SII-SWORD/CoKE huggingface dataset:
Pfam PF17929: Tetracyclin repressor-like, C-terminal domain (domain)
TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present in putative TetR family transcriptional regulators found in bacteria.
Pfam PF22705: Butyrophilin subfamily 3 member A2-like, Ig-C domain (domain)
This domain is found in human Butyrophilin subfamily 3 member A2 (BTN3A2), a protein that plays a role in T-cell responses in the adaptive immune response. BTN3A2 shows two extracellular domains: an N-terminal Ig-V like domain ([pfam:PF07686]) and a C-terminal Ig-C type domain that is located in the centre of the protein sequence.
Pfam PF03662: Glycosyl hydrolase family 79, N-terminal domain (domain)
Family of endo-beta-N-glucuronidase, or heparanase. Heparan sulfate proteoglycans (HSPGs) play a key role in the self- assembly, insolubility and barrier properties of basement membranes and extracellular matrices. Hence, cleavage of heparan sulfate (HS) affects the integrity and functional state of tissues and thereby fundamental normal and pathological phenomena involving cell migration and response to changes in the extracellular micro-environment.  Heparanase degrades HS at specific intra-chain sites. The enzyme is synthesised as a latent approximately 65 kDa protein that is processed at the N-terminus into a highly active approximately 50 kDa form. Experimental evidence suggests that heparanase may facilitate both tumour cell invasion and neovascularization, both critical steps in cancer progression. The enzyme is also involved in cell migration associated with inflammation and autoimmunity.
Wikipedia: In molecular biology, glycoside hydrolase family 79 is a family of glycoside hydrolases.
Pfam PF22974: Domain of unknown function (DUF7029) (domain)
This domain is found in uncharacterised proteins mainly from fungi. It is predicted to adopt a globular structure that has some similarity to SRA domain ([pfam:PF18491]). The function of this domain 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 PF14938: Soluble NSF attachment protein, SNAP (repeat)
The soluble NSF attachment protein (SNAP) proteins are involved in vesicular transport between the endoplasmic reticulum and Golgi apparatus. They act as adaptors between SNARE (integral membrane SNAP receptor) proteins and NSF (N-ethylmaleimide-sensitive factor). They are structurally similar to TPR repeats.
Pfam PF04268: Sarcosine oxidase, gamma subunit family (family)
Sarcosine oxidase is a hetero-tetrameric enzyme that contains both covalently bound FMN and non-covalently bound FAD and NAD(+).  This enzyme catalyses the oxidative demethylation of sarcosine to yield glycine, H2O2, and 5,10-CH2-tetrahydrofolate (H4folate) in a reaction requiring H4folate and O2.
Pfam PF03291: mRNA (guanine-N(7))-methyltransferase domain (domain)
This entry represents mRNA (guanine-N(7))-methyltransferase, which can either be found as a single domain protein, or as a domain within the mRNA-capping enzyme catalytic subunit. mRNA (guanine-N(7))-methyltransferase methylates the N7 position of the added guanosine to the 5'-cap structure of mRNAs. It binds RNA containing 5'-terminal GpppC. Viral mRNA capping enzymes, meanwhile, are multidomain proteins that catalyse the first two reactions in the mRNA cap formation pathway. They are heterodimers consisting of a large (catalytic) and small subunit.
Pfam PF12029: Domain of unknown function (DUF3516) (family)
This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 460 to 473 amino acids in length. This domain is found associated with [pfam:PF00270], [pfam:PF00271].
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 PF19274: PI4-kinase N-terminal region (family)
This entry represents the long non-catalytic N-terminal region in PI4K proteins. This region forms a large alpha solenoid structure.
Pfam PF12674: Putative zinc ribbon domain (domain)
This domain appears to be a zinc binding DNA-binding domain.
Pfam PF12069: Protein of unknown function (DUF3549) (family)
This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 340 amino acids in length. This protein has a conserved LDE sequence motif.
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 PF13010: Primase helical domain (domain)
This alpha helical domain is found in a set of bacterial plasmid replication proteins. The domain is found to the C-terminus of the primase/polymerase domain. Mutants of this domain are defective in template binding, dinucleotide formation and conformation change prior to DNA extension.
Pfam PF15410: Pleckstrin homology domain (domain)
This Pleckstrin homology domain is found in some fungal species.
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.
Pfam PF14855: Pilus-assembly fibrillin subunit, chaperone (domain)
PapJ is part of the Pap pilus assembly complex that plays an auxiliary role by ensuring the proper integration of PapA into the fimbrial shaft. PapA is the major shaft protein of the pilus.
Pfam PF07181: VirC2 protein (family)
This family consists of several VirC2 proteins which seem to be found exclusively in Agrobacterium species and Rhizobium etli. VirC2 is known to be involved in virulence in Agrobacterium species but its exact function is unclear.
Pfam PF13413: Helix-turn-helix domain (domain)
This domain is a helix-turn-helix domain that probably binds to DNA.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF12610: Suppressor of cytokine signalling (family)
This domain family is found in bacteria and eukaryotes, and is approximately 60 amino acids in length. The family is found in association with [pfam:PF07525], [pfam:PF00017]. The suppressors of cytokine signaling (SOCS) family play important roles in regulating a variety of signal transduction pathways that are involved in immunity, growth and development of organisms.
Pfam PF15255: WASH complex subunit CAP-Z interacting, central region (family)
This domain is found on WASH complex subunits FAM21 and CAP-ZIP proteins, as well as on VPEF (vaccinia virus penetration factor). This family of proteins is found in eukaryotes. Proteins in this family are typically between 305 and 1321 amino acids in length. The exact function of this region is not known.
Pfam PF07666: M penetrans paralogue family 26 (family)
These proteins include those ascribed to M penetrans paralogue family 26 in. This family contains a region of transmembrane helices.
Pfam PF20446: ATPase of the ABC class N-terminal (domain)
This is the N-terminal domain of various bacterial predicted ABC class ATPases which shows sequence and structural similarities to the N-terminal domain of MRB1590 (swiss:Q57ZF2) from kinetoplastids, a core protein of the multiprotein mitochondrial RNA binding complex 1 (MRB1) involved in kinetoplastid RNA (kRNA) editing. MRB1590 is a dimer and contains a central ABC ATPase fold ([pfam:PF09818]) between novel N- and C-terminal regions. The N-terminal domains combine and form a RNA-binding basic pore which involves an arginine patch that has been suggested to act as a chaperone to bind and stabilize ssRNA during kRNA editing processes. N-terminal MRB1590 shows structural similarity to chaperones.
Pfam PF04548: AIG1 family (domain)
Arabidopsis protein AIG1 appears to be involved in plant resistance to bacteria.
Wikipedia: The TIC and TOC complexes are translocons located in the chloroplast of a eukaryotic cell, that is, protein complexes that facilitate the transfer of proteins in and out through the chloroplast's membrane. It mainly transports proteins made in the cytoplasm into the chloroplast. The TIC complex (translocon on the inner chloroplast membrane) is located in the inner envelope of the chloroplast. The TOC complex (translocon on the outer chloroplast membrane) is located in the outer envelope of the chloroplast.
Pfam PF08763: Voltage gated calcium channel IQ domain (domain)
Voltage gated calcium channels control cellular calcium entry in response to changes in membrane potential.  The isoleucine-glutamine (IQ) motif in the voltage gated calcium channel IQ domain interacts with hydrophobic pockets of Ca2+/calmodulin.  The interaction regulates two self-regulatory calcium dependent feedback mechanism, calcium dependent inactivation (CDI), and calcium-dependent facilitation (CDF).
Pfam PF14027: Questin oxidase-like (family)
This family consists of oxidoreductases involved in the synthesis of different polyketides and derivatives. Questin oxidase GedK from Aspergillus terreus catalyzes the ring cleavage of the anthraquinone questin to form benzophenone desmethylsulochrin. It is part of the gene cluster that mediates the biosynthesis of geodin, an intermediate in the biosynthesis of other natural products. MdpL from Emericella nidulans is part of the gene cluster that mediates the biosynthesis of monodictyphenone.
Pfam PF09424: Yqey-like protein (domain)
The function of this domain found in the YqeY protein is uncertain.
Wikipedia: In molecular biology, YqeY is a type of protein domain of unknown function. It is thought to have a role in protein synthesis, facilitating the production of charged transfer RNA used in the process of translating mRNA into protein. It is present as a domain of glutaminyl-tRNA synthetase (GlnRS) in almost all eukaryotes.
Pfam PF04413: 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase) (domain)
Members of this family transfer activated sugars to a variety of substrates, including glycogen, fructose-6-phosphate and lipopolysaccharides.  Members of the family transfer UDP, ADP, GDP or CMP linked sugars.  The Glycos_transf_N region is flanked at the N-terminus by a signal peptide and at the C-terminus by Glycos_transf_1 ([pfam:PF00534]).  The eukaryotic  glycogen synthases may be distant members of this bacterial  family.
Pfam PF02369: Bacterial Ig-like domain (group 1) (domain)
This family consists of bacterial domains with an Ig-like fold. Members of this family are found in bacterial surface proteins such as intimins and invasins involved in pathogenicity.
Pfam PF14382: Exosome complex exonuclease RRP4 N-terminal region (domain)
ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology.
Pfam PF09003: Bacteriophage lambda integrase, Arm DNA-binding domain (domain)
The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage.
Pfam PF10638: Spindle body associated protein C-terminus (domain)
This C-terminal domain of spindle-body-associated protein Sfi1 has an important role to play in the bridge-splitting during bi-polar spindle assembly, and this separation event possibly requires interaction with integral components of the nuclear envelope, such as the Mps2-Bbp1 complex. Centrally to this domain is a region carrying centrin-binding repeats with repeating units containing tryptophan, family Sfi1_central, [pfam:PF08457].
Pfam PF15212: Spermatogenesis-associated protein 19, mitochondrial (family)
Spermatogenesis-associated protein 19 may have a role in spermiogenesis .
Pfam PF01302: CAP-Gly domain (domain)
Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein [swissprot:Q20728] CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove.
Pfam PF04503: Single-stranded DNA binding protein, SSDP (family)
This is a family of eukaryotic single-stranded DNA binding proteins with specificity to a pyrimidine-rich element found in the promoter region of the alpha2(I) collagen gene.
Pfam PF00698: Acyl transferase domain (domain)
Enzymes like bacterial malonyl CoA-acly carrier protein transacylase (2.3.1.39) and eukaryotic fatty acid synthase (2.3.1.85) that are involved in fatty acid biosynthesis belong to this group . Also included are the polyketide synthases 6-methylsalicylic acid synthase (2.3.1.165), a multifunctional enzyme that involved in the biosynthesis of patulin and conidial green pigment synthase (2.3.1) and several non-reducing polyketide synthases.
Pfam PF00085: Thioredoxin (domain)
Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. Some members with only the active site are not separated from the noise.
Wikipedia: Thioredoxin is a class of small redox proteins known to be present in all organisms. It plays a role in many important biological processes, including redox signaling. In humans, thioredoxins are encoded by TXN and TXN2 genes. Loss-of-function mutation of either of the two human thioredoxin genes is lethal at the four-cell stage of the developing embryo. Although not entirely understood, thioredoxin is linked to medicine through their response to reactive oxygen species (ROS). In plants, thioredoxins regulate a spectrum of critical functions, ranging from photosynthesis to growth, flowering and the development and germination of seeds. Thioredoxins play a role in cell-to-cell communication.
Pfam PF00627: UBA/TS-N domain (domain)
This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N.  The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC [swissprot:P70670] and MJ0280 [swissprot:Q57728].
Wikipedia: Ubiquitin-associated (UBA) domains are protein domains that non-covalently interact with ubiquitin through protein-protein interactions. Ubiquitin is a small protein that is covalently linked to other proteins as part of intracellular signaling pathways, often as a signal for protein degradation. UBA domains are among the most common ubiquitin-binding domains.
Pfam PF17931: Tetracyclin repressor-like, C-terminal domain (domain)
This is a C-terminal domain present in putative TetR family transcriptional regulators found in bacteria.
Pfam PF03114: BAR domain (domain)
BAR domains are dimerisation, lipid binding and curvature sensing modules found in many different protein families. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysin, endophilin, BRAP and Nadrin. BAR domains are also frequently found alongside domains that determine lipid specificity, like [pfam:PF00169] and [pfam:PF00787] domains in beta centaurins and sorting nexins respectively.
Wikipedia: In molecular biology, BAR domains are highly conserved protein dimerisation domains that occur in many proteins involved in membrane dynamics in a cell. The BAR domain is banana-shaped and binds to membrane via its concave face. It is capable of sensing membrane curvature by binding preferentially to curved membranes. BAR domains are named after three proteins that they are found in: Bin, Amphiphysin and Rvs.
Pfam PF04347: Flagellar biosynthesis protein, FliO (family)
FliO is an essential component of the flagellum-specific protein export apparatus. It is an integral membrane protein that acts as an assembly chaperone for the flagellar protein FliP ([pfam:PF00813]). It is crucial, although not strictly required, for efficient FliP assembly and, thus flagellar assembly and function.
Pfam PF09124: T4 recombination endonuclease VII, dimerisation (domain)
Members of this family, which are predominantly found in Bacteriophage T4 recombination endonuclease VII, adopt a helical secondary structure, with three alpha helices oriented parallel to each other. They mediate dimerisation of the protein, as well as binding to the DNA major groove.
Pfam PF02668: Taurine catabolism dioxygenase TauD, TfdA family (domain)
This family consists of taurine catabolism dioxygenases of the TauD, TfdA family.  TauD from E. coli [swissprot:P37610] is a alpha-ketoglutarate-dependent taurine dioxygenase.  This enzyme catalyses the oxygenolytic release of sulfite from taurine.  TfdA from Burkholderia sp. [swissprot:Q45423] is a 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase.              TfdA from Alcaligenes eutrophus JMP134 [swissprot:P10088] is a 2,4-dichlorophenoxyacetate monooxygenase. Also included are gamma-Butyrobetaine hydroxylase enzymes [ec:1.14.11.1].
Wikipedia: In molecular biology, TauD refers to a protein domain that in many enteric bacteria is used to break down taurine as a source of sulfur under stress conditions. In essence, they are domains found in enzymes that provide bacteria with an important nutrient.
Pfam PF04846: Herpesvirus pp38 phosphoprotein (family)
This protein represents a conserved region found in most herpesvirus pp38 phosphoproteins.
Pfam PF16043: Domain of unknown function (DUF4795) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 285 and 978 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 PF06814: GOST, seven transmembrane domain (domain)
This entry represents the transmembrane domain of a group of related proteins that share the same domain architecture, termed GOST (GOLD domain seven-transmembrane helix) proteins, including TMEM87A/B, GPR107/GPR108 from human and the homologues from yeast, PTM1. This entry also includes plant proteins, CAND6/7. Some members of this entry, such as TMEM87A/B, do not signal as a GPCR.
Pfam PF06542: Regulator protein PHA-1 (family)
This family represents the protein product of the gene pha-1 which coordinates with lin-35 Rb during animal development. The protein is expressed during embryonic development and functions in the cytoplasm. PHA-1 acts in a parallel pathway with UBC-18 to regulate the activity of a common cellular target.
Pfam PF10054: Predicted periplasmic lipoprotein (DUF2291) (family)
Members of this family of hypothetical bacterial 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 PF11720: Peptidase inhibitor I78 family (domain)
This family includes Aspergillus elastase inhibitor and belongs to MEROPS peptidase inhibitor family I78.
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 PF10915: Protein of unknown function (DUF2709) (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 PF09550: Phage tail assembly chaperone protein, TAC (family)
This is a family of phage tail assembly chaperone proteins largely derived from the Rhodobacter species viral agent GTA (gene transfer agent) gp10.