SII-SWORD/CoKE huggingface dataset:
Borrelia plasmid, OrfA (Borrelia_plasmid_OrfA)
Type: Family

The proteins in this entry are encoded by an open reading frame in plasmid borne DNA repeats of Borrelia species. This protein is known as ORF-A . The function of this putative protein is unknown.
Insect antifreeze protein motif (Insect_antifreeze_prot_motif)
Type: Repeat

Antifreeze proteins (AFPs) are a class of proteins that are able to bind to and inhibit the growth of macromolecular ice, thereby permitting an organism to survive subzero temperatures by decreasing the probability of ice nucleation in their bodies . These proteins have been characterised from a variety of organisms, including fish, plants, bacteria, fungi and arthropods. This entry represents insect AFPs of the type found in Tenebrio molitor (Yellow mealworm) and in Dendroides canadensis (Pyrochroid beetle).

The structure of these AFPs consists of a right-handed β-helix with 12 residues per coil. Each 12 residue-repeat contains two cys residues that form a disulphide bridge. The β-helices of insect AFPs present a highly rigid array of threonine residues and bound water molecules that can effectively mimic the ice lattice. As such, β-helical AFPs provide a more effective coverage of the ice surface compared to the α-helical fish AFPs .

A second insect antifreeze from Choristoneura fumiferana (Spruce budworm) (

) also consists of β-helices, however in these proteins the helices form a left-handed twist; these proteins show no sequence homology to the current entry, but may act by a similar mechanism. The β-helix motif may be used as an AFP structural motif in non-homologous proteins from other (non-fish) organisms as well.
Keratin (Keratin)
Type: Family

Keratins are a well known group of intermediate filament proteins. Like actin filaments, keratins are flexible but provide a firm cell skeleton. Unlike actin, however, no known keratins are associated with motor functions. This family represents avian keratin proteins , found in feathers, scale and claw. The avian keratins (F-ker, S-ker, C-ker and B-ker) are a complex mixture of very similar polypeptides.
Ornithine cyclodeaminase/mu-crystallin (ODC_Mu_crystall)
Type: Family

This entry represents the bacterial ornithine cyclodeaminase enzyme family, which catalyse the deamination of ornithine to proline . The family also includes archaeal alanine dehydrogenase and mu-crystallin, a mammalian homologue of bacterial ornithine cyclodeaminase , which is the major component of the eye lens in several Australian marsupials. mRNA for mu-crystallin has also been found in human retina .

This entry also includes protein SAR DEFICIENT 4 (SARD4) from Arabidopsis. SARD4 is involved in the biosynthesis of pipecolate (Pip), a metabolite that orchestrates defense amplification, positive regulation of salicylic acid (SA) biosynthesis, and priming to guarantee effective local resistance induction and the establishment of systemic acquired resistance (SAR) . It does not possess ornithine cyclodeaminase activity in vitro .
Paralytic/GBP/PSP peptide (GBP_PSP)
Type: Family

This family includes insect peptides that are short (23 amino acids) and contain 1 disulphide bridge. The family includes growth-blocking peptide (GBP) of Pseudaletia separata (Oriental armyworm) and the paralytic peptides from Manduca sexta (Tobacco hawkmoth), Heliothis virescens (Noctuid moth), and Spodoptera exigua (Beet armyworm) as well as plasmatocyte-spreading peptide (PSP1) . These peptides function to halt metamorphosis from larvae to pupae.
Muconolactone delta-isomerase (Muconolactone_d_Isoase)
Type: Family

This small enzyme forms a homodecameric complex, that catalyses the third step in the catabolism of catechol to succinate- and acetyl-coa in the beta-ketoadipate pathway (

).
Proteinase inhibitor I20 (Prot_inh_I20)
Type: Family

Members of the potato peptidase inhibitor II family are proteinase inhibitors that belong to MEROPS inhibitor family I20, clan IA and are restricted to plants. They inhibit serine peptidases belonging to MEROPS peptidase family S1 (

). They have a multidomain structure , which permits circular permutation of the sequences. It was been shown that some naturally occurring Pin2 proteins, have an `ancestral' circularly permuted structure . Circular permutation/ rearrangements of sequences has also been observed between species, such as favin from Vicia faba and the lectin concanavalin A from Canavalia ensiformis or amongst members of the plant aspartyl proteinases and human lung surfactant proteins .
K88 fimbrial minor subunit FaeH (Fimbrial_K88_FaeH)
Type: Family

Fimbriae (also know as pili) are polar filaments radiating from the surface of the bacterium to a length of 0.5-1.5 micrometers, that enable bacteria to colonise the epithelium of specific host organs . This family represents the K88 minor fimbrial subunit FaeH and related proteins.
Cytochrome c oxidase, monohaem subunit/FixO (Cyt_c_oxidase_monohaem-su/FixO)
Type: Family

Cytochrome cbb3 oxidases are found almost exclusively in Proteobacteria, and represent a distinctive class of proton-pumping respiratory haem-copper oxidases (HCO) that lack many of the key structural features that contribute to the reaction cycle of the intensely studied mitochondrial cytochrome c oxidase (CcO) . Cytochrome cbb3 oxidases are required both to support symbiotic nitrogen fixation, whilst ensuring that the oxygen-labile nitrogenase is not compromised. Cytochrome cbb3 oxidases consist of four subunits: FixN (or CcoN), FixO (or CcoO), FixP (or CcoP) and FixQ (or CcoQ). The catalytic core is comprised of subunits FixN, FixO and FixP, where FixN acts as the catalytic subunit, and Fix O and FixP are membrane-bound mono-and di-haem cytochromes c, respectively. The FixQ subunit protects the core complex in the presence of oxygen from proteolytic degradation . This entry represents the mono-haem FixO subunit.
Glycoside hydrolase, family 68 (Glyco_hydro_68)
Type: Family

This family consists of the glycosyl hydrolase 68 family (

), including several bacterial levansucrase enzymes, and invertase from Zymomonas. Levansucrase (

), also known as beta-D-fructofuranosyl transferase, catalyses the conversion of sucrose and (2,6-beta-D-fructosyl)(N) to glucose and (2,6-beta-D-fructosyl)(N+1), where other sugars can also act as fructosyl acceptors. Invertase, or extracellular sucrase (

), catalyses the hydrolysis of terminal non-reducing beta-D-fructofuranoside residues in beta-D-fructofuranosides.

O-Glycosyl hydrolases (

) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.
Adenovirus E3 region protein CR2 (Adeno_E3_CR2)
Type: Domain

Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host . This region called CR1 (conserved region 1) is found three times in Human adenovirus 19 (a subgroup D adenovirus) 49kDa protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain.
Adenovirus E3 region protein CR1 (Adeno_E3_CR1)
Type: Domain

Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host . This region called CR1 (conserved region 1) is found three times in Human adenovirus 19 (a subgroup D virus) 49 Kd protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain.
Virion membrane protein, poxvirus L1-related (Virion_mem_poxvirus_L1)
Type: Family

The four families of large eukaryotic DNA viruses, Poxviridae, Asfarviridae, Iridoviridae, and Phycodnaviridae, referred to collectively as nucleocytoplasmic large DNA viruses or NCLDV, have all been shown to have a lipid membrane, in spite of the major differences in virion structure. The paralogous genes L1R and F9L encode membrane proteins that have a conserved domain architecture, with a single, C-terminal transmembrane helix, and an N-terminal, multiple-disulphide-bonded domain. The conservation of the myristoylated, disulphide-bonded protein Entry-fusion complex associated protein OPG095 (L1R)/EFC-associated protein OPG053 (F9L) in most of the NCLDV correlates with the conservation of the thiol-disulphide oxidoreductase E10R which, in vaccinia virus, is required for the formation of disulphide bonds in L1R and F9L .

This entry also includes Inner membrane protein pE248R from African swine fever virus. This protein is essential for viral fusion with host endosomal membrane and core release .
Quinolinate synthetase A (NadA)
Type: Family

Quinolinate synthetase catalyses the second step of the
de novo
biosynthetic pathway of pyridine nucleotide formation. In particular, quinolinate synthetase is involved in the condensation of dihydroxyacetone phosphate and iminoaspartate to form quinolinic acid . This synthesis requires two enzymes, an FAD-containing "B protein" and an "A protein". B protein converts L-aspartate to iminoaspartate. The A protein, NadA, converts iminoaspartate to quinolate. NadA harbours a [4Fe-4S] cluster .
Gluconate transporter (Glcn_transporter)
Type: Family

This is a family of integral membrane permeases that are involved in gluconate uptake. Escherichia coli contains several members of this family including GntU, a low affinity transporter and GntT, a high affinity transporter .
Insect protein of unknown function (Insect_Unk)
Type: Family

This family of insect proteins are each about 100 amino acids long and have 6 conserved cysteine residues. They all have a predicted signal peptide and are probably excreted. The function of the proteins is unknown .
Glycoside hydrolase, family 42 (Glyco_hydro_42)
Type: Family

O-Glycosyl hydrolases (

) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.

This group of beta-galactosidase enzymes (

) belong to the glycosyl hydrolase 42 family

. The enzyme catalyses the hydrolysis of terminal, non-reducing terminal beta-D-galactosidase residues.
mRNA interferase PemK-like (PemK-like)
Type: Family

PemK is a growth inhibitor in Escherichia coli known to bind to the promoter region of the Pem operon, auto-regulating synthesis. It is responsible for mediating cell death through inhibiting protein synthesis through the cleavage of single-stranded RNA. PemK is part of the PemK-PemI system, where PemI is an antitoxin that inhibits the action of the PemK toxin . PemK homologues have been found in a wide range of bacteria, which together form an endonuclease family that interfere with mRNA function. This family consists of the PemK protein in addition to ChpA, ChpB, Kid and MazF.
Outer capsid sigma 1s (Capsid_sigma_1s)
Type: Family

The reoviral gene S1 encodes for haemagglutinin (sigma 1 protein), an outer capsid protein and a major factor in determining virus-host cell interactions. Sigma 1s is one of two translation products of the S1 gene.
Pre-hexon-linking protein IIIa (Hex_IIIa)
Type: Family

The major capsid protein of the adenovirus strain is also known as a hexon. This entry represents protein IIIa, which is a hexon-associated protein that is likely to participate in vertex stabilisation and genome packaging. It stabilises vertices by tethering the penton bases to neighbouring peripentonal hexons, and lashes peripentonal hexons to the neighbouring hexons through its interaction with hexon-linking protein. During virus assembly, it seems to play a role in packaging of viral DNA via its interaction with packaging protein 3 .
Flagellar hook-associated protein 2, N-terminal (FliD_N)
Type: Domain

The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria . This entry represents the N-terminal region of this family of proteins.
Transcription factor WhiB (Whib)
Type: Family

WhiB is a putative transcription factor in Actinobacteria, required for differentiation and sporulation. The process of mycelium formation in Streptomyces, which occurs in response to nutrient limitation, is controlled by a number of whi genes, named for the white colour of aerial hyphae when mutations occur in these genes. The normal colour is grey. The exact role of WhiB is not clear, but a mutation in the gene results in white, tightly coiled aerial hyphae .
Borrelia outer surface protein E/F (OspEF)
Type: Family

This is a family of outer surface proteins (Osp) from the Borrelia spp. spirochete . The family includes OspE, OspF, and OspEF-related proteins (Erp) . These proteins are coded for on different circular plasmids in the Borrelia genome.

Borrelia burgdorferi spirochetes, that cause Lyme borreliosis, survive for a long time in human serum due to their ability to succesfully evade the complement system, an important arm of innate immunity. The outer surface protein E (OspE) of B. burgdorferi is required for this since it recruits complement regulator factor H (FH) onto the bacterial surface to evade complement-mediated cell lysis .
N-acyltransferase NodA (NodA)
Type: Family

Rhizobial nodulation (Nod) factors are signalling molecules secreted by root-nodulating rhizobia in response to flavanoids excreted by the host plant. They induce various symbiotic responses on the roots of the leguminous host plant at low concentrations, and are required for successful infection . Nodulation factors are lipo-chitooligosaccharides made by bacterial nitrogen-fixing bacteria as a signal to plant hosts. Nod factors differ slightly from system to system and serve as host range determinants.

All members of this family belong to NodABC systems .
Herpesvirus US2, varicellovirus-type (Herpes_US2_varicellovirus)
Type: Family

This is a family of unique short (US) region proteins from Herpesviridae strains. The US2 family has no known function.
Nucleocapsid N protein (Nairo_nucleocap)
Type: Family

The nucleoprotein of the ssRNA negative-strand Nairovirus is an internal part of the virus particle.
Phosphoprotein, pneumoviral (Pprotein_pneumovir)
Type: Family

This family represents a phosphoprotein from Paramyxoviridae, which could be a putative RNA polymerase alpha subunit that may function in template binding .
DNA recombination-mediator protein A (DprA)
Type: Family

DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation . In Helicobacter pylori, DprA is required for natural chromosomal and plasmid transformation . It has now been shown that DprA binds cooperatively to single-stranded DNA (ssDNA) and interacts with RecA. In the process, DprA-RecA-ssDNA filaments are produced and these filaments catalyse the homology-dependent formation of joint molecules. While the Escherichia coli SSB protein limits access of RecA to ssDNA, DprA alleviates this barrier . DprA has a role not only in ensuring production of transformants via interaction with RecA, it is also involved in competence shut-off via interaction with ComE .
Ribosome hibernation promoting factor/RaiA (RHF/RaiA)
Type: Family

This family consists of ribosome hibernation promoting factor (RHF). RHF promotes and stabilizes dimerization of 70S ribosomes by the ribosome modulation factor (RMF), leading to the formation of inactive 100S ribosomes during the stationary phase .
Rhabdovirus non-virion protein (Rhabd_NV)
Type: Family

Infectious hematopoietic necrosis virus (IHNV) is a member of the family Rhabdoviridae. The non-virion protein (NV) is coded for by one of the six genes of the IHNV genome , but is absent in vesiculovirus-like rhabdovirus .
Replication initiation protein-like, C-terminal (REP-like_C)
Type: Domain

Plasmid replication is initiated by the replication initiation factor (REP). This entry represents the C-terminal domain of Replication initiation protein from Staphylococcus aureus and similar proteins mainly found in firmicutes and proteobacteria. Many members are probable specific topoisomerase that make a sequence-specific single-stranded nick in the plasmid DNA at the origin of replication. Putative DNA relaxase NicK from Bacillus subtilis, which is involved in the transfer of the integrative and conjugative element ICEBs1 and probably mediates conjugation of ICEBs1 by nicking at oriT on the conjugative element and facilitates the translocation of a single strand of ICEBs1 DNA through a transmembrane conjugation pore into the recipient cell .
Herpesvirus glycoprotein H (Herpes_gH)
Type: Family

Herpesviruses are enveloped by a lipid bilayer that contains at least a dozen glycoproteins. The virion surface glycoproteins mediate recognition of susceptible cells and promote fusion of the viral envelope with the cell membrane, leading to virus entry. No single glycoprotein associated with the virion membrane has been identified as the fusogen .

Glycoprotein L (gL) forms a non-covalently linked heterodimer with glycoprotein H (gH). This heterodimer is essential for virus-cell and cell-cell fusion since the association of gH and gL is necessary for correct localisation of gH to the virion or cell surface. gH anchoring the heterodimer to the plasma membrane through its transmembrane domain. gL lacks a transmembrane domain and is secreted from cells when expressed in the absence of gH .

This entry represents Herpesvirus glycoprotein H (gH), which is a virion associated envelope glycoprotein . Heterodimer formation between gH and gL has been demonstrated in both virions and infected cells . Heterodimer formation between gL and gH is important for the proper folding of gH and its insertion into the membrane because the anti-gH conformation-dependent monoclonal antibodies (mAbs) 53S and LP11 bind gH only when gL is present .
SHS2 domain inserted in FtsA (SHS2_FtsA)
Type: Domain

FtsA is essential for bacterial cell division, and co-localises to the septal ring with FtsZ. The SHS2 domain, also known as subdomain 1C , is inserted into the RNAseH fold of FtsA , and is involved in protein-protein interaction .
CobW/HypB/UreG, nucleotide-binding domain (CobW/HypB/UreG_nucleotide-bd)
Type: Domain

This domain is found in HypB, a hydrogenase expression/formation protein, and urease accessory protein UreG. Both these proteins contain a P-loop nucleotide binding motif . HypB has GTPase activity and is a guanine nucleotide binding protein . UreG is a GTPase in charge of nucleotide hydrolysis required for activation of the urease enzyme . Both GTPases are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression . UreG is required for functional incorporation of the urease nickel metallocentre . GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins .

Other proteins containing this domain include P47K (

), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, CobW (

), which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans , and YjiA . Both CobW and YjiA are members of the metal homeostasis-associated COG0523 family of GTPases .
ABA/WDS induced protein (ABA_WDS)
Type: Family

This is a family of plant proteins induced by water deficit stress (WDS) , or abscisic acid (ABA) stress and ripening . The Ip3 cDNA clone is expressed at high levels in the roots, and is induced by ABA under WDS.
BRO N-terminal domain (BRO_N_domain)
Type: Domain

The baculovirus Bro proteins are encoded by a multigene family. The typical Bro proteins that have been experimentally investigated are BroA, BroC and BroD from Bombyx mori uclear polyhedrosis virus (BmNV). They contain distinct amino- and carboxy-terminal domains (Bro-N and Bro-C, respectively) that are present independently of each other and in distinct contexts in a variety of other viral proteins. The Bro-N domain occurs in a stand-alone form or combined with other domains in proteins from temperate phages that infect Gram-positive bacteria and Myxococcus xanthus, and proteins encoded in the genomes of proteobacteria and Gram-positive bacteria. The Bro-N domain appears to define a distinct superfamily of widespread viral DNA-binding domains .
Probable DNA packing protein, C-terminal (DNA_pack_C)
Type: Domain

This family includes proteins that are probably involved in DNA packing in Herpesviridae. This domain is found at the C terminus of the protein.
Probable DNA packing protein, N-terminal (DNA_pack_N)
Type: Domain

This family includes proteins that are probably involved in DNA packing in Herpesviridae. This domain is normally found at the
N terminus of the protein.
Sugar-phosphate isomerase, RpiB/LacA/LacB family (RpiB_LacA_LacB)
Type: Family

This entry represents the sugar isomerase enzymes ribose 5-phosphate isomerase B (RpiB), galactose isomerase subunit A (LacA) and galactose isomerase subunit B (LacB).

Galactose-6-phosphate isomerase (

) is a heteromultimeric protein consisting of subunits LacA and LacB, and catalyses the conversion of D-galactose 6-phosphate to D-tagatose and 6-phosphate in the tagatose 6-phosphate pathway of lactose catabolism . Galactose-6-phosphate isomerase is induced by galactose or lactose.

Ribose 5-phosphate isomerase (

) forms a homodimer and catalyses the interconversion of D-ribose 5-phosphate and D-ribulose 5-phosphate in the non-oxidative branch of the pentose phosphate pathway. This reaction permits the synthesis of ribose from other sugars, as well as the recycling of sugars from nucleotide breakdown. Two unrelated enzymes can catalyse this reaction: RpiA (found in most organisms) and RpiB (found in some bacteria and eukaryotes). RpiB is also involved in metabolism of the rare sugar, allose, in addition to ribose sugars. The structures of RpiA and RpiB are distinct, RpiB having a Rossmann-type α/β/α sandwich topology .
Phosphotransferase system, EIIB component, type 2/3 (PTS_EIIB_2/3)
Type: Domain

The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes. The fold of IIB cellobiose shows similar structure to mammalian tyrosine phosphatases. This signature is often found downstream of

.