SII-SWORD/CoKE huggingface dataset:
Peroxisomal membrane protein PEX14, central, plants (PEX14-like_M_plants)
Type: Domain

This domain is centrally located in Peroxisomal membrane protein PEX14 from Arabidopsis thaliana and similar plant sequences. PEX14 is a component of the PEX13-PEX14 docking complex, a translocon channel that specifically mediates the import of peroxisomal cargo proteins bound to PEX5 receptor. It is often found C-terminal to

and is predicted to adopt an all-α helical configuration.
Cap-snatching endonuclease, N-terminal (CapSnatchArena_N)
Type: Domain

The cap-snatching endonuclease family is a group of enzymes found in segmented negative strand RNA viruses of the arena-, bunya-, and orthomyxovirus families. The viruses use cap-snatching to transcribe viral mRNA, which involves cleaving the host mRNA near its 5' end and is accomplished by an endonuclease (EN) domain located in the N-terminal region of the viral polymerase. The cap-snatching ENs belong to the PD-D/ExK superfamily of cation-dependent nucleases and have an active site configuration that includes two divalent metal ions and a histidine residue. The available structures of the influenza orthomyxovirus and LACV orthobunyavirus show the canonical conformation of the active site, while the arenavirus ENs show differences in their active sites, such as the replacement of the metal-coordinating histidine with an acidic residue in arenavirus ENs. The Hantaan virus cap-snatching EN has been structurally characterised, revealing high endonuclease activity, while the Lassa virus endonuclease has low intrinsic activity due to its non-canonical coordination of the catalytic metal ions.
Transcriptional regulator LmrA/YxaF-like, C-terminal domain (YxaF_TetR_C)
Type: Domain

This entry represents the C-terminal domain found in a group of TetR transcription regulators, including YxaF (also known as T1414) and LmrA from Bacillus subtilis, which are paralogous to each other . LmrA and YxaF are repressors that bind specifically to almost the same cis sequences, LmrA/YxaF boxes, located in the promoter regions of the lmrAB operon, the yxaF gene, and the yxaGH operon .
AGAO-like, N2 domain (AGAO-like_N2)
Type: Domain

This entry represents the first N-terminal domain (N2) of a group of copper amine oxidases, including PAOX from Arthrobacter globiformis (

, also known as AGAO) .
B12-dependent ribonucleotide reductase, insertion domain (RNR-II_ins_dom)
Type: Domain

This entry represents the insertion domain of adenosylcobalamin-dependent ribonucleoside-triphosphate reductases (class II RNRs) from Lactococcus leichmannii and related sequences. RNR's are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA, a rate-limiting step of DNA biosynthesis. RNRs are classified in class I, II and III . Class II RNRs are less complex and function as a monomer in contrast to class I and III RNRs, which controls substrate specificity as efficiently as a multimeric enzymes. This insertion domain provides the interface responsible for effector binding that, in oligomeric RNRs, is formed in the dimer interface .
PTEN upstream open reading frame MP31 (MP31)
Type: Family

This protein family represents human PTEN upstream open reading frame MP31, a micropeptide that inhibits lactate dehydrogenase (LDH)-mediated conversion of lactate to pyruvate in mitochondria by competing with mitochondrial LDH for binding to NAD+, and also inhibits cellular lactate utilisation .
MrkD-like, receptor binding domain (MrkD_recept-bd)
Type: Domain

This entry represents the receptor binding domain of MrkD from Klebsiella pneumoniae and similar sequences . MkrD is an adhesin protein that specifically interacts with type IV and/or V collagen .
Small regulatory polypeptide of amino acid response (SPAR)
Type: Family

This family represents human small regulatory polypeptide of amino acid response (SPAR) and similar sequences from vertebrates. SPAR interacts with the lysosomal v-ATPase to negatively regulate the activation of the signalling complex mTORC1 upon stimulation with amino acids. It also acts as a regulator of muscle regeneration following injury .
DUF6293, C-terminal winged helix domain (DUF6293_C)
Type: Domain

This domain is found C-terminal in functionally uncharacterised archaeal proteins. This domain is predicted to adopt a winged helix domain structure. It is usually associated to

.
LPP20 lipofamily protein, C-terminal domain (HP1454-like_C)
Type: Domain

This domain is found at the C-terminal end of LPP20 lipofamily protein

from Helicobacter pylori (HP1454) and similar sequences predominantly found in epsilonproteobacteria. HP1454 is a secreted protein composed of three distinct domains: the N-terminal (

), the middle domain (

) and this domain, which shows a β-sheet flanked by two α-helices .
Restriction endonuclease BpuSI, specificity domain (BpuSI_TRD)
Type: Domain

This domain is found at the C-terminal of the restriction endonuclease BpuSI from Bacillus pumilus (

) and similar bacterial sequences. BpuSI is a Type IIG restriction endonuclease that consists of three functional domains: an N-terminal domain

, a N-6 DNA methylase domain

and a C-terminal specificity domain (TRD, this entry), which includes a final domain with a mixed α/β structure and unknown function .
LPP20 lipofamily protein, middle domain (HP1454-like_M)
Type: Domain

This domain is found in LPP20 lipofamily protein

from Helicobacter pylori (HP1454) and similar sequences mainly found in epsilonproteobacteria. HP1454 is a secreted protein composed of three distinct domains: the N-terminal (

), this domain and the C-terminal (

). This domain forms an anti-parallel three-helix bundle .
Tyrosine-protein kinase receptor torso, third FN3 domain (Tor_FN3_3nd)
Type: Domain

This domain is found in the Tyrosine-protein kinase receptor torso from Bombyx mori (Tor), which is involved in the initiation of metamorphosis during postembryonic development. This protein is organised into three consecutive fibronectin type III (FN3) domains and a C-terminal Kinase domain. This entry represents the third FN3 domain .
Tyrosine-protein kinase receptor torso, first FN3 domain (Tor_FN3_1st)
Type: Domain

This domain is found in the Tyrosine-protein kinase receptor torso from Bombyx mori (Tor), which is involved in the initiation of metamorphosis during postembryonic development. This protein is organised into three consecutive fibronectin type III (FN3) domains and a C-terminal kinase domain. This entry represents the first FN3 domain. This domain has an N-terminal α-helical extension .
PG_1098 ferredoxin-like domain (PG_1098_Fer)
Type: Domain

This entry represents a ferredoxin-like domain found in a group of poorly characterised sequences, including the putative methyltransferase PG_1098 from Porphyromonas gingivalis (

,

). Members of this entry contain a THUMP-like domain at the C-terminal (

), following this domain.
1,4-alpha-glucan branching enzyme GlgB, N-terminal domain (GlgB_N)
Type: Domain

This is the N-terminal β-sandwich domain of 1,4-alpha-glucan branching enzyme GlgB and related proteins. This domain has a differential preference in substrate recognition and binding during amylase activity, when amylose is used as a substrate .
RlmL, ferredoxin-like domain (RlmL_1st)
Type: Domain

This entry represents the ferredoxin-like domain found at the N-terminal of RmlL, referred to as NFLD domain usually fused to the THUMP domain . Ribosomal RNA large subunit methyltransferase K/L from E.coli (also known as YcbY) specifically methylates the guanine in positions 2445 and 2069 of 23S rRNA before its assembly into 50S subunits .
RbmA-like, FnIII domain (RbmA-like_FnIII)
Type: Domain

This entry represents both fibronectin type III (FnIII) domains found in Vibrio cholerae scaffolding protein RbmA (

), a biofilm matrix protein essential for both maintenance of rugose colony morphology and development of wild-type biofilm architecture . RbmA contains two FnIII domains connected by a linker segment. The two folds run antiparallel to each other but do not form extensive interactions. Each FnIII domain shows a β-sandwich comprised of three β-sheets plus four β-sheets .
Major capsid protein VP16-like (VP16-like)
Type: Family

This family includes the major capsid protein VP16 from Thermus virus P23-77, which shows two turrets, producing a crenellated appearance .
ThiI, ferredoxin-like domain (ThiI_fer)
Type: Domain

This entry represents the ferredoxin-like domain found at the N-terminal of ThiI proteins (NFLD) . ThiI is responsible for the formation of the modified base S(4)U (4-thiouridine) found at position 8 in some prokaryotic tRNA. This domain connects the C-terminal catalytic PP-loop pyrophosphatase domain with the THUMP (

). NFLD and the THUMP domains jointly form the tRNA-binding surface shaped like a channe which may be of particular importance in ThiI for the correct orientation and distance between residues involved in RNA binding and the active site of the enzyme .
Alpha-amylase-like, C-terminal domain (Alpha-amylase-like_C)
Type: Domain

This is the C-terminal domain of Anoxybacillus alpha-amylase (

) and related enzymes. This domain follows the catalytic β/α domain. It folds into a β-sandwich with a greek key topology (

) .
NS3 RNA helicase, C-terminal helical domain (NS3_helicase_C)
Type: Domain

This entry represents the C-terminal all-α helical domain (referred to as domain 3) of hepatitis C virus RNA helicase (NS3) .

NS3 helicase consists of three domains, separated by a series of clefts. Bound ssDNA lies in a channel that separates domain 3 from domains 1 and 2. The 5' end of the oligonucleotide resides at the interface of domains 2 and 3 and its 3' end is positioned at the interface of domains 1. This domain is associated with domain 2 by a pair of antiparallel β-strands .
Inner capsid protein lambda-1/VP3 (Lamba1_VP3)
Type: Domain

The reovirus inner capsid protein lambda-1 displays nucleoside triphosphate phosphohydrolase (NTPase), RNA-5'-triphosphatase (RTPase), and RNA helicase activity and may play a role in the transcription of the virus genome, the unwinding or reannealing of double-stranded RNA during RNA synthesis. Lambda1 is an Orthoreovirus core protein, VP3 is the homologous core protein in aquareoviruses .
Uncharacterized protein B-129, C2H2 zinc finger (B129_C2H2-Znf)
Type: Domain

This entry represents a C2H2 zinc finger found at the C-terminal of a group of poorly characterised viral and archaeal proteins, including the uncharacterised protein B-129 from Sulfolobus spindle-shape virus 1 (SSV1).
Lpg0393-like, VPS9-like domain (Lpg0393-like_VPS9)
Type: Domain

This entry represents the N-terminal domain of Lpg0393 and related proteins. Lpg0393 (

) consists of two domains both of which are composed of α-helices. The N-terminal domain contains of seven helices and makes roughly a 90-degree angle with the C-terminal domain, that forms a helical bundle structure . The N-terminal domain is similar to Vps9 domain of Rabex-5. Lpg0393 exhibits a GEF activity toward Rab5, Rab21 and Rab22, and this activity is associated with a VPS9-like domain of the protein.
PSD13, N-terminal (PSD13_N)
Type: Domain

This entry represents the N-terminal domain of PSD13 from human and its orthologues from yeast, RPN9, consisting of helical repeats .

These proteins are a component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. This domain mediates interaction with the ubiquitin receptor Rpn10 (also known as PSMD4 in human) .
DNA-binding protein H-NS-like, N-terminal domain (H-NS-like_N)
Type: Domain

This entry corresponds to the N-terminal oligomerisation domain of H-NS histone-like proteins .

The histone-like nucleoid-structuring (H-NS) protein is a DNA-binding protein implicated in transcriptional repression (silencing) as well as in bacterial chromosome organisation . H-NS binds tightly to AT-rich dsDNA, increases its thermal stability and inhibits transcription. It also binds to ssDNA and RNA but with a much lower affinity .
Domain of unknown function DUF6888 (DUF6888)
Type: Domain

This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved N-terminal MPT sequence motif. AlphaFold predicts that this protein is composed of an N-terminal α-helix followed by a four stranded β-sheet. AlphaFold also predicts the protein forms a strong dimer interface. It shows some weak structural similarity to the N-terminal domain of RnlA toxin.
Protein of unknown function DUF6889 (DUF6889)
Type: Family

This entry represents a family of small proteins that are largely composed of a single α-helix. Some members of the family are found on phage. The function of these proteins is unknown.
Protein of unknown function DUF6890 (DUF6890)
Type: Family

This entry represents a family of small proteins composed largely of a single α-helix. Some proteins in this family are annotated as from phage. The function of these proteins is unknown.
Domain of unknown function DUF6891 (DUF6891)
Type: Domain

This entry represents a domain of unknown function from uncharacterised proteins mainly found in bacteria.
Domain of unknown function DUF6892 (DUF6892)
Type: Domain

This entry represents a domain found in uncharacterised bacterial proteins.
Protein of unknown function DUF6893 (DUF6893)
Type: Family

This entry represents a family of small proteins that are likely to have a signal peptide that takes up most of the sequence. Thus, a small peptide might be released from these proteins.
Domain of unknown function DUF6894 (DUF6894)
Type: Domain

This entry represents a small protein domain found mainly in alphaproteobacteria. Its structure is composed of a four stranded β-sheet packed on one side by an α-helix. The function of these proteins is unknown.
Domain of unknown function DUF6895 (DUF6895)
Type: Domain

This entry represents a domain found in a set of uncharacterised bacterial proteins. These proteins have a predicted 6-helical hairpin fold found in a wide range of glycosyl hydrolase enzymes, suggesting a potential function.
Domain of unknown function DUF6896 (DUF6896)
Type: Domain

This entry represents a domain found in bacterial proteins of unknown function. The domain structure includes a four stranded β-sheet which has two conserved aspartates in a DXDXG motif close to a highly conserved histidine. These three residues may for the potential active site.
Protein of unknown function DUF6897 (DUF6897)
Type: Family

This entry represents a family of small prokaryotic proteins. They are predicted to adopt an SH3-like barrel structure that shows similarity to the C-terminal domain of the ribosomal chaperone RimP

.
Domain of unknown function DUF6898 (DUF6898)
Type: Domain

This entry represents a small protein that has a domain with a structure resembling a double stranded RNA-binding domain such as

. Thus suggesting this protein may also have a dsRNA binding function. This is supported by the presence of several conserved positively charged residues.
Protein of unknown function DUF6899 (DUF6899)
Type: Family

This entry represents uncharacterised proteins of unknown function.
Domain of unknown function DUF6900 (DUF6900)
Type: Domain

This entry represents a small domain found in a range of bacterial and phage proteins. In a few proteins it is associated with

. This region is composed of two α-helices.
Protein of unknown function DUF6901 (DUF6901)
Type: Family

This entry represents a family of uncharacterised bacterial proteins. The possess a β-sheet packed against an α-helical subdomain. This alignment contains three fully conserved cysteines that look like they form an Fe-S cluster or zinc-binding site in the predicted structures.
Protein of unknown function DUF6902 (DUF6902)
Type: Family

This entry represents a family of bacterial proteins that have an α/α(6) toroid structure. This suggests that these proteins are probably members of an uncharacterised family of glycosyl hydrolases.
Protein of unknown function DUF6903 (DUF6903)
Type: Family

This entry represents a family of small putative bacterial integral membrane proteins with two transmembrane helices.
Protein of unknown function DUF6904 (DUF6904)
Type: Family

This entry represents an uncharacterised family of bacterial proteins. Members of the family are about 250 residues in length and predicted to adopt an α/β globular structure.
Protein of unknown function DUF6905 (DUF6905)
Type: Family

This entry represents a family of proteins that are annotated as Putative glycerol transporters (

). Members of the family contain four potential transmembrane helices.
Domain of unknown function DUF6906 (DUF6906)
Type: Domain

This entry represents a small domain found in a range of phage and bacterial proteins. Structurally it is composed of a three stranded β-meander packed against an α-helix. The function of these proteins is unknown.
Protein of unknown function DUF6907 (DUF6907)
Type: Family

This entry represents a family of Actinobacterial proteins of unknown function. AlphaFold predicts a confident dimeric arrangement. This family appears to be distantly related to

.
Domain of unknown function DUF6908 (DUF6908)
Type: Domain

This family of proteins are uncharacterised. This family is distantly related to

currently known as DUF1249.
Protein of unknown function DUF6909 (DUF6909)
Type: Family

This is a family of uncharacterised proteins. They are predicted to adopt a globular structure consisting of two domains. The predicted C-terminal domain share similarity with the catalytic domains of purine and uridine phosphorylases.
Protein of unknown function DUF6911 (DUF6911)
Type: Family

This entry represents a family of uncharacterised proteins. Proteins in this family are primarily found in Proteobacteria. The structure of these proteins contains a six stranded antiparallel β-sheet and α-helices packed on one side of the sheet.
Protein of unknown function DUF6912 (DUF6912)
Type: Family

This is a family of uncharacterised bacterial proteins. Their predicted structure shows some similarity to ADP-rybosylating toxins.
Protein of unknown function DUF6913 (DUF6913)
Type: Family

This is a family of uncharacterised bacterial proteins. They share remote similarity to both domains of proteins members of UDP-glycosyltransferase superfamily. In contrast to them, these proteins are predicted to consist of a single standalone domain.
Protein of unknown function DUF6914 (DUF6914)
Type: Family

This is a family of uncharacterised eukaryotic proteins. They are predicted to adopt a globular structure that resembles the conserved core of the PPPDE superfamily (after Permuted Papain fold Peptidases of DsRNA viruses and Eukaryotes) consisting of thiol peptidases with a circularly permuted papain-like fold.
Domain of unknown function DUF6916 (DUF6916)
Type: Domain

This is a domain of unknown function found in bacterial proteins. It is predicted to adopt a RIFT-type β(6)-barrel topology with a greater similarity to FAD-binding domains.
Domain of unknown function DUF6917 (DUF6917)
Type: Domain

This entry represents a domain in uncharacterised proteins is found in prokaryotes. Proteins in this family are typically between 135 and 154 amino acids in length. These proteins share significant sequence similarity to the central part of mammalian cell entry (MCE) protein MlaD.
Protein of unknown function DUF6918 (DUF6918)
Type: Family

This is a family of uncharacterised bacterial proteins with a length of ~140-150 residues. They are predicted to adopt an α-helical structure consisting of two structural repeats.
Domain of unknown function DUF6919 (DUF6919)
Type: Domain

This domain is found standalone or in combination with other domains mainly from bacteria. Its function is unknown but it has a significant sequence similarity to the C-terminal SAM-binding regulatory domain of 5,10-methylenetetrahydrofolate reductase (MTHFR).
Protein of unknown function DUF6920 (DUF6920)
Type: Family

This entry represents a set of uncharacterised proteins found in prokaryotes. They share remote similarity to LolA and LolB outer-membrane lipoproteins. Similar to LolA and LolB these proteins are predicted to have a hydrophobic cavity consisting of an unclosed β-barrel and an α-helical lid.
Domain of unknown function DUF6921 (DUF6921)
Type: Domain

This family of proteins is based on the known structure of a protein from Ruminococcus gnavus (

). The structure shows similarity to solute binding proteins. The exact function of these proteins is not yet known.
Domain of unknown function DUF6923 (DUF6923)
Type: Domain

This entry represents a β-propeller domain composed of five blades. It is often found in large extracellular proteins in one or more copies. It is uncertain whether this domain might have an enzymatic function or a ligand binding function. Structurally this domain appears to have a sixfold symmetry, but one of the blades takes up the space of normal repeats. This unusual blade is composed of three β-strands of the first repeat and a final C-terminal β-strand from the last repeat.
Domain of unknown function DUF6930 (DUF6930)
Type: Domain

This domain is found C-terminal in uncharacterised bacterial proteins. It is remotely related to the integrase core domain with a partly conserved active site architecture.
Domain of unknown function DUF6937 (DUF6937)
Type: Domain

This domain is found N-terminal in a family of uncharacterised proteins. This domain has a significant sequence similarity to the N-terminal domains of a number of proteins members of UDP-Glycosyltransferase/glycogen phosphorylase superfamily. It is predicted to adopt the same α/β structure.
Domain of unknown function DUF6938 (DUF6938)
Type: Domain

This domain is found C-terminal in a family of uncharacterised proteins mainly from bacteria. This domain has a significant sequence similarity to the C-terminal domains of a number of proteins members of UDP-Glycosyltransferase/glycogen phosphorylase superfamily. It is predicted to adopt the same α/β structure.
Protein of unknown function DUF6939 (DUF6939)
Type: Family

This entry represents a family of proteins with unknown function found mainly in bacteria. They share sequence similarity with the N-terminal part of NADAR domain and are predicted to adopt structure that is globally similar to the structure of E.coli protein YbiA, a member of the NADAR domain family.
Protein of unknown function DUF6940 (DUF6940)
Type: Family

This is a family of uncharacterised proteins found in bacteria and eukaryotes. These proteins are probably distantly related to HIT-containing uridylyltransferases and are likely to adopt the same structure.
Protein of unknown function DUF6941 (DUF6941)
Type: Family

This is a family of uncharacterised bacterial proteins. They share sequence similarity to Ig-like domains found in a number of proteins such as xylosyltransferase, alkylpurine DNA glycosylase, cycloisomaltooligosaccharide glucanotransferase and are predicted to adopt the same structure.
Protein of unknown function DUF6942 (DUF6942)
Type: Family

This is a family of uncharacterised bacterial proteins. They are probably distantly related to uracil-DNA glycosylases and other related DNA glycosylases given their predicted structure.
Protein of unknown function DUF6943 (DUF6943)
Type: Family

This is a family of uncharacterised bacterial proteins. They share significant sequence similarity with each of the specificity subunit target recognition domains of type I restriction-modification enzymes and are predicted to adopt the same structure.
Protein of unknown function DUF6944 (DUF6944)
Type: Family

This is a family of uncharacterised proteins found mainly in Gram-positive bacteria. They are predicted to be associated with the membrane and to adopt structure that has topological similarity to the common structural core of Succinate-acetate permease (SatP) superfamily proteins.
Domain of unknown function DUF6947 (DUF6947)
Type: Domain

This is a domain found in a group of uncharacterised bacterial sequences whose function is unknown. This domain adopts a galactose-binding-like structure (

).