SII-SWORD/CoKE huggingface dataset:
Domain of unknown function DUF5009 (DUF5009)
Type: Domain

Proteins containing this DUF5009 domain are not characterised.
Fragile X-related 1 protein, C-terminal region 3 (FXR_C3)
Type: Domain

This is a small highly conserved region at the very C terminus of Fragile X-related proteins 1 and 2, FRX1, FRX2. It is found in association with

and

.
Domain of unknown function DUF5010 (DUF5010)
Type: Domain

Proteins containing this DUF5010 domain are uncharacterised.
Pesticidal crystal protein Cry22Aa, Ig-like domain (Cry22Aa_Ig-like)
Type: Domain

This domain can be found in Pesticidal crystal protein Cry22Aa from Bacillus thuringiensis, a protein with a toxic effect on several insect larvae . It is also present in Chitinase 60 from Moritella marina (

), responsible for degradation of krill chitin. BT_2262 from Bacteroides thetaiotaomicron (

) contains this domain at the N-terminal end . This entry represents the bacterial immunoglobulin-like domain .
BT_2262-like, C-terminal domain (BT_2262-like_C)
Type: Domain

This entry represents a domain found at the C-terminal end of proteins found in Bacteroidetes, including BT_2262 from Bacteroides thetaiotaomicron (

), a small outer membrane lipoprotein located on the periphery of the SusCD complex, which is essential for the import of oligosaccharides and for glycan degradation. This domain shows an eight-stranded β-barrel with structural similarity to lipid binding domains. Its specific function remains unknown .
Domain of unknown function DUF5013 (DUF5013)
Type: Domain

DUF5013 is an uncharacterised domain found mainly in various Bacteroides and Prevotella species.
Domain of unknown function DUF5014 (DUF5014)
Type: Domain

DUF5014 is an uncharacterised domain found in various Bacteroides species.
PKD-like family (PKD-like)
Type: Family

This is a PKD-like family of proteins found in various Bacteroides, Odoribacter and Prevotella species.
Domain of unknown function DUF5016 (DUF5016)
Type: Domain

This domain, functionally uncharacterised, is found at the N-terminal end of a group of proteins from Bacteroides. It is often found associated with

and

.
Domain of unknown function DUF5017 (DUF5017)
Type: Domain

DUF5017 is an uncharacterised domain mainly found Bacteroidetes species.
Domain of unknown function DUF5018 (DUF5018)
Type: Domain

DUF5018 is an uncharacterised domain found in various eubacteria.
Outer membrane protein SusF/SusE-like, C-terminal (SusF/SusE-like_C)
Type: Domain

This entry represents the C-terminal region of Outer membrane protein SusE/SusF from Bacteroides thetaiotaomicron and similar sequences from bacteroidetes. It consists of three β-sandwich CBMs .

SusE and SusF are two outer membrane proteins composed of tandem starch specific carbohydrate-binding modules (CBMs) with no enzymatic activity. They are are likely to play an important role in starch metabolism in Bacteroides. It has been speculated that they could compete for starch in the human intestinal tract by sequestering starch at the bacterial surface and away from competitors . SusE has higher affinity for starch compared to SusF.
DNA mismatch repair protein Mlh1, C-terminal (Mlh1_C)
Type: Domain

This is the C-terminal domain of DNA mismatch repair protein Mlh1, which belongs to the MutL family. This domain forms part of the endonuclease active site .
Niemann-Pick C1, N-terminal (NPC1_N)
Type: Domain

This is the N-terminal domain of Niemann-Pick C1 family proteins, which mediate transport of cholesterol from the intestinal lumen to enterocytes. This domain contains a cholesterol-binding pocket .
CCR4-NOT transcription complex subunit 1, CAF1-binding domain (CNOT1_CAF1_bind)
Type: Domain

This is the CAF1-binding domain of CCR4-NOT transcription complex subunit 1, which is a scaffolding component of the CCR4-NOT complex. This domain adopts a MIF4G (middle portion of eIF4G) fold .
GUN4, N-terminal ARM-like repeat domain (GUN4_N)
Type: Domain

This entry represents the ARM-repeat like N-terminal domain of Gun4 proteins from cyanobacteria . It contains five helices arranged in an alternating antiparallel pattern that resembles ARM or HEAT repeats, though the functional importance of this poorly conserved domain in Gun4 is not currently known .
CCR4-NOT transcription complex subunit 1, TTP binding domain (CNOT1_TTP_bind)
Type: Domain

This entry represents the TTP binding domain of CCR4-NOT transcription complex subunit 1. It adopts a MIF4G (middle portion of eIF4G) fold .
CCR4-NOT transcription complex subunit 1, HEAT repeat (CNOT1_HEAT)
Type: Domain

This domain is a HEAT repeat found in CCR4-NOT transcription complex subunit 1 .
CCR4-NOT transcription complex subunit 1, HEAT repeat 1 (CNOT1_HEAT_N)
Type: Domain

This domain is a HEAT repeat found in fungal CCR4-NOT transcription complex subunit 1 .
Fragile X messenger ribonucleoprotein 1, C-terminal region 2 (FMR1_C2)
Type: Domain

This is a small highly conserved region at the very C terminus of fragile X messenger ribonucleoprotein 1 (FMR1) .
Ubiquitin-like modifier-activating enzyme Atg7, N-terminal (Atg7_N)
Type: Domain

This is the N-terminal domain of ubiquitin-like modifier-activating enzyme ATG7. In Arabidopsis this domain binds the E2 enzymes ATG10 and ATG3 .
E2F transcription factor, CC-MB domain (E2F_CC-MB)
Type: Domain

This is the coiled coil (CC) - marked box (MB) domain of E2F transcription factors. This domain forms a heterodimer with the corresponding domain of the DP transcription factor, the heterodimer binds the C terminus of retinoblastoma protein .
RecQ-mediated genome instability protein 1, C-terminal OB-fold domain (RMI1_C)
Type: Domain

The dissolvasome is a protein complex that consists of BLM, a RecQ helicase that is product of the gene mutated in Bloom syndrome, topoisomerase IIIalpha (Top3alpha) and the RMI (RecQ-mediated genome instability) subcomplex, comprised of RMI1 and RMI2. The dissolvasome acts on double Holliday junction intermediates in homologous recombination, creating non-crossover products in a process termed 'dissolution' .

This entry represents the C-terminal oligo-nucleotide binding domain of Recq-mediated genome instability protein RMI1. This domain interacts with RMI2-OB folds to make up the RMI core complex. The RMI core interface is crucial for dissolvasome assembly and may have additional cellular roles as a docking hub for other proteins .
Transcription factor COE, DNA-binding domain (COE_DBD)
Type: Domain

This entry represents the DNA-binding domain of COE1, COE2, COE3 and COE4 (also known as Ebf1, Ebf2, Ebf3 and Ebf4), they belong to the early B cell factor family. COE1 is a key transcriptional determinant of B-lymphocyte differentiation . COE3 is a transcription factor involved in neuronal differentiation and maturation .
Transcription factor COE, helix-loop-helix domain (COE_HLH)
Type: Domain

This is the helix-loop-helix domain of transcription factor COE. It is responsible for dimerisation .
Family of unknown function DUF5021 (DUF5021)
Type: Family

This family consists of Prepilin-type cleavage/methylation N-terminal domain proteins around 200 residues in length and is mainly found in various Eubacterium species. The function of this family is unknown.
Protein of unknown function (DUF5022) (DUF5022)
Type: Family

This family consists of uncharacterised proteins around 350 in length. The function of this family is unknown.
Protein of unknown function DUF5023 (DUF5023)
Type: Family

This family consists of uncharacterised proteins around 300 residues in length and is found in Eubacterium.
Protein of unknown function DUF5024 (DUF5024)
Type: Family

This family consists of several uncharacterised proteins around 150 or 200 in length and is mainly found in Bacteroidales. The function of this family is unknown.
Protein of unknown function DUF5025 (DUF5025)
Type: Family

This family consists of several uncharacterised proteins around 200 in length and is mainly found in Parabacteroides and Bacteroides spp. The function of this family is unknown.
Protein of unknown function DUF5026 (DUF5026)
Type: Family

This family consists of several uncharacterised proteins around 100 residues in length and is mainly found in various Clostridiales species. The function of this family is unknown.
Protein of unknown function DUF5027 (DUF5027)
Type: Family

This family consists of several uncharacterised proteins around 180 in length mainly found in Firmicutes. The function of this family is unknown.
Protein of unknown function DUF5028 (DUF5028)
Type: Family

This family consists of several uncharacterised proteins around 200 in length. The function of this family is unknown.
Protein of unknown function DUF5029 (DUF5029)
Type: Family

This family consists of several uncharacterised proteins around 550 in length and is mainly found in Bacteroides fragilis and sp. The function of this family is unknown.
Protein of unknown function DUF5030 (DUF5030)
Type: Family

This family consists of several uncharacterised proteins around 300 in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Protein of unknown function DUF5031 (DUF5031)
Type: Family

This family consists of several uncharacterised proteins around 380 in length and is mainly found in Bacteroides. The function of this family is unknown.
Protein of unknown function DUF5032 (DUF5032)
Type: Family

This family consists of several uncharacterised proteins around 270 in length and is mainly found in various Bacteroides and Parabacteroides species. The function of this family is unknown.
Protein of unknown function DUF5033 (DUF5033)
Type: Family

This family consists of several uncharacterised proteins around 200 in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Protein of unknown function DUF5034 (DUF5034)
Type: Family

This family consists of several uncharacterised proteins around 190 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Protein of unknown function DUF5035 (DUF5035)
Type: Family

This family consists of several uncharacterised proteins around 170 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Protein of unknown function DUF5036 (DUF5036)
Type: Family

This family consists of several uncharacterised proteins around 240 residues in length and is mainly found in various Bacteroides and Parabacteroides species. The function of this family is unknown.
Protein of unknown function DUF5037 (DUF5037)
Type: Family

This family consists of several uncharacterised proteins around 270 residues in length and is mainly found in various Clostridiales species. The function of this family is unknown.
Protein of unknown function DUF5038 (DUF5038)
Type: Family

This family consists of several uncharacterised proteins around 200 residues in length and is mainly found in various Clostridiales species. The function of this family is unknown.
Protein of unknown function DUF5039 (DUF5039)
Type: Family

This family consists of several uncharacterised proteins around 240 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Protein of unknown function DUF5040 (DUF5040)
Type: Family

This family consists of several uncharacterised proteins around 260 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Protein of unknown function DUF5041 (DUF5041)
Type: Family

This family consists of several uncharacterised proteins around 230 residues in length and is mainly found in various Bacteroidales species. The function of this family is unknown.
TNRC6, PABC binding domain (TNRC6_PABC-bd)
Type: Domain

This entry represents a natively unstructured region found in TNRC6 protein that carries the binding motif for the interaction with PABC (polyadenylate-binding protein 1). TNRC6 are trinucleotide repeat-containing gene 6 proteins required for miRNA-mediated gene silencing that are localised to the P bodies (processing bodies). P bodies are cytoplasmic mRNP aggregates that are involved in general mRNA translation repression and decay, including nonsense-mediated decay. The interaction motif that binds to PABC is SINWPPEFHPGVPWKGLQ . This region lies between a Q-rich region and the RRM, or RNA-recognition motif.
Caskin-1, CASK-interaction domain (Caskin1-CID)
Type: Domain

The Caskin1 protein interacts with the CASK protein via this region . CASK and Caskin1 are synaptic scaffolding proteins. The binding motif on human Caskin1 is EEIWVLRK. A similar motif is found on protein MINT1 and protein TIAM1, both shown to be able to bind to CASK though the motif. However, MINT1 and TIAM1 are not included in this entry . This region is predicted to be natively unstructured.

This entry also matches Caskin2, a Caskin1 homologue deprived of the CASK interaction domain (CID) . Caskin1 and caskin2 consist of multiple ankyrin repeats, two SAM domains and one SH3 domain. In Caskin1 the CID is located between the SH3 and SAM domains .
CRISPR-associated endonuclease Cas9, PAM-interacting domain (Cas9_PI)
Type: Domain

This entry represents a domain found in the C-terminal of bacterial type II CRISPR system Cas9 endonuclease. This domain adopts a novel protein fold that is unique to the Cas9 family. It is positioned in the structure-DNA-complex to recognise the PAM sequence on the non-complementary DNA strand of the crRNA. PAM sequence is protospacer-adjacent motifs on DNA. Cas9 carries two nuclease domains, HNH and RuvC, which cleave the DNA strands that are complementary and non-complementary to the 20 nucleotide guide sequence in crRNAs, respectively .
Putative ATP-synthase-associated protein (ATP-synth_Z)
Type: Family

This is a family of short highly conserved plant proteins that might be associated with ATP-synthase atp operon.
CRISPR-associated endonuclease Cas9, bridge helix (Cas9-BH)
Type: Domain

This entry represents the bridge helix between the NUC and the REC lobes of Cas9 (CRISPR-associated endonuclease Cas9). The REC lobe and the NUC lobe of Cas9 fold to present a positively charged groove at their interface which accommodates the negatively charged sgRNA:target DNA heteroduplex . CRISPR (clustered regularly interspaced short palindromic repeat)-Cas system occurs naturally in bacteria as a defence against invasion by phages or other mobile genetic elements. Cas9 is targeted to specific genomic locations by sgRNAs or single guide RNAs, in order to complex with invading DNA in order to cleave it and render it inactive.
CRISPR-associated endonuclease Cas9, REC lobe (Cas9_REC)
Type: Domain

The REC lobe of Cas9 includes the REC1 and REC2 domains. REC1 forms an elongated, α-helical structure consisting of 25 α helices and two β-sheets, whereas REC2 inserted within REC1 adopts a six-helix bundle structure. The REC lobe and the NUC lobe of Cas9 fold to present a positively charged groove at their interface which accommodates the negatively charged sgRNA:target DNA heteroduplex . CRISPR (clustered regularly interspaced short palindromic repeat)-Cas system occurs naturally in bacteria as a defence against invasion by phages or other mobile genetic elements. Cas9 is targeted to specific genomic locations by sgRNAs or single guide RNAs, in order to complex with invading DNA in order to cleave it and render it inactive.
Protein of unknown function DUF5042 (DUF5042)
Type: Family

This family consists of several uncharacterised proteins around 460 residues in length and is found in various Bacteroides species. The function of this family is unknown.
Protein of unknown function DUF5043 (DUF5043)
Type: Family

This family consists of several uncharacterised proteins around 200 residues in length and is found in various Bacteroides species. The function of this family is unknown.
Protein of unknown function DUF5044 (DUF5044)
Type: Family

This family consists of several uncharacterised proteins around 220 residues in length and is mainly found in various Clostridiales species. The function of this family is unknown.
LapD/MoxY, periplasmic domain (LapD_MoxY_N)
Type: Domain

This entry represents the N-terminal periplasmic domain of the LapD and MoxY receptor proteins .
RecQ-mediated genome instability protein 2 (RMI2)
Type: Family

The dissolvasome is a protein complex that consists of BLM, a RecQ helicase that is product of the gene mutated in Bloom syndrome, topoisomerase IIIalpha (Top3alpha) and the RMI (RecQ-mediated genome instability) subcomplex, comprised of RMI1 and RMI2. The dissolvasome acts on double Holliday junction intermediates in homologous recombination, creating non-crossover products in a process termed 'dissolution' .

RMI2 is an OB3, oligo-nucleotide-binding protein. It is an essential component of the RMI complex .
Domain of unknown function DUF4822 (DUF4822)
Type: Domain

This is lipocain-like domain found in functionally uncharacterised bacterial proteins, often as a repeat of two domains. Proteins with this domain are found in a wide range of bacteria and are often annotated as S-layer proteins, but the origin of this annotation is not clear.
Protein of unknown function DUF4823 (DUF4823)
Type: Family

This family consists of hypothetical lipoproteins around 210 residues of length and is mainly found in various Pseudomonas species. The function of this family is unknown.
Protein of unknown function DUF4824 (DUF4824)
Type: Family

This family consists of several hypothetical lipoproteins around 270 residues in length and is mainly found in Pseudomonas species. The function of this family is unknown.
Domain of unknown function DUF4825 (DUF4825)
Type: Domain

This domain forms the N-terminal, extracellular domain of some homologues of Staph BlaR1 proteases, where it replaces the penicillin-binding domain of BlaR1. It is also found in many uncharacterised proteins in a broad range of bacteria. Its association with BlaR1 homologues suggests it may be involved in substrate-, possibly antibiotic-binding, but this prediction has not been verified experimentally.
Protein of unknown function DUF4826 (DUF4826)
Type: Family

This family consists of uncharacterised proteins around 150 residues in length and is mainly found in various Shewanella and Pseudoalteromonas species. The function of this protein is unknown.
Protein of unknown function DUF4827 (DUF4827)
Type: Family

This family consists of uncharacterised proteins around 200 residues in length and is mainly found in Bacteroidales. Distant homology prediction algorithms consistently suggest a homology between this family and FKBP-type peptidyl-prolyl cis-trans isomerases (

), but this relation is as yet not confirmed. The function of this family is unknown.
Exocrine gland-secreted peptide Esp1/Esp22 (Esp1/Esp22)
Type: Family

Exocrine gland-secreting peptide Esp1 is produced by the rodent male extraorbital lacrimal gland to be secreted into the tear fluid. Other mice including females detect these peptides through receptors in the vomeronasal organ, and the receptors report information on mouse-strain, sex and species . Esp22 is produced by juveniles and functions as a mating inhibitor . The peptides are short, all carrying an N-terminal signal peptide to indicate they are for secretion which accounts for much of the common conservation.
Protein of unknown function DUF4828 (DUF4828)
Type: Family

This family consists of uncharacterised proteins around 120 residues in length and is mainly found in various Enterococcus and Lactobacillus species. The function of this family is unknown.
Helical bimodular sensor domain (HBM)
Type: Domain

The HBM sensor domain has been identified primarily in bacterial chemoreceptors but is also present on histidine kinases. Characteristic features of this domain are its size of approximately 250 amino acids and its location in the bacterial periplasm . The McpS chemoreceptor of Pseudomonas putida KT2440 was found to possess an HBM sensor domain and its 3D structure in complex with physiologically relevant ligands has been reported . This domain is composed of 2 long and 4 short helices that form two modules each composed of a 4-helix bundle. The McpS chemoreceptor mediates chemotaxis towards a number of organic acids . Both modules of the McpS HBM domain contain a ligand binding site. Chemo-attractants binds to each of these sites and their binding was shown to trigger a chemotactic response . This domain is primarily found in different proteobacteria but also in archaea. Interestingly, amino acids in both ligand binding sites showed a high degree of conservation suggesting that members of this family sense similar ligands.
Domain of unknown function DUF4829 (DUF4829)
Type: Domain

This domain is mainly found in various Clostridium species. Its function is unknown.
Domain of unknown function DUF4830 (DUF4830)
Type: Domain

This domain is mainly found in Clostridium, Eubacterium, and Ruminococcus species. The function of this domain is unknown.
17kDa common-antigen outer membrane protein (DUF5061)
Type: Family

This entry represents an uncharacterised family of bacterial 17kDa common-antigen proteins.
Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type (HIBYL-CoA-H)
Type: Family

The enoyl-CoA hydratase/isomerase family contains a diverse set of enzymes including: enoyl-CoA hydratase, napthoate synthase, carnitate racemase, 3-hydroxybutyryl-CoA dehydratase and dodecanoyl-CoA delta-isomerase. This entry represents a subset of the enoyl-CoA hydratase/isomerase family. Proteins in this entry includes 3-hydroxyisobutyryl-CoA hydrolases (HIBYL-CoA-H) from eukaryotes and their homologues from bacteria.

The EHD3 protein, found in Saccharomyces cerevisiae, has been recognised as a constituent of the mitochondrial ribosome. Hence, it is alternatively referred as small ribosomal subunit mS47 .
Domain of unknown function DUF5060 (DUF5060)
Type: Domain

This is the N-terminal domain of putative glycoside hydrolases. It is found in a number of different bacteria.
Zinc-regulated secreted antivirulence protein, C-terminal (ZirS_C)
Type: Domain

This entry represents the C-terminal domain of ZirS, zinc-regulated secreted protein, that is part of a type V-like secretion system. The domain adopts a bacterial Ig-like fold. This domain interacts with its transporter ZirT, and ZirS also interacts directly with ZirU, the third component of this antivirulence complex. ZirT is the zinc-regulated transporter through which ZirS is secreted .
ATP-citrate synthase, citrate-binding domain (Citrate-bd)
Type: Domain

This is a conserved domain containing the citrate-binding sites found in the ATP-citrate synthases (also known as ATP citrate lyases). This domain has a Rossmann fold .

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.
Menaquinone biosynthesis protein MenD, middle domain (MenD_middle)
Type: Domain

This entry represents the middle domain of menaquinone biosynthesis protein MenD, an enzyme that belongs to the thiamine pyrophosphate (TPP) enzyme family, but is not captured by

. This enzyme is necessary for the first step of the biosynthesis of menaquinone, or vitamin K2, an important cofactor in electron transport in bacteria .
Protein of unknown function DUF4831 (DUF4831)
Type: Family

This family consists of several uncharacterised proteins around 350 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Putative cytidyltransferase-related, C-terminal region (HIGH_NTase1_ass)
Type: Domain

This domain is found as the C-terminal portion of some putative cytidyltransferase-related domain proteins. The exact function is not known.