SII-SWORD/CoKE huggingface dataset:
Protein of unknown function DUF4252 (DUF4252)
Type: Family

This family of proteins is functionally uncharacterised.
Domain of unknown function DUF4253 (DUF4253)
Type: Domain

This presumed domain is functionally uncharacterised.
Protein of unknown function DUF4254 (DUF4254)
Type: Family

This family of proteins is functionally uncharacterised.
Pvc16, N-terminal (Pvc16_N)
Type: Domain

Contractile injection systems (CISs) are cell-puncturing nanodevices that share ancestry with contractile tail bacteriophages. Photorhabdus virulence cassette (PVC) represents one group of extracellular CISs that are present in both bacteria and archaea . This entry represents the N-terminal domain of TPvc16, which forms part of a contractile injection system . This domain alone in Pvc16 is able to produce PVC particles with normal length but without the outer sheath, indicating the main function of this N-terminal domain in terminating the tube growth .
Protein of unknown function DUF4256 (DUF4256)
Type: Family

This family of proteins is functionally uncharacterised.
Protein of unknown function DUF4257) (DUF4257)
Type: Family

This family of proteins is functionally uncharacterised.
Protein of unknown function DUF4258 (DUF4258)
Type: Family

This family of proteins is functionally uncharacterised.
Protein of unknown function DUF4259 (DUF4259)
Type: Family

This family of proteins is functionally uncharacterised.
Protein of unknown function DUF4260 (DUF4260)
Type: Family

This family of integral membrane proteins is functionally uncharacterised. There is a conserved GLK sequence motif.
Domain of unknown function DUF4261 (DUF4261)
Type: Domain

This presumed domain is functionally uncharacterised.
Protein of unknown function DUF4262 (DUF4262)
Type: Family

This family of proteins is functionally uncharacterised.
Shedu protein SduA, C-terminal (SduA_C)
Type: Domain

This entry represents the C-terminal domain of SduA, the only component of antiviral defense system Shedu. Expression of Shedu in B.subtilis (strain BEST7003) confers resistance to phages phi105, phi29, rho14 and to a lesser extent to SPP1 . This domain may have endonuclease activity.
Protein of unknown function DUF4265 (DUF4265)
Type: Family

This family of proteins is functionally uncharacterised.
Domain of unknown function DUF4266 (DUF4266)
Type: Domain

This presumed domain is functionally uncharacterised.
Protein of unknown function DUF4267 (DUF4267)
Type: Family

This family of putative integral membrane proteins is functionally uncharacterised.
Domain of unknown function DUF4268 (DUF4268)
Type: Domain

This presumed domain is functionally uncharacterised.
Protein of unknown function DUF4269 (DUF4269)
Type: Family

This family of proteins is functionally uncharacterised. There is a conserved KTE sequence motif.
Protein of unknown function DUF4270 (DUF4270)
Type: Family

This family of putative lipoproteins is functionally uncharacterised.
Protein of unknown function DUF4271 (DUF4271)
Type: Family

This family of putative integral membrane proteins is functionally uncharacterised.
Protein of unknown function DUF4272 (DUF4272)
Type: Family

This family of proteins is functionally uncharacterised.
Domain of unknown function DUF4274 (DUF4274)
Type: Domain

This presumed domain is functionally uncharacterised.
Transcriptional regulator SgrR, N-terminal HTH domain (SgrR_HTH_N)
Type: Domain

Small, non-coding RNA molecules play important regulatory roles in a variety of physiological processes in bacteria. This entry represents the N-terminal domain of the SgrR family of proteins which regulate the transcription of these sRNAs, in particular SgrS. This domain contains a helix-turn-helix motif characteristic of winged-helix DNA-binding transcriptional regulators. SgrS is a small RNA required for recovery from glucose-phosphate stress in bacteria . In examining the regulation of SgrR expression it was found that SgrR negatively auto-regulates its own transcription in the presence and absence of stress, and thus SgrR coordinates the response to glucose-phosphate stress by binding specifically to sgrS promoter DNA .
BT_3044-like, C-terminal (BT_3044-like_C)
Type: Domain

This entry represents a domain found at the C-terminal end of a group of proteins from bacteroidetes. Some members of this group also contain

, including BT_3044 from Bacteroides thetaiotaomicron (

), a glycan binding enzyme that could degrade oligosaccharides or even large molecular size glycans . Many other members also contain

, including the auxiliary nutrient binding protein BT3507 from Bacteroides thetaiotaomicron (

,

) and BACOVA_03322 from Bacteroides ovatus (

). This domain was previously known as DUF4361.
Protein of unknown function DUF4362 (DUF4362)
Type: Family

This family of proteins mainly found in firmicutes is functionally uncharacterised. There is a conserved IRIV sequence motif.
Protein of unknown function DUF4363 (DUF4363)
Type: Family

This family of proteins is functionally uncharacterised.
Protein of unknown function DUF4364 (DUF4364)
Type: Family

This family of proteins is functionally uncharacterised.
Domain of unknown function DUF4365 (DUF4365)
Type: Domain

The function of this domain is not known. There is a single completely conserved residue D that may be functionally important.
Mobile element protein CD1107-like domain (CD1107-like_dom)
Type: Domain

This domain is found in the mobile element protein CD1107 from Clostridioides difficile (

,

) and similar proteins mainly found in firmicutes.
Domain of unknown function DUF4367 (DUF4367)
Type: Domain

The function of this domain is not known.
Domain of unknown function DUF4368 (DUF4368)
Type: Domain

The function of this domain is not known. There is a single completely conserved residue G that may be functionally important.
Protein of unknown function DUF4295 (DUF4295)
Type: Family

This family of functionally uncharacterised proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. There are two completely conserved residues (K and Y) that may be functionally important.
Domain of unknown function DUF4369 (DUF4369)
Type: Domain

The function of this domain is not known.
Domain of unknown function DUF4296 (DUF4296)
Type: Domain

This presumed domain is functionally uncharacterised. It is found in bacterial proteins, and is approximately 90 amino acids in length.
CD-NTase associated protein 4-like, DNA endonuclease domain (Cap4-like_endonuclease_dom)
Type: Domain

This entry corresponds to the N-terminal domain found in CD-NTase associated protein 4 (Cap4) from Enterobacter cloacae. This is the effector domain which has dsDNA nuclease activity, sharing structural homology with type II restriction endonucleases and it has the putative active-site conserved residues required for divalent metal coordination. It has a mixed β-sheet arrangement with α-helical bundles on the sides. This domain is inactive as a monomer; after Cap4 signal recognition through its C-terminal SAVED domain, it oligomerizes to closely locate two nuclease effector domains. This domain does not participate in ligand specificity and it has a promiscuous DNA cleavage response . This domain can also be found in uncharacterised proteins from bacteria and archaea.

CD-NTase-associated protein 4 (Cap4) is a member of a diverse family of bacterial receptors that specifically recognises nucleotide second messenger signals synthesised by cGAS/DncV-like nucleotidyltransferases (CD-NTases), that functions in CBASS immunity. It plays an essential role protecting bacteria from phage infections degrading dsDNA through its DNA endonuclease domain which is activated after ligand-induced oligomerization . This domain is found in LmuA and AbpA proteins, which confer resistance to phage infections.
MrpA C-terminal/MbhD (MrpA_C/MbhD)
Type: Domain

Hydrogen gas-evolving membrane-bound hydrogenase (MBH) is a respiratory complex homologous to the quinone-reducing Complex I which share a common ancestor, the Mrp antiporter . Like Complex I, MBH has peripheral and membrane arms. MBH is made of 14 subunits (MbhA-N). MbhJ, K, L, N and M form the Membrane-anchored hydrogenase module. MbhJ, K, L, N are predicted to be exposed to the cytoplasm and form the peripheral arm. The remaining 10 subunits are predicted to be integral membrane proteins forming the membrane arm, made of 44 transmembrane helices (TMH) [2, 3]. MbhA, B, C and F form the Sodium translocation module. MbhD, E, G and H form the Proton translocation module. MbhI is the linker between the hydrogenase module and the proton-translocating membrane module. It anchors the discontinuous TMH7 of MbhH via its middle lateral helix and the C-terminal of TMH2, found in MbhE. MbhD and MbhE together are equivalent to Nqo10 of Complex I and the C-terminal of MrpA . MbhD has three TM helices .
Protein of unknown function DUF4298 (DUF4298)
Type: Family

This family of bacterial proteins includes sHIP (

) from Streptococcus pyogenes. This protein is though to play an important role in the virulence of the bacteria. This protein shows a unique tetrameric organisation composed of four helix-loop-helix motifs .
Domain of unknown function DUF4092 (DUF4092)
Type: Domain

This presumed domain is functionally uncharacterised. It is found in accessory colonisation factor AcfD and uncharacterised proteins from Proteobacteria.
Protein of unknown function DUF4299 (DUF4299)
Type: Family

This family is functionally uncharacterised. It contains two conserved sequence motifs (RGF and DAY), and two completely conserved residues (P and D) that may be functionally important.
Alginate export domain (Alginate_export_dom)
Type: Domain

This domain forms an 18-stranded β-barrel pore which is likely to act as an alginate export channel .
Domain of unknown function DUF4300 (DUF4300)
Type: Domain

This entry represents a domain of unkown function found in lipoproteins. It is found in bacteria. They are typically between 281 and 303 amino acids in length and contain two conserved sequence motifs: NCR and PYQ.
DSC E3 ubiquitin ligase complex subunit 3, C-terminal (Dsc3_C)
Type: Domain

This is the C-terminal domain of DSC E3 ubiquitin ligase complex subunit 3 (Dsc3), which contains two transmembrane helices and a characteristic GFDRL sequence motif. Dsc3 is a component of the DSC E3 ubiquitin ligase complex (a Golgi-specific protein ubiquitination system) that functions in protein homeostasis under non-stress conditions, playing a role in protein quality control through endosome and Golgi-associated degradation pathway (EGAD) which targets membrane proteins at Golgi and endosomes for degradation by cytosolic proteasomes . Dsc3 is also involved in endocytic protein trafficking .

Yeast DSC E3 ubiquitin ligase complex is the homologue of Hrd1 E3 ligase complex from mammals, in which Dsc1, Dsc2 and Dsc3 corresponds to Hrd1, Der1, and Usa1, respectively. Dsc3 is a Herp-like protein that acts as a bridge between Dsc1 and Dsc2 for their interaction .
Domain of unknown function DUF4123 (DUF4123)
Type: Domain

This presumed domain is functionally uncharacterised.
Domain of unknown function DUF4124 (DUF4124)
Type: Domain

This presumed domain is functionally uncharacterised, but it may have an Ig-like fold.
Domain of unknown function DUF4301 (DUF4301)
Type: Domain

This domain is functionally uncharacterised. It is found in bacteria.
Protein of unknown function DUF4127 (DUF4127)
Type: Family

This protein family is functionally uncharacterised.
PPhage tail terminator protein-like (Phage_tail_terminator-like)
Type: Family

This family of proteins is functionally uncharacterised. The structure of family member

reveals a tail terminator protein gpU fold, which suggests that the protein could have a bacteriophage origin.
Protein of unknown function DUF4302 (DUF4302)
Type: Family

This family of proteins is functionally uncharacterised. They contain two completely conserved residues (R and L) that may be functionally important.
Succinate dehydrogenase subunit 5, mitochondrial (SDH5)
Type: Family

Complex II [succinate dehydrogenase (succinate-ubiquinone oxidoreductase); SDH] is the only enzyme shared by both the electron transport chain and the tricarboxylic acid (TCA) cycle in mitochondria. In plants, this complex is considered unusual because it has accessory subunits (SDH5-SDH8), in addition to the catalytic subunits of SDH found in all eukaryotes (SDH1-SDH4) .

This family represents the accessory complex II subunit Succinate dehydrogenase subunit 5, mitochondrial from plants .
Domain of unknown function DUF4371 (DUF4371)
Type: Domain

This domain is found in animal and plant proteins.
Domain of unknown function DUF4372 (DUF4372)
Type: Domain

This domain of unknown function often occurs at the N terminus of putative transposases.
Lin1244/Lin1753-like, N-terminal (Lin1244/Lin1753-like_N)
Type: Domain

The function of this domain is not known. It is found at the N-terminal of the uncharacterised phage-related protein Lin1244/Lin1753 which contains a DnaD domain (

) at the C-terminal.
Protein of unknown function DUF4374 (DUF4374)
Type: Family

This family of proteins is functionally uncharacterised.
DNA mimic protein DMP19, C-terminal (DMP19_C)
Type: Domain

This entry represents the C-terminal domain in DMP19 from Neisseria meningitidis (NMB0541) and similar proteins. This domain is also found in other bacterial uncharacterised proteins.

DMP19 is a DNA mimic protein able to prevent the transcription factor NHTF from binding to a recognition box, playing a role in gene regulation in the bacterial nitrogen response. It is an acidic protein with an all-α structure. The protein adopts a dimeric configuration, and its surface-charge distribution reveals a dsDNA-like topology .
Protein-glutamine gamma-glutamyltransferase-like, C-terminal (TgpA-like_C)
Type: Domain

This entry represents a domain found at the C-terminal end a group of prokaryotic proteins, including Protein-glutamine gamma-glutamyltransferase from Pseudomonas aeruginosa (TgpA) and similar proteins that contain a transglutaminase core domain (

). TgpA displays transglutaminase activity in vitro and plays a critical role in the viability of the bacteria. It might contribute to an essential function linked to the cell wall .

This domain is also found in may uncharacterised sequences that lack the ransglutaminase-like domain.

The function of this domain, previously known as DUF4129, is unknown. It has a conserved TXXE motif.
Domain of unknown function DUF4130 (DUF4130)
Type: Domain

This presumed domain is functionally uncharacterised.
Domain of unknown function DUF4131 (DUF4131)
Type: Domain

This functionally uncharacterised domain is frequently found in the N-terminal section of bacterial proteins involved in competence.
Domain of unknown function DUF4132 (DUF4132)
Type: Domain

This presumed domain is functionally uncharacterised.
Protein of unknown function DUF4133 (DUF4133)
Type: Family

This entry represents proteins of unknown function found primarily in Bacteroides species. The B. thetaiotaomicron gene appears to be upregulated in the presence of host or other bacterial species compared to growth in pure culture .
Protein of unknown function DUF4134 (DUF4134)
Type: Family

This entry represents proteins of unknown function found primarily in Bacteroides species. The B. thetaiotaomicron gene appears to be upregulated in the presence of host or other bacterial species compared to growth in pure culture .
Protein of unknown function DUF4303 (DUF4303)
Type: Family

This family of proteins is functionally uncharacterised.
Lantibiotic biosynthesis protein, dehydration domain (Lant_dehyd)
Type: Domain

This domain is found in proteins involved in the synthesis of lantibiotic compounds. It is found at the N terminus of NukM, the post-translational modification enzyme of lantibiotic nukacin ISK-1, where it has been shown to be mainly responsible for substrate recognition and dehydration .
Domain of unknown function DUF4136 (DUF4136)
Type: Domain

This domain is found in bacterial lipoproteins and PDZ domain-containing proteins. Its function is not known.
Protein of unknown function DUF4304 (DUF4304)
Type: Family

This family of proteins is functionally uncharacterised.
YpzG-like protein (YpzG-like)
Type: Family

The YpzG-like protein family includes the Bacillus subtilis YpzG protein

, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length and contain a conserved QVNG sequence motif.
YpzI-like protein (YpzI-like)
Type: Family

The YpzI-like protein family includes the Bacillus subtilis YpzI protein

, which is functionally uncharacterised. Proteins in this family are approximately 40 amino acids in length.
Protein of unknown function DUF4141 (DUF4141)
Type: Family

This entry represents proteins of unknown function found primarily in Bacteroides species. The B. thetaiotaomicron gene appears to be upregulated in the presence of host or other bacterial species compared to growth in pure culture .
YqzM-like protein (YqzM)
Type: Family

The YqzM-like protein family includes the Bacillus subtilis YqzM protein

, which is functionally uncharacterised. Proteins in this family are approximately 40 amino acids in length.
YrzO-like protein (YrzO-like)
Type: Family

The YrzO-like protein family includes the Bacillus subtilis YrzO protein

, which is functionally uncharacterised.
YrhC-like protein (YrhC-like)
Type: Family

The YrhC-like protein family includes the Bacillus subtilis YrhC protein

, which is functionally uncharacterised. YrhC is on the same operon as the MccA and MccB genes, which are involved in the conversion of methionine to cysteine. Expression of this operon is repressed in the presence of sulphate or cysteine .
Domain of unknown function DUF4142 (DUF4142)
Type: Domain

This presumed domain is functionally uncharacterised.
Domain of unknown function DUF4143 (DUF4143)
Type: Domain

This domain is often found C-terminal to an ATPase core domain.
Protein of unknown function DUF4148 (DUF4148)
Type: Family

This protein family is functionally uncharacterised.
Transcription factor TGA like domain (TGA_domain)
Type: Domain

This entry represents a domain found in plant transcription factors, including TGA proteins and protein PERIANTHIA. In Arabidopsis thaliana, there are seven TGA paralogues (TGA 1-7), which are transcriptional activators that binds specifically to the DNA sequence 5'-TGACG-3' . Another Arabidopsis thaliana protein in this entry, PERIANTHIA, binds to the 5'-AAGAAT-3' cis-acting element found in AG promoter and is involved in the determination of floral organ number .
TMEM205-like (TMEM205-like)
Type: Domain

This entry represents a transmembrane domain found in TMEM205 from animals , its homologue from yeast YPR098C and in uncharacterised bacterial sequences. This domain is functionally uncharacterised.
YrhK domain (YrhK_domain)
Type: Domain

Bacillus subtilis YrhK protein

is functionally uncharacterised. Its expression is under the control of the motility sigma factor sigma-D . This entry represents domain found in YrhK, where it comprises the whole length of the protein, and other sequences.
Protein of unknown function DUF4305 (DUF4305)
Type: Family

This family includes the Bacillus subtilis YdiK protein

, which is functionally uncharacterised. This is not a homologue of Escherichia coli YdiK, which belongs to

.
Protein of unknown function DUF4160 (DUF4160)
Type: Family

The function of these proteins is not known.
Sporulation protein YhaL (Spore_YhaL)
Type: Family

This family of proteins is involved in sporulation. In Bacillus subtilis its expression is regulated by the early mother-cell-specific transcription factor sigma-E .
Domain of unknown function DUF4165 (DUF4165)
Type: Domain

This presumed domain is functionally uncharacterised.
Domain of unknown function DUF4167 (DUF4167)
Type: Domain

This presumed domain is functionally uncharacterised.
YhdB-like protein (YhdB-like)
Type: Family

The YhdB-like protein family includes the Bacillus subtilis YhdB protein

, which is functionally uncharacterised. Proteins in this family are typically between 57 and 82 amino acids in length and contain two conserved sequence motifs: LMVRT and FLHAY.
YhfH-like protein (YhfH-like)
Type: Family

The YhfH-like protein family includes the Bacillus subtilis YhfH protein

, which is functionally uncharacterised. Its expression is repressed by the Spx paralogue MgsR, which regulates genes involved in stress response .
Domain of unknown function DUF4168 (DUF4168)
Type: Domain

This presumed domain is functionally uncharacterised.
YesK-like protein (YesK-like)
Type: Family

The YesK-like protein family includes the Bacillus subtilis YesK protein

, which is functionally uncharacterised. Its expression is regulated by the sporulation-specific sigma factor sigma-E .
YfhD-like protein (YfhD-like)
Type: Family

The YfhD-like protein family includes the Bacillus subtilis YfhD protein

, which is functionally uncharacterised. Its expression is regulated by the sporulation-specific sigma factor sigma-F . The proteins in this family contain a single completely conserved residue E that may be functionally important.
Domain of unknown function DUF4179 (DUF4179)
Type: Domain

This presumed domain is functionally uncharacterised.
YfhE-like protein (YfhE-like)
Type: Family

The YfhE-like protein family includes the Bacillus subtilis YfhE protein

, which is functionally uncharacterised. Its expression may be regulated by the sigma factor sigma-B, which regulates the expression of stress-response proteins . The proteins in this family contain a conserved QEV sequence motif.
Domain of unknown function DUF4180 (DUF4180)
Type: Domain

This presumed domain is functionally uncharacterised.
Spore coat protein CotO (Spore_coat_CotO)
Type: Family

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. CotO has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly .
Protein of unknown function DUF4306 (DUF4306)
Type: Family

This family includes the Bacillus subtilis YjdJ protein

, which is functionally uncharacterised. This is not a homologue of Escherichia coli YjdJ, which belongs to

. The proteins in this family are found in bacteria and they are functionally uncharacterised.
Protein of unknown function DUF4181 (DUF4181)
Type: Family

This protein family is functionally uncharacterised.
Domain of unknown function DUF4185 (DUF4185)
Type: Domain

This presumed domain is functionally uncharacterised.
Protein of unknown function DUF4307 (DUF4307)
Type: Family

This family of proteins is functionally uncharacterised Proteins in this family are typically between 132 and 153 amino acids in length and contain a single completely conserved residue C that may be functionally important.
Monooxygenase af470-like (Monooxy_af470)
Type: Family

This family consists of proteins from bacteria and fungi. It includes monooxygenase af470 from Aspergillus fumigatus, which is part of the fma gene cluster that mediates the biosynthesis of fumagillin, a meroterpenoid with numerous biological activities . It has been suggested that af470 mediates the oxidative cleavage of the terminal alkene of the dodecapentaenoate side chain into the carboxylic acid present in fumagillin .
Protein of unknown function DUF4191 (DUF4191)
Type: Family

This protein family is functionally uncharacterised.
Antirepressor AbbA (Antirep_AbbA)
Type: Family

AbbA inactivates the repressor AbrB, which represses genes switched on during the transition from the exponential to the stationary phase of growth. It binds to AbrB and prevents it from binding to DNA .
Protein of unknown function DUF4192 (DUF4192)
Type: Family

This protein family is functionally uncharacterised.
YmzC-like protein (YmzC-like)
Type: Family

The YmzC-like protein family includes the Bacillus subtilis YmzC protein

, which is functionally uncharacterised. The proteins in this family contain a conserved ELR sequence motif.