SII-SWORD/CoKE huggingface dataset:
Pfam PF06945: Protein of unknown function (DUF1289) (family)
This family consists of a number of hypothetical bacterial proteins.  The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N-terminus. The function of this family is unknown. Structural modelling suggests this domain may bind nucleic acids.
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 PF24561: TRAPPC8, C-terminal, arthropods (domain)
This entry represents the C-terminal domain of TRAPPC8 from Drosophila melanogaster and related sequences from arthropods. TRAPPC8 is the orthologue of human TRAPPC8 which is not included in this entry. This is a TRAPPIII-specific subunit, a complex that consists of Transport Protein Particle (TRAPP) GEFs (nucleotide exchange factors). TRAPPIII activates Rab1, a master regulator of both the early secretory pathway and autophagy. This domain may adopt a beta-sandwich fold.
Pfam PF10193: Telomere length regulation protein (family)
This family is the central conserved 110 amino acid region of a group of proteins called telomere-length regulation or clock abnormal protein-2 which are conserved from plants to humans. The full-length protein regulates telomere length and contributes to silencing of sub-telomeric regions. In vitro the protein binds to telomeric DNA repeats.
Pfam PF17234: Mitochondrial peculiar membrane protein 1 (family)
This family contains  mitochondrial peculiar membrane proteins, found predominantly in Saccharomycetales.
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 PF01989: Aconitase X swivel domain (domain)
This is a putative aconitase X swivel domain, which has been predicted by comparative genomic analysis. The domain is mainly found in archaeal and proteobacterial proteins. As such, the prediction should be treated with caution. One member of this entry from Aeropyrum pernix which has been annotated as a putative aconitase, has been characterised in vitro and catalyses the dehydration of mevalonate 5-phosphate to form trans-anhydromevalonate 5-phosphate, a previously unknown intermediate, being involved in a "modified" mevalonate pathway.
Pfam PF07104: Protein of unknown function (DUF1366) (family)
This family consists of several hypothetical Streptococcus thermophilus bacteriophage proteins of around 130 residues in length. One of the sequences in this family, from phage Sfi11 ([swissprot:O80186]) is known as Gp149. The function of this family is unknown.
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 PF02182: SAD/SRA domain (domain)
The domain goes by several names including SAD, SRA  and YDG. It adopts a beta barrel, modified PUA-like, fold that is  widely present in eukaryotic chromatin proteins and in bacteria. Versions of this domain are known to bind hemi-methylated CpG  dinucleotides and also other 5mC containing dinucleotides. The  domain binds DNA by flipping out the methylated cytosine base from  the DNA double helix.The conserved tyrosine and aspartate  residues and a glycine rich patch are critical for recognition of  the flipped out base. Mammalian UHRF1 that contains this  domain plays an important role in maintenance of methylation at  CpG dinucleotides by recruiting DNMT1 to hemimethylated sites associated with replication forks. The SAD/SRA domain has been combined with other domains involved in the ubiquitin pathway on multiple occasions and such proteins link recognition of DNA  methylation to chromatin-protein ubiquitination. The domain is also found in species that lack DNA methylation, such as certain apicomplexans, suggestive of other DNA-binding modes or functions. A highly derived and distinct version of the domain is also found in fungi where it is fused to AlkB-type 2OGFeDO domains. In bacteria, the domain is usually fused or associated with restriction endonucleases, many of which target methylated or   hemi-methylated DNA.
Wikipedia: In molecular biology, this protein domain has been termed SRA-YDG, which is the abbreviation for SET and Ring finger Associated, YDG motif. Additional characteristics of the domain include conservation of up to 13 evenly spaced glycine residues and a VRV(I/V)RG motif. The protein domain is mainly found in plants and animals and in bacteria.
Pfam PF08921: Domain of unknown function (DUF1904) (domain)
This domain is found in a set of hypothetical bacterial 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 PF15532: Bacterial toxin 30 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems.  The toxin possesses an all-beta fold and two conserved histidines present in an RxH and THIP motif. The domain additionally has a highly conserved arginine residue. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 6 or type 7 secretion systems.
Pfam PF09431: SPIN90/Ldb17, leucine-rich domain (domain)
This is the conserved leucine-rich domain (LRD) within the C-terminal domain of SPIN90 (also known as NCK interacting protein with SH3 domain (NCKIPSD)) from animals, Ldb17 from budding yeasts and Dip1 from fission yeasts. Ldb17 is involved in the regulation of endocytosis in yeast. SPIN90 is an F-actin binding protein that regulates actin polymerization and endocytosis. It associates with and activates the Arp2/3 complex, without requiring a preformed actin filament. This LRD, within the C-terminal armadillo repeat (ARM) domain of SPIN90, is important for activation of Arp2/3 complex.
Pfam PF20112: Family of unknown function (DUF6502) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 269 and 295 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 PF19533: Rab3 GTPase-activating protein catalytic subunit C-terminal (domain)
This domain corresponds to the C-terminal region of the catalytic subunit of the GTPase activating protein that has specificity for Rab3 subfamily and converts active Rab3-GTP to the inactive form Rab3-GDP. Rab3 proteins are involved in regulated exocytosis of neurotransmitters and hormones.
Pfam PF02167: Cytochrome C1 family (family)
Cytochrome bc1 complex (ubiquinol:ferricytochrome c oxidoreductase) is found in mitochondria, photosynthetic bacteria and other prokaryotes. It is minimally composed of three subunits: cytochrome b, carrying a low- and a high-potential haem group; cytochrome c1 (cyt c1); and a high-potential Rieske iron-sulphur protein. The general function of the complex is electron transfer between two mobile redox carriers, ubiquinol and cytochrome c; the electron transfer is coupled with proton translocation across the membrane, thus generating proton-motive force in the form of an electrochemical potential that can drive ATP synthesis. In its structure and functions, the cytochrome bc1 complex bears extensive analogy to the cytochrome b6f complex of chloroplasts and cyanobacteria; cyt c1 plays an analogous role to cytochrome f, in spite of their different structures .
This entry also includes Nitrosomonas europaea petC, which is a subunit of the ammonia monooxygenase complex that catalyzes the oxidation of ammonia to hydroxylamine, the first reaction in the process of ammonia oxidation to nitrite .
Wikipedia: The coenzyme Q : cytochrome c – oxidoreductase, sometimes called the cytochrome bc1 complex, and at other times complex III, is the third complex in the electron transport chain, playing a critical role in biochemical generation of ATP. Complex III is a multisubunit transmembrane protein encoded by both the mitochondrial and the nuclear genomes. Complex III is present in the mitochondria of all animals and all aerobic eukaryotes and the inner membranes of most bacteria. Mutations in Complex III cause exercise intolerance as well as multisystem disorders. The bc1 complex contains 11 subunits, 3 respiratory subunits, 2 core proteins and 6 low-molecular weight proteins.
Pfam PF09152: Domain of unknown function (DUF1937) (domain)
This domain is found in a set of hypothetical bacterial proteins. Their exact function has not, as yet, been described.
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 PF19740: Family of unknown function (DUF6229) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000385) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It  includes a member from the lysobactin biosynthetic gene cluster  from Lysobacter sp. ATCC 53042. This family 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 PF08640: U3 small nucleolar RNA-associated protein 6 (repeat)
This is a family of U3 nucleolar RNA-associated proteins which are involved in nucleolar processing of pre-18S ribosomal RNA.
Pfam PF15072: Homologous recombination OB-fold protein (family)
This family represents Homologous recombination OB-fold protein (HROB). During homologous recombination, HROB acts by recruiting the MCM8-MCM9 helicase complex to sites of DNA damage to promote DNA repair synthesis.
Pfam PF23308: THS7A/B C-terminal TSP1 domain (domain)
This entry represents the C-terminal Thrombospondin type-1 (TSP1) domain of Thrombospondin type-1 domain-containing protein 7A and 7B. THSD7A is a neural protein that affects endothelial migration and vascular patterning during development. THSD7A is a membrane-associated N-glycoprotein with a soluble form, the latter promotes endothelial cell migration during angiogenesis via a FAK-dependent mechanism which implies that it may be a novel neuroangiogenic factor. THSD7A has been associated with membranous nephropathy.
Pfam PF11652: FAM167 (family)
This entry describes a eukaryotic protein family of unknown function designated FAM167.
Pfam PF23116: RTEL1, HHD domain (domain)
RTEL1 is an essential DNA helicase that disassembles a variety of DNA secondary structures to facilitate DNA replication, repair, and recombination processes, and to maintain telomere integrity. It is also required for the export and the correct cytoplasmic trafficking of the small nuclear (sn) RNA pre-U2, a component of the major spliceosome complex. This entry represents the harmonin homology domain which is predicted to mediate protein-protein In human and some other mammals as well as in some fish species, this domain is found as two tandem ones, referred to as HHD1 and HHD2 (or HNL1/2), while in plants and arthropods it is found as a single domain. It has been shown that the HHD1 domain mediates interaction of RTEL1 with SLX4 which prevents replication-transcription collision through R-loop dissolution. The HHD2 domain of RTEL1 interacts with RPA, which binds to single-stranded DNA with high affinity in a sequence-independent manner. Mutations in these domain are associated with associated with Hoyeraal-Hreidarsson syndrome and pulmonary fibrosis.
Pfam PF11137: Protein of unknown function (DUF2909) (family)
This is a family of proteins conserved in Proteobacteria of unknown 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 PF07492: Neutral trehalase Ca2+ binding domain (domain)
Neutral trehalases mobilise trehalose accumulated by fungal cells as a protective and storage carbohydrate. This family represents a calcium-binding domain similar to EF hand. Residues 97 and 108 in [swissprot:O42893] have been implicated in this interaction. It is thought that this domain may provide a general mechanism for regulating neutral trehalase activity in yeasts and filamentous fungi.
Pfam PF10833: Protein of unknown function (DUF2572) (family)
This bacterial 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 PF07145: Ataxin-2 C-terminal region (conserved_site)
The PABP-interacting motif PAM2 has been identified in various eukaryotic proteins as an important binding site for [pfam:PF00658]. It has been found in a wide range of eukaryotic proteins. Strikingly, this motif appears to occur solely outside of globular domains.
Pfam PF19710: PIK3 catalytic subunit gamma adaptor-binding domain (domain)
This is the N-terminal domain from PI3-kinase catalytic subunit gamma (PIK3CG, also known as p110 catalytic subunit gamma) which contains the  adaptor-binding domain (ABD). This is a globular domain with an alpha/beta sandwich topology, common to all catalytic subunits of PIK3s, and it is similar to ubiquitin-like domains. This domain interacts with the regulatory subunit of the p101 type.
Pfam PF15101: Telomere-associated protein TERB2 (family)
TERB2 is a meiosis-specific telomere-associated protein involved in meiotic telomere attachment to the nucleus inner membrane, a crucial step for homologous pairing and synapsis.
Pfam PF14040: Deoxyribonuclease NucA/NucB (family)
NucB is a non-specific endonuclease, which can hydrolyse both single- and double-stranded DNA substrates, in a divalent cation-dependent manner and to be expressed in late stage II of sporulation. NucB and NucA show structural similarity with other His-Me finger nucleases which are characterized by a common beta-beta-alpha motif. The beta-beta-alpha motif contains a central pair of anti-parallel beta-strands flanked by a conserved distal alpha-helix that sits in the major groove of DNA; the loop connecting the two beta-strands is variable in length and conformation. Direct magnesium co-ordination are highly conserved in NucB sequences in DRDE and DNRG (DD) motifs. The conserved Glu94 in B.subtilis NucB, corresponds to the conserved His in the His-Me finger family. Mutation of individual amino acids in these motifs in B. subtilis-NucB (Asp93 and Glu94 from motif 1, and Asn117 from motif 2) abrogates enzyme activity completely.
Pfam PF17018: Spore wall protein (family)
This is a family of microsporidial spore-wall proteins.
Pfam PF22889: Telomere ends associated, middle domain (domain)
This entry represents a presumed domain, mostly alpha-helical, found near the middle region of protein telomere ends associated (Tea) found in Drosophila species and related fly sequences. It protects telomeres from fusion and it likely functions as a component of the MTV complex along with moi and ver. The complex binds single-stranded DNA in a sequence-independent manner and can protect it from DNA degradation.
Pfam PF08115: SFI toxin family (family)
This family consists of the SFI family of spider toxins. This family of toxins might share structural, evolutionary and functional relationships with other small, highly structurally constrained spider neurotoxins. These toxins are highly selective agonists/antagonists of different voltage-dependent calcium channels and are extremely valuable reagents in the analysis of neuromuscular function.
Pfam PF14625: Lustrin, cysteine-rich repeated domain (domain)
This repeated domain is found in proteins from lower eukaryotes in lustrin, perlucin, pearl nacre, and other similar protein-types. Each repeat lies between Kunitz-BPTI repeats, in certain species, which are also cysteine-rich. The cysteines may form the disulfide bonds observed for other members of this superfamily.
Pfam PF24457: Family of unknown function (DUF7572) (domain)
This entry represents a family of uncharacterised mycophage proteins. These proteins form a compact domain composed of 5 or 6 antiparallel beta strands that curve around a C-terminal alpha-helix.
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 PF14186: Axin interactor dorsalisation-associated protein, C-terminal (domain)
This is the C-terminal domain of the axin-interacting protein family, and is a distinct version of the C2 domain. This domain is critical for interactions with cytoskeletal in the context of cellular adhesion points, thus it is combined with diverse domains related to cytoskeletal functions. This domain has predominantly a beta-strand globular fold composed of an antiparallel beta-sandwich with two beta-sheets, and three short alpha-helices to stabilize the conformation.
Pfam PF17645: Arylmalonate decarboxylase (family)
This entry contains members such as the arylmalonate decarboxylases (AMDase; EC 4.1.1.76), which belong to the family of carboxy-lyases (EC 4.1). Amdases are capable of decarboxylating a range of alpha-disubstituted malonic acid derivates to enantiopure products without the need for any cofactor. AMDases are members of the widespread Asp/Glu racemase family [pfam:PF01177] together with aspartate (EC 5.1.1.13) and glutamate racemases (EC 5.1.1.3), hydantoin racemases (EC 5.1.99.5) and maleate isomerases (EC 5.2.1.1).
Wikipedia: The enzyme arylmalonate decarboxylase (EC 4.1.1.76) catalyzes the chemical reaction2-aryl-2-methylmalonate  2-arylpropanoate + CO2
Pfam PF21685: Fungal virus Capsid protein, N-terminal domain (domain)
This domain is found at the N-terminal end of Capsid protein from Penicillium chrysogenum virus (P2), which self-assembles to form an icosahedral capsid with a T=1 symmetry. It is organised into two domains with similar alpha-beta  morphology.
Pfam PF11954: Domain of unknown function (DUF3471) (family)
This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 98 to 114 amino acids in length. This domain is found associated with [pfam:PF00144].
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 PF12447: Protein of unknown function (DUF3683) (family)
This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with [pfam:PF02754], [pfam:PF01565], [pfam:PF02913].
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 PF19942: Family of unknown function (DUF6404) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001055) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the yersiniabactin biosynthetic gene  cluster from Escherichia coli. This family appears to be  predominantly found in 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 PF19596: Family of unknown function (DUF6101) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found primarily in Alphaproteobacteria. Proteins in this family are typically between 173 and 189 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.