SII-SWORD/CoKE huggingface dataset:
Pfam PF14882: Integrase repeat unit (repeat)
This repeat family is found on integrase proteins in up to 15 copies. The function is not known.
Pfam PF11066: Protein of unknown function (DUF2867) (family)
This bacterial family of 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 PF08762: CRPV capsid protein like (domain)
This is a family of capsid proteins found in positive stranded ssRNA viruses such as cricket paralysis virus (CRPV).  It forms an all beta sheet structure.
Pfam PF22052: Domain of unknown function (DUF6937) (domain)
This domain is found N-terminal in a family of uncharacterised bacterial proteins. This domain has a significant sequence similarity to the N-terminal domains of a number of proteins members of UDP-Glycosyltransferase/glycogen phosphorylase superfamily. It is predicted to adopt the same alpha/beta structure.
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 PF24686: Fluoroquinolones export permease protein family (family)
The Fluoroquinolones export permease protein family is involved in the export of fluoroquinolones as part of an ABC transporter complex. This family is likely responsible for the translocation of substrates across the membrane and confers resistance to various fluoroquinolones, including ciprofloxacin, norfloxacin, moxifloxacin, and sparfloxacin.
Pfam PF11480: Colicin-E5 Imm protein (family)
Imms bind specifically to cognate colicins in order to protect their host cells. Imm-E5 is a specific inhibitor protein of colicin E5. It binds to E5 C-terminal ribonuclease domain (CRD) to prevent cell death. The binding mode of E5-CRD and Imm-E5 mimics that of mRNA and tRNA suggesting an evolutionary pathway from the RNA-RNA interaction through the RNA-protein interaction of tRNA/E5-CRD.
Pfam PF11896: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S (family)
This entry represents domain N and S of GlgE. GlgE is a homodimer and a member of the GH13_3 CAZy subfamily. Each subunit of GlgE is composed of five domains, domain A is a (beta/alpha)8 barrel, typical of the catalytic domain of this family of enzymes, that forms part of the dimer interface. Domain B corresponds to an insertion after the third beta-strand of domain A. In GlgE, domain B is fairly typical for a GH13 enzyme in having a pair of anti-parallel strands and one short helix. The C-terminal domain C has a beta-sandwich fold. The N-terminal domain N, which also consists of a beta-sandwich fold, forms the core of the dimer interface. The final domain arises from an insertion within domain N and forms a four-helix bundle where the last helix is discontinuous and slightly kinked. This domain, which will henceforth be referred to as domain S, participates in the dimer interface and interacts directly with domain B of the neighbouring subunit.
Pfam PF21837: Domain of unknown function (DUF6896) (domain)
This entry represents a family of bacterial proteins of unknown function. The domain structure includes a four stranded beta sheet which has two conserved aspartates in a DXDXG motif close to a highly conserved histidine. These three residues may for the potential active site.
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 PF11724: YvbH-like oligomerisation region (family)
This region is found at the C-terminus of a group of bacterial PH domains. This region is composed of a helical hairpin that appears to mediate oligomerisation based on the known structure. This elaboration of the bacterial PH domain is only found in Bacillales.
Pfam PF19969: vWA-MoxR associated protein middle region (VMAP-M) 8 (family)
Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities.
Pfam PF17934: Tetracyclin repressor-like, C-terminal domain (domain)
This entry represents the C-terminal domain present in putative HTH-type transcriptional regulator. Family members are found in bacilli.
Pfam PF19033: Intu longin-like domain 3 (domain)
This entry represents a longin-like domain found in Intu and related proteins.
Pfam PF20955: Phage tail base-plate attachment protein C-terminal barrel domain (domain)
Caudo_bapla16 is a family of ORF16 tail-phage P2-like proteins that forms part of the base-plate at the tip of the phage tail. The whole base-plate complex is involved in host recognition and attachment, and consists of several proteins derived from consecutive open-reading-frames.  This entry represents the C-terminal RIFT barrel domain.
Pfam PF10213: Mitochondrial ribosomal subunit protein (family)
This is a conserved region of approx. 125 residues of one of the proteins that makes up the small subunit of the mitochondrial ribosome. In Saccharomyces cerevisiae the protein is MRP-S24 whereas in humans it is MRP-S28. The human mitochondrial ribosome has 29 distinct proteins in the small subunit and these have homologues in, for example, Drosophila melanogaster, Caenorhabditis elegans, and in the genomes of several fungi.
Pfam PF03998: Utp11 protein (family)
This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome.
Pfam PF13317: Protein of unknown function (DUF4088) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 258 and 300 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 PF09461: Phytotoxin PcF protein (domain)
PcF is a 52 residue protein factor of two alpha helices, containing a 4-hydroxyproline and three cysteine bridges. The presence of the hydroxyproline is unique in relation to other fungal phytotoxic proteins. The protein has a high content of acidic side-chains implying a lack of binding with lipid-rich components of membranes and appears to be an extracellular phytotoxin that causes leaf necrosis in strawberries.
Pfam PF21375: Protection of telomeres protein 1 (POT1), C-terminal insertion domain (domain)
POT1  is responsible for binding to and protecting the 3' single-stranded DNA (ssDNA) overhang at most eukaryotic telomeres. This is an insertion domain found at the C-terminal, described as Holliday junction resolvase-like domain (HJRL) in.
Pfam PF04611: Mating type protein A alpha Y mating type dependent binding region (family)
This region is important for the mating type dependent binding of Y protein to the A alpha Z protein of another mating type in Schizophyllum commune.
Pfam PF21517: Transposable element Tc3 transposase, HTH (domain)
Tc3 is transposase with a specific DNA-binding domain. It binds specifically to the terminal nucleotides of the TC3 inverted repeat and acts by making double strand breaks at the ends of TC3 element. It has two DNA-binding domains at the N-terminal, the first one represented in [pfam:PF11427] and the second one in this entry. They both bind to the major groove on a single DNA oligomer, separated by a linker  that interacts closely with the minor groove.
Pfam PF10440: Ubiquitin-binding WIYLD domain (domain)
This presumed domain has been predicted to contain three alpha helices. The domain was named the WIYLD domain based on the pattern of most conserved residues. It binds ubiquitin. In the Arabidopsis thaliana histone-lysine N-methyltransferase SUVR4, [swissprot:Q8W595], binding of ubiquitin to this domain stimulates enzymatic activity and converts its activity from a strict dimethylase to a di/trimethylase.
Pfam PF14518: Iron-containing redox enzyme (family)
The CADD, Chlamydia protein associating with death domains, crystal structure reveals a dimer of seven-helical bundles. Each bundle contains a di-iron centre adjacent to an internal cavity that forms an active site similar to that of methane mono-oxygenase hydrolase.
Pfam PF09585: Conserved hypothetical protein (Lin0512_fam) (family)
This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a well conserved motif GxGxDxHG near the N-terminus.
Pfam PF20367: Family of unknown function (DUF6662) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 296 and 311 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 PF24717: Family of unknown function (DUF7672) (family)
This family of uncharacterised proteins is found in bacteria (Bacteroidota and Chloroflexi). Proteins in this family are approximately 80 amino acids in length. The proteins are likely to be integral membrane proteins with two transmembrane alpha helices.  Structural modelling suggests that these proteins form a dimeric arrangement with the pairs of alpha helices tilted at close to 45 degrees angle compared to the lipid membrane. Based on the positive inside rule it is likely that the N and C-terminii of the proteins have a cytoplasmic location. Given the geometry of the protein complex it may not span the entire membrane.
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 PF02252: Proteasome activator PA28, C-terminal (domain)
Proteasome activator 28 (PA28), also known as 11s regulator of REG, binds to the 20S proteasome and simulates peptidase activity in an ATP-independent manner. This entry represents a the C-terminal domain found in PA28 subunits, including PA28alpha/beta/gamma (also known as Proteasome activator complex subunit 1-3).
Pfam PF08641: Kinetochore protein Mis14 like (family)
Mis14 is a kinetochore protein which is known to be recruited to kinetochores independently of CENP-A.
Pfam PF19772: Family of unknown function (DUF6258) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000974) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the crocacin biosynthetic  gene cluster from Chondromyces crocatus.
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 PF13027: Protein of unknown function (DUF3888) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 111 and 149 amino acids in length.
Pfam PF02211: Nitrile hydratase beta subunit, C-terminal (domain)
Nitrile hydratases (NHase) [ec:4.2.1.84] are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit. Beta subunit consists of an N-terminal helical domain and a C-terminal SH3-like domain (represented in this entry). Thiocyanate hydrolase (SCNase) is a member of the NHase family, comprises alpha, beta and gamma subunits which share amino acid sequence similarities with NHase beta subunit C-terminal, beta subunit N-terminal and NHase alpha subunit, respectively.
Wikipedia: Nitrile hydratases are mononuclear iron or non-corrinoid cobalt enzymes that catalyse the hydration of diverse nitriles to their corresponding amides:R-C≡N + H2O → R-C(O)NH2
Pfam PF13555: P-loop containing region of AAA domain (domain)
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF15794: Coiled-coil domain-containing protein 106 (family)
CCDC106, coiled-coil domain-containing protein 106, is a family of eukaryote proteins. Yeast two-hybrid screening has identified CCDC106 as a p53-interacting partner. CCDC106 is a negative regulator of p53 and may be involved in tumourigenesis in some cancers by promoting the degradation of p53 protein and inhibiting its transactivity.
Pfam PF02887: Pyruvate kinase, alpha/beta domain (domain)
Pyruvate kinase catalyses the final step in glycolysis, the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP. The structure of several pyruvate kinases from various organisms have been determined. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain (represented in this entry). This domain is at the C-terminal of pyruvate kinases and contains the FBP (fructose 1,6-bisphosphate) binding site.
Pfam PF08493: Aflatoxin regulatory protein (family)
This domain is found in the aflatoxin regulatory protein (AflR) which is involved in the regulation of the biosynthesis of aflatoxin in the fungal genus Aspergillus.  It occurs together with the fungal Zn(2)-Cys(6) binuclear cluster domain ([pfam:PF00172]).
Pfam PF20822: CRISPR RNA silencing complex Cmr2 subunit, first helical domain (domain)
The prokaryotic CRISPR RNA-Cas protein (Cmr) complex provides protection against mobile genetic elements by cleaving foreign RNA. Its largest subunit is Cmr2. This protein shows a N-terminal HD (histidine-aspartate) domain, two RRM domains resembling adenylate cyclase and two alpha-helical domains. This entry represents the first alpha-helical domain, which is similar to the thumb of DNA polymerases.
Pfam PF05584: Sulfolobus plasmid regulatory protein (family)
This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Pfam PF04803: Cor1/Xlr/Xmr conserved region (coiled_coil)
Cor1 is a component of the chromosome core in the meiotic prophase chromosomes.  Xlr is a lymphoid cell specific protein. Xlm is abundantly transcribed in testis in a tissue-specific and developmentally regulated manner. The protein is located in the nuclei of spermatocytes, early in the prophase of the first meiotic division, and later becomes concentrated in the XY nuclear subregion where it is in particular associated with the axes of sex chromosomes.
Wikipedia: Synaptonemal complex protein 3 is a protein that in humans is encoded by the SYCP3 gene. It is a component of the synaptonemal complex formed between homologous chromosomes during the prophase of meiosis.
Pfam PF18794: DNA mismatch repair protein HSM3, C terminal domain (repeat)
Hsm3 is a proteasome-dedicated chaperone that forms a base precursor, Hsm3-Rpt1-Rpt2-Rpn1. Hsm3 consists of 23 alpha-helices forming 11 repeats similar to HEAT repeats. This entry include the last 5  repeats at the C terminal.
Pfam PF06897: Protein of unknown function (DUF1269) (family)
This family consists of several bacterial and archaeal proteins of around 200 residues in length. The function of this family is unknown. The family carries a repeated glycine-zipper sequence- motif, GxxxGxxxG, where the x following the G is frequently found to be an alanine. As glycine-zippers occur in membrane proteins, this family is likely to be found spanning a membrane.
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 PF05529: Bap31/Bap29 transmembrane region (family)
Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8.  Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31. This family also contains the Bap29 protein that forms a heterodimer with Bap 31.
Pfam PF15191: Synaptonemal complex central element protein 3 (family)
Synaptonemal complex central element protein 3 (SYCE3), also known as testis-specific expressed gene 2, is a major component of the transverse central element (CE) of meiosis-specific synaptonemal complexes. SYCE3 enables chromosome loading of the other CE-specific proteins, which in turn promotes synapsis between homologous chromosomes . SYCE3 may participate in the apoptosis of spermatogenic cells and the pathogenesis of cryptorchidism .
Wikipedia: The synaptonemal complex (SC) is a protein structure that forms between homologous chromosomes during meiosis and is thought to mediate synapsis and recombination during prophase I during meiosis in eukaryotes. It is currently thought that the SC functions primarily as a scaffold to allow interacting chromatids to complete their crossover activities.
Pfam PF16471: JNK-interacting protein leucine zipper II (coiled_coil)
This is the second leucine zipper domain (LZII) of several JNK-interacting proteins (JIP). It interacts with the small GTP-binding protein ARF6.
Pfam PF19815: Family of unknown function (DUF6298) (family)
This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 664 and 1043 amino acids in length. Some members of this family are thought to be pectin/pectate lyases.
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 PF02515: CoA-transferase family III (family)
CoA-transferases are found in organisms from all lines of descent. Most of these enzymes belong to two well-known enzyme families, but recent work on unusual biochemical pathways of anaerobic bacteria has revealed the existence of a third family of CoA-transferases. The members of this enzyme family differ in sequence and reaction mechanism from CoA-transferases of the other families. Currently known enzymes of the new family are a formyl-CoA: oxalate CoA-transferase, a succinyl-CoA: (R)-benzylsuccinate CoA-transferase, an (E)-cinnamoyl-CoA: (R)-phenyllactate CoA-transferase, and a butyrobetainyl-CoA: (R)-carnitine CoA-transferase. In addition, a large number of proteins of unknown or differently annotated function from Bacteria, Archaea and Eukarya apparently belong to this enzyme family. Properties and reaction mechanisms of the CoA-transferases of family III are described and compared to those of the previously known CoA-transferases.
Pfam PF08042: PqqA family (family)
This family consists of proteins belonging to the coenzyme Pyrroloquinoline quinone A (pqqA) family. PQQ is the non-covalently bounded prosthetic group  of many quinoproteins catalysing reactions in the periplasm of Gram-negative bacteria. PQQ is formed by the fusion of glutamate and tyrosine and synthesis of PQQ require the proteins encoded by the pqqABCDEF operon but details of the biosynthetic pathway are  unclear.
Pfam PF13077: Protein of unknown function (DUF3909) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length.
Pfam PF05922: Peptidase inhibitor I9 (domain)
This family includes the proteinase B inhibitor from Saccharomyces cerevisiae and the activation peptides from peptidases of the subtilisin family.  The subtilisin propeptides are known to function as molecular chaperones, assisting in the folding of the mature peptidase, but have also been shown to act as 'temporary inhibitors'.
Wikipedia: In biology and biochemistry, protease inhibitors, or antiproteases, are molecules that inhibit the function of proteases. Many naturally occurring protease inhibitors are proteins.
Pfam PF24031: IL27B N-terminal FN3 domain (domain)
This entry represents the Fibronectin type III (FN3) domain found at the N-terminal of Interleukin-27 subunit beta (IL27B), from animals. This domain may be found in association with a C-terminal FN3 ([pfam:PF00041]). Also known as EBI3, IL27B binds p28 to form the heterodimeric cytokine IL-27, which plays an important role in innate immunity by inducing naive CD4+ T cells proliferation. IL-27 binds GP130 and IL-27Ra, acting as a bridge, to activate the JAK/STAT signaling cascade. EBI3 stabilizes the complex by binding a positively charged surface of IL-27Ra and Domain 1 of GP130.