SII-SWORD/CoKE huggingface dataset:
Small ribosomal subunit protein uS11, bacterial-type (Ribosomal_uS11_bac-type)
Type: Family

This entry represents bacterial ribosomal uS11 proteins, and also some (though not all) chloroplast and mitochondrial equivalents as well.

Small ribosomal subunit protein uS11, previously known as Ribosomal protein S11 , plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small 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 .
Proteasome alpha subunit, archaeal (Proteasome_asu_arc)
Type: Family

The proteasome (or macropain) (

) is a multicatalytic proteinase complex in eukaryotes and archaea, and in some bacteria, that is involved in an ATP/ubiquitin-dependent non-lysosomal proteolytic pathway. In eukaryotes the 20S proteasome is composed of 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700kDa. Proteasome subunits can be classified on the basis of sequence similarities into two groups, alpha (A) and beta (B). The proteasome consists of four stacked rings composed of α/β/β/α subunits. There are seven different alpha subunits and seven different beta subunits . Three of the seven beta subunits are peptidases, each with a different specificity. Subunit beta1c (MEROPS identifier T01.010) has a preference for cleaving glutaminyl bonds ("peptidyl-glutamyl-like" or "caspase-like"), subunit beta2c (MEROPS identifier T01.011) has a preference for cleaving arginyl and lysyl bonds ("trypsin-like"), and subunit beta5c (MEROPS identifier T01.012) cleaves after hydrophobic amino acids ("chymotrypsin-like") . The proteasome subunits are related to N-terminal nucleophile hydrolases, and the catalytic subunits have an N-terminal threonine nucleophile.

This entry represents the alpha subunit of the archaeal proteasome (MEROPS identifier T01.970). This protein has so far been found in all completely sequenced archaeal genomes and is occasionally duplicated. The two different alpha subunits of Haloferax volcanii may have distinct physiological roles .
Peptidase T1A, proteasome beta-subunit, archaeal (Pept_T1A_Psome_bsu_arc)
Type: Family

The proteasome (or macropain) (

) is a multicatalytic proteinase complex in eukaryotes and archaea, and in some bacteria, that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). These are arranged in four rings of seven proteins, consisting of a ring of alpha subunits, two rings of beta subunits, and a ring of alpha subunits. In eukaryotes, each alpha and each beta ring consists of different proteins. Three of the beta subunits are peptidases in subfamily T1A, and each has a distinctive specificity (trypsin-like, chymotrypsin-like and glutamyl peptidase-like). The peptidases are N-terminal nucleophile hydrolases in which the N-terminal threonine is the nucleophile in the hydrolytic reaction . In the immunoproteasome, the catalytic components are replaced by three specialist, catalytic beta subunits . In bacteria and archaea there is only one alpha subunit and one beta subunit, and each ring is a homoseptamer.

This entry includes the beta subunit of the archaean proteasome (MEROPS identifier T01.002). The archaean proteasome consists of four stacked rings each of which contains a homoheptamer of either alpha or beta components, so that the rings are stacked in the order alpha, beta, beta, alpha. Alpha and beta subunits are homologous to one another, but only beta subunits are proteolytically active. The beta subunits are arranged so that the active sites are directed towards the centre of each ring. The proteasome is therefore a torus structure with a large cavity, and entrance and exit pores at the top and bottom. A dentured protein enters through the top pore, is degraded by the beta subunits into short peptides which exit from the bottom pore. The archaean proteasome is therefore similar to, but a simplified version of, the eukaryote proteasome. The crystal structure of the proteasome from
Thermoplasma acidophylum
was the first to be solved, showing a structure similar to that of N-terminal nucleophile hydrolases , and the beta subunit was found to be the first threonine peptidase .
Small ribosomal subunit protein uS17, bacteria/chloroplast (Ribosomal_uS17_bact/chlr)
Type: Family

This entry represents ribosomal S17 proteins from bacteria and chloroplasts .

The ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA . The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein uS17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence has revealed that uS17 has virtually no groups exposed on the ribosomal surface.
Large ribosomal subunit protein uL23 (Ribosomal_uL23)
Type: Family

This entry represent archaeal and eukaryotic ribosomal uL23 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 .
Protein YloV-like (YloV-like)
Type: Family

This entry represents a protein family of bacterial sequences that includes Protein YloV from Bacillus subtilis and a number of proteins of unknown function. YloV is a metal-dependent endoribonuclease that catalyses the cleavage of single-stranded RNA, preferentially at U residues . Most members of this family that contain an N-terminal DhaL domain (

).
GTP-binding protein, ribosome biogenesis, YsxC (GTP-bd_ribosome_bio_YsxC)
Type: Family

This entry represents a family of GTPases associated with ribosome biogenesis, as typified by YsxC from Bacillus subtilis . This family is widely distributed among bacteria, being found in around eighty percent of currently sequenced bacterial genomes. The proteins are commonly annotated as EngB based on their homology to EngA, one of several other GTPases involved in ribosome biogenesis. Some eukaryotic proteins are included in this entry and probably represent organellar sequences.
GTP-binding protein, riobosome biogenesis, YqeH (GTP-bd_ribosome_bgen_YqeH)
Type: Family

This entry represents the YqeH GTPase family, a subset of a larger family of GTPases involved in ribosome biogenesis . Like YqlF GTPases, these proteins are circularly permuted. This protein family is found in a relatively small number of bacterial species, including Bacillus subtilis but not Escherichia coli.
CRISPR-associated protein Cas8a1/Csx13, Myxan subtype, N-terminal (CRISPR-assoc_Csx13_N)
Type: Domain

Members of the Myxococcus xanthus subtype of the Cas8a1/Csx13 family are found among cas (CRISPR-Associated) genes close to CRISPR repeats in Leptospira interrogans (a spirochete), Myxococcus xanthus (a delta-proteobacterium), and Lyngbya sp. PCC 8106 (a cyanobacterium). They are found with other cas genes in Anabaena variabilis ATCC 29413. In Myxococcus xanthus Cas8a1 is also known as DevT (developmental protein T) where stimulates synthesis of a signal transduction protein required for fruiting body morphogenesis (formation of fruiting bodies within the rod-shaped cells under starvation conditions that differentiate into spherical spores) .

This entry corresponds to the N-terminal domain of the proteins; the C-terminal domain is described by

. In Lyngbya sp., the protein is split into two tandem genes, and this entry corresponds to the upstream gene in these species.
GTP-binding protein, ribosome biogenesis (GTP-bd_ribosome_bgen)
Type: Family

This entry represents a family GTP-binding proteins involved in ribosome biogenesis, typified by the essential Bacillus subtilis protein YlqF . They are related to Era, EngA, and other GTPases involved in ribosome biogenesis, but are circularly permuted. This family is not universal, and is not present in Escherichia coli, so it is not as well studied as some other GTPases.
Mycoides cluster lipoprotein, LppA/p72 (Mycoides_lipoprot_LppA/p72)
Type: Family

Members of this protein family occur in Mycoplasma mycoides, Mycoplasma hyopneumoniae, and related Mycoplasmas in small paralogous families that may also include truncated forms and/or pseudogenes. Members are predicted lipoproteins with a conserved signal peptidase II processing and lipid attachment site . Note that the name for certain characterised members, p72, reflects an anomalous apparent molecular weight, given a theoretical MW of about 61kDa.
RecB family nuclease, TM0106, putative (RecB_nuclease_TM0106_put)
Type: Family

Members of this uncharacterised protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Lipid-A-disaccharide synthase-related protein, putative (Lipid-A-disac_synthase-rel_put)
Type: Family

This entry represents a family of proteins mainly found in cyanobacterial species, in one or two copies. These proteins show some sequence similarity, especially toward the C terminus, to lipid-A-disaccharide synthase (

or

). The function is unknown.
Cellulose biosynthesis, BcsF/YhjT (Cellulose_BcsF/YhjT)
Type: Family

Members of this protein family are found invariably together with genes of bacterial cellulose biosynthesis, and are presumed to be involved in the process . Members average about 63 amino acids in length and are not uncharacterised. The gene has been designated both YhjT and BcsF (bacterial cellulose synthesis F).
Salicylate synthase (Salicylate_synthase)
Type: Family

Members of this protein family are salicylate synthases, bifunctional enzymes that make salicylate, in two steps, from chorismate. Members are homologous to anthranilate synthase component I from Trp biosynthesis. Members typically are found in gene regions associated with siderophore or other secondary metabolite biosynthesis .
Membrane insertase YidC (Membr_insert_YidC)
Type: Family

YidC is required for the insertion of integral membrane proteins into the membrane. It may also be involved in protein secretion processes .
Anthranilate synthase component I-like (Anth_synth_I-like)
Type: Family

This entry represents the anthranilate synthase component 1 protein

and its homologues, including aminodeoxychorismate synthase component 1

, 2-amino-4-deoxychorismate synthase

and isochorismate synthase/isochorismate-pyruvate lyase MbtI

.

Anthranilate synthase component 1 is a tetramer comprising two copies of component I and two copies of component II. Component I catalyses the formation of anthranilate using ammonia rather than glutamine, while component II provides glutamine amidotransferase activity.
Bacteriophage P2, LysB (Phage_P2_LysB)
Type: Family

This entry represents LysB from Bacteriophage P2 , also known as Probable spanin, inner membrane subunit, and similar sequences from taile bacteriophages and proteobacterial prophages.

Members of this protein family are Rz-like phage lysis system spanin subunits of the inner membrane (i-spanin). Similar systems, with components also termed Rz for the i-spanin and Rz1 for the o-spanin, are found in lambda-like and in T7-like phage, and share the property that the gene for the o-spanin is fully embedded or heavily overlapped by the gene for the i-spanin. The gene for this Rz-like phage lysis system protein may overlap extensively with the gene for the other spanin subunit, the Rz1-like protein in the outer membrane .
ATPase, alpha/beta subunit, nucleotide-binding domain, active site (ATPase_a/bsu_AS)
Type: Active_site

This entry represents a 10 amino acid region that is essential for catalysis. The signature pattern contains two highly conserved serines. The first serine seems to be important for catalysis - in the ATPase alpha-chain at least - as its mutagenesis causes catalytic impairment.

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

This group of proteins include the alpha and beta subunits found in the F1, V1, and A1 complexes of F-, V- and A-ATPases, respectively (sometimes called the A and B subunits in V- and A-ATPases), as well as Type 3 secretion system ATPase and Flagellum-specific ATP synthase.
Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (UDP-GlcNAc_Epase)
Type: Family

This entry represents a protein that catalyzes the combined epimerization and UDP-hydrolysis of UDP-N-acetylglucosamine to N-acetylmannosamine . This is in contrast to the related enzyme WecB (

) which retains the UDP moiety. NeuC acts in concert with NeuA and NeuB to synthesize CMP-N5-acetyl-neuraminate.

NeuC folds into two Rossmann-like domains and forms dimers and tetramers as does the epimerase part of the bifunctional UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE) that is also member of this family .
Flagellar export ATPase FliI, clade 1 (FliI_clade1)
Type: Family

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis . The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Flagellar biosynthesis protein FlhF (FlhF)
Type: Family

This entry represents the flagellar biosynthetic protein FlhF. The assembly of flagella is a multi-step process and relies on a complex type III export machinery located in the cytoplasmic membrane. The FlhF protein is essential for the placement and assembly of polar flagella and has been classified as a signal-recognition particle (SRP)-type GTPase . It is similar to the 54 kd subunit (SRP54) of the SRP that mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes . SRP recognises N-terminal signal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognate receptor (SR). FlhF activities and the net effect of FlhF on flagellation phenotypes appear to be different among polar flagellates .
NeuB/NeuA acid synthase (NeuB/NeuA)
Type: Family

This entry represents NeuB and NeuA enzymes. The majority of the proteins identified in this entry are observed adjacent to both the NeuA and NeuC genes which together effect the biosynthesis of CMP-N-acetylneuraminate from UDP-N-acetylglucosamine.

NeuB is the prokaryotic N-acetylneuraminic acid synthase. It catalyses the direct formation of N-acetylneuraminic acid (Neu5Ac), the most common sialic acid, by condensation of phosphoenolpyruvate (PEP) and N-acetylmannosamine (ManNAc). Mammals synthesise the 9-phosphate form, Neu5Ac-9-P, and utilise ManNAc-6-P instead of ManNAc . The bacterial and mammalian enzymes share 30%-40% sequence identity and are composed of two distinct domains. The N-terminal domain (NeuB domain,

) consists of ~250 amino acid residues, and is considered to bind the sugar substrates. The C-terminal domain consists of ~75 amino acid residues, and is called the antifreeze-like (AFL) domain, since it is similar to those observed in a variety of functional type III antifreeze proteins (AFPs) .
GlyGly-CTERM domain (GlyGly_CTERM)
Type: Domain

This homology domain, GlyGly-CTERM, shares a species distribution with rhombosortase (

), a subfamily of rhomboid-like intramembrane serine proteases . It is probably a recognition sequence for protein sorting and then cleavage by rhombosortase. Shewanella species have the largest number of target proteins per genome, up to thirteen. The domain occurs at the extreme carboxyl-terminus of a diverse set of proteins, most of which are enzymes with conventional signal sequences and with hydrolytic activities: nucleases, proteases, agarases, etc. The agarase AgaA from Vibro sp. strain JT0107 is secreted into the medium, while the same protein heterologously expressed in E. coli is retained in the cell fraction . This suggests cleavage and release in species with this domain. Both this suggestion, and the chemical structure of the domain (motif, hydrophobic predicted transmembrane helix, cluster of basic residues) closely parallels that of the LPXTG/sortase system and the PEP-CTERM/exosortase(EpsH) system. For this reason, the putative processing enzyme is designated rhombosortase.
VolA/Pla-1/cef phospholipase (VolA/Pla-1/cef)
Type: Family

This entry represents a family of extracellular lipoproteins mainly from gammaproteobacteria, including Lysophospholipase VolA from Vibrio cholerae, lipase Pla-1 from Aeromonas hydrophila , and CHO cell elongation factor (cef) from Vibrio hollisae . VolA (for Vibrio outer membrane lysophospholipase A) functions as a lipase that cleaves exogenous lysophosphatidylcholine (LPC) and generates free fatty acids, which are then transported into the cell by fatty acid transporters such as FadL, and used in various metabolic pathways .
Conserved hypothetical protein CHP03503 (CHP03503)
Type: Family

This set of conserved hypothetical protein has a phylogenetic range that closely matches that of

, and has a putative C-terminal protein targeting signal.
FimV, C-terminal domain (FimV_C)
Type: Domain

This domain is found at the C-terminal in FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis .

FimV is an inner membrane protein that plays a role in twitching motility, type IV pilus assembly, and type II secretion in bacteria like Pseudomonas aeruginosa. Disruption of FimV blocks twitching motility from type IV pili, which suggests a role in peptidoglycan layer remodelling required by type IV fimbrial systems . The C-terminal of FimV proteins is represented by

. In between is a highly variable, often repeat-filled region rich in the negatively charged amino acids Asp and Glu.
FimV, LysM domain (LysM_FimV)
Type: Domain

This entry represents the LysM domain in FimV from Pseudomonas aeruginosa, TspA of Neisseria meningitidis, and related proteins .

FimV is an inner membrane protein that plays a role in twitching motility, type IV pilus assembly, and type II secretion in bacteria like Pseudomonas aeruginosa. Disruption of FimV blocks twitching motility from type IV pili, which suggests a role in peptidoglycan layer remodelling required by type IV fimbrial systems . The C-terminal of FimV proteins is represented by

. In between is a highly variable, often repeat-filled region rich in the negatively charged amino acids Asp and Glu.
Flagellar hook-basal body protein, FlgE/F/G (Flagellar_FlgE/F/G)
Type: Family

This entry represents three closely related flagellar proteins usually denoted FlgE, FlgF and FlgG. The names have often been mis-assigned, however. Three models,

,

and

, separate the individual forms into three genome-context consistent groups. The major differences between these genes are architectural, with variable central sections between relatively conserved N- and C-terminal domains. More distantly related are two other flagellar apparatus familis, FlgC (

) which consists of little else but the N- and C-terminal domains and FlgK (

) with a substantial but different central domain.