SII-SWORD/CoKE huggingface dataset:
Domain of unknown function DUF4470 (DUF4470)
Type: Domain

This domain of unknown function is conserved from fungi to Metazoa and plants. It is sometimes found in proteins that have a zinc-finger domain, Znf-MYND (

) at their very C terminus. In other cases it is associated with

, as in axonemal dynein assembly factor 3 .
TMEM71 protein family (TMEM71)
Type: Family

The function of this family, TMEM71, is not known. However, it is predicted to be a transmembrane protein. This family of proteins is found in eukaryotes. Proteins in the family vary between 41 and 291 amino acids in length.
TATA box-binding protein-associated factor 1D (TAF1D)
Type: Family

TAF1D is a component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription .
Protein of unknown function DUF4621 (DUF4621)
Type: Family

This family of proteins is functionally uncharacterised. It is found in bacteria (Bacteroidales). Proteins in this family are approximately 350 amino acids in length.
Protein of unknown function DUF4644 (DUF4644)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 143 and 191 amino acids in length.
Protein of unknown function DUF4655 (DUF4655)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 533 and 570 amino acids in length.
RACo, C-terminal (RACo_C)
Type: Domain

This entry represents the C-terminal domain of CoFeSP (RACo,

). This domain is also known as DUF4445 domain. Structure analysis of RACo indicate that it contains 4 regions: N-terminal region that binds the [2Fe-2S] cluster, a linker region, the middle region, and the large C-terminal domain. This entry represents the C-terminal domain which harbours the ATP-binding site. Structural studies show that the C-terminal domain contains the conserved topology characteristic of the ASKHA (acetate and sugar kinases/heat shock protein 70/actin). Despite the low-sequence identity shared between members of the ASKHA superfamily, they show a common central fold. Members of the ASKHA include proteins that catalyze phosphoryl transfers or hydrolysis of ATP in a variety of biological contexts. Asp, Asn, Glu, and Gln residues are well conserved in the core of the ASKHA proteins, where they interact with the phosphates of ATP and the bound Mg2+ ions .

Proteins containing this domain, such as PGA1_c15200 from Phaeobacter inhibens, is suggested to be involved in vitamin B12 reactivation .
Protein of unknown function DUF4446 (DUF4446)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 165 and 176 amino acids in length.
TMEM95 family (TMEM95)
Type: Family

TMEM95 and its homologues can be found in eukaryotes. They have a conserved LGG sequence motif. TMEM95 is a sperm membrane protein required for sperm-oocyte fusion and is essential for mammalian fertilization .
Rab15 effector (Rab15_effector)
Type: Family

This family of proteins has a role in receptor recycling from the endocytic recycling compartment .
T-cell activation inhibitor, mitochondrial (TCAIM)
Type: Family

T-cell activation inhibitor, also known as tolerance associated gene-1, is a mitochondrial protein that may have a role in regulation of T cell activation or apoptosis .
Interleukin-31 (IL-31)
Type: Family

This entry represents interleukin 31 (IL-31), it is a four-helix bundle cytokine that is preferentially produced by T helper type 2 cells . It is associated with pruritus, a characteristic feature of atopic dermatitis , and with other types of allergic contact dermatitis-provoked skin inflammation .
Transcription factor BREVIS RADIX, N-terminal domain (BRX_N)
Type: Domain

This entry represents the N-terminal α-helical domain of the BREVIS RADIX (BRX), which was characterised as being a transcription factor in plants regulating the extent of cell proliferation and elongation in the growth zone of the root . BRX maintains a rate-limiting brassinosteroid biosynthesis enzyme expression to keep brassinosteroid biosynthesis above a critical threshold . BRX has a ubiquitous, although quantitatively variable role in modulating the growth rate in both the root and the shoot .
Domain of unknown function DUF4461 (DUF4461)
Type: Domain

This domain is found in eukaryotic proteins, including T-cell activation inhibitor, which may have a role in regulation of T cell activation or apoptosis .
Protein of unknown function DUF4633 (DUF4633)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 94 and 123 amino acids in length.
Domain of unknown function DUF4488 (DUF4488)
Type: Domain

In most proteins, this domain covers almost the whole sequence, but a few sequences also carry a TonB domain (

).
Possible tRNA binding domain (tRNA_bind_dom)
Type: Domain

This domain, found at the C terminus of tRNA(Met) cytidine acetyltransferase, may be involved in tRNA-binding . tRNA(Met) cytidine acetyltransferase TmcA catalyses the formation of N(4)-acetylcytidine (ac4C) at the wobble position of tRNA(Met), by using acetyl-CoA as an acetyl donor and ATP (or GTP) .
Protein of unknown function DUF4495 (DUF4495)
Type: Family

This family is found in eukaryotes, and is typically between 322 and 336 amino acids in length. There are two conserved sequence motifs: QMW and DLW. Proteins in this family vary in length from 793 to 1184 amino acids.
WxL domain (WxL_dom)
Type: Domain

The WxL motif appears in two or three copies in these bacterial proteins and confers a cell surface localisation function. It seems likely that this region is the cell wall-binding domain of Gram-positive bacteria, and may interact with the peptidoglycan .
Galactosyltransferase, N-terminal (Galactosyl_T_N)
Type: Domain

This entry represents the N-terminal domain of the galactosyltransferases with three related galactosyltransferases activities, all three of which are possessed by one sequence in some cases: N-acetyllactosamine synthase (

), beta-N-acetylglucosaminyl-glycopeptide beta-1,4- galactosyltransferase (

), and lactose synthase (

). Proteins containing this domain include Beta-1,4-galactosyltransferase 1-7, Beta-1,4-N-acetylgalactosaminyltransferase bre-4 and Beta-N-acetyl-D-glucosaminide beta-1,4-N-acetylglucosaminyl-transferase.
Tubulin epsilon and delta complex protein 1 domain (TEDC1_dom)
Type: Domain

This entry represents a domain found in TEDC1 (Tubulin epsilon and delta complex protein 1). TEDC is a complex required for centriole maintenance and it is a component of several ciliary structures. It acts as a positive regulator of hedgehog signalling, which play key roles in embryonic development and in cancers . Additionally, this protein may play a role in counteracting perturbation of actin filaments, such as after treatment with the actin depolymerising microbial metabolite Chivosazole F .
Protein Largen/Inhibitory synaptic factor 1 (Largen/INSYN1)
Type: Family

This entry includes protein Largen and INSYN1 (inhibitory synaptic factor 1). Largen regulates cell size control . INSYN1 is part of the complex that mediates postsynaptic inhibition .
Respiration factor 1 (Rsf1_fungi)
Type: Family

This is a family of transcriptional regulators that may interact with transcription factors to mediate the transition from fermentative to glycerol-based respiratory growth . They localise to both the nucleus and mitochondrion .
Pma1 stabilization in the Golgi protein 1 (Pma1)
Type: Family

This is a family of predicted membrane glycoproteins from fungi. Proteins in this family include the yeast plasma membrane H+-ATPase Pma1. It is the major regulator of cytoplasmic pH and plasma membrane potential and the most abundant protein in the plasma membrane . Exp1 (ER eXport of Pma1) and Psg1 (Pma1 Stabilization in the Golgi) are involved in Pma1 maturation process .
Stabilizer of axonemal microtubules 5 (SAXO5)
Type: Family

This family (previously DUF4601) represents the homologs of Stabilizer of axonemal microtubules 5 (SAXO5, also known as C19orf45, TEX45). SAXO5 is a member of the SAXO superfamily of stabilizers that is ubiquitous in axonemal DMTs as well as stable microtubules of neurons and parasites. SAXO5 is a filamentous SAXO protein that binds along protofilament A04 with 96-nm periodicity . A typical feature of SAXO proteins is the presence of Mn motif which forms 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 . SAXO5 contains 11 Mn motifs and therefore has 96-nm periodicity, matching the external periodicity of the axoneme .
Myb/SANT-like DNA-binding domain 5 (Myb_DNA-bind_5)
Type: Domain

This predicted domain appears to be related to other Myb/SANT like DNA binding domains.
Keratinocyte differentiation factor 1 (KDF1)
Type: Family

KDF1 plays a role in the regulation of the epidermis formation during early development. It is required both as an inhibitor of basal cell proliferation and a promoter of differentiation of basal progenitor cell progeny .
Protein of unknown function DUF4643 (DUF4643)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 254 and 462 amino acids in length.
N-acetyltransferase ESCO, zinc-finger (AcTrfase_ESCO_Znf_dom)
Type: Domain

This entry represents the zinc-inger domain of the acetyl-transferase ESCO. N-acetyltransferase ESCO1 and ESCO2 are required for the establishment of sister chromatid cohesion and couple the processes of cohesion and DNA replication to ensure that only sister chromatids become paired together. They act by mediating the acetylation of cohesin component SMC3 . They feature a conserved C-terminal domain consisting of a H2C2 zinc finger motif and an acetyltransferase domain (

), while the diverse N-terminal domain is involved in chromosome binding and could target these proteins to different chromosome structures .
Centrosomal protein 15-like (CEP15-like)
Type: Family

This entry represents Centrosomal protein 15 (CEP15) and similar proteins from animals. In humans, CEP15 (also known as C3orf14) has been found to interact with CEP89 protein at the centrosome-cilium interface . This family was formerly known as DUF4570.
Domain of unknown function DUF4459 (DUF4459)
Type: Domain

This domain appears only on sequences from Salmonella species. These sequences also carry a YARHG domain (

).
Protein of unknown function DUF4441 (DUF4441)
Type: Family

This family is largely made up of uncharacterised proteins from the Ciliophora. The function is not known.
N-acetyltransferase ESCO, acetyl-transferase domain (ESCO_Acetyltransf_dom)
Type: Domain

This entry represents the acetyl-transferase domain of the acetyl-transferase ESCO. N-acetyltransferase ESCO1 and ESCO2 are required for the establishment of sister chromatid cohesion and couple the processes of cohesion and DNA replication to ensure that only sister chromatids become paired together. They act by mediating the acetylation of cohesin component SMC3 . They feature a conserved C-terminal domain consisting of a H2C2 zinc finger motif (

) and an acetyltransferase domain, while the diverse N-terminal domain is involved in chromosome binding and could target these proteins to different chromosome structures .
Gamma-secretase-activating protein, C-terminal domain (GSAP_C_dom)
Type: Domain

The gamma-secretase-activating protein (GSAP) family includes the mammalian GSAPs and the insect pigeon proteins (also known as linotte proteins). GSAP is a gamma-secretase regulator. It specifically activates the production of beta-amyloid protein through interactions with both gamma-secretase and its substrate, the amyloid precursor protein carboxy-terminal fragment (APP-CTF) . This has led to interest in the protein as potential therapeutic target for the treatment of Alzheimer's disease . Pigeon/linotte was initially identified as a gene that functions in adult Drosophila during associative learning .

This entry represents a domain found in the C-terminal of GSAP family members.
Domain of unknown function DUF4476 (DUF4476)
Type: Domain

This domain is functionally uncharacterised. It is found in eukaryotic and bacterial sequences.
Transcription regulator Rua1, C-terminal (Rua1_C)
Type: Domain

This entry represents a domain that can be found at the C terminus of fungal proteins such as meiotic expression up-regulated protein 26 from Schizosaccharomyces pombe , Ecm8 from Saccharomyces cerevisiae and Rua1 from Ustilago maydis.

Rua1 is a transcription factor and part of the gene cluster that mediates the biosynthesis of the glycolipid biosurfactant ustilagic acid (UA) .
Protein of unknown function DUF4437 (DUF4437)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are typically between 152 and 283 amino acids in length and have a RmlC-like jelly roll fold.
Transmembrane protein 255 (TMEM255)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 241 and 349 amino acids in length. The function of this family is unknown.
CCDC84-like (CCDC84-like)
Type: Family

This entry includes CCDC84 from animals and TITAN-like protein (TTL; At4g24900) from Arabidopsis. TTL is a key regulator for endosperm and embryo nuclear divisions . CCDC84 has been shown to constrain centriole number by modulating APC/CCdh1-mediated HsSAS-6 degradation .
Protein of unknown function DUF4646 (DUF4646)
Type: Family

This is a family of proteins largely from fungi. The function is not known.
Protein of unknown function DUF4508 (DUF4508)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 117 and 253 amino acids in length.
ASX, DEUBAD domain (ASX_DEUBAD_dom)
Type: Domain

This entry represents the DEUBiquitinase ADaptor (DEUBAD) domain from Asx and homologues, which contain a characteristic LXXLL motif , detected in diverse transcription factors, coactivators and co-repressors and is implicated in mediating interactions between them . This domain interacts with the UCH37-like domain (ULD) from Calypso and BAP1 deubiquitinases (DUBs), an interaction that is required for DUB activity activation .
Katanin p80 subunit, C-terminal (Katanin_C-terminal)
Type: Domain

This entry represents the C-terminal domain of katanin 80kDa subunit.

Katanin is a microtubule-severing protein consist of a 60kDa ATPase subunit (katanin-p60) and a 80kDa subunit (katanin-p80) ,

]. Katanin-p80 is composed of an N-terminal WD40 repeat domain, a central proline-rich domain and a C-terminal domain required for dimerisation with the catalytic katanin-p60 . The katanin complex associates with a specific subregion of the mitotic spindle leading to increased microtubule disassembly and targeting of katanin-p60 to the spindle poles . Katanin is a crucial regulator of early embryonic development, and recessive mutations or deletions in the KATNB1 gene cause severe microcephaly or microlissencephaly . Katanin forms a complex with another microcephaly-associated protein, ASPM (abnormal spindle-like microcephaly-associated) that controls spindle pole organization, poleward spindle flux, and spindle positioning, processes that when misregulated could perturb proliferation of neuronal progenitors and lead to microcephaly. Katanin also interacts with CAMSAPs (calmodulin-regulated spectrin-associated proteins) and is required for limiting the length of CAMSAP-bound MT minus-end stretches during interphase . In plants it also plays an important role as it is required for the bending of the plant axis toward the light source.
Protein of unknown function DUF4600 (DUF4600)
Type: Family

Some members of this family are also annotated as coiled-coil domain-containing protein 169 (CCDC169).
Lysosomal enzyme trafficking factor (LYSET)
Type: Family

This family of proteins includes lysosomal enzyme trafficking factor (formerly known as UPF0694 transmembrane protein C14orf109, or transmembrane protein 251) are required for mannose-6-phosphate-dependent trafficking of lysosomal enzymes . LYSET bridges GlcNAc-1-phosphate transferase (GNPTAB), to the membrane-bound transcription factor site-1 protease (MBTPS1), thus allowing proteolytic activation of the GNPTAB. GNPTAB is involved in the regulation of M6P-dependent Golgi-to-lysosome trafficking of lysosomal enzymes . Members of this entry are essential factors for maturation and delivery of lysosomal hydrolases .
FAM229 protein (FAM229)
Type: Family

The FAM229 (also known as UPF0731) family of uncharacterised proteins is found in mammals.
Domain of unknown function DUF4502 (DUF4502)
Type: Domain

This domain of unknown function is found in eukaryotic proteins that are, as yet, uncharacterised.
Sperm microtubule associated protein 1 (SPMAP1)
Type: Family

This family (previously DUF4542) represents the homologs of Sperm microtubule associated protein 1 (SPMAP1 also known as C17orf98). These proteins contain a conserved IPPYN sequence motif. The EM structure of sperm DMTs shows that SPMAP1 interacts directly with the tubulin lattice at the A-tubule seam (between protofilaments A09/A10) where outer dense fibers (ODFs) are connected to dynein-decorated doublet microtubules (DMTs) .
Protein of unknown function DUF4450 (DUF4450)
Type: Family

This is a family of bacterial proteins of unknown function.
Signal transducer CD24 (CD24)
Type: Family

Signal transducer CD24 (also known as cluster of differentiation 24) is a cell adhesion molecule that has been implicated in tumor invasion and metastasis of various solid tumours .
Domain of unknown function DUF4592 (DUF4592)
Type: Domain

This domain of unknown function lies to the N terminus of the protein. This domain is found in eukaryotes and contains two completely conserved residues (L and A) that may be functionally important.
Domain of unknown function DUF4460 (DUF4460)
Type: Domain

This domain of unknown function has a conserved HPD sequence motif. There are two completely conserved residues (N and F) that may be functionally important. The domain is found in eukaryotic proteins, including T-cell activation inhibitor which may have a role in regulation of T cell activation or apoptosis .
Domain of unknown function DUF4503 (DUF4503)
Type: Domain

This domain of unknown function is found in eukaryotic proteins that are, as yet, uncharacterised.
Domain of unknown function DUF4462 (DUF4462)
Type: Domain

This domain is found in plant proteins, and is approximately 30 amino acids in length. In some sequences, this domain is repeated.
CCDC81, HU domain 1 (HU-CCDC81)
Type: Domain

This is the first of two HU domains found in the CCDC81-like proteins. CCDC81 has been experimentally linked to the centrosome; eukaryotic CCDC81 HU domains are predicted to function in protein-protein interactions in centrosome organization and potentially contribute to cargo-binding in conjunction with Dynein-VII. A striking lineage-specific expansion of the domain is observed in birds, where the HU domains could function in recognition of non-self molecules .
Distal membrane-arm assembly complex protein 1-like domain (DMAC1-like_dom)
Type: Domain

This entry represents a domain found in a group of animal and fungal proteins, including human Distal membrane-arm assembly complex protein 1 (DMAC1, also known as C9orf123) and its orthologue in Schizosaccharomyces pombe Tam6. DMAC1 is required for the assembly of the mitochondrial NADH:ubiquinone oxidoreductase complex (complex I). It is involved in the assembly of the distal region of complex I . Tam6, also known as Dmo2, is required for the stability and maturation of Cox2p, the second subunit of the COX complex . This domain, previously known as DUF4536, is predicted to fold into an α-helical configuration.
Antitoxin Rv0909/MT0933 (Antitoxin_Rv0909/MT0933)
Type: Family

Proteins in this family are found in bacteria, including the antitoxin Rv0909/MT0933. It is an antitoxin component of a toxin-antitoxin (TA) module .
TM140 protein family (TM140)
Type: Family

This family of uncharacterised membrane proteins are called transmembrane protein 140. Their function is unknown.
Coiled-coil domain containing protein 32 (CCDC32)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 160 and 188 amino acids in length. The gene that encodes this protein is C15orf57, but its protein product is called CCDC32 (Coiled-coil domain containing protein 32). The exact function of this protein is unknown.
Type 2 DNA topoisomerase 6 subunit B-like (TopoVIB-like)
Type: Family

This family of animal proteins is known as TOPOVIB-like as it shares strong structural similarity to the TopoVI DNA topoisomerase subunit B. TOPOVIB-like interacts and forms a complex with SPO11 and is required for meiotic DNA double-strand break formation . TOPOVIB-like may be involved in the regulation of DNA cleavage.
WD repeat and coiled-coil-containing protein family (WDCP)
Type: Family

This family includes WD repeat and coiled-coil-containing protein (WDCP, previously known as C2orf44), which is found in eukaryotes and consists of around 721 amino acids. The N-terminal contains two WD (tryptophan-aspartic acid) repeats (WD1 and WD2). WD repeats may be involved in a range of biological functions including apoptosis, transcriptional regulation and signal transduction. The C-terminal contains a proline-rich sequence (PPRLPQR), and is predicted to have leucine-rich coiled coil region (CC) .

WDCP was identified in a proteomic screen to find signalling components that interact with Hck (hematopoietic cell kinase), a non-receptor tyrosine kinase. WDCP was shown to bind tightly and specifically to the SH3 domain of Hck in U937 human monocytic cells. WDCP was also shown to exist as an oligomer when expressed in mammalian cells. While the function of WDCP is unknown, it has been identified in a gene fusion event with anaplastic lymphoma kinase (ALK) in colorectal cancer patients .
Protein of unknown function DUF4639 (DUF4639)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 161 and 601 amino acids in length.
ATPase PAAT-like (PAAT-like)
Type: Family

This family is found in eukaryotes. It represents the ATPase protein associated with ABC transporters (PAAT) and related proteins. PAAT is formed of a nucleotide-binding domain (NBD)-like domain and a signal for intramitochondrial sorting. PAAT interacts with the mitochondrial inner membrane ABC proteins: ABCB7, ABCB8, and ABCB10. It is involved in maintenance of mitochondrial homeostasis and cell survival .
Domain of unknown function DUF4444 (DUF4444)
Type: Domain

This domain is found in bacteria (Rhodobacteraceae family). It is typically found at the C terminus and is approximately 40 amino acids in length. It contains a conserved LIPL sequence motif and two completely conserved G residues that may be functionally important.
Homologous recombination OB-fold protein (HROB)
Type: Family

During homologous recombination, HROB acts by recruiting the MCM8-MCM9 helicase complex to sites of DNA damage to promote DNA repair synthesis .
Immunity protein 75 (Imm75)
Type: Family

Proteins in this family may be immunity proteins from bacteria, associated with polymorphic toxin systems .
Latrotoxin, C-terminal domain (Latrotoxin_C_dom)
Type: Domain

A toxin domain present in arthropod alphaproteobacterial and gammaproteobacterial endosymbionts, and also at the C termini of the latrotoxins of the black widow spider. The domain is characterised by a conserved, hydrophobic helix and is predicted to associate with the cell membrane .
HNH/Endo VII superfamily nuclease toxins (Tox-HNH-EHHH)
Type: Domain

A predicted toxin of the HNH/Endonuclease VII fold present in bacterial polymorphic toxin systems with a characteristic conserved [ED]H motif and two histidine residues. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5, type 6, type 7 or Photorhabdus virulence cassette (PVC)-type secretion system .