SII-SWORD/CoKE huggingface dataset:
Cysteine-rich DPF motif domain (CDPF1_dom)
Type: Domain

This entry represents the cysteine-rich DPF motif domain (CDPF1) in CDPF1-containing proteins found in a range of organisms, including human, chicken and Drosophila . It contains between six and eight highly conserved cysteine residues and a characteristic DPF sequence motif. The function of this protein has not been clarified yet.
Mitochondrial K+-H+ exchange-related (Mit_KHE1)
Type: Family

This entry represents a family of proteins from fungi, plants and bacteria, including Uncharacterized protein YDL183C from Saccharomyces cerevisiae, which may be part of an active mitochondrial K+/H+ exchanger (KHE) system .
Protein of unknown function DUF2371, TMEM200 (DUF2371_TMEM200)
Type: Family

This family of proteins with no known function is conserved from nematodes to humans. It includes members of the TMEM200 family of transmembrane proteins.
Proteasome assembly chaperone 3 (Proteasome_assmbl_chp_3)
Type: Family

Proteasome assembly chaperone 3 (PSMG3) promotes assembly of the 20S proteasome . It may cooperate with PSMG1-PSMG2 heterodimers to orchestrate the correct assembly of proteasomes.
Flocculin 11 domain (Flo11)
Type: Domain

Fungal cells need to be able to adhere to their surroundings, be it either abiotic surfaces or living tissues, in order to remain firmly attached to their source of nutrients. Adhesive properties in fungi are conveyed by a group of cell-surface proteins called adhesins (sometimes also referred to as
agglutinins or flocculins). Adhesins are generally rich in serine and threonine residues that allow extensive O-linked glycosylation. Some fungal adhesins also carry discernable ligand-binding domains that determine their substrate specificity and allows some degree of sequence classification of the different groups of adhesins.

Flocculin 11 is the major adhesin for controlling filamentous growth, mat, and biofilm formation of Baker's yeast. Although its amino acid sequence shows less similarity with the other flocculins, Flo11 belongs to the flocculin family. However, the N-terminal domain contains the 'Flo11 domain', but not the mannose-binding PA14 domain, which is present in most other flocculins (Flo1, Flo5, Flo9 and Flo10). Flo11 domains are only found within the ascomycetes orders of Saccharomycetales, which include the budding yeasts as well as the Schizosaccharomycetales, i.e. the fission yeast Schizosaccharomyces pombe. In the majority of its family members, the Flo11 domain is located at the N- terminal ends of glycosylphosphatidylinositol (GPI)-anchored cell wall proteins, although some yeasts such as Clavispora lusitaniae or Spathaspora passalidarum have arrays of up to three Flo11 domains within their adhesins. The Flo11 domain is not a mannose-binding module but can make homotypic
interactions .

The Flo11 domain consists of some 160 amino acids. It is O-glycosylated and is structurally composed mainly of β-sheets, which is typical for the members of the flocculin family. The Flo11 domain structure corresponds to a globular, wedge-shaped domain with a complex folding motif that consists of three antiparallel β-sheets. The sheets I and II form a β-sandwich as core domain, whereas the four-pleated sheet III forms a unique,
neck-like subdomain along the lower end of the β-sandwich. The core domain, namely the β-sandwich formed by the anti-parallel β-sheets I and II, was
assigned to the class of fibronectin type III-like domains (FN3) .
Protein of unknown function DUF2358 (DUF2358)
Type: Family

This entry represents a family of conserved proteins. The function is unknown.
UV radiation resistance protein/autophagy-related protein 14 (UV_resistance/autophagy_Atg14)
Type: Family

This entry includes Atg14 (autophagy-related protein 14) from budding yeasts and their homologues, Atg14L/Bakor (beclin-1-associated autophagy-related key regulator) and UVRAG (UV irradiation resistance-associated gene), from animals.

Atg14 is a hydrophilic protein with a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole .

Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated . UVRAG is also a Beclin-1 binding protein that positively stimulate starvation-induced autophagy . Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer.
Nuclear protein 1-like (NUPR1-like)
Type: Family

This entry represents a group of nuclear proteins that are conserved from nematodes to humans. They can form a helix-loop-helix motif and are related to, yet distinct from, the HMG-I/Y-like subfamily of HMG proteins. This entry includes two human nuclear proteins, NUPR1 (also known as p8) and NUPR2. Similar to several HMGs, NUPR1 binds DNA, however, it has a low affinity and poor sequence specificity for DNA binding . NUPR1 is multifunctional protein that interacts with several partners to target different signalling pathways, such as the NUPR1/RELB/IER3 survival pathway and the PI3K/AKT signaling pathway . It also binds to and inhibits MSL1, a protein with 53BP1-dependent DNA-repair activity .
Cytochrome c oxidase assembly protein PET191 (Cyt_c_oxidase_assmbl_Pet191)
Type: Family

This entry represents a family of conserved proteins found from nematodes to humans. Cytochrome c oxidase assembly protein Pet191 carries six highly conserved cysteine residues. Pet191 is required for the assembly of active cytochrome c oxidase but does not form part of the final assembled complex .
Uncharacterised protein family UPF0538 (UPF0538)
Type: Family

This entry consists of small proteins of approximately 150 amino acids whose function is unknown.
Uncharacterized protein KIAA2013-like (K2013-like)
Type: Family

This entry represents Uncharacterized protein KIAA2013 and similar proteins from animals. K2013 might be related to cannabinoid receptors and neurodegenerative disorders such as ALS . The function of this protein is still unknown.
Cytochrome c oxidase assembly factor 8 (COA8)
Type: Family

Apoptogenic protein 1 (Apop1, also known as cytochrome c oxidase assembly factor 8), previously thought to induce apoptosis through the Cyclophilin-D-dependent pathway , is required for cytochrome c oxidase (COX) assembly and function. Apop1 is controlled by the ubiquitination-proteasome system (UPS) . In Drosophila melanogaster, Apop1 is also involved in neurological impairment, COX enzymatic activity, and resistance to oxidative stress conditions .
FAM98 (FAM98)
Type: Family

FAM98A, B and C are glycine-rich proteins found from worms to humans. FAM98A contains a tubulin-binding calponin homology domain. It interacts with PLEKHM1 and functions in lysosome positioning in osteoclasts . FAM98A and FAM98B are included in a novel complex with DDX1 and C14orf166 and are involved in colorectal cancer progression .
Multivesicular body subunit 12 (MVB12A/B)
Type: Family

MVB12A (also known as CFBP) and MVB12B are subunits of the ESCRT-I complex, which mediates the sorting of ubiquitinated cargo protein from the plasma membrane to the endosomal vesicle . MVB12A plays a key role in the ligand-mediated internalization and down-regulation of the EGF receptor .
TRAF3-interacting protein 1 (TRAF3IP1)
Type: Family

TRAF3-interacting protein 1 (TRAF3IP1, also known as IFT54) recruits TRAF3 (tumour necrosis factor receptor-associated factor 3) and DISC1 (Disrupted-In-Schizophrenia 1) to the microtubules and is conserved from worms to humans . The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved . In humans, it plays an inhibitory role on IL13 signaling by binding to IL13RA1. It is involved in suppression of IL13-induced STAT6 phosphorylation, transcriptional activity and DNA-binding .
Proline-rich protein PRCC (PRCC)
Type: Family

This family constitutes the major, conserved, portion of PRCC proteins. In humans, this family interacts with MAD2B, the mitotic checkpoint protein . In Schizosaccharomyces pombe this protein is part of the Cwf-complex that is known to be involved in pre-mRNA splicing .
E3 ubiquitin-protein ligase TM129 (TM129)
Type: Family

TM129 (also known as TMEM129) is a tri-spanning ER-membrane protein that can serve as an E3 ligase involved in ER-associated protein degradation .
Latarcin precursor (Latarcin_precursor)
Type: Family

This entry represents the precursor proteins for a number of short antimicrobial peptides called Latarcins. Latarcins were discovered in the venom of the spider Lachesana tarabaevi . Latarcins are likely to adopt amphipathic α-helical structure in the plasma membrane.
Ish1/Msc1-like (Ish1/Msc1-like)
Type: Repeat

Proteins containing this repeat include the stress response protein Ish1 from fission yeasts and meiotic sister chromatid recombination protein 1 (Msc1) from budding yeasts. Proteins containing this repeat also include some uncharacterised proteins from Acinetobacter baumannii.

Ish1 has a role in maintaining cell viability during stationary phase induced by stress response. It can be activated by the spc1 MAPK pathway .
Luciferase catalytic domain (Luciferase_cat)
Type: Domain

This entry represents the catalytic domain of dinoflagellate luciferase. Luciferase is involved in catalysing the light emitting reaction in bioluminescence. The structure of this domain has been solved . The core part of the domain is a 10 stranded β barrel that is structurally similar to lipocalins and FABP .
Cell wall protein YJL171C/Tos1, C-terminal (YJL171C/Tos1_C)
Type: Domain

This entry represents a domain found in a group of fungal cell wall proteins, including Probable circularly permuted 1,3-beta-glucanase Tos1 and YJL171C from budding yeasts . They contain 5 highly conserved cysteines, two of which form a characteristic CGC sequence motif. This proteins are related to glycosyl hydrolases .
Cell wall protein YJL171C/Tos1, N-terminal (YJL171C/Tos1_N)
Type: Domain

This entry represents a domain found in a group of fungal cell wall proteins, including Probable circularly permuted 1,3-beta-glucanase Tos1 and YJL171C from budding yeasts. This proteins are related to glycosyl hydrolases . The function of this glycine-rich domain is unknown.
Muniscin, C-terminal (Muniscin_C)
Type: Domain

The muniscins are a family of endocytic adaptors that is conserved from yeast to humans.This C-terminal domain is structurally similar to mu homology domains, and is the region of the muniscin proteins involved in the interactions with the endocytic adaptor-scaffold proteins Ede1-eps15. This interaction influences muniscin localisation. The muniscins provide a combined adaptor-membrane-tubulation activity that is important for regulating endocytosis .
Protein of unknown function DUF2406 (DUF2406)
Type: Family

This entry represents a family of small proteins conserved in fungi. The function is not known.
Uncharacterised protein family UPF0662 (UPF0662)
Type: Family

This entry represents a family of proteins conserved in fungi whose function is unknown. It includes Cu(2+) suppressing and bleomycin sensitive protein 1 thought to be involved in bleomycin tolerance with links to DNA repair and/or proteasome function.
MIOREX complex component 11 (MRX11)
Type: Family

MIOREX complex component 11 (MRX11) associates with mitochondrial ribosome . Its function is not clear.

MIOREX complex is a large expressome-like assembly of ribosomes with factors involved in all the steps of post-transcriptional gene expression.
Swiss Army Knife RNA repair protein, HAD domain (SAK_HAD)
Type: Domain

This entry represents the HAD domain found in the so-called 'Swiss Army Knife' (SAK) repair protein, which is predicted to play a role in RNA repair. SAK may be involved in phosphate group removal during RNA re-ligation . There are two characteristic sequence motifs, GGWW and TGR.
Protein of unknown function DUF5427 (DUF5427)
Type: Family

In Saccharomyces cerevisiae, maintenance of telomere capping protein 1 (Mtc1) may interact with ribosomes and is synthetically lethal with cdc13-1 .
Increased loss of mitochondrial DNA protein 1 (Incr_loss_mito_DNA_1)
Type: Family

This is a family of proteins of approximately 200 residues that are conserved in fungi. Ilm1 is part of the peroxisome, a complex that is the sole site of beta-oxidation in Saccharomyces cerevisiae (Baker's yeast) and known to be required for optimal growth in the presence of fatty acid. Ilm1 may participate in the control of the C16/C18 ratio since it interacts strongly with Mga2p, a transcription factor that controls expression of Ole1, the sole fatty acyl desaturase in S. cerevisiae responsible for conversion of the saturated fatty acids stearate (C18) and palmitate (C16) to oleate and palmitoleate, respectively .
Splicing factor cactin, central domain (Cactin_central)
Type: Domain

This entry represents the conserved central domain of the splicing factor cactin. It contains two of three predicted coiled-coil motifs. Most proteins containing this domain also have

at the C-terminal end. Upstream of this domain in Drosophila proteins are a serine-rich region, some non-typical RD motifs and three predicted bipartite nuclear localisation signals, none of which are well-conserved.

Cactin associates with IkappaB-cactus as one of the intracellular members of the Rel (NF-kappaB) pathway which is conserved in invertebrates and vertebrates. In mammals, this pathway controls the activities of the immune and inflammatory response genes as well as viral genes, and is critical for cell growth and survival. In Drosophila, the Rel pathway functions in the innate cellular and humoral immune response, in muscle development, and in the establishment of dorsal-ventral polarity in the early embryo .
7TM GPCR, serpentine receptor class z (Srz) (7TM_GPCR_serpentine_rcpt_Srz)
Type: Family

G protein-coupled receptors (GPCRs) constitute a vast protein family that encompasses a wide range of functions, including various autocrine, paracrine and endocrine processes. They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups . The term clan can be used to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence . The currently known clan members include rhodopsin-like GPCRs (Class A, GPCRA), secretin-like GPCRs (Class B, GPCRB), metabotropic glutamate receptor family (Class C, GPCRC), fungal mating pheromone receptors (Class D, GPCRD), cAMP receptors (Class E, GPCRE) and frizzled/smoothened (Class F, GPCRF) . GPCRs are major drug targets, and are consequently the subject of considerable research interest. It has been reported that the repertoire of GPCRs for endogenous ligands consists of approximately 400 receptors in humans and mice . Most GPCRs are identified on the basis of their DNA sequences, rather than the ligand they bind, those that are unmatched to known natural ligands are designated by as orphan GPCRs, or unclassified GPCRs .

The nematode Caenorhabditis elegans has only 14 types of chemosensory neuron, yet is able to sense and respond to several hundred different chemicals because each neuron detects several stimuli . Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' . Chemoreception in C. elegans is mediated by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs). More than 1300 potential chemoreceptor genes have been identified in C. elegans, which are generally prefixed sr for serpentine receptor. The receptor superfamilies include Sra (Sra, Srb, Srab, Sre), Str (Srh, Str, Sri, Srd, Srj, Srm, Srn) and Srg (Srx, Srt, Srg, Sru, Srv, Srxa), as well as the families Srw, Srz, Srbc, Srsx and Srr . Many of these proteins have homologues in Caenorhabditis briggsae.

This entry represents serpentine receptor class z (Srz), a solo family amongst the superfamilies of chemoreceptors . The genes encoding Srz appear to be under strong adaptive evolutionary pressure .
Sin3 binding protein (Stb3)
Type: Family

This entry represents Sin3 binding proteins conserved in fungi. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex . Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein .
Nur1/Mug154 (Nur1/Mug154)
Type: Family

This entry includes Nur1 from budding yeasts and Mug154 from fission yeasts. Nur1 is part of the perinuclear network that controls recombination at multiple loci to maintain genome stability . Mug15 may has a role in meiosis .
Brefeldin A sensitivity protein-related, domain of unknown function DUF2421 (BRE4-related_DUF2421)
Type: Domain

This domain is found in several uncharacterised proteins and in Brefeldin A-sensitivity protein 4, which is a zinc finger protein containing five transmembrane domains. Brefeldin A-sensitivity protein 4 null mutant exhibits strongly fragmented vacuoles and sensitivity to brefeldin A, a drug which is known to affect intracellular transport .
Domain of unknown function DUF294, putative nucleotidyltransferase substrate-binding (DUF294_put_nucleoTrafse_sb-bd)
Type: Domain

This entry is found associated with presumed nucleotidyltransferase domains and seems to be distantly related to other helical substrate binding domains.
Uncharacterised protein family UPF0646 (UPF0646)
Type: Family

This entry represents a family of proteins conserved in fungi. Their function is not known.
Putative ER transporter, 6TM, N-terminal (ArAE_2_N)
Type: Domain

This domain is found in proteins conserved in fungi. Their function is not known. This entry represents the N-terminal half of some member proteins which contain the DUF2421 domain (

) at their C terminus. These proteins are putative endoplasmic reticulum tranpsorters, with a total of 12 TMs.
Conidiation-specific protein 6 (Conidiation-specific_6)
Type: Family

This entry represents a conserved region found in fungal conidiation-specific protein 6 . This protein is expressed approximately 6 hours after the induction of development and is induced just prior to major constriction-chain growth .
Domain of unknown function DUF2427 (DUF2427)
Type: Domain

This entry represents the N-terminal region of a family of proteins conserved in fungi. Several of these proteins are annotated as being Ftp1 but this could not be confirmed. Their function is not known.
Protein YTP1-like, C-terminal (YTP1_C)
Type: Domain

This entry represents a conserved sequence region found a family of poorly characterised fungal proteins, including YTP1 from S. cerevisiae. It appears to contain regions similar to mitochondrial electron transport proteins. The C-terminal domain is hydrophobic and negatively charged. There are consensus sites for both N-linked glycosylation and cAMP-dependent protein kinase phosphorylation .
Required for respiratory growth protein 7, mitochondrial (RRG7)
Type: Family

These family represents a group of mitochondrial fungal proteins, including RRG7, whose function is not yet known.
Domain of unknown function DUF2433 (DUF2433)
Type: Domain

This entry represents a conserved domain of 120 residues from a family fungal proteins. Their function is not known.
Protein of unknown function DUF2434 (DUF2434)
Type: Family

This entry represents a family of proteins conserved in fungi. Their function is not known.
Uncharacterised protein family NKWYS (Uncharacterised_NKWYS)
Type: Family

This entry contains proteins of no known function. They are found predominantly in Vibrio and cyanobacterial species and are characterised by having a NKWYS sequence motif.
Peptidase C25, gingipain, C-terminal (Pept_C25_gingipain_C)
Type: Domain

Gingipains R and K are endopeptidases with specificity for arginyl and lysyl bonds, respectively. Like other cysteine peptidases, they require reducing conditions for activity. They are maximally active at approximately neutral pH. Gingipains R and K are secreted by the bacterium Porphyromonas gingivalis (Bacteroides gingivalis). The bacterium is a major pathogen in periodontal disease, and the many ways in which the activities of the gingipains may contribute to the disease processes have been reviewed . These enzymes are also involved in the hemagglutinating activity of the organisms.
Rv2993c-like, N-terminal (Rv2993c-like_N)
Type: Domain

This entry represents the N-terminal 50 amino acids of a group of bacterial proteins, including protein Rv2993c from Mycobacterium tuberculosis. Some members of this entry are annotated as fumarylacetoacetate hydrolase-containing enzymes.
DNA/RNA-binding domain, Est1-type (DNA/RNA-bd_Est1-type)
Type: Domain

This entry represents a DNA/RNA binding domain found in the telomere elongation protein EST1 and related sequences, such as the nonsense-mediated mRNA decay pathway proteins SMG5 and SMG7 .
RNA-binding domain, putative (RNA-binding_domain_put)
Type: Domain

This entry represents a putative RNA-binding domain found only in fungi. It occurs in proteins annotated as Nrd1, which are known to carry RNA recogntion motif (RRM) domains. It is not homologous with any of the other RRM domains, e.g.

.
Necrogenic protein Nec1 (Necrogenic_Nec1)
Type: Family

The Nec1 protein has necrogenic activity on excised potato tuber tissue, and the encoding gene is highly conserved in plant-pathogenic Streptomyces spp. The G+C content of nec1 indicates lateral transfer from an unrelated taxon, but its origins are unclear. Deletion analysis of nec1 demonstrated that the 151-amino-acid C-terminal region of the Nec1 protein is sufficient to confer necrogenic activity. Streptomyces turgidiscabies containing a nec1 deletion was greatly compromised in virulence on Arabidopsis thaliana (Mouse-ear cress), Nicotiana tabacum (Common tobacco), and Raphanus sativus (Radish) seedlings. The wild-type strain, S. turgidiscabies Car8, aggressively colonized and infected the root meristem of radish, whereas the delta-nec1 mutant Car811 did not. Taken together, the data suggest that Nec1 is a secreted virulence protein with a conserved plant cell target that acts early in plant infection .
Transcription factor CRF1/IFH1 (TF_CRF1/IFH1)
Type: Family

CRF1 and IFH1 are transcription factors that control ribosomal gene regulation in S. cerevisiae. CRF1 binds FHL1 via the TOR signalling pathway and protein kinase A, and co-represses ribosomal genes . Contrarily, IFH1 binds FHL1 under rich growth conditions and induces ribosomal protein expression . CRF1 and IFH1 are derived from the duplication and subsequent specialisation of a single ancestral protein .