SII-SWORD/CoKE huggingface dataset:
Pfam PF00765: Autoinducer synthase (family)
Bacterial species have many methods of controlling gene expression and cell growth. Regulation of gene expression in response to changes in cell density is termed quorum sensing . Quorum-sensing bacteria produce, release and respond to hormone-like molecules (autoinducers) that accumulate in the external environment as the cell population grows. Once a threshold of these molecules is reached, a signal transduction cascade is triggered that ultimately leads to behavioural changes in the bacterium . Autoinducers are thus clearly important mediators of molecular communication.

Conjugal transfer of Agrobacterium octopine-type Ti plasmids is activated by octopine, a metabolite released from plant tumours . Octopine causes conjugal donors to secrete a pheromone, Agrobacterium autoinducer (AAI), and exogenous AAI further stimulates conjugation. The putative AAI synthase and an AAI-responsive transcriptional regulator have been found to be encoded by the Ti plasmid traI and traR genes, respectively. TraR and TraI are similar to the LuxR and LuxI regulatory proteins of Vibrio fischeri, and AAI is similar in structure to the diffusable V. fischeri autoinducer, the inducing ligand of LuxR. TraR activates target genes in the presence of AAI and also activates traR and traI themselves, creating two positive-feedback loops. TraR-AAI-mediated activation in wild-type Agrobacterium strains is enhanced by culturing on solid media, suggesting a possible role in cell density sensing .

Production of light by the marine bacterium V. fischeri and by recombinant hosts containing cloned lux genes is controlled by the density of the culture . Density-dependent regulation of lux gene expression has been shown to require a locus consisting of the luxR and luxI genes.

In these and other Gram-negative bacteria, N-(3-oxohexanoyl)-L-homoserine lactone (OHHL) acts as the autoinducer by binding to transcriptional regulatory proteins and activating them . OHHL and related molecules, such as N-butanoyl- (BHL), N-hexanoyl- (HHL) and N-oxododecanoyl- (PAI) homoserine lactones, are produced by a family of proteins that share a high level of sequence similarity.

Proteins which currently members of this family include:


 * luxI from V. fischeri.
 * ahyI and asaI from Aeromonas species, which synthesize BHL and whose targets are ahyR and asaR respectively.
 * carI from Erwinia carotovora. The target of OHHL is carR which activates genes involved in the biosynthesis of carbapenem antibiotics.
 * eagI from Enterobacter agglomerans. The target of OHHL is not yet known.
 * esaI from Erwinia stewartii.
 * expI from Erwinia carotovora.
 * lasI from Pseudomonas aeruginosa, which synthesizes PAI and whose target is lasR which activates the transcription of the elastase gene.
 * rhlI (or vsmI) from P. aeruginosa, which synthesizes BHL and HHL and whose target is rhlR.
 * swrI from Serratia liquefaciens, which synthesizes BHL.
 * yenI from Yersinia enterocolitica.
Pfam PF02582: RMND1/Sif2-Sif3/Mrx10, DUF155 (domain)
This entry represents a domain found in RMND1 from mammals, Sif2/Sif3 from fission yeasts and Rmd1/Rmd8/YDR282C (Mrx10) from budding yeasts. RMND1 and its yeast homologue, Mrx10, are mitochondrial proteins required for mitochondrial translation. Rmd1 and Rmd8 are cytoplasmic proteins required for sporulation.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF04935: Surfeit locus protein 6 (family)
The surfeit locus protein SURF-6 is shown to be a component of the  nucleolar matrix and has a strong binding capacity for nucleic acids.
Pfam PF14226: non-haem dioxygenase in morphine synthesis N-terminal (family)
This is the highly conserved N-terminal region of proteins with 2-oxoglutarate/Fe(II)-dependent dioxygenase activity.
Pfam PF13066: Protein of unknown function (DUF3929) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length.
Pfam PF22779: Shieldin complex subunit 2, second OB fold domain (domain)
This entry represents the second OB fold domain found in the middle of Shieldin complex subunit 2 (SHLD2, formerly known as FAM35A). SHLD2 is a component of the shieldin complex, which plays an important role in repair of DNA double-stranded breaks (DSBs). In some homologues, this domain has undergone changes and decay and have lost the barrel-like shape.
Pfam PF20685: Gamma-Tubulin ring complex non-core subunit mod21, C-terminal (domain)
GCP5-Mod21 is a non-core subunit of the larger gamma-tubulin ring complex that effects microtubule nucleation from both centrosomal and non-centrosomal sites. This subunit, unlike GCP2 and and GCP3 and others, is not essential for viability in the fission yeast, and may not be expressed in very high concentrations. Fission yeast can form a large gamma-Tubulin complex C similar to that found in higher eukaryotes and this complex is important for maintaining normal levels of microtubule nucleation in vivo. This entry represents the C-terminal domain of Mod21 from fission yeast. This domain may consist of an alpha-helical bundle.
Pfam PF20206: Tra1 HEAT repeat ring region (repeat)
This entry represents part of the Tra1 protein composed of alpha solenoid repeats that form a ring region.
Pfam PF03653: Uncharacterised protein family (UPF0093) (family)
This entry includes HemJ (P72793) from Synechocystis sp. (strain PCC 6803 / Kazusa). It is essential for protoporphyrinogen IX oxidase activity  and is functionally coupled with coproporphyrinogen III oxidase .
Pfam PF05215: Spiralin domain (domain)
This entry represents a repeated domain found in Spiralin proteins found in spiroplasma bacteria. Spiroplasmas are helically shaped pathogenic bacteria related to the mycoplasmas. The surface of spiroplasma bacteria is crowded with the membrane-anchored lipoprotein spiralin whose structure and function are unknown although its cellular function is thought to be a structural and mechanical one rather than a catalytic one.
Pfam PF18938: Atypical Rib domain (domain)
This entry contains atypical Rib (aRib) domains.  These are found in a variety of bacterial cell surface proteins. These proteins share a conserved motif with the Rib domain (YPDXXD). The structure of the aRib domain has been solved from two proteins, the SrpA adhesin and the GspB adhesin. In these proteins this domain has been termed the unique domain due to its lack of similarity to any other known structures at the time. The aRib domain from SrpA has been shown to mediate a dimer interaction. This family has been added to the E-set clan based on its similarity to the Rib domain, although it does not contain the Ig fold.
Pfam PF12956: Domain of Unknown Function with PDB structure (family)
Member PDB:3GF6 has statistically significant similarity  to TNF-like jelly roll fold may indicate an immunomodulatory function or a bioadhesion role
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF23972: Domain of unknown function (DUF7298) (domain)
This entry represents an uncharacterised phage domain.  In some members of the family this domain is found at the C-terminus of a longer protein which also contains [pfam:PF14594].
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF11373: Protein of unknown function (DUF3175) (family)
This family of proteins with unknown function appears to be restricted to Proteobacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF11696: Protein of unknown function (DUF3292) (family)
This eukaryotic family of proteins has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF24230: Phage zinc binding domain (domain)
This entry represents a conserved domain found in proteins from various bacteriophages, primarily infecting Mycobacterium and Gordonia species.  The domain is approximately 65-77 amino acids in length and contains highly conserved histidine and three cysteine residues in a CXH and CXXC motif that may form a zinc binding site.  The function of this domain is currently unknown. Structure prediction shows the domain has an unusual fold composed of two three stranded beta sheets that although adjacent are not hydrogen bonded together. There is an unusual side chain hydrogen bond between the threonine in the WXT motif in one sheet that bonds to the backbone of the other sheet. Overall the surface of the protein is highly negatively charged.
Pfam PF14969: Domain of unknown function (DUF4508) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 117 and 253 amino acids in length.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF08441: Integrin alpha Ig-like domain 1 (domain)
This domain is found in integrin alpha and integrin alpha precursors to the C terminus of a number of [pfam:PF01839] repeats and to the N-terminus of the [pfam:PF00357] cytoplasmic region. This region is composed of an immunoglobulin-like domain.
Wikipedia: Integrins are transmembrane receptors that help cell–cell and cell–extracellular matrix (ECM) adhesion. Upon ligand binding, integrins activate signal transduction pathways that mediate cellular signals such as regulation of the cell cycle, organization of the intracellular cytoskeleton, and movement of new receptors to the cell membrane. The presence of integrins allows rapid and flexible responses to events at the cell surface.
Pfam PF14641: Helix-turn-helix DNA-binding domain of SPT6 (domain)
This helix-turn-helix represents the first of two DNA-binding domains on the SPT6 proteins.
Pfam PF17803: Bacterial cadherin-like domain (domain)
This entry contains numerous bacterial cadherin-like domains found in extracelullar proteins.
Pfam PF01853: MOZ/SAS family (family)
This region of these proteins has been suggested to be homologous to acetyltransferases.
Pfam PF07651: ANTH domain (repeat)
AP180 is an endocytotic accessory proteins that has been implicated in the formation of clathrin-coated pits.       The domain is involved in phosphatidylinositol 4,5-bisphosphate binding and is a universal adaptor for nucleation of clathrin coats.
Wikipedia: The ANTH domain is a membrane binding domain that shows weak specificity for PtdIns(4,5)P2. It was found in AP180 endocytotic accessory protein that has been implicated in the formation of clathrin-coated pits. The domain is involved in phosphatidylinositol 4,5-bisphosphate binding and is a universal adaptor for nucleation of clathrin coats.
Pfam PF08696: DNA replication factor Dna2 (family)
Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, ( 5'-flap endonuclease) and helicase activities.  It is required for Okazaki fragment processing and is involved in DNA repair pathways.
Pfam PF05478: Prominin (family)
The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration.
Pfam PF09667: Domain of unknown function (DUF2028) (family)
This region of similarity is found in the vertebrate homologues of the drosophila Bobby Sox.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF02165: Wilm's tumour protein (family)
Wilm's tumour (WT) is an embryonal malignancy of the kidney, affecting around 1 in 10,000 infants. It occurs in both sporadic and hereditary forms. Inactivation of WT1 is one of the causes of Wilm's tumour. Defects in the WT1 gene are also associated with Denys-Drash Syndrome (DDS), which is characterised by typical nephropathy and genital abnormalities. The WT1 gene product shows similarity to the zinc fingers of the mammalian growth regulated EGR1 and EGR2 proteins .
Wikipedia: Wilms tumor protein (WT33) is a protein that in humans is encoded by the WT1 gene on chromosome 11p.
Pfam PF17187: Svf1-like C-terminal lipocalin-like domain (domain)
Family of proteins that are involved in survival during oxidative stress. This entry corresponds to the the C-terminal domain of a pair of lipocalin domains.
Pfam PF19496: Family of unknown function (DUF6031) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000919) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). This family  includes a protein from the phaseolotoxin biosynthetic gene cluster  from Pseudomonas syringae and appears to be predominantly found in  bacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF16286: Domain of unknown function (DUF4932) (family)
This family consists of uncharacterized proteins around 460 residues in length and is mainly found in various Bacteroides species, such as Bacteroides fragilis, Bacteroides sp. and so on. Several members are annotated as putative metalloproteases, but the specific function of this family is unknown.
Pfam PF03124: EXS family (family)
We have named this region the EXS family after (ERD1, XPR1, and SYG1). This family includes C-terminus portions from the SYG1 G-protein associated signal transduction protein from Saccharomyces cerevisiae, and sequences that are thought to be murine leukaemia virus (MLV)  receptors (XPR1). N-terminus portions from these proteins are aligned in the SPX [pfam:PF03105] family. The previously noted similarity between SYG1 and MLV receptors over their whole sequences is thus borne out in [pfam:PF03105] and this family. While the N-termini aligned in [pfam:PF03105] are thought to be involved in signal transduction, the role of the C-terminus sequences aligned in this family is not known. This region of similarity contains several predicted transmembrane helices. This family also includes the ERD1 (ERD: ER retention  defective) yeast proteins [swissprot:P16151].  ERD1 proteins are involved in the localisation of endogenous endoplasmic reticulum (ER) proteins. erd1 null mutants secrete such proteins even though they possess the C-terminal HDEL ER lumen localisation label sequence. In addition, null mutants also exhibit defects in the Golgi-dependent processing of several glycoproteins, which led to the suggestion that the sorting of luminal ER proteins actually occurs in the Golgi, with subsequent return of these proteins to the ER via  `salvage' vesicles.
Pfam PF01955: Adenosylcobinamide amidohydrolase (family)
This prokaryotic protein family includes CbiZ which converts adenosylcobinamide (AdoCbi) to adenosylcobyric acid (AdoCby), an intermediate of the de novo coenzyme B12 biosynthetic route.
Wikipedia: Cobalamin biosynthesis is the process by which bacteria and archea make cobalamin, vitamin B12. Many steps are involved in converting aminolevulinic acid via uroporphyrinogen III and adenosylcobyric acid to the final forms in which it is used by enzymes in both the producing organisms and other species, including humans who acquire it through their diet.
Pfam PF09646: Gp37 protein (domain)
This protein of 154 residues consists of a unit of helices and beta sheets that crystallises into a beautiful asymmetrical dodecameric barrel-structure, of two six-membered rings one on top of the other. It is expressed in bacteria but is of viral origin as it is found in phage BcepMu and is probably a pathogenesis factor.
Pfam PF01580: FtsK/SpoIIIE family (domain)
FtsK has extensive sequence similarity to wide variety of proteins from prokaryotes and plasmids, termed the FtsK/SpoIIIE family.  This domain contains a putative ATP binding P-loop motif. It is found in the FtsK cell division protein from E. coli [swissprot:P46889] and the stage III sporulation protein E SpoIIIE [swissprot:P21458] which has roles in regulation of prespore specific gene expression in B. subtilis. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer.
Pfam PF00689: Cation transporting ATPase, C-terminus (family)
Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport. This family represents 5 transmembrane helices.
Wikipedia: The P-type ATPases, also known as E1-E2 ATPases, are a large group of evolutionarily related ion and lipid pumps that are found in bacteria, archaea, and eukaryotes. P-type ATPases are α-helical bundle primary transporters named based upon their ability to catalyze auto- (or self-) phosphorylation (hence P) of a key conserved aspartate residue within the pump and their energy source, adenosine triphosphate (ATP). In addition, they all appear to interconvert between at least two different conformations, denoted by E1 and E2. P-type ATPases fall under the P-type ATPase (P-ATPase) Superfamily (TC# 3.A.3) which, as of early 2016, includes 20 different protein families.
Pfam PF03549: Translocated intimin receptor (Tir) intimin-binding domain (domain)
Intimin and its translocated intimin receptor (Tir) are bacterial proteins that mediate adhesion between mammalian cells and attaching and effacing (A/E) pathogens. A unique and essential feature of A/E bacterial pathogens is the formation of actin-rich pedestals beneath the intimately adherent bacteria and localised destruction of the intestinal brush border. The bacterial outer membrane adhesin, intimin, is necessary for the production of the A/E lesion and diarrhoea. The A/E bacteria translocate their own receptor for intimin, Tir, into the membrane of mammalian cells using the type III secretion system. The translocated Tir triggers additional host signalling events and actin nucleation, which are essential for lesion formation. This family represents the Tir intimin-binding domain (Tir IBD) which is needed to bind intimin and support the predicted topology for Tir, with both N- and C-terminal regions in the mammalian cell cytosol.
Pfam PF18133: Hydrogen maturase F tetramerization domain (domain)
This is the C-terminal domain found in Hydrogen maturase F (HydF) present in Thermotoga neapolitana. HydF is a GTPase, containing an FeS cluster-binding motif, that is able to are able to activate HydA produced so that HydA can drive the reversible reduction of protons to molecular H2. This domain is known as domain III, and is primarily responsible for homotetramer formation. Interactions between the two FeS cluster-binding domains worth noting are the interactions between beta-2 strands, the initial part of the long loop that connects strand beta-2 to strand beta-3, and the loop that connects strand beta-1 to helix alpha-3. There are three highly conserved cysteine residues (Cys-302, Cys-353, and Cys-356) that represent the FeS cluster-binding site which form a superficial pocket.
Pfam PF02378: Phosphotransferase system, EIIC (family)
The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The sugar-specific permease of the PTS consists of three domains (IIA, IIB and IIC). The IIC domain catalyses the transfer of a phosphoryl group from IIB to the sugar substrate.
Wikipedia: The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The PTS catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred to enzyme-I (EI) of PTS which in turn transfers it to a phosphoryl carrier protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease which consists of at least three structurally distinct domains which can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The IIC domain catalyzes the transfer of a phosphoryl group from IIB to the sugar substrate.
Pfam PF03020: LEM domain (domain)
The LEM domain is 50 residues long and is composed of two parallel alpha helices.  This domain is found in inner nuclear membrane proteins. It is called the LEM domain after LAP2 [swissprot:Q62733], Emerin [swissprot:P50402] and Man1.
Pfam PF21756: Probable sensor domain DacZ_T (domain)
This is a probable sensor domain found at the N-terminal of archaeal diadenylate cyclases, which are typically followed by the DAC ([pfam:PF02457]) domain. It is distantly related to PK_C ([pfam:PF02887]) and DacZ_N ([pfam:PF19294]).