SII-SWORD/CoKE huggingface dataset:
Domain of unknown function DUF4832 (DUF4832)
Type: Domain

This domain is mainly found in various Bacteroides species. Its function is unknown. Distant homology analysis suggests a possible similarity of proteins from this family to TIM barrel glycoside hydrolases and, subsequently its involvement in carbohydrate metabolism. The domain lies downstream of glycosyl hydrolases 42, suggesting that as a domain it might represent the carbohydrate-binding region of the enzyme.
Capsid polyprotein VP90, C-terminal (VP90_C)
Type: Domain

This entry represents a domain found at the C terminus of the capsid polyprotein VP90 from Turkey astrovirus. This is a globular domain found on the surface of the viral capsid that forms the capsid projections or spikes. Astroviruses cause diarrhoea in a variety of mammals and birds, and are small, non-enveloped, single-stranded RNA viruses. The spike carries three conserved patches on its surface which could be candidates for avian receptor-binding sites .
Domain of unknown function DUF4833 (DUF4833)
Type: Domain

This domain is around 170 residues in length and it is found both in prokaryotes, mainly Bacteroidetes, and lower eukaryotes such as water moulds and protozoa. Its function is unknown.
AMPK, C-terminal adenylate sensor domain (AMPK_C)
Type: Domain

This domain can be found at the C terminus of yeast SNF1 and animal 5'-AMP (adenosine monophosphate)-activated protein kinase (AMPK) subunit alpha . The yeast SNF1 kinase is a prototype of AMPKs that regulate cellular responses to a variety of nutritional and environmental stresses .
Domain of unknown function DUF4987 (DUF4987)
Type: Domain

This entry represents a domain found in the C terminus of some uncharacterised proteins in Bacteroidales. The function of this domain remains unknown.
Protein of unknown function DUF4834 (DUF4834)
Type: Family

This family consists of uncharacterised proteins around 90 residues in length and is mainly found in various Bacteroides and Prevotella species. Protein in this family are characterised by a strongly conserved KDEGEYVD motif on the C terminus and a very divergent N terminus. The function of this family is unknown.
Fragilysin, N-terminal (Fragilysin_N)
Type: Domain

This entry represents the N-terminal domain of fragilysin, which is an extracellular metalloprotease toxin from B. fragilis, an oportunistic pathogen of human gut. This domain inhibits fragilysin and is cleaved in a mature, virulent form .
Protein of unknown function DUF4835 (DUF4835)
Type: Family

This family consists of uncharacterised proteins of around 300 residues in length and is mainly found in bacteria from the Cytophaga-Flavobacteria-Bacteroides (CFB) group, both environmental and from human microbiome. The function of this family is unknown.
Domain of unknown function DUF4986 (DUF4986)
Type: Domain

This domain can be found in the glycoside hydrolase BT0349 from Bacteroides thetaiotaomicron

and other bacterial proteins. It shows an α/β structure and locates C-terminal to

. The function of this domain remains unknown.
Protein of unknown function DUF4836 (DUF4836)
Type: Family

This family consists of several uncharacterised proteins around 520 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Small ribosomal subunit protein eS4, C-terminal domain (Ribosomal_eS4_C)
Type: Domain

This domain is found at the C terminus of eukaryotic small ribosomal subunit protein eS4 (also known as 40S ribosomal protein S4).
Protein-glutamine deamidase Cif (Cif)
Type: Family

Cycle inhibiting factors (Cifs), produced by diverse pathogenic bacteria, are cyclomodulins that inhibit the eukaryotic host cell cycle and also hijack other key cellular processes such as those controlling the actin network and apoptosis . It acts by mediating the side chain deamidation of 'Gln-40' of host NEDD8, converting it to glutamate, thereby abolishing the activity of cullin-RING-based E3 ubiquitin-protein ligase complexes (CRL complexes). The hijacking of the ubiquitin-dependent degradation pathway of host cells results in the modulation of various cellular functions such as epithelium renewal, apoptosis and immune response .
Domain of unknown function DUF4985 (DUF4985)
Type: Domain

This domain of around 100 residues locates in the C terminus of some uncharacterised proteins in various Bacteroides, Alistipes and Prevotella species. Its function remains unknown.
Small ribosomal subunit protein uS2, C-terminal domain (Ribosomal_uS2_C)
Type: Domain

This domain is found at the C terminus of eukaryotic small ribosomal subunit protein uS2 (also known as 40S ribosomal protein SA) .
Hydroxyacylglutathione hydrolase, C-terminal domain (HAGH_C)
Type: Domain

This domain is found at the C terminus of hydroxyacylglutathione hydrolase enzymes. Substrate binding occurs at the interface between this domain and the catalytic domain (

) .
Domain of unknown function DUF4984 (DUF4984)
Type: Domain

This domain can be found at the C terminus of some uncharacterised proteins from Bacteroidales. The function of this domain remains unknown.
ATP-dependent DNA helicase RecQ, zinc-binding domain (RecQ_Zn-bd)
Type: Domain

This domain is the zinc-binding domain of ATP-dependent DNA helicase RecQ .
Calcineurin-like phosphoesterase, N-terminal (Metallophos_N)
Type: Domain

This entry represents the N-terminal domain of calcineurin-like phosphoesterases. The function of this domain is unknown.
Protein of unknown function DUF4837 (DUF4837)
Type: Family

This family consists of uncharacterised proteins around 350 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Protein of unknown function DUF4838 (DUF4838)
Type: Family

This family consists of several uncharacterised proteins found mainly in various Bacteroides species. The function of this family is unknown.
Calcineurin-like phosphoesterase, C-terminal (Metallophos_C)
Type: Domain

This entry represents the C-terminal domain of calcineurin-like phosphoesterases. The function of this domain is unknown.
Protein of unknown function DUF4839 (DUF4839)
Type: Family

This family consists of uncharacterised proteins around 300 residues in length. The function of this family is unknown.
Extracellular endo-alpha-(1->5)-L-arabinanase, C-terminal (Abn2_C)
Type: Domain

Bacillus subtilis extracellular endo-alpha-(1->5)-L-arabinanase Abn2 comprises two domains, an N-terminal catalytic domain, with a 3D fold similar to that observed for other endo-1,5-alpha-L-arabinanases, and an additional C-terminal domain . This entry represents the C-terminal domain. It is around 100 residues in length and its function is unknown.
Cytoplasmic polyadenylation element-binding protein 1, N-terminal (CEBP1_N)
Type: Domain

This is the N-terminal domain of cytoplasmic polyadenylation element-binding protein 1 (CPEB1), a sequence-specific RNA-binding protein that regulates mRNA translation and cell differentiation .
Protein of unknown function DUF4840 (DUF4840)
Type: Family

This family consists of uncharacterised proteins around 220 residues in length and is mainly found in various Prevotella and Bacteroides species. The function of this family is unknown.
Domain of unknown function DUF4841 (DUF4841)
Type: Domain

This domain is found in the N-terminal region of several uncharacterised proteins found in various Bacteroides species. The solved structure of one of them (PDB entry 3oqq, BACOVA_00967, from Bacteroides ovatus) shows a small β barrel with an immunoglobulin-like fold. DUF4841 domain shows weak overlap with DUF4114 (

), suggesting a possible distant relation. Function of this domain is unknown.
Domain of unknown function DUF4842 (DUF4842)
Type: Domain

This domain is found at the C terminus of large number of uncharacterised proteins with broad phylogenetic distribution, which includes human gut Bacteroides, gammaproteobacteria (Vibrio and Shewanella) and also spirochetes from Leptospira genus. Solved structure of Bacteroides ovatus protein BACOVA_00967 (PDB entry 3oqq) shows a large β barrel with an immunoglobulin-like fold and significant structural similarity to collagen-binding domain of adhesin from S. aureus (1amx), but with several additional long loops and secondary structure elements. The function of this domain is unknown.
Cytoplasmic polyadenylation element-binding protein, ZZ domain (CEBP_ZZ)
Type: Domain

This ZZ-type zinc finger domain binds zinc via two conserved histidines in the C-terminal part of the domain .
Torus domain (Torus)
Type: Domain

This domain is found in pre-mRNA-splicing factor CWC2. It includes a CCCH-type zinc finger .
EutK-Ctail domain (EutK_C)
Type: Domain

Bacterial microcompartments (BMCs) are large proteinaceous structures comprised of a roughly icosahedral shell and a series of encapsulated enzymes. They function as organelles by sequestering particular metabolic processes within the cell. A shell or capsid, which is composed of a few thousand protein subunits, surrounds a series of sequentially acting enzymes and controls the diffusion of substrates and products (including toxic or volatile intermediates) into and out of the lumen. One BMC, which is dedicated to ethanolamine utilization (Eut), is present in several bacteria, including Salmonella enterica and Escherichia coli. The cellular function of the Eut microcompartment is to metabolize ethanolamine without allowing the release of acetaldehyde into the cytosol, thus mitigating the potentially toxic effects of excess aldehyde in the bacterial cytosol and also preventing the volatile acetaldehyde from diffusing across the cell membrane and leading to a loss of carbon. The shells of BMCs are made primarily of a family of proteins whose structural core is the BMC domain. Four homologous proteins (EutS, EutL, EutK, and EutM) are thought to be the major shell constituents of a functionally complex Eut microcompartment. A fifth protein, EutN is a minor shell component but not homologous to the BMC shell proteins .

The EutK shell protein is distinct among the shell proteins in the Eut microcompartment. First, although all other BMC proteins studied to date form hexamers (or pseudohexamers, like EutL), EutK is a monomer in solution. The apparent inability of EutK to assemble into a hexamer by itself suggests that different BMC paralogs might form mixed hexamers during assembly of the shell. Second, EutK has an extra protein domain (EutK-Ctail) of about 60 amino acids following the conserved BMC domain. The EutK-Ctail domain is a helix-turn- helix domain that might bind nucleic acids .
Protein of unknown function DUF4843 (DUF4843)
Type: Family

This family consists of uncharacterised proteins around 220 residues in length and is mainly found in various Bacteroides species. Distant homology analysis suggest distant relation between this family and other families of proteins with immunoglobulin-like folds, which are often involved in substrate binding. However, specific function of this family is unknown.
Cell surface antigen, C-terminal (Antigen_C)
Type: Domain

This repeated domain is found at the C terminus of cell surface antigens . In the Streptococcus mutans antigen I/II there are three repeats of this domain, a cleft between the first two of these forms a binding site for the human salivary agglutinin (SAG) .
Protein of unknown function DUF4844 (DUF4844)
Type: Family

This family consists of short uncharacterised proteins found mostly in different strains of Acinetobacter bumanii, but also in several Shewanella species and in some bacteria from the CFB group. Solved structure of ABAYE3784 protein from Acinetobacter baumannii AYE (

) shows a five helical bundle with a very strong structural similarity to a bromodomain domain. However, the specific function of proteins from this family is unknown.
THO complex subunit 2, N-terminal domain (THOC2_N)
Type: Domain

This entry represents the N terminus of THO complex subunit 2 (THO2, THOC2) .

THO/TREX, a nuclear protein complex conserved from yeast to humans, plays an important role in mRNP biogenesis connecting transcription elongation, mRNA export and preventing genetic instability. THO could be relevant to different mRNA processing steps, including the 3'-end formation, transcript release and export .
YaiA protein (YaiA)
Type: Family

This family of proteins is found in Enterobacteriaceae, where they are immediately downstream of a Shikimate kinase.
Subtilase, N-terminal (Peptidase_S8_N)
Type: Domain

This is the N-terminal domain found in some putative subtilisin-like proteases, mainly from the Bacteroidales order of bacteria. It is around 100 residues in length from various. The function of this domain is unknown.
GTP-binding protein, middle domain (GTP-bd_M)
Type: Domain

This entry represents a domain found in a group of GTP-binding proteins. Proteins containing this domain includes GTPase HflX, which associates with the 50S ribosomal subunit and may have a role during protein synthesis or ribosome biogenesis . This function of this domain is not known.
Phosphotransferase RcsD, RcsD-ABL domain (RcsD_ABL)
Type: Domain

This domain is part of the RcsD phosphotransferase. RcsD is a phosphotransfer intermediate between the sensor kinase RcsC and the response regulator RcsB. This domain recognises and interacts with the DNA-binding domain of RcsB .
Putative PepSY TM-like protein (PepSY_TM-like_2)
Type: Family

This is a family of bacterial proteins with three PepSY-like transmembrane (TM) regions.
Tify domain-binding domain (TDBD)
Type: Domain

This entry contains a C-terminal presumed zinc binding domain from the NINJA and related proteins, which interacts with the Tify domain of JAZ1 . This domain appears to be necessary and sufficient for JAZ protein interaction. Proteins included in this entry play a role in stress-related and growth-related signalling cascades .
Domain of unknown function DUF4983 (DUF4983)
Type: Domain

This entry represents a domain found in a group of uncharacterised proteins around 600 residues in length, mainly from Bacteroidetes. The function of this domain is unknown.
Ninja/AFP-like, putative nuclear localisation signal (NLS_NINJA_AFP-like)
Type: Conserved_site

This entry represents a likely nuclear localisation motif that is found in the plant NINJA and AFP proteins. NINJA proteins are Novel INteractor of JAZ proteins found in plants. NINJA proteins act as transcriptional repressors, the activity of which is mediated by a functional TPL-binding EAR repression motif upstream from this domain .
Domain of unknown function DUF4982 (DUF4982)
Type: Domain

This domain is found towards the C terminus of Beta-glucuronidase from Formosa agariphila (P17_GH2) and similar proteins mainly from bacteria and fungi. P17_GH2 is involved in the degradation of ulvan, the main polysaccharide component of the Ulvales (green seaweed) cell wall . The function of this domain is unknown.
Beta-galactosidase, domain 4 (LacZ_4)
Type: Domain

This entry represents domain 4 found in beta-galactosidase and it is organised in a jelly-roll type barrel (Rutkiewicz-Krotewicz M. Crystals 2018, 8(1), 13, https://doi.org/10.3390/cryst8010013).
Domain of unknown function DUF4980 (DUF4980)
Type: Domain

This domain is found in a group of putative glycosyl hydrolase family 32 proteins, mainly from Bacteroides species. The function of this domain is unknown.
Protein of unknown function DUF4845 (DUF4845)
Type: Family

This family consists of uncharacterised proteins around 120 residues in length and mainly found in Proteobacteria. Distant homology analysis suggests that proteins from this family are related to pilin type IV proteins from the Bundlin (

) family; this prediction is however not confirmed by any experimental evidence.
Protein of unknown function DUF4846 (DUF4846)
Type: Family

This family consists of uncharacterised proteins around 260 residues in length found in bacteria. Its function is unknown.
Protein of unknown function DUF4847 (DUF4847)
Type: Family

Uncharacterised proteins in this family conserved in Bacteroidetes are similar to Shigella flexneri MxiM, a pilot protein for S. flexneri MxiD, an outer membrane (OM)-associated ring-forming secretin and component of the type-III secretion system. MxiM, also an OM protein, binds lipids and MxiD. This subgroup belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large β-barrel ligand-binding cavity .
RND efflux pump, membrane fusion protein, barrel-sandwich domain (CusB_D23)
Type: Domain

This entry represents a domain comprising the combined domains 2 and 3 of the membrane-fusion proteins CusB from E.coli and related proteins. It is formed by a barrel-sandwich domain which is inserted in a RIFT-like domain. The barrel-sandwich domain, itself, contains an insert of a three-helical bundle subdomain. CusB proteins are membrane fusion proteins of the CusCFBA copper efflux system in E.coli and related bacteria. The whole molecule hinges between D2 and D3. Efflux systems of this resistance-nodulation-division group - RND - have been developed to excrete poisonous metal ions, and in E.coli the only one that deals with silver and copper is the CusA transporter. The transporter CusA works in conjunction with a periplasmic component that is a membrane fusion protein, eg CusB, and an outer-membrane channel component CusC in a CusABC complex driven by import of protons.

CusB can be divided into four different domains. The first three domains of the protein are mostly β-strands. However, the fourth domain forms an all α-helical domain, which is folded into a three-helix bundle secondary structure .
Protein of unknown function DUF4848 (DUF4848)
Type: Family

A small family of uncharacterised proteins around 310 residues in length and found mainly in various Bacteroidales species. The function of this family is unknown.
Clp1, P-loop domain (CLP1_P)
Type: Domain

This entry represents the P-loop containing domain of Clp1. This domain carries the P-loop, suggesting it is the region that binds adenine or guanine nucleotide .

Polyribonucleotide 5-hydroxyl-kinase Clp1 is a component of the cleavage factor IA (CF IA) complex, which is involved in the endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation . It is involved in both the endonucleolyitc cleavage and polyadenylation steps of mRNA 3'-end maturation . Human Clp1 can also function as a tRNA splicing enzyme . In human, mutations in Clp1 affect tRNA biogenesis and lead to impairment of both peripheral and central nervous system function, causing severe motor-sensory defects, cortical dysgenesis and microcephaly . Clp1 contains three domains, a small N-terminal β sandwich domain involved in DNA binding , a C-terminal domain containing a novel α/β-fold and a central domain that binds ATP .
Glycoside hydrolase family 18, BT1044-like (GH18_BT1044-like)
Type: Family

This entry represents a family of glycosyl hydrolases (GH) from CAZy family 18 that are mainly found in Bacteroidetes, including the endoglycosidase BT1044 from Bacteroides thetaiotaomicron (

). This protein folds into the canonical (β/α)8 barrel (TIM barrel) fold common to many GH structures, with the N-terminal a discrete extended structure that would orientate the lipoprotein on the cell surface with the active site facing the extracellular environment .
Centrosomal protein of 290kDa, coiled-coil region (Cep209_CC5)
Type: Domain

Cep290 and similar centrosomal proteins carry a number of coiled-coil regions, and this is the fifth along the length of the protein. It is thought that the proteins are involved in cilia biosynthesis .
Protein of unknown function DUF4850 (DUF4850)
Type: Family

This family consists of several uncharacterised proteins around 250 residues in length and is mainly found in various Acinetobacter species. The function of this family is unknown.
Protein of unknown function DUF4851 (DUF4851)
Type: Family

This family consists of several uncharacterised proteins around 250 residues in length and is mainly found in various Desulfovibrio species. The function of this family is unknown.
Clp1, N-terminal (Clp1_N)
Type: Domain

This entry represents the short N-terminal domain of the pre-mRNA cleavage complex II protein Clp1.

Polyribonucleotide 5-hydroxyl-kinase Clp1 is a component of the cleavage factor IA (CF IA) complex, which is involved in the endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation . It is involved in both the endonucleolyitc cleavage and polyadenylation steps of mRNA 3'-end maturation . Human Clp1 can also function as a tRNA splicing enzyme . In human, mutations in Clp1 affect tRNA biogenesis and lead to impairment of both peripheral and central nervous system function, causing severe motor-sensory defects, cortical dysgenesis and microcephaly . Clp1 contains three domains, a small N-terminal β sandwich domain involved in DNA binding , a C-terminal domain containing a novel α/β-fold and a central domain that binds ATP .
Protein of unknown function DUF4852 (DUF4852)
Type: Family

This family consists of several uncharacterised proteins around 350 residues in length and is mainly found in various bacteria. The function of this family is unknown.
Protein of unknown function DUF4853 (DUF4853)
Type: Family

This family consists of uncharacterised proteins around 220 residues in length and is mainly found in various Actinomyces species. The function of this family is unknown.
Protein of unknown function DUF4854 (DUF4854)
Type: Family

This family consists of uncharacterised proteins found in firmicutes and high GC Gram-positive bacteria associated with human and animal guts. The function of this family is unknown.
Protein of unknown function DUF4855 (DUF4855)
Type: Family

This family consists of uncharacterised proteins around 400 residues in length and is mainly found in various Bacteroides and Paenibacillus species.
Elongation factor G-binding protein, C-terminal treble-clef zinc-finger (EF-G-binding_C)
Type: Domain

This entry represents the C-terminal domain of the FusB (

) from Staphylococcus aureus. FusB is an elongation factor G (EF-G) binding protein that is linked to the fusidic acid (FA) resistance in S. aureus .

FusB forms an extended four-cysteine zinc-finger with a unique structural fold. It binds to the C terminus of EF-G through its C-terminal zinc-finger . FusB release ribosomes by competing with them for EF-G .
Protein of unknown function DUF4856 (DUF4856)
Type: Family

This family consists of uncharacterised proteins around 400 residues in length and is mainly found in various Bacteroidetes and Proteobacteria species. The function of this family is unknown.
Gram-positive pilin backbone subunit 3, Cna-B-like domain (GramPos_pilinD3)
Type: Domain

This is one of the major backbone units of Gram-positive pili, such as those from S.pneumoniae . There are three major pilin subunits that form the polymeric backbone of the pilin from S. pneumoniae, constructed of three transthyretin-like, CnaB, domains along with a crucial N-terminal domain, D1. The three Cna-B like domains are stabilised by internal Lys-Asn isopeptdie bonds, Gram-positive pili are formed from a single chain of covalently linked subunit proteins (pilins), usually comprising an adhesin at the distal tip, a major pilin that forms the polymer shaft and a minor pilin that mediates cell wall anchoring at the base .
Protein of unknown function DUF4857 (DUF4857)
Type: Family

This family consists of uncharacterised proteins around 340 residues in length and is mainly found in various bacteria. The function of this family is unknown.