SII-SWORD/CoKE huggingface dataset:
Pfam PF17399: Domain of unknown function (DUF5405) (domain)
This domain family is found in Enterobacteriaceae. This protein may have a phage origin being found in bacteriophage P2 [swissprot:Q06425]. The majority of proteins have a conserved cysteine residue close to their C-terminus which may have functional significance.
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 PF10504: Protein of unknown function (DUF2452) (family)
This protein is found in eukaryotes but its function 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 PF09921: Uncharacterized protein conserved in archaea (DUF2153) (family)
This domain, found in various hypothetical archaeal 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 PF16174: Intracellular hyaluronan-binding protein 4 N-terminal (family)
IHABP4_N is the N-terminal region of intracellular hyaluronan-binding protein 4-like and SERPINE1 mRNA binding protein 1-like proteins. This region carries nuclear localisation sites, and may also be involved in the binding to some of the partners in the translational machinery.
Pfam PF00357: Integrin alpha cytoplasmic region (family)
This family contains the short intracellular region of integrin alpha chains.
Wikipedia: Integrins are transmembrane receptors that help cell–cell and cell–extracellular matrix (ECM) adhesion. Upon ligand binding, integrins activate signal transduction pathways that mediate cellular signals such as regulation of the cell cycle, organization of the intracellular cytoskeleton, and movement of new receptors to the cell membrane. The presence of integrins allows rapid and flexible responses to events at the cell surface.
Pfam PF04113: Gpi16 subunit, GPI transamidase component (family)
GPI (glycosyl phosphatidyl inositol) transamidase is a multi-protein complex.  Gpi16, Gpi8 and Gaa1 for a sub-complex of the GPI transamidase. GPI transamidase  that adds glycosylphosphatidylinositols (GPIs) to newly  synthesised proteins.  Gpi16 is an essential N-glycosylated transmembrane glycoprotein. Gpi16 is largely found on the lumenal side of the ER. It has a single C-terminal transmembrane domain and a small C-terminal, cytosolic extension with an ER retrieval motif.
Pfam PF04480: Protein of unknown function (DUF559) (family)
This entry represents a domain of unknown function found in Type II nicking enzyme V.HpaIIP from Haemophilus parainfluenzae, an endonuclease that may nick HpaII sequences that contain GT mismatches resulting from m5C-deamination and play a role in the very short patch (VSP) repair process, counteracting mutations . GT mismatches can lead to C-to-T transition mutations if not repaired. VSR repairs the mismatches in favour of the G-containing strand. In Escherichia coli, this endonuclease nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue, which is mismatched to 2'-deoxyguanosine . The incision is mismatch-dependent and strand specific. The structure of VSR is similar to the core structure of restriction endonucleases, which have a 3-layer Î±/Î²/Î± topology . Several catalytic residues from VSR endonucleases are conserved in this domain and form the composite sequence motif EDxHD .

This domain can also be found in some uncharacterised proteins, such as HI_0925 from Haemophilus influenzae.
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 PF11301: Protein of unknown function (DUF3103) (family)
This family of proteins with unknown function appear 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 PF14511: Type II restriction endonuclease EcoO109I (family)
This is a family of Type II restriction endonucleases.
Pfam PF14474: RTC4-like domain (domain)
This presumed domain is found in the RTC4 protein from yeasts. In Saccharomyces cerevisiae, Cdc13 binds telomeric DNA to recruit telomerase and to "cap" chromosome ends. RTC4 was identified in a screen to identify novel proteins and pathways that cap telomeres, or that respond to uncapped telomeres. This domain is also found in proteins that contain a DNA-binding myb domain.
Pfam PF09268: Clathrin, heavy-chain linker (repeat)
Members of this family adopt a structure consisting of alpha-alpha superhelix. They are predominantly found in clathrin, where they act as a heavy-chain linker domain.
Wikipedia: Clathrin is a protein that plays a role in the formation of coated vesicles. Clathrin was first isolated by Barbara Pearse in 1976. It forms a triskelion shape composed of three clathrin heavy chains and three light chains. When the triskelia interact they form a polyhedral lattice that surrounds the vesicle. The protein's name refers to this lattice structure, deriving from Latin clathri meaning lattice. Barbara Pearse named the protein clathrin at the suggestion of Graeme Mitchison, selecting it from three possible options. Coat-proteins, like clathrin, are used to build small vesicles in order to transport molecules within cells. The endocytosis and exocytosis of vesicles allows cells to communicate, to transfer nutrients, to import signaling receptors, to mediate an immune response after sampling the extracellular world, and to clean up the cell debris left by tissue inflammation. The endocytic pathway can be hijacked by viruses and other pathogens in order to gain entry to the cell during infection.
Pfam PF06206: CpeT/CpcT family (DUF1001) (domain)
This family consists of proteins of proteins belonging to the CpeT/CpcT family. These proteins are around 200 amino acids in length.  The proteins contain a conserved motif PYR in the amino terminal half of the protein that may be functionally important. The species distribution of the family is interesting.  So far it is restricted to cyanobacteria, cryptomonads and plants. It has been shown that CpcT encodes a bilin lyase responsible for attachment of phycocyanobilin to the beta subunit of phycocyanin.
Pfam PF20751: Structural protein 2 second domain (domain)
This entry represents the second domain of structural protein 2 of the hepatitis E virus. This domain has a RIFT like fold.  The high basic amino acid content of this protein has lead to the suggestion of a role in viral genomic RNA encapsidation.
Pfam PF25064: TT21 fifth ARM repeats domain (repeat)
This is the fifth ARM-repeats domain found towards the C-terminal of Tetratricopeptide repeat protein 21 (TT21) from human and its homologues. TT21 is an intraflagellar transport (IFT)-associated protein required for spermatogenesis. It is involved in sperm flagellar formation and intraflagellar transport.
Pfam PF12347: Holliday junction regulator protein family C-terminal repeat (domain)
Although this family is conserved in the Holliday junction regulator, HJURP, proteins in higher eukaryotes, alongside an Scm3, [pfam:PF10384], family, its exact function is not known. The C-terminal region of Scm3 proteins has been evolving rapidly, and this short repeat at the C-terminal end can be present in up to two copies in the higher eukaryotes.
Pfam PF11267: Domain of unknown function (DUF3067) (domain)
This family of proteins found in plants and cyanobacteria has no known function. The structure of this domain has been solved by NMR for the alr2454 protein. The structure was determined to be a novel fold composed of four alpha helices and a sheet of three anti-parallel beta-strands.
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 PF03962: Mnd1 HTH domain (domain)
This family of proteins includes  MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.
Pfam PF21762: DNA polymerase III subunit epsilon-like, C-terminal domain (domain)
This domain is found at the C-terminal end of QDE-2-interacting protein from Neurospora crassa, DNA polymerase III subunit epsilon from Treponema pallidum (DnaQ) and similar fungal proteins that belong to the DnaQ-like (or DEDDh) exonuclease superfamily. These proteins catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. This domain shows an alpha -beta configuration.
Pfam PF08833: Axin beta-catenin binding motif (conserved_site)
This motif is found on the scaffolding protein Axin which is a component of the beta-catenin destruction complex.  It competes with the tumour suppressor adenomatous polyposis coli protein (APC) for binding to beta-catenin.
Pfam PF23455: Domain of unknown function (DUF7129) (domain)
This domain is found in a group of small proteins mainly from Halobacteria. It contains highly conserved cysteine residues arranged in two CxxC motifs that likely coordinate zinc. The first motif could be more broadly defined as YECxxCG. This domain is predicted to adopt zinc ribbon fold.
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 PF11183: Polymyxin resistance protein PmrD (family)
PmrB forms a two-component system (TCS) with PmrA that allows Gram-negative bacteria to survive the cationic antimicrobial peptide polymyxin G. The TCS is linked to another one via the polymyxin resistance protein PmrD. PmrD is the first protein identified to mediate the connectivity between the two TCSs.  It binds to the N terminal domain of the PmrA response regulator which prevents its dephosphorylation, thereby promoting the the transcription of genes involved in polymyxin resistance.
Pfam PF19783: Domain of unknown function (DUF6268) (domain)
This family of integral membrane beta-barrel proteins is functionally uncharacterised. This family of proteins is found in Bacteroidetes bacteria. Proteins in this family are typically between 300 and 313 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 PF03146: Agrin NtA domain (domain)
Agrin is a multidomain heparan sulphate proteoglycan, that is a key organiser for the induction of postsynaptic specialisations at the neuromuscular junction. Binding of agrin to basement membranes requires the amino terminal (NtA) domain. This region mediates high affinity interaction with the coiled-coil domain of laminins. The binding of agrin to laminins via the NtA domain is subject to tissue-specific regulation. The NtA domain-containing form of agrin is expressed in non-neuronal cells or in neurons that project to non-neuronal cell such as motor neurons. The structure of this domain is an OB-fold.
Wikipedia: Agrin is a large proteoglycan whose best-characterised role is in the development of the neuromuscular junction during embryogenesis. Agrin is named based on its involvement in the aggregation of acetylcholine receptors during synaptogenesis. In humans, this protein is encoded by the AGRN gene.
Pfam PF14987: NADH dehydrogenase 1 alpha subcomplex subunit 3 (family)
This family of proteins are accessory subunits of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I). This subunit is not believed to be catalytic.
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF09280: XPC-binding domain (domain)
Members of this family adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair.
Wikipedia: In molecular biology, the XPC binding domain is thought to play a role in DNA damage discrimination and in the enhancement of cell survival. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair (NER). Members of this entry adopt a structure consisting of four alpha helices, arranged in an array.
Pfam PF12694: Circularly permutated YpsA SLOG family (family)
The structure of proteins in this family contain central beta strands with flanking alpha helices.  The structure is similar to that of a molybdenum cofactor carrier protein.This family belongs in the SLOG superfamily, circularly-permuted version of YspA famiy showing fusions to NAD utilization and ADP-ribosylation domains including NUDIX, NADAR and MACRO. Members of this family are predicted to function as sensors of nucleotide, nucleotide-derived ligands, or nucleic acids, which are potentially processed/modified by associating effectors.
Pfam PF17830: STI1/HOP, DP domain (domain)
This entry corresponds to the STI1/HOP aspartate/proline-rich (DP) domain that is found in two copies in the Sti1 protein and are referred to as DP1 and DP2. STI1/HOP proteins are cochaperones that belong to the foldosome, a system consisting in Hsp70 and Hsp90 chaperones. STI1/HOP acts as an adapter protein capable of transferring client proteins from the first to the second molecular chaperone. This domain (and specifically DP2 from STI1) is involved in client activation.
Pfam PF19750: Family of unknown function (DUF6237) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001214) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the marformycin A biosynthetic gene cluster  from Streptomyces drozdowiczii.
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 PF19225: Spo16 protein, N-terminal (domain)
This entry represents proteins related to yeast Spo16. Spo16 forms a complex with Zip2 and Zip4. Zip2 and Spo16, form a meiosis-specific XPF-ERCC1-like complex. The recombinant Zip2 XPF domain together with Spo16 preferentially binds branched DNA structures, such as D loops and HJs. The Spo16 protein contains a nuclease-like domain similar to that in ERCC1, represented in this entry, and a C-terminal HHH motif.
Pfam PF15307: Sperm acrosome-associated protein 7 (family)
SPACA7 is a family of eukaryotic proteins expressed in the testes. Proteins in this family are typically between 104 and 195 amino acids in length. There is a conserved DEIL sequence motif. The function is not known.
Pfam PF19963: vWA-MoxR associated protein middle region (VMAP-M) 1 (family)
Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities.
Pfam PF22425: Hypothetical protein ORF126-like (family)
This protein family includes the uncharacterised protein [swissprot:Q6ZYF6] from Pyrobaculum spherical virus (PSV), also known as ORF126, which forms an alpha-beta two-layer sandwich.
Pfam PF05320: Poxvirus DNA-directed RNA polymerase 19 kDa subunit (family)
This family contains several DNA-directed RNA polymerase 19 kDa polypeptides. The Poxvirus DNA-directed RNA polymerase (EC: 2.7.7.6)  catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
Pfam PF04747: Protein of unknown function, DUF612 (family)
This family includes several uncharacterised proteins from Caenorhabditis elegans.
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 PF17395: Family of unknown function (DUF5403) (family)
This is a family of unknown function 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 PF03000: NPH3 family (family)
Phototropism of Arabidopsis thaliana seedlings in response to a blue light source is initiated by nonphototropic hypocotyl 1 (NPH1), a light-activated serine-threonine protein kinase. Mutations in NPH3 disrupt early signaling occurring downstream of the NPH1 photoreceptor. The NPH3 gene encodes a NPH1-interacting protein. NPH3 is a member of a large protein family, apparently specific to higher plants, and may function as an adapter or scaffold protein to bring together the enzymatic components of a NPH1-activated phosphorelay.
Pfam PF07422: Sexual stage antigen s48/45 domain (domain)
This family contains sexual stage s48/45 antigens from Plasmodium (approximately 450 residues long). These are surface proteins expressed by Plasmodium male and female gametes that have been shown to play a conserved and important role in fertilisation. This domain contains 6 conserved cysteines suggesting 3 disulphide bridges.
Pfam PF07973: Threonyl and Alanyl tRNA synthetase second additional domain (domain)
The catalytically active from of threonyl/alanyl tRNA synthetase is a dimer. Within the tRNA synthetase class II dimer, the bound tRNA interacts with both monomers making specific interactions with the catalytic domain, the C-terminal domain, and this domain (the second additional domain).  The second additional domain is comprised of a pair of perpendicularly orientated antiparallel beta sheets, of four and three strands, respectively, that surround a central alpha helix that forms the core of the domain.
Pfam PF02721: Domain of unknown function DUF223 (domain)
This entry represents the first OB fold found Replication protein A 70 kDa DNA-binding subunit B/D from plants which are similar to human RPA1 (also called RPA70) and are part of the RPA complex. RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70kDa (RPA1), 32kDa (RPA2), and 14kDa (RPA3) . The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
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 PF05413: Putative closterovirus papain-like endopeptidase (family)
Corresponds to Merops family C34. Putative closterovirus papain-like  endopeptidase from the apple chlorotic  leaf spot closterovirus.
Pfam PF15939: Putative antitoxin of bacterial toxin-antitoxin system (family)
YmcE_antitoxin is the putative antitoxin for the supposed bacterial toxin GnsA, UniProtKB:P0AC92, family [pfam:PF08178].
Wikipedia: A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).