SII-SWORD/CoKE huggingface dataset:
Pfam PF24299: Domain of unknown function (DUF7483) (repeat)
This entry includes uncharacterised bacterial sequences that may adopt a novel fold consisting on three repeat units, each of them are type of beta-sandwich with three beta-strands on one side and four or five on the other.
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 PF23430: Family of unknown function (DUF7117) (family)
This family represents a group of proteins from halobacteria. It has several conserved motifs WSYY, RxYxR and HxK/RR. Members are predicted to show a predominantly alpha configuration.
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 PF11466: Prion-like protein Doppel (domain)
Dpl is a homologue related to the prion protein (PrP). Dpl is toxic to neurons and is expressed in the brains of mice that do not express PrP. In DHPC and SDS micelles, Dpl shoes about 40% alpha-helical structure however in aqueous solution it consists of a random coil. The alpha helical segment can adopt a transmembrane localisation also in a membrane. The unprocessed Dpl protein is thought to posses a possible channel formation mechanism which may be related to toxicity through direct interaction with cell membranes and damage to the cell membrane. It is suggested that the peptide is neither in an entirely random coil nor in a completely alpha-helical conformation, possible continuously interchanging between the two conformations.
Pfam PF00404: Dockerin type I domain (domain)
The dockerin repeat is the binding partner of the cohesin domain [pfam:PF00963]. The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome. The dockerin repeats, each bearing homology to the EF-hand calcium-binding loop bind calcium. This family contains two copies of the repeat.
Wikipedia: Dockerin is a protein domain found in the cellulosome cellular structure of anaerobic bacteria. It is found on many endoglucanase enzymes. The dockerin's binding partner is the cohesin domain, located on the scaffoldin protein. This interaction between the dockerin domains of the enzyme constituents of the cellulosome and the cohesin domains of the scaffoldin protein is essential to the construction of the cellulosome complex. The Dockerin domain has two in-tandem repeats of a non-EF hand calcium binding motif. Each motif is characterized by a loop-helix structure. The three-dimensional structure of dockerin has been determined in solution, as well as in complex with Cohesin.
Pfam PF23161: Double HTH domain (domain)
This entry represents a double HTH domain found in a set of largely bacterial ribonuclease II domain proteins.
Pfam PF05782: Extracellular matrix protein 1 (ECM1) (family)
This family consists of several eukaryotic extracellular matrix protein 1 (ECM1) sequences. ECM1 has been shown to regulate endochondral bone formation, stimulate the proliferation of endothelial cells and induce angiogenesis. Mutations in the ECM1 gene can cause lipoid proteinosis, a disorder which causes generalised thickening of skin, mucosae and certain viscera. Classical features include beaded eyelid papules and laryngeal infiltration leading to hoarseness.
Pfam PF23596: Domain of unknown function (DUF7138) (domain)
This domain is found in uncharacterised proteins mainly from plants. It has sequence similarity to PB1 domain and it is predicted to adopt similar structure with typical ubiquitin-like topology.
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 PF07250: Glyoxal oxidase N-terminus (repeat)
This family represents the N-terminus (approximately 300 residues) of a number of plant and fungal glyoxal oxidase enzymes. Glyoxal oxidase catalyses the oxidation of aldehydes to carboxylic acids, coupled with reduction of dioxygen to hydrogen peroxide. It is an essential component of the extracellular lignin degradation pathways of the wood-rot fungus Phanerochaete chrysosporium.
Pfam PF12227: Protein of unknown function (DUF3603) (family)
This protein is found in bacteria and eukaryotes. Proteins in this family are about 250 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 PF06300: Tsp45I type II restriction enzyme (family)
This family consists of several type II restriction enzymes.
Pfam PF15133: TLR adaptor interacting with SLC15A4 on the lysosome (family)
In humans, TASL (TLR adaptor interacting with SLC15A4 on the lysosome) is encoded by CXorf21 that is associated with systemic lupus erythematosus. It is an immune adaptor that is required for recruitment and activation of IRF5 by TLR7, TLR8 and TLR9, in mechanistic analogy to IRF3 and its three adaptors STING, MAVS and TRIF. TASL interacts with the endolysosomal transporter SLC15A4 forming the SLC15A4-TASL complex, which is required for endolysosomal TLR signalling. TASL contains a pLxIS motif that is important for its function.
Pfam PF06664: Wntless-like, transmembrane domain (domain)
This entry represents the seven transmembrane domain of wntless (WLS) from Drosophila and its homologues, also known as MIG-14 in C.elegans which regulates endocytosis and secretion of the wnt ligand egl-20. Newly synthesised EGL-20/Wnt binds to MIG-14 in the Golgi, targetting the Wnt to the cell membrane for secretion. AP-2-mediated endocytosis and retromer retrieval at the sorting endosome would recycle MIG-14 to the Golgi, where it can bind to EGL-20/Wnt for next cycle of secretion. WLS is a membrane trafficking and secretion chaperone for lipidated Wnt signaling proteins. It regulates Wnt proteins sorting and secretion in a feedback regulatory mechanism. This entry also includes TMEM181, a cell surface protein associated with Escherichia coli CDT toxicity. Members of this entry are homologous to GPR180 and TMEM145, and together with TMEM87A/B, GPR107 and GPR108, they have been described as GOLD domain seven-transmembrane helix (GOST) proteins given their domain architecture similarities. They all consist of a GOLD domain atop of a seven-transmembrane helix domain.
Pfam PF18419: ATP-grasp-like domain (domain)
Glutathione biosynthesis is achieved in most organisms via a conserved two-step approach relying on the capacity of two independent and unrelated ligases to perform peptide synthesis coupled to ATP hydrolysis. In a first and rate-limiting step, gamma-glutamylcysteine ligase (gamma-ECL) (or GshA; [ec:6.3.2.2]) uses l-glutamate and l-cysteine to form gamma-glutamylcysteine (gamma-EC), which, in a second step, is condensed with glycine to glutathione by glutathione synthetase (GS) (or GshB; [ec:6.3.2.3]). However, several pathogenic and free-living bacteria carry out glutathione biosynthesis based on a single enzyme that catalyzes both the gamma-ECL and the GS reactions. Such bifunctional glutathione-synthesizing enzymes have been termed gamma-GCS-GS or GshF. Hybrid GshF contains a typical gamma-proteobacterial gamma-ECL fused to an ATP-grasp-like domain. The ATP-grasp-like module is responsible for the ensuing formation of glutathione from gamma-glutamylcysteine and glycine. The ATP-grasp-like domain has an antiparallel beta-sheet in the GshF structures in contrast to all structurally characterized members of the ATP-grasp superfamily.
Pfam PF24240: Domain of unknown function (DUF7448) (domain)
This entry represents a conserved viral protein domain of unknown function (DUF4241). The domain is approximately 130-160 amino acids in length and is found in various bacteriophages and large DNA viruses.  The alignment shows several conserved residues, including a highly conserved DCC motif. The protein contains a beta sandwich domain structural.
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 PF03831: PhnA domain (domain)
This entry represents the C-terminal domain of YjdM. YjdM is not involved in phosphonate metabolism .
Pfam PF15024: Glycosyltransferase family 18 (family)
Enzymes belonging to glycosyltransferase family 18 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase) contribute to the creation of branches in complex-type N-glycans. This domain is responsible for the catalytic activity of the enzyme.
Pfam PF20013: GTPase-associated protein 1, N-terminal domain type 2 (domain)
One of two types of domain found at the N-terminus of the GTPase-associated protein 1 (GAP1) of the GTPase-centric ternary systems, a class of NTP-dependent biological conflict systems. This domain is predicted to mediate effector-GAP1 interactions.
Pfam PF24402: Inactive HKD-Rease (domain)
This entry represents an inactive HKD-REase domain typically fused to the ParB-CE domain and predicted to be involved in conflict.
Pfam PF16636: Unstructured region on APC between APC_crr regions 5 and 6 (disordered)
APC_u15 is a short region of natively unstructured sequence lying between the fifth and sixth creatine-rich, APC_crr, [pfam:PF05923], domains on APC or adenomatous polyposis coli proteins in higher eukaryotes. The function is not known.
Pfam PF07668: M penetrans paralogue family 1 (family)
This family of paralogous proteins identified in Mycoplasma penetrans includes homologues of p35.
Pfam PF15208: Rab15 effector (family)
This family of proteins has a role in receptor recycling from the endocytic recycling compartment.
Pfam PF17367: NiFe-hydrogenase-type-3 Eha complex subunit A (family)
Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. Energy-converting [NiFe] hydrogenases function as ion pumps, catalyzing the reduction of ferredoxin with H2 driven by the proton-motive force or the sodium-ion-motive force. Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA, EhaB, EhaC, EhaD, EhaE, EhaF, EhaG, EhaI, EhaK, EhaL) and four hydrophobic subunits (EhaM, EhaR, EhS, EhT). Eha and Ehb catalyse the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases. Based on sequence similarity and genome context analysis, other organisms such as Methanopyrus kandleri, Methanocaldococcus jannaschii, and Methanothermobacter marburgensis also encode Eha-like [NiFe]-hydrogenase-3-type complexes and have very similar eha operon structure. This domain family can be found on the small membrane proteins that are predicted to be the EhaA trans-membrane subunits of multisubunit membrane-bound [NiFe]-hydrogenase Eha complexes.
Pfam PF21621: Mannose-6-phosphate isomerase, cupin domain (domain)
This domain is found in Mannose-6-phosphate isomerase from Archaeoglobus fulgidus (MPI) and similar bacterial sequences. This enzyme catalyses the interconversion of mannose 6-phosphate and fructose 6-phosphate. This entry represents the C-terminal domain, which is found associated with PFam:PF20511. This domain shows an all-beta structure.
Pfam PF07546: EMI domain (domain)
The Pfam alignment is truncated at the C-terminus and does not include the final cysteine defined in Callebaut et al. This is to stop the family overlapping with other domains.
Wikipedia: In molecular biology, the EMI domain, first named after its presence in proteins of the EMILIN family, is a small cysteine-rich protein domain of around 75 amino acids. The EMI domain is most often found at the N terminus of metazoan extracellular proteins that are forming or are compatible with multimer formation. It is found in association with other domains, such as C1q, laminin-type EGF-like, collagen-like, FN3, WAP, ZP or FAS1. It has been suggested that the EMI domain could be a protein-protein interaction module, as the EMI domain of EMILIN-1 was found to interact with the C1q domain of EMILIN-2.
Pfam PF03804: Viral proteins of unknown function (family)
This is a family of uncharacterised proteins from Alphabaculovirus.
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 PF10451: Telomere regulation protein Stn1 (domain)
The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA.  Structural profiling has predicted an OB-fold. This domain is the N-terminal part of the molecule, which adopts the OB fold. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution.
Pfam PF11649: Virus neck protein (family)
This family of protein represents gene product 14, a major component of the neck in T4-like viruses along with gene product 13. Gene product 14 is rich is beta-sheets. The formation of the neck to the head of the bacteriophage is crucial for the tail attachment.
Pfam PF08994: T4 gene Gp59 loader of gp41 DNA helicase C-term (domain)
Bacteriophage T4 gene-59 helicase assembly protein is required for recombination-dependent DNA replication, which is the predominant mode of DNA replication in the late stage of T4 infection. T4 gene-59 helicase assembly protein accelerates the loading of the T4 gene-41 helicase during DNA synthesis by the T4 replication system in vitro.  T4 gene-59 helicase assembly protein binds to both T4 gene-41 helicase and T4 gene-32 single-stranded DNA binding protein, and to single and double-stranded DNA. The structure of T4 gene-59 helicase assembly protein reveals a novel alpha-helical bundle fold with two domains of similar size, this being the C-terminal domain that consists of seven alpha-helices with short intervening loops and turns. The surface of the domain contains large regions of exposed hydrophobic residues and clusters of acidic and basic residues. The hydrophobic region on the 'bottom' surface of the domain near the C-terminal helix binds the leading strand DNA, whilst the hydrophobic region on the 'top' surface of the domain lies between the two arms of the fork DNA, allowing for T4 gene 41 helicase binding and assembly into a hexameric complex around the lagging strand.
Pfam PF15922: YjeJ-like (family)
YjeJ is a family of bacterial proteins. The domains and proteins in this family vary in length from 283 to 284 amino acids. The function is not yet known. All proteins are Gammaproteobacteria.
Pfam PF11684: Protein of unknown function (DUF2380) (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 PF09085: Adhesion molecule, immunoglobulin-like (domain)
Members of this family are found in a set of mucosal cellular adhesion proteins and adopt an immunoglobulin-like beta-sandwich structure, with seven strands arranged in two beta-sheets in a Greek-key topology. They are essential for recruitment of lymphocytes to specific tissues.
Wikipedia: In molecular biology, the adhesin molecule (immunoglobulin-like) is a protein domain. This domain is found in mucosal vascular addressin cell adhesion molecule 1 proteins (MAdCAM-1). These are cell adhesion molecules expressed on the endothelium in mucosa that guide the specific homing of lymphocytes into mucosal tissues. MAdCAM-1 belongs to a subclass of the immunoglobulin superfamily (IgSF), the members of which are ligands for integrins. The crystal structure of this domain has been reported; it adopts an immunoglobulin-like beta-sandwich structure, with seven strands arranged in two beta-sheets in a Greek-key topology.
Pfam PF04877: HrpZ (family)
HrpZ from the plant pathogen Pseudomonas syringae binds to lipid bilayers and forms a cation-conducting pore in vivo.  This pore-forming activity may allow nutrient release or delivery of virulence factors during bacterial colonisation of host plants. The family of hairpinN proteins, Harpin, has been merged into this family. HrpN is a virulence determinant which elicits lesion formation in Arabidopsis and tobacco and triggers systemic resistance in Arabidopsis.
Pfam PF08051: Erythromycin resistance leader peptide (family)
This family consists of erythromycin resistance gene leader peptides.  These leader peptides are involved in the translational attenuation of erythromycin resistance genes. Interestingly, the consensus sequence of peptides conferring erythromycin resistance is similar to that of the leader peptides, thus indicating that a similar type of interaction between the nascent peptide and antibiotics can occur in both cases. This family also includes a small number of regions from within larger proteins from actinomycetes.
Pfam PF17755: UvrA DNA-binding domain (domain)
This is the DNA-binding domain found in the UvrABC system protein A.
In Eubacteria and some Archaea, the first steps in nucleotide excision repair are carried out by the coordinated action of the UvrA, UvrB, and UvrC proteins. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB Î²-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage .
Pfam PF22531: Family of unknown function (DUF7002) (family)
This is a family of uncharacterised bacterial proteins. They share sequence similarity with DarT toxin and are likely to adopt the same structure.
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 PF01769: Divalent cation transporter (family)
This region is the integral membrane part of the eubacterial MgtE family of magnesium transporters. Related regions are found also in archaebacterial and eukaryotic proteins. All the archaebacterial and eukaryotic examples have two copies of the region. This suggests that the eubacterial examples may act as dimers. Members of this family probably transport Mg2+ or other divalent cations into the cell. The alignment contains two highly conserved aspartates that may be involved in cation binding (Bateman A unpubl.)
Pfam PF02467: Transcription factor WhiB (family)
WhiB is a putative transcription factor in Actinobacteria, required for differentiation and sporulation.
Pfam PF02048: Heat-stable enterotoxin ST (family)
This family consists of the heat stable enterotoxin ST from Escherichia coli. ST is a small peptide of 18 or 19 amino acid residues produced by enterotoxigenic E. coli and is one of the causes of acute diarrhoea in infants and travellers in developing countries. ST triggers a biological response by binding to a membrane-associated guanylyl cyclase C which is located on intestinal epithelial cell membranes.
Wikipedia: Heat-stable enterotoxins (STs) are secretory peptides produced by some bacterial strains, such as enterotoxigenic Escherichia coli which are in general toxic to animals.
Pfam PF19480: Domain of unknown function (DUF6016) (domain)
This presumed domain is related to proteins in the Cupin superfamily. These proteins contain 1 or 2 copies of the domain. This family of proteins is found in Proteobacteria and Bacteroidetes. Proteins in this family are typically between 132 and 162 amino acids in length.
Wikipedia: The cupin superfamily is a diverse superfamily of proteins named after its conserved barrel domain. The superfamily includes a wide variety of enzymes as well as non-enzymatic seed storage proteins.
Pfam PF19098: Family of unknown function (DUF5785) (family)
Family of unknown function predominantly found in Halobacteria.
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 PF00603: Influenza RNA-dependent RNA polymerase subunit PA (family)
This entry includes the polymerase acidic (PA) protein and PA-X protein from Influenza. PA plays an essential role in viral RNA transcription and replication by forming the heterotrimeric polymerase complex together with PB1 and PB2 subunits .