SII-SWORD/CoKE huggingface dataset:
Non-structural protein 11/12 (Pns11/12)
Type: Family

This is a family of unknown function found in Phytoreovirus. Family members include the Rice dwarf virus Pns11 and Pns12 proteins. Rice dwarf virus (RDV) is an icosahedral, double-layered particle. The viral genome consists of 12 segmented dsRNAs that encode seven structural (P1, P2, P3, P5, P7, P8 and P9) and five non-structural (Pns4, Pns6, Pns10, Pns11 and Pns12) proteins. Pns11 is known to bind nucleic acids and Pns12 is a phosphorylated protein. The non-structural proteins Pns6, Pns11 and Pns12 of RDV are the major constituents of the matrix of viral inclusions in which the assembly of progeny virions and the synthesis of viral RNA are thought to occur .
TSX (TSX)
Type: Family

The Tsx gene resides at the X-inactivation centre and once thought to encode a protein expressed in testis. However, this was disputed upon further analysis. ORF and immunostaining analysis concluded that Tsx may be non-coding. Tsx long transcript is abundantly expressed in meiotic germ cells, embryonic stem cells, and brain .
Gene product 79 (Gp79)
Type: Family

This is a family of unknown function found in Mycobacterium phages. Family members include the full Gp79 protein found in Mycobacteriophage L5

. Mycobacteriophage L5 is a phage isolated from Mycobacterium smegmatis. It forms stable lysogens in M. smegmatis and has a broad host range among the pathogenic mycobacteria. L5 encodes gene products (gp) toxic to the host M. smegmatis. Expression of gp79 interferes with the cell membrane or cell-wall synthesis of M. smegmatis, leading to altered cell morphology. It also has a bactericidal effect on E. coli. The N-terminal segment of gp79 (amino acids 1-41) shares sequence similarity with the signal peptide of the D-alanyl-D-alanine carboxypeptidase of Bacillus licheniformis. This enzyme removes C-terminal D-alanyl residues from sugarpeptide cell-wall precursors and is also a penicillin-binding protein (PBP). The homology of the hydrophobic N-terminal part of gp79 to a PBP (penicillin-binding protein) signal peptide may indicate an interaction of gp79 with proteins or metabolites involved in the peptidoglycan synthesis of M. smegmatis .
Protein of unknown function DUF5424 (DUF5424)
Type: Family

This is a family of unknown function specific to Rickettsia.
Protein of unknown function DUF5423 (DUF5423)
Type: Family

This is a family of unknown function found in Chlamydia. Family members have 4 predicted trans-membrane regions.
Lacto-N-biose phosphorylase, C-terminal domain (LBP_C)
Type: Domain

This entry represent the C-terminal domain of 1,3-beta-galactosyl-N-acetylhexosamine phosphorylase (InpA) from Bifidobacterium and D-galactosyl-beta-1->4-L-rhamnose phosphorylase (Cphy_1920) from Lachnoclostridium phytofermentans.

LnpA can reversibly phosphorolyzes lacto-N-biose to Gal1-P and N-acetylglucosamine (GlcNAc) and galacto-N-biose to Gal1-P and N-acetylgalactosamine (GalNAc). It is involved in the lacto-N-biose I/galacto-N-biose (LNB/GNB) degradation pathway, which is important for host intestinal colonization by bifidobacteria .

Cphy_1920 can reversibly phosphorolyzes beta-D-galactosyl-(1->4)-L-rhamnose to form alpha-D-galactose 1-phosphate and L-rhamnose. But it does not phosphorolyze galacto-N-biose or lacto-N-biose .
Protein of unknown function DUF5422 (DUF5422)
Type: Family

This is a family of unknown function found in Chlamydia. Members of this family have 1-4 predicted trans-membrane regions.
Protein of unknown function DUF5421 (DUF5421)
Type: Family

This is a family of unknown function found in Chlamydia.
Protein of unknown function DUF5420 (DUF5420)
Type: Family

This is a family of unknown function mainly found in Gammaproteobacteria.
Honey bee toxin (Bee_toxin)
Type: Family

Bee venom contains a variety of peptides such as melittin, apamin, adolapin and mast cell degranulating peptide . Bee venom has been used in the treatment of major neurodegenerative disorders, including Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis and amyotrophic lateral sclerosis . Secondary structure analysis of apamin, mast cell degranulating peptide, tertiapin and secapin have been studied. The predicted structure for mast cell degranulating peptide is almost spherical with the eight positive centres evenly distributed over the surface. It has also been suggested that these four peptides share a common folding pattern, which is centred on a β-turn covalently linked to an α-helical segment by two disulphide links. It is further suggested that apamin, mast cell degranulating peptide and tertiapin form a single molecular class .

This family includes apamin and mast cell degranulating peptide. Apamin, the most widely studied member of this family has been shown to be a selective blocker of small-conductance Ca2-activated K (KCa2.X or SK) channels . It is a promising anti neuroinflammatory agent that could be used to prevent and treat various neurological disorders . Apamin also blocks Kv1.3 channels and is able to inhibit neuromuscular transmission by a mechanism independent of the blockade of SK channels, which may involve the activation of inhibitory muscarinic M2 receptors on motor nerve terminals .
Protein KleE (KleE)
Type: Family

Proteins in this family are mostly from Proteobacteria. Family Members are predicted to contain two trans-membrane regions.
Lacto-N-biose phosphorylase, central domain (LBP_M)
Type: Domain

This entry represents the central domain found in lacto-N-biose phosphorylase (lnpA) from Bifidobacterium . Proteins containing this domain also include D-galactosyl-beta-1->4-L-rhamnose phosphorylase (Cphy_1920) from Lachnoclostridium phytofermentans .

LnpA can reversibly phosphorolyzes lacto-N-biose to Gal1-P and N-acetylglucosamine (GlcNAc) and galacto-N-biose to Gal1-P and N-acetylgalactosamine (GalNAc). It is involved in the lacto-N-biose I/galacto-N-biose (LNB/GNB) degradation pathway, which is important for host intestinal colonization by bifidobacteria .

Cphy_1920 can reversibly phosphorolyzes beta-D-galactosyl-(1->4)-L-rhamnose to form alpha-D-galactose 1-phosphate and L-rhamnose. But it does not phosphorolyze galacto-N-biose or lacto-N-biose .
Glycosyl hydrolase 101, beta-sandwich domain (Beta_sandwich_GH101)
Type: Domain

Virulence of pathogenic organisms such as the Gram-positive Streptococcus pneumoniae is largely determined by the ability to degrade host glycoproteins and to metabolise the resultant carbohydrates. Endo-alpha-N-acetylgalactosaminidase (

) belongs to the GH101 family of glycoside hydrolases, and specifically cleaves Gal-beta-1,3-GalNAc-alpha-Ser/Thr (T-antigen, galacto-N-biose), the core 1 type O-linked glycan common to mucin glycoproteins .

This entry represents a β-sandwich domain in GH101 family proteins.
Protein of unknown function DUF5407 (DUF5407)
Type: Family

This is a family of unknown function mostly found in Chlamydiia.
Protein of unknown function DUF5408 (DUF5408)
Type: Family

This is a family of unknown function found in Helicobacteraceae. Family members are predicted to contain one trans-membrane region.
Nrap protein, domain 2 (Nrap_D2)
Type: Domain

This entry represents a conserved domain found in Nrap.

Nucleolar RNA-associated proteins (Nrap) are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript .
Nrap protein, domain 3 (Nrap_D3)
Type: Domain

This entry represents a conserved domain found in Nrap.

Nucleolar RNA-associated proteins (Nrap) are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript .
Nrap protein, domain 4 (Nrap_D4)
Type: Domain

This entry represents a conserved domain found in Nrap.

Nucleolar RNA-associated proteins (Nrap) are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript .
Nrap protein, domain 5 (Nrap_D5)
Type: Domain

This entry represents a conserved domain found in Nrap.

Nucleolar RNA-associated proteins (Nrap) are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript .
Nrap protein, domain 6 (Nrap_D6)
Type: Domain

This entry represents a conserved domain found in Nrap.

Nucleolar RNA-associated proteins (Nrap) are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript .
Malonyl-CoA decarboxylase, N-terminal (MCD_N)
Type: Domain

This entry represents the N-terminal domain of Malonyl-CoA decarboxylase .

Malonyl-CoA, in addition to being an intermediate in the
de novo
synthesis of fatty acids, is an inhibitor of carnitine palmitoyltransferase I, the enzyme that regulates the transfer of long-chain fatty acyl-CoA into mitochondria, where they are oxidised. After exercise, malonyl-CoA decarboxylase participates with acetyl-CoA carboxylase in regulating the concentration of malonyl-CoA in liver and adipose tissue, as well as in muscle. Malonyl-CoA decarboxylase is regulated by AMP-activated protein kinase (AMPK) .
Alpha galactosidase A, C-terminal domain (Melibiase/NAGA_C)
Type: Domain

Alpha-galactosidase (melibiase) catalyses the hydrolysis of melibiose into galactose and glucose . Alpha-N-acetylgalactosaminidase catalyses the hydrolysis of terminal non-reducing N-acetyl-D-galactosamine residues in N-acetyl-alpha-D-galactosaminides .

This entry represents the C-terminal domain of these enzymes .
Protein VraX (VraX)
Type: Family

This entry represents the VraX proteins from Staphylococcus aureus. The vraX gene belongs to the vra operon together with the vraA gene encoding for a long chain fatty acid-CoA ligase, which is up-regulated in the VISA (vancomycin-intermediate S. aureus) . The gene product, a 55-amino acids protein,is upregulated in the stress response to cell wall-active antibiotics and other surface-interactive molecules. VraX harbours a putative phosphorylation site, and could therefore be involved in regulatory processes within the cell. However, no exact function has been demonstrated .
MatP, C-terminal ribbon-helix-helix domain (MatP_C)
Type: Domain

This entry represents the C-terminal ribbon-helix-helix domain of MatP.

MatP organises the macrodomain Ter of the chromosome of bacteria such as E coli. In these bacteria, insulated macrodomains influence the segregation of sister chromatids and the mobility of chromosomal DNA. Organisation of the Terminus region (Ter) into a macrodomain relies on the presence of a 13 bp motif called matS repeated 23 times in the 800-kb-long domain. MatS sites are the main targets in the E. coli chromosome of YcbG or MatP (macrodomain Ter protein). MatP accumulates in the cell as a discrete focus that co-localises with the Ter macrodomain. The effects of MatP inactivation reveal its role as the main organiser of the Ter macrodomain: in the absence of MatP, DNA is less compacted, the mobility of markers is increased, and segregation of the Ter macrodomain occurs early in the cell cycle. A specific organisational system is required in the Terminus region for bacterial chromosome management during the cell cycle .
NigD-like, C-terminal domain (NigD_C)
Type: Domain

This entry represents the C-terminal β-sandwich domain of NigD1 (BT_4005) from Bacteroides thetaiotaomicron and related proteins.

NigD1 is a protein encoded adjacent to genes required for biosynthesis and regulation of lipopolysaccharides (LPS) and phospholipids. This protein was shown to be involved in controlling outer membrane vesicles (OMV) production and act as a molecular switch for OMV biogenesis . NigD1 controls, via currently unknown mechanisms, the amount of LPS, proteins, and lipids allocated to OMVs .
Herpesvirus Glycoprotein B, PH-like domain 1 (Glycoprot_B_PH1)
Type: Domain

This entry represents first PH-like fold domain found in Herpesvirus glycoprotein B.

Glycoprotein B is an envelope glycoprotein that plays a role in host cell entry, cell to-cell virus transmission, and fusion of infected cells .
Uncharacterized protein YrzK-like (YrzK-like)
Type: Family

This is a family of unknown function found in Bacillus.
Uncharacterized protein YkpC-like (YkpC-like)
Type: Family

This is a family of unknown function found in Bacillus.
Late transcription unit A (LtuA)
Type: Family

This entry represents Late transcription unit A and similar sequences found in Chlamydia. Its specific function is unknown.
Herpesvirus Glycoprotein B, PH-like domain 2 (Glycoprot_B_PH2)
Type: Domain

This entry represents the second PH-like fold domain found in Herpesvirus glycoprotein B.

Glycoprotein B is an envelope glycoprotein that plays a role in host cell entry, cell to-cell virus transmission, and fusion of infected cells .
Mating factor A1 (MFA1)
Type: Family

Many pathogenic fungi undergo morphological changes in order to infect their hosts. The Ustilago maydis pathogenic cycle starts when two mating compatible haploid yeast cells recognize each other via a pheromone-receptor system which is encoded by two sets of genes a and b . The a locus (a1 and a2) controls the cell fusion by encoding intercellular recognition system consisting of precursors (mfa1 and mfa2) and receptors (pra1 and pra2) of lipopeptide pheromones . The open reading frame codes for a 42-amino acid precursor, which is processed to a shorter peptide of 13 amino acids. The terminal CAAX motif is typical of farnesylated fungal pheromones, in which the last three amino acids are removed during farnesylation of the cysteine residue. This terminal cysteine is known to be O-methylated in several fungal pheromones . Mating leads to the formation of a dikaryon filament, whose apical tip differentiates into a specialized structure for plant penetration known as the appressorium. Once inside the plant, U. maydis proliferates, inducing the formation of tumours and eventually develops into diploid spores . This mating process requires cross-talk between cAMP and mitogen-activated protein kinase (MAPK) signaling . Upstream regulation of a locus has been demonstrated where Hos2 (Histone deacetylases (HDACs) plant homologue) directly regulates the expression of U. maydis mating-type genes downstream of the cAMP-PKA pathway . Furthermore, pheromone recognition blocks cell cycle progression in U. maydis cells in order to prepare mating partners for conjugation where cells undergo arrest in G2 phase .

This family includes Mfa1 proteins from Ustilgo maydis and U. hordei.
Methylamine utilization protein MauJ (MauJ)
Type: Family

The exact function of the MauJ proteins is unknown but thought to be involved in methylamine utilization. MauJ is predicted to be a cytoplasmic protein.
Uncharacterized protein YhdX-like (YhdX-like)
Type: Family

This is a family of unknown function found in Bacillus.
Herpesvirus U62/UL91, functional domain (U62/UL91)
Type: Domain

Human herpesvirus 6A (HHV-6A) and HHV-6B are classified as roseoloviruses and are highly prevalent in the human population. Roseolovirus reactivation in an immunocompromised host can cause severe pathologies . Human cytomegalovirus (HCMV) is responsible for significant diseases in developing fetus as well as in an immunocompromised host. During their productive cycle, herpesviruses have a regulated temporal cascade of gene expression that can be divided into three general stages: immediate-early (IE), early (E), and late (L). Following viral DNA replication, late viral genes that mainly encode structural proteins start to be transcribed, ultimately leading to the assembly and release of infectious particles .

This domain is found in Human herpesvirus 6A and 6B (HHV-6A/B) as well as HCMV. Family members are shown to be involved in late gene expression such as UL91 in Human Cytomegalovirus (

). This functional domain is located on the N-terminal (1-71 amino acids) of full-length UL91. It has been found to suffice for transcriptional activation of true-late genes within the nucleus of infected cells. In other words, UL91 is fully functional as a 71-aa N-terminal polypeptide. This small 71-aa polypeptide contains all protein-protein interaction motifs crucial to mediate transcriptional activation .
Arm, DNA-binding domain (Arm-DNA-bind_5)
Type: Domain

This domain is the N-terminal Arm DNA-binding domain found in various tyrosine recombinases.
Protein of unknown function DUF5406 (DUF5406)
Type: Family

This is a family of unknown function mostly found in Bacteria.
Swarming motility protein SwrA (SwrA)
Type: Family

SwrA is a transcription factor involved in swarming motility (a multicellular movement of hyper-flagellated cells on a surface). It acts synergistically with DegU to drive the fla/che operon encoding flagella components, chemotaxis constituents and the alternative sigma factor sigmaD, which is regarded as the primary event in the development of motility . LonA protease of Bacillus subtilis inhibits SwrA by proteolytically restricting its accumulation . SwrA does not contain any known DNA binding domain, and it has been shown to interact with the N-terminal domain of DegU. Anecdotally, in most laboratory strains, e.g. 168, the swrA coding sequence contains a nucleotide insertion that prematurely interrupts its reading frame, causing a non-swarming phenotype strain .
Protein of unknown function DUF5411 (DUF5411)
Type: Family

This is a family of unknown function found in Bacteria.
Thiol-activated cytolysin C-terminal (Thiol_cytolys_C)
Type: Domain

This domain has an immunoglobulin like fold. It is found at the C terminus of the thiol-activated cytolsin protein.

Thiol-activated cytolysins are toxins produced by a variety of Gram-positive bacteria and are characterised by their ability to lyse cholesterol-containing membranes, their reversible inactivation by oxidation and their capacity to bind to cholesterol. All these proteins contain a single cysteine residue, located in their C-terminal section, which has been shown to be essential for the binding to cholesterol.
Arylsulfotransferase, N-terminal domain (Arylsulfotran_N)
Type: Domain

This entry represents the small N-terminal domain found in arylsulfotransferases. Arylsulphotransferase (ASST) transfers a sulphate group from phenolic sulphate esters to a phenolic acceptor substrate . Each ASST monomer consists of a small, N-terminal 7-stranded β-sandwich domain, and a large C-terminal, 6-bladed β-propeller domain .
Protein of unknown function DUF5417 (DUF5417)
Type: Family

This is a family of unknown function found in Proteobacteria and virus.
Protein of unknown function DUF5416 (DUF5416)
Type: Family

This is a family of unknown function found in Campylobacteria.
Glycosyl hydrolase family 59, central domain (Glyco_hydro_59_dom)
Type: Domain

This entry represents the central domain of the glycosyl hydrolase family 59 members.

Glycoside hydrolase family 59

comprises enzymes with only one known activity; galactocerebrosidase (

).

Globoid cell leukodystrophy (Krabbe disease) is a severe, autosomal recessive disorder that results from deficiency of galactocerebrosidase (GALC) activity . GALC is responsible for the lysosomal catabolism of certain galactolipids, including galactosylceramide and psychosine .
Protein of unknown function DUF5415 (DUF5415)
Type: Family

This is a family of unknown function found in Enterococcus.
Alpha-L-rhamnosidase, six-hairpin glycosidase domain (Bac_rhamnosid6H)
Type: Domain

The six-hairpin glycoside transferase domain contains up to seven α-hairpins arranged in closed circular array. Proteins containing this domain include bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are important bioactive compounds. For example, terpenyl glycosides, the glycosidic precursor of aromatic terpenoids, act as important flavouring substances in grapes. Other rhamnosides act as cytotoxic rhamnosylated terpenoids, as signal substances in plants or play a role in the antigenicity of pathogenic bacteria .
CT_584-like (CT_584-like)
Type: Family

This entry represents a protein family specific to Chlamydiales, including CT_584 from Chlamydia trachomatis, a type III secretion system (T3SS)-associated protein. CT_584 shows a four α-helix bundle at the N-terminal, a three-stranded antiparallel β-sheet, and two α-helices arranged in a kinked antiparallel manner at the C-terminal .
Alpha-L-rhamnosidase C-terminal domain (Bac_rhamnosid_C)
Type: Domain

This entry represents the C-terminal domain of the bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are important bioactive compounds. For example, terpenyl glycosides, the glycosidic precursor of aromatic terpenoids, act as important flavouring substances in grapes. Other rhamnosides act as cytotoxic rhamnosylated terpenoids, as signal substances in plants or play a role in the antigenicity of pathogenic bacteria .
Protein of unknown function DUF5413 (DUF5413)
Type: Family

This is a family of unknown function found in Bradyrhizobiaceae. Family members contain 3 or 4 predicted trans-membrane regions.
Urocanase, N-terminal domain (Urocanase_N)
Type: Domain

This entry represents the N-terminal domain found in Urocanase. It is found also in S-methyl thiourocanate hydratase which cannot use urocanate or thiourocanate as substrate and catalyses the conversion of S-methyl thiourocanate, to S-methyl-thiohydantoin-5-propanoate .

Urocanase (also known as imidazolonepropionate hydrolase or urocanate hydratase) is the enzyme that catalyses the second step in the degradation of histidine, the hydration of urocanate into imidazolonepropionate:

urocanate + H
2
O = 4,5-dihydro-4-oxo-5-imidazolepropanoate

Urocanase is found in some bacteria (gene hutU) , in the liver of many vertebrates, and has also been found in the plant Trifolium repens (white clover). Urocanase is a protein of about 60 Kd, it binds tightly to NAD
+
and uses it as an electrophil cofactor. A conserved cysteine has been found to be important for the catalytic mechanism and could be involved in the binding of the NAD
+
.
Urocanase, C-terminal domain (Urocanase_C)
Type: Domain

This entry represents the C-terminal domain found in Urocanase. It is found also in S-methyl thiourocanate hydratase which cannot use urocanate or thiourocanate as substrate and catalyses the conversion of S-methyl thiourocanate, to S-methyl-thiohydantoin-5-propanoate .

Urocanase (also known as imidazolonepropionate hydrolase or urocanate hydratase) is the enzyme that catalyses the second step in the degradation of histidine, the hydration of urocanate into imidazolonepropionate:

urocanate + H
2
O = 4,5-dihydro-4-oxo-5-imidazolepropanoate

Urocanase is found in some bacteria (gene hutU) , in the liver of many vertebrates, and has also been found in the plant Trifolium repens (white clover). Urocanase is a protein of about 60 Kd, it binds tightly to NAD
+
and uses it as an electrophil cofactor. A conserved cysteine has been found to be important for the catalytic mechanism and could be involved in the binding of the NAD
+
.