SII-SWORD/CoKE huggingface dataset:
Pfam PF16042: Domain of unknown function (DUF4794) (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 74 and 92 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 PF10335: Putative nucleotidyltransferase substrate binding domain (domain)
This domain is found associated with presumed nucleotidyltransferase domains and seems to be distantly related to other helical substrate binding 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 PF16939: Putative porin (family)
Porin_6 is a family of putative porins from Leptospira species.
Pfam PF07942: Carnosine N-methyltransferase (family)
This family includes Carnosine N-methyltransferase (E.C:2.1.1.22), conserved from yeast to human, that catalyses the formation of anserine (beta-alanyl-N(Pi)-methyl-L-histidine) from carnosine. Anserine, a methylated derivative of carnosine (beta-alanyl-L-histidine), is an abundant constituent of vertebrate skeletal muscles. It also methylates other L-histidine-containing di- and tripeptides such as Gly-Gly-His, Gly-His and homocarnosine (GABA-His).
Pfam PF16121: 40S ribosomal protein S4 C-terminus (family)
This domain is found at the C-terminus of 40S ribosomal protein S4.
Pfam PF09907: HigB_toxin, RelE-like toxic component of a toxin-antitoxin system (family)
HigB_toxin is a family of RelE-like prokaryotic proteins that function as mRNA interferases. HigB cleaves translated mRNA only, and cleavage depended on translation of the target RNAs. HigB belongs to the RelE super-family of RNases. The toxin-antitoxin gene-pair is induced by environmental stress factors.
Wikipedia: A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
Pfam PF02159: Oestrogen receptor (family)
The oestrogen receptors (ERs) are steroid or nuclear hormone receptors that act as transcription regulators involved in diverse physiological functions. Oestrogen receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. The ER consists of three functional and structural domains: an N-terminal modulatory domain, a highly conserved DNA-binding domain that recognises specific sequences (IPR001628), and a C-terminal ligand-binding domain (IPR000536).
This entry represents the N-terminal modulatory domain of the estrogen receptor, which spans the first 180 residues and contains the activation function 1 (AF1) region. Nuclear receptors differ considerably with respect to AF1 activity and regulation, as it is a poorly conserved region . There is another activation function region, namely AF2, which resides in the C-terminal end of the ligand-binding domain. Transcription activation is facilitated by both AF1 and AF2, which appear to act synergistically in the ER complex . For example, the ER can recruit TIF2 (transcription intermediary factor 2) via the AF1 and AF2 regions, whose synergistic action results in the activation of transcription.
Wikipedia: Estrogen receptors (ERs) are proteins found in cells that function as receptors for the hormone estrogen (17β-estradiol). There are two main classes of ERs. The first includes the intracellular estrogen receptors, namely ERα and ERβ, which belong to the nuclear receptor family. The second class consists of membrane estrogen receptors (mERs), such as GPER (GPR30), ER-X, and Gq-mER, which are primarily G protein-coupled receptors. This article focuses on the nuclear estrogen receptors.
Pfam PF22996: BIRD-IDD transcription factor, second C2H2 zinc finger (family)
This C2H2 zinc finger domain is found in the BIRD/INDETERMINATE DOMAIN (IDD) transcription factor family. Members of this BIRD/IDD family such as JACKDAW (JKD)/IDD10, BALDIBIS (BIB), MAGPIE (MGP)/IDD3 are required for asymmetric cell division of ground tissue and QC specification by direct protein-protein interaction with SHR and/or SCR to control ground tissue patterning during root growth. SHR-SCR functions as a transcription cofactor by binding to the zinc finger domains of these transcription factors. Members of the BIRD/IDD family contain 4 zinc finger domains, two classical C2H2 followed by two C2HC zinc finger domains. This entry represents the second C2H2 zinc finger domain that is involved in DNA binding.
Pfam PF14712: Snapin/Pallidin (family)
This family of proteins includes Snapin, this protein is associated with the SNARE complex, which mediates synaptic vesicle docking and fusion. It also includes the yeast snapin-like protein SNN1, which is a part of a complex involved in endosomal cargo sorting. The family also includes pallidin, a component of a complex involved in biogenesis of lysosome-related organelles.
Pfam PF18263: MCM6 C-terminal winged-helix domain (domain)
The minichromosome maintenance (Mcm) complex is the replicative helicase in eukaryotic species, that plays essential roles in the initiation and elongation phases of DNA replication. During late M and early G(1), the Mcm complex is loaded onto chromatin to form prereplicative complex in a Cdt1-dependent manner. This entry represents the C-terminal domain of human Mcm6 which is the Cdt1 binding domain (CBD). The structure of CBD exhibits a typical winged helix fold that is generally involved in protein-nucleic acid interaction. The CBD failed to interact with DNA in experiments. The CBD-Cdt1 interaction involves the helix-turn-helix motif of CBD.
Pfam PF04027: Domain of unknown function (DUF371) (family)
Archaeal domain 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 PF06474: MltD lipid attachment motif (conserved_site)
This short motif is a lipid attachment site.
Pfam PF13272: Putative 2/3 transmembrane domain holin (family)
Holin_2-3 is a putative holins with 2 or 3 transmembrane segments.  It consists of many proteobacterial proteins ranging in size from about 70 aas to 120 aas. They have 2 or 3 predicted TMSs. Although some are annotated as phage proteins or holins, none appears to be functionally characterised.
Pfam PF22569: 2'-deoxycytidine 5'-triphosphate deaminase (DCD), C-terminal domain (domain)
This entry includes several bacterial 2'-deoxycytidine 5'-triphosphate deaminase proteins ([ec:3.5.4.13]) (DCD) which consist of two dUTPase-like domains (PDBe:2r9q). This entry represents the C-terminal domain.
Pfam PF03223: V-ATPase subunit C (family)
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.
V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra-and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release . V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins .
This entry represents the C subunit that is part of the V1 complex, and is localised to the interface between the V1 and V0 complexes . This subunit does not show any homology with F-ATPase subunits. The C subunit plays an essential role in controlling the assembly of V-ATPase, acting as a flexible stator that holds together the catalytic (V1) and membrane (V0) sectors of the enzyme . The release of subunit C from the ATPase complex results in the dissociation of the V1 and V0 subcomplexes, which is an important mechanism in controlling V-ATPase activity in cells.
Wikipedia: Vacuolar-type ATPase (V-ATPase) is a highly conserved evolutionarily ancient enzyme with remarkably diverse functions in eukaryotic organisms. V-ATPases acidify a wide array of intracellular organelles and pumps protons across the plasma membranes of numerous cell types. V-ATPases couple the energy of ATP hydrolysis to proton transport across intracellular and plasma membranes of eukaryotic cells. It is generally seen as the polar opposite of ATP synthase because ATP synthase is a proton channel that uses the energy from a proton gradient to produce ATP. V-ATPase however, is a proton pump that uses the energy from ATP hydrolysis to produce a proton gradient.
Pfam PF11659: Protein of unknown function (DUF3261) (domain)
This family of proteins with unknown function appears to be restricted to Proteobacteria. The family is related to the LolB family suggesting a role in lipoprotein insertion in the outer 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 PF14399: Butirosin biosynthesis protein H, N-terminal (family)
BtrH_N is the N-terminus of the acyl carrier protein:aminoglycoside acyltransferase BtrH. Alternatively it can be referred to as butirosin biosynthesis protein H. BtrH transfers the unique (S)-4-amino-2-hydroxybutyrate (AHBA) side chain, which protects the antibiotic butirosin from several common resistance mechanisms. Butirosin, an aminoglycoside antibiotic produced by Bacillus circulans, exhibits improved antibiotic properties over its parent molecule and retains bactericidal activity toward many aminoglycoside-resistant strains. Butirosin is unique in carrying the AHBA side-chain. BtrH transfers the AHBA from the acyl carrier protein BtrI to the parent aminoglycoside ribostamycin as a gamma-glutamylated dipeptide.
Pfam PF01507: Phosphoadenosine phosphosulfate reductase family (family)
This domain is found in phosphoadenosine phosphosulfate (PAPS) reductase enzymes or PAPS sulfotransferase. PAPS reductase is part of the adenine  nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. The enzyme uses thioredoxin as an electron  donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP). It is also found in NodP nodulation protein P from Rhizobium which has ATP sulfurylase activity (sulfate adenylate transferase).
Pfam PF21367: Zinc finger 512, zinc fingers (domain)
This zinc finger is found in Zinc finger protein 512, whose function is not yet known.
Pfam PF09292: Endonuclease VIII-like 1, DNA bind (domain)
Members of this family are predominantly found in Endonuclease VIII-like 1 and adopt a glucocorticoid receptor-like fold. They allow for DNA binding.
Pfam PF14598: PAS domain (domain)
This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), which binds to an LXXLL motif in the C-terminal region of STAT6 (Signal transducer and activator of transcription 6).
Pfam PF09718: Lambda phage tail tape-measure protein (Tape_meas_lam_C) (domain)
This represents a relatively well-conserved region near the C terminus of the tape measure protein of a lambda and related phage. The protein, which controls phage tail length, is typically about 1000 residues in length. Both low-complexity sequence and insertion/deletion events appear common in this family. Mutational studies suggest a ruler or template role in the determination of phage tail length. Similar behaviour is attributed to proteins from distantly related or unrelated families in other phage.
Pfam PF01558: Pyruvate ferredoxin/flavodoxin oxidoreductase (domain)
This family includes a region of the large protein pyruvate-flavodoxin oxidoreductase and the whole pyruvate ferredoxin oxidoreductase gamma subunit protein.  It is not known whether the  gamma subunit has a catalytic or regulatory role. Pyruvate oxidoreductase (POR) catalyses the final step in the fermentation of carbohydrates in anaerobic microorganisms. This involves the oxidative decarboxylation of pyruvate with the participation of thiamine followed by the transfer of an acetyl moiety to coenzyme A for the synthesis of acetyl-CoA. The family also includes  pyruvate flavodoxin oxidoreductase as encoded by the nifJ gene in cyanobacterium which is required for growth on molecular nitrogen when iron is limited.
Pfam PF01212: Beta-eliminating lyase (domain)
This domain is found in many tryptophanases (tryptophan indole-lyase, TNase), tyrosine phenol-lyases (TPL) and threonine aldolases. It is involved in the degradation of amino acids. The glycine cleavage system is composed of four proteins: P, T, L and H. In Bacillus subtilis, the P 'protein' is an heterodimer of two subunits. The glycine cleavage system catalyses the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein
Pfam PF21157: DnaK suppressor protein DksA, N-terminal domain (domain)
DksA is a transcription factor that directly binds RNA polymerase and controls the bacteria response to stress and starvation. DksA is all helical and comprises a coiled-coil (CC) and globular domains. This is the N-terminal domain which extends through the secondary channel toward the RNAP active site and serves as a conduit for the substrate NTPs. This domain consists of two helices arranged in an antiparallel alpha-hairpin with left-handed twist.
Pfam PF10825: Protein of unknown function (DUF2752) (family)
This family is conserved in bacteria. Many members are annotated as being putative membrane 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 PF03862: SpoVAC/SpoVAEB sporulation membrane protein (family)
Members of this family are all transcribed from the spoVA operon. Bacillus and Clostridium are two well studied endospore forming bacteria. Spore formation provides a resistance mechanism in response to extreme or unfavourable environmental conditions such as heat, radiation, and chemical agents or nutrient deprivation.  The reverse process termed germination takes place where spores develop into growing cells in response to nutrient availability or stress reduction. Nutrient germinant receptors (GRs) and the SpoVA proteins are important players in the germination process. In B.subtilis the SpoVAC and SpoVAEB, belonging to this domain family, are predicted to be membrane proteins, with two to five membrane spanning. Biophysical and biochemical studies suggest that SpoVAC acts as a mechano-sensitive channel with properties that would allow the release of Ca-DPA (dipicolinic acid) and amino acids during germination of the spore. The release of Ca-DPA is a crucial event during spore germination. When expressed in E.coli SpoVAC provides protection against osmotic downshift. Furthermore, SpoVAC acts as channel that facilitates the efflux down the concentration gradient of osmolytes up to a mass of at least 600 Da. Another conserved SpoVA protein in all spore-forming bacteria is SpoVAEb, which appears to be an integral membrane protein with no known function.
Pfam PF04108: Autophagy protein ATG17-like domain (domain)
This domain is found in the autophagy-related proteins ATG17 and ATG11, conserved across eukaryotes. ATG17 forms a complex with ATG29 and ATG31, critical for both PAS (preautophagosomal structure) formation and autophagy. Together with ATG13, it is required for ATG1 kinase activation. ATG11 is a scaffold protein required for the cytoplasm-to-vacuole targeting (Cvt) pathway during starvation and to recruit ATG proteins to the pre-autophagosome. It is also required for ATG1 kinase activation. In many eukaryotes, ATG11 (the orthologue in mammals is RB1-inducible coiled-coil protein 1 (RB1CC1) and in S. pombe is Taz1-interacting factor 1 (taf1)) is essential for bulk autophagy, except in S.cerevisiae. ATG17 and ATG11 are large similar proteins, both predicted to be almost entirely helical, containing conserved coiled-coil regions and lack obvious functional motifs.
Pfam PF11136: Protein of unknown function (DUF2889) (family)
This bacterial family of 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 PF12482: Phage integrase protein (family)
This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with [pfam:PF00589].
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 PF08638: Mediator complex subunit MED14 (family)
Saccharomyces cerevisiae RGR1 mediator complex subunit affects chromatin structure, transcriptional regulation of diverse genes and sporulation, required for glucose repression, HO repression, RME1 repression and sporulation.  This subunit is also found in higher eukaryotes and Med14 is the agreed unified nomenclature for this subunit. Med14 is found in the tail region of Mediator.
Wikipedia: Mediator of RNA polymerase II transcription subunit 14 is an enzyme that in humans is encoded by the MED14 gene.
Pfam PF20406: Kinase suppressor RAS 1 N-terminal helical hairpin (domain)
Pseudokinases kinase suppressor of Ras 1 and 2 (KSR1/2) are scaffolds that bridge RAF isoforms and their substrate, mitogen-activated protein kinase kinase (MEK). They dimerize with kinase-competent RAFs (ARAF, BRAF and CRAF) to stimulate catalysis allosterically . This entry represents the N-terminal helical hairpin which, together with the SAM-like domain (IPR025561) constitutes the N-terminal regulatory region that mediates heterodimerization of BRAF with KSR1. Additionally, MEK binding to the kinase domain of KSR1 asymmetrically drives BRAF-KSR1 heterodimerization, resulting in the concomitant stimulation of BRAF catalytic activity towards free MEK molecules .
Pfam PF18672: N-terminal PilZ-like domain PilZN1 (domain)
This domain is found in PilZ domain-containing proteins from Deltaproteobacteria, such as swiss:Q748G9 from Geobacter sulfurreducens. This domain is located N-terminal to a canonical PilZ domain, with a PilZ-related structure comprising the beta-barrel fold, lacking the C-terminal alpha-helix and both c-d-GMP-binding motifs. This domain also has a N-terminal loop that forms a short alpha-helix (3 residues).
Pfam PF07105: Protein of unknown function (DUF1367) (family)
This family consists of several highly conserved, hypothetical phage proteins of around 200 residues in length. The function of this family is unknown. Some proteins are annotated as IrsA (intracellular response to stress).
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 PF06503: Protein of unknown function (DUF1101) (family)
This family consists of several hypothetical Fijivirus proteins 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 PF20283: C-terminal domain 7 of the ABC-three component (ABC-3C) systems (domain)
C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector.