SII-SWORD/CoKE huggingface dataset:
Spike glycoprotein S1, coronavirus (Spike_S1_CoV)
Type: Domain

The type I glycoprotein S of Coronavirus, trimers of which constitute the typical viral spikes, is assembled into virions through noncovalent interactions with the M protein. The spike glycoprotein is translated as a large polypeptide that is subsequently cleaved to S1 and S2

. Both chimeric S proteins appeared to cause cell fusion when expressed individually, suggesting that they were biologically fully active . The spike is a type I membrane glycoprotein that possesses a conserved transmembrane anchor and an unusual cysteine-rich (cys) domain that bridges the putative junction of the anchor and the cytoplasmic tail .

The coronavirus (SARS-CoV) S1 subunit is composed of two distinct domains: an N-terminal domain (S1 NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Each of these domains have been implicated in binding to host receptors. However, most coronaviruses are not known to utilise both the S1 NTD and S1 RBD for viral entry . SARS-CoV makes use of its S1 RBD to bind to the human angiotensin-converting enzyme 2 (ACE2) as its host receptor .
Clathrin/coatomer adaptor, adaptin-like, N-terminal (Clathrin/coatomer_adapt-like_N)
Type: Domain

Proteins synthesized 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 .

This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer α/α fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily . The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity . It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles.
Protein phosphatase 2A, regulatory B subunit, B56 (PP2A_B56)
Type: Family

Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits, this family is called the B56 family .
Arterivirus GP3 envelope glycoprotein (Arteri_GP3)
Type: Family

This family consists of envelope proteins from Arterivirus, including glycoprotein 3 (GP3) from Porcine reproductive and respiratory syndrome virus (PRRSV) and Lactate dehydrogenase-elevating virus (LDV) structural glycoprotein . Arteriviruses consists of positive ssRNA and do not have a DNA stage.
Chitin binding domain (Chitin-bd_dom)
Type: Domain

This entry represents a chitin binding domain . It is found in the Peritrophin-A chitin binding proteins, particularly the peritrophic matrix proteins of insects and animal chitinases and related proteins. Copies of the domain are also found in some baculoviruses. It is an extracellular domain characterised by a six-cysteine motif and several aromatic residues . Chitin-binding activity has been confirmed in a protein that contains just two of these domains .
I/LWEQ domain (ILWEQ_dom)
Type: Domain

The I/LWEQ domain is a ~250-residue actin-binding module that is found in the C termini of functionally diverse proteins from yeast to mammals. The I/LWEQ domain contains four conserved blocks and has been named after the conserved initial residues of blocks 1-4. The I/LWEQ domain is generally found near the C terminus and in association with other domains, such as FERM or ENTH. The I/LWEQ domain has been shown to bind to F-actin and to bundle actin filaments .

The I/LWEQ domain contains a proteolysis resistant-core that has an all-α-helical structure composed of five long down-up-down-up-down antiparallelhelices connected by short loops and one short connecting α helix arranged in a progressive topology. The proteolysis-resistant core is
followed by a C-terminal latch region that adopts an α-helical conformation. The latch region can mediate oligomerization of I/LWEQ domains,
possibly as dimers, and this seems to enhance the F-actin-binding ability of the proteolysis-resistant core .

It's worth noting that the I/LWEQ domain has also been called the talin-HIP1/R/Slap2p actin- tethering C-terminal homology (THATCH) domain (HIP1/R/Slap2p denotes similarity of Slap2p to HIP1 and HIP1R) .
Transposase IS4-like domain (Transposase_11)
Type: Domain

Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families . This family includes the IS4 transposase.
Transposase IS204/IS1001/IS1096/IS1165, DDE domain (Transposase_DDE)
Type: Domain

This entry represents the DDE domain found in the IS204/IS1001/IS1096/IS116 transposases. Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families . This family includes the IS204 , IS1001 , IS1096 and IS1165 transposases.
Filoviruses glycoprotein, extracellular domain (GPC_filovir-type_extra_dom)
Type: Domain

This entry represents an extracellular domain from the envelope glycoprotein of Ebola virus sp. and Lake Victoria marburgvirus. The extracellular domain is also produced as a separate transcript that gives rise to a non-structural, secreted glycoprotein, which is produced in large amounts and has an unknown function . Processing of the protein may be involved in viral pathogenicity .
3'-5' exonuclease domain (3'-5'_exonuclease_dom)
Type: Domain

This entry represents the domain that is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes which catalyse the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI and is also found in the Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN (also known as Werner syndrome helicase), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) .

Werner syndrome is a human genetic disorder causing premature ageing; the WRN protein has helicase activity in the 3'-5' direction . The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homologue of the WRN protein . RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.

This domain is also found in some DNA polymerases from phages, including the DNA polymerase from Escherichia phage T5, exonucleolytic activity , and the DNA polymerase DpoZ from Acinetobacter phage SH-Ab 15497, which preferentially incorporates the non-canonical base aminoadenine/dZTP instead of adenine into the synthesized DNA .
Flavin reductase like domain (Flavin_Rdtase-like_dom)
Type: Domain

This domain can be found in NAD(P)H-flavin oxidoreductases (flavin reductases), a class of enzymes capable of producing reduced flavin for bacterial bioluminescence and other biological processes, and various other oxidoreductase and monooxygenase enzymes .

This domain consists of a β-barrel with Greek key topology, and is related to the ferredoxin reductase-like FAD-binding domain. The flavin reductases have a different dimerisation mode than that found in the PNP oxidase-like family, which also carries an FMN-binding domain with a similar topology.
Orbivirus NS3 (Orbi_NS3)
Type: Family

This is a family of Orbivirus non structural protein of unknown function, but which may play a role in release of the virus from infected cells .
Msp4/OMP-like (Msp4_OMP-like)
Type: Domain

This entry includes a number of bacterial surface antigens expressed on the surface of pathogens. The Anaplasma marginale surface proteins are targets of protective immune responses but are antigenically polymorphic . They display a β-barrel like fold.
Envelope glycoprotein K (GK)
Type: Family

Human herpesvirus 1 (HHV-1) (Human herpes simplex virus 1) glycoprotein K (gK) plays an essential role in viral replication and cell fusion. gK is a very hydrophobic membrane protein that contains a signal sequence and several hydrophobic regions. gK contains three transmembrane domains (amino acids 125-139, 226-239, and 311-325) and another hydrophobic domain (amino acids 241-265), which is relatively less hydrophobic and much longer compared with the transmembrane sequences located in the extracellular loop. The domains may interact with each other to form a complex tertiary structure that is critical for the biological function of gK .
Carlavirus nucleic acid-binding protein (Carla-bd)
Type: Family

This family of carlavirus nucleic acid binding proteins includes a motif for a potential C-4 type zinc finger this has four highly conserved cysteine residues and is a conserved feature of the carlaviruses 3' terminal ORF . These proteins may function as viral transcriptional regulators. The carlavirus family includes Garlic latent virus and Potato virus S and Potato virus M, these viruses are positive strand, ssRNA with no DNA stage.
Peptide methionine sulphoxide reductase MsrA domain (Met_Sox_Rdtase_MsrA_dom)
Type: Domain

Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine . It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set .

The domains MsrA and MsrB reduce different epimeric forms of methionine sulphoxide. This group represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution .

In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (

) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate.
Heat-inducible transcription repressor HrcA (HrcA)
Type: Family

Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer.
Domain of unknown function DUF22 (DUF22)
Type: Domain

This region is found in 1 to 3 copies in archaeal proteins whose function is unknown. It only appears in multiple copies in proteins from Archaeoglobus fulgidus.
M matrix/glycoprotein, coronavirus (M_CoV)
Type: Family

This family consists of various coronavirus matrix proteins which are transmembrane glycoproteins . The membrane (M) protein is the most abundant structural protein and defines the shape of the viral envelope. It is also regarded as the central organiser of coronavirus assembly, interacting with all other major coronaviral structural proteins. M proteins play a critical role in protein-protein interactions (as well as protein-RNA interactions) since virus-like particle (VLP) formation in many CoVs requires only the M and envelope (E) proteins for efficient virion assembly . Interaction of spike (S) with M is necessary for retention of S in the ER-Golgi intermediate compartment (ERGIC)/Golgi complex and its incorporation into new virions, but dispensable for the assembly process. Binding of M to nucleocapsid (N) proteins stabilises the nucleocapsid (N protein-RNA complex), as well as the internal core of virions, and, ultimately, promotes completion of viral assembly. Together, M and E protein make up the viral envelope and their interaction is sufficient for the production and release of virus-like particles (VLPs) .
Aminoglycoside phosphotransferase (Aminoglycoside_PTrfase)
Type: Domain

This entry consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides they include:- aminoglycoside 3'-phosphotransferase or kanamycin kinase / neomycin-kanamycin phosphotransferase and streptomycin 3''-kinase or streptomycin 3''-phosphotransferase. The aminoglycoside phosphotransferases inactivate aminoglycoside antibiotics via phosphorylation . The proteins are found in a range of taxonomic groups.
Helix-turn-helix, HxlR type (HTH_HxlR)
Type: Domain

The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde . The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH .
Peptide methionine sulphoxide reductase MrsB domain (Met_Sox_Rdtase_MsrB_dom)
Type: Domain

Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine . It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set .

The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A . The overall structure shows no resemblance to the structures of MsrA (

) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin.

In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains.
Herpesvirus UL24 (Herpes_UL24)
Type: Family

This entry consists of the human herpes virus protein UL24 and its orthologues, which are universally present in avian, mammalian and reptilian herpes viruses. Though the functions of these proteins are not known, computational analysis suggests that they may belong to the restriction endonuclease-like fold superfamily, which contains a variety of endonucleases, DNA repair enzymes and exonucleases . Proteins in this entry contain an absolutely conserved PD-(D/E)XK motif thought to be critical for nucleotide-cleaving activity.
Holo-[acyl carrier protein] synthase (ACPS)
Type: Family

Holo-acyl carrier protein synthase (ACPS) transfers the 4'-phosphopantetheine (4'-PP) moiety from coenzyme A (CoA) to Ser-36 of acyl carrier protein (ACP) in Escherichia coli. This post-translational modification renders holo-ACP capable of acyl group activation via thioesterification of the cysteamine thiol of 4'-PP . In eukaryotes such as the yeast
Neosartorya fumigata
, ACPS is mitochondrial .
Small ribosomal subunit protein bS20 (Ribosomal_bS20)
Type: Family

This family consists of bacterial (and chloroplast) examples of the ribosomal small subunit protein bS20. Bacterial ribosomal protein bS20 forms part of the 30S ribosomal subunit, and interacts with 16S rRNA.

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 .
Cytochrome ubiquinol oxidase subunit 1 (Cyt-d_ubiquinol_oxidase_su_1)
Type: Family

This family are the alternative oxidases found in many bacteria which oxidise ubiquinol and reduce oxygen as part of the electron transport chain. This family is the subunit I of the oxidase. E. coli has two copies of the oxidase, bo and bd. Only bd is represented here In some nitrogen fixing bacteria.

Cytochrome bd may play an important role in microaerobic nitrogen fixation in the enteric bacterium Klebsiella pneumoniae, where it is expressed under all conditions that permit diazotrophy . Subunit I binds a single b-haem, through ligands at His186 and Met393 (using

numbering). In addition His19 is a ligand for the haem b found in subunit II (

).
CobQ/CobB/MinD/ParA nucleotide binding domain (CobQ/CobB/MinD/ParA_Nub-bd_dom)
Type: Domain

This domain is found in various cobyrinic acid a,c-diamide synthases. These include CbiA (

) and CbiP (

) from S. typhimurium , and CobQ (

) from R. capsulatus . These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria .
Myo-inositol-1-phosphate synthase (Myo-inos-1-P_Synthase)
Type: Family

Myo-inositol 1-phosphate synthase (

), also known as Inositol-3-phosphate synthase 1 (INO1), is a key enzyme in myo-inositol biosynthesis pathway that catalyses the conversion of glucose 6-phosphate to 1D-myo-inositol 3-phosphate in a NAD-dependent manner . The enzyme exists in a cytoplasmic form in a wide range of plants, animals, and fungi. It has also been detected in several bacteria and a chloroplast form is observed in alga and higher plants. Inositol phosphates play an important role in signal transduction.

In Saccharomyces cerevisiae (Baker's yeast), the transcriptional regulation of the INO1 gene has been studied in detail and its expression is sensitive to the availability of phospholipid precursors as well as growth phase. The regulation of the structural gene encoding 1L-myo-inositol-1-phosphate synthase has also been analysed at the transcriptional level in the aquatic angiosperm, Spirodela polyrrhiza (Giant duckweed) and the halophyte, Mesembryanthemum crystallinum (Common ice plant) .
Alphavirus-like methyltransferase domain (Alphavirus-like_MT_dom)
Type: Domain

This domain is found at the N terminus of the non-structural poly-protein of Tymoviruses, it spans the RNA methyltransferase domain of the replicase large subunit, which is a RNA-dependent RNA polymerase active in viral RNA replication is found in a wide range of ssRNA viruses (Tymovirales), including Hordeivirus, Tobravirus, Tobamovirus, Bromovirus, Closterovirus and Calicivirus. The poly-protein is processed into the replicase small subunit, which is the methyltransferase active in RNA capping and a RNA helicase. Methyltransferase displays a cytoplasmic capping enzyme activity. This function is necessary since all viral RNAs are synthesized in the cytoplasm, and host capping enzymes are restricted to the nucleus. The helicase region probably, which is immediately adjacent to the methyltransferase domain exhibits NTPase and RNA unwinding activities.