SII-SWORD/CoKE huggingface dataset:
Pfam PF18156: pPIWI_RE three-gene island domain Y (domain)
Poorly-understood domain observed N-terminal to restriction endonuclease (REase) domain, which is part of a conserved three-gene island also containing a DinG-type helicase and the pPIWI_RE module. This three gene island is predicted to form a conflict system which targets R-loop formation of invasive plasmids during plasmid replication.
Pfam PF19564: Family of unknown function (DUF6086) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000721) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a  protein from the tobramycin biosynthetic gene cluster from  Streptoalloteichus tenebrarius and appears to be predominantly  found in Actinobacteria.
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 PF19704: DNA-PKcs, CC5 (repeat)
This entry represents the C-terminal region of the circular cradle segment (CC, also known as M-HEAT repeats) from DNA-dependent protein kinase catalytic subunit (DNA-PKcs), containing most of the supersecondary structure CC4 and the complete CC5. DNA-PKcs is involved in DNA nonhomologous end joining (NHEJ), required for double-strand break (DSB) repair. It interacts with the C-terminal peptide of Ku80 which presents the DNA ends for repair. The structures in this entry contain Ku-binding site B and one of the caspase-3 cleavage sites.
Pfam PF18307: Transcription factor Tfb2 (p52) C-terminal domain (domain)
This is the C-terminal domain of Transcription factor Tfb2 present in Saccharomyces cerevisiae. Tfb2 is referred to as p52 in humans. The interaction between p8-Tfb5 and p52-Tfb2 has a key role in the maintenance of the transcription factor TFIIH architecture and TFIIHs function in nucleotide-excision repair (NER) pathway. The C-terminal domain of Tfb2 is thought to have a crucial role in DNA repair.
Wikipedia: In molecular biology, this protein domain represents Tbf5 which stands for TTDA subunit of TFIIH basal transcription factor complex, and Rex1 a type of nucleotide excision repair (NER) proteins. Nucleotide excision repair is a major pathway for repairing UV light-induced DNA damage in most organisms. The function of this protein is to aid transcription.
Pfam PF14176: YxiJ-like protein (family)
The YxiJ-like protein family includes the B. subtilis YxiJ protein [swissprot:P42320], which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length.
Pfam PF10944: Protein of unknown function (DUF2630) (family)
This bacterial family of proteins have 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 PF04657: Putative inner membrane exporter, YdcZ (family)
DMT_YdcZ is a family of putative inner membrane exporters from both Gram-positive and Gram-negative bacteria.
Pfam PF17975: Ribonucleotide reductase alpha domain (domain)
This is the alpha helical domain of ribonucleotide reductases. Family members include Ribonucleotide reductase (RNR, [ec:1.17.4.1]) which catalyse the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs divide into three classes on the basis of their metallocofactor usage. This domain is found in Class II.  Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Many organisms have more than one class of RNR present in their genomes. Ribonucleotide reductase is an oligomeric enzyme composed of a large sub-unit (700 to 1000 residues) and a small sub-unit (300 to 400 residues) - class II RNRs are less complex, using the small molecule B12 in place of the small chain. Some family members carry ATP cone domain which acts as a functional regulator. Competitive binding of ATP and dATP to an N-terminal ATP-cone domain determines enzyme activity. As the ratio of dATP to ATP increases above a certain threshold, the enzyme activity is turned off. Substrate nucleotides are recognised by relatively simple H-bonding interactions at the N-terminus of one or more alpha helices. In the monomeric class II RNR, the effector binds in a pocket formed by helices in a 130 amino acid insertion which constitutes this domain.
Wikipedia: Ribonucleotide reductase (RNR), also known as ribonucleoside diphosphate reductase, is an enzyme that catalyzes the formation of deoxyribonucleotides from ribonucleotides. It catalyzes this formation by removing the 2'-hydroxyl group of the ribose ring of nucleoside diphosphates. This reduction produces deoxyribonucleotides. Deoxyribonucleotides in turn are used in the synthesis of DNA. The reaction catalyzed by RNR is strictly conserved in all living organisms. Furthermore, RNR plays a critical role in regulating the total rate of DNA synthesis so that DNA to cell mass is maintained at a constant ratio during cell division and DNA repair. A somewhat unusual feature of the RNR enzyme is that it catalyzes a reaction that proceeds via a free radical mechanism of action. The substrates for RNR are ADP, GDP, CDP and UDP. dTDP is synthesized by another enzyme from dTMP.
Pfam PF15949: Domain of unknown function (DUF4757) (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 145 and 166 amino acids in length. The family is found in association with [pfam:PF00412]. There are two completely conserved residues (W and L) that may be functionally important.
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 PF24521: KRIT1 ankyrin-repeats domain (repeat)
KRIT1, also known as CCM1, a Rap1-binding protein, is expressed in endothelial cells where it is present in cell-cell junctions and associated with junctional proteins. Together with CCM2/MGC4607 and CCM3/PDCD10, KRIT1 constitutes a set of proteins whose mutations are found in cerebral cavernous malformations, characterised by cerebral hemorrhages and vascular malformations in the central nervous system. KRIT-1 localization is mediated by its FERM domain. This entry represents an ankyrin-repeats domain found in the central region of KRIT1. This entry also includes HOS4 from yeast, whose function is unknown.
Pfam PF08485: Polysaccharide biosynthesis protein C-terminal (family)
This domain is found to the C-terminus of the [pfam:PF02719] domain in bacterial polysaccharide biosynthesis enzymes including the capsule protein CapD and several putative epimerases/dehydratases.
Pfam PF04512: Baculovirus polyhedron envelope protein, PEP, N terminus (family)
Polyhedra are large crystalline occlusion bodies containing nucleopolyhedrovirus virions, and surrounded by an electron-dense  structure called the polyhedron envelope or polyhedron calyx.  The  polyhedron envelope (associated) protein PEP is thought to be an  integral part of the polyhedron envelope. PEP is concentrated at the surface of polyhedra, and is thought to be important for the proper  formation of the periphery of polyhedra.  It is thought that PEP may  stabilise polyhedra and protect them from fusion or aggregation.
Pfam PF22136: Bacterial argonaute protein N-terminal domain (domain)
Argonaute proteins are key effectors of eukaryotic RNA interference and, in prokaryotes, function in host genome defense.  This entry represents a domain found at the N-terminus of the Marinitoga piezophila Argonaute (MpAgo) protein that uses 5'-hydroxylated guide RNAs to recognise and cleave single-stranded target sequences  rather than the 5'-phosphorylated guides used by all known Argonautes. This domain adopts alpha/beta structure consisting of four-stranded beta-sheet and two helices. Compared to other Argonaute proteins, this domain differs in both its secondary structure and its orientation relative to the MID/PIWI lobe.
Pfam PF05635: 23S rRNA-intervening sequence protein (family)
This family consists of bacterial proteins encoded within an intervening sequence present within some 23S rRNA genes. It folds into an anti-parallel four-helix bundle and forms homopentamers.
Pfam PF03953: Tubulin C-terminal domain (domain)
This family includes the tubulin alpha, beta and gamma chains. Members of this family are involved in polymer formation. Tubulins are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules. (The FtsZ GTPases have been split into their won family).
Pfam PF15150: Phorbol-12-myristate-13-acetate-induced (family)
This family carries a BH3 domain between residues 23 and 40.
Wikipedia: Phorbol-12-myristate-13-acetate-induced protein 1 is a protein that in humans is encoded by the PMAIP1 gene, and is also known as Noxa.
Pfam PF24550: Dynamin-like GTPase MGM1-like, lipid interacting stalk (domain)
This is the lipid-interacting stalk (LIS) domain of Dynamin-like GTPase MGM1, mitochondrial from Saccharomyces cerevisiae and similar fungal sequences. MGM1 is essential for normal mitochondrial morphology by mediating fusion of the mitochondrial inner membranes. This domain has been implicated in lipid binding with several key lysine residues.
Pfam PF02674: Colicin V production protein (family)
Colicin V production protein is required in E. Coli for colicin V production from plasmid pColV-K30. This protein is coded for in the purF operon.
Pfam PF19178: Family of unknown function (DUF5860) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in viruses.
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 PF18342: Endo-beta-N-acetylglucosaminidase LytB SH3 domain (domain)
This domain has can be found in endo-beta-N-acetylglucosaminidase LytB (EC 3.2.1.96) of S. pneumoniae and other gram positive bacteria. This domain adopts an SH3-like structure.
Pfam PF05694: 56kDa selenium binding protein (SBP56) (repeat)
This family consists of several selenium binding proteins from eukaryotes, bacteria and archaea. It is thought that SP56 participates in late stages of intra-Golgi protein transport. The Lotus japonicus homologue of SBP56, LjSBP, is thought to have more than one physiological role and can be implicated in controlling the oxidation/reduction status of target proteins, in vesicular Golgi transport. Human selenium-binding protein 1 (SELENBP1) is a methanethiol oxidase (MTO) that converts methanethiol to H2O2, formaldehyde, and H2S.
Pfam PF04828: Glutathione-dependent formaldehyde-activating enzyme (domain)
The GFA enzyme catalyzes the first step in the detoxification of formaldehyde. This domain has a beta-tent fold.
Pfam PF22911: Proline-rich AKT1 substrate 1, N-terminal domain (domain)
This entry represents a domain found in the N-terminal region of the PRAS (Proline-rich AKT1 substrate 1) family. PRAS is a proline-rich family that can be phosphorylated by AKT, and in the phosphorylated state binds to 14-3-3. The AKT signalling pathway contributes to regulation of apoptosis after a variety of cell death stimuli, and PRAS is found to be a substrate. PRAS plays an important role in regulating cell survival downstream of the PI3-K/Akt pathway after re-perfusion injury after transient focal cerebral ischemia. Copper/zinc-SOD (SOD1), a cytosolic isoenzyme of superoxide dismutase, SOD, is highly protective against ischemia and re-perfusion injury after transient focal cerebral ischemia, and SOD1 thus contributes to the inhibition of direct oxidation of PRAS and the activation of its signalling pathway. PRAS is also a mTOR binding partner, and PRAS phosphorylation by AKT and its association with 14-3-3, a cytosolic anchor protein, are crucial for insulin to stimulate mTOR (mammalian target of rapamycin).
Pfam PF22732: MSL3 chromodomain-like (domain)
This domain is found in Male-specific lethal-3 (MSL3) and other related proteins such as MRG15 transcription factor. MSL3 resides in the MSL (male-specific lethal) complex, which upregulates transcription by spreading the histone H4 Lys16 acetyl mark. The MSL3 chromo domain implicated in chromatin targeting and its deletion leads to the disruption of MSL targeting. The MRG15 chromo domain is involved in chromatin remodelling and transcription regulation. This domain consists of a SH3-like beta-barrel and a long alpha-helix.
Pfam PF02262: CBL proto-oncogene N-terminal domain 1 (domain)
Cbl is an adaptor protein that binds EGF receptors (or other tyrosine kinases) and SH3 domains, functioning as a negative regulator of many signaling pathways. The N-terminal domain is evolutionarily conserved, and is known to bind to phosphorylated tyrosine residues. Cbl_N is comprised of 3 structural domains of which this is the first - a four helix bundle.
Wikipedia: In molecular biology, the Cbl TKB domain, also known as the phosphotyrosine binding (PTB) domain is a conserved region found at the N-terminus of Cbl adaptor proteins. This N-terminal region is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle domain, an EF hand-like domain and a SH2-like domain, which together are known to bind to phosphorylated tyrosine residues.
Pfam PF08402: TOBE domain (family)
The TOBE domain (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum (eg [swissprot:P46930]) and sulphate ([swissprot:P16676]). Found in ABC transporters immediately after the ATPase domain. In this family a strong RPE motif is found at the presumed N-terminus of the domain.
Pfam PF17518: Family of unknown function (DUF5443) (family)
This is a family of unknown function found in Mycoplasma.
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 PF23540: DesK N-terminal domain (domain)
The protein family includes sensor histidine kinases that function as part of two-component regulatory systems. These kinases are involved in sensing environmental stimuli and initiating appropriate cellular responses. Specifically, one member of the family, DesK, is responsible for detecting changes in membrane fluidity during cold stress and activating the response regulator DesR by phosphorylation, which leads to the induction of the des gene for Delta5 acyl-lipid desaturase. Another member, YvfT, is part of the YvfT/YvfU regulatory system and likely activates the response regulator YvfU by phosphorylation. These kinases play a critical role in adapting to environmental changes by modulating the activity of their respective response regulators.  This domain is composed of 5 transmembrane helices.
Pfam PF04932: O-Antigen ligase (family)
This group of bacterial proteins is involved in the synthesis of O-antigen, a lipopolysaccharide found in the outer membrane in gram-negative bacteria. This family includes O-antigen ligases such as E. coli RfaL.
Pfam PF22103: ElaD/SseL N-terminal domain (repeat)
This entry represents the N-terminal helical domain found in a group of CE proteases from human pathogens, including ElaD from E.coli, SseL from Salmonella typhimurium and ShiCE from Shigella, which are dedicated deubiquitinases (DUBs), proteases that reverse the addition of ubiquitin to substrates, and effectively hijacks the host's ubiquitination processes. This domain is structurally similar to VHS domains and it serves to localise the catalytic domain ([pfam:PF22102]) through an additional Ub binding site.
Pfam PF22509: CARDS D2, beta trefoil domain (domain)
This entry represents a beta-trefoil domain (called D2) present in the CARDS toxin, a vacuolating cytotoxin from Mycoplasma pneumoniae.
Pfam PF24858: Alkylglycerol monooxygenase C-terminal (domain)
This entry includes Alkylglycerol monooxygenase (AGMO, also known as TMEM195) which is a glyceryl-ether monooxygenase that cleaves the O-alkyl bond of ether lipids. These lipids are essential components of brain membranes. This is the C-terminal domain which may adopt a four helical bundle fold.
Pfam PF22341: GSPII protein E, N1E domain (domain)
GSPE is an ATPase component of the type II secretion system required for the energy-dependent secretion of extracellular factors such as proteases and toxins from the periplasm. This entry represents the N1E domain at its N-terminal end which associates with the cytoplasmic domain of the inner membrane protein GspL.
Pfam PF11699: Mif2/CENP-C like (domain)
CENP-C_C is a C-terminal family of fungal and eukaryote proteins necessary for centromere formation. CENP-C is the inner-kinetochore centromere (CEN) binding protein.  In the budding-yeast, Mif2, the yeast homologue, binds in the CDEIII region of the centromere, and has been shown to recruit a substantial subset of all inner and outer kinetochore proteins. Mif2 adopts a cupin fold and is extremely similar both in polypeptide chain conformation and in dimer geometry to the dimerisation domain of a bacterial transcription factor. The Mif2 dimer appears to be part of an enhanceosome-like structure that nucleates kinetochore assembly in budding yeast. This C-terminal domain is the region via which CENP-C localises to centromeres throughout the cell cycle 2,3].
Pfam PF20396: Family of unknown function (DUF6689) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in gamma proteobacteria. Proteins in this family are typically between 273 and 287 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 PF21261: Mammalian exosome complex component RRP40, N-terminal (domain)
Exosome complex component RRP40 is a non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude  of cellular RNA processing and degradation events. It consists of a N-terminal beta-sandwich hybrid domain, a central S1 domain and a C-terminal KH domain ([pfam:PF15985]). This entry represents the N-terminal domain of mammalian RRP40.
Pfam PF14261: Domain of unknown function (DUF4351) (family)
This domain is found in bacteria, and is approximately 60 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 PF07697: 7TM-HD extracellular (domain)
This entry represents the extracellular domain of the 7TM-HD (7TM Receptors with HD hydrolase).
Pfam PF06782: Uncharacterised protein family (UPF0236) (family)
This is a family of unknown function found in Bacteria. Some family members are thought to be transposases.
Pfam PF07875: Coat F domain (domain)
The Coat F proteins, which contribute to the Bacillales spore coat.  It occurs multiple times in the genomes it is found in.
Pfam PF08799: pre-mRNA processing factor 4 (PRP4) like (domain)
This small domain is found on PRP4 ribonuleoproteins.  PRP4 is a U4/U6 small nuclear ribonucleoprotein that is involved in pre-mRNA processing.
Pfam PF02311: AraC-like ligand binding domain (domain)
This family represents the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif [pfam:PF00165]. This domain is distantly related to the Cupin domain [pfam:PF00190].
Pfam PF00635: MSP (Major sperm protein) domain (domain)
Major sperm proteins are involved in sperm motility. These proteins oligomerise to form filaments. This family contains many other proteins.
Wikipedia: Major sperm protein (MSP) is a nematode specific small protein of 126 amino acids with a molecular weight of 14 kDa. It is the key player in the motility machinery of nematodes that propels the crawling movement/motility of nematode sperm. It is the most abundant protein present in nematode sperm, comprising 15% of the total protein and more than 40% of the soluble protein. MSP is exclusively synthesized in spermatocytes of the nematodes. The MSP has two main functions in the reproduction of the helminthes: i) as cytosolic component it is responsible for the crawling movement of the mature sperm, and ii) once released, it acts as hormone on the female germ cells, where it triggers oocyte maturation and stimulates the oviduct wall to contract to bring the oocytes into position for fertilization. MSP has first been identified in Caenorhabditis elegans.
Pfam PF08617: Kinase binding protein CGI-121 (domain)
CGI-121 has been shown to bind to the p53-related protein kinase (PRPK).  PRPK is a novel protein kinase which binds to and induces phosphorylation of the tumour suppressor protein p53. CGI-121 is part of a conserved protein complex, KEOPS. The KEOPS complex is involved in telomere uncapping and telomere elongation.  Interestingly this family also include archaeal homologues, formerly in the DUF509 family. A structure for these proteins has been solved by structural genomics.
Wikipedia: In molecular biology, the kinase binding protein CGI-121 family of proteins includes the kinase binding protein CGI-121 and its homologues. CGI-121 has been shown to bind to the p53-related protein kinase (PRPK). CGI-121 is part of a conserved protein complex, KEOPS. The KEOPS complex is involved in telomere uncapping and telomere elongation. This family of proteins also include archaeal homologues.