SII-SWORD/CoKE huggingface dataset:
Pfam PF21995: B12-dependent ribonucleotide reductase, insertion domain (domain)
This entry represents the insertion domain of adenosylcobalamin-dependent ribonucleoside-triphosphate reductases (class II RNRs) from Lactococcus leichmannii and related sequences. RNR's are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA, a rate-limiting step of DNA biosynthesis. RNRs are classified in class I, II and III. Class II RNRs are less complex and function as a monomer in contrast to class I and III RNRs, which controls substrate specificity as efficiently as a multimeric enzymes. This insertion domain provides the interface responsible for effector binding that, in oligomeric RNRs, is formed in the dimer interface.
Pfam PF01353: Green fluorescent protein (domain)
The green fluorescent protein (GFP) is found in the jellyfish (Aequorea victoria), and functions as an energy-transfer acceptor. It fluorescesin vivoupon receiving energy from the Ca2+-activated photoprotein aequorin. The protein absorbs light maximally at 395 nm and exhibits a smaller absorbance peak at 470 nm. The fluorescence emission spectrum peaks at 509 nm with a shoulder at 540 nm. The protein is produced in the photocytes and contains a chromophore, which is composed of modified amino acid residues. The chromophore is formed upon cyclisation of the residues ser-dehydrotyr-gly. There are several other members of the GFP family, which are able to fluoresce different colours, several of which are non-fluorescent . These proteins are all essentially encoded by single genes, since both the substrate and the catalytic enzyme for pigment biosynthesis are provided within a single polypeptide chain .
Wikipedia: The green fluorescent protein (GFP) is a protein that exhibits green fluorescence when exposed to light in the blue to ultraviolet range. The label GFP traditionally refers to the protein first isolated from the jellyfish Aequorea victoria and is sometimes called avGFP. However, GFPs have been found in other organisms including corals, sea anemones, zoanithids, copepods and lancelets.
Pfam PF13070: Protein of unknown function (DUF3934) (disordered)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There are two conserved sequence motifs: GTG and SKG.
Pfam PF22083: DNA endonuclease I-HmuI-like, NUMOD-like domain (domain)
This entry represents a C-terminal NUMOD1-like DNA-binding (HTH superfamily) domain present in a set of intron-encoded endonucleases (homing endonucleases) such as I-HmuI from Bacteriophage SP01 and similar proteins.
Pfam PF13542: Helix-turn-helix domain of transposase family ISL3 (domain)
This entry represents the HTH (helix-turn-helix) domain found in the IS204 , IS1001 , IS1096  and IS1165  transposases.
Pfam PF00520: Ion transport protein (family)
This family contains sodium, potassium and calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g.  Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane.
Wikipedia: The transmembrane cation channel superfamily was defined in InterPro and Pfam as the family of tetrameric ion channels. These include the sodium, potassium, calcium, ryanodine receptor, HCN, CNG, CatSper, and TRP channels. This large group of ion channels apparently includes families 1.A.1, 1.A.2, 1.A.3, and 1.A.4 of the TCDB transporter classification.
Pfam PF13762: Mitochondrial splicing apparatus component (family)
MNE1 is a novel component of the mitochondrial splicing apparatus responsible for the processing of a COX1 group I intron in yeast. Yeast cells lacking MNE1 are deficient in intron splicing in the gene encoding the Cox1 subunit of cytochrome oxidase but do contain wild-type levels of the bc1 complex.
Pfam PF06764: Protein of unknown function (DUF1223) (family)
This family consists of several hypothetical proteins of around 250 residues in length which are found in both plants and bacteria. The function of this family is unknown. Structurally it lies in the Thioredoxin-like superfamily.
Wikipedia: The thioredoxin fold is a protein fold common to enzymes that catalyze disulfide bond formation and isomerization. The fold is named for the canonical example thioredoxin and is found in both prokaryotic and eukaryotic proteins. It is an example of an alpha/beta protein fold that has oxidoreductase activity. The fold's spatial topology consists of a four-stranded antiparallel beta sheet sandwiched between three alpha helices. The strand topology is 2134 with 3 antiparallel to the rest.
Pfam PF13956: Toxin Ibs, type I toxin-antitoxin system (family)
The Ibs (induction brings stasis) proteins are a family of toxic peptides. Their expression is inhibited by the Sib antisense RNAs, which act as antitoxins.
Wikipedia: Sib RNA refers to a group of related non-coding RNA. They were originally named QUAD RNA after they were discovered as four repeat elements in Escherichia coli intergenic regions. The family was later renamed Sib when it was discovered that the number of repeats is variable in other species and in other E. coli strains.
Pfam PF03045: DAN domain (domain)
This domain contains 9 conserved cysteines and is extracellular. Therefore the cysteines may form disulphide bridges.  This family of proteins has been termed the DAN family after the first member to be reported. This family includes DAN, Cerberus and Gremlin. The gremlin protein is an antagonist of bone morphogenetic protein signaling.  It is postulated that all members of this family antagonise different TGF beta [pfam:PF00019] ligands. Recent work shows that the DAN protein is not an efficient antagonist of  BMP-2/4 class signals, we found that DAN was able to interact with  GDF-5 in a frog embryo assay, suggesting that DAN may regulate signaling by the GDF-5/6/7 class of BMPs in vivo.
Pfam PF08462: Carmovirus coat protein (family)
This domain is found to the C-terminus of the [pfam:PF00729] domain in Carmoviruses.
Pfam PF22209: CPV, RNA-directed RNA polymerase, N-terminal (domain)
This domain is found at the N-terminal of RNA-directed RNA polymerase (RdRP) from Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) and similar sequences from reovirus. This protein adopts a closed cage-like structure consisting of a central polymerase domain sandwiched between N-terminal and C-terminal bracelet domains. This domain adopts a predominantly alpha-helical configuration.
Pfam PF15156: Ceroid-lipofuscinosis neuronal protein 6 (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 190 and 310 amino acids in length.
Wikipedia: Ceroid-lipofuscinosis neuronal protein 6 is a protein that in humans is encoded by the CLN6 gene.
Pfam PF20860: Dicers, N-terminal domain (domain)
This domain is found at the N-terminal of hypothetical proteins from yeast that are thought to be the noncanonical Dicers found in these organisms. These proteins adopt a homodimer assembly similar to bacterial ribonuclease III but extended by a unique N-terminal domain that consists of five alpha-helices.
Pfam PF07136: Protein of unknown function (DUF1385) (family)
This family contains a number of hypothetical bacterial proteins of unknown function approximately 300 residues in length. Some family members are predicted to be metal-dependent.
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 PF13004: Putative binding domain, N-terminal (domain)
The BACON (Bacteroidetes-Associated Carbohydrate-binding Often N-terminal) domain is an all-beta domain found in diverse architectures, principally in combination with carbohydrate-active enzymes and proteases. These architectures suggest a carbohydrate-binding function which is also supported by the nature of BACON's few conserved amino-acids. The phyletic distribution of BACON and other data tentatively suggest that it may frequently function to bind mucin. Further work with the characterised structure of a member of glycoside hydrolase family 5 enzyme, PDB:3ZMR, has found no evidence for carbohydrate-binding for this domain.
Pfam PF04260: Protein of unknown function (DUF436) (domain)
Family of bacterial proteins with undetermined 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 PF22976: RRM domain (domain)
This entry represents the fourth RRM domain found in the hnRNP L protein.
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 PF20963: Acanthaporin (domain)
Acanthaporin is a pore-forming toxin from acanthamoebae, an opportunistic pathogen. This protein is cytotoxic for neuronal cells in humans and shows antimicrobial activity against diverse bacterial strains by permeabilising their membranes. It folds into a disulfide-bonded four-alpha-helix monomeric structure that dimerises at pH 8.0 due to the deprotonation of some histidine residues, which leads to a conformational change.
Pfam PF16257: tagaturonate epimerase (family)
This family consists of uncharacterized proteins around 500 residues in length and is mainly found in various Bacteria species, such as Thermotoga, Paenibacillus and Rhodothermus.  A newly recognized enzyme from the galacturonate utilization pathway in T. maritima with tagaturonate epimerase activity.
Pfam PF10931: Protein of unknown function (DUF2735) (family)
Some members in this family of proteins are annotated as glutamine synthetase translation inhibitor however this function can not be confirmed.
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 PF07369: Protein of unknown function (DUF1488) (family)
This family consists of several hypothetical bacterial proteins of around 85 residues in length. 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 PF05266: Protein of unknown function (DUF724) (family)
This family contains several uncharacterised proteins found in Arabidopsis thaliana and other plants. This region is often found associated with Agenet domains and may contain coiled-coil.
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 PF10409: C2 domain of PTEN tumour-suppressor protein (domain)
This is the C2 domain-like domain, in greek key form, of the PTEN protein, phosphatidyl-inositol triphosphate phosphatase, and it is the C-terminus. This domain may well include a CBR3 loop which means it plays a central role in membrane binding. This domain associates across an extensive interface with the N-terminal phosphatase domain DSPc ([pfam:PF00782]) suggesting that the C2 domain productively positions the catalytic part of the protein onto the membrane.
Pfam PF07096: Protein of unknown function (DUF1358) (family)
This family consists of several hypothetical eukaryotic proteins of around 125 residues in length. 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 PF04386: Stringent starvation protein B (family)
Escherichia coli stringent starvation protein B (SspB), is thought to enhance the specificity of degradation of tmRNA-tagged proteins by the ClpXP protease.  The tmRNA tag, also known as ssrA, is an 11-aa peptide added to the C terminus of proteins stalled during translation, targets proteins for degradation by ClpXP and ClpAP.  SspB a cytoplasmic protein that specifically binds to residues 1-4 and 7 of the tag. Binding of SspB enhances degradation of tagged proteins by ClpX, and masks sequence elements important for ClpA interactions, inhibiting degradation by ClpA. However, more recent work has cast doubt on the importance of SspB in wild-type cells. SspB is encoded in an operon whose synthesis is stimulated by carbon, amino acid, and phosphate starvation.  SspB may play a special role during nutrient stress, for example by ensuring rapid degradation of the products of stalled translation, without causing a global increase in degradation of all ClpXP substrates.
Pfam PF13571: Domain of unknown function (DUF4133) (family)
Based on Bacteroides thetaiotaomicron gene BT_0094, a putative uncharacterized protein as seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), It appears to be upregulated in the presence of host or vs when in culture.
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 PF05044: Homeo-prospero domain (domain)
Prospero is a large drosophila transcription factor protein that is expressed in all neural lineages of drosophila embryos.  It is needed for correct expression of several neural proteins and in determining the cell fates of neural stem cells. Homologues of prospero are found in a wide range of animals including humans with the highest level of similarity being found in the C-terminal 160 amino acids. This region was identified as containing an atypical homeobox domain followed by a prospero domain.  However, the structure shows that these two regions form a single stable structural domain as defined here. This homeo-prospero domain binds to DNA.
Pfam PF16414: Niemann-Pick C1 N terminus (domain)
This is the N-terminal domain of Niemann-Pick C1 family proteins. This family of proteins mediates transport of cholesterol from the intestinal lumen to enterocytes. This domain contains a cholesterol-binding pocket.
Pfam PF15519: linker between RRM2 and RRM3 domains in RBM39 protein (domain)
A conserved linker between the second and the third RRM domain in human RBM39 (CAPER) protein, also present in other RNA binding proteins, especially those involved in RNA splicing. This linker was implicated in interactions with ESR1 and ESR2. Preliminary results from JCSG suggest that this is a structured domain with a well defined fold.
Pfam PF18923: Domain of unknown function (DUF5673) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 90 amino acids in length. The domain is usually found C-terminal to a pair of transmembrane helices.
Pfam PF02508: Rnf-Nqr subunit, membrane protein (family)
This is a family of integral membrane proteins including Rhodobacter-specific nitrogen fixation (rnf) proteins RnfA and RnfE and Na+-translocating NADH:ubiquinone oxidoreductase (Na+-NQR) subunits NqrD and NqrE.
Pfam PF10983: Protein of unknown function (DUF2793) (family)
This is a bacterial family of proteins with 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 PF24567: ANKLE2 third alpha/beta domain (domain)
This domain is found in the human Ankyrin repeat and LEM domain-containing protein 2 (ANKLE2) and related proteins. Human ANKLE2 is involved in mitotic nuclear envelope reassembly by promoting dephosphorylation of BAF/BANF1 during mitotic exit. The domain represented by this entry is predicted to adopt globular alpha/beta structure consisting of a five-stranded antiparallel beta-sheet and helices packed on one side of it.
Pfam PF13289: SIR2-like domain (family)
This family of proteins are related to the sirtuins.
Pfam PF24513: Domain of unknown function (DUF7593) (domain)
This domain of unknown function is found in uncharacterised fungal sequences.
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 PF13605: Domain of unknown function (DUF4141) (family)
Based on Bacteroides thetaiotaomicron gene BT_4772, a putative uncharacterized protein. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or vs when in culture.
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 PF12976: Domain of Unknown Function with PDB structure (DUF3860) (family)
A protein family created to cover PDB:2OD5. 2OD5 is a hypothetical protein (JCVI_PEP_1096688149193) from an environmental metagenome (unidentified marine microbe).
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 PF12130: Bivalent Mical/EHBP Rab binding domain (domain)
A variety of different effector proteins interact specifically with GTP-bound Rab proteins and mediate their versatile roles in membrane trafficking, including budding of vesicles from a donor membrane, directed transport through the cell and finally tethering and fusion with a target membrane. The 'bivalent Mical/EHBP Rab binding' (bMERB) domain is a Rab effector domain that is present in proteins of the Mical and EHBP families, both known to act in endosomal trafficking. The bMERB domain displays a preference for Rab8 family proteins (Rab8, 10, 13 and 15) and at least some of the bMERB domains contain two separate binding sites for Rab-proteins, allowing Micals and EHBPs to bind two Rabs simultaneously. The strong similarity between the two binding sites within one bMRB domain strongly suggests an evolutionarily development via duplication of a common ancestor supersecondary structure element. The bMERB domain has a completely alpha-helical fold consisting of a central helix and N- and C-terminal helices folding back on this central helix.
Pfam PF22234: Mycothiol-dependent nitroreductase Rv2466c (domain)
Mycothiol-dependent nitroreductase Rv2466c is a key oxidoreductase that mediates the reductive activation of TP053, a thienopyrimidine derivative that kills replicating and non-replicating Mycobacterium tuberculosis. This enzyme transforms nitro-containing compounds to their corresponding amine and uses as  a cofactor, a low molecular weight sugar thiol, mycothiol. The Rv2466c structure adopts a thioredoxin-like fold but it forms an unique homodimer in which the C-terminal beta-strand is swapped between the thioredoxin domains of each subunit. Rv2466c undergoes significant conformational changes upon formation of its oxidized state.
Pfam PF18658: Spin-doc zinc-finger (domain)
This is a zinc finger domain C2H2 type which can be found in SPIN1 docking protein (SPIN-DOC) and Epm2a-interacting protein 1 (Epm2aip1). SPIN-DOC is a Spindlin1 (SPIN1) regulator that directly binds and strongly disrupts its histone methylation reading ability, causing it to disassociate from chromatin. Epm2aip1 is a glycogen synthase (GS)-associated protein. In the absence of Epm2aip1, the sensitivity of the liver to insulin, in which GS is a principal actor, is impaired.
Pfam PF20097: Domain of unknown function (DUF6487) (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. This domain is likely to be a zinc-binding domain.
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 PF23360: BBS7 GAE domain (domain)
This entry represents the gamma-adaptin ear (GAE) domain of BBS7. BBS7 is one of the BBS proteins that form the BBSome complex found in vertebrates and nematodes, including humans, mice, and Caenorhabditis elegans. The BBSome complex is required for ciliogenesis, as well as the assembly and movement of intraflagellar transport proteins along the ciliary membrane [].
Pfam PF18813: phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease4 (domain)
A predicted endoRNase of the Barnase-EndoU-ColicinE5/D-RelE like nuclease fold found in polyvalent proteins of phages and conjugative elements. The predicted active site contains a conserved histidine residue.