SII-SWORD/CoKE huggingface dataset:
Photosystem II PsbJ (PSII_PsbJ)
Type: Family

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 .

This entry represents the low molecular weight transmembrane protein PsbJ found in PSII. PsbJ is one of the most hydrophobic proteins in the thylakoid membrane, and is located in a gene cluster with PsbE, PsbF and PsbL (PsbEFJL). Both PsbJ and PsbL (

) are essential for proper assembly of the OEC. Mutations in PsbJ cause the light-harvesting antenna to remain detached from the PSII dimers . In addition, both PsbJ and PsbL are involved in the unidirectional flow of electrons, where PsbJ regulates the forward electron flow from D2 (Qa) to the plastoquinone pool, and PsbL prevents the reduction of PSII by back electron flow from plastoquinol protecting PSII from photo-inactivation .
PsbP, C-terminal (PsbP_C)
Type: Domain

In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants .

This entry represents the C-terminal domain found in PSII OEC protein PsbP. Both PsbP and PsbQ (

) are regulators that are necessary for the biogenesis of optically active PSII. PsbP increases the affinity of the water oxidation site for chloride ions and provides the conditions required for high affinity binding of calcium ions . The crystal structure of PsbP from Nicotiana tabacum (Common tobacco) revealed a two-domain structure, where domain 1 may play a role in the ion retention activity in PSII, the N-terminal residues being essential for calcium and chloride ion retention activity . PsbP is encoded in the nuclear genome in plants.

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 .

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 .
Biotin synthase/Biotin biosynthesis bifunctional protein BioAB (Biotin_synth/BioAB)
Type: Family

This family consists of biotin synthase B-like and bifunctional biotin synthase AB proteins.

Biotin synthase

works with flavodoxin, S-adenosylmethionine, and possibly cysteine to catalyze the last step of the biotin biosynthetic pathway. The reaction consists of the introduction of a sulphur atom into dethiobiotin, thus requiring activation of C-H bonds . Biotin (vitamin H) is a prosthetic group in enzymes catalysing carboxylation and transcarboxylation reactions .

Biotin synthase from Escherichia coli is a homodimer of 76kDa, with each polypeptide chain carrying an oxygen-sensitive (4Fe-4S) cluster, probably ligated by three cysteines of a CXXXCXXC box conserved among all known BioB sequences and a fourth still not identified ligand. BioB displays a pyridoxal phosphate-dependent cysteine desulphurase activity, which allows mobilisation of the sulphur atom from free cysteine .
Glycosyl transferase, family 15 (Glyco_trans_15)
Type: Family

This entry represents a family of fungi mannosyl-transferases involved in N-linked and O-linked glycosylation of proteins. They belong to the glycosyltransferase family 15 (

). Some of the enzymes in this family have been shown to be involved in O- and N-linked glycan modifications in the Golgi .

The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates ([ec:2.4.1.-]) and related proteins into distinct sequence based families has been described . This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'.
Transposase IS200-like (Transposase_17)
Type: Domain

Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This entry represents a domain found in transposases for IS200 from Escherichia coli .
Nop domain (Nop_dom)
Type: Domain

This entry represents the Nop domain.

The Nop domain is present in various pre-RNA processing ribonucleoproteins (RNP):

Eukaryotic Prp31, part of a tri-snRNP complex. It is involved in pre-mRNA splicing.

Eukaryotic Nucleolar proteins 56 and 58 (Nop56 and Nop58), components of box C/D small nucleolar ribonucleoprotein (snoRNP) particles.

Archaeal Nop5, an homologue of Nop56/Nop58.

The Nop domain is a RNP binding module, exhibiting RNA and protein binding surfaces. It is oval-shaped and exclusively α-helical .

U4/U6 small nuclear ribonucleoprotein Prp31 (PRPF31) is involved in pre-mRNA splicing as component of the spliceosome . This protein is required for the assembly of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome . It is associated with a progressive pigmentary retinopathy characterised by night vision blindness and loss of midperipheral visual field .

Nucleolar protein 56 and 58 (NOP56/58) are required for 60S ribosomal subunit synthesis . They are core components of box C/D small nucleolar ribonucleoprotein (snoRNP) particles . In humans, NOP56 is associated with a type of slowly progressive neurodegenerative disorder characterised by late-onset ataxia followed by variable involvement of the motor neuron system .
Herpesvirus capsid protein 2 (Herpes_capsid_2)
Type: Family

This family consist of various capsid proteins from members of the Herpesviridae. The capsid protein 2 (formerly known as VP23) in Human herpesvirus 1 (HHV-1) (Human herpes simplex virus 1) forms a triplex together with VP19C these fit between and link together adjacent capsomers as formed by VP5 and VP26 . VP3 along with the scaffolding proteins helps to form normal capsids by defining the curvature of the shell and size of the particle .
Penicillin/GL-7-ACA/AHL/aculeacin-A acylase (S45)
Type: Family

This entry represents a number of acylases which all belong to MEROPS peptidase family S45 (clan PB).

Penicillin G acylase precursor and cephalosporin acylase precursor, more precisely termed glutaryl-7-aminocephalosporanic acid (GL-7-ACA) acylase, are self-cleaving proteins that spontaneously form the heterodimeric subunits of the mature acylases. They are not known to hydrolyse peptide bonds in other substrates, although they may have the capacity to do so.

This family also includes acyl-homoserine lactone (AHL) acylase PvdQ and QuiP, and aculeacin-A acylase, which has been shown to have penicillin acylase activity .
Paramyxovirinae P phosphoprotein C-terminal domain (Paramyxo_PProtein_C)
Type: Domain

The subfamily Paramyxovirinae of the family Paramyxoviridae now contains as main genera the Rubulaviruses, avulaviruses, respiroviruses, Henipavirus-es and morbilliviruses. Protein P is the best characterised, structurally of the replicative complex of N, P and L proteins and consists of two functionally distinct moieties, an N-terminal PNT, and a C-terminal PCT . The P protein is an essential part of the viral RNA polymerase complex formed from the P and L proteins . P protein plays a crucial role in the enzyme by positioning L onto the N/RNA template through an interaction with the C-terminal domain of N. Without P, L is not functional.The C-terminal part of P (PCT) is only functional as an oligomer and forms with L the polymerase complex. PNT is poorly conserved and unstructured in solution while PCT contains the oligomerisation domain (PMD) that folds as a homotetrameric coiled coil containing the L binding region and a C-terminal partially folded domain, PX (residues 474 to 568), identified as the nucleocapsid binding site. Interestingly, PX is also expressed as an independent polypeptide in infected cells. PX has a C-subdomain (residues 516 to 568) that consists of three {alpha}-helices arranged in an antiparallel triple-helical bundle linked to an unfolded flexible N-subdomain (residues 474 to 515).
Zinc finger, CHC2-type (Znf_CHC2)
Type: Domain

This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses.

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
Bifunctional purine biosynthesis protein PurH-like (PurH-like)
Type: Family

This is a family of bifunctional enzymes catalysing the last two steps in
de novo
purine biosynthesis. The bifunctional enzyme is found in both prokaryotes and eukaryotes. The second last step is catalysed by 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase

(AICARFT), this enzyme catalyses the formylation of AICAR with 10-formyl-tetrahydrofolate to yield FAICAR and tetrahydrofolate . The last step is catalysed by IMP (Inosine monophosphate) cyclohydrolase

(IMPCHase), cyclizing FAICAR (5-formylaminoimidazole-4-carboxamide ribonucleotide) to IMP .
Membrane protein insertion efficiency factor YidD-like (Membr_insert_effic_factor_YidD)
Type: Family

This family consists of membrane insertion efficiency factor proteins, such as YidD which may be involved in insertion of integral membrane proteins into the membrane . They contain three conserved cysteine residues.
5-formyltetrahydrofolate cyclo-ligase (FTHF_cligase)
Type: Family

5-formyltetrahydrofolate cyclo-ligase or methenyl-THF synthetase

catalyses the interchange of 5-formyltetrahydrofolate (5-FTHF) to 5-10-methenyltetrahydrofolate, this requires ATP and Mg
2
. 5-FTHF is used in chemotherapy where it is clinically known as Leucovorin .

This entry also includes the 5-formyltetrahydrofolate cyclo-ligase-like protein COG0212 (At1g76730) from Arabidopsis. It does not possess the 5-formyltetrahydrofolate cyclo-ligase activity in vitro and does not complement the growth defect or the characteristic 5-formyltetrahydrofolate accumulation of a 5-FCL-deficient Escherichia coli strain. Instead, it may play a role in thiamin metabolism .
ATPase, V1 complex, subunit D (V_ATPase_D)
Type: Family

This is a family of D subunits from various ATP synthases, including V-type H+ transporting and Na+ transporting . This family is found in eukaryota, bacteria and archaea . The V-type ATPase can use a proton gradient to synthesize ATP, but the primary biological role is to acidify some compartment, such as yeast vacuole (a lysosomal homologous) or the interior of a prokaryote. Subunit D is suggested to be an integral part of the catalytic sector of the V-ATPase .

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.

The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V-ATPase folding, localisation, and stability is made possible through the formation of a luminal glycan coat by the glycolipids and the glycosylated V0 subunits . The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis . The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases.
Chorismate mutase II, prokaryotic-type (CM_II_prokaryot)
Type: Domain

This entry represents the CM type 2 domain, mainly from prokaryotes. It does not include the CM from plants and or Baker's yeast.

Chorismate mutase (CM) is a regulatory enzyme (

) required for biosynthesis of the aromatic amino acids phenylalanine and tyrosine. CM catalyzes the Claisen rearrangement of chorismate to prephenate, which can subsequently be converted to precursors of either L-Phe or L-Tyr. In bifunctional enzymes the CM domain can be fused to a prephenate dehydratase (P-protein for Phe biosynthesis), to a prephenate dehydrogenase (T-protein, for Tyr biosynthesis), or to 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase. Besides these prokaryotic bifunctional enzymes, monofunctional CMs occur in prokaryotes as well as in fungi, plants and nematode worms . The sequence of monofunctional chorismate mutase aligns well with the N-terminal part of P-proteins .

The type II or AroQ class of CM has an all-helical 3D structure, represented by the CM domain of the bifunctional Escherichia coli P-protein. This type is named after the Enterobacter agglomerans monofunctional CM encoded by the aroQ gene . All CM domains from bifunctional enzymes as well as most monofunctional CMs belong to this class, including archaeal CM.

Eukaryotic CM from plants and fungi form a separate subclass of AroQ, represented by the Baker's yeast allosteric CM. These enzymes show only partial sequence similarity to the prokaryotic CMs due to insertions of regulatory domains, but the helix-bundle topology and catalytic residues are conserved and the 3D structure of the E. coli CM dimer resembles a yeast CM monomer . The E. coli P-protein CM domain consists of 3 helices and lacks allosteric regulation. The yeast CM has evolved by gene duplication and dimerization and each monomer has 12 helices. Yeast CM is allosterically activated by Trp and inhibited by Tyr .
Translation repressor RegA (Transl_repress_RegA)
Type: Family

The translational regulator protein RegA, found in Bacteriophage T4 and related phages, binds to a region of messenger RNA (mRNA) that includes the initiator codon. RegA is unusual in that it represses the translation of about 35 early T4 mRNAs but does not affect nearly 200 other mRNAs .
Levivirus coat protein (Levivir_coat)
Type: Family

This entry represents the coat proteins of the leviviruses (phage MS2) and alloleviruses (phage Qbeta and phage F1).
Peptidase C7 domain (Peptidase_C7_dom)
Type: Domain

This entry represents a peptidase C7 domain, which is found in HAV papain-like proteases p48 and p29 .

Hypoviruses are positive-strand RNA mycoviruses that attenuate virulence of their pathogenic fungal hosts [E1]. They employ a gene expression strategy that involves the autocatalytic processing of the N-terminal portion of encoded polyproteins by papain-like protease domains. The prototypic hypovirus CHV-1/EP713, responsible for virulence attenuation (hypovirulence) of the chestnut blight fungus Cryphonectria parasitica, encodes two contiguous open reading frames (ORFs) designated ORF A and ORF B, which contain N-terminal proteases p29 and p48, respectively. Protease p29 functions as a suppressor of the RNA silencing defense response, while p48 is required for viral RNA replication .
DNA-repair protein Xrcc1, N-terminal (Xrcc1_N)
Type: Domain

DNA-repair protein Xrcc1 functions in the repair of single-strand DNA breaks in mammalian cells and forms a repair complex with beta-Pol, ligase III and PARP . The NMR solution structure of the Xrcc1 N-terminal domain (Xrcc1 NTD) shows that the structural core is a β-sandwich with β-strands connected by loops, three helices and two short two-stranded β-sheets at each connection side. The Xrcc1 NTD specifically binds single-strand break DNA (gapped and nicked) and a gapped DNA-beta-Pol complex .
Homocysteine biosynthesis enzyme, sulfur-incorporation (HcyBio)
Type: Domain

This presumed domain (used to be named as DUF39) is about is about 360 residues long. The function of this domain is not clear. It is found at N terminus in some proteins that have two C-terminal cystathionine beta-synthase (CBS) domains, such as MJ0100 from Methanocaldococcus jannaschii. This domain can also be found in proteins that contain two C-terminal inserted Fe4S domains .

In Methanocaldococcus jannaschii, MJ0100 and its ortholog MA1821 from Methanosarcina acetivorans are involved in Hcy (homocysteine) biosynthesis. MJ0100 CBS domains bind S-adenosyl-l-methionine (SAM) and 5'-methylthioadenosine (MTA), which induce a conformational change consistent with regulatory function. Another protein in the homocysteine biosynthesis pathway, MJ0099 and its ortholog MA1822, is involved in the reduction of the disulfide formed in MJ0100/MA1821 during the conversion of Asa (aspartate semialdehyde) to Hcy .

The DUF39-CBS and DUF39-ferredoxin architectures repeatedly occur together in the genomes of methanogenic Archaea, suggesting they may be of diverged function. This is consistent with a phylogenetic reconstruction of the DUF39 family, which clearly distinguishes the CBS-associated and ferredoxin-associated DUF39s .
Dilute domain (Dilute_dom)
Type: Domain

The myosin superfamily consists of at least 15 distinct classes of presumed actin-based molecular motors. All members of the superfamily share a similar motor domain and a tail portion which is diagnostic of the class .

Class V myosins are actin-based molecular motors that function in relatively long-range movements of many intracellular cargoes including organelles, membrane vesicles, and mRNA . These motors are ubiquitously found in all eukaryotes. Class V myosins are characterised by the presence of a conserved globular domain at the C terminus of the tail portion: the dilute domain . Myosin V moves via attachment of its amino terminal head (motor) domain to actin cables; its carboxyl terminal dilute domain anchors it to cargoes via attachments to organelle-specific receptors .

The dilute domain is also found in the afadin family. Afadins are nectin and actin filament-binding proteins that connect nectin to the actin cytoskeleton . The dilute domain of afadin appears to be responsible for actin stress fibre formation .
HNH endonuclease (HNH)
Type: Domain

HNH endonuclease is found in bacteria and viruses . This entry represents the catalytic core of these enzymes that folds into a typical ββα-fold . It spans the conserved catalytic HNH motif and the Zn-binding site. This minimal catalytic core is found in site-specific homing endonucleases, restriction enzymes, pyocins, colicins and anaredoxins. Bacterial HNH domains are known to act as both site-specific DNA nucleases (in homing nucleases for example, or in the RNA-guided DNA endonuclease Cas9), as well as non-specific nucleases (in colicins, a subgroup of bacterial toxins) .
Toxin CcdB (CcdB)
Type: Family

CcdB protein is a topoisomerase poison from Escherichia coli .
It is responsible for killing plasmid-free segregants, and interferes with the activity of DNA gyrase. It acts to inhibit partitioning of the chromosomal DNA.
FF domain (FF_domain)
Type: Domain

The FF domain may be involved in protein-protein interaction . It often occurs as multiple copies and often accompanies WW domains

. PRP40 from yeast encodes a novel, essential splicing component that associates with the yeast U1 small nuclear ribonucleoprotein particle .