SII-SWORD/CoKE huggingface dataset:
Photosystem II PsbR (PSII_PsbR)
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 family represents the low molecular weight intrinsic protein PsbR found in PSII, which is also known as the 10kDa polypeptide. The PsbR gene is found only in the nucleus of green algae and higher plants. PsbR may provide a binding site for the extrinsic oxygen-evolving complex protein PsbP to the thylakoid membrane. PsbR has a transmembrane domain to anchor it to the thylakoid membrane, and a charged N-terminal domain capable of forming ion bridges with extrinsic proteins, allowing PsbR to act as a docking protein. PsbR may be a pH-dependent stabilising protein that functions at both donor and acceptor sides of PSII .
Microvirus J protein-like (Microvir_J-like)
Type: Family

This entry represents the Microvirus J protein and related proteins from bacteria.
ELMO domain (ELMO_dom)
Type: Domain

This entry represents the ELMO (EnguLfment and Cell MOtility) domain, which is found in a number of eukaryotic proteins involved in the cytoskeletal rearrangements required for phagocytosis of apoptotic cells and cell motility, including CED-12, ELMO-1 and ELMO-2.
Lipoprotein leucine-zipper (Lipoprotein_leucine-zipper_dom)
Type: Domain

This is leucine-zipper is found in the enterobacterial outer membrane lipoprotein LPP . It is likely that this domain oligomerises and is involved in protein-protein interactions. As such it is a bundle of α-helical coiled-coils, which are known to play key roles in mediating specific protein-protein interactions for in molecular recognition and the assembly of multi-protein complexes .
Histone chaperone ASF1-like (ASF1-like)
Type: Family

This family includes the yeast and human ASF1 protein. These proteins have histone chaperone activity . ASF1 participates in both the replication-dependent and replication-independent pathways. The structure three-dimensional has been determined as a compact immunoglobulin-like β-sandwich fold topped by three helical linkers .
Agrobacterium VirD5 protein (Agro_VirD5)
Type: Family

The virD operon in Agrobacterium encodes a site-specific endonuclease, and a number of other poorly characterised products . This family represents the VirD5 protein.
Caudal-like activation domain (Caudal_activation_dom)
Type: Domain

This domain occurs at the N-terminal of proteins belonging to the caudal-related homeobox protein family. This region is thought to mediate transcription activation. The level of activation caused by mouse Cdx2 (

) is affected by phosphorylation at serine 60 via the mitogen-activated protein kinase pathway . Caudal family proteins are involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium, and are important in differentiation and maintenance of the intestinal epithelial lining. Caudal proteins always have a homeobox DNA binding domain (

).
Intermediate filament head, DNA-binding domain (Intermed_filament_DNA-bd)
Type: Domain

This entry represents the N-terminal head domain of intermediate filaments. Intermediate filament heads bind DNA . Vimentin heads are able to alter nuclear architecture and chromatin distribution, and the liberation of heads by HIV-1 protease liberates may play an important role in HIV-1 associated cytopathogenesis and carcinogenesis . Phosphorylation of the head region can affect filament stability . The head has been shown to interaction with the rod domain of the same protein .
Coatomer, epsilon subunit (Coatomer_esu)
Type: Family

This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex .

Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer . While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins . For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi . Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes . COPI coated vesicle assembly is initiated by recruitment of the small GTPase Arf1 which recruits the coatomer protein complex from the cytoplasm and anchors it at the membrane. Then, Arf1 is activated by a guanine exchange factor and hydrolyses GTP to mediate uncoating of the vesicle which subsequently fuses with its target membrane . As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits, and can be subdivided into an outer-coat and an adaptor subcomplex .
Neutral/alkaline nonlysosomal ceramidase (Ceramidase_alk)
Type: Family

This family represents a group of neutral/alkaline ceramidases found in both bacteria and eukaryotes . They hydrolyse the sphingolipid ceramide into sphingosine and free fatty acid.
DNA helicase, Baculovirus (DNA_helicase_Baculovir)
Type: Family

Baculovirus P143 is a DNA helicase essential for virus DNA replication . It has distinct roles during infection and contributes to host range determination .
Eclosion hormone (Eclosion)
Type: Family

Eclosion hormone is an insect neuropeptide that triggers the performance of ecdysis behaviour, which causes shedding of the old cuticle at the end of a molt .
Lantibiotic dehydratase, N-terminal (Lant_deHydtase_N)
Type: Domain

Lantibiotics are ribosomally synthesised antimicrobial agents derived from ribosomally synthesised peptides . They are produced by bacteria of the Firmicutes phylum, and include mutacin, subtilin, and nisin. Lantibiotic peptides contain thioether bridges termed lanthionines that are thought to be generated by dehydration of serine and threonine residues followed by addition of cysteine residues . This family constitutes the N terminus of the enzyme proposed to catalyse the dehydration step via glutamylation of the substrate during lantibiotic biosynthesis. The enzyme dehydrates Ser/Thr residues in the precursor by glutamylation .
Association with the SNF1 complex (ASC) domain (ASC_dom)
Type: Domain

Association with the SNF1 complex (ASC) domain is found in the Sip1/Sip2/Gal83/AMPKbeta subunits of the SNF1/AMP-activated protein kinase (AMPK) complex . SNF1/AMPK are heterotrimeric enzymes composed of a catalytic alpha-subunit, a regulatory gamma-subunit and a regulatory/targeting beta-subunit . Saccharomyces cerevisiae encodes three beta-subunit genes, Sip1, Sip2 and Gal83 . The beta-subunits function as target selective adaptors that recruit the catalytic kinase and regulator Snf4/gamma-subunits. The ASC domain is required for interaction with Snf4 .

The SNF1 kinase complex is required for transcriptional, metabolic, and developmental adaptations in response to glucose limitation . As glucose levels decrease, Snf1 is activated and promotes the use of alternative carbon sources.
LXG domain (LXG_dom)
Type: Domain

This domain is present at the N-terminal region of a group of polymorphic toxin proteins in bacteria . LXG toxins mediate intraspecies competition in biofilms and may also help to avoid warfare between strains in biofilms .
InvH outer membrane lipoprotein (InvH)
Type: Family

This family of proteins includes SPI-1 type 3 secretion system pilotin (also known as outer membrane lipoprotein InvH) from Salmonella, which is required for the localisation to outer membrane of InvG, which is involved in a type III secretion apparatus mediating host cell invasion .
Ammonia monooxygenase/particulate methane monooxygenase, subunit B (NH3_CH4_mOase_B)
Type: Family

Ammonia monooxygenase and the particulate methane monooxygenase are both integral membrane proteins, occurring in ammonia oxidisers and methanotrophs respectively, which are thought to be evolutionarily related . These enzymes have a relatively wide substrate specificity and can catalyse the oxidation of a range of substrates including ammonia, methane, halogenated hydrocarbons and aromatic molecules . These enzymes are composed of 3 subunits -A (

), B (

) and C (

) -and contain various metal centres, including copper. Particulate methane monooxygenase from Methylococcus capsulatus str. Bath is an ABC homotrimer, which contains mononuclear and dinuclear copper metal centres, and a third metal centre containing a metal ion whose identity in vivo is not certain.

The soluble regions of these enzymes derive primarily from the B subunit. This subunit forms two antiparallel β-barrel-like structures and contains the mono- and di- nuclear copper metal centres .
VITF-3 subunit protein (Pox_A8)
Type: Family

This is a family of Chordopoxvirus proteins composing one of the two subunits that make up VITF-3, a virally encoded complex necessary for intermediate stage transcription .
Domain of unknown function DUF575 (DUF575)
Type: Domain

This represents a conserved region found in a number of Chlamydophila pneumoniae proteins.
Protein of unknown function DUF612 (DUF612)
Type: Family

This family includes several uncharacterised proteins from Caenorhabditis elegans.
Divergent polysaccharide deacetylase (Divergent_DAC)
Type: Family

This family contains an uncharacterised protein

from Bacillus halodurans, an uncharacterised protein

from Agrobacterium tumefaciens C58, and other bacterial hypothetical proteins. Although their functions are still unknown, structural superposition and sequence comparison suggest that BH1492 and ATU2773 might be divergently related to the 7-stranded barrel catalytic domain of polysaccharide deacetylases (DACs) from the carbohydrate esterase 4 (CE4) superfamily, which remove N-linked acetyl groups from cell wall polysaccharides.
ADTRP/AIG1 (ADTRP_AIG1)
Type: Family

This family includes the androgen-dependent TFPI-regulating protein (ADTRP) and AIG1 protein which were first described as the homologues of hamster androgen-induced FAR-17a protein . AIG1 and ADTRP hydrolyzes bioactive fatty-acid esters of hydroxy-fatty acids (FAHFAs), but not other major classes of lipids, with preference for FAHFAs with branching distal from the carboxylate head group of the lipids . In vitro, ADTRP can regulate the expression and the cell-associated anticoagulant activity of the inhibitor TFPI in endothelial cells .
Dual-action ribosomal maturation protein DarP (DarP)
Type: Family

The entry represents the Dual-action ribosomal maturation protein DarP (also known as YjgA) from Escherichia coli and related proteins. This protein binds pre-50S ribosomal subunits near the 23S rRNA L1 stalk, where it may mediate correct positioning of the L1 stalk . It plays a dual role in the late stages of assembly of the 50S ribosomal subunit where it promotes peptidyl transferase centre maturation by modulating the docking of 23S rRNA helix H68, and maintains the stability of helix H89 with the help of uL16 (rplP), facilitating the final maturation of the peptidyl transferase centre .
Glutathione-specific gamma-glutamylcyclotransferase (ChaC)
Type: Family

The ChaC family of proteins function as gamma-glutamyl cyclotransferases acting specifically to degrade glutathione but not other gamma-glutamyl peptides . It is is conversed across all phyla and represents a new pathway for glutathione degradation in living cells.
Coronavirus nonstructural protein NS2 (Corona_NS2)
Type: Family

This is a family of Coronavirus nonstructural protein NS2. Phosphoamino acid analysis confirmed the phosphorylated nature of NS2 and identified serine and threonine as its phosphorylated amino acid residues . It was also demonstrated that the ns2 gene product is not essential for Murine hepatitis virus replication in transformed murine cells .
Transposase (putative), YhgA-like (Transposase_31)
Type: Domain

This is a domain found in a group of putative transposases, including the YhgA sequence from Escherichia coli (

) and several prokaryotic homologues .
Plastid lipid-associated protein/fibrillin conserved domain (PAP/fibrillin_dom)
Type: Domain

This entry represents a conserved domain found in a number of plastid lipid-associated proteins (PAPs), including Fibrillin-5 (FBN5) from Arabidopsis and CHRC from Oncidium hybrid cultivar. Fibrillins accumulate in chromoplasts and sequester carotenoids during the development of flowers and fruits . FBN5 has been shown to be involved in PQ-9 (Plastoquinone-9) biosynthesis in Arabidopsis and rice . CHRC is a corolla-specific carotenoid-associated protein and a major component of carotenoid-lipoprotein complexes in Cucumis sativus chromoplasts .
Pex, N-terminal (Pex_N)
Type: Domain

This region is the N-terminal part of a number of peroxisomal biogenesis proteins, including Pex2, Pex10 and Pex12, which contain two predicted transmembrane segments. The majority of these proteins have a C-terminal ring finger domain

.
Small ribosomal subunit protein eS30 (Ribosomal_eS30)
Type: Family

This entry is for the ribosomal protein eS30.

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 .
Translation initiation factor IF-2, N-terminal (IF2_N)
Type: Domain

This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms . Its function is unknown.
Transcription regulator, putative, lactococcus phage-type (Transcrpt_reg_put_lact_phage)
Type: Family

This family represents a number of putative transcription repressor proteins found in several Lactococcus bacteriophages. Horizontal transfer may account for the presence of similar proteins in Lactococcus species .
Elongator complex protein 1 (Elp1)
Type: Family

Elongator complex protein 1 (also known as Iki3) is a component of the RNA polymerase II elongator complex, which is a major histone acetyltransferase component of the RNA polymerase II (RNAPII) holoenzyme. The eukaryotic elongator complex has been associated with many cellular activities, including transcriptional elongation , but its main function is tRNA modification . It is required for the formation of 5-methoxy-carbonylmethyl (mcm5) and 5-carbamoylmethyl (ncm5) groups on uridine nucleosides present at the wobble position of many tRNAs .
Domain of unknown function DUF562 (DUF562)
Type: Domain

This represents a conserved region found in a number of Chlamydophila pneumoniae proteins.
Protein of unknown function DUF613 (DUF613)
Type: Family

This is a family of chloroplast proteins of unknown function. Some members have two copies of the conserved region.
Alkaline ceramidase TOD1/Probable hexosyltransferase MUCI70 (TOD1_MUCI70)
Type: Family

The entry represents a group of proteins mainly found in plants, including MUCI70 and TOD1 from Arabidopsis. They share a Rossmann-like fold found in glycosyltransferases.

MUCI70 is a predicted glycosyltransferase essential for the accumulation of seed mucilage, a gelatinous wall rich in unbranched rhamnogalacturonan I (RG I), and for shaping the surface morphology of seeds . Together with IRX14, itis required for xylan and pectin synthesis in seed coat epidermal (SCE) cells.

TOD1 is an endoplasmic reticulum ceramidase that catalyses the hydrolysis of ceramides into sphingosine and free fatty acids at alkaline pH (e.g. pH 9.5) . It is involved in the regulation of turgor pressure in guard cells and pollen tubes .
Poxin, virus (Poxin_vir)
Type: Family

This entry represents Poxin (poxvirus immune nucleases) from Baculovirus and Vaccinia virus. Poxin is a nuclease that cleaves host 2',3'-cGAMP . In human hosts, enzyme cGAS recognizes cytosolic DNA and synthesizes 2'3' cGAMP to activate STING-dependent interferon and NF-kappaB immune responses. Poxin is the viral factor responsible for 2'3' cGAMP degradation . Interestingly, in some poxviruses the poxin is expressed as a poxin-schlafen fusion protein.
Phosphoprotein F17 (Phosphoprotein_F17)
Type: Family

This is a family of poxvirus proteins required for virus morphogenesis and infectivity . Phosphoprotein F17 is necessary for proteolytic processing of the major viral structural proteins, P4a and P4b . F17 binds and sequesters Raptor and Rictor, regulators of mammalian target of rapamycin complexes mTORC1 and mTORC2, respectively, which constitutes a poxvirus strategy to evade cytosolic sensing .
Vertebrate-like NAGS Gcn5-related N-acetyltransferase (GNAT) domain (Vertebrate-like_GNAT_dom)
Type: Domain

The N-acetyltransferases (NAT) (EC 2.3.1.-) are enzymes that use acetyl coenzyme A (CoA) to transfer an acetyl group to a substrate, a reaction implicated in various functions from bacterial antibiotic resistance to mammalian circadian rhythm and chromatin remodeling. The Gcn5-related N-acetyltransferases (GNAT) catalyze the transfer of the acetyl from the CoA donor to a primary amine of the acceptor. The GNAT proteins share a domain composed of four conserved sequence motifs A-D . This GNAT domain is named after yeast GCN5 (from General Control Nonrepressed) and related histone acetyltransferases (HATs) like Hat1 and PCAF. HATs acetylate lysine residues of amino terminal histone tails, resulting in transcription activation. Another category of GNAT, the aminoglycoside N-acetyltransferases, confer antibiotic resistance by catalyzing the acetylation of amino groups in aminoglycoside antibiotics . GNAT proteins can also have anabolic and catabolic functions in both prokaryotes and eukaryotes .

The acetyltransferase/GNAT domain forms a structurally conserved fold of 6 to 7 β strands (B) and 4 helices (H) in the topology B1-H1-H2-B2-B3-B4-H3-B5-H4-B6, followed by a C-terminal strand which may be from the same monomer or contributed by another . Motifs D (B2-B3), A (B4-H3) and B (B5-H4) are collectively called the HAT core , while the N-terminal motif C (B1-H1) is less conserved.

This entry represents the vertebrate-like NAGS-type GNAT domain .
Mating-type protein MAT alpha 1, HMG-box (MATalpha_HMGbox)
Type: Domain

This entry represents the MAT Alpha1 domain, which is diverged from the MATA HMG-box domain . All ascomycete MAT idiomorphs encode proteins with confirmed or putative DNA-binding motifs . The HMG-box domain can be found in a wide variety of DNA-binding proteins.
Chicken anaemia virus VP-3 protein (CAV_VP3)
Type: Family

Chicken anaemia virus (CAV) is a circovirus which can cause severe depletion of some cell types, such as lymphocytes, by the induction of apoptosis . Studies indicate that expression of the viral VP3 protein, also known as apoptin, is sufficient to induce apoptosis in susceptible cells and to produce the doughnut-shaped apoptosis body formations observed in cells during CAV infections. This protein induces apoptosis in tumor cells and transformed cells, but is incapable of inducing apoptosis in normal cells unless tranforming signals are supplied which induce its phosphorylation. Cell death occurs in a p53- and Bcl-2-independent manner . Apoptin contains putative nuclear localisation and nuclear export domains, and has a positively charged C terminus which is thought to allow direct interaction with nucleic acids. Localisation to the nucleus appears to be necessary for apoptosis, but is not sufficient on its own. The biologically active form of the protein appears to be large complexes of 30-40 molecules which form distinct superstructures upon DNA binding. A number of cellular factors including Nmi, and several death domain superfamily proteins, have been shown to interact apoptin. It has been suggested that in the nucleus, it this binding of phosphorylated apoptin to DNA and other factors which starts the apoptotic machinery, triggering cell death.