SII-SWORD/CoKE huggingface dataset:
Estrogen receptor beta-like, N-terminal (ER-beta-like_N)
Type: Domain

This entry represents the N-terminal domain of Estrogen receptor beta (ER-beta) and similar proteins from eukaryotes. This domain has approximately 110 amino acids in length and is usually found in association with

,

. There is a conserved IPS sequence motif and there are two completely conserved residues (Y and W) that may be functionally important.

ER-beta is a nuclear hormone receptor that binds estrogens with an affinity similar to that of ER-alpha, and activates expression of reporter genes containing estrogen response elements in an estrogen-dependent manner. ER-beta acts as a transcription factor once bound to its ligand and it can dimerise with ER-alpha . In humans, these receptors may play an important role in the development, treatment, and prognosis of breast cancer and other disorders such as osteoporosis, delayed bone age and continuous growth in adulthood, and multiple ovarian cysts in women .

This entry algo includes Estrogen receptor gamma (ER-gamma) from Micropogonias undulatus (Atlantic croaker).
Fertility inhibition protein FinO, N-terminal (Fertility_inhibition_FinO_N)
Type: Domain

This entry represents the N-terminal of the Fertility inhibition protein FinO, found in bacteria, and is typically between 62 and 102 amino acids in length.
Fungal protease inhibitor-1 (FPI1)
Type: Family

This entry represents fungal proteinase inhibitors found mainly in arthropodes, including fungal protease inhibitor-1 (FPI-1) from Antheraea mylitta (Tasar silkworm). FPI1 inhibits trypsin and chymotrypsin proteases from the fungi Aspergillus oryzae and Rhizopus oryzae. However, they do not inhibit papain-like proteases from the bacterium Bacillus licheniformis . The crystal structure of this protein was solved using the single isomorphous replacement with anomalous scattering (SIRAS), which revealed that it is a single domain protein possessing a unique fold that consists of three helices and five β-strands stabilized by a network of six disulfide bonds . Members of this family belong to MEROPS inhibitor family I83, clan JH.
Glycosyltransferase, GlcNAc (Glycosyltransferase)
Type: Family

GlcNAc is an enzyme that carries out the first glycosylation step of hydroxylated Skp1; it is found in the cytoplasm and results in a pentasaccharide-linked 'HyPro-143.
HTH DNA binding domain (HTH_DNA-bd)
Type: Domain

This entry represents the C-terminal helix-turn-helix DNA binding domain of a group of bacterial uncharacterised proteins, including Uncharacterized protein y4cF from Sinorhizobium fredii.
ImpA, C-terminal (ImpA_C)
Type: Domain

This entry represents a conserved region located towards the C-terminal end of ImpA and related proteins. ImpA is an inner membrane protein, which has been suggested to be involved with proteins that are exported and associated with colony variations in Actinobacillus actinomycetemcomitans . Note that many members are hypothetical proteins.
Killing trait, RebB (Killing_trait_RebB)
Type: Family

R-bodies are highly insoluble protein ribbons which coil into cylindrical structures in the cell and the genes for their synthesis and assembly are encoded on a plasmid. One of these three proteins is RebB, which this entry represents.

RebB is one of three proteins necessary for the production of R- bodies, refractile inclusion bodies produced by a small number of bacterial species, essential for the expression of the killing trait of the endosymbiont bacteria that produce them for attack upon the host Paramecium. Note that many members are uncharacterised proteins .
Low molecular weight S layer protein, N-terminal (Low_molc_weight_S-layer_N)
Type: Domain

Clostridial species have a layer of surface proteins surrounding their membrane. This layer is comprised of a high molecular weight protein and a low molecular weight protein. It is a structural domain. This domain is the N-terminal domain of the low molecular weight protein. There is a conserved LGDG sequence motif .
Melanoma associated antigen, N-terminal (MAGE_N)
Type: Domain

This domain is found N-terminal in various melanoma associated antigens from eukaryotes, and is typically between 82 and 96 amino acids in length. These are tumour rejection antigens which are expressed on HLA-A1 of tumour cells and they are recognised by cytotoxic T lymphocytes (CTLs) .
Murid betaherpesvirus 1, M157 (MuHV-1_M157)
Type: Family

This entry represents the M157 glycoprotein, a divergent form of MHC class I-like proteins which is the protein product of Murid betaherpesvirus 1. This protein is unique in its ability to engage both activating (Ly49H) and inhibitory (Ly49I) natural killer cell receptors. M157 is involved in intra- and intermolecular interacts within and between its domains to form a compact MHC-like molecule . This entry also includes proteins found in Muromegalovirus.
Formate dehydrogenase, delta subunit (Formate_DH_dsu)
Type: Family

FdsD is the delta subunit of the enzyme formate dehydrogenase. This subunit may play a role in maintaining the quaternary structure by means of electrostatic interactions with the other subunits . The delta subunit is not involved in the active centre of the enzyme .
Bocavirus non-capsid protein, NP1 (Bocavirus_NP1)
Type: Family

This entry represents the bocavirus non-capsid protein NP1 .
Parvovirus non-structural protein 1, N-terminal (Parvovirus_NS1_N)
Type: Domain

This entry represents a domain of the parvovirus Initiator protein 1 (NS1, also known as non-structural protein 1). It is found immediately N-terminal to the helicase domain and binds to the origin of replication . Parvoviral NS1 regulates host gene expression through histone acetylation .

Parvoviruses are some of the smallest viruses containing linear, non-segmented single-stranded DNA genomes, with an average genome size of 5000 nucleotides. Parvoviruses have been described that infect a wide range of invertebrates and vertebrates and are well known for causing enteric disease in mammals. Genomes contain two large ORFs: NS1 and VP1; other ORFs are found in some sub-types and different gene products can arise from splice variants and the use of different start codons .
Bacteriophage phi-Lf, Orf112 (Phage_phi-Lf_Orf112)
Type: Family

This entry represents a phage protein found in bacteria and viruses, they are typically between 112 and 194 amino acids in length. Note that many members are hypothetical proteins.
Membrane-integrating protein Mistic (Membrane-integrating_Mistic)
Type: Family

Mistic is an integral membrane protein that folds autonomously into the membrane . It is conserved in the Bacilli bacteria. The protein forms a helical bundle with a polar lipid-facing surface. Mistic can be used for high-level production of other membrane proteins in their native conformations .
Methanol-cobalamin methyltransferase, B subunit (MeOH-cob_MeTrfase_bsu)
Type: Family

This entry represents a family of methanol-cobalamin methyltransferase B subunit (MtaB) proteins found in bacteria and archaea. Proteins in this family are approximately 460 amino acids in length. MtaB folds as a TIM barrel and contains a novel zinc-binding motif. Zinc(II) lies at the bottom of a funnel formed at the C-terminal β-barrel end and ligates to two cysteinyl sulphurs (Cys-220 and Cys-269) and one carboxylate oxygen (Glu-164). The function of this protein is to catalyse the cleavage of the C-O bond in methanol by an SN2 mechanism. It complexes with MtaA and MtaC to perform this function .
Minor capsid protein (Minor_capsid_protein)
Type: Family

This entry represents a family of minor capsid proteins found in a number of bacteriophages including Bacteriophage A118. The function of these proteins is not known.
Nepovirus subgroup A, RNA2 polyprotein, Protein 2A (Nepovirus_subgr_A_2A)
Type: Domain

Nepoviruses are plant viruses that, together with comoviruses and picornaviruses, are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. Its genome consist of two single-stranded RNAs, both required for infection .

RNA2 from the subgroup A of these viruses encode the polyprotein P2, which includes Protein 2A, the cell-to-cell movement protein and the coat protein .

This entry includes the N-terminal region of the RNA2 polyprotein, termed Protein 2A, which is implicated in the replication RNA2 . This domain is normally found in association with

,

and

.
Protein GAPT (Protein_GAPT)
Type: Family

Protein GAPT (also known as Growth-factor Receptor-Bound protein 2 (GRB2)-binding adaptor protein, transmembrane) belongs to a class of transmembrane (TM) adaptor proteins that couple antigen receptor engagement to downstream signalling cascades in lymphocytes . Expressed in B cells and myeloid cells, GAPT negatively regulates B-cell proliferation following stimulation through the B-cell receptor; it may also play an important role in the proper maintenance of marginal zone B-cells .

GAPT has an extracellular domain, a TM domain, and a cytoplasmic tail with multiple GRB2-binding motifs; it constitutively associates with GRB2 SH3 domains via a proline-rich region . Its cytosolic domain contains 7 tyrosine residues (4 of them within GRB2-binding motifs), and 2 cysteines in the juxta-membrane region, which may be palmitoylated .
Nuclear abundant poly(A) RNA-binding protein Nab2, N-terminal (Nab2_N)
Type: Domain

Nab2 is a yeast heterogeneous nuclear ribonucleoprotein that modulates poly(A) tail length and mRNA. This is the N-terminal domain of the protein which mediates interactions with the C-terminal globular domain, Myosin-like protein 1 and the mRNA export factor, Gfd1 . The N-terminal domain of Nab2 shows a structure of a helical fold. The N-terminal domain of Nab2 is thought to mediate protein:protein interactions that facilitate the nuclear export of mRNA . An essential hydrophobic Phe73 patch on the N-terminal domain is thought to be an important component of the interface between Nab2 and Mlp1 .
Het-s prion-forming domain (Het-s_prion_dom)
Type: Domain

This entry represents the prion domain of Het-s. Het-s plays a role in heterokaryon incompatibility, which prevents different forms of parasitism . The C terminus of Het-s is unstructured in solution but, in vitro, amyloid fibrils from the prion-forming domain form a structure consisting of a left-handed β-solenoid which contains two windings per molecule .
AvrE-family Type-III effector protein (AvrE_T3Es)
Type: Family

This family is secreted by Gram-negative Gammaproteobacteria such as Pseudomonas syringae of tomato and Erwinia amylovora (Fire blight bacteria), amongst others. It is an essential pathogenicity factor of approximately 198kDa. Its injection into the host-plant is dependent upon the bacterial type III or Hrp secretion system . The family is long and carries a number of predicted functional regions, including an ERMS or endoplasmic reticulum membrane retention signal at both the C- and the N termini, a leucine-zipper motif from residues 539-560, and a nuclear localisation signal at 1358-1361. This conserved AvrE-family of effectors is among the few that are required for full virulence of many phytopathogenic pseudomonads, erwinias and pantoeas .

A double β-propeller structure is found towards the N terminus . Furthermore, AvrE1, an AvrE-family T3E from Pseudomonas syringae pv. tomato strain DC3000, associates with specific PP2A B- subunit proteins from its susceptible host Arabidopsis. In a similar fashion, the WtsE (AvrE-family T3E from the maize pathogen Pantoea stewartii subsp. Stewartii) has been shown to target maize protein phosphatase 2A (PP2A) heterotrimeric enzyme complexes via direct interaction with B- regulatory subunits. Taken together, it has been indicated that that sub-component specific PP2A complexes are targeted by bacterial T3Es, including direct targeting by members of the widely conserved AvrE-family. Additionally, DspE, a type-III effector encoded by the broad-host-range bacterial soft-rot pathogen Pectobacterium carotovorum subsp. carotovorum (Pcc), has been indicated to be required and sufficient for disease-associated cell death in host plants .
Accessory protein p12I (p12I)
Type: Family

This entry represents viral proteins of approximately 100 amino acids in length. p12I binds to the immature beta and gamma-c chains of the interleukin-2 receptor retarding their translocation to the plasma membrane. p12I forms dimers which bind to these chains .
Uncharacterised protein family PixA/AidA (Uncharacterised_PixA/AidA)
Type: Family

This entry represents bacterial proteins that are typically between 173 and 191 amino acids in length. PixA is thought to be specifically produced in Xenorhabdus nematophila. It is an inclusion body protein . This entry also matches AidA.
Osteocrin (Osteocrin)
Type: Family

Osteocrin, also known as Musclin, is a muscle derived secretory peptide which induces insulin resistance in vitro. It encodes a 130 amino acid sequence including a N-terminal 30 amino acid signal sequence. Musclin expression level is tightly regulated by nutritional changes .
Bacteriocin, lactococcin-G (Bacteriocin_lactococcin-G)
Type: Family

This entry represents Lactococcin-G subunit beta, which together with subunit alpha constitutes the two-peptide bacteriocin lactococcin G. This family of proteins represents the N-terminal domain which has an α-helical structure and is amphiphilic. Both peptides have a GxxxG motif which they use for interaction through a helix-helix structure . It is thought to kill Lactococci .
SLy proteins associated disordered region (SPIDER)
Type: Domain

This entry represents the SLy proteins associated disordered region (SPIDER), which is conserved in the SLy protein family. It has a disordered nature and ranges from 143 to 154 residues long. The region includes a conserved LGKK motif of unknown function as well as a nuclear localisation sequence . In most members of this group of proteins from vertebrates, this region is followed by SH3 (

) and SAM (

) domains, suggesting a role in the signalling function of these proteins . SPIDER is a part of the SASH1 protein that plays essential roles in tumour cell adhesion and migration . Multiple disease variants in the SPIDER of SASH1 suggest that it may be involved in the regulation of skin pigmentation .
Mercury ion transport, MerF (Mercury_ion_transport_MerF)
Type: Family

This entry represents Mercury ion transport protein MerF. This protein, the smallest encoded by the mer operon in bacteria, plays a role in the resistance to environmental mercury toxicity by importing Hg2+ and reducing it to volatile Hg(0) . It has also been related to the trasport of cadmium . MerF has a core helix-loop-helix domain. It also has two vicinal pairs of cysteine residues which are involved in the transport of Hg(II) across the membrane and are exposed to the cytoplasm .
NADH-quinone oxidoreductase, subunit15 (NADH_quinone_OxRdtase_su15)
Type: Family

This entry represents subunit 15 of NADH-quinone oxidoreductase, also known as Complex I. The nqo15 subunit has probably a role in complex stabilisation, and may be also involved in the storage of iron for iron-sulphur cluster regeneration in the complex .
NPR1/NIM1-like, C-terminal (NPR1/NIM1-like_C)
Type: Domain

This entry represents the NPR1/NIM1 like defence protein, which is found in many plant species . The eukaryotic proteins are typically between 251 and 588 amino acids in length.

NPR1/NIM1 like defence protein mediates the binding of TGA factors to the as-1 motif, found in the pathogenesis-related PR-1 gene which leads to the transcriptional regulation of the gene defence. Controls the onset of systemic acquired resistance (SAR) .
Domain of unknown function DUF3734 (DUF3734)
Type: Domain

This entry represents a domain found in bacterial proteins and it is approximately 110 amino acids in length. This domain is found in association with

, localised to the C-terminal. There are two completely conserved residues (F and G) that may be functionally important. Proteins containing this domain are frequently annotated as patatin family phospholipases however there is little accompanying literature to confirm this.
Vibrio phage VSK, Orf152 (Vibrio_phage_VSK_Orf152)
Type: Family

This entry is represented by Vibrio phage VSK, Orf152. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
CPH domain (CPH_domain)
Type: Domain

The CPH domain is found in the Cullin-7, PARC and HERC2 proteins, which are all components of known or predicted E3-ubiquitin ligases. The CPH domain is a protein-protein interaction module that binds the teramerisation domain of the tumour suppressor protein p53 . Structurally it forms a β-barrel fold similar to the SH3, Tudor and KOW and domains. Unlike the SH3 and Tudor domains, which bind to small peptides, the CPH domain appears to bind to an extended surface on p53.
Bacteriophage P22, Gp10, DNA-stabilising (Phage_P22_Gp10)
Type: Family

This entry represents the Bacteriophage P22, Gp10, DNA-stabilising protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

Members of this family are phage proteins involved with stabilising the head assembly unit and condensed DNA within the capsid .
Plant organelle RNA recognition domain (PORR_domain)
Type: Domain

The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts . It seems likely that most PORR proteins function in organellar RNA metabolism .
N-glycosylation protein EOS1 (N-glycosylation_EOS1)
Type: Family

The Saccharomyces cerevisiae EOS1 (Endoplasmic Reticulum-localised and Oxidants Sensitive) gene is not essential for cell growth, but the EOS1 deletion strain YNL080c confers, to some degree, a slow growth phenotype . The gene product, localised to the ER membrane, is involved in oxidative stress tolerance , and may also be involved in N-glycosylation of cellular proteins. Its deduced amino acid sequence contains four potential transmembrane (TM) domains. Although its precise molecular function has not yet been established, it may be involved in cellular homeostasis .
Optomotor-blind protein, N-terminal (Optomoror-blind_N)
Type: Domain

Optomotor-blind is one of the essential toolkit proteins for coordinating development in diverse animal taxa. In Drosophila, where it has been characterised in the most detail, it plays a key role in establishing the abdominal pigmentation pattern, in development of the central nervous system and leg and wing imaginal disc-formation . This entry represents the N-terminal domain of the optomotor-blind protein in Drosophila and other flies. It does not include the T-box-containing transcription factor that plays a part in DNA-binding.
Peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase A (PNGase_A)
Type: Family

Peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase A (PNGase A), unlike many other amidases, is capable of hydrolysing glycopeptides with an alpha-1,3-fucosylated asparagine-bound N-acetylglucosamine (GlcNAc). PNGase A is a heterodimer composed of a large and small subunit . This entry represents the PNGase A precursor, which contains both subunits and is activated by proteolytic cleavage.
Argonaute PAZ domain, archaea (PAZ_arc)
Type: Domain

This entry corresponds to the PAZ domain found in some archaeal argonaute proteins, such as

and

. It is an siRNA binding domain.
KfrA, N-terminal DNA-binding domain (KfrA_DNA-bd_N)
Type: Domain

The KfrA family of proteins are encoded on plasmids, generally in or near gene clusters involved in stable inheritance functions. These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning .

This entry represents the N-terminal DNA-binding domain.
Protein Ste5, Fus3-binding domain (Ste5_Fus3-bd_dom)
Type: Domain

The Saccharomyces cerevisiae pheromone response pathway involves a cascade of 3 MAP kinases Ste11, Ste7, and Fus3. Ste5 is an essential element of this cascade, acting as a scaffold for each of the MAP kinases prior to signalling . This entry represents the Fus3-binding domain of Ste5, also known as the minimal scaffold domain. It acts as a co-catalyst, binding Fus3 and promoting its phosphorylation by Ste7 . In the absence of this domain, Fus3 is an extremely poor substrate for Ste7. The requirement for both Ste7 and this domain in Fus3 activation ensures that Fus3 is selectively activated by the mating pathway and not by other pathways that also utilise Ste7.
Restriction endonuclease, type II, HinP1I (Restrct_endonuc_II_HinP1I)
Type: Family

There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , as summarised below:

Type I enzymes (

) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (

) activities.

Type II enzymes (

) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.

Type III enzymes (

) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (

).

Type IV enzymes target methylated DNA.

Type II restriction endonucleases (

) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four β-strands and one α-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin . However, there is still considerable diversity amongst restriction endonucleases . The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone .

Hinp1I is a type II restriction endonuclease that recognises and cleaves a palindromic tetranucleotide sequence (G/CGC) resulting in 2 nt 5' overhanging ends . Structurally HinP1I consists of a conserved catalytic core domain, containing an active site motif SDC18QXK, and a DNA-binding domain .