SII-SWORD/CoKE huggingface dataset:
Pfam PF22899: SMCHD1, ribosomal S5 domain 2-like domain (domain)
This domain is found in the homologues of human SMCHD1 protein. SMCHD1 is an epigenetic repressor that may participate in structural manipulation of chromatin in an ATP-dependent manner as a part of its role in gene expression regulation. This domain follows the SMCHD1 ATPase module and adopts a globular alpha/beta structure consisting of five-stranded mixed beta-sheet with alpha helices packed on both sides. This domain is involved in dimerisation.
Pfam PF17584: Bacillus competence protein S (family)
ComS is crucial for competence development as it prevents proteolytic degradation of ComK, the key transcriptional activator of all genes required for the uptake and integration of DNA. This family includes members of the Bacillus comS proteins such as [swissprot:P80355].
Pfam PF11453: Protein of unknown function (DUF2950) (family)
This is a bacterial family of uncharacterised proteins.
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 PF18315: Integron cassette protein VCH_CASS1 chain (domain)
This domain is a chain that forms part of the integron cassette protein VCH_CASS14 present in Vibrio cholerae. In each monomer lies a deep binding pocket for small molecule substrates formed by helices alpha-1 and alpha-2 and residues from the central four strands of the beta-sheet. The pocket is extensively lined with hydrophobic side chains.
Pfam PF14948: RESP18 domain (family)
This domain is found in the glucocorticoid-responsive protein regulated endocrine-specific protein 18 (RESP18) and in the N-terminal extracellular region of receptor-type tyrosine-protein phosphatases containing the protein-tyrosine phosphatase receptor IA-2 domain ([pfam:PF11548]).
Pfam PF15049: Protein of unknown function (DUF4534) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in mammals. Proteins in this family are typically between 170 and 190 amino acids in length. The protein includes the human integral membrane TMEM217 protein.
Pfam PF24359: Domain of unknown function (DUF7515) (domain)
This domain is found in a group of uncharacterised metazoan proteins. It has a detectable sequence similarity to HTH winged helix domains and it is predicted to adopt similar 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 PF23200: Domain of unknown function (DUF7061) (domain)
This entry represents a domain found towards the N-terminal of a group of proteins from nematodes such as Trichuris suis and Trichinella britovi, members of the BPI/LBP/Plunc family of proteins which share homology with cholesterol ester transfer protein (CETP) and phospholipid transfer protein (PLTP). The exact function of these proteins is unknown, however, according to their structure predictions and homology to CEPT/PLTP, they may be involved in lipid binding.
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 PF22139: DNA repair helicase XPD, arch domain (domain)
This domain is found in DNA repair helicase XPD from Sulfurisphaera tokodaii ([swissprot:Q971R4]) and similar archaeal proteins. XPD, which functions as a 5'-3' DNA helicase, shows three major domains. This entry represents the central domain, called Arch domain, which folds into a mixed alpha/beta topology with a four-stranded antiparallel beta-sheet and four alpha -helices. The other two canonical motor domains are represented by [pfam:PF06733] at the N-terminal end and [pfam:PF13307] at the C-terminal end.
Pfam PF19840: Family of unknown function (DUF6317) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001740) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the phthoxazolin biosynthetic gene cluster from Streptomyces avermitilis.
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 PF10640: mRNA capping enzyme catalytic subunit, RNA triphosphatase domain (domain)
mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the methylation of the GpppN cap. It consists of an N-terminal RNA triphosphatase (TPase)-guanylyltransferase (GTase) module, and a C-terminal guanine-N7-methyltransferase (MTase) module ([pfam:PF03291]). The N-terminal module comprises a TPase domain, represented in this entry, followed by the GTase at the C-terminal, which consists of the nucleotidyltransferase (NTPase, [pfam:PF21004]) and OB fold ([pfam:PF21005]) domains. This domain catalyses the hydrolysis of the the 5' triphosphate end of the pre-mRNA.
Pfam PF01755: Glycosyltransferase family 25 (LPS biosynthesis protein) (family)
Members of this family belong to Glycosyltransferase family 25 This is a family of glycosyltransferases involved in lipopolysaccharide (LPS) biosynthesis. These enzymes catalyse the transfer of various sugars onto the growing LPS chain during its biosynthesis.
Pfam PF10543: ORF6N domain (domain)
This domain was identified by Iyer and colleagues.
Pfam PF21352: Thioredoxin 2, N-terminal (domain)
This entry represents the N-terminal domain of thioredoxin 2, which is a zinc finger domain, unusual in thioredoxin proteins. Thio2 reduces disulfide bonds and is an efficient electron donor for the essential enzyme ribonucleotide reductase. This domain may mediate protein-protein interactions.
Pfam PF12067: Sox 17/18 central domain (family)
This is the central region of eukaryotic SOX17 and 18 transcription factor proteins. It lies just downstream of the HMG-box family, [pfam:PF00505], and is followed by a C-terminal domain.
Wikipedia: SOX genes encode a family of transcription factors that bind to the minor groove in DNA, and belong to a super-family of genes characterized by a homologous sequence called the HMG-box. This HMG box is a DNA binding domain that is highly conserved throughout eukaryotic species. Homologues have been identified in insects, nematodes, amphibians, reptiles, birds and a range of mammals. However, HMG boxes can be very diverse in nature, with only a few amino acids being conserved between species.
Pfam PF09010: Anti-Sigma Factor A (domain)
Anti-sigma factor A is a transcriptional inhibitor that inhibits sigma 70-directed transcription by weakening its interaction with the core of the host's RNA polymerase. It is an all-helical protein, composed of six helical segments and intervening loops and turns, as well as a helix-turn-helix DNA binding motif, although neither free anti-sigma factor nor anti-sigma factor bound to sigma-70 has been shown to interact directly with DNA. In solution, the protein forms a symmetric dimer of small (10.59 kDa) protomers, which are composed of helix and coil regions and are devoid of beta-strand/sheet secondary structural elements.
Pfam PF12943: Protein of unknown function (DUF3839) (family)
This is a family of uncharacterised proteins that are found in Trichomonas.
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 PF06195: Protein of unknown function (DUF996) (family)
Family of uncharacterised bacterial and archaeal proteins.
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 PF09602: Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg) (family)
This entry describes a protein found in polyhydroxyalkanoic acid (PHA) gene regions and incorporated into PHA inclusions in Bacillus cereus and Bacillus megaterium. The role of the protein may include amino acid storage.
Pfam PF11771: Protein of unknown function (DUF3314) (family)
This small family contains human, mouse and fish members but the function is not known.
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 PF03450: CO dehydrogenase flavoprotein C-terminal domain (domain)
Proteins containing this domain form structural complexes with other known families, such as IPR008274 and IPR001041. The carbon monoxide (CO) dehydrogenase of Oligotropha carboxidovorans is a heterotrimeric complex composed of a apoflavoprotein, a molybdoprotein, and an iron-sulphur protein. It can be dissociated with sodium dodecylsulphate . CO dehydrogenase catalyses the oxidation of CO according to the following equation :CO + H2O = CO2 + 2e + 2H+

Subunit S represents the iron-sulphur protein of CO dehydrogenase and is clearly divided into a C- and an N-terminal domain, each binding a  cluster .
Pfam PF16791: Connexin 40 C-terminal domain (domain)
This is the C-terminal domain of connexin 40. It interacts with the C-terminal and cytoplasmic loop domains of connexin 43 and with the cytoplasmic loop pf connexin 40.
Pfam PF09767: Predicted membrane protein (DUF2053) (family)
This entry is of the conserved N-terminal 150 residues of proteins conserved from plants to humans. The function is unknown although some annotation suggests it to be a transmembrane protein.
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 PF02534: Type IV secretory system Conjugative DNA transfer (family)
These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation.  These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems.  The C-terminus of this domain interacts with the relaxosome component TraM via the latter's tetramerisation domain. TraD is a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore. The family contains a number of different DNA transfer proteins.
Pfam PF19637: Family of unknown function (DUF6140) (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.
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 PF25119: Heparan sulfate-N-deacetylase, N-terminal domain (domain)
This entry represents the N-terminal domain of Bifunctional heparan sulfate N-deacetylase/N-sulfotransferases, which is related to the N-terminal domain of Agd3 from A. fumigatus, a carbohydrate binding module (CBM), the founding member of CBM family 87.
Pfam PF16881: N-terminal domain of lipoyl synthase of Radical_SAM family (family)
LIAS_N is found as the N-terminal domain of the Radical_SAM family in the members that are lipoyl synthase enzymes, particularly the mitochondrial ones in metazoa but also those in bacteria.
Pfam PF08776: VASP tetramerisation domain (coiled_coil)
Vasodilator-stimulated phosphoprotein (VASP) is an actin cytoskeletal regulatory protein.  This region corresponds to the tetramerisation domain which forms a right handed alpha helical coiled coil structure.
Wikipedia: ENA/VASP homology proteins or EVH proteins are a family of closely related proteins involved in cell motility in vertebrate and invertebrate animals. EVH proteins are modular proteins that are involved in actin polymerization, as well as interactions with other proteins. Within the cell, ENA/VASP proteins are found at the leading edge of lamellipodia and at the tips of filopodia. ENA, the founding member of the family, was discovered in a fruit fly genetic screen for mutations that act as dominant suppressors of the AB non receptor tyrosine kinase. Invertebrate animals have one Ena homologue, whereas mammals have three, named Mena, VASP, and Evl.
Pfam PF22712: Short NACHT-associated C-Terminal domain, family 7 (domain)
The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors.
Pfam PF07914: Uncharacterized oxidoreductase dhs-27 (family)
The region featured in this family is found in a number of  C. elegans proteins, in one case ([swissprot:Q19034]) as a repeat. In many of the family members, this region is associated with the CHK region described by SMART as being found in ZnF_C4 and HLH domain-containing kinases. In fact, one member of this family ([swissprot:Q9GUC1]) is annotated as being a member of the nuclear hormone receptor family, and contains regions typical of such proteins  (Interpro:IPR000536, Interpro:IPR008946, and Interpro:IPR001628).
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 PF23934: Domain of unknown function (DUF7270) (domain)
This entry represents and uncharacterised family of phage proteins.
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 PF20039: Family of unknown function (DUF6441) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 210 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 PF04972: BON domain (domain)
This domain is found in a family of osmotic shock protection proteins (e.g. [swissprot:P27291]). It is also found in some Secretins and a group of potential haemolysins. Its likely function is attachment to phospholipid membranes.
Pfam PF20378: Family of unknown function (DUF6673) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is typically between 47 and 65 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 PF08130: Type A lantibiotic family (family)
This family consists of the type A lantibiotic peptides. Both Pep5  and epicidin-280 are ribosomally-synthesised antimicrobial peptides  produced by Gram-positive bacteria that are characterised by the  presence of lanthionine and/or methyllanthionine residues. The  lantibiotics family has a highly specific activity against multi- drug resistant bacteria and has potential to be utilised in a wide range of medical applications.
Pfam PF18286: Type III secretion system ExsE (domain)
This domain is found in ExsE present in Pseudomonas aeruginosa. ExsE forms part of the ExsACDE signaling cascade which acts as an important regulatory switch that ensures timely expression of the Type III secretion system (T3SS) and so plays a critical role in facilitating infection. Prior to host-cell contact, the T3SS is inactive and ExsE and Type III Secretion Chaperone (ExsC) form a stable complex. ExsC forms a compact homodimer and ExsE wraps around one face of this dimer.
Pfam PF21388: Spermatogenesis-associated protein 2, PUB-like domain (domain)
This domain is found at the N-terminal end of Spermatogenesis- associated protein 2 from humans (SPATA2) and similar proteins from animals. This protein interacts with the deubiquitinase CYLD through its non-canonical PUB domain (this entry) and activates CYLD-mediated hydrolysis of ubiquitin chains. This domain shows an all-helical fold.
Pfam PF21910: GH85 endohexosaminidases, C-terminal domain (domain)
This entry represents the C-terminal domain of GH85 endohexosaminidases.These enzymes cleave the glycosidic linkage between the two N-acetylglucosamine units that make up the chitobiose core of N-glycans. The C-terminal domain adopts a typical fibronectin Ig-like fold.
Pfam PF08789: PBCV-specific basic adaptor domain (domain)
The small PBCV-specific basic adaptor domain is found fused to S/T protein kinases and the 2-Cysteine domain.
Pfam PF20324: Family of unknown function (DUF6619) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 100 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 PF09770: Topoisomerase II-associated protein PAT1 (repeat)
Members of this family are necessary for accurate chromosome transmission during cell division.
Pfam PF08868: YugN-like family (domain)
This family of proteins related to B. subtilis YugN are functionally uncharacterised.
Pfam PF23149: Cdr2 UBA domain (domain)
The protein kinase Cdr2 from S.pombe promotes mitotic entry by organising cortical oligomeric nodes that lead to inhibition of Wee1 which itself inhibits the cyclin-dependent kinase Cdk1. Cdr2 may act as a dosage-dependent regulator of cell size by sequestering its substrate Wee1 in cytoplasmic clusters, away from Cdk1 in the nucleus. This protein consists of a kinase domain at the N-terminal, followed by a ubiquitin-associated domain (UBA) and a KA1 domain at the C-terminal. This entry represents the UBA domain which is thought to be necessary for kinase activity.
Pfam PF24598: DOP1 C-terminal (repeat)
DOP1 is the founding member of the Dopey family and is required for correct cell morphology and spatiotemporal organisation of multicellular structures in the filamentous fungus Emericella nidulans (Aspergillus nidulans). In S. cerevisiae, it is required for normal cellular morphogenesis. Loss of Dop1 activity affects endosome to Golgi transport and causes a severe perturbation of the organization of the endoplasmic reticulum; Mon2 a relative of large Arf exchange factors, recruits Dop1 to the Golgi apparatus. Dop1 homologues are found in mammals, where they may play a role in regulating membrane trafficking of cargo proteins. Together with ATP9A and MON2, it regulates SNX3 retromer-mediated endosomal sorting of WLS away from lysosomal degradation. This entry represents the C-terminal domain of DOP1, which consists of TPRs.
Pfam PF03153: Transcription factor IIA, alpha/beta subunit (family)
Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in [pfam:PF02268] and [pfam:PF02751], respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription.