SII-SWORD/CoKE huggingface dataset:
Pfam PF21559: DNA-binding protein reb1, Myb-associated domain (domain)
This domain is found in DNA-binding protein reb1 from Schizosaccharomyces pombe and similar proteins from yeast. Reb1 mediate transcription termination and is also involved in replication termination and transcription activation. This protein, almost entirely alpha-helical, is organised into five domains: two Myb-associated domains (MybADs, this entry), each consisting of four alpha-helices, two Myb repeats (MybRs, [pfam:PF00249]) and a final C-terminal domain.
Pfam PF20619: Family of unknown function (DUF6804) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 98 and 195 amino acids in length and adopt a helix-rich bundle structure and share a  similar fold with a flagellin homologue, hook-associated protein.
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 PF03730: Ku70/Ku80 C-terminal arm (family)
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 C terminal arm. This alpha helical region embraces the beta-barrel domain [pfam:PF02735] of the opposite subunit.
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 PF12560: RAG1 importin binding (family)
This region of RAG1 is responsible for binding to importin alpha.
Pfam PF18962: Secretion system C-terminal sorting domain (domain)
Species that include Porphyromonas gingivalis, Fibrobacter succinogenes, Flavobacterium johnsoniae, Cytophaga hutchinsonii, Gramella forsetii, Prevotella intermedia, and Salinibacter ruber have on average twenty or more copies of this C-terminal domain, associated with sorting to the outer membrane and covalent modification. This domain targets proteins to type IX secretion systems and is secreted then cleaved off by a C-terminal signal peptidease. Based on similarity to other families it is likely that this domain adopts an immunoglobulin like fold.
Pfam PF19281: Phytanoyl-CoA hydroxylase-interacting protein C-terminus (family)
This entry includes PHYHIP and PHYHIPL from humans. PHYHIP interacts with DYRK1A and may contribute to new cellular functions of DYRK1A.
Pfam PF10396: GTP-binding protein TrmE N-terminus (family)
This family represents the shorter, B, chain of the homo-dimeric structure which is a guanine nucleotide-binding protein that binds and hydrolyses GTP.  TrmE is homologous to the tetrahydrofolate-binding domain of N,N-dimethylglycine oxidase and indeed binds formyl-tetrahydrofolate. TrmE actively participates in the formylation reaction of uridine and regulates the ensuing hydrogenation reaction of a Schiff's base intermediate.  This B chain is the N-terminal portion of the protein consisting of five beta-strands and three alpha helices and is necessary for mediating dimer formation within the protein.
Pfam PF15293: FMR1-interacting protein 2 (family)
FMR1-interacting protein 2 (NUFIP2, also known as 82-FIP) is an RNA binding protein that shows a cell cycle-dependent intracellular localisation .
Wikipedia: Nuclear fragile X mental retardation-interacting protein 2 is a protein that in humans is encoded by the NUFIP2 gene.
Pfam PF16982: Putative Flagellin, Flp1-like, domain (family)
This entry represents the Flp1-like domain of putative Flagellin proteins.
Pfam PF03910: Adenovirus minor core protein PV (family)
The Adenoviruses nucleoprotein core consists of genomic dsDNA and six proteins. Protein V is one of the most important proteins in the core due to its involvement in core condensation. Protein V also bridges the viral DNA core with the outer capsid by interacting with protein VI. It plays an important role in capsid assembly and in the formation of infectious virions .
Pfam PF17726: Dam-replacing HTH domain (domain)
Dam-replacing protein (DRP) is an restriction endonuclease that is flanked by pseudo-transposable small repeat elements.  The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis. This domain represents the C-terminal HTH domain.
Pfam PF04023: FeoA domain (domain)
This family includes FeoA a small protein, probably involved in Fe2+ transport. This presumed short domain is also found at the C-terminus of a variety of metal dependent transcriptional regulators.  This suggests that this domain may be metal-binding. In most cases this is likely to be either iron or manganese.
Pfam PF07006: Protein of unknown function (DUF1310) (family)
This family consists of several hypothetical proteins of around 125 residues in length. Members of this family seem to be specific to Listeria and Streptococcus species. The function of this family is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF10285: Luciferase catalytic domain (domain)
This domain is the catalytic domain of dinoflagellate luciferase . Luciferase is involved in catalysing the light emitting reaction in bioluminescence. The structure of this domain has been solved. The core part of the domain is a 10 stranded beta barrel that is structurally similar to lipocalins and FABP.
Pfam PF19099: Family of unknown function (DUF5786) (family)
Family of unknown function predominantly found in Halobacteria.
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 PF12785: Variant erythrocyte surface antigen-1 (family)
This family represents the N-terminal of the variant erythrocyte surface antigen 1, versions a and b, of Babesia. Babesia bovis is a tick-borne, intra-erythrocytic, protozoal parasite of cattle that shares many lifestyle parallels with the most virulent of the human malarial parasites, Plasmodium falciparum. Babesia uses antigenic variation to establish consistent infections of long duration. The two variants of VESA1, a and b, are expressed from different but closely related genes, and variation is achieved through the involvement of a segmental gene conversion mechanism and low-frequency epigenetic in situ switching of transcriptional activity from the VESA1 gene-pair to a possible other gene pair.
Pfam PF06869: Protein of unknown function (DUF1258) (family)
This family represents a conserved region approximately 260 residues long within a number of hypothetical proteins of unknown function that seem to be specific to C. elegans. Note that this family contains a number of conserved cysteine and histidine residues.This family corresponds to the Mirage group of putative transposases and family members are relatively close homologs of Transposase_21 ([pfam:PF02992]) proteins (1).
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 PF19052: BMP/retinoic acid-inducible neural-specific protein (family)
This entry represents the BMP/retinoic acid-inducible neural-specific protein (BRINP) family, including BRINP1/2/3. They are predominantly and widely expressed in both the central nervous system (CNS) and peripheral nervous system (PNS). They inhibit neuronal cell proliferation by negative regulation of the cell cycle G1/S transition.
Pfam PF04068: Possible Fer4-like domain in RNase L inhibitor, RLI (family)
Possible metal-binding domain in endoribonuclease RNase L inhibitor.  Found at the N-terminal end of RNase L inhibitor proteins, adjacent to the 4Fe-4S binding domain, fer4, [pfam:PF00037]. Also often found adjacent to the DUF367 domain [pfam:PF04034] in uncharacterised proteins. The RNase L system plays a major role in the anti-viral and anti-proliferative activities of interferons, and could possibly play a more general role in the regulation of RNA stability in mammalian cells.  Inhibitory activity requires concentration-dependent association of RLI with RNase L.
Pfam PF00194: Eukaryotic-type carbonic anhydrase (domain)
This entry represents a domain characteristic of alpha class carbonic anhydrases. The dominating secondary structure is a 10-stranded, twisted Î²-sheet, which divides the molecules into two halves . Alpha-CAs contain a single zinc atom bound to three conserved histidine residues. The catalytically active group is the zinc-bound water which ionizes to a hydroxide group. In the mechanism of catalysis, nucleophilic attack of CO2 by a zinc-bound hydroxide ion is followed by displacement of the resulting zinc-bound bicarbonate ion by water; subsequent deprotonation regenerates the nucleophilic zinc-bound hydroxide ion .

A carbonic anhydrase-like domain with striking homology to that of the alpha class carbonic anhydrases is also found in receptor-type tyrosine-protein phosphatase gamma and zeta. In this case it may have a different function, as only one of the three His residues that ligate the zinc atom and are required for catalytic activity is conserved .
Carbonic anhydrases (CA: 4.2.1.1) are zinc metalloenzymes which catalyse the reversible hydration of carbon dioxide to bicarbonate . The alpha-CAs are found predominantly in animals but also in bacteria and green algae. There are at least 15 isoforms found in mammals, which can be subdivided into cytosolic CAs (CA-I, CA-II, CA-III, CA-VII and CA XIII), mitochondrial CAs (CA-VA and CA-VB), secreted CAs (CA-VI), membrane-associated (CA-IV, CA-IX, CA-XII and CA-XIV) and those without CA activity, the CA-related proteins (CA-RP VIII, X and XI).
Wikipedia: The carbonic anhydrases form a family of enzymes that catalyze the interconversion between carbon dioxide and water and the dissociated ions of carbonic acid. The active site of most carbonic anhydrases contains a zinc ion. They are therefore classified as metalloenzymes. The enzyme maintains acid-base balance and helps transport carbon dioxide.
Pfam PF08968: Domain of unknown function (DUF1885) (domain)
This domain is found in a set of hypothetical proteins produced by bacteria of the Bacillus genus.
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 PF08039: Mitochondrial proteolipid (family)
This family consists of proteins with similarity to the mitochondrial proteolipids. Mitochondrial proteolipid consists of about 60 amino acids residues and is about 6.8 kDa in size.
Pfam PF21742: Family of unknown function (DUF6868) (domain)
This entry represents a small bacterial integral membrane protein of unknown function that is composed of two transmembrane helices. The function of this protein is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF14829: Glycerol-3-phosphate acyltransferase N-terminal (domain)
GPAT_N is the N-terminal domain of glycerol-3-phosphate acyltransferases, and it forms a four-helix bundle. Glycerol-3-phosphate (1)-acyltransferase(G3PAT) catalyses the incorporation of an acyl group from either acyl-acyl carrier proteins or acyl-CoAs into the sn-1 position of glycerol 3-phosphate to yield 1-acylglycerol-3-phosphate. G3PATs can either be selective, preferentially using the unsaturated fatty acid, oleate (C18:1), as the acyl donor, or non-selective, using either oleate or the saturated fatty acid, palmitate (C16:0), at comparable rates. The differential substrate-specificity for saturated versus unsaturated fatty acids seen within this enzyme family has been implicated in the sensitivity of plants to chilling temperatures. The exact function of this domain is not known. it lies upstream of family Acyltransferase, [pfam:PF01553].
Pfam PF17878: Phage single-stranded DNA-binding protein (domain)
Family members include single-stranded DNA binding protein encoded by the filamentous Pseudomonas bacteriophage Pf3.
Pfam PF20561: Domain of unknown function (DUF6771) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 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 PF15412: Binding domain of Nse4/EID3 to Nse3-MAGE (domain)
This family includes Nse4 and EID3 members, that bind over this region to the Nse3 pocket, in MAGE family [pfam:PF01454].
Pfam PF14573: Acyl-carrier (domain)
This entry represents the phosphopantetheine binding ACP domain. This domain forms a small negatively charged four helical bundle.
Acyl carrier protein (ACP) is an essential cofactor in the synthesis of fatty acids by the fatty acid synthetases systems in bacteria and plants. In addition to fatty acid synthesis, ACP is also involved in many other reactions that require acyl transfer steps, such as the synthesis of polyketide antibiotics, biotin precursor, membrane-derived oligosaccharides, and activation of toxins, and functions as an essential cofactor in lipoylation of pyruvate and alpha-ketoglutarate dehydrogenase complexes . Phosphopantetheine (or pantetheine 4' phosphate) is the prosthetic group of acyl carrier proteins (ACP) in some multienzyme complexes where it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups . Phosphopantetheine is attached to a serine residue in these proteins. The core structure of ACP consists of a four-helical bundle, where helix three is shorter than the others.

Several other proteins share structural homology with ACP, such as the bacterial apo-D-alanyl carrier protein, which facilitates the incorporation of D-alanine into lipoteichoic acid by a ligase, necessary for the growth and development of Gram-positive organisms ; and the thioester domain of the bacterial peptide carrier protein (PCP) found within large modular non-ribosomal peptide synthetases, which are responsible for the synthesis of a variety of microbial bioactive peptides .
Pfam PF15839: Testis-expressed sequence 29 protein (family)
TEX29, testis-expressed sequence 29 protein, is a family of proteins found in eukaryotes. Proteins in this family are typically between 39 and 150 amino acids in length.
Pfam PF23646: TRAPP trafficking subunit Trs65 IgD2 (domain)
This entry includes Trp65, an essential subunit of the TRAPP Golgi trafficking complex. TRAPP subunits are found in three forms-core TRAPP/TRAPPI, TRAPPII, and TRAPPIII and they function in various vesicle trafficking pathways. TRAPPI mediates transport from endoplasmic reticulum to cis-Golgi by tethering COPII-coated vesicles; TRAPPII interacts with COPI-coated vesicles in mammalian cells and aids in endosome-to-Golgi transport, and TRAPPIII plays a unique role in autophagy. TRAPP complexes act as GEFs and play an essential role in catalysing nucleotide exchange for Ypt/Rab GTPase. The three complexes share a core of six different proteins (Bet3, Bet5, Trs20, Trs23, Trs31, and Trs33) that make up core TRAPPI. TRAPPII contains four additional proteins (Trs120, Trs130, Trs65, and Tca17), and TRAPPIII has one additional Trs85 in yeast. while Trp65 has been implicated in cell wall biogenesis and stress response, the role of Trs65 in TRAPPII is supported by the findings that the protein co-localises with Trs130p, and deletion of Trs65 in yeast leads to a conditional lethal phenotype if either one of the other TRAPPII-specific subunits is modified. Trs65 is essential to the formation of TRAPPII dimer and consists of three Ig-like  domains (IgD1, IgD2 and IgD3). This entry represents IgD2 domain.
Pfam PF15507: Domain of unknown function (DUF4649) (family)
This family of Firmicute sequences has members that are annotated as ribose-phosphate pyrophosphokinase; however there is no evidence for this attribution. Member proteins are all shorter than 100 residues 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 PF14732: Ubiquitin/SUMO-activating enzyme ubiquitin-like domain (domain)
This is the C-terminal domain of ubiquitin-activating enzyme and SUMO-activating enzyme 2. It is structurally similar to ubiquitin. This domain is involved in E1-SUMO-thioester transfer to the SUMO E2 conjugating protein.
Pfam PF19320: Galactofuranosyltransferase-2, domain 3 (domain)
This entry represents the third domain of GlfT2 (Rv3808c), a polymerising galactofuranosyltransferase that synthesises the galactan portion of the peptidoglycan complex of the mycobacteria cell wall. It consists of eight alpha-helices, five of which immediately follow the glycosyltransferase (GT) domain and form the central portion of domain 3. Three helices at the C terminus of the polypeptide chain wrap around these core helices to complete the domain. The first helix in domain 3 anchors loop 1 and is conserved in many GT-A proteins. The flanking domains and many hydrophobic residues found at the interface between domains 2 and 3 of this protein are conserved among many proteins of mycobacteria, related Actinobacteria and more distantly related species, suggesting conserved structure structure and function relationships. The alpha2- and alpha6-helices from domain 3 and alpha1 from domain 4 contribute with a patch of exposed hydrophobic residues which probably generate a binding site for the hydrophobic acyl chains of membrane phospholipids. These surface-exposed hydrophobic residues may also contribute to the specificity and affinity binding of UDP donors.
Pfam PF06788: Uncharacterised protein family (UPF0257) (family)
This is a group of proteins of unknown function.
Pfam PF09904: Winged helix-turn helix (family)
This family, found in various hypothetical prokaryotic proteins, is a probable winged helix DNA-binding domain.
Pfam PF19454: Family of unknown function (DUF5992) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 105 and 116 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 PF05463: Sclerostin (SOST) (family)
This family contains several mammalian sclerostin (SOST) proteins. SOST is thought to suppress bone formation. Mutations of the SOST gene lead to sclerosteosis, a progressive sclerosing bone dysplasia with an autosomal recessive mode of inheritance. Radiologically, it is characterised by a generalised hyperostosis and sclerosis leading to a markedly thickened and sclerotic skull, with mandible, ribs, clavicles and all long bones also being affected. Due to narrowing of the foramina of the cranial nerves, facial nerve palsy, hearing loss and atrophy of the optic nerves can occur. Sclerosteosis is clinically and radiologically very similar to van Buchem disease, mainly differentiated by hand malformations and a large stature in sclerosteosis patients.
Wikipedia: Sclerostin is a protein that in humans is encoded by the SOST gene. It is a secreted glycoprotein with a C-terminal cysteine knot-like (CTCK) domain and sequence similarity to the DAN family of bone morphogenetic protein (BMP) antagonists. Sclerostin is produced primarily by the osteocyte but is also expressed in other tissues, and has anti-anabolic effects on bone formation.
Pfam PF14843: Growth factor receptor domain IV (domain)
This is the fourth extracellular domain of receptor tyrosine protein kinases. Interaction between this domain and the furin-like domain ([pfam:PF00757]) regulates the binding of ligands to the receptor L domains ([pfam:PF01030]).
Pfam PF08547: Complex I intermediate-associated protein 30 (CIA30) (family)
This protein is associated with mitochondrial Complex I intermediate-associated protein 30 (CIA30) in human and mouse. The family is also present in Schizosaccharomyces pombe which does not contain the NADH dehydrogenase component of complex I, or many of the other essential subunits.    This means it is possible that this family of protein may not be directly involved in oxidative phosphorylation.