SII-SWORD/CoKE huggingface dataset:
Domain of unknown function DUF7812 (DUF7812)
Type: Domain

This domain is found in uncharacterised plant proteins. It is predicted to fold into an α-helical structure with similarity to α-solenoid domains.
Protein of unknown function DUF7813 (DUF7813)
Type: Family

This entry represents uncharacterised proteins found in plants. They are predicted to adopt structures similar to choline-like transporters.
Domain of unknown function DUF7814 (DUF7814)
Type: Domain

This domain is found in uncharacterised bacterial proteins. It is predicted to fold into array of helices. It has similarity to helical domain found in MmeI restriction-modification enzymes.
Domain of unknown function DUF7815 (DUF7815)
Type: Domain

This domain is found in uncharacterised plant proteins. It contains two pairs of conserved cysteines that may be involved in metal coordination. It is predicted to adopt a structure typical for zinc ribbon domains.
NEDD4-binding protein 2, DUF7816 (DUF7816)
Type: Domain

This domain is found towards the C terminus of human NEDD4-binding protein 2 (N4BP2), which has 5'-polynucleotide kinase and nicking endonuclease activity and may play a role in DNA repair or recombination . This domain is predicted to adopt an α configuration. Its specific function is unknown. It is normally found N-terminal to

.
NEDD4-binding protein 2, DUF7817 (DUF7817)
Type: Domain

This domain is found towards the C terminus of human NEDD4-binding protein 2 (N4BP2), which has 5'-polynucleotide kinase and nicking endonuclease activity and may play a role in DNA repair or recombination . This domain is often found N-terminal to

and

.
NEDD4-binding protein 2, DUF7818 (DUF7818)
Type: Domain

This domain is found towards the C terminus of human NEDD4-binding protein 2 (N4BP2), which has 5'-polynucleotide kinase and nicking endonuclease activity and may play a role in DNA repair or recombination . This domain is often found associated with

,

and

.
Calcium homeostasis endoplasmic reticulum protein, DUF7819 (DUF7819)
Type: Domain

This domain is found towards the C-terminal end of human Calcium homeostasis endoplasmic reticulum protein (CHERP), which is involved in calcium homeostasis, growth and proliferation . This domain is usually found associated with

. Its specific function is unknown. It shows highly conserved GWE and GLYE/DxY/F motifs.
Domain of unknown function DUF7820 (DUF7820)
Type: Domain

This domain is found in uncharacterised proteins from fungi. It contains three pairs of conserved cysteine residues that are predicted to form disulfide bonds. It also contains a long region that is predicted to be disordered.
Domain of unknown function DUF7821 (DUF7821)
Type: Domain

This domain is found N-terminal in the uncharacterised protein PM0657 and its paralogue PM1082 from Pasteurella multocida and related bacterial proteins. It is predicted to adopt a α/β globular structure consisting of a central antiparallel β-sheet and helices packed on both sides.
Domain of unknown function DUF7822 (DUF7822)
Type: Domain

This domain is found N-terminal in uncharacterised bacterial proteins. It is predicted to adopt a globular structure consisting of a curved β-sheet and α-helices packed on one side of it.
Domain of unknown function DUF7823 (DUF7823)
Type: Domain

This domain is found in uncharacterised proteins from Gammaproteobacteria. This domain is found usually associated with

.
Repeat of unknown function DUF7824 (DUF7824)
Type: Domain

This is a presumed domain found in the middle region of bacterial sequences, which have a

at the N-terminal.
Repeat of unknown function DUF7825 (DUF7825)
Type: Domain

This is a presumed domain found at the C-terminal of a group of uncharacterised sequences from bacteria. It may adopt a TPR-like fold. It is found associated with

at the N-terminal and

in the middle.
Iron export permease protein FetB (FetB)
Type: Family

This entry includes the probable iron export permease protein FetB from Escherichia coli and similar proteins specific to gammaproteobacteria. FetB (Fe Transport B) is one subunit of the iron efflux ABC transporter FetAB. FetA is the ATP-binding subunit and FetB is the permease subunit. FetB is thought to be responsible for the translocation of the substrate across the membrane . Proteins in this family are encoded next to FetA.
Mannose-1-phosphate guanyltransferase, C-terminal domain (GMPPB_C)
Type: Domain

This entry represents the C-terminal domain of Mannose-1-phosphate guanyltransferase MPG1 from fungi and Mannose-1-phosphate guanylyltransferase catalytic subunits alpha and beta (GMPPA/B) from animals. This domain consists of a left-handed parallel β-helix composed of tandem repeats of a [LIV]-G-X(4) hexapeptide .

GMPPA is the regulatory subunit of the GMPPA-GMPPB mannose-1-phosphate guanylyltransferase complex which reduces the catalytic activity of GMPPB when part of the complex . It mediates allosteric feedback inhibition of GMPPB catalytic activity upon binding GDP-alpha-D-mannose . GMPPA, together with GMPPB, regulates GDP-alpha-D-mannose levels . GMPPB is the catalytic subunit of the GMPPA-GMPPB mannose-1-phosphate guanylyltransferase complex. It catalyses the formation of GDP-mannose, an essential precursor of glycan moieties of glycoproteins and glycolipids . In S. pombe, it is required for proper septum structure and is involved cell cycle progression through cell-size checkpoint . In budding yeasts, Mgp1 (also known as Psa1) plays an important part in maintenance of cell-wall integrity .
DUF2096, C-terminal KH-like domain (DUF2096_C)
Type: Domain

This domain, found in various hypothetical archaeal proteins, has no known function. Many members belong to

. The domain shows structural similarity to KH domains suggesting it may have an RNA-binding function.
DUF2096, N-terminal four-helical bundle domain (DUF2096_N)
Type: Domain

This domain, found in various hypothetical archaeal proteins, has no known function. Many members belong to

. This N-terminal domain is predicted to be composed of four α helices.
Attractin, GBD domain (GBD_ATRN)
Type: Domain

This entry represents a domain found towards the C terminus of attractin (ATRN) and attractin-like proteins. ATRN is involved in the initial immune cell clustering during inflammatory response and may regulate chemotactic activity of chemokines. It may play a role in melanocortin signalling pathways that regulate energy homeostasis and hair color . It was thought to have dipeptidase activity but it was shown later to lack that activity . This domain is predicted to adopt a β-sandwich fold similar to galactose-binding domains.
N-acetylneuraminate epimerase (NANM)
Type: Family

This entry includes N-acetylneuraminate epimerase (NANM) from Haemophilus influenzae, E. coli and its homologues. It converts alpha-N-acetylneuranimic acid (Neu5Ac) to the β-anomer, accelerating the equilibrium between the α- and β-anomers . The structure of NANM comprises a dimeric 6-bladed unclosed β-propeller

.
Sucrose synthase, N-terminal (SUS_N)
Type: Domain

This entry represents the N-terminal domain of sucrose synthases, which corresponds to the cellular targeting domain (CTD, also referred to as SSN1) and together with the EPBD domain (SSN2,

), they have regulatory functions in plant species, however, the function of these domains in cyanobacteria is not yet clear . Sucrose synthases are sucrose-cleaving enzymes that provide UDP-glucose and fructose for various metabolic pathways.
Sucrose synthase, EPBD domain (SUS_EPBD)
Type: Domain

This entry represents the EPBD domain (ENOD40 peptide binding domain, also referred to as SSN2) of sucrose synthases, which corresponds to the second domain and together with the N-terminal one (

), referred to as the cellular targeting domain (CTD) have regulatory functions in plant species, however, the function of these domains in bacteria is not yet clear . Sucrose synthases are sucrose-cleaving enzymes that provides UDP-glucose and fructose for various metabolic pathways. Members of this group are found in plants and cyanobacteria.
Attractin/MKLN-like, beta-propeller domain (Beta-prop_ATRN-MKLN-like)
Type: Domain

This entry represents the β-propeller domain (made up of Kelch repeats) found in attractin (ATRN), muskelin (MKLN), among others. ATRN is involved in the initial immune cell clustering during inflammatory response and may regulate chemotactic activity of chemokines. It may play a role in melanocortin signalling pathways that regulate energy homeostasis and hair color . It was thought to have dipeptidase activity but it was shown later to lack that activity . Muskelin is a component of the CTLH E3 ubiquitin-protein ligase complex that selectively accepts ubiquitin from UBE2H and mediates ubiquitination and subsequent proteasomal degradation of the transcription factor HBP1 . It also acts as a mediator of cell spreading and cytoskeletal responses to the extracellular matrix component THBS1 .

This domain can be found in a number of other proteins, such as KLH25, a substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex involved in various processes, such as translation homeostasis and lipid synthesis .
NfeD1b, N-terminal domain (NfeD1b_N)
Type: Domain

This domain is found N-terminal in the membrane protein NfeD1b from B. subtilis and related bacterial proteins.

The NfeD1b is composed of an N-terminal cytoplasmic ClpP serine protease-like domain, transmembrane domain, and a C-terminal OB (oligosaccharide/oligonucleotide-binding) fold domain. NfeD1b is a member of the NfeD (nodulation formation efficiency D) family which was divided into two groups: long and short forms. Long-form NfeD homologs contain a putative ClpP serine protease-like domain while short-form homologs have in common the C-terminal OB fold domain (

). Despite global similarity to ClpP serine proteases, this domain lacks the typical for these enzymes Ser, His, Asp catalytic triad and of these, has only Ser residue conserved in equivalent position.
NfeD, integral membrane domain (NfeD_membrane)
Type: Domain

This entry represents the central integral membrane domain found in the NfeD protein and related proteins.

The NfeD1b is composed of an N-terminal cytoplasmic ClpP serine protease-like domain, transmembrane domain, and a C-terminal OB (oligosaccharide/oligonucleotide-binding) fold domain. NfeD1b is a member of the NfeD (nodulation formation efficiency D) family which was divided into two groups: long and short forms. Long-form NfeD homologs contain a putative ClpP serine protease-like domain while short-form homologs have in common the C-terminal OB fold domain (

). Despite global similarity to ClpP serine proteases, this domain lacks the typical for these enzymes Ser, His, Asp catalytic triad and of these, has only Ser residue conserved in equivalent position.
Dihydroxy-acid/6-phosphogluconate dehydratase, C-terminal (ILV_EDD_C)
Type: Domain

This is the C-terminal domain of Ilv/ED dehydratase protein family which includes dihydroxy-acid/6-phosphogluconate dehydratases, and pentonate dehydratases . This domain is composed of a β-sheet consisting of six parallel and two anti-parallel β-strands that are arranged like a β-barrel .

Members of this entry are involved in various biosynthetic and carbohydrate metabolic pathways . Dihydroxy-acid dehydratase catalyses the fourth step in the biosynthesis of isoleucine and valine, the dehydration of 2,3-dihydroxy-isovaleic acid into alpha-ketoisovaleric acid. 6-Phosphogluconate dehydratase catalyses the first step in the Entner-Doudoroff pathway, the dehydration of 6-phospho-D-gluconate into 6-phospho-2-dehydro-3-deoxy-D-gluconate. They consist of two domains, N- and C-terminal, the latter contains residues (Ser490 and Thr492) that participate in the formation of the substrate binding site.
Bridge-like lipid transfer protein family member 1, middle region (BLTP1_M)
Type: Domain

This entry represents the middle region of a group of very long animal proteins, including human BLTP1.

Bridge-like lipid transfer protein family member 1 (BLTP1, formerly known as Tweek/KIAA1109/FSA in human) is a tube-forming lipid transport protein which provides phosphatidylethanolamine for glycosylphosphatidylinositol (GPI) anchor synthesis in the endoplasmic reticulum. It plays a role in endosomal trafficking and endosome recycling and it is also involved in the actin cytoskeleton and cilia structural dynamics . BLTP1 also acts as a regulator of phagocytosis . In humans, it has been associated with rheumatoid arthritis . Mutations of the BLTP1 gene has been associated with Alkuraya-Kucinskas syndrome (MIM 617822), a severe disorder of brain development and arthrogryposis .

Members of this entry belong to the repeating β-groove (RBG) superfamily together with VPS13, ATG2, SHIP164, BLTP2/FMP27, which are all conserved lipid transfer proteins containing long hydrophobic grooves . They all share the same structure comprising multiple repeating modules consisting of five β-sheets followed by a loop.
Bridge-like lipid transfer protein family member 1, C-terminal (BLTP1_C)
Type: Domain

This entry represents the C-terminal region of a group of very long eukaryotic proteins, including the human BLTP1 and similar animal sequences.

Bridge-like lipid transfer protein family member 1 (BLTP1, formerly known as Tweek/KIAA1109/FSA in human) is a tube-forming lipid transport protein which provides phosphatidylethanolamine for glycosylphosphatidylinositol (GPI) anchor synthesis in the endoplasmic reticulum. It plays a role in endosomal trafficking and endosome recycling and it is also involved in the actin cytoskeleton and cilia structural dynamics . BLTP1 also acts as a regulator of phagocytosis . In humans, it has been associated with rheumatoid arthritis . Mutations of the BLTP1 gene has been associated with Alkuraya-Kucinskas syndrome (MIM 617822), a severe disorder of brain development and arthrogryposis .

Members of this entry belong to the repeating β-groove (RBG) superfamily together with VPS13, ATG2, SHIP164, BLTP2/FMP27, which are all conserved lipid transfer proteins containing long hydrophobic grooves . They all share the same structure comprising multiple repeating modules consisting of five β-sheets followed by a loop.
TRM5/TYW2-like, methyltransferase domain (TRM5-TYW2-like_MTfase)
Type: Domain

This is the methyltransferase domain of TRM5/TYW2 proteins, SAM-dependent methyltransferases that are involved in tRNA methylation . Members are found in all cellular organisms.
TRM5/TYW2-like, N-terminal domain (TRM5/TYW2-like_N)
Type: Domain

This is the N-terminal domain of of TRM5/TYW2 proteins, SAM-dependent methyltransferases that are involved in tRNA methylation and related sequences found in archaea and eukaryotes . This domain consists of six β-strands and three α-helices.
TYW2, N-terminal domain (TYW2_N)
Type: Domain

This entry represents the N-terminal domain of tRNA wybutosine-synthesizing protein 2 homolog (TWY2) and similar sequences from vertebrates. TWY2 is a SAM-dependent transferase that acts as a component of the wybutosine biosynthesis pathway . This domain may consist of three β-sheets and two α-helices.
Surface presentation of antigen domain (SPAN_dom)
Type: Domain

Surface presentation of antigens protein (SPAN), also know as invasion protein invJ, is a Salmonella secretory pathway protein involved in presentation of determinants required for mammalian host cell invasion. This entry represents a C-terminal domain found in these proteins. This domain is predicted to be composed of a 4-stranded β sheet followed by an α helix.
VPS13-like, middle region (VPS13-like_M)
Type: Domain

This entry represents the middle region of the VPS13 proteins.

VPS13 proteins have been implicated in processes including vesicle fusion, autophagy, and actin regulation. They bind phospholipids and act as channels that mediate the transfer of lipids between membranes at organelle contact sites . It has been proposed that members of this entry have the capacity to bind and likely transfer tens of glycerolipids at once. Yeast VPS13 acts at multiple cellular sites, namely the interface between mitochondria and the vacuole, on endosomes, on the nuclear-vacuole junction and the vacuole, depending on the carbon source and metabolic state. VPS13A, VPS13C and VPS13D from mammals localise at contacts at contacts between the ER and other organelles, i.e. VPS13A and VPS13D bridge the ER to mitochondria, VPS13C bridges the ER to late endosomes and lysosomes and VPS13B may localise to endosome-endosome contacts . Mutations in human VPS13 proteins cause different diseases such as Chorea-acanthocytosis, Cohen syndrome, Parkinson's disease, and spastic ataxia .
Intermembrane lipid transfer protein VPS13-like, C-terminal (VPS13-like_C)
Type: Domain

This entry represents the C-terminal PH-like domain from VPS13 which weakly binds to phosphatidylinositol 4,5-bisphosphate and contributes to membrane recruitment . Truncation of this domain in VPS13A are causative for chorea-acanthocytosis, which suggests that it plays an important function .

VPS13 proteins have been implicated in processes including vesicle fusion, autophagy, and actin regulation. They bind phospholipids and act as channels that mediate the transfer of lipids between membranes at organelle contact sites . It has been proposed that members of this entry have the capacity to bind and likely transfer tens of glycerolipids at once. Yeast VPS13 acts at multiple cellular sites, namely the interface between mitochondria and the vacuole, on endosomes, on the nuclear-vacuole junction and the vacuole, depending on the carbon source and metabolic state. VPS13A, VPS13C and VPS13D from mammals localise at contacts at contacts between the ER and other organelles, i.e. VPS13A and VPS13D bridge the ER to mitochondria, VPS13C bridges the ER to late endosomes and lysosomes and VPS13B may localise to endosome-endosome contacts . Mutations in human VPS13 proteins cause different diseases such as Chorea-acanthocytosis, Cohen syndrome, Parkinson's disease, and spastic ataxia .
ATP-citrate synthase, ATP-grasp domain (Citrate_synth_N)
Type: Domain

This entry represents the N-terminal ATP-grasp domain of ATP-citrate synthases.

The ATP-citrate synthase family is responsible for the synthesis of cytosolic acetyl-CoA, a crucial substrate for de novo lipid synthesis, including cholesterol and fatty acids. In animals, these enzymes typically have a homomeric structure, whereas in plants, they are composed of distinct alpha and beta chains. These proteins play a central role in lipid metabolism, contributing to the elongation of fatty acids and the biosynthesis of various compounds such as isoprenoids and flavonoids. They are characterised by its membership in the succinate/malate CoA ligase subunit families, with distinct N-terminal and C-terminal sections.
ESF1, RRM domain (RRM_ESF1)
Type: Domain

This domain is found in the yeast Pre-rRNA-processing protein ESF1 and related eukaryotic proteins. ESF1 is involved in the 18S rRNA synthesis and required for the early cleavages at sites A0, A1 and A2 . This domain has a detectable similarity to known RNA binding domains.
ERT1/acuK family, PAS domain (PAS_13)
Type: Domain

This entry represents a C-terminal PAS domain found in ERT1/acuK proteins. The ERT1/acuK family consists of transcription factors that play a crucial role in regulating nonfermentable carbon utilization. These proteins act as activators of gluconeogenetic genes, facilitating the conversion of non-carbohydrate substrates into glucose . Members of this family are involved in various metabolic pathways, including gluconeogenesis and the tricarboxylic acid (TCA) cycle . Some proteins in this family also participate in processes such as drug resistance and cell wall remodeling. The family includes proteins that bind specific DNA sequences in promoter regions, thereby influencing gene expression. Additionally, certain members are involved in iron acquisition and metabolism, contributing to the organism's virulence and adaptation to glucose starvation conditions.
Elongation factor-like GTPase 1 domain (EFL1)
Type: Domain

This domain is found in human Elongation factor-like GTPase 1 (EFL1) and similar eukaryotic proteins, including yeast homologue known as Ribosome assembly protein 1. EFL1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes. Together with SBDS, triggers the GTP-dependent release of EIF6 from 60S pre-ribosomes in the cytoplasm, thereby activating ribosomes for translation competence by allowing 80S ribosome assembly and facilitating EIF6 recycling to the nucleus, where it is required for 60S rRNA processing and nuclear export .
DrmE-like, N-terminal domain (DrmE_N)
Type: Domain

This domain is found in DISARM (Defense Island System Associated with Restriction-Modification) protein DrmE and related proteins from Halobacteria . It is predicted to adopt a globular structure composed of a central parallel β-sheet and α-helices packed on both sides of it.
DSCAM/DSCAML, C-terminal domain (DSCAM/DSCAML_C)
Type: Domain

This entry represents a Fn3-like domain found at the C-terminal of DSCAM and DSCAML. DSCAM and DSCAML are cell adhesion molecules that play a role in neuronal self-avoidance. They promote repulsion between specific neuronal processes of either the same cell or the same subtype of cells .
dsRNA binding domain (DSRM_2)
Type: Domain

This entry represents a a set of divergent dsRNA binding domains. They are found in functionally diverse proteins such as Dicer-like protein 1/2, ATP-dependent RNA helicase DHX30 and Small RNA 2'-O-methyltransferase HEN1 .
DUF2110, central domain (DUF2110_central)
Type: Domain

This domain, found in various hypothetical archaeal proteins, has no known function. This domain is the middle of three domains found in the DUF2110 family proteins. It has an OB-like fold.
DUF2110, C-terminal domain (DUF2110_C)
Type: Domain

This domain, found in various hypothetical archaeal proteins, has no known function. It is found at the C-terminal of DUF2110 family proteins.
DUF2110, N-terminal domain (DUF2110_N)
Type: Domain

This domain, found in various hypothetical archaeal proteins, has no known function. It is found at the N-terminal of the DUF2110 family proteins.
Dynein axonemal heavy chain 2/5/8, coiled-coil domain (DYH2-5-8_CC)
Type: Domain

This entry represents a coiled-coil region found in Dynein axonemal heavy chains 2/5/8 and related proteins, including Dynein gamma and Dynein-1-beta heavy chain. These proteins are involved in sperm and flagella motility. DYH2 is part of the axonemal inner dynein arm complex and plays a central role in ciliary beat .
E3 ubiquitin-protein ligase XB3-like, RING finger (RING_XB3-like)
Type: Domain

This entry represents the RING finger domain found at the C-terminal end of E3 ubiquitin-protein ligase XB3 from rice and its plant homologues, including XBAT31/32/33 from Arabidopsis thaliana. XB3 is an E3 ubiquitin-protein ligase required for full accumulation of the LRR receptor kinase XA21 and XA21-mediated disease resistance. Binding to XA21 may stabilise the receptor kinase and maintain its protein level . XBAT31 regulates thermoresponsive hypocotyl growth through mediating degradation of the thermosensor ELF3 .
E3 UFM1-protein ligase-like, C-terminal domain (Ufl1-like_C)
Type: Domain

This domain is found C-terminal in human E3 UFM1-protein ligase 1 (Ufl1) and similar eukaryotic sequences. This domain is predicted to adopt a globular structure consisting of an array of α-helices.

The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme (Ufl1) . Ufl1 mediates the covalent attachment of the ubiquitin-like modifier Ufm1 to lysine residues on target proteins and plays a key role in reticulophagy (also called ER-phagy) induced in response to endoplasmic reticulum stress .