SII-SWORD/CoKE huggingface dataset:
Armadillo repeat-containing domain (ARM-rpt_dom)
Type: Domain

This domain contains armadillo-like repeats . Proteins containing this domain interact with numerous other proteins, through these interactions they are involved in a wide variety of processes including carcinogenesis , control of cellular ageing and survival , regulation of circadian rhythm and lysosomal sorting of G protein-coupled receptors .
Harbinger transposase-derived protein (Harbinger_derived_prot)
Type: Family

The majority of members of this family are from plants, including putative members of the PIF/Ping-Pong family .
CENP-V/GFA domain (CENP-V/GFA)
Type: Domain

Centromere protein (CENP)-V is a kinetochore protein that drives the progression of mitosis by coordinating chromatin condensation, positioning of sister chromatid centromeres and targeting of the chromosome passenger complex (CPC), a machinery that regulates the attachment of spindle microtubules (MTs) to kinetochores. CENP-V homologues are found in all vertebrates as well as in plants and nematodes. At the C-terminal end, CENP-V possesses an evolutionally conserved domain that comprises an array of seven cysteines and shows high structural similarity to glutathione-dependent formaldehyde-activating enzyme (Gfa), an enzyme responsible for formaldehyde detoxification in prokaryotes. CENP-V could be an enzyme that scavenges the formaldehyde produced in histone demethylation reactions. The three central cysteines and the flanking four cysteines separately coordinate to zinc, forming a catalytic centre and a structural fold for a tertiary structure, respectively .
VENN motif-containing domain (VENN_dom)
Type: Domain

This domain represents a conserved region found in many bacterial polymorphic toxins which is located before the C-terminal toxin modules .
Domain of unknown function DUF637, haemagglutinin putative (DUF637_hemagglutn_put)
Type: Domain

This entry represents a conserved region found in a bacterial proteins which may be hemagglutinins or hemolysins.
POPDC1-3 (POPDC1-3)
Type: Family

This entry represents the POPDC family of proteins, also known as the Popeye (POP) family, which includes POPDC1, 2 and 3 and is mainly restricted to vertebrates. It is preferentially expressed in developing and adult striated muscle . These proteins act as cAMP effectors and play a role in cardiac pacemaking and conduction. The POPDC proteins have been shown to regulate potassium and sodium channels .

POPDC1 has been associated with phenotypes including limb-girdle muscular dystrophy-25 (), cardiac arrhythmias and changes in POPDC protein expression have been linked to many cancers .

POPDC3 may play a role in the maintenance of heart function mediated, at least in part, through cAMP-binding and it is also important for skeletal muscle function. It may play a role in the regulation of KCNK2/TREK-1-mediated current amplitude. Pathogenic variants in POPDC3 are responsible for a novel type of autosomal recessive limb girdle muscular dystrophy .
SOUL heme-binding protein (SOUL_heme-bd)
Type: Family

This family represents a group of heme-binding proteins . It includes archaeal and bacterial homologues.

HEBP1-2 are part of the heme-binding protein HBP/SOUL family, which represents a group of evolutionary conserved putative heme-binding proteins. In humans, HEBP1 binds metalloporphyrins, free porphyrins and N-methylprotoporphyrins with similar affinities . HEBP2, in humans, can promote mitochondrial permeability transition and facilitate necrotic cell death under different types of stress conditions .
COBRA, plant (COBRA_pln)
Type: Family

This entry represents the COBRA family proteins. In Arabidopsis thaliana, members of the family are all extracellular glycosyl-phosphatidyl inositol-anchored proteins (GPI-linked) . COBRA is involved in determining the orientation of cell expansion, probably by playing an important role in cellulose deposition. It may act by recruiting cellulose synthesizing complexes to discrete positions on the cell surface. Some members of this family are annotated as phytochelatin synthase, but these annotations are incorrect .
Poxvirus A9 (Poxvirus_A9)
Type: Family

This entry represents a family of Chordopoxvirus A9 proteins. Chordopoxvirus belongs to the family Poxviridae and is the cause of vertebrate infections .
Interferon-related developmental regulator, C-terminal (Interferon-rel_develop_reg_C)
Type: Domain

This entry represents the C-terminal domain of IFRD1 and similar sequences predominantly found in animals.

Interferon-related developmental regulator (IFRD1) is the human homologue of the Rattus norvegicus early response protein PC4 and its murine homologue TIS7 . IFRD1 is a transcriptional coactivator/repressor controlling patterns of gene expression by interacting with transcription factors or histone deacetylase (HDAC) complexes . This entry also contains IFRD2 and its murine equivalent SKMc15, which are highly expressed soon after gastrulation and in the hepatic primordium, suggesting an involvement in early hematopoiesis . Members of this group are generally described as transcriptional regulators implicated in cellular differentiation and various human diseases .
Mobilization protein MbeB-like (MbeB-like)
Type: Family

This family consists of Mbe/Mob proteins. These proteins are essential for specific plasmid transfer.
Baculoviridae late expression factor 5, N-terminal (Baculo_LEF5_N)
Type: Domain

This is the N-terminal domain of Baculoviridae late expression factor 5, required for late and very late gene expression.
Small ribosomal subunit protein cS23-like (Ribosomal_cS23-like)
Type: Family

This small acidic protein is found in 30S ribosomal subunit of cyanobacteria and plant plastids.

In plants it has been named plastid-specific ribosomal protein 3 (PSRP-3), and in cyanobacteria it is named Ycf65, with both also known as small ribosomal subunit protein cS23. Plastid-specific ribosomal proteins may mediate the effects of nuclear factors on plastid translation. The acidic PSRPs are thought to contribute to protein-protein interactions in the 30S subunit, and are not thought to bind RNA .
Vps16, C-terminal (Vps16_C)
Type: Domain

Vps16 forms part of the Class C vacuolar protein sorting (Vps) complex. It is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast . The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport . The role of VPS16 in this complex is not known.

The C-terminal domain of Vps16 binds to Vps33 for integration into the HOPS complex .
Vps16, N-terminal (Vps16_N)
Type: Domain

This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast . The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport . The role of VPS16 in this complex is not known.
Protein of unknown function DUF639 (DUF639)
Type: Family

The sequences in this family are plant proteins of unknown function.
Herpesvirus large tegument protein, USP domain (Herpes_teg_USP)
Type: Domain

All herpesviruses contain a Ubiquitin (Ub)-specific cysteine protease (USP) domain embedded within their large tegument protein. The herpesvirus tegument ubiquitin (Ub)-specific protease (htUSP) domain of ~200 amino acids adopts an α-β-α sandwich fold that features a central catalytic cleft, ideally suited to accommodate the C-terminal stretch of Ub. The catalytic triad Cys-His-Asp is strictly conserved, along with a putative oxyanion hole-forming Gln residue. The htUSP domain is a member of peptidase family C76 of clan CA .
Herpesvirus pp38 phosphoprotein (Herpes_pp38)
Type: Family

Members of this family contain a conserved region found in most herpesvirus pp38 phosphoproteins.
Calcipressin (Calcipressin)
Type: Family

Calcipressins (RCANs) are a novel family of calcineurin regulators that have been suggested as key factors contributing to Down syndrome in humans. Three human calcipressins have been identified, calcipressin 1-3. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 . Calcipressins contain an N-terminal RNA recognition motif (RRM), a highly conserved SP repeat domain containing the phosphorylation site by GSK-3, a well-known PxIxIT motif responsible for docking many substrates to calcineurin, and a C-terminal TxxP motif .

Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In doing so, it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation .
Holliday junction resolvase, A22 (HJ-resolvase_A22)
Type: Family

This family representis the Poxvirus A22 protein, a Holliday junction resolvase also known as Resolvase OPG149, and similar proteins from poxvirus. It specifically cleaves and resolves four-way DNA Holliday junctions into linear duplex products .
HAP1, N-terminal (HAP1_N)
Type: Domain

This entry represents a N-terminal conserved region found in huntingtin-associated protein 1 (HAP1), trafficking Kinesin proteins TRAK1 and TRAK2 (vertebrate), Milton (Drosophila) and similar proteins from animals .

HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner . It is involved in intracellular trafficking . HAP1 is also linked to Alzheimer's disease. It regulates amyloid precursor protein subcellular trafficking to the non-amyloidogenic pathway and may negatively regulate Abeta production in neurons .

TRAK1 binds to both kinesin-1 and dynein/dynactin, is prominently localized in axons, and is needed for normal axon outgrowth, whereas TRAK2 predominantly interacts with dynein/dynactin, is more abundantly present in dendrites, and is required for dendritic development .
Baculovirus ODV-E66, C-terminal domain (ODV-E66_C_baculovirus)
Type: Domain

This entry represents the C-terminal domain of Non-sulfated chondroitin lyase E66 from Autographa californica nuclear polyhedrosis virus (ODV-E66) and similar sequences from baculovirus. This domain, predominantly formed by β-strands, is often found associated with

.

ODV-E66 is a component of the polyhedra envelope that plays an essential role in oral infectivity. It may digest, with its chondroitin lyase activity, the chondroitin sulfate barrier of the peritrophic matrix of the host midgut to facilitate viral infection in the epithelial cells .

Baculovirus occlusion-derived virus (ODV) derives its envelope from an intranuclear membrane source. N-terminal amino acid sequences of the Autographa californica MNPV nuclear polyhedrosis virus (AcMNPV) envelope protein ODV-E66 is highly hydrophobic. This defined hydrophobic domain was shown to direct the protein, E66, to induce membrane microvesicles within a baculovirus-infected cell nucleus and the viral envelope. In addition, it was suggested that movement of this protein into the nuclear envelope may initiate through cytoplasmic membranes, such as endoplasmic reticulum, and that transport into the nucleus may be mediated through the outer and inner nuclear membrane .
Helicase/UvrB, N-terminal (Helicase/UvrB_N)
Type: Domain

This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (

), the Res subunit of type III endonucleases (

), and the B subunit of the UvrABC system (UvrB) .
ALOG domain (ALOG_dom)
Type: Domain

The 125-residue ALOG (Arabidopsis LSH1 and oryza G1) domain is rich in basic amino acids, especially arginine, and is highly conserved among land plants. Members of the ALOG family of proteins function as key developmental regulators. It has been proposed that the ALOG domain originated from the N- terminal DNA-binding domains of integrases belonging to the tyrosine recombinase superfamily encoded by a distinct type of DIRS1-like LTR retrotransposon found in several eukaryotes. Secondary structure predictions revealed an all-α helical domain with four conserved helices .

Some proteins known to contain an ALOG domain are listed below:

Arabidopsis thaliana LIGHT_DEPENDENT SHORT HYPOCOTYLS1 (LSH1), involved in phytochrome-dependent light signalling.

Oryza G1, involved in the specification of sterile lemma identity.

Plant defence proteins.
Protein of unknown function DUF624 (DUF624)
Type: Family

This family consists of uncharacterised or hypothetical bacterial proteins.
SNF5/SMARCB1/INI1 (SNF5)
Type: Family

SNF5 is a component of the yeast SWI/SNF complex, which is an ATP-dependent nucleosome-remodelling complex that regulates the transcription of a subset of yeast genes. SNF5 is a key component of all SWI/SNF-class complexes characterised so far . This family consists of the conserved region of SNF5, including a direct repeat motif. SNF5 is essential for the assembly promoter targeting and chromatin remodelling activity of the SWI-SNF complex . SNF5 is also known as SMARCB1, for SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1, and also INI1 for integrase interactor 1. Loss-of function mutations in SNF5 are thought to contribute to oncogenesis in malignant rhabdoid tumours (MRTs) .
Securin sister-chromatid separation inhibitor (Securin_separation_inhibitor)
Type: Family

Securin, also known as pituitary tumour-transforming gene product is a regulatory protein which plays a central role in chromosome stability in the p53/TP53 pathway, and in DNA repair. It probably acts by blocking the action of key proteins, for example, during mitosis it blocks Separase/ESPL1 function preventing the proteolysis of the cohesin complex and the subsequent segregation of the chromosomes. At the onset of anaphase, it is ubiquitinated, leading to its destruction and to the liberation of ESPL1. Its function is however not limited to an inhibitory activity, since it is required to activate ESPL1. The negative regulation of the transcriptional activity and related apoptosis activity of TP53 may explain the strong transforming capability of the protein when it is overexpressed. Over-expression of securin is associated with a number of tumours, and it has been proposed that this may be due to erroneous chromatid separation leading to chromosome gain or loss .
Ribonuclease CAF1 (RNase_CAF1)
Type: Family

The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 (also known as CCR4-associated factor 1) is an RNase of the DEDD superfamily, and a subunit of the CCR4-NOT complex that mediates 3' to 5' mRNA deadenylation . In yeast, CAF1 (

) is also known as POP2, and encodes a critical component of the major cytoplasmic deadenylase . It is required for normal mRNA deadenylation
in vivo
and localises to the cytoplasm. CAF1 copurifies with a CCR4-dependent poly(A)-specific exonuclease activity. The crystal structure of Saccharomyces cerevisiae POP2 has been resolved .

Some members of this family contain a single-stranded nucleic acid binding domain, R3H, such as poly(A)-specific ribonuclease (PARN), which also contains an RRM domain . PARN is only conserved in vertebrates and may be important in regulated deadenylation such as early developmentand DNA damage response .
TH1 protein (TH1)
Type: Family

TH1 is a highly conserved but uncharacterised metazoan protein. No homologue has been identified in Caenorhabditis elegans . TH1 binds specifically to A-Raf kinase .
Domain of unknown function DUF641, plant (DUF641_pln)
Type: Domain

This conserved region is found in a number of plant proteins of unknown function.
Bacteriophage/Gene transfer agent portal protein (Phage/GTA_portal)
Type: Family

This is a family of bacteriophage, prophage and Gene Transfer Agent (GTA) portal proteins. Positioned at one of the twelve icosahedral vertices, of the viral capsid, is a dodecameric complex of the virus encoded portal protein. This dodecameric complex, known as the portal or connector complex, forms the channel through which the viral DNA is packaged into the capsid, and through which it exits during infection. While the portal proteins from different phage show relatively little sequence homology and vary widely in molecular weight, portal complexes display significant morphological similarity as determined by electron microscopy. Morphologically, they present as disk-like structures approximately 150 Angstroms in diameter with radially arranged projections and a 30 Angstroms central channel. The packaging reaction is energy dependent and typically involves several components. ATP hydrolysis provides the driving force, and it is estimated that one ATP molecule is required for every base pair that is packaged. It appears that the portal motor may represent a new and extremely powerful class of motor which couples rotation to DNA translocation .
DUF642 L-galactono-1,4-lactone-responsive gene 2-like domain (DGR2-like_dom)
Type: Domain

This entry represents a domain found twice in the protein DUF642 L-galactono-1,4-lactone-responsive gene 2 from Arabidopsis thaliana (DGR2) and similar proteins found in plants and bacteria. DGR2 is involved in the regulation of testa rupture during seed germination and in the development of roots and rosettes . This domain was previously known as DUF642.
Alliinase, EGF-like domain (EGF_alliinase)
Type: Domain

Allicin is a thiosulphinate that gives rise to dithiines, allyl sulphides and ajoenes, the three groups of active compounds in Allium species. Allicin is synthesised from sulphoxide cysteine derivatives by alliinase, whose C-S lyase activity cleaves C(beta)-S(gamma) bonds. It is thought that this enzyme forms part of a primitive plant defence system .

This entry represents the N-terminal EGF-like domain .
Alliinase, C-terminal (Alliinase_C)
Type: Domain

Allicin is a thiosulphinate that gives rise to dithiines, allyl sulphides and ajoenes, the three groups of active compounds in Allium species. Allicin is synthesised from sulphoxide cysteine derivatives by alliinase, whose C-S lyase activity cleaves C(beta)-S(gamma) bonds. It is thought that this enzyme forms part of a primitive plant defence system .
Baseplate protein J-like (Baseplate_J-like)
Type: Domain

The temperate bacteriophage P2 has four defined tail genes: V, J, W and I. Their order is the late gene promoter, VWJI, followed by the tail fibre genes H and G and then a transcription terminator. BAP V protein is the small spike at the tip of the tail and basal plate assembly protein J lies at the edge of the baseplate . This family also includes a number of bacterial homologues, which are thought to have been horizontally transferred.
Rotavirus non-structural protein 6 (Rotavirus_NSP6)
Type: Family

This family comprises the 11kDa non-structural proteins found in segment S11 of the Rotavirus genome. They may form part of a complex that is involved in the replication of the genome.
Protein of unknown function DUF643 (DUF643)
Type: Family

These are proteins of unknown function found in Borrelia burgdorferi (Lyme disease spirochete)
Retinal cGMP phosphodiesterase, gamma subunit (PDE6_gamma)
Type: Family

Retinal rod and cone cGMP phosphodiesterases function as the effector enzymes in the vertebrate visual transduction cascade. This family represents the inhibitory gamma subunit , which is also expressed outside retinal tissues and has been shown to interact with the G-protein-coupled receptor kinase 2 signalling system to regulate the epidermal growth factor- and thrombin-dependent stimulation of p42/p44 mitogen-activated protein kinase in human embryonic kidney 293 cells .
Vesicle tethering protein Uso1/P115-like, head domain (Vesicle_Uso1_P115_head)
Type: Domain

This domain identifies a group of proteins, which are described as: General vesicular transport factor, Transcytosis associated protein (TAP) or Vesicle docking protein, this myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region . p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the Golgi stack. This domain is found in the head region. The head region is highly conserved, but its function is unknown. It does not seem to be essential for vesicle tethering . The N-terminal part of the head region contains context-detected Armadillo/beta-catenin-like repeats.
Moulting cycle mlt-10-like (Mlt-10-like)
Type: Family

This entry represents a family of proteins from nematodes, including Molting protein mlt-10 from Caenorhabditis elegans. Mlt-10 plays a role in the moulting cycle, which involves the synthesis of a new collagen-rich cuticle underneath the existing cuticle and the subsequent removal of the old cuticle .
Uso1/p115-like vesicle tethering protein, C-terminal (Uso1_p115_C)
Type: Domain

This domain identifies a group of proteins, which are described as: General vesicular transport factor, Transcytosis associate protein (TAP) and Vesicle docking protein. This myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region . p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the Golgi stack. This domain is found in the acidic C-terminal region, which binds to the golgins giantin and GM130. p115 is thought to juxtapose two membranes by binding giantin with one acidic region, and GM130 with another .
Poxvirus L5 (Poxvirus_L5)
Type: Family

This family represents Protein L5 from variola (smallpox), vaccinia virus, and similar proteins from poxvirus. L5, also known as Entry-fusion complex protein OPG094, is a component of the entry fusion complex (EFC), which consists of 11 proteins. During cell infection, this complex mediates entry of the virion core into the host cytoplasm by a two-step mechanism consisting of lipid mixing of the viral and cellular membranes and subsequent pore formation .
Ethylene insensitive 3 (EIN3)
Type: Family

Ethylene insensitive 3 (EIN3) proteins are a family of plant DNA-binding proteins that regulate transcription in response to the gaseous plant hormone ethylene, and are essential for ethylene-mediated responses . In the presence of ethylene, dark-grown dicotyledonous seedlings undergo dramatic morphological changes collectively known as the 'triple response'. In Arabidopsis, these changes consist of a radial swelling of the hypocotyl, an exaggeration in the curvature of the apical hook, and the inhibition of cell elongation in the hypocotyl and root .
Mak16 protein (Mak16)
Type: Family

In budding yeasts, Mak16 forms part of the 66S pre-ribosomal particles and functions as a transacting actor involved in rRNA processing . The Schistosoma mansoni (Blood fluke) Mak16 has been shown to target protein transport to the nucleolus .
Protein of unknown function DUF645 (DUF645)
Type: Family

This family contains uncharacterised proteins from Vibrio cholerae.
Major non-capsid protein, tenuivirus (Major_non-capsid_tenuivirus)
Type: Family

This entry contains the tenuivirus major non-capsid protein. Proteins accumulate in large amounts in tenuivirus infected cells. They are found in the inclusion bodies that are formed after infection .
Harpin, HrpN/Z (HrpN/Z)
Type: Family

HrpZ (harpin elicitor) from the plant pathogen Pseudomonas syringae binds to lipid bilayers and forms a cation-conducting pore in vivo. This pore-forming activity may allow nutrient release or delivery of virulence factors during bacterial colonisation of host plants .