SII-SWORD/CoKE huggingface dataset:
Pfam PF15277: Exocyst complex component SEC3 N-terminal PIP2 binding PH (domain)
This is the N-terminal domain of fungal and eukaryotic Sec3 proteins. Sec3 is a component of the exocyst complex that is involved in the docking of exocytic vesicles with fusion sites on the plasma membrane.This N-terminal domain contains a cryptic pleckstrin homology (PH) fold, and all six positively charged lysine and arginine residues in the PH domain predicted to bind the PIP2 head group are conserved. The exocyst complex is essential for many exocytic events, by tethering vesicles at the plasma membrane for fusion. In fission yeast, polarised exocytosis for growth relies on the combined action of the exocyst at cell poles and myosin-driven transport along actin cables.
Pfam PF24872: DUF2110 N-terminal domain (domain)
This domain, found in various hypothetical archaeal proteins, has no known function. It is found at the N-terminus of the DUF2110 family 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 PF21458: Selenocysteine-specific elongation factor, winged helix 1/3 (domain)
This domain is found twice in Selenocysteine-specific elongation factor from Escherichia coli (SelB) and in similar proteins mainly found in proteobacteria. SelB is a translation factor necessary for the incorporation of selenocysteine into proteins. SelB is composed of a N-terminal region, which contains [pfam:PF00009] and [pfam:PF03144], and a C-terminal extension that consists of four winged-helix (WH) domains arranged in tandem. This entry represents the first and third of these motifs, each containing three helices flanked by a three-stranded antiparallel beta-sheet.
Pfam PF22512: Colicin S4 translocation domain (domain)
This entry represents the N-terminal translocation domain of Colicin S4 from Escherichia coli (Csa), a polypeptide toxin produced and active against E.coli. This protein consists of four distinct domains, this domain, two receptor-binding domains ([pfam:PF20761]) and the C-terminal pore-forming domain ([pfam:PF01024]). This domain shows an antiparallel beta-sheet formed by three strands, an extended, glycine-rich loop structure and a short helix.
Pfam PF25041: E3 UFM1-protein ligase 1 C-terminal domain (domain)
This domain is found C-terminal in human E3 UFM1-protein ligase 1 (UFL1) and similar eukaryotic sequences. UFL1 mediates ufmylation, the covalent attachment of the ubiquitin-like modifier UFM1 to lysine residues on target proteins, which plays a key role in reticulophagy induced in response to endoplasmic reticulum stress. UFL1 is a component of the UFM1 ribosome E3 ligase (UREL) complex which is involved in the release and recycling of stalled or terminated ribosomes from the ER membrane. This domain is predicted to adopt globular structure consisting of an array of alpha-helices.
Pfam PF16170: Domain of unknown function (DUF4873) (domain)
This family consists mostly of short uncharacterized proteins found in various high GC Gram positive bacteria, primarily Mycobacterium species. However in some proteins, such as for instance Rv0943c proteins from Mycobacterium tuberculosis H37Rv, DUF4873 domain is found at the C-terminus, following the flavin-binding monooxygenase-like domain [pfam:PF00743], which is why probably many proteins with DUF4873 domains are annotated as monooxygenases.  However these functions are not confirmed experimentally and the function of DUF4873 domain is still unknown.
Pfam PF18992: Family of unknown function (DUF5725) (family)
A highly conserved domain of unknown function found in Platyhelminthes.
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 PF16620: Unstructured linker between I-set domains 2 and 3 on MYLCK (disordered)
23ISL is a natively unstructured region lying between the second and third I-set domains on higher eukaryotic myosin light chain kinase (MYLCK) proteins. The function is not known.  It carries a highly conserved TSSTITLQ sequence motif which might be a binding domain.
Pfam PF18953: SAP domain-containing new25 (domain)
This family includes Schizosaccharomyces specific SAP domain containing proteins such as gene product new25 . SAP ( SAF-A/B, Acinus and PIAS) motif is a DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins. For instance, the SAP domain of SUMO E3 ligase PIAS1 from human is shown to bind an A/T-rich DNA.
Pfam PF18114: Suv3 helical N-terminal domain (domain)
This is the N-terminal domain of Suv3 present in Homo sapiens. Suv3 is an NTP-dependent RNA/DNA helicase that is necessary for the degradation of mature mtRNAs. Suv3 has been found to interact in vitro with polynucleotide phosphorylase.
Pfam PF06651: Protein of unknown function (DUF1163) (family)
This family represents the C-terminus of hypothetical Arabidopsis thaliana 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 PF18746: Alpha-glutamyl/putrescinyl thymine pyrophosphorylase clade 3 (domain)
An alpha helical domain related to the alpha-helical DNA glycosylases, predicted to catalyze the in situ synthesis of hypermodified bases such as alpha-glutamyl, putrescinyl thymine, 5-(2-aminoethoxy)methyluridine or 5-(2-aminoethyl)uridine. The enzyme is predicted to utilize a high-energy pyrophosphate DNA base intermediate which is subject to a nucleophilic attack by the modifying moiety. Mainly found in bacterial mobile operons.
Pfam PF07972: NrdI Flavodoxin like (domain)
Ribonucleotide reductases (RNRs) are enzymes that catalyse the conversion of ribonucleotides to the corresponding deoxyribonucleotides to provide the precursors of DNA synthesis. There are three classes (I-III) of RNRs and four known subclasses within class I RNRs (Ia-Id) , which differ by their metal cofactor, their stable organic radical and sequence . Class I consists of two homodimeric subunits: alpha2, which catalyses the reversible one-electron oxidation of a conserved cysteine residue to a thiyl radical, which is initiated by a dinuclear metallocofactor and tyrosyl radical positioned in the beta2 subunit. Class Ib RNR is encoded in four different genes: nrdH, nrdI, nrdE (alpha subunit) and nrdF (beta subunit)  and has Mn2 in the dimetal cluster to oxidize a nearby tyrosine residue to a stable radical.

This family represents NrdI, a flavoprotein activase which provides superoxide that binds to the beta subunit and forms a hydrophilic channel connecting their active sites .
Pfam PF11974: Bacterial alpha-2-macroglobulin MG3 domain (domain)
This is the MG3 domain from bacterial alpha2-macroglobulins.
Pfam PF20728: Nairovirus NSm (domain)
This is a protein of unknown function found in the glycoprotein precursor complex (GPC) encoded in the M segment of nairovirus genome, located between [pfam:PF20726] and [pfam:PF01561].
Pfam PF11747: Killing trait (family)
RebB is one of three proteins necessary for the production of R- bodies, refractile inclusion bodies produced by a small number of bacterial species, essential for the expression of the killing trait of the endosymbiont bacteria that produce them for attack upon the host Paramecium. R-bodies are highly insoluble protein ribbons which coil into cylindrical structures in the cell and the genes for their synthesis and assembly are encoded on a plasmid. One of these three proteins is RebB.
Pfam PF10302: DSC E3 ubiquitin ligase complex subunit 3, ubiquitin-like domain (domain)
This is the N-terminal ubiquitin-like domain of DSC E3 ubiquitin ligase complex subunit 3 (Dsc3). Dsc3 is a component of the DSC E3 ubiquitin ligase complex (a Golgi-specific protein ubiquitination system) that functions in protein homeostasis under non-stress conditions, playing a role in protein quality control through endosome and Golgi-associated degradation pathway (EGAD). Yeast DSC E3 ubiquitin ligase complex is the homologue of Hrd1 E3 ligase complex from mammals, in which Dsc1, Dsc2 and Dsc3 corresponds to Hrd1, Der1 and Usa1, respectively. Dsc3 is a Herp-like protein that acts as a bridge between Dsc1 and Dsc2 for their interaction.
Pfam PF11166: Protein of unknown function (DUF2951) (family)
This family of proteins has no known function. It has a highly conserved sequence.
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 PF12273: Chitin synthesis regulation, resistance to Congo red (family)
RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5.
Pfam PF10097: Predicted membrane protein (DUF2335) (family)
Members of this family of hypothetical bacterial proteins have 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 PF06621: Single-minded protein C-terminus (family)
This family represents the C-terminal region of the eukaryotic single-minded (SIM) protein. Drosophila single-minded acts as a positive master gene regulator in central nervous system midline formation. There are two homologues in mammals: SIM1 and SIM2, which are members of the basic-helix-loop-helix PAS family of transcription factors. SIM1 and SIM2 are novel heterodimerisation partners for ARNT in vitro, and they may function both as positive and negative transcriptional regulators in vivo, during embryogenesis and in the adult organism. SIM2 is thought to contribute to some specific Down syndrome phenotypes. This family is found in conjunction with a [pfam:PF00989] domain and associated [pfam:PF00785] motif.
Pfam PF13316: Protein of unknown function (DUF4087) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 140 and 280 amino acids in length. There is a conserved RCGW 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 PF05007: Mannosyltransferase (PIG-M) (family)
PIG-M has a DXD motif. The DXD motif is found in many glycosyltransferases that utilise nucleotide sugars. It is thought that the motif is involved in the binding of a manganese ion that is required for association of the enzymes with nucleotide sugar substrates.
Pfam PF06916: FAM210A/B-like domain (domain)
This domain is found in mitochondrial proteins, including FAM210A and B, which contains a transmembrane peptide. Its function is not clear. FAM210A, a protein essential in maintaining skeletal muscle structure and strength, interacts with mitochondrial translation elongation factor EF-Tu and promotes mitochondrial protein expression. In FAM210A, this domain is responsible for binding EF-Tu. FAM210B plays a role in erythroid differentiation and is involved in cell proliferation and tumour cell growth suppression.
Pfam PF09582: Iron only nitrogenase protein AnfO (AnfO_nitrog) (family)
Proteins in this entry include Anf1 from Rhodobacter capsulatus (Rhodopseudomonas capsulata) and AnfO from Azotobacter vinelandii. They are found exclusively in species which contain the iron-only nitrogenase, and are encoded immediately downstream of the structural genes for the nitrogenase enzyme in these species.
Pfam PF24460: Domain of unknown function (DUF7575) (domain)
This domain is found in uncharacterised eu- and prokaryotic proteins. It contains four invariant cysteines and it is predicted to adopt a Zn-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 PF01617: Surface antigen (family)
This family includes a number of bacterial surface antigens expressed on the surface of pathogens.
Pfam PF17116: Type 9 secretion system plug protein 1st domain (domain)
This is a family of Bacteroidetes proteins that appear to form a plug in the type 9 secretion system pore.
Pfam PF00805: Pentapeptide repeats (8 copies) (repeat)
These repeats are found in many cyanobacterial proteins. The repeats were first identified in hglK. The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix. The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid.
Wikipedia: Pentapeptide repeats are a family of sequence motifs found in multiple tandem copies in protein molecules. Pentapeptide repeat proteins are found in all species, but they are found in many copies in cyanobacterial genomes. The repeats were first identified by Black and colleagues in the hglK protein. The later Bateman et al. showed that a large family of related pentapeptide repeat proteins existed. The function of these repeats is uncertain in most proteins. However, in the MfpA protein a DNA gyrase inhibitor it has been suggested that the pentapeptide repeat structure mimics the structure of DNA. The repeats form a regular right handed four sided beta helix structure known as the Rfr-fold.
Pfam PF20475: Family of unknown function (DUF6717) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 115 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 PF03589: Antitermination protein (domain)
This entry consists of antitermination proteins found in bacteriophages, such as protein Q from phage lambda, and some bacterial homologues. Protein Q positively regulates expression of the phage late gene operon by binding to the bacterial host RNA polymerase (RNAP) and modifying it. This protein binds a specific DNA Q-binding element (QBE) and interacts with RNAP. The modified RNAP can read without pausing and through transcription terminators preceding late genes . It participates in the lysis-lysogeny decision by activating the expression of the late lytic genes . The structure of Q from bacteriophage 21 revealed that it forms a torus, that narrows and extends the RNAP RNA-exit channel and extrudes the linked RNA, preventing the formation of pause and terminator hairpins .
Pfam PF02057: Glycosyl hydrolase family 59 (family)
This entry represents the catalytic domain found in a group of proteins from animals, fungi and bacteria that belong to the Glycoside hydrolase family 59 GH59. This family comprises enzymes with only one known activity: galactocerebrosidase (3.2.1.46).

Globoid cell leukodystrophy (Krabbe disease) is a severe, autosomal recessive disorder that results from deficiency of galactocerebrosidase (GALC) activity . GALC is responsible for the lysosomal catabolism of certain galactolipids, including galactosylceramide and psychosine .
O-Glycosyl hydrolases (3.2.1.) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.
Wikipedia: In molecular biology, glycoside hydrolase family 59 is a family of glycoside hydrolases.
Pfam PF06451: Moricin (domain)
Moricin is a antibacterial peptide that is highly basic. The structure of moricin reveals that it is comprised of a long alpha-helix.  The N-terminus of the helix is amphipathic, and the C-terminus of the helix is predominately hydrophobic.  The amphipathic N-terminal segment of the alpha- helix is mainly responsible for the increase in permeability  of the bacterial membrane which kills the bacteria.
Wikipedia: Moricin is a highly basic antibacterial peptide that was isolated from the silkworm Bombyx mori. It consists of a long alpha-helix with 8 turns from a 42 amino acid sequence over almost the entire protein. The amphipathic N-terminal segment of the alpha- helix is mainly responsible for the increase in permeability of the bacterial membrane which kills the bacteria. Moricin functions as an antibacterial peptide against Gram-positive and Gram-negative bacteria, with its main activity being towards Gram-positive bacteria.
Pfam PF20841: NtrZ (family)
This family represents the periplasmic protein NtrZ which functions to regulate the activity of the NtrY-NtrX two-component system. NtrZ inhibits NtrY phosphatase activity.
Pfam PF22445: Ssol_1539-like, second domain (domain)
This domain is found in Ssol_1539 from Saccharolobus solfataricus and similar archaeal sequences. Ssol_1539 is organised into two domains. The N-terminal domain contains two subdomains separated by a central helix. This entry represents the second subdomain, which shows an all-alpha configuration.
Pfam PF25070: Domain of unknown function (DUF7794) (domain)
This domain is found in uncharacterised plant proteins. It is predicted to fold into a globular structure with significant structural similarity to alkaline phosphatases.
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 PF02344: Myc leucine zipper domain (coiled_coil)
This family consists of the leucine zipper dimerisation domain found in both cellular c-Myc proto-oncogenes and viral v-Myc oncogenes.  Dimerisation via the leucine zipper motif with other basic helix-loop-helix-leucine zipper (b/HLH/lz) proteins such as  Max [swissprot:P25912] is required for efficient DNA binding.  The Myc-Max dimer is a transactivating complex activating expression of growth related genes promoting cell proliferation. The dimerisation is facilitated via interdigitating leucine residues every 7th position of the alpha helix.  Like charge repulsion of  adjacent residues in this region perturbs the formation of homodimers  with heterodimers being promoted by opposing charge attractions.
Pfam PF03571: Peptidase family M49 (family)
Peptidase family M49 contains exopeptidases that remove dipeptides from the N terminus of peptides and proteins and are known as dipeptidyl-peptidases (DPP). The best characterized of these is dipeptidyl-peptidase III and represents the prototype for the M49 family of metallopeptidases. It consists of two domains that form a wide cleft containing the catalytic metal ion (DPPIII; 3.4.14.4; MEROPS identifier M49.001) . The exopeptidases in M49 are metal-dependent, and bind a single zinc ion via the histidines in an HEXXXH motif, in which the distance between the histidines in one residue longer than in the HEXXH zinc-binding motif found in endopeptidases of clan MA. The importance of the histidines and the glutamic acid was identified by site-directed mutagenesis . Some members of family M49, notably from bacteria such asColweliaand plants possess the more usual HEXXH motif . A third zinc ligand occurs within a motif that has been described as EECRAE . DPPIII releases N-terminal dipeptides sequentially from peptides such as angiotensins II and III, Leu-enkephalin, prolactin and alpha-melanocyte-stimulating hormone, but tripeptides are poor substrates and polypeptides of more than ten residues are not cleaved . DPPIII is a soluble, cytosolic enzyme with a housekeeping role, but is elevated in retroplacental serum may participate in the increased angiotensin hydrolysis seen during pregnancy .

This family also includes Nudix hydrolase 3 (NUDT3) from plants, which is thought to hydrolyse nucleoside diphosphate derivatives because of the presence of a Nudix box. Isopentenyl diphosphate (IPP), a universal precursor for the biosynthesis of isoprenoid compounds, is hydrolysed; purine nucleotides such as 8-oxo-dATP are dephosphorylated; and the enzyme acts as a dipeptidyl-peptidase against dipeptidyl-2-arylamide substrates .
Pfam PF13569: Domain of unknown function (DUF4132) (domain)
This domain might be involved in the biosynthesis of the molybdopterin cofactor in E.coli.
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.