SII-SWORD/CoKE huggingface dataset:
DNA helicase Pif1-like, 2B domain (Pif1-like_2B_dom)
Type: Domain

Pif1 is a DNA helicase conserved from bacteria to humans. It suppresses both G-quadruplex-associated DNA damage and telomere lengthening. In budding yeast, it exists in two forms, nuclear and mitochondrial. Its nuclear form inhibits telomerase, while its mitochondrial is involved in repair and recombination of mitochondrial DNA. These proteins belong to the helicase superfamily 1 (SF1) and contain RecA-like domains (1A and 2A) which, together with two additional domains, 1B and 2B, form the helicase core . This entry represents domain 2B, which adopts a SH3-like fold.
Glycosyl hydrolase family 78 alpha-rhamnosidase, N-terminal domain (Glyco_hydro_78_N)
Type: Domain

This entry represents the N-terminal domain found in a group of fungal and bacterial alpha-rhamnosidase sequences that belong to the Glycosyl hydrolase family 78 . This domain is involved in dimerisation of the enzyme .
Glycosyl hydrolases family 39, active site (GH39_as)
Type: Active_site

This entry represents the active site of glycosyl hydrolases from the family 39, including mammalian lysosomal alpha-L-iduronidase (

) and beta-xylosidase (

) (gene xynB) from Thermoanaerobacter saccharolyticum. This region is located in the N-terminal section and contains a glutamic acid residue which probably acts as the proton donor in the catalytic mechanism .
Glycosyl hydrolases family 39, N-terminal catalytic domain (GH39_cat)
Type: Domain

This entry represents the N-terminal catalytic domain of Glycoside hydrolase family 39 proteins.

Glycoside hydrolase family 39 (

) comprises enzymes with several known activities such as alpha-L-iduronidase (

), beta-xylosidase (

), and alpha-1,4-L-rhamnosidase .

The most highly conserved regions in these enzymes are located in their N-terminal parts. These contain a glutamic acid residue which, on the basis of similarities with other families of glycosyl hydrolases , probably acts as the proton donor in their catalytic mechanism.
Alpha-L-iduronidase, C-terminal domain (GH39_C)
Type: Domain

This entry represents the C-terminal Ig-like domain of animal Alpha-L-iduronidase enzymes .
Glycosyl hydrolase family 134 (Glyco_hydro_134)
Type: Family

This entry represents glycoside hydrolase family 134 which contains beta-1,4-mannanase enzymes. This enzyme has a lysozyme-like fold.
Glycoside hydrolase 120, insertion domain (Glyco_hydro_120_ins)
Type: Domain

This insertion domain is found in a group of bacterial glycoside hydrolases from the CAZy family 120, including Parallel beta-helix repeat protein from Thermoanaerobacterium saccharolyticum (also known as xylosidase) (

). It is often found associated to

.
Transcription regulator GlnR, N-terminal domain (GlnR_N)
Type: Domain

This domain is found at the N-terminal end of Transcription regulator GlnR from Amycolatopsis mediterranei (

) and similar sequences predominantly found in actinobacteria. GlnR plays a key role in the global regulation of nitrogen metabolism. It belongs to the OmpR/PhoB subfamily. This domain shows five alternating β-strands and α-helices that form a five-stranded parallel β-sheet in the middle surrounded by two α-helices on one side and three on the other, showing great structure similarity with most of the known structures of the typical RR receiver domains . This domain is usually found associated with

.
Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, C-terminal (GLGE_C)
Type: Domain

This entry represents the C-terminal domain of alpha-1,4-glucan:maltose-1-phosphate maltosyltransferases (GLGE) which has an all-β fold . This domain, referred to domain C, together with the catalytic one, is involved in the binding of alpha-glucan chains .
Domain of unknown function DUF6857, plants (DUF6857_pln)
Type: Domain

This is a domain of unknown function found at the C-terminal of uncharacterised plant proteins. These sequences have a OB fold-like domain at the N-terminal (

). This domain may consist of 5-6 α-helices.
Endonuclease NucS, N-terminal domain superfamily (NucS_N_sf)
Type: Homologous_superfamily

This superfamily represents the N-terminal domain of endonuclease NucS, which adopts a β-barrel structure. This domain is involved in dimerisation achieved via domain swapping. The dimer formation it likely critical for the folding and stabilisation of the NucS structure.

NucS cleaves both 3' and 5' ssDNA extremities of branched DNA structures and it binds to ssDNA .
Non-reducing end beta-L-arabinofuranosidase-like (Beta-AFase-like)
Type: Family

This entry represents the homologues of enzymes belonging to the glycosyl hydrolase 127 family, including non-reducing end beta-L-arabinofuranosidase from Bifidobacterium longum (

, also known as Beta-AFase) .

Beta-AFase, an unusual beta-L-arabinofuranosidase enzyme (

), releases l-arabinose from the l-arabinofuranose (Araf)-beta1,2-Araf disaccharide and also transglycosylates 1-alkanols with retention of the anomeric configuration. Terminal beta-l-arabinofuranosyl residues have been found in arabinogalactan proteins from a number of different plant species. Beta-l-Arabinofuranosyl linkages with 1-4 arabinofuranosides are also found in the sugar chains of extensin and solanaceous lectins, hydroxyproline (Hyp)2-rich glycoproteins that are widely observed in plant cell wall fractions. The critical residue for catalytic activity is Glu-338, in a ET/SCAS sequence context .
FAM171, C-terminal (FAM171_C)
Type: Domain

This is the C-terminal domain of a family of proteins that includes FAM171A1, FAM171A2 and FAM171B. FAM171A1 is a type 1 transmembrane glycoprotein also known as astroprincin (APCN) due to abundant expression in astrocytes. APCN is also expressed in placental trophoblasts, skeletal and heart muscle, kidney and pancreas . APCN is involved in the regulation of the cytoskeletal dynamics, playing a role in actin stress fibre formation.
Conserved oligomeric Golgi complex subunit 5, N-terminal (COG5_N)
Type: Domain

This entry represents the domain found at the N-terminal of Conserved oligomeric Golgi complex subunit 5 (COG5) and includes the LLR motif which is important to interact with COG7 .

The COG complex, the peripheral membrane oligomeric protein complex involved in intra-Golgi protein trafficking, consists of eight subunits arranged in two lobes bridged by Cog1. Cog5 is in the smaller B lobe, bound in with Cog6-8, and is itself bound to Cog1 as well as, strongly, to Cog7 . Disruption of COG5-COG7 interface does not impair lobe B but causes aberrant cell surface glycosylation with major deficits in the trafficking of Golgi glycosyltransferases .
MgtC/SapB/SrpB/YhiD, N-terminal domain (MgtC_SapB_SrpB_YhiD_N)
Type: Domain

This entry represents the N-terminal domain found in a group of similar bacterial proteins, including Protein MgtC from Salmonella typhimurium and Protein SapB from Bacillus subtilis. MgtC is a virulence factor required for growth in low Mg2+ medium and for intramacrophage survival. It may be involved in regulating membrane potential by activating Na+/K+-ATPase .
Picobirnavirus capsid protein superfamily (CP_picobirnavirus_sf)
Type: Homologous_superfamily

This entry represents a group of proteins from picobirnavirus, including Capsid protein precursor from Human picobirnavirus.

Picobirnaviruses have a unique layer with icosahedral architecture consisting of 60 quasi-symmetric dimers of a its Capsid protein (CP). This protein is organised into two domains, a shell (S) domain that contains all of the α-helices and two β-sheets, and a projecting (P) domain that includes the remaining β-sheets. The dimer is stabilised by domain swapping .
T2SS protein K, second SAM-like domain (T2SSK_SAM-like_2nd)
Type: Domain

This entry represents a SAM-like domain found in proteins involved in the Type II protein secretion system (T2SS), including Type II secretion system protein K from Escherichia coli. The T2SK family includes proteins such as ExeK, PulK, OutX and XcpX. They consist of three domains, two of which are arranged in tandem and share structural similarity to SAM-like domains (

) . This entry represents the second SAM-like domain.
Phosphoribosyl-dephospho-CoA transferase MdcG, C-terminal (MdcG_C)
Type: Domain

This entry represents the C-terminal catalytic domain of MdcG, which is a phosphoribosyl-dephospho-CoA transferase that is involved in the biosynthesis of the prosthetic group of malonate decarboxylase . Malonate decarboxylase from Klebsiella pneumoniae contains an acyl carrier protein (MdcC) to which a 2'-(5-triphosphoribosyl)-3'-dephospho-CoA prosthetic group is attached via phosphodiester linkage. MdcG catalyses the following reaction:

2'-(5-triphosphoribosyl)-3'-dephospho-CoA apo-[acyl-carrier-protein] = holo-[acyl-carrier-protein] diphosphate.
Transcriptional regulator SutA, RNAP-binding domain (SutA_RBD)
Type: Domain

This domain (previously known as DUF6813) is found in the transcriptional regulator SutA from Pseudomonas aeruginosa (

) and similar proteins mainly from gammaproteobacteria. In Pseudomonas aeruginosa, SutA adapts bacteria to hypoxia and nutrition-limited environment during chronic infection by increasing transcription activity of an RNA polymerase (RNAP) holoenzyme comprising the stress-responsive sigma factor sigma-S (RNAP-sigma-S). SutA interacts with both RNAP-sigma-A and RNAP-sigma-S holoenzymes and the RNAP-β protrusion is its primary anchor site. This domain, known as RNAP-binding domain of SutA (SutA-RBD), comprises an α-helix and a β-strand and is responsible for interaction with RNAP-β protrusion . It contains a conserved FLxxGG sequence motif that appears to be located near the C-terminal helix cap. The SutA-RBD α-helix binds to hydrophobic groove on RNAP-β protrusion .
Domain of unknown function DUF4246, C-terminal (DUF4246_C)
Type: Domain

This domain is functionally uncharacterised, found mainly in fungi and bacteria. Proteins in this family are typically between 392 and 644 amino acids in length. According to structure predictions, this domain may have a cupin-like fold.
Domain of unknown function DUF6855 (DUF6855)
Type: Domain

This entry represents a domain protein found in a range of group of prokaryotic sequences. It is functionally uncharacterised and covers the whole length of the protein in most members.
Protein of unknown function DUF6856 (DUF6856)
Type: Family

This entry includes a set of mycoplasma lipoproteins related to uncharacterised Mycoplasma genitalium lipoprotein MG348.
NAD(+)--protein-arginine ADP-ribosyltransferase Tre1-like, N-terminal domain (Tre1-like_N)
Type: Domain

This entry represents the N-terminal domain of NAD(+)--protein-arginine ADP-ribosyltransferase Tre1 from Pseudomonas putida, the toxic component of a contact-dependent interbacterial competition system (also called effector-immunity systems). This protein acts by ADP-ribosylating a number of target proteins in target cells .

This domain is also found associated with

or toxin domains such as

in other proteobacterial proteins and centrally located in the uncharacterised protein slr0273 from Synechocystis sp and similar bacterial sequences.

It is a likely integral membrane domain that contains a glycine-zipper motif.
Domain of unknown function DUF6863 (DUF6863)
Type: Domain

This entry represents an α-helical bundle domain found at the N-terminal of a small group of putative toxins from Legionellales. The function of this domain is unknown.
Protein of unknown function DUF6864 (DUF6864)
Type: Family

This entry represents a family of bacterial proteins that adopt a β-sandwich domain. The function of these proteins is currently unknown.
Protein of unknown function DUF6865 (DUF6865)
Type: Family

This entry represents a small family of uncharacterised proteins from plants. AlphaFold predictions suggest that the protein contains two non-contacting α-helices.
DUF6866, N-terminal domain (DUF6866_N)
Type: Domain

This entry represents the N-terminal α+β domain found in DUF6866 family. The function of these proteins is unknown. Proteins in this family are primarily found in Proteobacteria.
DUF6866, C-terminal domain (DUF6866_C)
Type: Domain

This entry represents the C-terminal α-helical domain found in the DUF6866 family. The function of these proteins remains unknown. Proteins belonging to this family are primarily identified in Proteobacteria.
Domain of unknown function DUF6867 (DUF6867)
Type: Domain

This entry represents a likely integral membrane protein. These proteins are predicted to be composed of three α-helices followed by a short β-hairpin. This family is called DUF6867. Proteins in this family are found in proteobacteria.
Domain of unknown function DUF6817 (DUF6817)
Type: Domain

This presumed domain is functionally uncharacterised, mainly found in bacteria and plants. It has two conserved sequence motifs, HL and GLxHxxY.
Domain of unknown function DUF6818 (DUF6818)
Type: Domain

This presumed domain is functionally uncharacterised. It is found in proteins from fungi, and is typically between 39 and 76 amino acids in length. There are several conserved motifs, Y/FxN, KF and KPTG and a highly conserved W residue at the N-terminal. Structural predictions indicate this domain may fold into three α-helices.
Protein of unknown function DUF6858 (DUF6858)
Type: Family

This family of proteins are distantly related to

. Their function is as yet unknown.
Vacuolar sorting protein Vps3844, N-terminal domain (Vps3844_N)
Type: Domain

This domain is found at the N-terminal of the uncharacterised endoplasmic reticulum membrane protein C1709.03 from S. pombe, which was renamed to vacuolar sorting protein Vps3844, which is important for protein trafficking to the vacuole . From AlphaFold structure prediction, it can be inferred that this domain may adopt an α/β structure consisting of six antiparallel β-strands surrounded by three or four α-helices.
Domain of unknown function DUF6860 (DUF6860)
Type: Domain

This entry represents the N-terminal domain of uncharacterised bacterial proteins such as YhiL from E.coli (SwissProt:

). According to AlphaFold predictions, this domain may have an α/β structure consisting of five β-sheets and three short α-helices.
Domain of unknown function DUF4246, N-terminal (DUF4246_N)
Type: Domain

This presumed domain, found N-terminal of

, may consist of four helices. Proteins in this group are found mainly in fungi and bacteria.
Domain of unknown function DUF6819 (DUF6819)
Type: Domain

This entry represents a domain of unknown function mainly found in bacteria. It is usually located at the C-terminal of InterPro:

and it may have an α-helical fold.
Protein of unknown function DUF6812 (DUF6812)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family are found in bacteria. There is a conserved RxxD sequence motif.
Protein of unknown function DUF6814 (DUF6814)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family are predominantly found in Bacteroidetes and are approximately 80 amino acids in length. There are several conserved motifs: IxxGL, FGxY and GEY.
Domain of unknown function DUF6815 (DUF6815)
Type: Domain

This presumed domain is functionally uncharacterised and is found in bacteria and eukaryotes. It may contain an ATP-grasp-like fold which suggest an ATP-binding function. There are several conserved motifs: EGxxR, PxxWxxDF and ExNCSCV.
Domain of unknown function DUF6816 (DUF6816)
Type: Domain

This presumed domain is functionally uncharacterised and it is found in bacterial (predominantly cyanobacterial) and eukaryotic (mainly plant) sequences. AlphaFold structure prediction suggests that this domain may have a START-like (StAR-related lipid-transfer) fold consisting of an α/β structure of a helix-grip fold, that forms cavities for hydrophobic substrates or ligands which may indicate a possible function for this domain.
Domain of unknown function DUF6808 (DUF6808)
Type: Domain

This entry represents a domain of unknown function that is mainly found in bacteria. This domain is typically around 110 amino acids in length. There are two conserved motifs, RW and VSG.
Protein of unknown function DUF6809 (DUF6809)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family are found in bacteria, are typically around 85 amino acids in length and have a conserved motif FxxGF.
Domain of unknown function DUF6810 (DUF6810)
Type: Domain

This entry represents a conserved domain of unknown function mainly found in bacteria from the phylum Chloroflexota. This domain contains the motifs ExRFY and WxEG.
DUF5575, N-terminal domain (DUF5575_N)
Type: Domain

This entry represents the N-terminal domain from a family of chordate proteins that includes human C19orf68 (also.known as ZSWIM9) (SwissProt:

). This domain appears to be related to the WRKY-like DNA-binding domains (InterPro:

). These proteins are functionally uncharacterised.
DUF5575, C-terminal domain (DUF5575_C)
Type: Domain

This entry represents the C-terminal domain from a family of chordate proteins that includes human C19orf68 (also.known as ZSWIM9) (SwissProt:

). These proteins are functionally uncharacterised.
Domain of unknown function DUF6841, NTF2-like (DUF6841)
Type: Domain

This entry represents a domain found in NTF2-like proteins (

) whose function is unknown. It is mainly found in bacteria.
Domain of unknown function DUF6868 (DUF6868)
Type: Domain

This entry represents a small bacterial integral membrane domain of unknown function that is composed of two transmembrane helices. The function of this domain is unknown.
Domain of unknown function DUF6869 (DUF6869)
Type: Domain

This entry represents a domain found in bacterial proteins. It contains an α-helical solenoid structure. The function of these proteins is unknown.
Domain of unknown function DUF6870 (DUF6870)
Type: Domain

This entry represents a small domain of unknown function. Proteins in this family are primarily found in Bacillota bacterias
Domain of unknown function DUF6820 (DUF6820)
Type: Domain

This domain is functionally uncharacterised. It is found in eukaryotes (predominantly in the marine diatom Thalassiosira) and is approximately 50 amino acids in length. There are several conserved motifs: TSAGR/QARxM, FAV and DNxGRRAM/IG.
Domain of unknown function DUF6821 (DUF6821)
Type: Domain

This presumed domain is functionally uncharacterised. This domain is found mainly in plants, such as in At4g13530 (

) from Arabidopsis and is approximately 300 amino acids in length. It contains a predicted transmembrane helix.
Family of unknown function DUF6822 (DUF6822)
Type: Family

This entry represents a family of functionally uncharacterised proteins. This family of proteins is found in eukaryotes (predominantly in the Dinoflagellate Symbiodinium microadriaticum). There are several highly conserved W residues.
Family of unknown function DUF6823 (DUF6823)
Type: Family

This entry represents a family of functionally uncharacterised proteins. This protein family is found in green algae. There are highly conserved motifs: QQE and RFDLR.
Domain of unknown function DUF6824 (DUF6824)
Type: Domain

This domain is functionally uncharacterised, found mainly in diatoms (phylum Bacillariophyta). There are highly conserved motifs: DxxxGR/KG, HxGN and GRFL; and three highly conserved residues: W, K and R at the C-terminal.
Domain of unknown function DUF6826 (DUF6826)
Type: Domain

This presumed domain is functionally uncharacterised and is found in fungal sequences, N-terminal to a kinase domain (InterPro:

). There are two conserved motifs: PD and QPxR.
Domain of unknown function DUF6827 (DUF6827)
Type: Domain

This domain lacks functional characterisation and is predominantly present in Apicomplexa. There are highly conserved motifs: NWxD, EDxxDH and GxGLAI/LLRQ.
DUF5581, N-terminal domain (DUF5581_N)
Type: Domain

This entry represents the N-terminal helical domain found in the human Fibronectin type III domain-containing protein 11 (FNDC11) (also known as C20orf195) (Swissprot:

) and its homologues in chordates. FNDC11 is functionally uncharacterised.
Family of unknown function DUF6829 (DUF6829)
Type: Family

This family is functionally uncharacterised, mainly found in fungi, and consists of approximately 420 amino acids in length. Structurally, this family is composed of α-helices.
Domain of unknown function DUF6830 (DUF6830)
Type: Domain

This domain is functionally uncharacterised, predominantly found in Basidiomycetes. There are several highly conserved residues: P, W, Q and G. Some proteins containing the DUF6830 domain have been classified as members of the Plavaka family (InterPro:

)
Domain of unknown function DUF6832 (DUF6832)
Type: Domain

This domain is functionally uncharacterised, predominantly found in eukaryotic sequences mostly from Alveolates (phylum Apicomplexa). There are several highly conserved motifs: FGFNSFWS, FKxxxYD, PRxxY and YRC. Predictions of its structure suggest it folds into seven α-helices.
Domain of unknown function DUF6850 (DUF6850)
Type: Domain

This entry corresponds to a functionally unknown domain found in bacteria, and it is probable that it folds as an outer-membrane β-barrel.(OMBBs). OMBBs are found in the outer membrane of gram-negative bacteria and eukaryotic organelles. OMBBs fold as antiparallel β-sheets that close onto themselves, forming pores that traverse the membrane.
DUF2264, C-terminal domain (DUF2264_C)
Type: Domain

This entry represents a domain found at the C-terminal of DUF2264 family. This domain adopts a β-sandwich domain that is structurally related to InterPro:

, suggesting that DUF2264 proteins are oligosaccharide degrading enzymes.
Domain of unknown function DUF6873 (DUF6873)
Type: Domain

This entry represents a domain with a five fold symmetric α/β propeller fold found in family of uncharacterised proteins belonging to the GME (guanidino-group modifying enzymes) superfamily . Members of this group are mainly found in Bacillota.
Domain of unknown function DUF6874 (DUF6874)
Type: Domain

This entry represents a functionally uncharacterised domain found in bacterial and viral sequences, that is predicted to fold into a small α-helical bundle.
Domain of unknown function DUF6875 (DUF6875)
Type: Domain

This entry represents a domain present in uncharacterised proteins mostly found in bacteria. They share an N-terminal CPF/Y motif that is characteristic of the NCPF superfamily of proteins.
Domain of unknown function DUF6876 (DUF6876)
Type: Domain

This entry represents a domain present in uncharacterised proteins primarily found in bacteria. This domain exhibits structural similarity to

.
Domain of unknown function DUF6877 (DUF6877)
Type: Domain

This entry represents a small domain present in short, uncharacterised proteins identified in bacteria and Clostridium phages. These proteins are predicted to adopt a three-helical structure.
Domain of unknown function DUF6878 (DUF6878)
Type: Domain

This entry represents a functionally uncharacterised bacterial domain (mainly present in phylum Pseudomonadota) that adopts a β-grasp fold.
Domain of unknown function DUF6879 (DUF6879)
Type: Domain

This entry represents a functionally uncharacterised domain found in bacteria, mainly within Actinomycetes. This domain is predicted to adopt a compact structure resembling the Phospholipase D domain (InterPro:

).
Family of unknown function DUF6880 (DUF6880)
Type: Family

This entry represents a family of proteins that form an α-helical solenoid structure of HEAT-like repeats. Proteins in this family are found in various bacterial species, but most commonly in proteobacteria.
DUF5580, middle domain (DUF5580_M)
Type: Domain

This is the middle calmodulin-like domain found in metazoan proteins of unknown function.
DUF5580, C-terminal domain (DUF5580_C)
Type: Domain

This entry represents a domain found in the C-terminal region of a family of unknown function found in metazoa.