SII-SWORD/CoKE huggingface dataset:
Pfam PF06861: BALF1 protein (family)
This family consists of several BALF1 proteins which seem to be specific to the Lymphocryptoviruses. BALF1, inhibits the antiapoptotic activity of EBV BHRF1 and of KSBcl-2.
Pfam PF24942: Dep-1 first Fn3-like domain (domain)
This domain is found in the Receptor-type tyrosine-protein phosphatase Dep-1 from Caenorhabditis elegans and related proteins. Dep-1 is involved in the dephosphorylation of the receptor let-23 and the beta-integrin subunit pat-3. It is involved in the regulation of the  cell fate during the development of the vulva and the excretory system. It is also involved indirectly in the negative regulation of let-23 signaling and vulval induction. Dep-1 is a multidomain protein which is predicted to contain a number of Fn3-like domains arranged in tandem. This entry represents the first of them.
Pfam PF16683: Transglutaminase elicitor (domain)
TGase_elicitor is a family of largely oomycete sequences from plant pathogens that elicit transglutaminase/acyltransferase activity. The enzyme classification is E.C:2.3.2.13. From the presence of sequences from Vibrio spp one can propose a lateral gene transfer event having occurred between bacteria and oomycetes to the probable selective advantage of the pathogen.
Pfam PF12579: Protein of unknown function (DUF3755) (family)
This domain family is found in eukaryotes, and is approximately 40 amino acids in length. There is a single completely conserved residue N that may be functionally important.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF13288: DXP reductoisomerase C-terminal domain (domain)
This is the C-terminal domain of the 1-deoxy-D-xylulose-5-phosphate reductoisomerase enzyme. This domain forms a left handed super-helix.
Pfam PF22013: PG_1098 ferredoxin-like domain (domain)
This entry represents a ferredoxin-like domain found in a group of poorly characterised sequences, including the putative methyltransferase PG_1098 from Porphyromonas gingivalis ([swissprot:Q7MVG6], PDB:3ll7). Members of this entry contain a THUMP-like domain at the C-terminal ([pfam:PF18096]), following this domain.
Pfam PF14517: Tachylectin (repeat)
This family of lectins binds N-acetylglucosamine and N-acetylgalactosamine and may be involved in innate immunity. It has a five-bladed beta-propeller structure with five carbohydrate-binding sites, one per beta sheet.
Pfam PF00400: WD domain, G-beta repeat (repeat)
WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed Î²-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised Î²-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein or protein-DNA interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins . The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a Î²-propeller), TAFII transcription factor, and E3 ubiquitin ligase . In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events.
Wikipedia: In structural biology, a beta-propeller (β-propeller) is a type of all-β protein architecture characterized by 4 to 8 highly symmetrical blade-shaped beta sheets arranged toroidally around a central axis. Together the beta-sheets form a funnel-like active site.
Pfam PF06564: Cellulose biosynthesis protein BcsQ (domain)
This is a family of bacterial proteins involved in cellulose biosynthesis. (Roemling U. and Galperin M.Y. "Bacterial cellulose biosynthesis. Diversity of operons and subunits" (manuscript in preparation)). A second component of the extracellular matrix of the multicellular morphotype (rdar) of Salmonella typhimurium and Escherichia coli is cellulose. The family does contain a P-loop sequence motif suggesting a nucleotide binding function, but this has not been confirmed.
Pfam PF02333: Phytase (repeat)
Phytase is a secreted enzyme which hydrolyses phytate to release inorganic phosphate. This family appears to represent a novel enzyme that shows phytase activity and has been shown to have a six- bladed propeller folding architecture.
Pfam PF12707: Protein of unknown function (DUF3804) (domain)
This family is approximately 130 residues.  Dali search indicates this protein carries a NTF2-fold with a hydrophobic cavity as a structural homologue to 1JB2, 2R4I, 3FSD and 2UX0. In this hydrophobic cavity, Arg 118 provides the H-bonding force to hold a PEG molecule from crystallisation. The interface interaction suggests that the biomolecule of [swissprot:Q46KI2] is a dimer. Two members of the family are annotated as putative EF-Tu domain 2 but there is no match to this family so this is likely to be a false assignment. There are two highly conserved tryptophan residues towards the C-terminal end of the family.
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 PF00251: Glycosyl hydrolases family 32 N-terminal domain (repeat)
This domain corresponds to the N-terminal domain of glycosyl hydrolase family 32 which forms a five bladed beta propeller structure.
Wikipedia: In molecular biology, glycoside hydrolase family 32 is a family of glycoside hydrolases EC 3.2.1., which 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 glycoside hydrolases, based on sequence similarity, has led to the definition of &gt;100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.
Pfam PF11308: Glycosyl hydrolases related to GH101 family, GH129 (family)
This family of bacterial and lower eukaryote glycosyl hydrolases is related to CAZy family GH129,and distantly to GH101, and is made up of sub-families GHL1-GHL3. In the example [swissprot:C02A26], the substrate-binding Asp is residue 596, the nucleophilic Asp is residue 706, and the proton donor Glu is residue 747.
Wikipedia: In molecular biology, glycoside hydrolase family 101 is a family of glycoside hydrolases.
Pfam PF00729: Viral coat protein (S domain) (domain)
The capsid proteins of plant icosahedral positive strand RNA viruses form 4 different domains, a positively charged, N-terminal 'R' domain, which interacts with RNA (66 residues); a connecting arm, 'a' (35 residues); a central, surface 'S' domain, which forms the virion shell; and a projecting, C-terminal 'P' domain . Some of the viruses lack either the R or P domains. The S domain contains from 158 to 166 amino acids and comprises 8 anti-parallel Î²-strands, which form a twisted sheet or jelly-roll fold. This structure is shared by a number of plant viral capsid proteins, which include: Carmovirus, Dianthovirus, Sobemovirus, Tombusvirus and an unidentified tobacco necrosis virus .
Pfam PF17277: Family of unknown function (DUF5342) (family)
This family of no known function is found in Bacilli.
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 PF15872: Serine-rich and transmembrane domain-containing protein 1 (family)
This family of proteins is found in eukaryotes. Proteins in this family are approximately 100 amino acids in length.
Pfam PF19902: Family of unknown function (DUF6375) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001020) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the muraymycin C1 biosynthetic gene  cluster from Streptomyces sp. NRRL 30471.
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 PF16440: Domain of unknown function (DUF5037) (family)
This family consists of several uncharacterized proteins around 270 residues in length and is mainly found in various Clostridiales 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 PF06545: Oxamate carbamoyltransferase subunit AllG (family)
This entry, previously known as DUF1116, represents Oxamate carbamoyltransferase subunit AllG and related bacterial proteins. AllG is a component of a carbamoyltransferase involved in the anaerobic nitrogen utilisation via the assimilation of allantoin. It is catalyses the conversion of oxalurate (N-carbamoyl-2-oxoglycine) to oxamate and carbamoyl phosphate.
Pfam PF05455: GvpH (family)
This family consists of archaeal GvpH proteins which are thought to be involved in gas vesicle synthesis.
Pfam PF20327: Family of unknown function (DUF6622) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are approximately 170 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 PF22591: eIF3a, PCI domain, TPR-like region (repeat)
This entry represents the TPR-like region of the PCI domain of the Eukaryotic translation initiation factor 3 subunit A from Saccharomyces cerevisiae (eIF3a), the RNA-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. This region folds into flatly arranged helical repeats.
Pfam PF09953: Uncharacterized protein conserved in bacteria (DUF2187) (family)
This domain, found in various hypothetical bacterial 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 PF16272: Domain of unknown function (DUF4925) (family)
This family consists of uncharacterized proteins around 400 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Pfam PF18876: AFF4, C-terminal homology domain (domain)
This entry consists of AFF (AF4/FMR2) family of proteins which includes AFF1-AFF4 and the Drosophila protein Lilliputian. Lilliputian acts in cytoskeleton regulation, segmentation and morphogenesis. All AFF proteins are localised in the cell nucleus and are involved in regulation of gene expression. They are scaffold proteins that mediate the multisubunit super-elongation complex (SEC) assembly. This entry represents the C-terminal homology domain (CHD, also known as C-terminal signature sequence), highly conserved among its members. This domain mediates the formation of an AFF4 homodimer or an AFF1-AFF4 heterodimer. This domain is essential for AFF4 interaction with Transcription Start Site (TSS)-associated histone H3K27 whose acetylation signals SEC to regulate transcriptional elongation of the ESR1 gene. Depletion of AFF4 reduces expression of ESR1, and, consequently inhibits breast cancer cell growth. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and FRAXE.
Pfam PF20920: Death domain-associated protein 6, histone binding domain (domain)
This domain is found in the mammalian Death domain-associated protein 6 (DAXX) and in similar proteins from animals. DAXX is a transcription corepressor and a histone chaperone that shows specificity for the conserved histone H3.3. This entry represents the histone binding domain, which adopts an all alpha-helical fold where the first two alpha-helices form a coiled coil.
Pfam PF01780: Ribosomal L37ae protein family (family)
This ribosomal protein is found in archaebacteria and eukaryotes. It contains four conserved cysteine residues that may bind to zinc.
Pfam PF08379: Bacterial transglutaminase-like N-terminal region (family)
This region is found towards the N-terminus of various archaeal and bacterial hypothetical proteins. Some of these are annotated as being transglutaminase-like proteins, and in fact contain a transglutaminase-like superfamily domain ([pfam:PF01841]).
Pfam PF12776: Myb/SANT-like DNA-binding domain (domain)
This presumed domain appears to be related to other Myb/SANT like DNA binding domains. In particular [pfam:PF10545] seems most related.  This family is greatly expanded in plants and appears in several proteins annotated as transposon proteins.
Pfam PF19686: Family of unknown function (DUF6188) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces  kanamyceticus. This family appears to be predominantly found in  bacteria.
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 PF15642: Toxin in Odyssella and Amoebophilus (family)
A predicted all-alpha fold toxin present in bacterial polymorphic toxin systems of the endosymbionts Odyssella and Amoebophilus.
Pfam PF22532: Nonstructural protein, WIV domain (domain)
This domain is found in Nonstructural protein from Lake Sinai virus and similar sequences from arthropod-infecting viruses and lower eukaryotes. It has been named 'Widespread, Intriguing, Versatile' (WIV) domain. This region is likely to play a role in viral infection of arthropods.
Pfam PF07803: GSG1-like protein (family)
This family contains sequences bearing similarity to a region of GSG1 ([swissprot:Q9Z1H7]), a protein specifically expressed in testicular germ cells. It is possible that overexpression of the human  homolog may be involved in tumourigenesis of human testicular germ cell tumours. The region in question  has four highly-conserved cysteine residues.
Pfam PF00076: RNA recognition motif (domain)
The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins ([swissprot:P05455]) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins ([swissprot:P05455]) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.
Wikipedia: RNA recognition motif, RNP-1 is a putative RNA-binding domain of about 90 amino acids that are known to bind single-stranded RNAs. It was found in many eukaryotic proteins.
Pfam PF00573: Ribosomal protein L4/L1 family (family)
This family includes Ribosomal L4/L1 from eukaryotes and archaebacteria and L4 from eubacteria. L4 from yeast has been shown to bind rRNA.
Pfam PF22415: PSV_Hypothetical protein ORF131-like domain (domain)
This domain is found in the uncharacterised protein [swissprot:Q6ZYH1] from Pyrobaculum spherical virus (PSV), also known as ORF131, and similar viral sequences. It adopts a two-layered alpha-beta configuration.
Pfam PF16837: Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 (domain)
SF3A3 is one of the components of the SF3a splicing factor complex of the mature U2 snRNP (small nuclear ribonucleoprotein particle). In yeast, SF3a shows a bifurcated assembly structure of three subunits, Prp9 (subunit 3), Prp11 (subunit 2) and Prp21 (subunit 1). Prp9 and Prp21 were not thought to interact with each other but the alpha1 helix of Prp9 does make important contacts with the SURP2 domain of Prp21, thus the two do interact via a bidentate-binding mode. Prp9 harbours a major binding site for stem-loop IIa of U2 snRNA.
Pfam PF04642: Protein of unknown function, DUF601 (family)
This family represents a conserved region found in several uncharacterised plant 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 PF23770: RIG first beta-propeller (repeat)
This entry represents the first beta-propeller found at the N-terminal of Protein rigor mortis (RIG) from Drosophila melanogaster. RIG is a nuclear receptor-interacting protein required for the response to steroid hormone ecdysone during larval development. This domain acts as a specific protein-protein interaction domain. Also included in this entry as partial matches are orthologues Gem-associated protein 5 (GEMI5) from animals. GEMI5 is a component of the survival of motor neurons (SMN) complex, that binds small nuclear RNAs (snRNAs). The SMN complex assembles the heptameric Sm protein core on snRNAs and plays a critical role in the biogenesis of small nuclear ribonucleoproteins (snRNPs).
Pfam PF24302: Family of unknown function (DUF7484) (family)
This entry represents an uncharacterised family of phage proteins. These proteins consist of two domains. The first is composed of four alpha helices that are contributed by both the N and C-terminus of the protein.  The second domain is a central beta domain. Structure prediction suggests that these proteins might form a large homo-oligomeric ring of 8-10 subunits, but the iPTM scores are marginal.
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 PF22714: Short NACHT-associated C-Terminal domain, family 8 (domain)
The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors.
Pfam PF23793: Rz1-like lysis system protein LysC (family)
This entry represents a group of proteins from tailed bacteriophages and bacterial prophages mainly found in proteobacteria, including LysC from Burkholderia phage ST79 (Bacteriophage ST79) ([swissprot:R4JDL9]). LysC is an Rz1-like component of a phage lytic system, substantially overlapping although not fully embedded in the gene for the Rz-like LysB component. The phage lysis defect in the absence of a functional LysB/LysC system appears in the presence of high concentrations of divalent cations.
Pfam PF06943: LSD1 zinc finger (domain)
This family consists of several plant specific LSD1 zinc finger domains. Arabidopsis lsd1 mutants are hyper-responsive to cell death initiators and fail to limit the extent of cell death. Superoxide is a necessary and sufficient signal for cell death propagation. LSD1 monitors a superoxide-dependent signal and negatively regulates a plant cell death pathway. LSD1 protein contains three zinc finger domains, defined by CxxCxRxxLMYxxGASxVxCxxC. It has been suggested that LSD1 defines a zinc finger protein subclass and that LSD1 regulates transcription, via either repression of a pro-death pathway or activation of an anti-death pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death.