SII-SWORD/CoKE huggingface dataset:
Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, N-terminal (PpnN_N)
Type: Domain

This domain can be found at the N terminus of pyrimidine/purine nucleotide 5'-monophosphate nucleosidase (PpnN, also known as YgdH) from bacteria. PpnN catalyses the hydrolysis of the N-glycosidic bond of diverse pyrimidine and purine nucleotide 5'-monophosphates, to form ribose 5-phosphate and the corresponding free base. It can use AMP, GMP, IMP, CMP, dTMP and UMP as substrates. This enzyme adopts a tetrameric configuration with allosteric (p)ppGpp binding sites located between subunits. The binding of this alarmone molecule, which play a role in the bacterial stringent response, gives rise to a large conformational change involving the terminal region that leads to the exposure of the catalytic pocket. The N-terminal
domain consists of a three-stranded anti-parallel β-sheet surrounded by α-helices .
Shieldin complex subunit 1 (SHLD1)
Type: Family

SHLD1, also known as RINN3, is a component of the shieldin complex, a vertebrate-specific protein complex which functions as a downstream effector in the 53BP1 pathway, regulates NHEJ (non-homologous end joining) .
Protein of unknown function DUF4641 (DUF4641)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 201 and 519 amino acids in length.
Domain of unknown function DUF4468 with TBP-like fold (DUF4468)
Type: Domain

This entry represents a domain found in a large family of (predicted) secreted proteins with unknown functions from human gut and oral cavity. In these proteins, the domain is typically found towards the N terminus, with a FMN-binding domain at the C terminus. Experimentally determined 3D structure of this domain shows a variant of a TATA box binding-like fold, but with no detectable sequence similarity to other proteins with this fold.
Domain of unknown function DUF4469 with IG-like fold (DUF4469)
Type: Domain

This entry represents the C-terminal domain of a large family of (predicted) secreted proteins with unknown functions, mainly from human gut bacteroides.
Protein of unknown function DUF4522 (DUF4522)
Type: Family

This family of mammalian proteins is functionally uncharacterised. In humans, this protein is known as C4orf36.
Domain of unknown function DUF4431 (DUF4431)
Type: Domain

This domain of unknown function is found in bacterial proteins.
Testis expressed protein 56 (Tex56)
Type: Family

This family of proteins is includes Testis expressed protein 56 (Tex56), whose function is not yet clear. This family of proteins is found in mammals.
Protein of unknown function DUF4465 (DUF4465)
Type: Family

This entry represents a large family of uncharacterised proteins mostly from human gut bacteroides, but also some environmental and water bacteria (Planctomycetes), as well as metagenomic samples. Most proteins from this family are secreted or located on the outer surface, and may participate in cell-cell interactions or cell-nutrient interactions. This function is supported by a solved structure of a Bacteroides ovatus homologue, which adopts a galactose binding (jelly-roll) β barrel structure.
Protein of unknown function DUF4625 (DUF4625)
Type: Family

Members of this family contain a likely bacterial Ig-like fold, suggesting it may be a family of lipoproteins.
C5orf34-like, N-terminal (C5orf34-like_N)
Type: Domain

This entry represents the N-terminal domain of a family of eukaryotic proteins, including the human uncharacterised protein C5orf34, which has been reported to be correlated with an unfavorable prognosis of patients from a variety of human malignancies . This domain was previously known as DUF4524. It is predicted to show an α/β structure.
Domain of unknown function DUF4485 (DUF4485)
Type: Domain

This domain of unknown function is found in eukaryotic proteins, and is approximately 90 amino acids in length.
MGT5A-like, N-terminal (MGT5A-like_N)
Type: Domain

This domain is found at the N-terminal end of human Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A (MGT5A) and similar sequences mainly found in vertebrates.

MGT5A, also known as GNT-V, is a glycosyltransferase family 18 enzyme that catalyses the addition of N-acetylglucosamine (GlcNAc) in beta 1-6 linkage to the alpha-linked mannose of biantennary N-linked oligosaccharides . This protein consists of a short N-terminal cytosolic region, a transmembrane (TM) domain, a stem region, the N domain and a large C-terminal catalytic region (

) . This entry covers the three N-terminal short domains. The activity of the signal-peptide peptidase-like-3 (SPPL3), responsible for the secretion of the protein, depends on the helical stability of the TM domain . The N domain has been reported to play a critical role in the recognition of glycoprotein substrates . This region shows an all-α configuration.

This domain is also found covering the whole length of the protein in human Coiled-coil domain-containing protein 126 (CC126) and related proteins.
Pre-T-cell antigen receptor (PTCRA)
Type: Family

The pre-T-cell antigen receptor (pre-TCR), expressed by immature thymocytes, has a pivotal role in early T-cell development, including TCR beta-selection, survival and proliferation of CD4(-)CD8(-) double-negative thymocytes, and subsequent alpha/beta T-cell lineage differentiation . This protein contains an immunoglobulin domain .
Transmembrane protein 174 (TMEM174)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in chordates and includes the human integral membrane protein TMEM174 protein.
Protein of unknown function DUF4529 (DUF4529)
Type: Family

This family of eukaryotic proteins is functionally uncharacterised. The proteins contain a conserved VLPPLK sequence motif.
Kinocilin protein (Kinocilin)
Type: Family

The kinocilin family of proteins is found in vertebrates. In mouse it has been shown that this protein is expressed primarily in the kinocilium of sensory cells in the inner ear .
Domain of unknown function DUF4585 (DUF4585)
Type: Domain

The function of this domain is yet to be characterised. It is often found in eukaryotes, and is approximately 70 amino acids in length. It has a conserved DPE sequence motif. This domain is putatively thought to lie in the C terminus of the DNA nucleotide repair protein, Xeroderma pigmentosa complementation group A (XPA). The function of XPA is to bind to DNA and repair any mismatched base pairs. In humans, this protein is encoded for in chromosome 5 open reading frame 65. Mutations in the gene lead to myelodysplastic syndromes, where there is inefficient stem cell production in the bone marrow. This suggests that the protein may have a role in forming blood cells .
Protein of unknown function DUF4432 (DUF4432)
Type: Family

This family of proteins has not been characterised.
Protein of unknown function DUF4493 (DUF4493)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are typically between 264 and 710 amino acids in length. Many of them have a lipid attachment site suggesting they are lipoproteins.
Interleukin-17 receptor C/E, N-terminal (IL-17_rcpt_C/E_N)
Type: Domain

This domain is found at the N terminus (extracellular region) of interleukin-17 receptor C and interleukin-17 receptor E. This is the presumed ligand-binding domain . Human putative interleukin-17 receptor E-like consists only of this domain.
HAM1-like, C-terminal domain (HAM1-like_C)
Type: Domain

This entry represents a domain found at the C-terminal end of the putative cell signalling protein HAM1 from Cryptococcus neoformans and similar fungal sequences. HAM1 may act as a negative regulator of mating during vegetative growth . Proteins with this domain often also contain an N-terminal domain (

).
Domain of unknown function DUF4440 (DUF4440)
Type: Domain

This entry represents a domain found in uncharacterised proteins from bacteria, archaea and eukaryotes, including NTF2-Like SgcJ protein from Streptomyces carzinostaticus, which plays a role in the biosynthesis of the 9-membered enediyne antitumor antibiotic C-1027. It shows a cone-like α+β barrel structure with a long N-terminal α-helix, a curved six-stranded antiparallel β-sheet and two additional shorter α-helices. Its specific function is still unkown .
Integrator complex subunit 15 (INTS15)
Type: Family

Integrator complex subunit 15 is likely a component of the Integrator (INT) complex, which is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing .
Protein of unknown function DUF4548 (DUF4548)
Type: Family

This family of proteins is found in eukaryotes. The human member of this family is C1orf105.
Cytochrome b-245 chaperone 1 (Cybc1)
Type: Family

Cytochrome b-245 chaperone 1, also known as Eros in mice, is a transmembrane protein that may play a central role as a chaperone critical for expression of gp91phox and p22phox and hence for the cytochrome b558 heterodimer .
Protein of unknown function DUF4545 (DUF4545)
Type: Family

This family of proteins is found in eukaryotes. The human member of this family is C1orf141.
Protein of unknown function DUF4494 (DUF4494)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are typically between 154 and 172 amino acids in length. They contain two conserved sequence motifs (VDA and EAE) and a single completely conserved residue E that may be functionally important.
Domain of unknown function DUF4434 (DUF4434)
Type: Domain

This entry represents a domain of unknown function found in a group of uncharacterised proteins from bacteria.
Protein of unknown function DUF4504 (DUF4504)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 253 and 329 amino acids in length. There are two conserved sequence motifs: LLGYP and SFS.
Protein of unknown function DUF4628 (DUF4628)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 152 and 673 amino acids in length.
Steroid receptor-associated and regulated protein (C1ORF64)
Type: Family

Steroid receptor-associated and regulated protein is also known as ER-related factor, ERRF, or C1orf64. It is thought to regulate the transcriptional function of androgen and estrogen receptors . Proteins in this family are typically between 145 and 169 amino acids in length, and have a conserved IDC sequence motif.
Protein of unknown function DUF4492 (DUF4492)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. Their function is unknown.
Short transmembrane mitochondrial protein 1 (STMP1)
Type: Family

STMP1 may be a subunit of mitochondrial respiratory complexes .
Domain of unknown function DUF4479 (DUF4479)
Type: Domain

The function of this domain is not known. It is found in bacteria in association with a putative tRNA-binding domain (

).
Glutamate-rich protein 5 (Glu-rich_5)
Type: Family

This entry represents a group of uncharacterised proteins, including glutamate-rich protein 5.

Glutamate-rich protein 5, also known as ERICH5, is a protein in humans encoded by the ERICH5 gene, which is located on chromosome 8 at position 8q22.2.
Protein SPO16 homolog (SCRE)
Type: Family

This entry represents the Protein SPO16 homologue (SPO16, also known as Synaptonemal complex reinforcing element SCRE), including the mammalian orthologue of budding yeast Spo16. It plays a key role in reinforcing the integrity of the central element of the synaptonemal complex (SC), resulting in the SC stabilization which ensures the progression of meiotic prophase I in male and female germ cells [

. It promotes homologous recombination and crossing-over in meiotic prophase I via its association with SHOC1 . It is also required for the localization of TEX11 and MSH4 to recombination intermediates .
Protein BRAWNIN (BRAWNIN)
Type: Family

BRAWNIN (also known as ubiquinol-cytochrome-c reductase complex assembly factor 6, UQCC6) is essential for respiratory chain complex III (CIII) assembly . It is also required for cytochrome c oxidase complex (complex IV) assembly .
KATNIP domain (KATNIP_dom)
Type: Domain

This domain can found in eukaryotic proteins such as KATNIP. It repeats several times in the vertebrate KATNIP.

KATNIP is a microtubule-associated ciliary base protein probably involved in microtubule regulation .
Domain of unknown function DUF4429 (DUF4429)
Type: Domain

This presumed domain is functionally uncharacterised. It is found in bacteria, archaea and viruses, and is approximately 90 amino acids in length. This domain is often found in two tandem copies.
Cation channel sperm-associated auxiliary subunit TMEM249 (TMEM249)
Type: Family

This family of transmembrane proteins is found in eukaryotes and includes Cation channel sperm-associated auxiliary subunit TMEM249 (also referred to as C8orfK29). It is an auxiliary component of the CatSper complex, a complex involved in sperm cell hyperactivation . TMEM249 contributes to the assembly of the CatSpermasome.
Protein of unknown function DUF4534 (DUF4534)
Type: Family

This family of functionally uncharacterised proteins is found in mammals. It includes human transmembrane TMEM217 and TMEM217B.
Protein of unknown function DUF4623 (DUF4623)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are approximately 470 amino acids in length. There are two conserved sequence motifs: HLL and RYL.
Protein of unknown function DUF4597 (DUF4597)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 63 and 76 amino acids in length. There is a conserved TPPTPT sequence motif.
C5orf34-like, C-terminal (C5orf34-like_C)
Type: Domain

This is the C-terminal domain of a family of eukaryotic proteins, including the human uncharacterised protein C5orf34, which has been reported to be correlated with an unfavorable prognosis of patients from a variety of human malignancies . This domain was previously known as DUF4520. It is predicted to show an α/β configuration.
Retroelement silencing factor 1 (RESF1)
Type: Family

RESF1 is involved in retroelement silencing. It regulates repressive epigenetic modifications associated with SETDB1 .
Spermatogenesis-associated protein 48 (SPATA48)
Type: Family

Spermatogenesis-associated protein 48 is also known as sperm microtubule inner protein 7 (SPMIP7) and post-meiotic spermatogenesis protein 1 . In humans, it is found in the chromosomal position, C7orf72.

Lack of this protein leads to small testis and defective spermatogenesis in mice. SPATA48 has homologs in humans, mice, chimpanzees and macaques but these proteins have no conserved domains and their function is unclear .
C2orf72-like, C-terminal (C2orf72-like_C)
Type: Domain

This entry represents a domain found at the C-terminal of the human uncharacterised protein C2orf72 and similar sequences from vertebrates. C2orf72 may be used for the diagnosis of prostate cancer . This domain was previously known as DUF4630.
TASL protein (TASL)
Type: Family

In humans, TASL (TLR adaptor interacting with SLC15A4 on the lysosome) is encoded by CXorf21 that is associated with systemic lupus erythematosus . It is an immune adaptor that is required for recruitment and activation of IRF5 by TLR7, TLR8 and TLR9, in mechanistic analogy to IRF3 and its three adaptors STING, MAVS and TRIF. TASL interacts with the endolysosomal transporter SLC15A4; the SLC15A4-TASL complex is required for endolysosomal TLR signalling. TASL contains a pLxIS motif that is important for its function .
Protein of unknown function DUF4543 (DUF4543)
Type: Family

This family of proteins is found in eukaryotes. The human member of this family is C17orf67.
Protein of unknown function DUF4603 (DUF4603)
Type: Family

This protein family is found in eukaryotes and has unknown function.
Domain of unknown function DUF4428 (DUF4428)
Type: Domain

This putative zinc finger domain is found in uncharacterised bacterial and viral proteins.
Protein PAXX (PAXX)
Type: Family

Protein PAXX is involved in DNA double-strand break (DSB) repair. PAXX interacts directly with the DSB-repair protein Ku and is recruited to DNA-damage sites in cells .
Testis-expressed sequence 35 protein (Tex35)
Type: Family

This family of proteins is found in eukaryotes. The mouse and human family members are specifically expressed in the testis .
Protein of unknown function DUF4547 (DUF4547)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 144 and 206 amino acids in length. The human member of this family is C3orf43, also annotated as single-pass membrane and coiled-coil domain-containing protein 1.
Domain of unknown function DUF4550 (DUF4550)
Type: Domain

This presumed domain is functionally uncharacterised. The domain contains an N-terminal HXE motif.
Small integral membrane protein 15 (Smim15)
Type: Family

This family of eukaryotic proteins is functionally uncharacterised. There is a conserved LSWKL sequence motif. This family includes human protein C5orf43. Family members are annotated as small integral membrane protein 15.
Protein of unknown function DUF4551 (DUF4551)
Type: Family

This metazoan family of proteins is functionally uncharacterised. This family includes human protein C12orf56.
Protein of unknown function DUF4649 (DUF4649)
Type: Family

This family of Firmicute proteins has members that are annotated as ribose-phosphate pyrophosphokinase; however there is no evidence for this attribution. Member proteins are all shorter than 100 residues in length.
Protein of unknown function DUF4635 (DUF4635)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 120 and 154 amino acids in length. There are two conserved sequence motifs: LEQ and DLE.
SOGA, coiled-coil domain (SOGA_CC)
Type: Domain

This entry represents a coiled-coil region of SOGA proteins.

The SOGA (suppressor of glucose by autophagy) family consists of proteins SOGA1, SOGA2, and SOGA3 (also known as Microtubule cross-linking factor 1-3). SOGA1 regulates autophagy by playing a role in the reduction of glucose production in an adiponectin-and insulin-dependent manner . SOGA1/2 are required for faithful chromosome segregation during mitosis . Members of this entry contain a long coiled-coil domain that dimerizes and holds two N-terminal domains that bind to microtubules .
SOGA 1/2-like, coiled-coil (SOGA1/2-like_CC)
Type: Domain

This entry represents a coiled-coil region found in microtubule cross-linking factors 1 and 2 (also known as SOGA1/2), which are members of the SOGA (suppressor of glucose by autophagy) family. SOGA1 regulates autophagy by playing a role in the reduction of glucose production in an adiponectin-and insulin-dependent manner . It is required for faithful chromosome segregation during mitosis . This entry also includes KIAA0408, an uncharacterised human protein.
Regulator of DNA class I crossover intermediates 1-like (Redic1-like)
Type: Family

This family of proteins mainly found in vertebrates includes mouse Regulator of DNA class I crossover intermediates 1 (Redic1). Redic1 is involved in recombination, probably acting by stabilising recombination intermediates during meiotic crossover formation. It is required for normal germline development and fertility as well as for meiotic progression, complete chromosomal synapsis and crossover formation . This protein binds double-stranded DNA .
Domain of unknown function DUF4614 (DUF4614)
Type: Domain

This domain is found in eukaryotes, and contains a conserved EALT sequence motif.
Uncharacterised protein family UPF0728 (UPF0728)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in metazoa. There is a conserved GPY sequence motif.
Sperm-associated microtubule inner protein 4 (SPMIP4)
Type: Family

This family (previously DUF4555) includes the homologs of human sperm-associated microtubule inner protein 4 (SPMIP4, also known as C7orf31) that is found predominantly in testis . SPMIP4 is a microtubule inner protein (MIP) part of the axonemal dynein-decorated doublet microtubules (DMTs).

Members of this family adopt rather extended conformation and contain a single or multiple Mn motifs. Each Mn motif consists of a 5- to 6-residue helix flanked by a Tyr/Phe residue on one end and by a Ser/Thr on the other that binds the shoulder of the α-tubulin S9/S10 loop . It was reported that a single Mn motif is sufficient for microtubule binding in vitro . Members of this family are likely to stabilise the microtubule structure in the sperm flagella .
Protein of unknown function DUF4464 (DUF4464)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family have a conserved YID sequence motif.
Protein of unknown function DUF4501 (DUF4501)
Type: Family

This family of proteins is found in eukaryotes. The exact function of the family members remains unknown, but they are thought to be a single-pass membrane proteins. This family contains many highly conserved cysteine residues.
Coiled-coil domain-containing glutamate-rich protein family 1 (CCER1)
Type: Family

This is a family of coiled-coil family proteins found in eukaryotes. Proteins in this family are typically between 160 and 397 amino acids in length.
Protein of unknown function DUF4491 (DUF4491)
Type: Family

This family of proteins is found in bacteria. There is a conserved EYY sequence motif.
Protein of unknown function DUF4645 (DUF4645)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 200 and 298 amino acids in length.
Maturin (Maturin)
Type: Family

Maturin is required for differentiation during primary neurogenesis .
EKC/KEOPS complex subunit GON7, metazoa (GON7_meta)
Type: Family

The KEOPS/EKC complex is a tRNA modification complex involved in the biosynthesis of N6-threonylcarbamoyladenosine (t6A). In eukaryotes, KEOPS is composed of OSGEP/Kae1, PRPK/Bud32, TPRKB/Cgi121, LAGE3/Pcc1 and GON7 . This family consists of subunit GON7 from Metazoa.
Protein of unknown function DUF4620 (DUF4620)
Type: Family

This entry represents a protein family of unknown function from primates.
Protein of unknown function DUF4533 (DUF4533)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in mammals and includes two human proteins: C12orf60 and C12orf69.
Ubiquinol-cytochrome-c reductase complex assembly factor 3 (UQCC3)
Type: Family

Complex III (cytochrome bc1) is a protein complex of the mitochondrial inner membrane that transfers electrons from ubiquinol to cytochrome c. UQCC3 functions in complex III assembly . It is also a potent antiviral protein independent of interferon production .
Protein of unknown function DUF4559 (DUF4559)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes and includes human protein CXorf38 which is associated with the transmembrane protein metal cation symporter ZIP8 malfunction .
Domain of unknown function DUF4629 (DUF4629)
Type: Domain

This domain is found in eukaryotes, and contains two conserved sequence motifs: MHML and LGKK.
Domain of unknown function DUF4458 (DUF4458)
Type: Domain

This entry represents a domain found in tandem repeats at the N terminus of secreted Leucine Rich repeat (LRR) proteins from human-associated Bacteroidetes.
Vexin domain (Vexin_dom)
Type: Domain

Proteins containing this domain include Xenopus laevis Vexin and its human homologue, C8orf46. Vexin is transiently expressed in differentiating progenitors in the developing central nervous system (CNS) and is required for neurogenesis in the neural plate and retina .

This entry corresponds to a presumed SH3 domain.
Cilia and flagella associated protein 90 (CFAP90)
Type: Family

This family of proteins is found in animals, including the cilia- and flagella-associated protein 90 (CFAP90) from human, which has been recently identified as a microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating .