SII-SWORD/CoKE huggingface dataset:
Large ribosomal subunit protein bL9, N-terminal (Ribosomal_bL9_N)
Type: Domain

This entry represents a domain located in the N-terminal section of proteins belonging to the ribosomal protein bL9 family from bacteria and eukaryotes.

This entry represents the large ribosomal subunit protein bL9. In Escherichia coli, bL9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities .

The crystal structure of Bacillus stearothermophilus bL9 shows the 149-residue protein comprises two globular domains connected by a rigid linker . Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an α-helix and a three-stranded mixed parallel, anti-parallel β-sheet packed against the central α-helix. The long central α-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends.

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 .
Uncharacterised protein family AF1718 (Uncharacterised_AF1718)
Type: Family

This entry represents a group of uncharacterised proteins found in the Archaea. Their function is unknown.
Uncharacterised protein family AF2234 (Uncharacterised_AF2234)
Type: Family

This entry contains uncharacterised prokaryotic proteins which have no known function at present.
Protein of unknown function DUF2768 (DUF2768)
Type: Family

This entry contains proteins with no known function.
Protein of unknown function DUF5436 (DUF5436)
Type: Family

This is a family of unknown function found in Orthopoxvirus.
Outer membrane adhesin/peptidase omptin (OM_adhesin/peptidase_omptin)
Type: Homologous_superfamily

This entry represents a transmembrane domain with a (10,12) β-barrel structure. This domain is found in:

Outer membrane peptidase omptin

Outer membrane adhesin OpcA

The outer membrane omptin belongs to the MEROPS family A26 (clan AF). The omptin family, comprises a number of novel outer membrane-associated serine peptidases that are distinct from trypsin-like peptidases in that they cleave polypeptides between two basically-charged amino acids . The enzyme is sensitive to the serine protease inhibitor diisopropylfluoro-phosphate, to divalent cations such as copper, zinc and iron , and is temperature regulated, activity decreasing at lower temperatures . Temperature regulation is most prominently shown in the Yersinia pestis coagulase/fibrinolysin protein, where coagulase activity is prevalent below 30 degrees Celsius, and fibrinolysin (protease) activity is prevalent above this point, the optimum temperature being 37 degrees . It is possible that this assists in 'flea blockage' and transmission of the bacteria to animals .

The outer membrane adhesin OpcA is Neisseria species-specific. OpcA (formerly called 5C) was isolated from Neisseria meningitidis, causative agent of meningococcal meningitis and septicemia. An outer membrane protein embedded in the lipid bilayer, OpcA was shown to play an important role in meningococcal adhesion and invasion of both epithelial and endothelial cells, mediating attachment to host cells by binding proteoglycan cell-surface receptors . OpcA forms a 10-stranded β-barrel with five highly mobile extracellular loops that protrude above the surface of the membrane . These extracellular loops combine to form a crevice in the external surface that is lined by positively charged residues, which is predicted to be a binding site for proteoglycan polysaccharides involved in pathogenesis. Conformational changes in the extracellular loops modulate the surface of OpcA, which could affect the proteoglycan binding site . These conformational changes could also lead to pore opening.
SsrA-binding protein, conserved site (SsrA-bd_prot_CS)
Type: Conserved_site

This entry represents SsrA-binding protein (aka small protein B or SmpB), which is a unique RNA-binding protein that is conserved throughout the bacterial kingdom and is an essential component of the SsrA quality-control system. Tight recognition of codon-anticodon pairings by the ribosome ensures the accuracy and fidelity of protein synthesis. In eubacteria, translational surveillance and ribosome rescue are performed by the 'tmRNA-SmpB' system (transfer messenger RNA-small protein B). SmpB binds specifically to the ssrA RNA (tmRNA) and is required for stable association of ssrA with ribosomes. SsrA RNA recognises ribosomes stalled on defective messages and acts to mediate the addition of a short peptide tag to the C terminus of the partially synthesised nascent polypeptide chain. Within a stalled ribosome, SmpB interacts with the three universally conserved bases G530, A1492 and A1493 that form the 30S subunit decoding centre, in which canonical codon-anticodon pairing occurs . The SsrA-tagged protein is then degraded by C-terminal-specific proteases. Formation of an SmpB-SsrA complex appears to be critical in mediating SsrA activity after aminoacylation with alanine but prior to the transpeptidation reaction that couples this alanine to the nascent chain . The SmpB protein has functional and structural similarities with initiation factor 1, and is proposed to be a functional mimic of the pairing between a codon and an anticodon.
S-adenosyl-L-homocysteine hydrolase, conserved site (S-Ado-L-homoCys_hydrolase_CS)
Type: Conserved_site

Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase,

) (AdoHcyase) is an enzyme of the activated methyl cycle, responsible for the reversible hydration of S-adenosyl-L-homocysteine into adenosine and homocysteine. This enzyme is ubiquitous, highly conserved, and may play a key role in the regulation of the intracellular concentration of adenosylhomocysteine. AdoHcyase requires NAD+ as a cofactor and contains a central glycine-rich region which is thought to be involved in NAD-binding. Since AdoHyc is a potent inhibitor of S-adenosyl-L-methionine dependent methyltransferases, AdoHycase plays a critical role in the modulation of the activity of various methyltransferases. The enzyme forms homotetramers, with each monomer binding one molecule of NAD+ .

This entry represents two highly conserved regions. The first pattern is located in the N-terminal section; the second is derived from a glycine-rich region in the central part of S-adenosyl-L-homocysteine hydrolase, a region thought to be involved in NAD-binding.
Large ribosomal subunit protein eL39, conserved site (Ribosomal_eL39_CS)
Type: Conserved_site

A number of eukaryotic and archaebacterial large subunit ribosomal proteins can be grouped on the basis of sequence similarities. This entry represents the large ribosomal subunit protein eL39, of about 50 residues long, being the smallest protein of eukaryotic-type ribosomes. In mammals, eL39 has been described as the RNA-binding component of the large ribosomal subunit .

This entry represents a conserved region in the C-terminal section of these proteins.

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 .
DNA delivery protein, P32/P34 (DNA_delivery_prot_P32/34)
Type: Family

This entry represents the DNA delivery proteins P32 and P34 that are found in the virion membrane. It is responsible for DNA delivery and viral infectivity . It is also required for DNA injection in the membrane transformation event. In Enterobacteria phage PRD1 virions, which are composed of a tail-less icosahedral capsid, an inner protein-lipid membrane, and a dsDNA genome which is located inside the lipid vesicle; the DNA is packaged into a preformed procapsid. The internal membrane plays an active role in DNA delivery to the host cell by forming a tubular structure used for injecting the DNA into the host cytoplasm.
Protein of unknown function DUF5487 (DUF5487)
Type: Family

This is a family of unknown function found in Myoviridae.
Pleiotrophin/Midkine, N-terminal domain (PTN/MK_N_dom)
Type: Domain

Several extracellular heparin-binding proteins involved in regulation of growth and differentiation belong to a new family of growth factors. These growth factors are highly related proteins of about 140 amino acids that contain 10 conserved cysteines probably involved in disulphide bonds, and include pleiotrophin (also known as heparin-binding growth-associated molecule HB-GAM, heparin-binding growth factor 8 HBGF-8, heparin-binding neutrophic factor HBNF and osteoblast specific protein OSF-1); midkine (MK) ; retinoic acid-induced heparin-binding protein (RIHB) ; and pleiotrophic factors alpha-1 and -2 and beta-1 and -2 from Xenopus laevis, the homologues of midkine and pleiotrophin respectively. Pleiotrophin is a heparin-binding protein that has neurotrophic activity and has mitogenic activity towards fibroblasts. It is highly expressed in brain and uterus tissues, but is also found in gut, muscle and skin. It is thought to possess an important brain-specific function. Midkine is a regulator of differentiation whose expression is regulated by retinoic acid, and, like pleiotrophin, is a heparin-binding growth/differentiation factor that acts on fibroblasts and nerve cells.

This entry represents the N-terminal domain of pleiotrophin and midkine .
Pleiotrophin/Midkine, C-terminal domain (PTN/MK_C_dom)
Type: Domain

Several extracellular heparin-binding proteins involved in regulation of growth and differentiation belong to a new family of growth factors. These growth factors are highly related proteins of about 140 amino acids that contain 10 conserved cysteines probably involved in disulphide bonds, and include pleiotrophin (also known as heparin-binding growth-associated molecule HB-GAM, heparin-binding growth factor 8 HBGF-8, heparin-binding neutrophic factor HBNF and osteoblast specific protein OSF-1); midkine (MK) ; retinoic acid-induced heparin-binding protein (RIHB) ; and pleiotrophic factors alpha-1 and -2 and beta-1 and -2 from Xenopus laevis, the homologues of midkine and pleiotrophin respectively. Pleiotrophin is a heparin-binding protein that has neurotrophic activity and has mitogenic activity towards fibroblasts. It is highly expressed in brain and uterus tissues, but is also found in gut, muscle and skin. It is thought to possess an important brain-specific function. Midkine is a regulator of differentiation whose expression is regulated by retinoic acid, and, like pleiotrophin, is a heparin-binding growth/differentiation factor that acts on fibroblasts and nerve cells.

This entry represents the C-terminal domain of pleiotrophin and midkine .
Pleiotrophin/Midkine disulphide-rich domain superfamily (PTN/MK_diS_sf)
Type: Homologous_superfamily

Several extracellular heparin-binding proteins involved in regulation of growth and differentiation belong to a new family of growth factors. These growth factors are highly related proteins of about 140 amino acids that contain 10 conserved cysteines probably involved in disulphide bonds, and include pleiotrophin (also known as heparin-binding growth-associated molecule HB-GAM, heparin-binding growth factor 8 HBGF-8, heparin-binding neutrophic factor HBNF and osteoblast specific protein OSF-1); midkine (MK) ; retinoic acid-induced heparin-binding protein (RIHB) ; and pleiotrophic factors alpha-1 and -2 and beta-1 and -2 from Xenopus laevis, the homologues of midkine and pleiotrophin respectively. Pleiotrophin is a heparin-binding protein that has neurotrophic activity and has mitogenic activity towards fibroblasts. It is highly expressed in brain and uterus tissues, but is also found in gut, muscle and skin. It is thought to possess an important brain-specific function. Midkine is a regulator of differentiation whose expression is regulated by retinoic acid, and, like pleiotrophin, is a heparin-binding growth/differentiation factor that acts on fibroblasts and nerve cells.

Pleiotrophin is structurally divided into two domains, both domains consisting of three antiparallel β-strands, but the C-terminal domain has a long flexible hairpin loop where a heparin-binding consensus sequence is located . This superfamily represents the all-β 3 antiparallel strands disulfide-rich fold found both in the N-terminal and C-terminal domains of pleiotrophin and midkine.
Pleiotrophin/Midkine heparin-binding growth factor, conserved site (PTN_MK_heparin-bd_GF_CS)
Type: Conserved_site

Several extracellular heparin-binding proteins involved in regulation of growth and differentiation belong to a new family of growth factors. These growth factors are highly related proteins of about 140 amino acids that contain 10 conserved cysteines probably involved in disulphide bonds, and include pleiotrophin (also known as heparin-binding growth-associated molecule HB-GAM, heparin-binding growth factor 8 HBGF-8, heparin-binding neutrophic factor HBNF and osteoblast specific protein OSF-1); midkine (MK) ; retinoic acid-induced heparin-binding protein (RIHB) ; and pleiotrophic factors alpha-1 and -2 and beta-1 and -2 from Xenopus laevis, the homologues of midkine and pleiotrophin respectively. Pleiotrophin is a heparin-binding protein that has neurotrophic activity and has mitogenic activity towards fibroblasts. It is highly expressed in brain and uterus tissues, but is also found in gut, muscle and skin. It is thought to possess an important brain-specific function. Midkine is a regulator of differentiation whose expression is regulated by retinoic acid, and, like pleiotrophin, is a heparin-binding growth/differentiation factor that acts on fibroblasts and nerve cells.

This entry represents two conserved sites found within pleiotrophin and midkine heparin-binding growth factors; these conserved sites include the majority of the conserved cysteines.
Pseudouridine synthase I, TruA, C-terminal (PsdUridine_synth_TruA_C)
Type: Homologous_superfamily

Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an α+β structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are :

Pseudouridine synthase I, TruA.

Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain.

Pseudouridine synthase RsuA. RluB, RluE and RluF are also part of this family.

Pseudouridine synthase RluA. TruC, RluC and RluD belong to this family.

Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific α+β subdomain.

This superfamily represents the Pseudouridine synthase I (TruA) C-terminal domain.

TruA from Escherichia coli modifies positions uracil-38, U-39 and/or U-40 in tRNA . TruA contains one atom of zinc essential for its native conformation and tRNA recognition and has a strictly conserved aspartic acid that is likely to be involved in catalysis . These enzymes are dimeric proteins that contain two positively charged, RNA-binding clefts along their surface. Each cleft contains a highly conserved aspartic acid located at its centre. The structural domains have a topological similarity to those of other RNA-binding proteins, though the mode of interaction with tRNA appears to be unique.
Pseudouridine synthase I, TruA, alpha/beta domain (PsdUridine_synth_TruA_a/b_dom)
Type: Domain

Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an α+β structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are :

Pseudouridine synthase I, TruA.

Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain.

Pseudouridine synthase RsuA. RluB, RluE and RluF are also part of this family.

Pseudouridine synthase RluA. TruC, RluC and RluD belong to this family.

Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific α+β subdomain.

This entry represents pseudouridine synthase I (TruA) α/β domain.

TruA from Escherichia coli modifies positions uracil-38, U-39 and/or U-40 in tRNA . TruA contains one atom of zinc essential for its native conformation and tRNA recognition and has a strictly conserved aspartic acid that is likely to be involved in catalysis . These enzymes are dimeric proteins that contain two positively charged, RNA-binding clefts along their surface. Each cleft contains a highly conserved aspartic acid located at its centre. The structural domains have a topological similarity to those of other RNA-binding proteins, though the mode of interaction with tRNA appears to be unique.
Protein of unknown function DUF5445 (DUF5445)
Type: Family

This is a family of unknown function found in Enterobacteriaceae.
Glucose-repressible protein Grg1 (Glc-repressible_Grg1)
Type: Family

This fungal protein increases during glucose deprivation. Its function is unknown .
Cytochrome b-c1 complex subunit 8, plants (Cyt_b-c1_8-plants)
Type: Family

This entry represents subunit 8 of the Cytochrome b-c1 complex. The ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) is part of the mitochondrial respiratory chain. This subunit, together with cytochrome b, binds to ubiquinone. In plants, the b-c1 complex contains 10 subunits: 3 respiratory subunits, 2 core proteins and 5 low-molecular weight proteins .
Uncharacterised protein YqgC-like (YqgC-like)
Type: Family

This is a family of unknown function found in Enterobacteriaceae such as E.coli and Shigella.
Protein of unknown function DUF5438 (DUF5438)
Type: Family

This is a family of unknown function found in Orthopoxvirus.
Spore coat protein CotD (Spore_coat_CotD)
Type: Family

This entry represents spore coat protein D; a capsid protein involved in sporulation.
Holin, r1t-type (Holin_r1t)
Type: Family

Holin is a phage membrane protein that is necessary for host cell lysis. This entry contains holins related to the holin from Lactococcus phage r1t (Bacteriophage r1t) .
Protein of unknown function DUF2883 (DUF2883)
Type: Family

This group of proteins currently have no known function and are found primarily in the T4-like bacteriophages.
Protein of unknown function DUF5439 (DUF5439)
Type: Family

This is a family of unknown function found in Orthopoxvirus.
Anti-sigma-F factor Fin (Fin)
Type: Family

Fin (formerly known as YabK) is a small protein required for efficient switching from sigma(F)- to sigma(G)-directed gene expression during sporulation in Bacillus subtilis. Fin has been proposed to be an anti-sigma(F) factor which, by disabling sigma(F), promotes the switch to late developmental gene expression in the forespore .
Uncharacterised protein family YncJ (Uncharacterised_YncJ)
Type: Family

This entry contains proteins with no known function.