is responsible for movement of nuclear encoded pre-proteins into mitochondria, is very complex with at least 19 components. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family represents the Tom22 proteins . The N-terminal region of Tom22 has been shown to have chaperone-like activity, and the C-terminal region faces the intermembrane face .
Integration host factor, alpha subunit (IHF_alpha)
Type: Family

Integration host factor (IHF) is a heterodimeric protein consisting of alpha and beta (

) subunits. IHF binds the minor groove of DNA in a sequence-specific manner to induce a large bend. This bending stabilises distinct DNA conformations that are required during several bacterial processes, such as recombination, transposition, replication and transcription. IHF is known to act as a transcription factor at many gene regulatory regions in E. coli. It is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups) . IHF is also involved in formation as well as maintenance of bacterial biofilms since it is found in complex with extracellular DNA (eDNA) within the extracellular polymeric substances (EPS) matrix of many biofilms .
Integration host factor, beta subunit (IHF_beta)
Type: Family

Integration host factor (IHF) is a heterodimeric protein consisting of alpha (

) and beta subunits. IHF binds the minor groove of DNA in a sequence-specific manner to induce a large bend. This bending stabilises distinct DNA conformations that are required during several bacterial processes, such as recombination, transposition, replication and transcription .
Mitochondrial import receptor subunit Tom40, fungi (Tom40_fungi)
Type: Family

Tom40 is a mitochondrion outer membrane protein and a component of the TOM (translocator of the outer mitochondrial membrane) complex, which is essential for import of protein precursors into mitochondria . In Saccharomyces cerevisiae, TOM complex is composed of the subunits Tom70, Tom40, Tom22, Tom20, Tom7, Tom6, and Tom5 . Tom40 is an integral membrane protein and the main structural component of the protein-conducting channel formed by the TOM complex . It is stabilised by other components, such as Tom5, Tom6, and Tom7 .
Mitochondrial outer membrane translocase complex, subunit Tom70 (Tom70)
Type: Family

The mitochondrial protein translocase (MPT) family, which brings nuclearly encoded preproteins into mitochondria, is very complex with 19 currently identified protein constituents. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tom70 proteins.
Chloroplast protein import component Toc34 (Toc34)
Type: Family

Two integral outer envelope GTPases, Toc34 and Toc86, are proposed to regulate the recognition and translocation of nuclear-encoded preproteins during the early stages of protein import into chloroplasts. The cytosolic region of Toc34 reveals 34% α-helical and 26% β-strand structure and is stabilised by intramolecular electrostatic interaction. Toc34 binds both chloroplast preproteins and isolated transit peptides in a guanosine triphosphate- (GTP-) dependent mechanism .
Chloroplast envelope protein translocase, IAP75 (IAP75)
Type: Family

Chloroplast function requires the import of nuclear encoded proteins from the cytoplasm across the chloroplast double membrane. This is accompished by two protein complexes, the Toc complex located at the outer membrane and the Tic complex loacted at the inner membrane . The Toc complex recognises specific proteins by a cleavable N-terminal sequence and is primarily responsible for translocation through the outer membrane, while the Tic complex translocates the protein through the inner membrane.

This entry represents Toc750, a core component of the Toc complex. This protein is deeply embedded in the outer membrane and forms the voltage-dependent translocation channel . Toc75 itself appears to be capable of at least some discrimination between substrate and non-substrate proteins, with recognition based on based on both conformational and electrostatic interactions.
Translocase of chloroplast Toc86/159 (Toc86_159)
Type: Family

This entry represents the translocase of chloroplast 159 family of proteins (Tocs), GTPases involved in protein precursor import into chloroplasts, which recognise chloroplast-destined precursor proteins and regulate their presentation to the translocation channel through GTP hydrolysis . They have three domains: the N-terminal A-domain is acidic, repetitive, weakly conserved, readily removed by proteolysis during chloroplast isolation, not required for protein translocation , and the other domains are designated G (GTPase) and M (membrane anchor) . The signature for this family includes most of the G domain and all of M. There are at least two distinct Toc159 subtypes, Toc159 and Toc132/Toc120. Toc159 is expressed in young photosynthetic tissues and seems to be specialised in the import of nuclear encoded photosynthetic preproteins from the cytoplasm to the chloroplast, whereas Toc132/Toc120 are expressed relatively prominent in nonphotosynthetic tissues and seem to be specialised in the import of nuclear encoded non-photosynthetic preproteins from the cytoplasm to the chloroplast .
Chloroplast protein import component Tic20 (Tic20)
Type: Family

Chloroplast function requires the import of nuclear encoded proteins from the cytoplasm across the chloroplast double membrane. This is accompished by two protein complexes, the Toc complex located at the outer membrane and the Tic complex loacted at the inner membrane . The Toc complex recognises specific proteins by a cleavable N-terminal sequence and is primarily responsible for translocation through the outer membrane, while the Tic complex translocates the protein through the inner membrane.

This entry represents Tic20, a core member of the Tic complex. This protein is deeply embedded in the inner envelope membrane and is thought to function as a protein conducting component of the Tic complex .
Chloroplast protein import component Tic22 (Tic22)
Type: Family

Chloroplast function requires the import of nuclear encoded proteins from the cytoplasm across the chloroplast double membrane. This is accompished by two protein complexes, the Toc complex located at the outer membrane and the Tic complex loacted at the inner membrane . The Toc complex recognises specific proteins by a cleavable N-terminal sequence and is primarily responsible for translocation through the outer membrane, while the Tic complex translocates the protein through the inner membrane.

This entry represents Tic22, a core member of the Tic complex. Tic22 is a soluble protein and the only Tic complex component of the intermembrane space that has been shown to interact with preproteins during import. It may also act as a chaperone that prevent misfolding or missorting of the preprotein to the intermembrane space and potentially serve as a component that links the Toc and Tic complexes .
Membrane fusion proteins, proteobacteria (MFP_proteobact)
Type: Family

This family of membrane fusion proteins (MFP) from proteobacteria includes Multidrug resistance protein MdtN and the efflux pump membrane proteins EmrA and EmrK . MdtN is thought to be involved in resistance to puromycin, acriflavine and tetraphenylarsonium chloride. The EmrAB transporter confer resistance to carbonylcyanide m-chlorophenylhydrazone, nalidixic acid, and a number of other toxic compounds . EmrA is predicted to have a short N-terminal cytoplasmic domain, a single transmembrane helix, and a large periplasmic domain .
Cobalt/zinc/cadmium resistance protein CzcB-like (Co/Zn/Cd_resistance_CzcB-like)
Type: Family

Gram-negative bacteria have evolved transport complexes that export macromolecules and toxic substances such as heavy metals across the two membranes of the cell envelope in a single energy coupled step. The process requires (1) a cytoplasmic membrane export system, (2) a membrane fusion protein (MFP), and (3) an outer membrane factor. Phylogenetic analyses reveal that the MFPs cluster in accordance with the type of cytoplasmic membrane transport systems with which they function -proteins in this family are associated with reisistance to heavy metal poisoning.
Secretion protein MesE/LcnD (MesE/LcnD)
Type: Family

Bacteriocins are antibacterial proteinaceous compounds produced by bacteria. In Gram-positive bacteria, they are divided into four classes. Within the class II, constituted by non-modified peptides produced mainly by lactic acid bacteria, bacteriocins of the subclass IIa (also known as pediocin-like bacteriocins), such as mesentericin Y105, are of particular interest. They are active against the foodborne pathogen Listeria monocytogenes and share a similar primary structure, with a conserved N-terminal motif (YGNGV). Subclass IIa bacteriocins induce membrane permeabilization of sensitive strains . Class-IId contains the one-peptide non-cyclic bacteriocins that show no sequence similarity to the pediocin-like bacteriocins, and include lactococcin A (LcnA) .

The translocation of most of the class II bacteriocins requires a type I secretion system which is composed of maturation and secretion protein and an accessory factor. MesD and MesE encode the dedicated transport system of mesentericin Y105 . Secretion and maturation of LcnA depends on the two membrane proteins LcnC and LcnD . This family consist of accessory factors such as MesE and LcnD. Their function remains unclear, but they are required for full production of these bacteriocins .
Homoserine O-succinyltransferase MetA (HST_MetA)
Type: Family

This family of enzymes, homoserine O-succinyltransferase, catalyses the first step in the biosynthesis of methionine:

Succinyl-CoA + L-homoserine = CoA + O-succinyl-L-homoserine

This enzyme is essential for the survival of bacteria, plants and fungi. Since they are not found in humans, they make a promising new target for antimicrobial drug development. Homoserine O-succinyltransferase (HST) is a representative from this class and has recently had the key amino acids involved in substrate specificity and catalysis elucidated .
Chaperone lipoprotein, PulS/OutS (Chap_lipoprot_PulS/OutS)
Type: Family

This family comprises lipoproteins from gamma proteobacterial species: pullulanase secretion protein PulS protein of Klebsiella pneumoniae (

), the lipoprotein OutS protein of Erwinia chrysanthemi (

) and the functionally uncharacterised type II secretion protein EtpO (

) from Escherichia coli O157:H7. PulS and OutS have been shown to interact with and facilitate insertion of secretins into the outer membrane, suggesting a chaperone-like, or piloting function for members of this family. These proteins consist of 4 α helices arranged into a slightly elongated, C-shaped helical bundle. Within PulS, the helices form a binding groove which interact with a disordered region on another protein, PulD, to form a PulS-PulD complex. PulD then oligomerises into a dodecameric outer membrane complex in the formation of a type II secretion system .
Exopolysaccharide biosynthesis protein ExoP-like (EPS_ExoP-like)
Type: Family

This group of proteins are part of a large genetic locus which is associated with exopolysaccharide (EPS) biosynthesis . This entry includes ExoP from Rhizobium meliloti and PssP from Rhizobium leguminosarum bv. trifolii. They belong to the PCP2a family involved in the synthesis of high-molecular-weight EPS . They contain a periplasmic domain flanked by two transmembrane regions and an additional cytoplasmic domain. ExoP is involved in polymerization and secretion of succinoglycan. Mutations in the Walker A ATP-binding motif found in the cytoplasmic domain of ExoP prevented ATPase activity of the ExoP protein .
Capsular polysaccharide biosynthesis protein CpsC-like (CpsC-like)
Type: Family

This entry includes some capsular polysaccharide biosynthesis proteins from the CpsC/CapA family, including CpsC from Streptococcus pneumoniae. CpsC (capsular polysaccharide biosynthesis protein C) is required for CpsD phosphorylation and is involved in the regulation of capsular polysaccharide biosynthesis. This protein is part of a trio of proteins that includes tyrosine kinase activity and that governs polymer length . It may be part of a complex that directs the coordinated polymerisation and export to the cell surface of the capsular polysaccharide . Members of this family are found in Bacilli.
Tyrosine-protein kinase Wzc-like, C-terminal domain (Wzc-like_C)
Type: Domain

This entry represents the C-terminal domain of Tyrosine-protein kinase wzc from Escherichia coli and similar bacterial sequences. Wzc in required for the extracellular polysaccharide colanic acid synthesis. It is probably involved in the export of colanic acid from the cell to medium . This domain covers the whole length of the protein in Tyrosine-protein kinase CpsD from Streptococcus agalactiae, which is involved in the regulation of capsular polysaccharide biosynthesis .

Wzc is an integral cytoplasmic membrane protein that belonds to the bacterial tyrosine kinase (BY-kinase) family. This enzyme is essential for extracellular polysaccharide colanic acid synthesis and export in Escherichia coli. The protein undergoes autophosphorylation at multiple tyrosine residues through a cooperative two-step mechanism involving both intra- and intermolecular phosphorylation events. Paradoxically, whilst the autophosphorylated form is required for colanic acid assembly, it is inactive for its actual production. The enzyme phosphorylates UDP-glucose dehydrogenase (Ugd), stimulating its activity and connecting colanic acid biosynthesis with polymer export from the cell to the medium. Wzc functions as a master regulator of polysaccharide assembly through the formation and dissociation of octameric complexes, driven by changes in the phosphorylation status of its C-terminal tyrosine-rich tail. .
Small ribosomal subunit protein uS3, eukaryotic/archaeal (Ribosomal_uS3_euk/arc)
Type: Family

Ribosomal protein uS3 is one of the proteins from the small ribosomal subunit. This family describes ribosomal protein uS3 found in eukaryotes and 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 .
Small ribosomal subunit protein uS3, bacterial-type (Ribosomal_uS3_bac-typ)
Type: Family

Ribosomal protein uS3 is one of the proteins from the small ribosomal subunit.
This family describes the bacterial type of ribosomal protein uS3 and also and many chloroplast forms. Chloroplast and mitochondrial forms have large, variable inserts between conserved N-terminal and C-terminal domains.

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 .
Polysaccharide export inner-membrane protein, BexC/CtrB/KpsE/VexD (BexC_CtrB_KpsE_VexD)
Type: Family

This family contains gammaproteobacterial proteins involved in ATP-dependent capsule polysaccharide export .