SII-SWORD/CoKE huggingface dataset:
Domain of unknown function DUF4049 (DUF4049)
Type: Domain

This presumed domain is functionally uncharacterised.
Gag1-like, clamp domain (Gag1-like_clamp)
Type: Domain

This entry represents a domain found in a group of sequences from fungi and plants, including Gag1 from Saccharomyces cerevisiae (YLR407W), which interacts with Cka2, the fourth subunit of the eukaryotic kinase CK2. Gag1 is organised into three domains: lock, Gag and Clap (this entry). This domain, previously known as DUF4050, has three regions: rear, hinge and front . It contains two conserved sequence motifs: IPL and FLVD.
Protein of unknown function DUF4052 (DUF4052)
Type: Family

This family of proteins is functionally uncharacterised.
Protein of unknown function DUF4054 (DUF4054)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family are found in bacteria and viruses.
Poxvirus B22R protein C-terminal domain (Poxvirus_B22R_C_dom)
Type: Domain

This domain represents a highly conserved region towards the C terminus of poxvirus proteins from Fowlpox virus, Myxoma virus, Lumpy skin disease, Variola virus and other members of the Poxviridae family of double-stranded, no-RNA stage poxviruses.
Domain of unknown function DUF4055 (DUF4055)
Type: Domain

This presumed domain is functionally uncharacterised.
Protein of unknown function DUF4056 (DUF4056)
Type: Family

This family of proteins is functionally uncharacterised.
Domain of unknown function DUF4057 (DUF4057)
Type: Domain

This entry represents a domain found in a group of plant proteins, including DNA oxidative demethylase ALKBH2 from Arabidopsis thaliana , a dioxygenase that repairs alkylated DNA containing 1-methyladenine and 1-ethenoadenine by oxidative demethylation .
Protein of unknown function DUF4058 (DUF4058)
Type: Family

This family of proteins is functionally uncharacterised.
Poxvirus B22R protein N-terminal domain (Poxvirus_B22R_N_dom)
Type: Domain

This domain represents the highly conserved N-terminal region of poxvirus proteins from Fowlpox virus, Myxoma virus, Lumpy skin disease, Variola virus and other members of the Poxviridae family of double-stranded, no-RNA stage poxviruses.
Protein of unknown function DUF4059 (DUF4059)
Type: Family

This family of proteins is functionally uncharacterised. There is a conserved DKT sequence motif.
Protein of unknown function DUF4060 (DUF4060)
Type: Family

This family of proteins is functionally uncharacterised. There are two conserved sequence motifs: VEVV and SYVAT.
MAP3K, TRAFs-binding domain (MAP3K_TRAF-bd)
Type: Domain

Apoptosis signal-regulating kinases (ASK1/2/3 or MAP3K5/6/15) are mitogen-activated protein kinase kinase kinases (MAP3Ks) that mediate cellular responses to redox stress and inflammatory cytokines and play a key role in innate immunity and viral infection. This kind of signalling kinases are regulated by oligomerization and regulatory domains. In its N-terminal there is a thioredoxin-binding domain that negatively regulates activity and a TNF receptor-associated factors (TRAFs)-binding domain which triggers ASK activation and kinase activity. TRAFs-binding domain is composed by 14 helices, which form seven tetratricopeptide repeats (TPRs), followed by a PH-like domain to complete de central regulatory domain of ASK. The central regulatory region promotes ASK1 activity via its PH domain but also facilitates ASK1 autoinhibition by bringing the thioredoxin-binding and kinase domains into close proximity. The PH-like domain, adjacent to the kinase domain, is required together with an intact TPR region for ASK1 activity.

The major role of the central regulatory region is to bring the thioredoxin-binding domain into close proximity to the kinase domain to inhibit its activity .

This domain corresponds to the TRAFs-binding domain found at the N terminus of some MAP3Ks. This domain includes seven tetratricopeptide repeats (TPRs) and, together with th PH-like domain, constitutes the central regulatory domain of ASK1.
Bacteriophage N4 adsorption protein A, C-terminal (NfrA_C)
Type: Domain

The function of this domain is unknown, but it is found at the C terminus of bacteriophage N4 adsorption protein A (NfrA) in association with an N-terminal region of Tetratricopeptide (TPR) repeats. NfrA serves as the phage receptor .
Domain of unknown function DUF4072 (DUF4072)
Type: Domain

This short domain of unknown function is normally found at the N terminus of putative phosphoserine phosphatases.
Domain of unknown function DUF4062 (DUF4062)
Type: Domain

This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 80 amino acids in length. There is a conserved SST sequence motif.

This domain can be found in telomerase protein component 1 (TEP1), which is a component of the telomerase ribonucleoprotein complex that is essential for the replication of chromosome termini .
Putative 2/3 transmembrane domain holin (Holin_2-3)
Type: Family

Holin_2-3 is a putative holins with 2 or 3 transmembrane segments. It consists of many proteobacterial proteins ranging in size from about 70 aas to 120 aas. They have 2 or 3 predicted TMSs. Although some are annotated as phage proteins or holins, none appears to be functionally characterised.
Domain of unknown function DUF4082 (DUF4082)
Type: Domain

This domain appears to be a parallel β-helix repeated region that is located between successive cadherin domains in some proteins.
Domain of unknown function DUF4073 (DUF4073)
Type: Domain

This domain is frequently found at the C terminus of bacterial proteins carrying the metallophosphoesterase domain

.
Protein of unknown function DUF4083 (DUF4083)
Type: Family

This protein family is functionally uncharacterised. Some members are putatively annotated as being MutT/Nudix. However, the characteristic Nudix motif of GX(5)EX(7)REUXEE is absent.
Protein of unknown function DUF4085 (DUF4085)
Type: Family

This family of proteins is functionally uncharacterised.
Protein of unknown function DUF4087 (DUF4087)
Type: Family

This family of proteins is functionally uncharacterised. There is a conserved RCGW sequence motif.
Protein of unknown function DUF4088 (DUF4088)
Type: Family

This family of proteins is functionally uncharacterised.
DNA packaging protein FI (Packaging_FI)
Type: Family

This family includes the lambda phage DNA-packaging protein FI .
1-carboxybiuret hydrolase subunit AtzG-like (AtzG-like)
Type: Family

AtzG is essential for the production of soluble, active AtzE, which is a 1-carboxybiuret hydrolase .
Protein of unknown function DUF4090 (DUF4090)
Type: Family

This family of proteins is found in cyanobacteria and is functionally uncharacterised. Proteins in this family are approximately 90 amino acids in length. A member of this family, the ssr1528 gene was found to be regulated by an sRNA NsiR4 . In addition, the expression of that gene was repressed under conditions of nitrogen depletion, suggesting it may have a role related to cellular nitrogen status .
Glycoside hydrolase 123, catalytic domain (GH123_cat)
Type: Domain

This entry, formerly known as DUF4091, represents the C-terminal end of members of the glycoside hydrolase family 123 (GH123). A member of this family, beta-D-N-acetylgalactosaminidase from Clostridium perfringens, removes specific terminal N-D-acetylgalactosamine from glycosphingolipids. This catalytic domain folds into a pair of α-helices and a two-stranded β-sheet .
ELYS-like domain (ELYS_dom)
Type: Domain

This domain is found in ELYS (embryonic large molecule derived from yolk sac), which is conserved from fungi such Aspergillus nidulans and Schizosaccharomyces pombe to humans . ELYS is important for the assembly of the nuclear pore complex . The domain is also found in other proteins, such as E3 ubiquitin-protein ligase HOS1.
Domain of unknown function DUF4084 (DUF4084)
Type: Domain

This presumed domain is functionally uncharacterised. It is found in proteins from Gram-positive bacteria.
Ead/Ea22-like protein (Ead_Ea22)
Type: Family

This family contains phage proteins and bacterial proteins that are likely to represent integrated phage proteins. This family includes the Lambda phage Ea22 early protein as well as the Bacteriophage P22 Ead protein.
Putative metallopeptidase domain (Put_metallopeptidase_dom)
Type: Domain

This putative metallopeptidase domain is found mainly in hypothetical bacterial proteins.
WxxW domain (WxxW_domain)
Type: Domain

This domain of unknown function carries a highly conserved WxxW sequence motif and also has at least six well conserved cysteine residues. It is found in variable numbers ranging from a single copy up to 32 consecutive copies, as in

, from Branchiostoma floridae.
Ribonuclease M5, C-terminal domain (RNase_M5_C)
Type: Domain

This domain lies at the C terminus of ribonuclease M5. The N-terminal domain of this enzyme is a Toprim domain .

Ribonuclease M5 is required for correct processing of both the 5' and 3' ends of 5S rRNA precursor. It cleaves both sides of a double-stranded region yielding mature 5S rRNA in one step .
Hemagglutinin repeat (Hemagglutinin_rpt)
Type: Repeat

This hemagglutinin repeat is found in hemolysins and filamentous hemagglutinin. Bacterial hemolysins are exotoxins that attack blood cell membranes and cause cell rupture by mechanisms not clearly defined. Filamentous hemagglutinins have a role in host-cell binding and infection.
Mg chelatase-related protein, C-terminal domain (Mg_chelat-rel_C)
Type: Domain

This domain is found in proteins of unknown function that are homologus to bacterial magnesium chelatase subunit ChlI.
Transcriptional regulator, AbiEi antitoxin (AbiEi_4)
Type: Family

AbiEi_4 is the cognate antitoxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and also present in archaea .
AATF leucine zipper-containing domain (AATF)
Type: Domain

This leucine zipper-containing domain is found in apoptosis antagonizing transcription factor (AATF, also known as Che-1) and related proteins. AATF may function as a general inhibitor of the histone deacetylase HDAC1 . AATF has been shown to inhibit the abberant production of the amyloid beta peptide 1-42 by direct interaction with Par4 . This interaction occurs via the leucine zipper.
Insertion element IS402-like domain (IS402-like_dom)
Type: Domain

This entry represents a domain found in Insertion element IS402 from Burkholderia cepacia and similar sequences mainly found in prokaryotes. Members of this group are putative transposases of the IS4/IS5 family.
Recombination activating protein 2, PHD domain (RAG2_PHD)
Type: Domain

RAG-2 is an essential component of the lymphoid-specific recombination activating gene RAG1/2 V(D)J recombinase mediating antigen-receptor gene assembly. It contains an acidic hinge region implicated in histone-binding, a non-canonical plant homeodomain (PHD) finger followed by a C-terminal extension of 40 amino acids that is essential for phosphoinositide (PtdIns)-binding. .

This domain, a non-canonical plant homeodomain (PHD) finger, is found at the C terminus of the Recombination activating gene 2 (RAG2) protein. The PHD finger is a chromatin-binding module that has been shown bound to histone H3 trimethylated at lysine 4 (H3K4me3) and influences V(D)J recombination .
Toastrack DUF4097 (Toastrack_DUF4097)
Type: Domain

This has a putative all-β structure with a twenty-residue repeat with a highly conserved repeating GD, gly-asp, motif that has been described as Toastrack DUF4097, whose function is unknown. In bacteria, it may form part of an adhesin. This entry also includes eukaryotic proteins, such as FAM185A from human and its orthologues in animals and other eukaryotes, as Toastrack has been transferred from bacteria to certain eukaryotes (Janani Ravi et.al, The Phage-shock-protein (PSP) Envelope Stress Response: Discovery of Novel Partners and Evolutionary History, doi:10.1101/2020.09.24.301986).
Domain of unknown function DUF4100 (DUF4100)
Type: Domain

This domain is found in a family of uncharacterised proteins mainly found in basidiomycetes.
Integrase, DNA-binding domain (Integrase_DNA_bind_dom)
Type: Domain

This domain is found at the N terminus of a wide variety of phage integrase proteins. It is predicted to bind DNA.
Fusion glycoprotein F0, Isavirus (Fusion_F0_Isavirus)
Type: Family

Fusion between viral and cellular membranes is mediated by viral membrane fusion glycoproteins. This entry represents fusion glycoprotein F0 from the infectious salmon anemia virus (ISAV). The precursor protein F0 is proteolytically cleaved to F1 and F2, which are held together by disulphide bridges .
Protein of unknown function DUF3925 (DUF3925)
Type: Family

This family of bacterial proteins is functionally uncharacterised. Proteins in this family are approximately 70 amino acids in length.
Protein of unknown function DUF3927 (DUF3927)
Type: Family

This family of proteins is found in bacteria and viruses and is functionally uncharacterised. The proteins contain a conserved SVL sequence motif and a single completely conserved residue D that may be functionally important.
Protein of unknown function DUF3928 (DUF3928)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family are found in bacteria and are approximately 100 amino acids in length.
Protein of unknown function DUF3929 (DUF3929)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family are approximately 70 amino acids in length and are found in bacteria.
Protein of unknown function DUF3930 (DUF3930)
Type: Family

This family consists of functionally uncharacterised bacterial proteins.
Protein of unknown function DUF3932 (DUF3932)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family are approximately 80 amino acids in length and are found in bacteria.
Protein of unknown function DUF3933 (DUF3933)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family are approximately 60 amino acids in length and are found in bacteria.
Protein of unknown function DUF3934 (DUF3934)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family are approximately 40 amino acids in length and are found in bacteria. They contain two conserved sequence motifs: GTG and SKG.
Protein of unknown function DUF3935 (DUF3935)
Type: Family

This family of bacterial proteins is functionally uncharacterised. Proteins in this family are approximately 90 amino acids in length and contain two conserved sequence motifs: FVF and LGV.
Cell division inhibitor MciZ (MciZ)
Type: Family

This family of bacterial proteins includes cell division inhibitor MciZ from
Bacillus subtilis
. MciZ is required during sporulation, blocking Z-ring formation in the mother cell by inhibiting the polymerization of FtsZ . FtsZ (filamentation temperature-sensitive Z) is the bacterial homologue of tubulin. Crystal structure reveals that MciZ binds to the C-terminal polymerization interface of FtsZ, the equivalent of the minus end of tubulin, causing shortening of protofilaments and blocking the assembly of higher-order FtsZ structures. Hence, MciZ provides a capping-based regulatory mechanism for FtsZ .
Lnb, N-terminal periplasmic domain (Lnb_N)
Type: Domain

This domain, previously known as DUF4105, is found N-terminal in Lipoprotein N-acyltransferase Lnb from Bacteroides and related uncharacterised bacterial proteins. Lnb functions as a lipoprotein N-acyltransferase in its native cell enviroument . It is composed of two domains, N-terminal (this entry) and C-terminal α-helical transmembrane domain. The domain represented by this entry contains a highly conserved histidine residue and a well-conserved NCT motif. Its predicted structure has a significant similarity to the papain-like cysteine peptidases. In addition, the putative catalytic triad Asn-His-Cys is highly conserved. This domain is also found in combination with other domains.
Protein of unknown function DUF4106 (DUF4106)
Type: Family

This family of proteins are found in large numbers in the Trichomonas vaginalis proteome. The function of this protein is unknown.
Protein of unknown function DUF4107 (DUF4107)
Type: Family

This family of putative proteins are found in Trichomonas vaginalis in large numbers. The function of this protein is unknown.
Protein of unknown function DUF4108 (DUF4108)
Type: Family

This family of putative proteins are found in Trichomonas vaginalis in large numbers. The function of this protein is unknown.
RNA polymerase-binding protein RbpA (RNApol-bd_RbpA)
Type: Family

RbpA binds to RNA polymerase (RNAP), stimulating transcription from principal, but not alternative sigma factor promoters . RbpA stimulates transcription from several principal sigma factor HrdB (SigA)-dependent promoters but not from a SigR-dependent promoter. Stimulation occurs in the presence of the transcription inititation inhibitor rifampicin .
Domain of unknown function DUF4110 (DUF4110)
Type: Domain

This domain is found predominantly at the C terminus of Kelch repeat-containing proteins. However, the exact function of this domain is not known.
Adenylyltransferase AadA, C-terminal domain (AadA_C)
Type: Domain

This domain is found at the C-terminal end of Aminoglycoside adenylyltransferase from Salmonella typhimurium (AadA) and other proteins associated with methicillin-resistant bacteria. AadA adenylates the 3''-hydroxyl group of the streptomycin glucosamine ring and the 9-hydroxyl group of the spectinomycin actinamine ring, mediating bacterial resistance to these antibiotics. This enzyme is organised into two domains: a N-terminal domain with a nucleotidyltransferase fold and a C-terminal domain. This domain consists of five α-helices forming an up-and-down α-helical bundle. It undergoes small conformational changes upon binding of ATP and magnesium that play a key role in the binding of the antibiotic compounds .

This entry also includes Spectinomycin 9-adenylyltransferase from Enterococcus faecalis (Aad9), which only mediates bacterial resistance to the antibiotic spectinomycin . This protein shows an overall and structure similar to AadA .
Protein of unknown function DUF4120 (DUF4120)
Type: Family

The function of this protein is not known, but the Bacteroides thetaiotaomicron gene appears to be upregulated in the presence of host or other bacterial species compared to pure culture .
Protein of unknown function DUF4119 (DUF4119)
Type: Family

The function of this protein is not known, but the Bacteroides thetaiotaomicron gene appears to be upregulated in the presence of host or other bacterial species compared to pure culture .
Protein of unknown function DUF4112 (DUF4112)
Type: Family

This uncharacterised protein family has several highly conserved GD sequence-motifs of unknown function.
Domain of unknown function DUF4113 (DUF4113)
Type: Domain

This domain of unknown function is usually found at the C terminus of DNA repair polymerase proteins.
Protein of unknown function DUF4121 (DUF4121)
Type: Family

The function of this protein is not known, but the Bacteroides thetaiotaomicron gene appears to be upregulated in the presence of host or other bacterial species compared to pure culture .
Protein of unknown function DUF4122 (DUF4122)
Type: Family

The function of this protein is not known, but the Bacteroides thetaiotaomicron gene appears to be upregulated in the presence of host or other bacterial species compared to pure culture .
Protein of unknown function DUF4125 (DUF4125)
Type: Family

This family of proteins is functionally uncharacterised.
Succinate dehydogenase/fumarate reductase N-terminal (Succ_DH/fum_Rdtase_N)
Type: Domain

This entry represents the 2Fe-2S iron-sulphur cluster binding domain found in members of the succinate dehydrogenase/fumarate reductase protein family. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated.
Domain of unknown function DUF4114 (DUF4114)
Type: Domain

This domain of unknown function is found in many different types of protein. There are highly conserved glutamate and aspartate residues suggesting that this domain might carry enzymic activity.
Cytoskeleton protein RodZ-like, C-terminal domain (RodZ-like_C)
Type: Domain

This short domain is often found at the C terminus of cytoskeleton RodZ proteins, which contain a helix-turn-helix domain. The function of this domain, previously known as DUF4115, is unknown.
GTA TIM-barrel-like domain (GTA_TIM_dom)
Type: Domain

This domain, which appears to have a TIM barrel fold, is found in the gene transfer agent protein. An unusual system of genetic exchange exists in the purple nonsulphur bacterium Rhodobacter capsulatus. DNA transmission is mediated by a small bacteriophage-like particle called the gene transfer agent (GTA) that transfers random 4.5-kb segments of the producing cell's genome to recipient cells, where allelic replacement occurs . The genes involved in this process appear to be found widely in bacteria .
Domain of unknown function DUF4126 (DUF4126)
Type: Domain

This presumed domain is functionally uncharacterised.
Domain of unknown function DUF4116 (DUF4116)
Type: Domain

This entry represents a domain found in proteins from lower eukaryotes and bacteria. The function of this domain is unknown.
Polyphosphate kinase N-terminal domain (PPK_N_dom)
Type: Domain

Polyphosphate kinase (PPK) catalyses the formation of polyphosphate from ATP, with polyphosphate chain lengths of up to a thousand or more orthophosphate molecules.

This entry represents the PPK N-terminal domain, which consists of three α helices .
DNA translocase FtsK, 4TM region (FtsK_4TM)
Type: Domain

This entry represents the integral membrane domain of the FtsK DNA tranlocases. During sporulation in Bacillus subtilis, the SpoIIIE protein is believed to form a translocation pore at the leading edge of the nearly closed septum. The E. coli FtsK protein is homologous to SpoIIIE, and can free chromosomes trapped in vegetative septa .
Polyphosphate kinase C-terminal domain 2 (PPK_C_dom2)
Type: Domain

Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. This C2-terminal domain has a structure similar to phospholipase D. It is one of two closely related carboxy-terminal domains (C1 and C2 domains). Both the C1 and C2 domains (residues 322-502 and 503-687, respectively) consist of a sevenstranded mixed β-sheet flanked by five α-helices. However, the structural topology and relative orientations of the helices to the β-sheet in these two domains are different. The C1 and C2 domains are highly conserved in the PPK family. Some of the residues previously shown to be crucial for the enzyme catalytic activity are located in these two domains .
Sensor protein KdpD, transmembrane domain (KdpD_TM)
Type: Domain

This domain is found in sensor protein KdpD. It is likely to be a transmembrane domain involved in ligand sensing.

KdpD is part of the two-component regulatory system KdpD/KdpE involved in the regulation of the kdp operon, a three-component K+ transport system. KdpD may function as a membrane-associated protein kinase that phosphorylates KdpE in response to environmental signals .
Phospholipase D-like domain (PLD-like_dom)
Type: Domain

Phospholipase D hydrolyses glycerol-phospholipids at the terminal phosphodiesteric bond. This entry represents a phospholipase D-like domain, found in phospholipase D and related proteins. In cardiolipin synthases it is found duplicated.