SII-SWORD/CoKE huggingface dataset:
Protein of unknown function DUF4487 (DUF4487)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 209 and 938 amino acids in length. There is a conserved WCF sequence motif and a single completely conserved residue W that may be functionally important.
Protein of unknown function DUF4566 (DUF4566)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes and includes human protein C6orf62.
Domain of unknown function DUF4587 (DUF4587)
Type: Domain

This entry represents a domain of unknown function. This domain is found in eukaryotes, and is typically between 64 and 79 amino acids in length. It contains two conserved sequence motifs: QNAQ and HHH.
Cilia- and flagella-associated protein 95 (CFAP95)
Type: Family

This family includes CFAP95, a microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating .
Protein of unknown function DUF4567 (DUF4567)
Type: Family

This family of proteins is functionally uncharacterised. It is found in some mammals.
BTB/POZ domain-containing protein 8, C-terminal (BTBD8_C)
Type: Domain

This domain is found in vertebrates. It is found at the C terminus of BTB/POZ domain-containing protein 8 (BTBD8, also known as AP2-interacting clathrin-endocytosis protein). BTBD8 is involved in clathrin-mediated endocytosis at the synapse and plays a role in neuronal development and in synaptic vesicle recycling in mature neurons, a process required for normal synaptic transmission . This domain contains a conserved ELET sequence motif and two completely conserved residues (S and E) that may be functionally important.
Protein of unknown function DUF4640 (DUF4640)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 99 and 306 amino acids in length.
Protein of unknown function DUF4447 (DUF4447)
Type: Family

This family of proteins is found in Shewanella species. Proteins in this family are approximately 170 amino acids in length.
YdiL domain superfamily (YdiL_sf)
Type: Homologous_superfamily

This superfamily represents a domain found in bacteria, named after the uncharacterised protein YdiL from Escherichia coli.
Domain of unknown function DUF4604 (DUF4604)
Type: Domain

This domain of unknown function is found in eukaryotes. It contains a conserved LSF sequence motif.
Cilia- and flagella-associated protein 54 (CFAP54)
Type: Family

CFAP54 is required for assembly and function of cilia and flagella .
Protein of unknown function DUF4473 (DUF4473)
Type: Family

This family is largely confined to Caenorhabditis proteins. Their function is not known. They have two well-conserved aspartate residues.
Domain of unknown function DUF4456 (DUF4456)
Type: Domain

This domain of unknown function has is a single completely conserved residue E that may be functionally important.
Protein of unknown function DUF4452 (DUF4452)
Type: Family

This fungal family has no known function. However, it is rich in paired, as CXXC, cysteines and histidines, but these do not fall in the conformation that might suggest zinc-binding.
Rhoptry, Protein kinase-like domain (Kinase-like_dom_ROP)
Type: Domain

This entry represents the kinase-like domain found in the Rhoptry (ROP) pseudokinases ROP4, ROP5, ROP17 AND ROP18 and kinases from the intracellular parasite Toxoplasma gondii .

ROP17 and ROP18 are protein kinases that function as virulence factors . In ROP18, this domain adopts the canonical protein kinase domain-fold with a predominantly α-helical C-terminal lobe and a smaller N-terminal lobe containing a central β-sheet .

ROP4 is localised to the rhoptries, secretory organelles at the apical end of the parasite, and is secreted from the parasite during host cell invasion . It has a typical bi-lobed protein kinase fold, but lack catalytic activity .

ROP5 is a pseudokinase that is essential for virulence in type I lineages of Toxoplasma gondii . It plays a critical role in promoting parasite survival within mouse monocytes and is required for the parasite's resistance to innate immune responses triggered by interferon-gamma (IFN-γ) in mice . ROP5 reduces the accumulation of immunity-related GTPases (IRGs), including IRGA6 (IIGP1) and IRGB6 (TGTP1/TGTP2), on the parasitophorous vacuole membrane, thereby limiting IRG-mediated killing of the parasite by mouse cells . It also regulates the activity of ROP18, an active kinase that directly targets IRGs to block their function and prevent parasite clearance. Additionally, ROP5 acts as an allosteric inhibitor of mouse IRGA6 (IIGP1) . Notably, ROP5 does not affect IFN-γ-mediated parasite killing in human cells, which lack the diverse IRG repertoire found in mice.
Small integral membrane protein 20 (SMIM20)
Type: Family

SMIM20, also known as MITRAC7, acts as a COX1-specific chaperone and is required for cytochrome c oxidase biogenesis .
Centriolar and ciliogenesis-associated protein HYLS1, C-terminal domain (HYLS1_C_dom)
Type: Domain

This entry represents the C-terminal domain of Centriolar and ciliogenesis-associated protein HYLS1. The HYLS1 gene shows alternative splicing and the transcript is found in multiple tissues during foetal development .
Protein of unknown function DUF4568 (DUF4568)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes.
Domain of unknown function DUF4453 (DUF4453)
Type: Domain

This short domain is found only on a small group of proteins from Proteobacteria that also carry a YARHG domain,

. They carry three conserved tryptophan and three conserved cysteine residues.
NOP protein chaperone 1 (NOPCHAP1)
Type: Family

This entry includes NOPCHAP1 from animals and New4 from fission yeast.

NOPCHAP1 is a client-loading PAQosome/R2TP complex cofactor that selects NOP58 to promote box C/D small nucleolar ribonucleoprotein (snoRNP) assembly . The function of New4 is not clear.
Proline-rich acidic protein 1 (PRAP)
Type: Family

PRAP, or proline-rich acidic protein 1, is a family of eukaryotic proteins. PRAP is abundantly expressed in the epithelial cells of the human liver, kidney, gastrointestinal tract, and cervix. It is significantly down-regulated in hepatocellular carcinoma and right colon adenocarcinoma compared with the respective adjacent normal tissues . It is expressed in the epithelial cells of the mouse and rat gastrointestinal tracts, and pregnant mouse uterus. PRAP plays an important role in maintaining normal growth suppression .
Hydrophobic seed protein domain (Hydrophob_seed_dom)
Type: Domain

This domain has a four-helix bundle structure. It contains four disulfide bonds, of which three function to keep the C- and N-terminal parts of the molecule in place .
Phage-like element PBSX protein, XkdF (XkdF)
Type: Domain

This domain is found in the phage-like element PBSX protein XkdF from Bacillus subtilis. This domain can also be found in the C-terminal of the N6 adenine-specific DNA methyltransferases. Its function is still not clear.
MCM, N-terminal domain (MCM_N)
Type: Domain

This entry represents the N-terminal region of MCM proteins. This region is composed of three structural domains. Firstly a four helical bundle, secondly a zinc binding motif and thirdly an OB-like fold .

MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication . In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins .
Uncharacterised protein YqbF, N-terminal domain (YqbF_N)
Type: Domain

This domain is found in N terminus of the uncharacterised protein YqbF from Bacillus subtilis. Its function is not known.
Vascular endothelial growth factor, heparin-binding domain (VEGF_C)
Type: Domain

This short domain is found at the C terminus of vascular endothelial growth factor (VEGF). It has been shown to have heparin binding activity .

Proteins containing this domain include VEGF-A, which is a growth factor active in angiogenesis, vasculogenesis and endothelial cell growth . VEGF-A also promotes a wide range of neuronal functions, including neurogenesis, neuronal migration, neuronal survival and axon guidance .
D-amino acid oxidase regulator (DAOA)
Type: Family

Members of this family were first described as activators of D-amino acid oxidase (DAO), however, it was later found that it acts as a repressor of DAO and SOD1 activity and promote their degradation . It may stimulate the degradation of DDO (D-aspartate oxidase) . DAO catalyzes the oxidative deamination of D-3,4-dihydroxyphenylalanine (D-DOPA) and D-serine, a precursor of dopamine and a participant in glutamatergic transmission, respectively . Variation in the DAO activator gene have been associated with bipolar disorder and major depression , although other studies have cast doubt on such a link .
Protein of unknown function DUF4609 (DUF4609)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 70 and 139 amino acids in length.
Domain of unknown function DUF4595 with porin-like fold (DUF4595)
Type: Domain

This entry represents a domain with a with porin-like fold found in a group of proteins from bacteroidetes. A 3D structure of a representative from Bacteroides uniformis has been deposited as

.
Protein of unknown function DUF4606 (DUF4606)
Type: Family

This family is found in eukaryotes.
Cellulose synthase, RING-type zinc finger (CES_Znf_RING)
Type: Domain

This RING-type zinc finger domain is frequently found in the catalytic subunit of cellulose synthase (

). This enzyme removes the glucose from UDP-glucose and adds it to the growing cellulose, thereby releasing UDP. The domain-structure is treble-clef like (PDB:1weo).
Di19, C-terminal (Di19_C)
Type: Domain

This entry represents the C-terminal domain in Di19 proteins. This domain contains an unstructured region followed by an α-helix.

Protein dehydration-induced19 (Di19) increases the sensitivity of plants to environmental stress, such as salinity, drought, osmotic stress and cold. The protein is also induced by an increased supply of stress-related hormones such as abscisic acid ABA and ethylene . Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought . It is phosphorylated by AtCPK11 in a Ca(2+)-dependent manner
Ephrin receptor, transmembrane domain (Eph_TM)
Type: Domain

This entry represents the left-handed dimer transmembrane domain of Ephrin receptors. This domain oligomerises and is important for the active signalling process .

Proteins containing this domain include the ephrin type-A and type-B receptors. Ephrin receptors (Ephs) are a group of receptor tyrosine kinases that are activated in response to binding ephrin ligands residing on adjacent cells . This binding leads to contact-dependent bidirectional signaling into neighbouring cells .
Photoreceptor disk component PRCD (PRCD)
Type: Family

PRCD is a secreted protein and a photoreceptor outer segment (OS) disc-specific protein involved in vision . Defects in the corresponding genes causes autosomal recessive retinal degeneration .
Adipogenin (Adipogenin)
Type: Family

This family of proteins is involved in the stimulation of adipocyte differentiation and development .
NMT1/THI5 family (NMT1/THI5)
Type: Family

The THI5 gene family of Saccharomyces cerevisiae comprises four highly conserved members named THI5, THI11, THI12 and THI13 . All are homologues of Schizosaccharomyces pombe Nmt1 (THI3), which is thought to function in the biosynthesis of hydroxymethylpyrimidine (HMP), a precursor of vitamin B1, thiamin . This entry includes the THI5 family, Nmt1 and other homologues , including bacterial homologues ThiY and RibY , which are substrate-binding components of ABC transporters for vitamins B1 and B2 respectively.

THI5 is responsible for the synthesis of 4-amino-5-(hydroxymethyl)-2-methylpyrimidine phosphate (HMP-P) in the thiamine biosynthetic pathway of eukaryotes .
Kita-kyushu lung cancer antigen 1 (KKLCAg1)
Type: Family

This is a family of cancer antigens .
Placenta-specific protein 9 (PLAC9)
Type: Family

This family of proteins has been identified as being enriched in placenta .
Sieve element occlusion, N-terminal (SEO_N)
Type: Domain

This entry represents the N terminus of the sieve element occlusion (SEO) proteins (also known as forisomes), which are phloem proteins accumulated during sieve element differentiation . This domain mediates homologous dimerisation of the forisome protein MtSEO-F, probably via hydrophobic interplay .
FAM209 family (FAM209)
Type: Family

This family of proteins is found in eukaryotes. Although the exact function of this family is unknown, it has been suggested that it may play a role in sperm acrosome biogenesis.
Sieve element occlusion, C-terminal (SEO_C)
Type: Domain

This entry represents the C terminus of the sieve element occlusion (SEO) proteins (also known as forisomes), which are phloem proteins accumulated during sieve element differentiation . This domain seems to be non-essential for dimerisation during forisome assembly .
SseB protein, C-terminal (SseB_C)
Type: Domain

This entry represents the C-terminal domain of the SseB protein found in Enterobacteria. SseB is known to enhance serine-sensitivity in Escherichia coli and is part of the Salmonella pathogenicity island 2 (SPI-2) translocon .
Oligogalacturonate lyase domain (Ogl_dom)
Type: Domain

This entry represents a domain found in oligogalacturonate lyases (also classified as pectate lyase family 22) (

) . It is involved in degradation of pectin .
TMEM240 family (TMEM240)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 54 and 175 amino acids in length. The function of this family is unknown.
Protein of unknown function (DUF4436) (DUF4436)
Type: Family

This is a family of membrane and transmembrane proteins. The function is not known.
Petal formation-expressed (Chloroplast_duf)
Type: Family

The members of this plant family from Arabidopsis thaliana appear to be proteins found in the chloroplast, expressed in the pollen tube during the petal differentiation and expansion stage. The function is not known.
Protein of unknown function DUF4576 (DUF4576)
Type: Family

This family of uncharacterised proteins is found in eukaryotes.
Nucleolus and neural progenitor protein-like, N-terminal domain (Nepro_N)
Type: Domain

This entry represents a domain found in Nucleolus and neural progenitor protein from mouse (Nepro) and similar eukaryotic sequences. Nepro may play a role in cortex development as part of the Notch signalling pathway. Downstream of Notch, it may repress the expression of proneural genes and inhibit neuronal differentiation thereby maintaining neural progenitors . It may also be involved in preimplentation embryo development . In humans, NEPRO (also known as Ribonuclease MRP subunit P64, Rmp64), which is required for the activity of human RNase MRP , interacts with multiple protein subunits of RMRP and is implicated in Anauxetic dysplasia 3 . The specific function of this domain, which is predicted to have a four-helix bundle structure, is still unknown.
Domain of unknown function DUF4632 (DUF4632)
Type: Domain

Proteins with this domain are found in eukaryotes. The length of these proteins is typically between 59 and 190 amino acids in length.
Domain of unknown function DUF4605 (DUF4605)
Type: Domain

This domain of unknown function is found in eukaryotes.
Transcobalamin-like, C-terminal domain (Transcobalamin-like_C)
Type: Domain

This domain of is found at the C-terminal of transcobalamin (TC), a vitamin B12-binding protein that transports cobalamin (Cbl/vitamin B12) into cells . TC consists of two domains, α and β, both of which contribute to Cbl binding, resulting in sub-picomolar affinity . This entry corresponds to the β-domain.

This domain is also found in several uncharacterised proteins, like

, that have an LPXTG-cell wall anchor at their C terminus, a polysaccharide lyase or glycosyltransferase structure associated with them in the middle region, as well as this domain at the N terminus.
Protein of unknown function DUF4636 (DUF4636)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 196 and 244 amino acids in length.
CIROZ (CIROZ)
Type: Family

This entry represents CIROZ proteins from animals. CIROZ is associated with several serious conditions, including primary ciliary dyskinesia .

CIROZ, formerly known as C1orf127, encodes a secreted protein characterised by an N-terminal signal peptide followed by three zona pellucida N domains (

), consistent with an extracellular localisation. It is specifically expressed in the left-right organiser (LRO) of several vertebrates, including mice, frogs and fish. Bi-allelic inactivation of CIROZ in humans is associated with heterotaxy and congenital heart defects, and knockout studies in mice confirm its essential role in establishing left-right embryonic asymmetry. However, targeted inactivation of the gene in zebrafish and Xenopus does not result in overt laterality defects, suggesting species-specific roles. Evolutionary analysis reveals that CIROZ is either absent or rendered non-functional in certain vertebrate lineages possessing motile cilia at the LRO, such as Carnivora, Atherinomorpha fish and jawless vertebrates. These findings highlight CIROZ as a key regulator of bilateral symmetry in mammals, with its loss or pseudogenisation reflecting divergent mechanisms of left-right axis specification across vertebrate evolution .
Protein of unknown function DUF4634 (DUF4634)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 98 and 133 amino acids in length.
Domain of unknown function DUF4657 (DUF4657)
Type: Domain

This domain is found in eukaryotic proteins with a typical protein length of between 305 and 370 amino acids.
Domain of unknown function DUF4627 (DUF4627)
Type: Domain

This domain is found in bacterial proteins and contains a conserved WYK sequence motif.
Protein of unknown function DUF4519 (DUF4519)
Type: Family

Proteins in this family contain two conserved sequence motifs, KET and VLP, and a single completely conserved residue P that may be functionally important.
Protein of unknown function DUF4442 (DUF4442)
Type: Family

This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 139 and 165 amino acids in length. There is a conserved PYF sequence motif. There is a single completely conserved residue N that may be functionally important.
Glutamate-rich protein 3 (ERICH3)
Type: Family

This entry includes human protein ERICH3 is a component of the mammalian primary cilium that regulates cilium length and the ciliary levels of Shh signaling molecules. It has been proposed that ERICH3 functions within retrograde intraflagellar transport-associated pathways to remove signaling proteins from cilia .
Meiosis-specific coiled-coil domain-containing protein MEIOC (MEIOC)
Type: Family

In mice, MEIOC is required for meiosis completion in both male and female germ cells . It interacts with YTHDC2 and maintains an extended meiotic prophase I in mice . In humans, it is encoded for on the chromosomal position C17orf104.
Sperm-associated microtubule inner protein 10 (SPMIP10)
Type: Family

This family (previously DUF4513) represents homologs of Sperm-associated microtubule inner protein 10 (SPMIP10). SPMIP10 is a microtubule inner protein (MIP) part of the axonemal dynein-decorated doublet microtubules (DMTs). It plays a role in the stabilisation of the interacting protomers of TEKTL1 - a tektin-like molecule that forms a filament in the cleft between protofilaments A11 and A12. In the EM structure of sperm DMTs, SPMIP10 cradles the inter-TEKTL1 interface while interacting with protofilaments A11 and A12 .
FANCD2 opposite strand protein (FANCD2OS)
Type: Family

This family of proteins of unknown function gets its name from its position in the mammalian genome: Fanconi anemia group D2 protein opposite strand transcript protein.
Protein of unknown function DUF4612 (DUF4612)
Type: Family

This protein family is a domain of unknown function, which is found in eukaryotes. Proteins in this family are typically between 109 and 323 amino acids in length.
Jhy protein (JHY)
Type: Family

Jhy protein is the protein product of the gene Jhy (previously known as 4931429I11Rik). This protein family is found in eukaryotes. In humans, the gene encoding this protein lies in the position chromosome 11 open reading frame 63. The function of Jhy protein is still to be determined.
Small membrane A-kinase anchor protein (Small_membr_AKAP)
Type: Family

Small membrane A-kinase anchor protein (sm) AKAP binds to type I regulatory subunits of protein kinase A (PKA-RI) and anchors them to the plasma membrane. This way provides spatio-temporal specificity for cAMP-dependent protein kinase (PKA) signalling . Small membrane AKAP is localised at the plasma membrane via potential myristoylation/palmitoylation anchors.
SPATA31-like (SPATA31-like)
Type: Domain

This domain of unknown function is found in proteins described as spermatogenesis-associated protein 31 (SPATA31) in mammalian such as

in homo sapiens.

Spermatogenesis-associated protein 3 (SPATA3), also known as Aep1, is a testis-specific protein primarily expressed during the haploid stage of spermatogenesis, from round spermatids to mature sperm. SPATA3 localizes to the acrosome region of developing spermatids and plays a role in spermiogenesis. While its precise function remains unclear, SPATA3 is involved in sperm formation and function. Deletion of the Spata3 gene in mice leads to in vitro fertility defects and ultrastructural anomalies in sperm . SPATA3 has been found to interact with beta-actin and syntaxin 1 in vitro .
Elongin BC and Polycomb repressive complex 2-associated protein EPOP-like (EPOP)
Type: Family

In mouse embryonic stem cells (mESCs), the transcriptional network can be divided into three functionally distinct modules: Polycomb, Core, and Myc, and the Polycomb module represses developmental genes . This family includes the polycomb repressive complex 2-associated factor EPOP (Elongin BC and Polycomb Repressive Complex 2 (PRC2) Associated Protein, also termed C17orf96, esPRC2p48, E130012A19Rik), a scaffold protein expressed in the inner cell mass of the mouse blastocyst serving as a bridging partner between the PRC2/EED-EZH2 complex and the elongin BC complex, and fine-tuning the transcriptional status of Polycomb group (PcG) target genes in embryonic stem cells. Both EPOP and Elongin BC are required to maintain low levels of expression at PRC2 genomic targets . EPOP interacts with the H2B deubiquitinase USP7 to modulate transcriptional processes in mESCs similar to MYC .

Another member of the family is the uncharacterised SKI/DACH domain-containing protein 1.
Protein of unknown function DUF4489 (DUF4489)
Type: Family

This family of uncharacterised proteins is found mainly in Clostridium.
40S small subunit processome assembly factor 1-like (FSAF1-like)
Type: Family

This entry represents human 40S small subunit processome assembly factor 1 (FSAF1), its homologue from Schizosaccharomyces pombe C3F10.08c, and similar proteins mainly found in animals. FSAF1 is part of the small subunit (SSU) processome, the first precursor of the small eukaryotic ribosomal subunit. During the assembly of the SSU processome in the nucleolus, many ribosome biogenesis factors, an RNA chaperone and ribosomal proteins associate with the nascent pre-rRNA and work in concert to generate RNA folding, modifications, rearrangements and cleavage as well as targeted degradation of pre-ribosomal RNA by the RNA exosome .