SII-SWORD/CoKE huggingface dataset:
Pfam PF00254: FKBP-type peptidyl-prolyl cis-trans isomerase (domain)
FKBP-type peptidylprolyl isomerases (5.2.1.8) in vertebrates, are receptors for the two immunosuppressants, FK506 and rapamycin. The drugs inhibit T cell proliferation by arresting two distinct cytoplasmic signal transmission pathways. Peptidylprolyl isomerases accelerate protein folding by catalysing the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides. These proteins are found in a variety of organisms .

This entry represents a domain found in FKBP-type peptidylprolyl isomerases.
Wikipedia: The FKBPs, or FK506 binding proteins, constitute a family of proteins that have prolyl isomerase activity and are related to the cyclophilins in function, though not in amino acid sequence. FKBPs have been identified in many eukaryotes, ranging from yeast to humans, and function as protein folding chaperones for proteins containing proline residues. Along with cyclophilin, FKBPs belong to the immunophilin family.
Pfam PF06886: Targeting protein for Xklp2 (TPX2) domain (domain)
This family represents a conserved region approximately 60 residues long within the eukaryotic targeting protein for Xklp2 (TPX2). Xklp2 is a kinesin-like protein localised on centrosomes throughout the cell cycle and on spindle pole microtubules during metaphase. In Xenopus, it has been shown that Xklp2 protein is required for centrosome separation and maintenance of spindle bi-polarity. TPX2 is a microtubule-associated protein that mediates the binding of the C-terminal domain of Xklp2 to microtubules. It is phosphorylated during mitosis in a microtubule-dependent way. The TPX domain appears to be truncated in fungal species.
Pfam PF20701: Het-E N-terminal domain (domain)
This entry corresponds to a domain found at the N-terminus of fungal Heteroincompatibility HetE proteins and in biological conflict systems of bacteria.
Pfam PF12194: Protein kinase Fus3-binding (domain)
This domain family is found in eukaryotes, and is approximately 190 amino acids in length. This domain is the penultimate C terminal domain from the protein ste5 which co-catalyses the phosphorylation of fus3 by ste7. It is involved in the MAPK pathways. This domain is the minimal scaffold domain of ste5. It binds to the mitogen activated protein kinase fus3 before it is phosphorylated.
Pfam PF14851: FAM176 family (family)
Members of the FAM176 family regulate autophagy and apoptosis.
Pfam PF09056: Prokaryotic phospholipase A2 (domain)
The prokaryotic phospholipase A2 domain is predominantly found in bacterial and fungal phospholipases, as well as various hypothetical and putative proteins. It enables the liberation of fatty acids and lysophospholipid by hydrolysing the 2-ester bond of 1,2-diacyl-3-sn-phosphoglycerides. The domain adopts an alpha-helical secondary structure, consisting of five alpha-helices and two helical segments.
Wikipedia: The prokaryotic phospholipase A2 domain is found in bacterial and fungal phospholipases. It enables the liberation of fatty acids and lysophospholipid by hydrolyzing the 2-ester bond of 1,2-diacyl-3-sn-phosphoglycerides. The domain adopts an alpha-helical secondary structure, consisting of five alpha-helices and two helical segments.
Pfam PF23461: ZMYND11 protein coiled-coil (coiled_coil)
This entry represents a coiled-coil that self associates to form a dimeric arrangement found in the ZMYND11 protein.  The coiled coil is adjacent to a MYND zinc finger.  The Zinc finger MYND domain-containing protein 11 family functions as a chromatin reader, specifically recognizing and binding to histone H3.3 trimethylated at Lys-36 (H3.3K36me3). It plays a role in regulating RNA polymerase II elongation, acting as a transcription corepressor by modulating the polymerase during the elongation stage. The family's PWWP domain adopts a five-bladed beta-barrel fold and binds to H3.3K36me3 via a conserved aromatic cage. The family is involved in the specific recognition of H3.3 histone by encapsulating the Ser 31 residue of H3.3 in a composite pocket formed by tandem bromo-PWWP domains. Additionally, the family has a role in tumor suppression by repressing transcriptional programs essential for tumor cell growth and can bind non-specifically to dsDNA. In the context of microbial infection, it can inhibit viral-mediated transcriptional activation and host cell proliferation.
Pfam PF04342: Putative member of DMT superfamily (DUF486) (family)
This family contains several proteins of uncharacterised function. The family is represented in the Transport classification database as 2.A.7.34, though the exact nature of what is transported is not known.
Pfam PF13770: Domain of unknown function (DUF4169) (family)
The function of these proteins is not known.
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 PF17673: Family of unknown function (DUF5532) (family)
This is a family of unknown function found in mammals.
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 PF12385: Papain-like cysteine protease AvrRpt2 (family)
This is a family of cysteine proteases, found in actinobacteria, protobacteria and firmicutes. Papain-like cysteine proteases play a crucial role in plant-pathogen/pest interactions. On entering the host they act on non-self substrates, thereby manipulating the host to evade proteolysis. AvrRpt2 from Pseudomonas syringae pv. tomato DC3000 triggers resistance to P. syringae-2-dependent defence responses, including hypersensitive cell death, by cleaving the Arabidopsis RIN4 protein which is monitored by the cognate resistance protein RPS2.
Pfam PF13084: Domain of unknown function (DUF3943) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 110 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 PF14637: Folliculin-interacting protein middle domain (family)
This is the middle domain of folliculin-interacting proteins.
Pfam PF18515: Rh5 coiled-coil domain (coiled_coil)
This is a helical coiled-coil domain found in reticulocyte-binding protein homolog 5 (RH5), a Plasmodium falciparum protein essential for erythrocyte invasion.
Pfam PF12934: FTO C-terminal domain (domain)
This domain is found at the C-terminus of the FTO protein which was shown to be associated with increased BMI and obesity risk in humans.  The N-terminal domain of this protein is a DNA demethylase and this domain is found to associate with the N-terminal domain in the crystal structure. This domain is alpha helical with three helices that form a bundle.
Wikipedia: Fat mass and obesity-associated protein, also known as alpha-ketoglutarate-dependent dioxygenase FTO, is an enzyme that in humans is encoded by the FTO gene located on chromosome 16. As one homolog in the AlkB family proteins, it is the first messenger RNA (mRNA) demethylase that has been identified. Certain alleles of the FTO gene appear to be correlated with obesity in humans.
Pfam PF19325: E3 ubiquitin-protein ligase RNF152 C-terminus (family)
This family represents the C-terminal region of the E3 ubiquitin ligase RNF152 containing the hydrophobic transmembrane domain, responsible for the lysosomal localisation of the protein as well as its ubiquitination activity. This protein polyubiquitinates several proteins and itself, which leads to proteasome degradation. It has been shown that RNF152 has also pro-apoptotic activity, dependent on its RING finger and transmembrane domains. In addition, the transmembrane domain of RNF152 is necessary for negative regulation of the mTORC1 pathway in an amino-acid-sensitive manner, as it mediates RNF152-RagA interaction and RagA ubiquitination.
Pfam PF04360: Serglycin (family)
Serglycin is the most prevalent proteoglycan produced in haemopoietic cells. Serglycin is a proteinase resistant secretory granule  proteoglycan.
Pfam PF19375: DurN substrate-assisted peptide maturase (family)
This entry represents a member of a biosynthetic gene cluster (BGC) involved in duramycin biosynthesis, a ribosomally synthesized and post-translationally modified peptide (RiPP) produced by various actinomycetes and marine symbionts. Duramycin binds phosphatidylethanolamine (PE), a major structural phospholipid in mammalian and microbial cell membranes which contains 19 amino acids and 5 post-translational modifications (PTMs). This entry represents DurN, an enzyme that forms (2S,9S)-Lal one of the two last PTMs. DurN catalyses stereospecific and diastereoselective Lal formation in an unusual substrate-assisted mechanism in  which the active site residues that make the reaction proceed come from the substrate itself, manoeuvred into position by DurN.
Pfam PF24688: SseK/NleB family (family)
This entry represents the bacterial effector proteins SseK and NleB and their homologues. SseK and NleB are bona fide protein-arginine N-acetylglucosaminyltransferases that glycosylate host proteins on arginine residues, leading to reduced NF-kappaB-dependent responses to infection. These proteins have different substrate specificity. They have a detectable sequence similarity and share similar structural core with glucosyltransferases family 88 ([pfam:PF16849]). A conserved HEN motif (His-Glu-Asn) in their active site is important for enzyme catalysis and bacterial virulence.
Pfam PF16972: Na+ channel auxiliary subunit TipE (family)
TipE appears to be a family of insect Na+ channel auxiliary subunit proteins.
Pfam PF18239: Hemagglutinin I (domain)
This domain is hemagglutinin I (HA1) present in Physarum polycephalum. Although the physiological function of the secreted HA1 remains to be established, HA1 recognizes cell wall polysaccharides of E. coli. The beta-sandwich fold of HA1, composed of two up and down beta-sheets, is conserved among other legume lectin-like proteins. The up and down beta-sheet region is a minimal carbohydrate recognition domain.
Pfam PF07721: Tetratricopeptide repeat (repeat)
This Pfam entry includes tetratricopeptide-like repeats not detected by the [pfam:PF00515], [pfam:PF07719] and [pfam:PF07720] models.
Pfam PF18958: Putative zinc dependent peptidase (DUF5700) (family)
This entry represents a group of putative zinc dependent peptidases that have the characteristic HEXXH motif. This family is most related to [pfam:PF10026].
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 PF21305: GspD-like, N0 domain (domain)
GspD is a type II general secretion pathway protein involved in protein export. This is the N0 domain found at the N-terminal of GspD type II secretins and its close homologues. These proteins form a dodecameric ring, in which the N0 domain mediate extensive contacts suggesting that dodecameric N0 ring is an important feature of T2SS secretins. This domain is also found in virion export proteins, proteins thought to form a channel across the host outer membrane for the purposes of extruding the bacteriophage.
Pfam PF24075: Domain of unknown function (DUF7367) (domain)
This entry represents a small family of uncharacterised phage proteins. These proteins range in length from 94 to 110 amino acids and adopt a small domain composed of four alpha helices.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF14491: Protein of unknown function (DUF4435) (domain)
This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 285 and 362 amino acids in length. This domain is sometimes associated with AAA domains.
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 PF12319: Tryptophan-Threonine-rich plasmodium antigen C terminal (family)
This protein is found in eukaryotes. Proteins in this family are typically between 254 to 536 amino acids in length. This family is the C terminal of a surface antigen of malarial Plasmodium species. It is currently being targeted for use as part of a subunit vaccine against Plasmodium falciparum, the main species involved in causing human malaria.
Pfam PF19911: Family of unknown function (DUF6384) (family)
This family of proteins is functionally uncharacterised. Proteins in this family are typically between 306 and 346 amino acids in length and they are predominantly found in Proteobacteria. There is a conserved sequence MDXXdTLRH at the N-terminal and a conserved sequence YxxVEA at the C-terminal.
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 PF22289: Dimethylamine monooxygenase subunit DmmA-like, C-terminal domain (domain)
This entry represents the C-terminal domain of the dimethylamine monooxygenase subunit DmmA from Methylocella silvestris (Msil_3607, [swissprot:B8EJ00]) and similar sequences, mainly found in proteobacteria and actinomycetes. Dimethylamine (DMA) monooxygenase is required for metabolism of trimethylamine N-oxide (TMAO).
Pfam PF01934: Ribonuclease HepT-like (family)
This family includes the toxic component HepT of a type II toxin-antitoxin (TA) system, which has RNase activity. These proteins contain a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain and are neutralised through tri-AMPylation by the cognate antitoxin MntA, containing a MNT (minimal nucleotidyltransferase) domain. HepT-MnA form an heterooctamer (at a 2:6 ratio), a rare organisation for this kind of TA systems. HepT dimerises and enables the formation of a deep cleft at the HEPN-domain interface, containing the RX4-6H motif (where X is any amino acid and the residue immediately after the conserved R is typically a polar amino acid) as the active site that functions as an RNA-cleaving RNase. This type II TA system regulates cell motility and confers plasmid stability. Due to the prevalence of these HEPN/MNT modules in bacteria and archaea, it has been suggested that these TA systems may also play a role in the environmental adaptation to extreme habitats.
Pfam PF11599: RRNA methyltransferase AviRa (family)
This family of proteins represents the methyltransferase AviRa from Streptomyces viridochromogenes. This protein mediates the resistance to the antibiotic avilamycin. AviRa methylates a specific guanine base within the peptidyl-transferase loop of the 23S ribosomal RNA.
Pfam PF17698: Family of unknown function (DUF5544) (family)
This is a family of unknown function found in primates.
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 PF01299: Lysosome-associated membrane glycoprotein 2-like, luminal domains (domain)
This domain is found in a group of animal proteins that includes Lysosome-associated membrane glycoprotein 2 from humans (Lamp2). Lamp2 is an integral membrane protein that plays an important role in chaperone-mediated autophagy (CMA), targeting pertinent proteins for lysosomal degradation. This protein is organised into two conserved luminal domains (this entry), a single transmembrane (TM) domain ([pfam:PF21222]), and a short C-terminal cytosolic tail. It adopts a trimeric configuration.
Wikipedia: Lysosome-associated membrane glycoproteins (LAMPs) are integral membrane proteins, specific to lysosomes, and whose exact biological function is not yet clear. Structurally, the lamp proteins consist of two internally homologous lysosome-luminal domains separated by a proline-rich hinge region; at the C-terminal extremity there is a transmembrane region (TM) followed by a very short cytoplasmic tail (C). In each of the duplicated domains, there are two conserved disulfide bonds. This structure is schematically represented in the figure below. +-----+ +-----+ +-----+ +-----+
 | | | | | | | |
 xCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxxxCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxx
 +--------------------------++Hinge++--------------------------++TM++C+
Pfam PF24829: Phage connector protein (domain)
This entry represents a family of phage proteins that are structurally related to the HK97 gp6 protein that forms a head to tail connection. It is likely that these proteins form large homo-oligomeric rings.
Pfam PF04964: Flp/Fap pilin component (family)
This entry is for the fimbriae associated protein Flp/Fap pilin component.
Pfam PF04580: Chordopoxvirinae D3 protein (family)
Chordopoxvirinae D3 protein conserved region.  Region occupies entire length of D3 protein.
Pfam PF00148: Nitrogenase component 1 type Oxidoreductase (domain)
Enzymes belonging to this family include cofactor-requiring nitrogenases and protochlorophyllide reductase. The key enzymatic reactions in nitrogen fixation are catalysed by the nitrogenase complex, which has two components, the iron protein (component 2), and a component (component 1) which is either a molybdenum-iron, vanadium-iron or iron-iron protein. The enzyme (1.18.6.1) forms a hexamer of two alpha, two beta and two delta chains. Protochlorophyllide reductase (1.3.1.33) is involved in the light-dependent accumulation of chlorophyll, probably at the step of reduction of protochlorophyllide to chlorophyllide.
Wikipedia: Nitrogenases are enzymes (EC 1.18.6.1EC 1.19.6.1) that are produced by certain bacteria, such as cyanobacteria (blue-green bacteria) and rhizobacteria. These enzymes are responsible for the reduction of nitrogen (N2) to ammonia (NH3). Nitrogenases are the only family of enzymes known to catalyze this reaction, which is a step in the process of nitrogen fixation. Nitrogen fixation is required for all forms of life, with nitrogen being essential for the biosynthesis of molecules (nucleotides, amino acids) that create plants, animals and other organisms. They are encoded by the Nif genes or homologs. They are related to protochlorophyllide reductase.
Pfam PF17160: Domain of unknown function (DUF5124) (family)
DUF5124 is a domain of unknown function found in proteins from Bacteroidales.
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 PF04241: Protein of unknown function (DUF423) (family)
This family of proteins with unknown function is a possible integral membrane protein from Caenorhabditis elegans. This family of proteins has GO references indicating the protein is involved in nematode larval development and is a positive regulator of growth rate.
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 PF17988: VEGFR-2 Transmembrane domain (domain)
This is a transmembrane domain (TMD) of vascular endothelial growth factor receptor 2 which regulates blood vessel homeostasis. Transmembrane signalling by receptor tyrosine kinases (RTKs) requires specific orientation of the intracellular kinase domains in active receptor dimers. Two mutants in VEGFR-2 TMD showed constitutive kinase activity, suggesting that precise TMD orientation is mandatory for kinase activation. Scanning mutagenesis and structural analysis indicated that introducing two polar amino acids in distinct positions of the TMD (G770E/F777E and I771E/L778E mutations) reorients transmembrane helices and leads to stable dimer formation. Therefore, it has been suggested that the transition between the inactive and the active dimeric state of VEGFR-2 implicates alternative dimeric TMD conformations.
Pfam PF03192: Pyrococcus protein of unknown function, DUF257 (family)
This family of proteins is 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 PF03611: PTS system sugar-specific permease component (family)
This family includes bacterial transmembrane proteins with a putative sugar-specific permease function, including and analogous to the IIC component of the PTS system. It has been suggested that this permease may form part of an L-ascorbate utilisation pathway, with proposed specificity for 3-keto-L-gulonate (formed by hydrolysis of L-ascorbate). This family includes the IIC component of the galactitol specific GAT family PTS system.
Wikipedia: The PTS L-Ascorbate (L-Asc) Family includes porters specific for L-ascorbate, and is part of the PTS-AG superfamily. A single PTS permease of the L-Asc family of PTS permeases has been functionally characterized. This is the SgaTBA system, renamed UlaABC by Yew and Gerlt.