SII-SWORD/CoKE huggingface dataset:
Small ribosomal subunit protein uS4 (Ribosomal_uS4)
Type: Family

This family includes the small ribosomal subunit protein uS4, also known as S9. U3 small nucleolar ribonucleoprotein protein IMP3, a component of the 60-80S U3 small nucleolar ribonucleoprotein (U3 snoRNP), is also included in this entry. It is required for the early cleavages during pre-18S ribosomal RNA processing .

Ribosomal protein uS4 is one of the proteins from the small ribosomal subunit. In Escherichia coli, uS4 is known to bind directly to 16S ribosomal RNA. Mutations in uS4 have been shown to increase translational error frequencies . uS4 is a protein of 171 to 205 amino-acid residues (except for NAM9, which is much larger). The crystal structure of a bacterial uS4 protein revealed a two domain molecule. The first domain is composed of four helices in the known structure. The second domain is in the middle of the first one and displays some structural homology with the ETS DNA binding domain .

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 uS4, archaeal (Ribosomal_uS4_arc)
Type: Family

This entry represents archaeal ribosomal S4 proteins, also known as uS4.

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 domain superfamily (Ribosomal_uL5_dom_sf)
Type: Homologous_superfamily

This superfamily represents the structural domain of uL5, which forms a 2 layer, mainly antiparallel β-sheet.

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 uL5, archaeal (Ribosomal_uL5_arc)
Type: Family

This entry represents the archaeal uL5 proteins.

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 .
Phosphoenolpyruvate carboxylase, bacterial/plant-type (PEP_COase_bac/pln-type)
Type: Family

Phosphoenolpyruvate carboxylase (PEPCase), an enzyme found in all multicellular plants, catalyses the formation of oxaloacetate from phosphoenolpyruvate (PEP) and a hydrocarbonate ion . This reaction is harnessed by C4 plants to capture and concentrate carbon dioxide into the photosynthetic bundle sheath cells. It also plays a key role in the nitrogen fixation pathway in legume root nodules: here it functions in concert with glutamine, glutamate and asparagine synthetases and aspartate amido transferase, to synthesise aspartate and asparagine, the major nitrogen transport compounds in various amine-transporting plant species .

This entry represents the family found primarily in bacteria and plants.
Dynamin (Dynamin)
Type: Family

Membrane transport between compartments in eukaryotic cells requires proteins that allow the budding and scission of nascent cargo vesicles from one compartment and their targeting and fusion with another. Dynamins are large GTPases that belong to a protein superfamily that, in eukaryotic cells, includes classical dynamins, dynamin-like proteins, OPA1, Mx proteins, mitofusins and guanylate-binding proteins/atlastins , and are involved in the scission of a wide range of vesicles and organelles. They play a role in many processes including budding of transport vesicles, division of organelles, cytokinesis and pathogen resistance.

The minimal distinguishing architectural features that are common to all dynamins and are distinct from other GTPases are the structure of the large GTPase domain (300 amino acids) and the presence of two additional domains; the middle domain and the GTPase effector domain (GED), which are involved in oligomerization and regulation of the GTPase activity.
Protein-export membrane protein SecD/SecF, archaeal and bacterial (SecD/SecF_arch_bac)
Type: Family

This entry represents archaeal and bacterial SecD and SecF protein export membrane proteins and their archaeal homologues . It is found in association with

SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC . SecD and SecF are required to maintain a proton motive force .

Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component . From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.
Protease inhibitor (Inh)
Type: Family

This family of proteins represent monomeric serralysin inhibitors of about 125 residues, which interact with specific metalloprotease which are synthesised by serralysin secretors and characterised by being plant, insect and animal pathogens. It is probable that the serralysin inhibitors protect the host from proteolysis during export of the protease. The members of this family belong to MEROPS proteinase inhibitor family I38, clan IK.

X-ray crystallography of a complex between the Serratia marcescens protease, SmaPI, and the inhibitor of Erwinia chrysanthemi, Inh, reveals that Inh is folded into an eight-stranded b-barrel with an N-terminal trunk of 10 residues. Residues 1-5 occupy part of the extended active site of the proteinase, thereby preventing access of the substrate. Residues 6-10 form a linker that connects the N-terminal proteinase-binding peptide to the body of the b-barrel. The backbone carbonyl of Ser-1 interacts with the catalytic zinc; the Ser-2 side chain occupies the S1'-binding site and also forms a hydrogen bond to the carboxyl end of the catalytic Glu, whereas Leu-3 occupies the S2' recognition site. Penetration of the trunk region further than 5 residues into the substrate binding cleft appears to be prevented by the b-barrel, which itself interacts with the proteinase near its Met turn (19). Peptide mimetics of the trunk at concentrations up to about 100 mM do not inhibit the protease, demonstrating that the barrel is essential for inhibitory activity .

Structurally and functionally these inhibitors are closely related to the lipocalins, fatty acid-binding proteins, avidins and the enigmatic triabin. Together these five protein families constitute the calycin superfamily . The proteins are characterised by their high specificity for small hydrophobic molecules and by their ability to form complexes with soluble macromolecules either through intramolecular disulphides or protein-protein interactions .
Condensin complex subunit 2/barren (Condensin_barren_su2)
Type: Family

This entry represents eukaryotic condensin complex subunit 2 proteins. Included in this group are several Barren protein homologues from several eukaryotic organisms. In Drosophila Barren (barr) is required for sister-chromatid segregation in mitosis. barr encodes a novel protein that is present in proliferating cells and has homologues in yeast and human. Mitotic defects in barr embryos become apparent during cycle 16, resulting in a loss of PNS and CNS neurons. Centromeres move apart at the metaphase-anaphase transition and Cyclin B is degraded, but sister chromatids remain connected, resulting in chromatin bridging. Barren protein localises to chromatin throughout mitosis. Colocalisation and biochemical experiments indicate that Barren associates with Topoisomerase II throughout mitosis and alters the activity of Topoisomerase II. It has been suggested that this association is required for proper chromosomal segregation by facilitating the decatenation of chromatids at anaphase .
Photosystem I Ycf3, assembly (PSI_Ycf3_assembly)
Type: Family

Photosystem I (PSI) is a large protein complex embedded within the photosynthetic thylakoid membrane formed by a core complex, peripheral light-harvesting complexes (LHCIs) and cofactors. It consists of 15 core and 4 LHCI subunits, ~150 chlorophylls (a and b) molecules, 2 phylloquinones, and 3 Fe4S4-clusters . The three dimensional structure of the PSI complex has been resolved at 2.5 A , which allows the precise localisation of each cofactor. PSI together with photosystem II (PSII) catalyses the light-induced steps in oxygenic photosynthesis - a process found in cyanobacteria, eukaryotic algae (e.g. red algae, green algae) and higher plants.

To date, three thylakoid proteins involved in the stable accumulation of PSI have been identified: BtpA (

) , Ycf3 , and Ycf4 . Because translation of the psaA and psaB mRNAs encoding the two reaction centre polypeptides, of PSI and PSII respectively, is not affected in mutant strains lacking functional ycf3 and ycf4, the products of these two genes appear to act at a post-translational step of PSI biosynthesis. The BtpA protein appears to act at the level of PSI stabilisation . It is an extrinsic membrane protein located on the cytoplasmic side of the thylakoid membrane . Homologs of BtpA are found in the crenarchaeota and euryarchaeota, where their function remains unknown. The Ycf4 protein is firmly associated with the thylakoid membrane, presumably through a transmembrane N-terminal domain . Together with Ycf3, it forms a core PSI assembly apparatus as an auxiliary factor. The Ycf3 is a TPR-containing protein loosely associated with the thylakoid membrane and, with its interacting partner Y3IP1, facilitates the assembly of reaction centre subunits. Ycf4 facilitates the integration of peripheral PSI subunits and LHCIs into the PSI reaction centre subcomplex .
Poxvirus Bcl-2-like (Poxvirus_Bcl-2-like)
Type: Family

This family represents a group of Poxvirus Bcl-2-like proteins that function as immunomodulators to evade the host innate immune response through the inhibition of apoptosis or blocking the activation of pro-inflammatory transcription factors, such as interferon (IFN) regulatory factor-3 (IRF-3) and nuclear factor-kappaB (NF-kappaB) . These proteins have low sequence identity but high structural similarity to the eukaryotic Bcl-2 protein family. They have a Bcl-2 fold which comprises a central hydrophobic α-helix that is surrounded by an additional layer of 6-7 amphipathic α-helices . Included in this family are proteins B14 , A52 , A46 , C6 , K7, N1, and N2 . Protein N1 has the unusual dual ability of modulating apoptosis and inflammatory signalling . Protein K7, in addition to its anti-inflammatory activity, forms a complex with RNA helicase DDX3 and antagonises interferon-beta promoter induction .
Uncharacterised protein family UPF0758, YicR subfamily (UPF0758_YicR)
Type: Family

UPF0758 was previously known as the radC family. The name was assigned according to the radC102 mutant of E. coli which was later demonstrated to be an allele of the transcription-repair-coupling factor recG . It has been described as a putative JAMM-family deubiquitinating enzyme, but its function remains to be determined .

This entry represents the YicR subfamily, found in the Enterobacteriaceae.
HTH-type transcriptional regulator MurR (Tscrpt_reg_HTH_MurR)
Type: Family

This entry contains MurR, which represses the expression of the murPQ operon involved in the uptake and degradation of N-acetylmuramic acid (MurNAc). It binds to two adjacent inverted repeats within the operator region. MurNAc 6-phosphate and GlcNAc-6-phosphate can bind to MurR and weaken the DNA binding ability of MurR .

MurR is paralogous to RpiR and has both HTH and SIS phosphosugar binding domains. The divergent murR and murQP transcripts have complementary 5' ends . It is required for swarming phenotype.
Lactate utilization protein A (LutA)
Type: Family

This entry represents lactate utilization protein A, which is involved in L-lactate degradation and allows cells to grow with lactate as the sole carbon source.
Lactate utilization protein C (LutC)
Type: Family

This entry represents lactate utilization protein C, which is involved in L-lactate degradation and allows cells to grow with lactate as the sole carbon source .
Multidrug resistance protein MdtA (Multidrug-R_MdtA)
Type: Family

This entry represents the multidrug resistance protein MdtA. MdtA is one subunit of the MdtABC tripartite complex which is a RND-type drug exporter. The complex consists of MdtB/C, which form a transmembrane heteromultimer and MdtA which is a membrane fusion protein . The mdtABC complex confers resistance against novobiocin and deoxycholate .
Lactate utilization protein B (LutB)
Type: Family

This entry represents lactate utilization protein B, which is involved in L-lactate degradation and allows cells to grow with lactate as the sole carbon source . It is thought to function as an electron transporter during oxidation of L-lactate.
3-deoxy-D-manno-octulosonic acid kinase (KDO_kinase)
Type: Family

Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process.
Protein kinases fall into three broad classes, characterised with respect to substrate specificity :

Serine/threonine-protein kinases

Tyrosine-protein kinases

Dual specificity protein kinases (e.g. MEK -phosphorylates both Thr and Tyr on target proteins)

Protein kinase function is evolutionarily conserved from Escherichia coli to human . Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation . Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved , leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases .

This entry represents 3-deoxy-D-manno-octulosonic acid kinase, which is responsible for the ATP-dependent phosphorylation of 3-deoxy-D-manno-octulosonic acid at the 4-OH position during lipopolysaccharide core biosynthesis.
Phycoerythrobilin:ferredoxin oxidoreductase (Phycoerythrobilin_Fdx_Rdtase)
Type: Family

This entry represents bacterial phycoerythrobilin:ferredoxin oxidoreductases. They are involved in the biosynthesis of photosynthetic antennae of cyanobacteria.
Thiazole biosynthetic enzyme, prokaryotic (Thi4_prok)
Type: Family

This entry represents bacterial and archaeal proteins related to eukaryotic THI4, involved in the biosynthesis of the thiamine precursor thiazole.

Archaea harbour structural homologues of both the bacterial (ThiS-ThiF) and eukaryotic (THI4) proteins for thiazole synthesis. Most archaea have homologues that cluster to the THI4 family of proteins, but lack the conserved cysteine residue of the yeast THI4p that is required for sulfur transfer in formation of the thiazole ring. Instead, they have a histidine residue that is well conserved. Initially, these archaeal histidine-cointaining THI4 homologues were reported to convert ribose-1,5-bisphosphate (R15P) into ribulose-1,5-bisphosphate, the substrate of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) , but this may not be correct and their function remains unknown . On the other hand, archaeal THI4 homologues with a conserved catalytic cysteine are linked to thiamine biosynthesis .
1,4-dihydroxy-2-naphthoyl-CoA hydrolase (DHNA_CoA_hydrolase)
Type: Family

This entry contains 1,4-dihydroxy-2-naphthoyl-CoA hydrolase, which catalyzes the hydrolysis of 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) to 1,4-dihydroxy-2-naphthoate (DHNA), a reaction involved in phylloquinone (vitamin K1) biosynthesis.
Indigoidine synthase A-like (Indigdn_synthA-like)
Type: Homologous_superfamily

The crystal structure of indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima represents a new fold . This protein has been shown to act also as a pseudouridine-5'-phosphate glycosidase .