SII-SWORD/CoKE huggingface dataset:
Pfam PF16303: Domain of unknown function (DUF4945) (family)
This small family consists of uncharacterized proteins around 140 residues in length and is mainly found in various Bacteroides species, such as Bacteroides fragilis and Bacteroides sp.. The function of this family is unknown.
Pfam PF19537: Family of unknown function (DUF6061) (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. Several proteins in this family are annotated as toxin-antitoxin system 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 PF02737: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain (domain)
This family also includes lambda crystallin.
Pfam PF17272: Family of unknown function (DUF5337) (family)
This family of unknown function is found in Rhodobacterales. Most members are predicted to have 2 trans-membrane regions.
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 PF23321: ABCA1-like, C-terminal R1 regulatory domain (domain)
This domain is found at the C-terminal end of human Phospholipid -transporting ATPase ABCA1 and similar sequences predominantly found in animals. ABCA1 catalyses the translocation of specific phospholipids from the cytoplasmic to the extracellular/lumenal leaflet of membrane coupled to the hydrolysis of ATP. This entry represents the regulatory domain R2 which shows a beta-sheet and two alpha-helices on one side.
Pfam PF02739: 5'-3' exonuclease, N-terminal resolvase-like domain (domain)
The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures ([prositedoc:PDOC00658]) are never found outside the '53EXO' domains. The latter are found in more diverse proteins . The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families.

In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures.
This entry represents the N-terminal resolvase-like domain, which has a 3-layer Î±/Î²/Î± core structure and contains an Î±-helical arch .
Pfam PF02911: Formyl transferase, C-terminal domain (domain)
Methionyl-tRNA formyltransferase (2.1.2.9) transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA. The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and by impairing its binding to EFTU-GTP. This family also includes formyltetrahydrofolate dehydrogenases, which produce formate from formyl-tetrahydrofolate. These enzymes contain an N-terminal domain in common with other formyl transferase enzymes (IPR002376). The C-terminal domain has an open Î²-barrel fold .
Pfam PF06076: Orthopoxvirus F14 protein (family)
This family consists of several short Orthopoxvirus F14 proteins. The function of this protein is unknown.
Pfam PF04155: Ground-like domain (domain)
This family consists of the ground-like domain and is specific to C.elegans. It has been proposed that the ground-like domain containing proteins may bind and modulate the activity of Patched-like membrane molecules, reminiscent of the modulating activities of neuropeptides.
Pfam PF18357: Diphteria toxin repressor SH3 domain (domain)
This is an SH3 domain which can be found in diphtheria toxin repressor (DtxR) proteins. DtxR) from Corynebacterium diphtheriae regulates the expression of the gene on corynebacteriophages that encodes diphtheria toxin (DT). Other genes regulated by DtxR include those that encode proteins involved in siderophore-mediated iron uptake.
Pfam PF17108: N-terminal small S protein of HET, non-prionic (family)
HET-S is an N-terminal domain on various fungal STAND proteins. The function is not known exactly.
Pfam PF19510: Protein of unknown function (DUF6044) (family)
This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 557 and 582 amino acids in length. There is a conserved YNG sequence motif.
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 PF13470: PIN domain (domain)
Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).
Wikipedia: In molecular biology the PIN domain is a protein domain that is about 130 amino acids in length. PIN domains function as nuclease enzymes that cleave single stranded RNA in a sequence- or structure-dependent manner.
Pfam PF09236: Alpha-haemoglobin stabilising protein (domain)
Alpha-haemoglobin stabilising protein (AHSP) acts a molecular chaperone for free alpha-haemoglobin, preventing the harmful aggregation of alpha-haemoglobin during normal erythroid cell development: it specifically protects free alpha-haemoglobin from precipitation. AHSP adopts a helical secondary structure consisting of an elongated antiparallel three alpha-helix bundle.
Pfam PF05792: Candida agglutinin-like (ALS) (repeat)
This family consists of several agglutinin-like proteins from different Candida species. ALS genes of Candida albicans encode a family of cell-surface glycoproteins with a three-domain structure. Each Als protein has a relatively conserved N-terminal domain, a central domain consisting of a tandemly repeated motif of variable number, and a serine-threonine-rich C-terminal domain that is relatively variable across the family. The ALS family exhibits several types of variability that indicate the importance of considering strain and allelic differences when studying ALS genes and their encoded proteins. Fungal adhesins, which include sexual agglutinins, virulence factors, and flocculins, are surface proteins that mediate cell-cell and cell-environment interactions. It is possible that both the serine/threonine-rich domain and the cysteine residues in the C-terminal and DIPSY [pfam:PF11763] participate in anchoring the terminal domains inside the wall, so that only the inner part of Map4p, including the repeat region, is sticking out as a fold-back loop then able to act in adhesing.
Pfam PF24811: DE-cadherin, Ig-like domain (domain)
Cadherins are calcium-dependent cell adhesion proteins. This immunoglobulin-like (Ig-like) domain is found in DE-cadherin from Drosophila melanogaster (Shg) and similar sequences.
Pfam PF12845: TBD domain (family)
The Tbk1/Ikki binding domain (TBD) is a 40 amino acid domain able to bind kinases, has been found to be essential for poly(I:C)-induced IRF activation. The domain is found in SINTBAD, TANK and NAP1 protein. This domain is predicted to form an a-helix with residues essential for kinase binding clustering on one side.
Pfam PF04377: Arginine-tRNA-protein transferase, C terminus (family)
This family represents the C terminal region of the enzyme arginine-tRNA-protein transferase (EC 2.3.2.8), which catalyses the post-translational conjugation of arginine to the N terminus of a protein. In eukaryotes, this functions as part of the N-end rule pathway  of protein degradation by conjugating a destabilising amino acid to the amino terminal aspartate or glutamate of a protein, targeting the protein for ubiquitin-dependent proteolysis.  N terminal cysteine is sometimes  modified.
Pfam PF11181: Heat induced stress protein YflT domain (domain)
YflT is a heat induced protein. According to AlphaFold this domain is composed of a core of four beta strands that form a central beta sheet with alpha helices packed on both side. This family shows sequence similarity to [pfam:PF11821] which includes the ActD protein which forms an accessory component of the Alternative complex III which catalyses the oxidation of membrane-bound quinol and the reduction of cytochrome c or an equivalent electron carrier. This suggests that members of this family may also be involved in forming larger redox complexes.
Pfam PF24538: Domain of unknown function (DUF7599) (domain)
This is a domain of unknown function found in a group of uncharacterised proteins from plants and some fungal species. This domain is usually found associated with [pfam:PF23704] and [pfam:PF04182].
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 PF08654: DASH complex subunit Dad2 (family)
The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro.
Pfam PF07944: Beta-L-arabinofuranosidase, GH127 catalytic domain (repeat)
This entry represents the catalytic domain of Non-reducing end beta-L-arabinofuranosidase from Bifidobacterium longum (Beta -AFase) and similar proteins that belong to the glycoside hydrolase family 127 (GH127). This domain folds into an (alpha /alpha)6 barrel. Beta-AFase has been characterised as an unusual beta-L-arabinofuranosidase enzyme, [ec:3.2.1.185]. It releases l-arabinose from the l-arabinofuranose (Araf)-beta1,2-Araf disaccharide and also transglycosylates 1-alkanols with retention of the anomeric configuration.
Pfam PF17895: Giardia Dicer N-terminal domain (domain)
This is the N-terminal domain found in dicer proteins from Giardia intestinalis. The N-terminal region (i.e. the platform domain) forms a flat surface composed of antiparallel beta sheet and three alpha helices. This surface contains a large positively charged region that could interact directly with the negatively charged phosphodiester backbone of the modeled dsRNA helix.
Pfam PF23889: Domain of unknown function (DUF7241) (domain)
This entry represents a family of small phage proteins found in a variety of mycobacteriophage genomes. The family members are typically around 70-75 amino acids in length. The function of these proteins is currently 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 PF10827: Protein of unknown function (DUF2552) (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 PF00639: PPIC-type PPIASE domain (domain)
Rotamases increase the rate of protein folding by catalysing the interconversion of cis-proline and trans-proline.
Wikipedia: Prolyl isomerase is an enzyme found in both prokaryotes and eukaryotes that interconverts the cis and trans isomers of peptide bonds with the amino acid proline. Proline has an unusually conformationally restrained peptide bond due to its cyclic structure with its side chain bonded to its secondary amine nitrogen. Most amino acids have a strong energetic preference for the trans peptide bond conformation due to steric hindrance, but proline's unusual structure stabilizes the cis form so that both isomers are populated under biologically relevant conditions. Proteins with prolyl isomerase activity include cyclophilin, FKBPs, and parvulin, although larger proteins can also contain prolyl isomerase domains.
Pfam PF05562: Cold acclimation protein WCOR413 (family)
This family consists of several WCOR413-like plant cold acclimation proteins.
Pfam PF06792: Uncharacterised protein family (UPF0261) N-terminal domain (domain)
This entry represents the N-terminal domain of ToMV resistance protein Tm-1 and the uncharacterised UPF0261 proteins. The tomato resistance protein Tm-1, which inhibits replication complex formation through its binding to tomato mosaic virus (ToMV) replication proteins. It contains an ATP-binding site required for interaction with ToMV proteins .
Pfam PF15177: Interleukin-28A (domain)
The protein family, Interleukin-28A, plays an important role in modulating the immune system. This protein family is induced by viral infection and interacts with a class II receptor. This family of proteins is found in eukaryotes. Proteins in this family are typically between 145 and 195 amino acids in length.
Wikipedia: The type III interferon group is a group of anti-viral cytokines, that consists of four IFN-λ (lambda) molecules called IFN-λ1, IFN-λ2, IFN-λ3, and IFN-λ4. They were discovered in 2003. Their function is similar to that of type I interferons, but is less intense and serves mostly as a first-line defense against viruses in the epithelium.
Pfam PF01140: Matrix protein (MA), p15 (domain)
Matrix proteins are produced as part of Gag precursor polyproteins.  During viral maturation, the Gag polyprotein is cleaved into major  structural proteins by the viral protease, yielding the matrix (MA),  capsid (CA), nucleocapsid (NC), and some smaller peptides.  Gag-derived proteins govern the entire assembly and release of the  virus particles, with matrix proteins playing key roles in Gag  stability, capsid assembly, transport and budding. Although matrix  proteins from different retroviruses appear to perform similar  functions and can have similar structural folds which predominantly  consist of four closely packed alpha-helices that are interconnected  through loops, their primary sequences can be very different. The matrix protein, p15, is encoded by the gag gene. MA is involved in pathogenicity.
Wikipedia: Retroviral matrix proteins are components of envelope-associated capsids of retroviruses. These proteins line the inner surface of viral envelopes and are associated with viral membranes.
Pfam PF24490: Domain of unknown function (DUF7585) (domain)
This is a presumed domain found at the N-terminal of uncharacterised sequences from Strongyloides species. This domain may consist of a beta-sandwich 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 PF03736: EPTP domain (repeat)
Mutations in the LGI/Epitempin gene can result in a special form of epilepsy, autosomal dominant lateral temporal epilepsy. The Epitempin protein contains a large repeat in its C terminal section.  The architecture and structural features of this repeat make it a likely member 7-bladed beta-propeller fold.
Pfam PF07054: Pericardin like repeat (repeat)
This family consists of several repeated sequences of around 34 residues in length. This repeat is found in multiple copies in the Drosophila pericardin and other extracellular matrix proteins.
Pfam PF14822: Vasohibin (domain)
This family of proteins function as angiogenesis inhibitors in animals. Reversible detyrosination of alpha-tubulin is crucial to microtubule dynamics and functions and defects have been implicated in cancer, brain disorganization, and cardiomyopathies. VASH1 and its homolog VASH2, when complexed with SVBP, exhibited robust and specific Tyr/Phe carboxypeptidase activity on microtubules.
Pfam PF04629: Islet cell autoantigen ICA69, C-terminal domain (domain)
This family includes a 69 kD protein which has been identified as an islet cell autoantigen in type I diabetes mellitus. Its precise function is unknown.
Pfam PF25106: von Willebrand factor A domain (domain)
This domain is found in a number of proteins including VWA7, HMCN1, HMCN2, irg-7 and others.
Wikipedia: The von Willebrand factor type A (vWA) domain is a protein domain named after its occurrence in von Willebrand factor (vWF), a large multimeric glycoprotein found in blood plasma. Mutant forms of vWF are involved in the aetiology of bleeding disorders. This type A domain is the prototype for a protein superfamily.
Pfam PF19182: Family of unknown function (DUF5864) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in Mimiviridae.
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 PF19455: Family of unknown function (DUF5993) (family)
This family of integral membrane proteins is found primarily in proteobacteria. Proteins in this family are approximately 50 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 PF14541: Xylanase inhibitor C-terminal (domain)
This domain is found C-terminal in some aspartic proteinases and in xylanase inhibitors. The activity of these proteins is vital for plant-survival as xylanase produced by phytopathogens destroys plant cells. In TAXI-type inhibitors, this domain is important for the differences in xylanase specificity.
Pfam PF21897: Domain of unknown function (DUF6919) (domain)
This domain is found standalone in bacteria. Its function is unknown but it has a significant sequence similarity to the C-terminal SAM-binding regulatory domain of 5,10-methylenetetrahydrofolate reductase (MTHFR).
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 PF20277: C-terminal domain 11 of the ABC-three component (ABC-3C) systems (domain)
C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector.
Pfam PF16999: Vacuolar (H+)-ATPase G subunit (coiled_coil)
This family represents vacuolar (H+)-ATPase G subunit from several bacterial and archaeal species. Subunit G is a component of the peripheral stalk of the ATPase complex
Pfam PF15336: Autism susceptibility gene 2 protein (family)
Auts2, or FBRSL2, Fibrosin-1-like protein 2, is a family of eukaryotic proteins associated both with a susceptibility to autism and with influencing the number of corpora lutea produced by breeding sows.
Pfam PF01005: Flavivirus non-structural protein NS2A (family)
NS2A is a hydrophobic protein about 25 kDa is size.  NS2A is cleaved from NS1 by a membrane bound host protease.  NS2A has been found to associate with the dsRNA within the vesicle packages.  It has also been found that NS2A associates with the known replicase components and so NS2A has been postulated to be part of this replicase complex.
Pfam PF13822: Acyl-CoA carboxylase epsilon subunit (family)
This family includes the epsilon subunits of propionyl-CoA carboxylase, [ec:6.4.1.3], and acetyl-CoA carboxylase, [ec:6.4.1.2]. These enzymes are involved in the biosynthesis of long-chain fatty acids. The epsilon subunit is necessary for an efficient interaction between the alpha and beta subunits of these enzymes.
Pfam PF22373: Organelle protein MG491, central domain (domain)
This domain is found in the organelle protein MG491 (also known as MG218.1) from Mycoplasma genitalium. MG491 plays a key role in the functioning, organisation and stabilisation of the terminal organelle, a protrusion of the bacterial cell membrane responsible for its flask-shaped morphology. This protein is organised into a 60-residue N-terminus, a central three-helix-bundle (this entry) and a C-terminal region.
Pfam PF07953: Clostridium neurotoxin, N-terminal receptor binding (domain)
The Clostridium neurotoxin family is composed of tetanus neurotoxin and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein.  The N-terminal catalytic domain ([pfam:PF01742]), the central translocation domains and two receptor binding domains. This domains is the N-terminal receptor binding domain,which is  comprised of two seven-stranded beta-sheets sandwiched together to form a jelly role motif. The role of this domain in receptor binding appears to be indirect.