SII-SWORD/CoKE huggingface dataset:
Pfam PF11949: Protein of unknown function (DUF3466) (repeat)
This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 564 to 612 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 PF16077: Spaetzle (family)
This family of proteins are nerve growth factor-like ligands required in the pathway that establishes the dorsal-ventral pattern of the embryo. They form a cystine knot structure.
Wikipedia: Spätzle or spaetzle is an evolutionarily-conserved arthropod protein first identified in Drosophila melanogaster. It plays a role in embryonic development and in the insect innate immune response. The name was coined by the Nobel laureate Christiane Nüsslein-Volhard after the Spätzle noodle-like form of homozygous mutant fly larvae.
Pfam PF18735: RiboL-PSP-HEPN (domain)
RiboL-PSP-HEPN. Fused to endoRNase L-PSP ; in operon with ParB.
Pfam PF05256: Uncharacterised protein family (UPF0223) (family)
This family of proteins is functionally uncharacterised.
Pfam PF17307: Small integral membrane protein 3 (family)
This domain family can be found in Smim3 proteins (Small integral membrane protein 3) also known as NID67 (NGF-induced differentiation clone 67). It is a primary response gene, hypothesized to be involved in forming or regulating ion channels in neuronal differentiation. It is strongly induced by NGF (Nerve Growth Factor) and FGF (Fibroblast Growth Factor), both of which cause these cells to differentiate. The amino acid sequence of NID67 is strongly conserved among rat, mouse and human. This family of small membrane proteins is only 60 amino acids long and analysis of the predicted peptide sequence reveals a stretch of 29 hydrophobic and uncharged residues which very likely comprise a trans-membrane region.
Pfam PF22555: Phage DNA Adenine Methylase-like domain 1 (domain)
This domain has been characterised as part of a nucleic acid modifying system in certain phages. This system may modify tRNAs that are encoded adjacent to the system on the genome. These tRNAs are then possibly packaged into the viral head, to render them resistant to host restriction.
Pfam PF05263: Protein of unknown function (DUF722) (family)
This family contains several bacteriophage proteins 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 PF17551: Family of unknown function (DUF5463) (family)
This is a family of unknown function found in Yersinia pestis.
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 PF02592: Putative vitamin uptake transporter (family)
This entry includes queuosine (Q) precursor transporter fromEscherichia coli, which is required for the import and rescue of the queuosine precursors 7-cyano-7-deazaguanine (preQ0) and 7-aminomethyl-7-deazaguanine (preQ1) . Membranes are impermeable to purines; therefore, transporters are required for the salvage of Q precursors.
Pfam PF14782: BBS2 GAE domain (domain)
This entry represents the gamma-adaptin ear (GAE) domain of BBS2. BBS2 is one of the BBS proteins that form the BBSome complex found in vertebrates and nematodes, including humans, mice, and Caenorhabditis elegans. The BBSome complex is required for ciliogenesis, as well as the assembly and movement of intraflagellar transport proteins along the ciliary membrane.
Pfam PF14270: Domain of unknown function (DUF4358) (family)
This domain family is found in bacteria, and is approximately 110 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 PF14004: Protein of unknown function (DUF4227) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.
Pfam PF15216: Thymic stromal lymphopoietin (domain)
Thymic stromal lymphopoietin (TSLP) is a cytokine that functions mainly on myeloid cells; it induces the release of T cell-attracting chemokines from monocytes and enhances the maturation of CD11c(+) dendritic cells . TSLP has proliferative effects on the myeloid cell line  and may initiate asthma or atopic dermatitis responses by directly activating mast cells .
Wikipedia: Thymic stromal lymphopoietin (TSLP) is an interleukin (IL)-2-like cytokine, alarmin, and growth factor involved in numerous physiological and pathological processes, primarily those of the immune system. It shares a common ancestor with IL-7.
Pfam PF03991: Copper binding octapeptide repeat region (disordered)
This repeat is found at the amino terminus of prion proteins. It has been shown to bind to copper.
Pfam PF09064: Thrombomodulin like fifth domain, EGF-like (domain)
Members of this family adopt a fold similar to other EGF domains, with a flat major and a twisted minor beta sheet. Disulphide pairing, however, is not of the usual 1-3, 2-4, 5-6 type; rather 1-2, 3-4, 5-6 pairing is found. Its extended major sheet (strands beta-2 and beta-3 and the connecting loop) projects into thrombin's active site groove. This domain is required for interaction of thrombomodulin with  thrombin, and subsequent activation of protein-C.
Pfam PF23639: Domain of unknown function (DUF7146) (domain)
This domain is found in uncharacterised bacterial proteins. It has significant sequence similarity to the alpha+beta domain found in DNA primases 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 PF17322: Family of unknown function (DUF5364) (family)
This family of unknown function is found 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 PF21111: CDI toxin restriction endonuclease-like domain (domain)
Contact-dependent growth inhibition (CDI) systems encode polymorphic toxin/immunity proteins that mediate competition between neighbouring bacterial cells. Despite sharing little sequence identity, the toxin domains are structurally similar and have homology to endonucleases. The EC869 toxin is a Zn(2+)-dependent DNase capable of completely degrading the genomes of target cells.
Pfam PF12358: Domain of unknown function (DUF3644) (domain)
This entry represents a HEPN-like domain found in bacterial proteins. The AlphaFold structures show this entry is a part of the Nucleotidyltransferase substrate binding domain superfamily.
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 PF00719: Inorganic pyrophosphatase (domain)
Inorganic pyrophosphatase (3.6.1.1) (PPase)  is the enzyme responsible for the hydrolysis of pyrophosphate (PPi) which is formed principally as the product of the many biosynthetic reactions that utilise ATP. All known PPases require the presence of divalent metal cations, with magnesium conferring the highest activity. Among other residues, a lysine has been postulated to be part of or close to the active site. PPases have been sequenced from bacteria such as Escherichia coli (homohexamer), Bacillus PS3 (Thermophilic bacterium PS-3) and Thermus thermophilus, from the archaebacteria Thermoplasma acidophilum, from fungi (homodimer), from a plant, and from bovine retina. In yeast, a mitochondrial isoform of PPase has been characterised which seems to be involved in energy production and whose activity is stimulated by uncouplers of ATP synthesis.

The sequences of PPases share some regions of similarities, among which is a region that contains three conserved aspartates that are involved in the binding of cations.
Wikipedia: Inorganic pyrophosphatase is an enzyme that catalyzes the conversion of one ion of pyrophosphate to two phosphate ions. This is a highly exergonic reaction, and therefore can be coupled to unfavorable biochemical transformations in order to drive these transformations to completion. The functionality of this enzyme plays a critical role in lipid metabolism, calcium absorption and bone formation, and DNA synthesis, as well as other biochemical transformations.
Pfam PF08423: Rad51 (domain)
Rad51 is a DNA repair and recombination protein and is a homologue of the bacterial ATPase RecA protein.
Pfam PF04507: Csa1 family (domain)
This family contains several uncharacterised staphylococcal proteins. These proteins have been called conserved staphylococcal antigens (Csa).
Pfam PF06569: Protein of unknown function (DUF1128) (family)
This family consists of several short, hypothetical bacterial proteins 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 PF15132: Domain of unknown function (DUF4568) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes.
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 PF00806: Pumilio-family RNA binding repeat (repeat)
Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA).  Other proteins that contain Puf domains are also plausible RNA binding proteins. [swissprot:P47135], for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognise all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure.
Pfam PF17782: DprA winged helix domain (domain)
This winged helix domain is found in the DprA protein.
Pfam PF08391: Ly49-like protein, N-terminal region (family)
The sequences making up this family are annotated as, or are similar to, Ly49 receptors (e.g. [swissprot:P20937]). These are type II transmembrane receptors expressed by mouse natural killer (NK) cells. They are classified as being activating (e.g.Ly49D and H) or inhibitory (e.g. Ly49A and G), depending on their effect on NK cell function. They are members of the C-type lectin receptor superfamily, and in fact in many family members this region is found immediately N-terminal to a lectin C-type domain ([pfam:PF00059]).
Pfam PF08899: Domain of unknown function (DUF1844) (domain)
This family of proteins are functionally uncharacterised.
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 PF23043: UBE2O, SH3-B domain (domain)
This domain is found in the human E3-independent E2 ubiquitin-conjugating enzyme UBE2O and related proteins. UBE2O is involved in the monoubiquitination of diverse targets to mediate important processes such as targeting proteins for quality control, regulation of nuclear trafficking of chromatin-associated proteins and clearing ribosomes during erythropoiesis. UBE2O is a multidomain protein composed of several SH3-like domains, UBC domain and a CR3 helix. The domain represented by this entry folds into an open beta-barrel with typical SH3 topology. It precedes the ubiquitin binding SH3-like domain.
Pfam PF22924: Acyl-CoA oxidase, C-alpha1 domain (domain)
This entry represents the C-alpha1 domain from acyl-CoA oxidases which has an all-alpha helical structure that a forms a four-helix bundle. This domain includes the FAD-binding and substrate-binding sites.
Pfam PF06121: Domain of Unknown Function (DUF959) (domain)
This N-terminal domain is not expressed in the 'Short' isoform of Collagen A.
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 PF00614: Phospholipase D Active site motif (family)
Phosphatidylcholine-hydrolysing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways.  PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, and/or asparagine residues which may contribute to the active site. aspartic acid.  An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not been achieved.
Wikipedia: Phospholipase D (EC 3.1.4.4, lipophosphodiesterase II, lecithinase D, choline phosphatase, PLD; systematic name phosphatidylcholine phosphatidohydrolase) is an anesthetic sensitive and mechanosensitive enzyme of the phospholipase superfamily that catalyses the following reactiona phosphatidylcholine + H2O = choline + a phosphatidate
Pfam PF12493: Protein of unknown function (DUF3709) (family)
This domain family is found in bacteria, and is approximately 30 amino acids in length. There are two conserved sequence motifs: RCLMK and LIEL.
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 PF18241: Flax-rust effector AvrM-A (domain)
This domain is found in AvrM-A present in Melampsora lini. AvrM-A is a natural variant of AvrM which is a secreted effector protein that can internalize into plant cells in the absence of the pathogen and bind to phosphoinositides. AvrM results in effector-triggered immunity. This domain makes up part of the C-terminal region, which is highly conserved in AvrM. The domain is required for M-dependent effector-triggered immunity.
Pfam PF07624: Protein of unknown function (DUF1585) (family)
A conserved sequence region at the C terminus of several cytochrome-like proteins in Rhodopirellula baltica.
Pfam PF02500: Probable DNA packing protein, N-terminus (family)
This family includes proteins that are probably involved in DNA packing in herpesvirus. This domain is normally found at the N-terminus of the protein.
Pfam PF12526: Protein of unknown function (DUF3729) (family)
This family of proteins is found in viruses. Proteins in this family are typically between 145 and 1707 amino acids in length. The family is found in association with [pfam:PF01443], [pfam:PF01661], [pfam:PF05417], [pfam:PF01660], [pfam:PF00978]. There is a single completely conserved residue 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 PF00651: BTB/POZ domain (domain)
The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger ([pfam:PF00096]) proteins and in proteins that contain the [pfam:PF01344] motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer.  The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.
Wikipedia: The BTB/POZ domain is a structural domain found in proteins across the domain Eukarya. Given its prevalence in eukaryotes and its absence in Archaea and bacteria, it likely arose after the origin of eukaryotes. While primarily a protein-protein interaction domain, some BTB domains have additional functionality in transcriptional regulation, cytoskeletal mobility, protein ubiquitination and degradation, and ion channel formation and operation. BTB domains have traditionally been classified by the other structural features present in the protein.
Pfam PF14680: FANCI helical domain 2 (repeat)
This is the helical domain 2 (HD2) of the Fanconi anemia group I protein.
Pfam PF19030: Thrombospondin type 1 domain (domain)
This subfamily of thrombospondin type 1 repeats are mainly found in ADAMTS proteins.
Pfam PF15622: Kinetochore assembly subunit CENP-C N-terminal (family)
CENP-C is a vertebrate family that forms a core component of the centromeric chromatin. On depletion of CENP-C proper formation of both centromeres and kinetochores is prevented. The N-terminal of CENP-C is necessary for recruitment of some but not all components of the Mis12 complex of the kinetochore.
Pfam PF19153: Family of unknown function (DUF5835) (family)
This entry represents a family of uncharacterised proteins of unknown function found in Lactobacillus salivarius. It is associated with the biosynthetic gene cluster for the bacteriocin salivaricin CRL 1328, which is similar to the gene cluster for the bacteriocin ABP118 .
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 PF15550: Draxin (family)
This family of proteins inhibit Wnt signaling and act as chemorepulsive axon guidance molecules.
Pfam PF06317: Arenavirus RNA polymerase (family)
This family consists of several Arenavirus RNA polymerase proteins ([ec:2.7.7.48]).
Pfam PF20850: Oedema factor (EF), alpha-helical domain (domain)
This domain is found in Oedema factor (EF), the exotoxin with adenylyl cyclase activity produced by Bacillus anthracis to increase the concentration of cyclic AMP in infected host cells and disrupts intracellular signalling pathways. EF consists of four domains: a PA-binding domain (PABD), two adenylate cyclase domains (ACD) and a helical domain (HD, this entry). HD moves and forms a large clamp that almost completely encircles EF's activator calmodulin (CaM), naturally present in host cells, stabilizing a disordered loop and leading to enzyme activation.
Pfam PF14547: Hydrophobic seed protein (domain)
This domain has a four-helix bundle structure. It contains four disulfide bonds, of which three function to keep the C- and N-terminal parts of the molecule in place.