SII-SWORD/CoKE huggingface dataset:
Wadjet protein JetB (JetB)
Type: Family

This family includes Wadjet protein JetB, a component of anti plasmid transformation system Wadjet type I, composed of JetA, JetB, JetC and JetD. Expression of Wadjet type I in B.subtilis (strain BEST7003) reduces the transformation efficiency of plasmid pHCMC05 .
YndJ-like protein (YndJ-like)
Type: Family

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

, which is functionally uncharacterised. The proteins in this family contain two completely conserved G residues that may be functionally important.
Domain of unknown function DUF4211 (DUF4211)
Type: Domain

This presumed domain is functionally uncharacterised.
Domain of unknown function DUF4218 (DUF4218)
Type: Domain

This presumed domain is functionally uncharacterised.
Protein of unknown function DUF4309 (DUF4309)
Type: Family

This family includes the Bacillus subtilis YjgB protein

, which is functionally uncharacterised. This is not a homologue of Escherichia coli YjgB,

. Expression of B. subtilis YjgB is regulated by the alternative transcription factor sigma-B .
Protein of unknown function DUF4275 (DUF4275)
Type: Family

This protein family is functionally uncharacterised.
Protein of unknown function DUF4276 (DUF4276)
Type: Family

This family of proteins is functionally uncharacterised. There is a single completely conserved residue E that may be functionally important.
Protein of unknown function DUF4310 (DUF4310)
Type: Family

The proteins in this family are functionally uncharacterised.
Domain of unknown function DUF4277 (DUF4277)
Type: Domain

This presumed domain is functionally uncharacterised. There is a conserved NGLGF sequence motif.
Protein of unknown function DUF4278 (DUF4278)
Type: Family

This family of proteins is functionally uncharacterised. There is a single completely conserved residue R that may be functionally important.
Protein of unknown function DUF4279 (DUF4279)
Type: Family

This protein family is functionally uncharacterised.
Protein of unknown function DUF4280 (DUF4280)
Type: Family

This family of proteins is functionally uncharacterised. There is a single completely conserved residue C that may be functionally important.
ABA DEFICIENT 4-like (ABA4-like)
Type: Family

This family of proteins is found in bacteria and plants. It includes abscisic acid (ABA)-deficient 4 protein (ABA4) from Arabidopsis thaliana, which has a role in neoxanthin synthesis and may be important for the de novo ABA synthesis specifically during dehydration .
Protein of unknown function DUF4313 (DUF4313)
Type: Family

The proteins in this family are functionally uncharacterised.
Domain of unknown function DUF4314 (DUF4314)
Type: Domain

This presumed domain has not been functionally characterised.
Protein of unknown function DUF4315 (DUF4315)
Type: Family

This family of proteins is functionally uncharacterised.
Domain of unknown function DUF4316 (DUF4316)
Type: Domain

This domain is functionally uncharacterised.
Protein of unknown function DUF4317 (DUF4317)
Type: Family

The proteins in this family are functionally uncharacterised. There is a single completely conserved residue P that may be functionally important.
Protein of unknown function DUF4318 (DUF4318)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family contain a single completely conserved residue F that may be functionally important.
Putative transposon-transfer assisting protein (TTRAP)
Type: Family

TTRAP is a family of small bacterial proteins largely from Clostrium difficile. From comparative and other structural studies of the PDB:

,

, it has been suggested that this family is required for interacting with other proteins in order to facilitate the transfer of the transposon CTn4 between different bacterial species. PDB:

comprises an α-helical fold of four α-helices leading to the production of two clefts, the larger of which displays two highly conserved residues in close proximity, Glu-8 and Lys-48. The gene concerned is part of an operon within transposon CTn4, and is expressed alongside a putative DNA primase, a DNA topoisomerase and conjugal transfer proteins .
Protein of unknown function DUF4320 (DUF4320)
Type: Family

This family is functionally uncharacterised. There are two completely conserved residues (G and Y) that may be functionally important.
Protein of unknown function DUF4321 (DUF4321)
Type: Family

The proteins in this family are functionally uncharacterised.
Domain of unknown function DUF4322 (DUF4322)
Type: Domain

This presumed domain is functionally uncharacterised. It has a conserved QTV sequence motif.
Domain of unknown function DUF4325 (DUF4325)
Type: Domain

This domain is functionally uncharacterised. It is found predominantly in bacteria but also some archaea.
Domain of unknown function DUF4326 (DUF4326)
Type: Domain

This entry represents a domain that is functionally uncharacterised. Proteins in this family have two completely conserved residues (P and C) that may be functionally important. This domain covers the whole length of the protein in some sequences and is found C-terminal to

in a small group of proteobacterial proteins.
Helitron helicase-like domain (Helitron_helicase-like)
Type: Domain

This domain is found in Helitrons, widespread eukaryotic DNA transposons that have significantly contributed to genome variability and evolution, as they perform a distinctive, replicative rolling-circle mechanism, which often mobilizes adjacent genes . Helitron transposases contain a single-stranded DNA (ssDNA)-specific HUH endonuclease domain, with structural similarity to viral replication initiator (Rep) proteins . In many instances a protein-coding gene is disrupted by their insertion.
Protein of unknown function DUF4327 (DUF4327)
Type: Family

This family of bacterial proteins is functionally uncharacterised
Circadian oscillating protein COP23 (COP23)
Type: Family

This family includes the circadian oscillating protein COP23 from Cyanothece sp. (strain PCC 8801),

. The levels of this peripheral membrane protein display a circadian oscillation .
Domain of unknown function DUF4329 (DUF4329)
Type: Domain

This domain is functionally uncharacterised. It contains a single completely conserved residue D and a highly conserved HTH motif which may be functionally important.
Protein of unknown function DUF4330 (DUF4330)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family have a single completely conserved residue G that may be functionally important.
Cell morphogenesis protein C-terminal (Cell_Morphogen_C)
Type: Domain

This domain represents the conserved C-terminal region of proteins that are involved in cell morphogenesis .
Lipase, eukaryotic (Lipase_euk)
Type: Family

This entry represents a family of eukaryotic lipases, including gastric triacylglycerol lipase , lysosomal acid lipase and triacylglycerol lipase 1 .
Domain of unknown function DUF4376 (DUF4376)
Type: Domain

The function of this domain is unknown.
Domain of unknown function DUF4377 (DUF4377)
Type: Domain

The function of this domain is unknown.
Domain of unknown function DUF4378 (DUF4378)
Type: Domain

This domain is found in protein LONGIFOLIA 2. The function of this domain is not known.
Treble clef zinc finger domain (DUF4379)
Type: Domain

This domain is found in bacteria, eukaryotes and viruses, and is approximately 60 amino acids in length. It contains a CXXCXH motif and a CPXC motif. It is predicted to adopt a treble clef fold. Some members have the second probable zinc binding residue replaced by histidine.

The specific function of this domain is yet unknown.
Protein of unknown function DUF4380 (DUF4380)
Type: Family

This family of proteins is functionally uncharacterised. There are two completely conserved residues (G and E) that may be functionally important.
Protein of unknown function (DUF4381 (DUF4381)
Type: Family

This family of proteins is functionally uncharacterised.
RQC P-site tRNA stabilizing factor (RqcP)
Type: Family

This entry represents the RQC P-site tRNA stabilizing factor (RqcP) found mainly in bacteria. RqcP is a component of the ribosome quality control system, a ribosome-associated complex that mediates the extraction of incompletely synthesised nascent chains from stalled ribosomes and their subsequent degradation . RqcP is associated with the translocation-like movement of the peptidyl-tRNA from the A-site into the P-site . In Bacillus subtilis, polyalanine tailing is catalysed by the NEMF family protein RqcH, in cooperation with RqcP and both are necessary and sufficient for processivity .
Domain of unknown function DUF4382 (DUF4382)
Type: Domain

The function of this domain is unknown.
Domain of unknown function DUF4384 (DUF4384)
Type: Domain

This presumed domain is functionally uncharacterised.
Protein of unknown function DUF4385 (DUF4385)
Type: Family

This family of proteins is functionally uncharacterised.
Protein of unknown function DUF4386 (DUF4386)
Type: Family

This family of proteins is functionally uncharacterised.
Protein of unknown function DUF4387 (DUF4387)
Type: Domain

This domain is functionally uncharacterised. There is a conserved RSKN sequence motif.
PatA-like, N-terminal (PatA-like_N)
Type: Domain

This entry represents the N-terminal domain of Protein PatA from Nostoc sp. and similar bacterial proteins. PatA controls heterocyst pattern formation. It is required for the differentiation of intercalary heterocysts but not for terminal heterocysts . This domain was previously known as DUF4388.
Protein of unknown function DUF4389 (DUF4389)
Type: Family

This family of proteins is functionally uncharacterised. There is a single completely conserved residue R that may be functionally important.
Pectin degradation protein KdgF (KdgF)
Type: Family

This entry represents pectin degradation protein KdgF, which may have a role in pathogenicity .
Protein of unknown function DUF4390 (DUF4390)
Type: Family

This family of proteins is functionally uncharacterised.
ATP binding protein MinD/FleN (MinD_FleN)
Type: Family

This entry represents an ATPase that includes both a MinD-type, and FleN-type.

MinD is a multifunctional cell division protein that guides correct placement of the septum. In Escherichia coli, the cell division site is determined by the cooperative activity of min operon products MinC, MinD, and MinE . MinD is a membrane-associated ATPase and is a septum site-determining factor through the activation and regulation of MinC and MinE. MinD is also known to undergo a rapid pole-to-pole oscillation movement in vivo as observed by fluorescent microscopy. In plants, chloroplast division requires the dimerisation of stromal MinD . Homologues can also be found in archaea, their exact role unknown.

FleN is involved in the maintenance of flagellar number in Pseudomonas aeruginosa

. It has been shown to be an anti-activator against FleQ, an important transcriptional regulator of flagellar genes

.
TldD (TldD)
Type: Family

The letD gene product of the F plasmid acts to inhibit partitioning of chromosomal DNA and cell division by inhibiting the DNA gyrase. TldD, together with TldE (also known as PmbA) and ZfiA, are host proteins that modulate the activity of the DNA Gyrase along with letD . It has been proposed that the zfiA gene product acts to inhibit interaction between the LetD protein and the A subunit of DNA gyrase, while the tldD and tldE gene products act to suppress the inhibitory activity of the zfiA.
Protein of unknown function DUF4391 (DUF4391)
Type: Family

This family of proteins is functionally uncharacterised.
D-glutamate cyclase-like, C-terminal (GLUCM_C)
Type: Domain

This entry represents the C-terminal domain found in mitochondrial D-glutamate cyclase (

), which converts D-glutamate to 5-oxo-D-proline . There are two completely conserved G residues that may be functionally important. This domain is also found in numerous uncharacterised proteins from bacteria.
FHIPEP conserved site (FHIPEP_CS)
Type: Conserved_site

A number of bacterial proteins seem to be involved in translocating specific proteins across the bacterial cell membrane by a distinct secretory mechanism that does not require the cleavage of a signal peptide. They belong to the FHIPEP family, which stands for Flagella/Hr/Invasion Proteins Export Pore .

The N-terminal half of these proteins is highly conserved and seems to contain 6 to 8 transmembrane domains. The C-terminal half is less conserved and seemingly devoid of transmembrane domains. It is possible that these proteins serve as pores for the export of specific proteins. This entry represents a highly conserved hydrophilic region between two transmembranes regions.
Abortive infection alpha (Abi_alpha)
Type: Family

Enterococci such as Enterococcus faecalis and Enterococcus faecium are part of the normal human gut microbiota. However they can also be a source of nosocomial infections specially in immunocompromised patients. Virulent bacteriophages, i.e., viruses that infect and obligatorily lyse bacteria might provide alternative options for combating them. Yet, bacterial resistance to phage is taking place in similar fashion to antibiotic resistance. This might be, in part due to temperate phages that are stably associated with their host. They compete for their bacterial host, in addition to repressor-dependent immunity against similar phages, some phage express genes conferring resistance to infection by more or less unrelated phages. They can encode abortive infection (Abi) mechanisms that cause an interruption of invasive phage development and a premature death of the infected bacteria. For instance, E. faecalis V583 prophage 6 confers resistance to the virulent phage Idefix infection mainly due to Abi-alpha protein. This entry represents a protein family that corresponds to Abi-alpha protein sequences which is mostly found in bacterial prophages, arguing that it is essentially a temperate phage weapon to fight against other phages .
Domain of unknown function DUF4394 (DUF4394)
Type: Domain

The function of this domain is not known.
Domain of unknown function DUF4395 (DUF4395)
Type: Domain

This domain is functionally uncharacterised. There are two completely conserved C residues that may be functionally important.
Domain of unknown function DUF4396 (DUF4396)
Type: Domain

The function of this domain is not known.
Domain of unknown function DUF4397 (DUF4397)
Type: Domain

This presumed domain is functionally uncharacterised.
Domain of unknown function DUF4398 (DUF4398)
Type: Domain

This presumed domain is functionally uncharacterised.
Domain of unknown function DUF4399 (DUF4399)
Type: Domain

This presumed domain is functionally uncharacterised.
Domain of unknown function DUF4401 (DUF4401)
Type: Domain

The function of this domain is not known. There is a single completely conserved residue K that may be functionally important.
Protein of unknown function DUF4402 (DUF4402)
Type: Family

This family of proteins is functionally uncharacterised.
Protein of unknown function DUF4403 (DUF4403)
Type: Family

This family of proteins is functionally uncharacterised. There is a single completely conserved residue W that may be functionally important.
Protein of unknown function DUF4404 (DUF4404)
Type: Family

This family of proteins is functionally uncharacterised. There are two completely conserved residues (P and G) that may be functionally important.
Flavinylation-associated cytochrome domain (DUF4405)
Type: Domain

This domain is found in a group of uncharacterised prokaryotic proteins. Proteins in this group are thought to mediate flavinylation-associated electron transfer in the cytoplasmic membrane and constitute a novel class of cytochromes. There are two conserved histidines in this domain, which are predicted to bind to two haem cofactors .
Protein of unknown function DUF4406 (DUF4406)
Type: Family

This family of proteins is functionally uncharacterised.
Protein of unknown function DUF4407 (DUF4407)
Type: Family

This family of proteins has not been characterised. There is a single completely conserved residue R that may be functionally important.
Domain of unknown function DUF4408 (DUF4408)
Type: Domain

This domain of unknown function is found at the N-terminal of the pathogen-associated molecular patterns-induced protein A70 from Arabidopsis thaliana and other plant proteins.
Neprosin activation peptide (Neprosin_propep)
Type: Domain

Pitcher plants are insectivorous and secrete a digestive fluid into the pitcher. This fluid contains a mixture of enzymes, including peptidases. One of these is neprosin, characterised by the pitcher plant Nepenthes ventrata. Neprosin is a glutamic endopeptidase that preferentially cleaves peptide bonds on the C-terminal side of proline residues . In contrast to most proline-cleaving enzymes, it effectively degrades proteins of any size . The peptidase is secreted and is presumed to possess an N-terminal activation peptide which is represented in this entry.
Protein of unknown function DUF4410 (DUF4410)
Type: Family

This family of proteins is functionally uncharacterised.
Domain of unknown function DUF4412 (DUF4412)
Type: Domain

This presumed domain is functionally uncharacterised.
hAT-like transposase, RNase-H fold (hAT-like_transposase_RNase-H)
Type: Domain

This domain is found as part of an RNase-H fold section in a number of hAT-like transposases, such as protein DAYSLEEPER (At3g42170) from Arabidopsis . Protein DAYSLEEPER is essential for plant development and can also regulate global gene expression . This entry also includes some uncharacterised fungal proteins.
DsrC-like domain superfamily (DsrC-like_dom_sf)
Type: Homologous_superfamily

The structure of DsrC, an archaeal homologue of the gamma subunit of dissimilatory sulphite reductase, consists of an orthogonal helical bundle with a β hairpin along one side .
HUWE1/REV1, ubiquitin-binding motif (HUWE1/Rev1_UBM)
Type: Conserved_site

This entry contains repetitive elements (RE) from a subgroup of HECT E3 ubiquitin ligases and the Y-family translesion polymerases, including human HUWE1 and REV1. Each of these repetitive elements are approximately 20 amino acids in length and contain two predicted helical segments separated by a Leu-Pro motif. The REs from the Y-family polymerases were shown to bind ubiquitin and were the basis for a novel ubiquitin-binding domain called the ubiquitin-binding motif (UBM) .
BrnA antitoxin of type II toxin-antitoxin system (BrnA_antitoxin)
Type: Family

BrnA is family of antitoxins that neutralises the toxin BrnT (

). It consists of 3 α-helices and a C-terminal ribbon-helix-helix DNA binding domain. As in other toxin-antitoxin systems, BrnA negatively autoregulates the brnTA operon and has higher affinity for the DNA operator when complexed with BrnT. It dimerises with two molecules of its toxin BrnT .
Protein of unknown function DUF4416 (DUF4416)
Type: Family

This family of proteins is functionally uncharacterised. There is a conserved DPG sequence motif that may be important for function.
Protein of unknown function DUF4417 (DUF4417)
Type: Family

This family of proteins is functionally uncharacterised. There is a single completely conserved glycine residue that may be functionally important.
Protein of unknown function DUF4418 (DUF4418)
Type: Family

This family of proteins is functionally uncharacterised.
Glucose-6-phosphate 1-epimerase (G6P_1-epimerase)
Type: Family

Glucose-6-phosphate 1-epimerase (

) has been shown to catalyse the interconversion between the alpha and beta anomers from at least three hexose 6-phosphate sugars (Glc6P, Gal6P, and Man6P) .
Protein of unknown function DUF4419 (DUF4419)
Type: Family

This family of proteins is functionally uncharacterised.
Putative PD-(D/E)XK family member (DUF4420) (DUF4420)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 310 and 334 amino acids in length. Advanced homology-detection methods supported with superfamily-wide domain architecture and horizontal gene transfer analyses have established this family to be a member of the PD-(D/E)XK superfamily .
Protein of unknown function DUF4421 (DUF4421)
Type: Family

This family of proteins is functionally uncharacterised.
Domain of unknown function DUF4422 (DUF4422)
Type: Domain

The function of this domain is not known.
Domain of unknown function DUF4423 (DUF4423)
Type: Domain

This presumed domain is functionally uncharacterised.
Domain of unknown function DUF4424 (DUF4424)
Type: Domain

This is a domain of unknown function is found in bacterial proteins.
YdgH protein (YdgH)
Type: Family

This family of uncharacterised proteins is found in Enterobacteria.
Fluoroacetyl-CoA thioesterase (FlK)
Type: Family

This family of fluoroacetyl-CoA thioesterases includes FlK from the fluoroacetate-producing Streptomyces cattleya. FlK selectively hydrolyses fluoroacetyl-CoA over acetyl-CoA. It has been suggested that FlK protects its host from fluoroacetate toxicity .
Propanediol/glycerol dehydratase, medium subunit (Ppandiol/glycerol_DHydtase_msu)
Type: Family

Diol dehydratase (

) and glycerol dehydratase (

) are two iso-functional enzymes that can each catalyse the conversion of 1,2-propanediol, 1,2-ethanediol and glycerol to the corresponding deoxy aldehydes (propionaldehyde, acetaldehyde and 3-hydroxypropionaldehyde, respectively). This reaction proceeds by a radical mechanism involving coenzyme B12 (adenosylcobalamin, AdoCbl) as an essential cofactor. Even though they catalyse the same reaction, these two enzymes (1) differ in their substrate preferences (diol dehydratase has a higher affinity for 1,2-propanediol and glycerol dehydratase for glycerol ); (2) they participate in different pathways (dihydroxyacetone [DHA] pathway for glycerol dehydratase and 1,2-propanediol degradation pathway for diol dehydratase); and (3) in those organisms where both enzymes are produced (such as Klebsiella and Citrobacter), the genes for them are independently regulated: glycerol dehydratase is induced when Klebsiella pneumoniae grows in glycerol-containing medium, whereas diol dehydratase is fully induced when it grows in propane-1,2-diol-containing medium, but only slightly in the glycerol medium .

Both diol dehydratase and glycerol dehydratase comprise three subunits: PduC/PduD/PduE or PddA/PddB/PddC for propanediol dehydratase, and GldA/Gld/B/GldC or DhaB/DhaC/DhaE for glycerol dehydratase.

This entry represents the medium subunit PduD/PddB/GldB/DhaC.
YacH protein (YacH)
Type: Family

The proteins in this family contain one UVR domain and are functionally uncharacterised. This family includes the YacH protein from Bacillus subtilis.
Dodecin-like (Dodecin-like)
Type: Homologous_superfamily

Dodecin flavoprotein is a small dodecameric flavin-binding protein from Halobacterium salinarium that contains two flavins stacked in a single binding pocket between two tryptophan residues to form an aromatic tetrade . This entry represents Dodecin and structurally related proteins, including the functionally uncharacterised proteins YdgH and YjfN.
YhzD-like protein (YhzD)
Type: Family

This family, named for the Bacillus subtilis YhzD protein, is functionally uncharacterised. Proteins in this family contain a conserved GKL sequence motif.
YozD-like protein (YozD)
Type: Family

The YozD-like protein family includes the B. subtilis YozD protein

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

The YqzH-like protein family includes the B. subtilis YqzH protein

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

The YtzH-like protein family includes the B. subtilis YtzH protein

, which is functionally uncharacterised. Proteins in this family are approximately 90 amino acids in length and contain a conserved DIL sequence motif.
YfkD-like protein (YfkD)
Type: Family

The YfkD-like protein family includes the B. subtilis YfkD protein

, which is functionally uncharacterised. Its expression is regulated by the sigma factor sigma-B, which regulates the expression of stress-response proteins, and by the forespore-specific sigma factor sigma-G .