SII-SWORD/CoKE huggingface dataset:
DNA polymerase III, beta sliding clamp, central (DNA_polIII_beta_cen)
Type: Domain

DNA polymerase III is a complex, multichain holoenzyme responsible for most of the replicative synthesis in bacteria . It functions by adding nucleotide triphosphate (dNTP) residues to the 5'-end of a growing DNA chain, using a complementary DNA as template. The elongation factor beta-clamp, also called beta subunit, is part of the DNA polymerase III holoenzyme. However, beta-clamp is not attached to polymerase III permanently like the other subunits. It is loaded on the DNA, by clamp loader, a subunit of DNA Pol III .

The beta clamp forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The bacterial beta clamp is a homodimer; each monomer consists of three globular domains to yield a six-domain ring . It is structurally similar to the trimeric ring formed by proliferating cell nuclear antigen (PCNA) (found in eukaryotes and archaea) and the processivity factor (found in bacteriophages T4 and RB69) . This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds.

This entry describes the central domain of the beta sliding clamp.
Cysteine and tyrosine-rich protein 1 (CYYR1)
Type: Family

Members in this family of proteins are annotated as cysteine and tyrosine-rich protein 1, however currently no function is known .
Chemotaxis receptor methyltransferase CheR, N-terminal (CheR_N)
Type: Domain

CheR proteins are part of the chemotaxis signaling mechanism in bacteria. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains . Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase , which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues .

The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A . The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal α/β domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel β-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region .

This entry represents the N-terminal domain of CheR.
Orn/DAP/Arg decarboxylase 2, C-terminal (De-COase2_C)
Type: Domain

These enzymes are collectively known as group IV decarboxylases . Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities . Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC , to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate-binding region .

This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.
Orn/DAP/Arg decarboxylase 2, N-terminal (De-COase2_N)
Type: Domain

These enzymes are collectively known as group IV decarboxylases . Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities . Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC , to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate-binding region .
Protein-export membrane protein SecD/SecF, bacterial (SecD/SecF_bac)
Type: Family

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.

This entry represents bacterial SecD and SecF protein export membrane proteins. 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 .
Protein-export membrane protein SecD/SecF/SecDF, conserved site (SecD/SecF_CS)
Type: Conserved_site

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.

This entry represents a GG-containing domain found in the N-terminal region of prokaryotic SecD and SecF protein export membrane proteins. 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 .
Recombinase Flp protein, N-terminal (Recombinase_Flp_N)
Type: Domain

This entry describes the N-terminal domain of recombinase Flp protein from fungi. Flp proteins catalyse recombination between large inverted repetitions of the plasmid.
Proliferating cell nuclear antigen, PCNA, N-terminal (Pr_cel_nuc_antig_N)
Type: Domain

Proliferating cell nuclear antigen (PCNA), or cyclin, is a non-histone acidic nuclear protein that plays a key role in the control of eukaryotic DNA replication . It acts as a co-factor for DNA polymerase delta, which is responsible for leading strand DNA
replication . The sequence of PCNA is well conserved between plants and animals, indicating a strong selective pressure for structure conservation, and suggesting that this type of DNA replication mechanism is conserved throughout eukaryotes . In Saccharomyces cerevisiae (Baker's yeast), POL30, is associated with polymerase III, the yeast analog of polymerase delta.

Homologues of PCNA have also been identified in the archaea (known as DNA polymerase sliding clamp) and in Paramecium bursaria Chlorella virus 1 (PBCV-1) and in nuclear polyhedrosis viruses.

The N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA .
Proliferating cell nuclear antigen, PCNA, C-terminal (Pr_cel_nuc_antig_C)
Type: Domain

Proliferating cell nuclear antigen (PCNA), or cyclin, is a non-histone acidic nuclear protein that plays a key role in the control of eukaryotic DNA replication . It acts as a co-factor for DNA polymerase delta, which is responsible for leading strand DNA
replication . The sequence of PCNA is well conserved between plants and animals, indicating a strong selective pressure for structure conservation, and suggesting that this type of DNA replication mechanism is conserved throughout eukaryotes . In Saccharomyces cerevisiae (Baker's yeast), POL30, is associated with polymerase III, the yeast analog of polymerase delta.

Homologues of PCNA have also been identified in the archaea (known as DNA polymerase sliding clamp) and in Paramecium bursaria Chlorella virus 1 (PBCV-1) and in nuclear polyhedrosis viruses.

The N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA .
S-layer protein, central domain (S_layer_central)
Type: Domain

This entry represents the central domain of archaeal S-layer proteins. Members of this family are found in (for example) Pyrococcus horikoshii (split into two tandem reading frames), Methanocaldococcus jannaschii (Methanococcus jannaschii), and related species. Some local similarity can be found to other S-layer protein families. This domain is found inserted in the outer domain (

).
S-layer protein, outer domain (S_layer_C)
Type: Domain

This entry represents the outer domain of archaeal S-layer proteins. Members of this family are found in (for example) Pyrococcus horikoshii (split into two tandem reading frames), Methanocaldococcus jannaschii (Methanococcus jannaschii), and related species. Some local similarity can be found to other S-layer protein families. This domain has the central domain (

) inserted.
Zinc finger, XPA-type, conserved site (Znf_XPA_CS)
Type: Conserved_site

Xeroderma pigmentosum (XP) is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30kDa nuclear protein called XPA (or XPAC) . The sequence of the XPA protein is conserved from higher eukaryotes to yeast (gene RAD14) . XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section.

This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to (

)
Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site (De-COase2_pyr-phos_BS)
Type: Binding_site

These enzymes are collectively known as group IV decarboxylases . Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities . Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. This site contains a conserved lysine residue which is known, in mouse ODC , to be the site of attachment of the pyridoxal-phosphate group.
Domain of unknown function DUF1553 (DUF1553)
Type: Domain

The function of this domain is not known. It is found associated with

. It is also found associated with the Planctomycete cytochrome C domain

.
XPA, C-terminal (XPA_C)
Type: Domain

Xeroderma pigmentosum (XP) is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30kDa nuclear protein called XPA (or XPAC) . The sequence of the XPA protein is conserved from higher eukaryotes to yeast (gene RAD14) . XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section.

This entry represents the uncharacterised C-terminal domain of the XPA protein.
Orn/DAP/Arg decarboxylase 2, conserved site (De-COase2_CS)
Type: Conserved_site

These enzymes are collectively known as group IV decarboxylases . Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities . Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. This conserved site contains a stretch of three consecutive glycine residues and has been proposed to be part of a substrate-binding region .
XPA, conserved site (XPA_CS)
Type: Conserved_site

Xeroderma pigmentosum (XP) is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30kDa nuclear protein called XPA (or XPAC) . The sequence of the XPA protein is conserved from higher eukaryotes to yeast (gene RAD14) . XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section.

This entry corresponds to the second conserved site in the XPA protein. It is a highly conserved region located some 12 residues after the zinc finger regio
Proliferating cell nuclear antigen, PCNA, conserved site (Pr_cel_nuc_antig_CS)
Type: Conserved_site

Proliferating cell nuclear antigen (PCNA), or cyclin, is a non-histone acidic nuclear protein that plays a key role in the control of eukaryotic DNA replication . It acts as a co-factor for DNA polymerase delta, which is responsible for leading strand DNA
replication . The sequence of PCNA is well conserved between plants and animals, indicating a strong selective pressure for structure conservation, and suggesting that this type of DNA replication mechanism is conserved throughout eukaryotes . In Saccharomyces cerevisiae (Baker's yeast), POL30, is associated with polymerase III, the yeast analog of polymerase delta.

Homologues of PCNA have also been identified in the archaea (known as DNA polymerase sliding clamp) and in Paramecium bursaria Chlorella virus 1 (PBCV-1) and in nuclear polyhedrosis viruses.

This entry represents two conserved regions located in the N-terminal section. The second one has been proposed to bind DNA.
Domain of unknown function DUF1581 (DUF1581)
Type: Domain

Several Rhodopirellula baltica proteins share this domain. They also match (

).
Methylaspartate ammonia-lyase, C-terminal (MeAsp_NH4-lyase_C)
Type: Domain

Methylaspartate ammonia-lyase

catalyses the second step of fermentation of glutamate. It is a homodimer. This domain represents the C-terminal region of methylaspartate ammonia-lyase and contains a TIM barrel fold similar to the

. This domain represents the catalytic domain and contains a metal binding site .
Dihydrodipicolinate reductase, C-terminal (DapB_C)
Type: Domain

This entry represents the C-terminal region of Dihydrodipicolinate reductase.

Dihydrodipicolinate reductase catalyzes the second step in the biosynthesis of diaminopimelic acid and lysine, the NAD or NADP-dependent reduction of 2,3-dihydrodipicolinate into 2,3,4,5-tetrahydrodipicolinate .

In Escherichia coli and Mycobacterium tuberculosis, dihydrodipicolinate reductase has equal specificity for NADH and NADPH, however in Thermotoga maritima there it has a greater affinity for NADPH . In addition, the enzyme is inhibited by high concentrations of its substrate, which consequently acts as a feedback control on the lysine biosynthesis pathway. In T. maritima, the enzyme also lacks N-terminal and C-terminal loops which are present in enzyme of the former two organisms.
Dihydrodipicolinate reductase, conserved site (DapB_N_CS)
Type: Conserved_site

Dihydrodipicolinate reductase catalyzes the second step in the biosynthesis of diaminopimelic acid and lysine, the NAD or NADP-dependent reduction of 2,3-dihydrodipicolinate into 2,3,4,5-tetrahydrodipicolinate .

In Escherichia coli and Mycobacterium tuberculosis, dihydrodipicolinate reductase has equal specificity for NADH and NADPH, however in Thermotoga maritima there it has a greater affinity for NADPH . In addition, the enzyme is inhibited by high concentrations of its substrate, which consequently acts as a feedback control on the lysine biosynthesis pathway. In T. maritima, the enzyme also lacks N-terminal and C-terminal loops which are present in enzyme of the former two organisms.

This entry represents a conserved site in the central region of the protein which is found in the substrate binding region.
Methylaspartate ammonia-lyase, N-terminal (MeAsp_NH4-lyase_N)
Type: Domain

Methylaspartate ammonia-lyase

catalyses the second step of fermentation of glutamate. It is a homodimer. This domain represents the N-terminal region of methylaspartate ammonia-lyase. This domain is structurally related to

. This domain is associated with the catalytic domain

.
Large ribosomal subunit protein uL2, RNA-binding domain (Ribosomal_uL2_RNA-bd_dom)
Type: Domain

This entry represents the N-terminal RNA-binding domain of the large ribosomal subunit protein uL2.

Ribosomal protein uL2 is one of the proteins from the large ribosomal subunit. The best conserved region is located in the C-terminal section of these proteins. In Escherichia coli, uL2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities , groups:

Eubacterial uL2 (old name L2).

Algal and plant chloroplast uL2 (old name L2).

Cyanelle uL2 (old name L2).

Archaebacterial uL2 (old name L2).

Plant uL2 (old name L2).

Slime mold uL2 (old name L2).

Marchantia polymorpha mitochondrial uL2m (old name L2).

Paramecium tetraurelia mitochondrial uL2m (old name L2).

Fission yeast K5, K37 and KD4.

Yeast YL6.

Vertebrate uL2 (old name L8).

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 .
Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr, N-terminal (ForMFR_H4MPT_ForTrfase_N)
Type: Domain

Formylmethanofuran:tetrahyromethanopterin formyltransferase (Ftr) is involved in C1 metabolism in methanogenic archaea, sulphate-reducing archaea and methylotrophic bacteria. It catalyses the following reversible reaction:

N-formylmethanofuran + 5,6,7,8-tetrahydromethanopterin = methanofuran + 5-formyl-5,6,7,8-tetrahydromethanopterin

Ftr from the thermophilic methanogen Methanopyrus kandleri (optimum growth temperature 98 degrees C) is a hyperthermophilic enzyme that is absolutely dependent on the presence of lyotropic salts for activity and thermostability. The crystal structure of Ftr, determined to a reveals a homotetramer composed essentially of two dimers. Each subunit is subdivided into two tightly associated lobes both consisting of a predominantly antiparallel β sheet flanked by α helices forming an α/β sandwich structure. The approximate location of the active site was detected in a region close to the dimer interface . Ftr from the mesophilic methanogen Methanosarcina barkeri and the sulphate-reducing archaeon Archaeoglobus fulgidus have a similar structure .

In the methylotrophic bacterium Methylobacterium extorquens, Ftr interacts with three other polypeptides to form an Ftr/cyclohydrolase complex which catalyses the hydrolysis of formyl-tetrahydromethanopterin to formate during growth on C1 substrates .

This entry represents the ferredoxin-like Ftr N-terminal domain.