SII-SWORD/CoKE huggingface dataset:
Zinc carboxypeptidases, zinc-binding region 2 (CARBOXYPEPT_ZN_2)
Type: Binding_site

There are two conserved sites matching these three zinc-ligands - this entry and

. If a protein includes both, the probability of it being a eukaryotic zinc carboxypeptidase is very high.

There are a number of different types of zinc-dependent carboxypeptidases (EC 3.4.17.-) . All these enzymes seem to be structurally and functionally related. Some enzymes that belong to this family are listed below.

Carboxypeptidase A1 (EC 3.4.17.1), a pancreatic digestive enzyme that can remove all C-terminal amino acids with the exception of Arg, Lys and Pro.

Carboxypeptidase A2 (EC 3.4.17.15), a pancreatic digestive enzyme with a specificity similar to that of carboxypeptidase A1, but with a preference for bulkier C-terminal residues.

Carboxypeptidase B (EC 3.4.17.2), also a pancreatic digestive enzyme, but that preferentially removes C-terminal Arg and Lys.

Carboxypeptidase N (EC 3.4.17.3) (also known as arginine carboxypeptidase), a plasma enzyme which protects the body from potent vasoactive and inflammatory peptides containing C-terminal Arg or Lys (such as kinins or anaphylatoxins) which are released into the circulation.

Carboxypeptidase H (EC 3.4.17.10) (also known as enkephalin convertase or carboxypeptidase E), an enzyme located in secretory granules of pancreatic islets, adrenal gland, pituitary and brain. This enzyme removes residual C-terminal Arg or Lys remaining after initial endoprotease cleavage during prohormone processing.

Carboxypeptidase M (EC 3.4.17.12), a membrane bound Arg and Lys specific
enzyme.

Mast cell carboxypeptidase (EC 3.4.17.1), an enzyme with a specificity to carboxypeptidase A, but found in the secretory granules of mast cells.

Streptomyces griseus carboxypeptidase (Cpase SG) (EC 3.4.17.-) , which combines the specificities of mammalian carboxypeptidases A and B.

Thermoactinomyces vulgaris carboxypeptidase T (EC 3.4.17.18) (CPT) , which also combines the specificities of carboxypeptidases A and B.

All of these enzymes bind an atom of zinc. Three conserved residues are implicated in the binding of the zinc atom: two histidines and a glutamic acid.
Alsin-like, PH-like domain (Alsin-like_PH)
Type: Domain

This entry represents the Pleckstrin Homology (PH) domain found in Alsin (ALS2) proteins and ALS2-like proteins. The PH domain is likely involved in membrane targeting through phospholipid binding .

Alsin functions as a guanine nucleotide exchange factor (GEF) for Rho family GTPases, particularly Rac1, in addition to its role as a Rab5 GEF. It contains a DH domain and a PH domain (

). This dual GEF activity links endocytic processes (via Rab5) and actin cytoskeleton remodelling (via Rac1), critical for neuronal membrane transport and motor neurone maintenance. Alsin's dysfunction is implicated in amyotrophic lateral sclerosis (ALS), where impaired GEF activity disrupts intracellular trafficking and cytoskeletal dynamics, contributing to neurodegeneration .
Androglobin, circularly permuted globin domain (Globin_CP_ADGB)
Type: Domain

This entry represents the circularly permuted globin-like domain found in Androglobin. Androglobin is a multidomain protein with a key role in spermatogenesis. It is required for sperm flagellum formation and maturation of elongating spermatids, both essential for male fertility .

Unlike classical globins, the androglobin globin domain has a rearranged sequence that folds into α-helices, resulting in a different topology while maintaining the overall globin fold. A disulfide bond, similar to that found in neuroglobin, forms a closed loop around the haem pocket, taking the place of androglobin's missing CD loop . This unique structural feature further supports the haem pocket structure and likely contributes to its stability.

The androglobin globin-like domain displays unusual ligand binding properties. It binds nitric oxide as a five-coordinate complex, which is rare among globins and similar to other haem proteins with nitric oxide storage functions . The haem iron is likely bis-histidyl six-coordinate, potentially allowing it to bind dioxygen, carbon monoxide, and nitric oxide . It exhibits rapid autoxidation and high nitrite reductase activity, suggesting a role in nitric oxide homeostasis or buffering rather than oxygen transport .
Zinc finger C2HC, NPR-type (Znf_C2HC_NPR-type)
Type: Domain

This entry represents the C2HC zinc finger found in NPR1 and related proteins.

The nonexpressor of pathogenesis-related genes 1 (NPR1) is a master regulator of the defence transcriptome induced by the plant immune signal salicylic acid (SA). It encodes a protein with two protein-protein interaction domains: a BTB/POZ domain at the N-terminal and an ankyrin repeat domain in the central region. In response to SA-induced redox changes, NPR1 protein is released from a quiescent oligomer to translocate into the nucleus, where it serves as a coactivator in complex with transcription factors (TFs), such as TGAs, a family of basic leucine zipper (bZIP) TGACG motif-binding transcription factors. NPR1 is the founding member of a unique family of proteins divided into three functionally distinct clades. Each of the three clades contains two family members with functional redundancy. In the first clade, NPR1 and NPR2 are SA receptors and act as transcriptional co-activators in plant immunity. In the second clade, NPR3 and NPR4 are also SA receptors and serve as transcriptional co-repressors in plant defence. In the third clade, NPR5/BOP2 and NPR6/BOP1 are involved in plant growth and development . A prominent feature of NPR proteins is the presence of a conserved cysteine cluster within the BTB domain. These cysteine residues, together with a conserved histidine (C-X-D-X(2,3)-C-X-H-X(2)-C) form a zinc finger motif that bridges the BTB domain with the ANKs .
FP protein, C-terminal domain (FP_C)
Type: Domain

This entry represents the C-terminal domain of the FP protein from Orgyia pseudotsugata multicapsid polyhedrosis virus, which is also found in other uncharacterised sequences predominantly from arthropods and baculovirus. The function of the FP protein is not known. The protein is missing in baculovirus FP (Few Polyhedra) mutants .
Competence protein CoiA, C-terminal domain (CoiA_C)
Type: Domain

This entry represents a domain found C-terminal in the Competence protein CoiA from Bacillus subtilis and related proteins predominantly found in Bacilli. This domain is predicted to fold in a mainly α-helical structure.

CoiA falls within a competence-specific operon in Streptococcus. It is required for optimal transformation .

Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions .
Competence protein CoiA-like, N-terminal domain (CoiA-like_N)
Type: Domain

This domain is found N-terminal in the Competence protein CoiA from Bacillus subtilis, Druantia protein DruB from Escherichia coli, and related bacterial proteins. It contains three highly conserved cysteine and histidine residues that are probably involved in metal coordination.

CoiA falls within a competence-specific operon in Streptococcus. It is required for optimal transformation .

Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions .

DruB is a component of antiviral defense system Druantia type I .
P5A-ATPase, transmembrane helical hairpin (2TM_P5A-ATPase)
Type: Domain

This entry represents a domain found in homologues of endoplasmic reticulum P5A-ATPase (Spf1 in yeast; ATP13A1 in humans). It consists of two transmembrane helices that form a helical hairpin. This domain seems to be loosely associated with the core transmembrane domain .

P5A-ATPase acts as a dislocase that mediates the ATP-dependent extraction of mislocalized mitochondrial transmembrane proteins from the endoplasmic reticulum membrane . It interacts directly with the TM of the mitochondrial tail-anchored proteins.
MtfA, enterobacterales (MtfA_enterob)
Type: Family

This entry represents Mlc titration factor A (MtfA, previously known as YeeI), which is found mainly in Enterobacteriaceae.

Mlc titration factor A (MtfA, previously known as YeeI) is a transcription factor A that binds Mlc (make large colonies), itself a repressor of glucose and hence a protein important in regulation of the phosphoenolpyruvate:glucose-phosphotransferase (ptsG) system, the major glucose transporter in E. coli. Mlc is a repressor of ptsG, and MtfA is found to bind and inactivate Mlc with high affinity . The membrane-bound protein EIICBGlc encoded by the ptsG gene is the major glucose transporter in Escherichia coli. MtfA is found to be a glucose-regulated peptidase , whose activity is regulated by binding to Mlc available in the cytoplasm, which in turn has been released from EIICBGlc during times when no glucose is taken up. A physiologically relevant target for this peptidase is not yet known.
Small ribosomal subunit protein cS23 (Ribosomal_cS23)
Type: Family

This entry describes probable ribosomal proteins or ribosome-associated proteins mostly found in cyanobacteria and some species from red and green algae.

In cyanobacteria, the small ribosomal subunit protein cS23 is named Ycf65. In red algae, the gene encoding this protein is Ycf65 . Plastid-specific ribosomal proteins may mediate the effects of nuclear factors on plastid translation. The acidic PSRPs are thought to contribute to protein-protein interactions in the 30S subunit, and are not thought to bind RNA .
Small ribosomal subunit protein uS3 (Ribosomal_uS3)
Type: Family

Ribosomal protein uS3 is one of the proteins from the small ribosomal subunit. This entry describes the ribosomal protein uS3 found in bacteria, archaea, and eukaryotes.

The ribosomal protein uS3 plays a crucial role in translation initiation as it positions the mRNA for translation by binding to the 30S and 70S ribosomal subunits and participates in the mRNA unwinding . In eukaroyes, it has also been reported to have extra-ribosomal functions. For example, uS3 has the ability to nick DNA. It also participates in the nuclear factor-kappa B (NF-kB) signalling pathway. Finally, it could be involved in the regulation of apoptosis .

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 .
Ribosomal protein L19e, N-terminal domain (Ribosomal_L19e)
Type: Domain

This domain is found at the N-terminal end of the large ribosomal subunit protein eL19 found in eukaryotes and archaea. This is an α-helical domain that assumes an orthogonal bundle topology.
Ribosomal protein L19e, C-terminal domain (Ribosomal_L19e_C)
Type: Domain

This domain is found at the C-terminal end of the large ribosomal subunit protein eL19 found in eukaryotes and archaea. This is an α-helical domain that assumes an orthogonal bundle topology.
Sororin-like, middle region (Sororin-like_M)
Type: Domain

This entry represents the middle region of Sororin and related animal proteins. According to structure predictions, this region is likely disordered.

Sororin is an essential, cell cycle-dependent mediator of sister chromatid cohesion . The protein is nuclear in interphase cells, dispersed from the chromatin in mitosis, and interacts with the cohesin complex . This protein protects cohesin from WAPL, which otherwise releases cohesin from DNA . This entry also includes dalmatian, a sororin-related protein from Drosophila melanogaster that combines protein functions of Sororin and Shugoshin to promote and protect cohesion .
Connectase MJ0548-like, N-terminal domain (MJ0548_N)
Type: Domain

This domain is found at the N-terminal end of Connectase MJ0548 from Methanocaldococcus jannaschii and similar archaeal sequences. MJ0548 is a distant, monomeric proteasome homologue which connects proteins in a sequence-specific manner .
C-terminal of Roc, COR-B domain (COR-B)
Type: Domain

This entry corresponds to COR-B, located at the C-terminal of COR. COR-B serves as the main dimerisation interface in the full-length LRRK2 structure . It interacts with the kinase domain, which is essential for LRRK2 kinase activity . COR-B consists of four flanked helices, a central seven-stranded antiparallel β-sheet, and a hairpin motif . This entry also describes related serine/theronine-protein kinases and cyclic GMP-binding protein C.

The C-terminal of Roc domain, COR, along with Roc functions as the putative regulator of kinase activity. It functions as a proper GTP-binding protein with a low GTPase activity somehow stimulating the kinase activity . COR is divided in two subdomains: COR-A and COR-B. The Roc-COR tandem is found in Roco-containing proteins from bacterias and eukaryotes. Its most prominent member is the leucine-rich repeat kinase 2 LRRK2 . It also contains Leucine-rich repeat kinase 1 LRKK1, Death-associated protein kinase 1 DAPK1 and Malignant fibrous histiocytoma amplified sequence 1 MFHAS1 .
Large ribosomal subunit protein uL24, C-terminal domain (Ribosomal_uL24_C)
Type: Domain

This entry describes the C-terminal domain in large ribosomal subunit protein uL24 (also known as RPL26).

RPL26 is one of the proteins from the large ribosomal subunit. In their mature form, these proteins have 103 to 150 amino-acid residues. RPL26 makes a very minor contributions to the biogenesis, structure, and function of 60s ribosomal subunits . However, RPL24 is essential to generate the first intermediate during 50s ribosomal subunits assembly . RPL26 have an extra-ribosomal function to enhances p53 translation after DNA damage .
Large ribosomal subunit protein uL22, archaeal-type (Ribosomal_uL22_arc-type)
Type: Family

This family describes the ribosomal protein uL22, previously known as L17 and L22. Proteins in this entry are found in archaea, animals and plants.

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 uL5, eukaryotic/archaeal-type (Ribosomal_uL5_euk/arc-type)
Type: Family

This entry represents uL5 proteins primarily found in eukaryotic and archaeal organisms.

Large ribosomal subunit protein uL5, previously known as Ribosomal protein L5, is ~180 amino acids in length. In Escherichia coli, uL5 is known to be involved in binding 5S RNA to the large ribosomal subunit .

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 uL18, archaeal (Rbsml_uL18_arch)
Type: Family

This entry represents ribosomal uL18 proteins from archaea.

The large ribosomal subunit protein uL18 is an essential component of the large subunit LSU, which is required in its formation and stabilisation. The LSU contains the ribosomal catalytic site termed the peptidyl transferase centre (PTC), which catalyses the formation of peptide bonds, thereby polymerising the amino acids delivered by tRNAs into a polypeptide chain. Additionally, uL18 is essential for binding and coordinating 5S rRNA into the ribosome, a key step in ribosome biogenesis and assembly .

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 .