SII-SWORD/CoKE huggingface dataset:
Photosystem II D2 (PSII_PsbD/D2)
Type: Family

This family represents the D2 protein (PsbD), which forms the reaction core of PSII as a heterodimer with the D1 protein. The accumulation of D2 protein appears to be a key step in the assembly of the PSII reaction centre complex . In higher plants, the N-terminal residues of both proteins, which are exposed to the stromal surface, can be reversibly phosphorylated. The D1/D2 core binds to a number of cofactors, including: a 4-atom manganese cluster, which is located on the lumenal surface of the D1 and D2 proteins ; two pheophytin molecules, only one of which is phytochemically active; non-haem iron; and two quinones, Qa (bound to D2) and Qb (bound to D1). Upon light excitation, an electron is transferred from the primary donor (chlorophyll a) via intermediate acceptor pheophytin to the primary quinone Qa, then to the secondary quinone Qb. At the oxidising side of PSII, a redox-active residue in the D1 protein reduces P680, the oxidised tyrosine then withdrawing electrons from a manganese cluster, which in turn withdraw electrons from water, leading to the splitting of water and the formation of molecular oxygen. PSII thus provides a source of electrons that can be used by photosystem I to produce the reducing power (NADPH) required to convert CO2 to glucose.

Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product .

PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane . Within the core of the complex, the chlorophyll and β-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection .
Photosystem II CP43 reaction centre protein (PSII_PsbC)
Type: Family

This family represents the intrinsic antenna protein CP43 (PsbC), which is one of two such proteins found in the reaction centre of PSII, both of which can bind to chlorophyll 'a' and beta-carotene, passing the excitation energy on to the reaction centre .

Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product .

PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane . Within the core of the complex, the chlorophyll and β-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection .
Cytochrome b6/f complex, subunit IV (Cyt_b6/f_cplx_suIV)
Type: Family

This entry describes subunit IV of the cytochrome b6/f complex. The cyt b6/f complex is central to the functions of oxygenic photosynthetic electron transport in cyanobacteria and its equivalents in algae and higher plants, mediating electron transfer between photosystem II (PSII) and photosystem I (PSI) reaction centre complexes. The cyt b6f complex consists of a cytochrome b core, in addition to cytochrome f, Rieske 2Fe-2S, and subunits IV, V, VI, VII. The complex has a central quinone exchange cavity, which is defined by two monomers that resemble the respiratory cytochrome bc1 complex . Cyt b6f has three prosthetic groups not found in cytbc1: chlorophyll-a, beta-carotene and a structurally unique covalently bound haem. The haem is thought to function in cyclic electron transport via anionic ferredoxin. Each monomer of the complex contains a molecule of chlorophyll-a and beta-carotene. Subunit IV is one of the principal subunits for the binding of the redox prosthetic groups.
Photosynthetic reaction centre, L subunit (Photo_RC_L)
Type: Family

This entry describes the photosynthetic reaction centre L subunit.

The photosynthetic apparatus in non-oxygenic bacteria consists of light-harvesting (LH) protein-pigment complexes LH1 and LH2, which use carotenoid and bacteriochlorophyll as primary donors . LH1 acts as the energy collection hub, temporarily storing it before its transfer to the photosynthetic reaction centre (RC) . Electrons are transferred from the primary donor via an intermediate acceptor (bacteriopheophytin) to the primary acceptor (quinine Qa), and finally to the secondary acceptor (quinone Qb), resulting in the formation of ubiquinol QbH2. RC uses the excitation energy to shuffle electrons across the membrane, transferring them via ubiquinol to the cytochrome bc1 complex in order to establish a proton gradient across the membrane, which is used by ATP synthetase to form ATP .

The core complex is anchored in the cell membrane, consisting of one unit of RC surrounded by LH1; in some species there may be additional subunits . RC consists of three subunits: L (light), M (medium), and H (heavy). Subunits L and M provide the scaffolding for the chromophore, while subunit H contains a cytoplasmic domain . In Rhodopseudomonas viridis, there is also a non-membranous tetrahaem cytochrome (4Hcyt) subunit on the periplasmic surface.
Archaeal/bacterial translation initiation factor SUI1 (SUI1_arc_bac)
Type: Family

This family of archaeal and bacterial proteins is homologous to the eukaryotic translation intiation factor SUI1 involved in directing the ribosome to the proper start site of translation by functioning in concert with eIF-2 and the initiator tRNA-Met. The function of non-eukaryotic family members is unclear. Escherichia coli YciH is a non-essential protein and was reported to be able to perform some of the functions of IF3 in prokaryotic initiation .
DENR, eukaryotes (DENR_eukaryotes)
Type: Family

This entry includes translation machinery-associated protein 22 (Tma22) from yeasts and density-regulated protein (DENR) from animals. DENR may be involved in the translation of target mRNAs by scanning and recognition of the initiation codon . DENR and MCT-1 form a heterodimer, which binds to the ribosome and is involved in unconventional translation initiation, reinitiation, and recycling .
Eukaryotic translation initiation factor SUI1 (SUI1_euk)
Type: Family

SUI1/eIF1 (eukaryotic initiation factor 1) plays an important role in accurate initiator codon recognition during translation initiation. eIF1 interacts with 18S rRNA in the 40S ribosomal subunit during eukaryotic translation initiation. Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown .

Cells have evolved elaborate mechanisms to rid themselves of aberrant proteins and transcripts. The nonsense-mediated mRNA decay pathway (NMD) is an example of a pathway that eliminates aberrant mRNAs. In addition to its role in recognition of the AUG codon during translation initiation and maintenance of the appropriate reading frame during translation elongation by directing the ribosome to the proper start site of translation by functioning in concert with eIF-2 and the initiator tRNA-Met, the SUI1 protein plays a role in the NMD pathway .
Phosphoribosylaminoimidazole carboxylase, ATPase subunit (PurK)
Type: Domain

Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This entry includes PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, which catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP.
YSIRK Gram-positive signal peptide (YSIRK_signal_dom)
Type: Domain

Many surface proteins found in Streptococcus, Staphylococcus, and related lineages share apparently homologous signal sequences. A motif resembling [YF]SIRKxxxGxxS[VIA] appears at the start of the transmembrane domain. The GxxS motif appears perfectly conserved, suggesting a specific function and not just homology.
Large ribosomal subunit protein uL1, bacterial-type (Ribosom_uL1_bac-type)
Type: Family

Ribosomal protein uL1 is the largest protein from the large ribosomal subunit. In Escherichia coli, uL1 is known to bind to the 23S rRNA. This model describe s bacterial and chloroplast ribosomal protein uL1. Most mitochondrial uL1 sequences are sufficiently divergent to be the contained in a different entry (

).

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 uL1, mitochondrial (Ribosomal_uL1_mit)
Type: Family

Ribosomal protein uL1 is the largest protein from the large ribosomal subunit. In Escherichia coli, uL1 is known to bind to the 23S rRNA. This model describes the mitochondrial uL1 protein.

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 uL2, bacterial/organellar-type (Ribosomal_uL2_bac/org-type)
Type: Family

The protein uL2 is found in all ribosomes and is one of the best conserved proteins of this mega-dalton complex. uL2 is elongated, exposing one end of the protein to the surface of the intersubunit interface of the 50 S subunit and is essential for the association of the ribosomal subunits and might participate in the binding and translocation of the tRNAs . This entry represents bacterial, chloroplast and mitochondrial forms.

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 .
Serine O-acetyltransferase (Ser_O-AcTrfase)
Type: Family

The biosynthesis of L-cysteine is the predominant way by which inorganic sulphur is incorporated into organic compounds. In this process, the most abundant utilizable source of sulphur, inorganic sulphate, is taken up and reduced to sulphide. Sulphide is used to produce L-cysteine, which serves for protein synthesis or the production of other sulphur-containing organic compounds. Two routes for cysteine biosynthesis in nature have been documented. Serine transacetylase (also known as serine O-acetyltransferase;

) catalyzes steps in pathway I, the activation of L-serine by acetyl-coenzyme A, yielding O-acetyl-L-serine.
Bifunctional protein GlmU (Bifunctional_GlmU)
Type: Family

N-Acetylglucosamine-1-PO(4) uridyltransferase (GlmU,

) is a trimeric bifunctional enzyme that catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-GlcNAc.

The X-ray crystal structure of Escherichia coli GlmU in complex with UDP-GlcNAc and CoA has been determined to 2.1 A resolution and reveals a two-domain architecture that is responsible for these two reactions . The C-terminal domain is responsible for the CoA-dependent acetylation of Glc-1-PO(4) to GlcNAc-1-PO(4) and displays the longest left-handed parallel β-helix (LbetaH or LbH) observed to date. The acetyltransferase active site defined by the binding site for CoA makes use of residues from all three subunits and is positioned beneath an open cavity large enough to accommodate the Glc-1-PO(4) acetyl acceptor. The N-terminal domain catalyzes uridyl transfer from UTP to GlcNAc-1-PO(4) to form the final products UDP-GlcNAc and pyrophosphate. This domain is composed of a central seven-stranded β-sheet surrounded by six α-helices in a Rossmann fold-like topology.
Type IV pilus inner membrane component PilM (PilM)
Type: Family

Bacterial type IV pili are surface filaments critical for diverse biological processes including surface and host cell adhesion, colonisation, biofilm formation, twitching motility, DNA uptake during natural transformation and virulence . The proteins necessary to form the type IV pili inner-membrane complex, are included in the pilMNOPQ operon which encodes the cytoplasmic actin-like protein PilM, PilN, PilO, the periplasmic lipoprotein PilP and the outer-membrane secretin PilQ. The inner-membrane PilM/N/O/P complex is required for the optimal function of the outer-membrane secretin PilQ. This cluster is highly conserved across the type IV pilus-producing bacterial species, and all of these proteins have been shown to be essential for twitching motility .

The type IV pilus inner membrane component PilM is required for competency and pilus biogenesis . PilM associates with PilNO heterodimers by binding the conserved cytoplasmic N terminus of PilN. Binding to PilN induce conformational changes that allow PilM to bind its own N-terminal and form dimers. It also binds ATP, which facilitates PilN interaction . This protein is required for the assembly of the type IV fimbria in P. aeruginosa and for a similar pilus-like structure in Synechocystis. It is also found in species such as Deinococcus described as having natural transformation (for which a type IV pilus-like structure is proposed) but not fimbria.

This entry also includes Competence protein A from Haemophilus influenzae in which this cluster is annotated as comA/B/C/D/E.
Fumarate reductase, flavoprotein subunit (Fum_red_fp)
Type: Family

In bacteria two distinct, membrane-bound, enzyme complexes are responsible for the interconversion of fumarate and succinate (

): fumaratereductase (Frd) is used in anaerobic growth, and succinate dehydrogenase (Sdh) is used in aerobic growth. Both complexes consist of two main components: a membrane-extrinsic component composed of a FAD-binding flavoprotein and an iron-sulphur protein; and an hydrophobic component composed of a membrane anchor protein and/or a cytochrome B.

In eukaryotes mitochondrial succinate dehydrogenase (ubiquinone) (

) is an enzyme composed of two subunits: a FAD flavoprotein and and iron-sulphur protein.

The flavoprotein subunit is a protein of about 60 to 70 Kd to which FAD is covalently bound to a histidine residue which is located in the N-terminal section of the protein . The sequence around that histidine is well conserved in Frd and Sdh from various bacterial and eukaryotic species .

The terms succinate dehydrogenase and fumarate reductase may be used interchangeably in certain systems. However, a number of species have distinct complexes, with the fumarate reductase active under anaerobic conditions. This model represents the fumarate reductase flavoprotein subunit from several such species in which a distinct succinate dehydrogenase is also found.
tRNA guanine(10)-N2-dimethyltransferase (TrmG10)
Type: Family

TrmG10 (tRNA (guanine(10)-N2)-dimethyltransferase or tRNA:G10 dimethyltransferase) catalyses the adenosylmethionine-dependent methylation of the exocyclic amino group (N(2)) of guanosine located at position 10. This enzyme is found in eukaryotes and archaea, but never in bacteria. It consists of a S-adenosylmethionine-dependent methyltransferase domain in the C terminus and a predicted RNA-binding THUMP (thiouridine synthases, RNA methyltransferases, and pseudouridine synthases) domain in the N terminus . This entry represents the archaeal TrmG10.
UDP-glucose 4-epimerase (UDP_G4E)
Type: Family

UDP-glucose 4-epimerase (

, also known as UDP-galactose 4-epimerase) interconverts UDP-glucose and UDP-galactose which are precursors of glucose-and galactose-containing exopolysaccharides (EPS) . Arabidopsis thaliana has five genes encoding functional UDP-D-glucose/UDP-D-galactose 4-epimerase .

A set of related proteins, some of which are tentatively identified as UDP-glucose-4-epimerase in Thermotoga maritima, Bacillus halodurans, and several archaea, but deeply branched from this set and lacking experimental evidence, are not included in this family.
Glycosyl hydrolase family 92, alpha-1,2-mannosidase, putative (GH92_a_mannosidase_put)
Type: Family

This entry represents a group of glycosyl hydrolases (glycosidases) from bacteria and fungi, including members characterised as mannosidases with various fine specificities . Most members of this family appear to have signal sequences and may, like the Microbacterium sp. M-90 protein, be secreted.