SII-SWORD/CoKE huggingface dataset:
Pfam PF24370: Family of unknown function (DUF7526) (family)
This family includes a group of short archaeal proteins. Members are predicted to adopt an alpha-beta configuration.
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 PF13955: Toxin Fst, type I toxin-antitoxin system (domain)
Fst (faecalis plasmid stabilization toxin), also known as RNA I, is a toxic peptide. Its N-terminus forms a transmembrane alpha helix, its C terminus is disordered and is likely to be cytosolic. Its translation is inhibited by the antisense RNA, RNA II, which acts as an antitoxin.
Wikipedia: The par stability determinant is a 400 bp locus of the pAD1 plasmid which encodes a type I toxin-antitoxin system in Enterococcus faecalis. It was the first such plasmid addiction module to be found in gram-positive bacteria.
Pfam PF12420: Fam-L, Fam-M like protein (family)
This entry represents a large set of plasmodium proteins found in high copy number in subtelomeric repeats. It has been suggested that these proteins may pair to form heterodimers. Structure prediction suggests these proteins are related to RH5 and therefore may also have an adhesion role, possibly binding host receptors.
Pfam PF07255: Benyvirus 14KDa protein (family)
This family consists of several Benyvirus specific 14KDa proteins of around 125 residues in length. Members of this family contain 9 conserved cysteine residues. The function of this family is unknown.
Pfam PF21184: Fungal HAT1, C-terminal (domain)
Histone acetyltransferase type B catalytic subunit (HAT1) is the catalytic subunit of the histone acetylase B (HAT-B) complex (composed on HAT1 and HAT2 at least). It DNA double-strand break repair. Yeast HAT1 specifically acetylates H4 at Lys5 and Lys12 residues. The C-terminal domain of HAT1 (this entry) is highly variable and not required for HAT activity. It consists of a bundle of helices and a short beta-strand. This entry includes HAT1 from Fungi.
Pfam PF12148: Tandem tudor domain within UHRF1 (domain)
TTD, tandem tudor domain within UHRF1 preferentially binds H3 histone tails trimethylated at Lys-9. It specifically recognises H3 tail peptides with the heterochromatin-associated modification state of trimethylated lysine 9 and unmodified lysine 4 (H3K4me0/K9me3). This domain is found in eukaryotes and is found in association with [pfam:PF00097], [pfam:PF02182], [pfam:PF00628], [pfam:PF00240].
Pfam PF03052: Adenoviral protein L1 52/55-kDa (family)
The adenoviral protein L1 52/55-kDa is expressed in both the early and late stages of infection which suggests that it could play multiple roles in the viral life cycle.  The L1 52/55 kDa protein interacts with the viral IVa2 protein and is required for DNA packaging. L1 53/55-kDa is required to mediate stable association between the viral DNA and empty capsid.
Pfam PF11798: IMS family HHH motif (conserved_site)
These proteins are involved in UV protection, eg ([swissprot:P07375]).
Pfam PF18586: Chromatin remodeling factor Mit1 C-terminal Zn finger 1 (domain)
The Snf2/Hdac Repressive Complex (SHREC) is the fission yeast nucleosome remodeling and deacetylation (NuRD) equivalent and plays a major role in transcriptional gene silencing (TGS) within S. pombe heterochromatin. SHREC consists of the chromatin remodeler Mit1, the HDAC Clr3, and Clr1 and Clr2 proteins. The Mit1 C terminus contains two zinc binding motifs (CCHC zinc fingers) at the C-terminus onto which the alpha helices from both Clr1 and Mit1 pack. The Mit1 chromatin remodeler uses its C-terminal domain to intimately bind to the N-terminal half of Clr1 to integrate into the SHREC complex. This is entry represents the first C-terminal zinc-binding domain found on Mit-1.
Pfam PF02916: DNA polymerase processivity factor (domain)
The DNA polymerase processivity factor is a replisome sliding clamp subunit, which is responsible for tethering the catalytic subunit of DNA polymerase to the DNA during high speed replication. The crystal structure of the Bacteriophage RB69 sliding clamp has been solved. It has shown that the peptide binds to the sliding clamp at the same position as that of a replication inhibitor peptide bound to PCNA. This suggests that the replication inhibitor protein p21CIP1 competes with eukaryotic polymerases for the same binding pocket on the clamp .
Wikipedia: A DNA clamp, also known as a sliding clamp, is a protein complex that serves as a processivity-promoting factor in DNA replication. As a critical component of the DNA polymerase III holoenzyme, the clamp protein binds DNA polymerase and prevents this enzyme from dissociating from the template DNA strand. The clamp-polymerase protein–protein interactions are stronger and more specific than the direct interactions between the polymerase and the template DNA strand; because one of the rate-limiting steps in the DNA synthesis reaction is the association of the polymerase with the DNA template, the presence of the sliding clamp dramatically increases the number of nucleotides that the polymerase can add to the growing strand per association event. The presence of the DNA clamp can increase the rate of DNA synthesis up to 1,000-fold compared with a nonprocessive polymerase.
Pfam PF17084: Topoisomerase I damage affected protein 11 (family)
Tda11 is a fungal protein family. The function is unknown.
Pfam PF03169: OPT oligopeptide transporter protein (family)
The OPT family of oligopeptide transporters is distinct from the ABC [pfam:PF00005] and PTR [pfam:PF00854] transporter families. OPT transporters were first recognised in fungi (Candida albicans and Schizosaccharomyces pombe), but this alignment also includes orthologues from Arabidopsis thaliana. OPT transporters are thought to have 12-14 transmembrane domains and contain the following motif: SPYxEVRxxVxxxDDP.
Pfam PF03477: ATP cone domain (domain)
The ATP-cone is an evolutionarily mobile, ATP-binding regulatory domain which is found in a variety of proteins including ribonucleotide reductases, phosphoglycerate kinases and transcriptional regulators .

In ribonucleotide reductase protein R1 (P28903) from Escherichia coli this domain is located at the N terminus, and is composed mostly of helices . It forms part of the allosteric effector region and contains the general allosteric activity site in a cleft located at the tip of the N-terminal region . This site binds either ATP (activating) or dATP (inhibitory), with the base bound in a hydrophobic pocket and the phosphates bound to basic residues. Substrate binding to this site is thought to affect enzyme activity by altering the relative positions of the two subunits of ribonucleotide reductase.
Wikipedia: In molecular biology, the ATP-cone is an evolutionarily mobile, ATP-binding regulatory domain which is found in a variety of proteins including ribonucleotide reductases, phosphoglycerate kinases and transcriptional regulators.
Pfam PF03973: Triabin (domain)
Triabin is a serine-protease inhibitor with a calycin fold.
Pfam PF09332: Mcm10, C-terminal zinc binding motif (domain)
This is the C-terminal zinc binding motif of Mcm10, a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha. This motif is structurally similar to the zinc ribbon in the N-terminal domain of eukaryotic and archaeal MCM helicases.
Pfam PF07935: ORF D-335-like protein (family)
The sequences featured in this family are similar to  a probable integrase ([swissprot:P20214]) expressed by the SSV1 virus of the archaebacterium Sulfolobus shibatae. This protein may be necessary for the integration of the virus into the host genome by a process of site-specific  recombination.
Pfam PF04186: FxsA cytoplasmic membrane protein (family)
This is a bacterial family of cytoplasmic membrane proteins. It includes two transmembrane regions. The molecular function of FxsA is unknown, but in Escherichia coli its over-expression has been shown to alleviate the exclusion of phage T7 in those cells with an F plasmid.
Pfam PF17244: Cell division control protein 24, OB domain 3 (domain)
This family contains OB-fold domains that bind to nucleic acids. The family includes a domain found in Cell division control protein 24 (Cdc24). Cdc24 plays an essential role in the progression of normal DNA replication and is required to maintain genomic integrity. Cdc24 has been reported to interact with replication factor C (RFC) as well as proliferating cell nuclear antigen (PCNA), and has been suggested to act as a target for the regulation of damage repair DNA synthesis.
Pfam PF13128: Protein of unknown function (DUF3954) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 60 amino acids in length.
Pfam PF09476: Pilus biogenesis CpaD protein (pilus_cpaD) (family)
Proteins in this entry consist of a pilus biogenesis protein, CpaD, from Caulobacter, and homologues in other bacteria, including three in the root nodule bacterium Bradyrhizobium japonicum. The molecular function of the homologues is not known.
Pfam PF01744: GLTT repeat (6 copies) (repeat)
This short repeat of unknown function is found in multiple copies in several C. elegans proteins. The repeat is five residues long and consists of XGLTT where X can be any amino acid.
Pfam PF04315: Elongation factor P hydroxylase (family)
This family catalyses the final step in the elongation factor P modification pathway. It hydroxylates Lys-34 of elongation factor P.  Members of this family have a conserved HEXXH motif, suggesting they are putative peptidases of zincin fold.
Pfam PF21990: SH2 domain (domain)
The SH2 domain is a protein module that folds to form a pocket into which a phosphorylated tyrosine residue fits. SH2 domains discriminate their targets by making important contacts with residues from position +1 up to +4 in the ligand peptide. SH2 domain comprises two alpha-helices packed against each side of a central beta-sheet.
Pfam PF23193: NOMO third transthyretin-like domain (domain)
This domain is found in the family of human Nodal modulators NOMO1, NOMO2, NOMO3 and in other related proteins. The Nodal modulators are components of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the membrane lipid bilayer. They play important role in the protein topogenesis and cells lacking these components show reduced multipass protein stability. The domain represented by this entry has a weak sequence similarity to Transthyretin-like domains and it is predicted to adopt similar structure that consists of seven-stranded beta-sandwich. Nodal modulators are predicted to contain a tandem of twelve Transthyretin-like domains and this domain is the third in the tandem.
Pfam PF01998: Protein of unknown function DUF131 (family)
This archaebacterial protein family has no known function. The proteins are predicted to contain two transmembrane helices.
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 PF04593: Selenoprotein P, C terminal region (family)
SelP is the only known eukaryotic selenoprotein that contains multiple selenocysteine (Sec) residues, and accounts for more than 50% of the selenium content of rat and human plasma. It is thought to be glycosylated. SelP may have antioxidant properties.  It can attach to epithelial cells, and may protect vascular endothelial cells against peroxynitrite toxicity. The high selenium content of SelP suggests that it may be involved in selenium intercellular transport or storage. The promoter structure of bovine SelP suggest that it may be involved in countering heavy metal intoxication, and may also have a developmental function. The N terminal region always contains one Sec residue, and this is separated from the C terminal region (9-16 sec residues) by a histidine-rich sequence.  The large number of Sec residues in the C-terminal portion of SelP suggest CC that it may be involved in selenium transport or storage. However, it is also possible that this region has a redox function.
Wikipedia: In molecular biology, the protein domain selenoprotein P (SelP) is the only known eukaryotic selenoprotein that contains multiple selenocysteine (Sec) residues. It is a secreted glycoprotein, often found in the plasma. Its precise function remains to be elucidated; however, it is thought to have antioxidant properties. This particular protein contains two domains: the C terminal and N terminal domain. The N-terminal domain is larger than the C terminal and the N-terminal is thought to be glycosylated.
Pfam PF08318: COG4 transport protein, middle alpha-helical bundle (repeat)
This region is found in conserved oligomeric golgi complex component 4. COG mediates the proper glycosylation of proteins trafficking through the Golgi apparatus and it is a member of the CATCHR (complexes associated with tethering containing helical rods) family, together with the exocyst, GARP and DSL1 complexes, sharing structural and functional features. They consist of alpha-helical bundles at the middle/C-terminal (described as domains A-D/E) and a N-terminal coiled-coil region. This entry represents the middle region comprising alpha-helical bundles corresponding to domains B and C. Mutations in COG4 cause fatal congenital disorders of glycosylation (CDGs) in humans.
Pfam PF23683: U exon (family)
This protein family includes U exon protein from Fowl aviadenovirus 4 and similar viral short sequences.
Pfam PF11285: Protein of unknown function (DUF3086) (family)
This family of proteins with unknown function appears to be restricted to Cyanobacteria.
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 PF11133: Head fiber protein (family)
This head fiber protein is also refereed to as Gp8.5. Gp8.5 is a structural protein in phage. It is a dispensable head protein.
Pfam PF13131: Protein of unknown function (DUF3951) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 56 and 71 amino acids in length. There is a conserved YTP sequence motif.
Pfam PF05669: SOH1 (family)
The family consists of Saccharomyces cerevisiae SOH1 homologues. SOH1 is responsible for the repression of temperature sensitive growth of the HPR1 mutant and has been found to be a component of the RNA polymerase II transcription complex. SOH1 not only interacts with factors involved in DNA repair, but transcription as well. Thus, the SOH1 protein may serve to couple these two processes.
Wikipedia: Mediator of RNA polymerase II transcription subunit 31 is a protein in humans encoded by the MED31 gene. It represents subunit Med31 of the Mediator complex. The family contains the Saccharomyces cerevisiae SOH1 homologues. SOH1 is responsible for the repression of temperature sensitive growth of the HPR1 mutant and has been found to be a component of the RNA polymerase II transcription complex. SOH1 not only interacts with factors involved in DNA repair, but transcription as well. Thus, the SOH1 protein may serve to couple these two processes.
Pfam PF25040: BLTP1-like family C-terminal region (repeat)
This entry represents the C-terminal region of a group of very long eukaryotic proteins, including the human BLTP1 (also known as KIAA1109) protein. These proteins are tube-forming lipid transport proteins that belong to theRBG (repeating beta-groove) superfamily. They consist of long hydrophobic grooves made of multiple repeating modules of five beta-sheets followed by a loop. BLTP1 is a tube-forming lipid transport protein which provides phosphatidylethanolamine for glycosylphosphatidylinositol (GPI) anchor synthesis in the endoplasmic reticulum. It plays a role in endosomal trafficking and endosome recycling and it is also involved in the actin cytoskeleton and cilia structural dynamics. BLTP1 also acts as a regulator of phagocytosis. In humans, it has been associated with rheumatoid arthritis. Mutations of the BLTP1 gene has been associated with Alkuraya-Kucinskas syndrome (MIM 617822), a severe disorder of brain development and arthrogryposis.
Pfam PF03731: Ku70/Ku80 N-terminal alpha/beta domain (domain)
The Ku heterodimer (composed of Ku70 [swissprot:P12956] and Ku80 [swissprot:P13010]) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface.  The domain comprises a six stranded beta sheet of the Rossman fold.
Wikipedia: Ku is a dimeric protein complex that binds to DNA double-strand break ends and is required for the non-homologous end joining (NHEJ) pathway of DNA repair. Ku is evolutionarily conserved from bacteria to humans. The ancestral bacterial Ku is a homodimer. Eukaryotic Ku is a heterodimer of two polypeptides, Ku70 (XRCC6) and Ku80 (XRCC5), so named because the molecular weight of the human Ku proteins is around 70 kDa and 80 kDa. The two Ku subunits form a basket-shaped structure that threads onto the DNA end. Once bound, Ku can slide down the DNA strand, allowing more Ku molecules to thread onto the end. In higher eukaryotes, Ku forms a complex with the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to form the full DNA-dependent protein kinase, DNA-PK. Ku is thought to function as a molecular scaffold to which other proteins involved in NHEJ can bind, orienting the double-strand break for ligation.
Pfam PF00928: Adaptor complexes medium subunit family (family)
This family also contains members which are coatomer subunits.
Wikipedia: In molecular biology, the adaptor complexes medium subunit domain is a protein domain found at the C-terminus of the mu subunit from various clathrin adaptor protein complexes and muniscins. The C-terminal domain has an immunoglobulin-like beta-sandwich fold consisting of 9 strands in 2 sheets with a Greek key topology, similar to that found in cytochrome f and certain transcription factors. The mu subunit regulates the coupling of clathrin lattices with particular membrane proteins by self-phosphorylation via a mechanism that is still unclear. The mu subunit possesses a highly conserved N-terminal domain of around 230 amino acids, which may be the region of interaction with other AP proteins; a linker region of between 10 and 42 amino acids; and a less well-conserved C-terminal domain of around 190 amino acids, which may be the site of specific interaction with the protein being transported in the vesicle.
Pfam PF16628: Unstructured region on maltose acetyltransferase (disordered)
Mac_assoc is a region of natively unstructured residues on fungal maltose acetyltransferase proteins.  It lies just upstream of the Mac, [pfam:PF12464], domain linking it with the upstream Zn_clus, [pfam:PF00172], the Zn(2)-Cys(6) binuclear cluster.  the function of this region is not known.
Pfam PF24599: Family of unknown function (DUF7621) (family)
This entry represents a small family of uncharacterised phage 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 PF18742: REase_DpnII-MboI (domain)
REase Fold fused to DpnII/MboI-NTD.
Pfam PF07340: Cytomegalovirus IE1 protein (family)
Expression from a human cytomegalovirus early promoter (E1.7) has been shown to be activated in trans by the IE2 gene product. Although the IE1 gene product alone had no effect on this early viral promoter, maximal early promoter activity was detected when both IE1 and IE2 gene products were present.  The IE1 protein from cytomegalovirus is also known as UL123.
Pfam PF03287: Poxvirus C7/F8A protein (family)
This family includes Poxvirus C7 and F8A proteins. The C7 protein, also known as Interferon antagonist OPG027, inhibits the antiviral activity induced by type I interferons .
Pfam PF15257: Domain of unknown function (DUF4590) (family)
This family of proteins remains to be characterised and is a domain of unknown function. This domain family is found in eukaryotes, and is approximately 120 amino acids in length. There are two conserved sequence motifs: CCE and PCY. In humans, the gene encoding this protein lies in the position, chromosome 1 open reading frame 173.
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 PF24105: CAF1B/HIR1 beta-propeller domain (repeat)
This entry represents the beta-propeller domain found in chromatin assembly factor 1 subunit CAF1B (also known as p60 subunit) from animals, and its homologues Cac2 from yeasts and FAS from plants. These proteins are involved in DNA synthesis-coupled chromatic assembly in S-phase and chromatin assembly following DNA repair alongside other CHAF proteins in what is known as CAF1 complex. In plants, the loss of activity of the CAF1 pathway causes delay and arrest of the cell cycle during pollen development. The CAF1 complex is also required for stable maintenance of telomeres and 45S rDNA in Arabidopsis. This domain is involved in CAF1B interactions with other CAF1 complex subunits. This entry also includes histone cell cycle regulator HIRA from animals and their yeast orthologues HIR1, which are required in replication-independent chromatic assembly. The beta-propeller of HIRA proteins is involved in the protein interactions with Ubinuclein-1 (UBN1) to achieve chromatic-remodelling pathway in senescent cells.
Pfam PF22015: O-succinylbenzoate synthase, N-terminal domain (domain)
This domain is found N-terminal in members of o-succinylbenzoate synthase (OSBS) family. It is also known as capping domain. In most members, this domain consists of a central three-stranded antiparallel beta-sheet packed on one side with two helices. The second helix is truncated or missing in some members of the family.