Tag: UniProtKB

Product Details Description: Anti-XRCC1 (CHICKEN) Antibody – 200-901-MG5 Synonyms: Chicken Anti-X-Ray Repair Cross Complementing 1 Antibody, X-Ray Repair Complementing Defective Repair In Chinese Hamster Cells 1, X-Ray Repair Cross-Complementing Protein 1, DNA Repair Protein XRCC1, SCAR26, RCC Host Species: Chicken Clonality: Polyclonal Format: IgY Target Details Gene Name: XRCC1  – View…

In recent decades, the development of computational and bioinformatics tools and websites for life sciences has increased exponentially. This great development has gone hand in hand with the availability of genome, proteome and macromolecule structure databases, and also of functional experiments, including microarray and RNAseq expression data, RNA-protein interactions, ChIP-seq,…

Product Data Locus ID 4781 Synonyms CTF; HMGIC/NFIB; MACID; NF-I/B; NF1-B; NFI-B; NFI-RED; NFIB2; NFIB3 Vector pGFP-V-RS E. coli Selection Kanamycin Mammalian Cell Selection Puromycin Format Retroviral plasmids Kit Components NFIB – Human, 4 unique 29mer shRNA constructs in retroviral GFP vector(Gene ID = 4781). 5µg purified plasmid DNA per…

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

Product Data Locus ID 59307 Synonyms IL-1R8; TIR8 Vector pGFP-C-shLenti Format Lentiviral particles RefSeq NM_001135053, NM_001135054, NM_021805, NM_021805.1, NM_021805.2, NM_001135053.1, NM_001135054.1, BC003591, BC003591.1, BC025953, BC106007, NM_001135054.2, NM_001135053.2 UniProt ID Q6IA17 Summary Acts as a negative regulator of the Toll-like and IL-1R receptor signaling pathways. Attenuates the recruitment of receptor-proximal signaling…

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

ID A0A8U0V2F9_MUSPF Unreviewed; 413 AA. AC A0A8U0V2F9; DT 12-OCT-2022, integrated into UniProtKB/TrEMBL. DT 12-OCT-2022, sequence version 1. DT 03-MAY-2023, entry version 4. DE SubName: Full=Protein C-ets-1 isoform X5 {ECO:0000313|RefSeq:XP_044936298.1}; GN Name=ETS1 {ECO:0000313|RefSeq:XP_044936298.1}; OS Mustela putorius furo (European domestic ferret) (Mustela furo). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC…

Transcribed image text: Part 2: UniProtKB/SwissProt and Protein Data Bank Analysis on SARS-CoV-2 Non-Structural Proteins Objective: Explore the structures, functions, and interactions of SARS-CoV-2 non-structural proteins using resources from UniProtKB/SwissProt and the Protein Data Bank, 1) Visit the PDB resource on SARS-CoV-2 proteins and select a non-structural protein (e.g., NSP3,…

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

You need to get the geneID first. For PDB structures, you may be able to retrieve it from RCSB PDB APIs. For AlphaFold UniProt IDs, you can do this way: `url = “rest.uniprot.org/uniprotkb/search?format=json&fields=xref_geneid,gene_names&query=” + structure; let geneData = await me.getAjaxPromise(url, ‘json’); let geneId = (geneData.results[0] && geneData.results[0].uniProtKBCrossReferences && geneData.results[0].uniProtKBCrossReferences[0]) ?…

Bar-On YM, Phillips R, Milo R. The biomass distribution on Earth. Proc Natl Acad Sci USA. 2018;115:6506–11. Article  CAS  PubMed  PubMed Central  Google Scholar  Ogawa H, Amagai Y, Koike I, Kaiser K, Benner R. Production of refractory dissolved organic matter by bacteria. Science. 2001;292:917–20. Article  CAS  PubMed  Google Scholar  Liang…

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

UniRef90 to UniRef50 conversion 1 Hi… i have a long list of UniRef90 IDs. Is it possible to convert all of them to their respective UniRef50IDs? If yes, how? Thanks Uniref Id_conversion uniprot • 66 views • link updated 2 hours ago by GenoMax 135k • written 7 hours ago…

biomaRT doesn’t report uniprot id 1 Hi all, I’m working with UniProtKB and would like to get the genomic coordinates of list of proteins. To my knowledge, the first step is to retrieve the mapping between uniprot and ensemble via biomaRT: annotLookup <- getBM( mart = mart, attributes = c(…

NM_005546.4(ITK):c.1741C>T (p.Arg581Trp) AND Autoinflammatory syndrome Based on: 1 submission [Details] Record status: current Accession: RCV002263636.3 Allele description [Variation Report for NM_005546.4(ITK):c.1741C>T (p.Arg581Trp)] NM_005546.4(ITK):c.1741C>T (p.Arg581Trp) Gene: ITK:IL2 inducible T cell kinase [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 5q33.3 Genomic location: Preferred name: NM_005546.4(ITK):c.1741C>T (p.Arg581Trp) HGVS:…

About the team/job Recent advances in technology and analysis have revealed significant opportunities to further our understanding of the diversity and impact of human genetics (such as the first full length telomere-to-telomere human genome and the first release of the human pangenome). As a result, we are excited to launch…

How to convert between UniRef50 to EC/enzyme number? 1 You can use the cluster representatives (P45148 in your case) which represent UniProtKB entries. Upload your list of UniProtKB IDs to the Batch Retrieval / IDmapping at www.uniprot.org/id-mapping and map from UniProtKB to UniProtKB. Once you have your results, you can…

Researchers from the European Bioinformatics Institute (EMBL-EBI), ETH Zurich’s Institute of Molecular Systems Biology, and Seoul National University’s School of Biological Sciences have made significant strides in protein research. They harnessed the power of AlphaFold’s vast database of AI-predicted 3D protein structures, shedding light on protein evolution and human immunity…

Revealing the secrets of protein evolution using the AlphaFold database. Credit: Karen Arnott/EMBL-EBI By developing an efficient way to compare all predicted protein structures in the AlphaFold database, researchers have revealed similarities between proteins across different species. This work aids our understanding of protein evolution and has uncovered new insights…

Structural clustering algorithm The clustering procedure is similar to MMseqs2’s clustering but, instead of using sequences, Foldseek’s 3Di alphabet (Extended Data Fig. 1) was used to represent the structures as one-dimensional sequences. The clustering algorithm combines Linclust17 and cascaded MMseqs2 (ref. 42) clustering. The pipeline applies this strategy to allow for efficient…

Overall structure of BPSL1038 The crystal structure of recombinant BPSL1038 (rBPSL1038) protein (~12 kDa) was determined by the single wavelength anomalous (SAD) dispersion method using the SeMet-BPSL1038 protein. The SeMet-BPSL1038 (smBPSL0138) and native BPSL1038 (rBPSL1038) crystals diffracted to 1.88 Å and 1.55 Å resolution, respectively. Both crystals belong to space group C2221 with…

ID A0A7F8Q8W3_LEPWE Unreviewed; 479 AA. AC A0A7F8Q8W3; DT 10-FEB-2021, integrated into UniProtKB/TrEMBL. DT 10-FEB-2021, sequence version 1. DT 03-MAY-2023, entry version 8. DE SubName: Full=Protein FAM118A isoform X2 {ECO:0000313|RefSeq:XP_030877677.1}; GN Name=FAM118A {ECO:0000313|RefSeq:XP_030877677.1}; OS Leptonychotes weddellii (Weddell seal) (Otaria weddellii). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Laurasiatheria;…

ID A0A6J2VJ84_CHACN Unreviewed; 220 AA. AC A0A6J2VJ84; DT 07-OCT-2020, integrated into UniProtKB/TrEMBL. DT 07-OCT-2020, sequence version 1. DT 28-JUN-2023, entry version 11. DE SubName: Full=Claudin-4-like {ECO:0000313|RefSeq:XP_030632049.1}; GN Name=LOC115813661 {ECO:0000313|RefSeq:XP_030632049.1}; OS Chanos chanos (Milkfish) (Mugil chanos). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Gonorynchiformes; OC Chanidae;…

UniProtKB/SwissProt variant VAR_086765 Dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit STT3A Gene: STT3A Feedback? Literature citations Active site variants in STT3A cause a dominant type I congenital disorder of glycosylation with neuromusculoskeletal findings. Wilson M.P.; Garanto A.; Pinto e Vairo F.; Ng B.G.; Ranatunga W.K.; Ventouratou M.; Baerenfaenger M.; Huijben K.; Thiel C.; Ashikov…

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

Uniprot Database for download 0 Hi All, I am looking for a database similar to GTF file for RNA-sequence data. I ‘d like to use this file to cross-reference all the protein accessions in my list with all that are available in the downloaded file and extract the protein names,…

No statistical methods were used to predetermine sample size. The experiments were not randomized and investigators were not blinded to allocation during experiments and outcome assessment. Expression constructs The coding sequence of mouse PIEZO1 (E2JF22, UniprotKB entry) was codon-optimized, synthesized and cloned into the pcDNA3.1 plasmid. An amber stop codon…

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

Genome sequencing and assembly After filtering the adapters and low-quality reads, approximately 30.58 Gb of clean reads (~100×) were retained by Illumina paired-end short-reads sequencing, and about 63.24 Gb of subreads (~200×) were obtained by PacBio long-reads sequencing. The PacBio reads had an average length of 16.34 kb, with an N50 length of…

dataset posted on 2023-07-17, 18:41 authored by Pieter Verschaffelt, Alessandro Tanca, Marcello Abbondio, Tim Van Den Bossche, Tibo Vande Moortele, Peter Dawyndt, Lennart Martens, Bart Mesuere Unipept Desktop 2.0 is the most recent iteration of the Unipept Desktop tool that adds support for the analysis of metaproteogenomics datasets. Unipept Desktop…

Hey everyone. So I am trying to design a function in python that uses information from Uniprot in regards to the features a given protein has. The features I am interested in accessing are regions, domains, and secondary structures. I can access the API already and get the amino acid…

Accepted Name acyl-[acyl-carrier protein]–UDP-2-acetamido-3-amino-2,3-dideoxy-alpha-D- glucopyranose N-acyltransferase Reaction catalysed a (3R)-hydroxyacyl-[ACP] + UDP-2-acetamido-3-amino-2,3-dideoxy-alpha-D-glucopyranose <=> a UDP-2-acetamido-3-{[(3R)-3-hydroxyacyl]amino}-2,3-dideoxy-alpha-D-glucopyranose + H(+) + holo-[ACP] Comment(s) The enzyme is found in bacterial species whose lipid A contains 2,3- diamino-2,3-dideoxy-D-glucopyranose. Some enzymes, such as that from Leptospira interrogans, are highly specific for 2,3-diamino-2,3-dideoxy-D-glucopyranose, while others, such as…

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

Accepted Name L-aspartate N-monooxygenase (nitrosuccinate-forming) Reaction catalysed 2 H(+) + L-aspartate + 3 NADPH + 3 O2 <=> 2-nitrobutanedioate + 4 H2O + 3 NADP(+) Comment(s) Requires FAD. The enzyme, found in some Actinobacteria, is involved in a pathway that forms nitrite, which is subsequently used to generate a diazo…

UniProtKB/SwissProt variant VAR_086244 Atrial natriuretic peptide receptor 3 Gene: NPR3 Feedback? Literature citations Bi-allelic Loss-of-Function Mutations in the NPR-C Receptor Result in Enhanced Growth and Connective Tissue Abnormalities. Boudin E.; de Jong T.R.; Prickett T.C.R.; Lapauw B.; Toye K.; Van Hoof V.; Luyckx I.; Verstraeten A.; Heymans H.S.A.; Dulfer E.;…

UniProtKB/SwissProt variant VAR_084861 Retinal-specific phospholipid-transporting ATPase ABCA4 Gene: ABCA4 Feedback? Literature citations Novel mutations in of the ABCR gene in Italian patients with Stargardt disease. Passerini I.; Sodi A.; Giambene B.; Mariottini A.; Menchini U.; Torricelli F.; Eye 24:158-164(2010) Cited for: VARIANTS STGD1 21-GLN–ASP-2273 DEL; LEU-68; HIS-96; LYS-96; SER-172; CYS-212;…

UniProtKB/SwissProt variant VAR_086367 Transportin-2 Gene: TNPO2 Feedback? Literature citations TNPO2 variants associate with human developmental delays, neurologic deficits, and dysmorphic features and alter TNPO2 activity in Drosophila. Goodman L.D.; Cope H.; Nil Z.; Ravenscroft T.A.; Charng W.L.; Lu S.; Tien A.C.; Pfundt R.; Koolen D.A.; Haaxma C.A.; Veenstra-Knol H.E.; Wassink-Ruiter…

UniProtKB/SwissProt variant VAR_086225 H(+)/Cl(-) exchange transporter 3 Gene: CLCN3 Feedback? Literature citations Unique variants in CLCN3, encoding an endosomal anion/proton exchanger, underlie a spectrum of neurodevelopmental disorders. Duncan A.R.; Polovitskaya M.M.; Gaitan-Penas H.; Bertelli S.; VanNoy G.E.; Grant P.E.; O’Donnell-Luria A.; Valivullah Z.; Lovgren A.K.; England E.M.; Agolini E.; Madden…

AlphaFold predicts the structure of almost every cataloged protein known to science. Credit: Karen Arnott/EMBL-EBI AI-powered predictions of the three-dimensional structures of nearly all cataloged proteins known to science have been made by DeepMind and EMBL’s European Bioinformatics Institute (EMBL-EBI). The catalog isfreely and openly available to the scientific community,…

DNA ligase 1 Gene: LIG1 Feedback? Literature citations Biallelic mutations in DNA ligase 1 underlie a spectrum of immune deficiencies. Maffucci P.; Chavez J.; Jurkiw T.J.; O’Brien P.J.; Abbott J.K.; Reynolds P.R.; Worth A.; Notarangelo L.D.; Felgentreff K.; Cortes P.; Boisson B.; Radigan L.; Cobat A.; Dinakar C.; Ehlayel M.;…

60S ribosomal protein L3-like Gene: RPL3L Feedback? Literature citations Bi-allelic missense disease-causing variants in RPL3L associate neonatal dilated cardiomyopathy with muscle-specific ribosome biogenesis. Ganapathi M.; Argyriou L.; Martinez-Azorin F.; Morlot S.; Yigit G.; Lee T.M.; Auber B.; von Gise A.; Petrey D.S.; Thiele H.; Cyganek L.; Sabater-Molina M.; Ahimaz P.;…

Mothers against decapentaplegic homolog 2 Gene: SMAD2 Feedback? Literature citations De novo mutations in histone-modifying genes in congenital heart disease. Zaidi S.; Choi M.; Wakimoto H.; Ma L.; Jiang J.; Overton J.D.; Romano-Adesman A.; Bjornson R.D.; Breitbart R.E.; Brown K.K.; Carriero N.J.; Cheung Y.H.; Deanfield J.; DePalma S.; Fakhro K.A.;…

Question briefly: Let is take an example of SRC human protein (P12931) – length 536 – on top of the blastP output we will see SRC itself – with score 1119 . Why ? What bothers me – diagonal of the blossum62 matrix – 4,5,6,9.. so in my mind output…

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

NLRP3 expression and purification Both wild-type NLRP3 and CAPS mutants were cloned in the mammalian expression vector pcDNA3.1HisB. Plasmid was purified using Qiagen Giga Prep up to 2000 ng/μl and subsequently transfected into Expi293 with Expifectamine per manufacturer instructions. Expression was allowed to proceed for 3 days before harvesting. Cells were…

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

Data sets To create data sets of sequences corresponding to compartments of photosynthetic plastids, we searched the UniProt database for proteins annotated as localized in the chloroplast. Importantly, the UniProt keyword ’Chloroplast’ includes not only chloroplasts of green algae and land plants but also plastids of Rhodophyta, haptophytes and the…

Uniprot API access to download .pdb files 0 Hey everyone, fairly new to Bioinformatics so please cut me some slack. Anyways, I am trying to work with the UniProt API and I am running into a bit of a wall. My goal is to write a URL that I can…

Accepted Name cyclopenase Reaction catalysed (-)-cyclopenine <=> H(+) + methyl isocyanate + viridicatin Comment(s) This fungal enzyme catalyzes a key reaction in the biosynthesis of quinolone compounds, converting the benzodiazepine structure into a quinolone structure. The enzyme is also active with (-)-4′-methoxycyclopenine. Cross-references BRENDA 4.1.99.27 EC2PDB 4.1.99.27 ExplorEnz 4.1.99.27 PRIAM…

Accepted Name L-fucono-1,5-lactonase Reaction catalysed H2O + L-fucono-1,5-lactone <=> H(+) + L-fuconate Comment(s) The enzyme, characterized from the bacterium Burkholderia multivorans, participates in an L-fucose degradation pathway. The enzyme exhibits catalytic activity for the hydrolysis of several lactones, including L-fucono-1,4-lactone, D-arabinono-1,4-lactone, L-xylono-1,4-lactone, and L-galactono-1,4-lactone, but L-fucono-1,5- lactone is the best…

Functional genomics analyses for SLC22A31 and SFTPD. a, Effect-size plot for the effect of multiple variants on SLC22A31 expression (eQTLgen, x axis) against increasing susceptibility to critical COVID-19 (βxy = 0.11; Pxy = 1.3 × 10−9). The color shows linkage disequilibrium (LD) with the missense variant rs117169628. b, Three cartoon views of an AlphaFold model of…

There is a brute force method for this. You could upload the fasta sequence in tblastn and keep a filter of 100% sequence cover and blast. Usually the first hit should give you the Genbank/Refsec ID for your protein sequence. The next one will require some scripting, but if you…

Due to maintenance work, this service will be unavailable Wednesday 10 between 18:00 and 21:00 – CET. Apologies for the inconvenience. Accepted Name sarcosine oxidase (5,10-methylenetetrahydrofolate-forming) Reaction catalysed (6S)-5,6,7,8-tetrahydrofolate + O2 + sarcosine <=> (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O2 Comment(s) The enzyme, found in some bacterial species, is composed of…

ID A0A2Y9QLR8_TRIMA Unreviewed; 522 AA. AC A0A2Y9QLR8; DT 12-SEP-2018, integrated into UniProtKB/TrEMBL. DT 12-SEP-2018, sequence version 1. DT 22-FEB-2023, entry version 12. DE SubName: Full=actin-binding protein IPP isoform X2 {ECO:0000313|RefSeq:XP_023582882.1}; GN Name=LOC101351470 {ECO:0000313|RefSeq:XP_023582882.1}; OS Trichechus manatus latirostris (Florida manatee). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Afrotheria;…

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

ID A0A6P7ILG0_9TELE Unreviewed; 421 AA. AC A0A6P7ILG0; DT 02-DEC-2020, integrated into UniProtKB/TrEMBL. DT 02-DEC-2020, sequence version 1. DT 22-FEB-2023, entry version 9. DE SubName: Full=transcriptional enhancer factor TEF-5 isoform X8 {ECO:0000313|RefSeq:XP_028261144.1}; GN Name=tead3 {ECO:0000313|RefSeq:XP_028261144.1}; OS Parambassis ranga (Indian glassy fish). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Actinopterygii; Neopterygii;…

ID A0A6P8XQ90_DROAB Unreviewed; 717 AA. AC A0A6P8XQ90; DT 02-DEC-2020, integrated into UniProtKB/TrEMBL. DT 02-DEC-2020, sequence version 1. DT 22-FEB-2023, entry version 9. DE SubName: Full=RUN and FYVE domain-containing protein 2 isoform X5 {ECO:0000313|RefSeq:XP_034113470.1}; GN Name=LOC117574004 {ECO:0000313|RefSeq:XP_034113470.1}; OS Drosophila albomicans (Fruit fly). OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; OC…

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

Accepted Name L-cysteine–[L-cysteinyl-carrier protein] ligase Reaction catalysed ATP + holo-[peptidyl-carrier protein] + L-cysteine <=> AMP + diphosphate + L-cysteinyl-[peptidyl-carrier protein] Comment(s) The adenylation domain of the enzyme catalyzes the activation of L-cysteine to (L-cysteinyl)adenylate, followed by the transfer of the activated compound to the free thiol of a phosphopantetheine arm…

Hey, There are two approaches here. 1, org.At.tair.db You can use the annotation DB packages from Bioconductor, specifically org.At.tair.db. Copying my own answer from here: A: Biomart query returns NA when searching for entrez_id, while manual search works library(org.At.tair.db) genes <- c(“AT2G14610″,”AT4G23700″,”AT3G26830”, “AT3G15950″,”AT3G54830″,”AT5G24105”) keytypes(org.At.tair.db) mapIds(org.At.tair.db, keys = genes, column =…

Accepted Name indoleacetaldoxime dehydratase Alternative Name(s) (indol-3-yl)acetaldehyde-oxime hydro-lyase 3-indoleacetaldoxime hydro-lyase indole-3-acetaldehyde-oxime hydro-lyase indole-3-acetaldoxime hydro-lyase indoleacetaldoxime hydro-lyase Reaction catalysed (E)-(indol-3-yl)acetaldehyde oxime <=> (indol-3-yl)acetonitrile + H2O Comment(s) Formerly EC 4.99.1.6. Cross-references BRENDA 4.8.1.3 EC2PDB 4.8.1.3 ExplorEnz 4.8.1.3 PRIAM enzyme-specific profiles 4.8.1.3 KEGG Ligand Database for Enzyme Nomenclature 4.8.1.3 IUBMB Enzyme Nomenclature 4.8.1.3…

I am trying to run some commands in Python using the urllib library in order to access the API of the Uniprot protein database. All the code does is send in the Uniprot IDs and get back the pertinent gene names (e.g. P08603 would correspond with the gene name of…

Ribonuclease SLFN12Gene: SLFN12 Variant information Variant position:  168 The position of the amino-acid change on the UniProtKB canonical protein sequence. Type of variant:  LB/B The variants are classified into three categories: LP/P, LB/B and US. LP/P: likely pathogenic or pathogenic. LB/B: likely benign or benign. US: uncertain significance Residue change:  From Cysteine (C)…

Sequence information Variant position:  384 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  788 The length of the canonical sequence. Location on the sequence:   LGVSGASLGVPLEEEEGLLS  S HWEARLLQGSLMTATFDGAQ The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

Hi all, I am trying to generate a count.matrix for sorted bam files, using featureCounts on linux. I have a non-modal organism (bacteria), so I generated the annotation.file using both PROKKA and RAST. I used all the following files in featurecounts; PROKKA.gff, RAST.gff RAST.gtf gffread converted-PROKKA.gtf file But still facing…

Accepted Name aliphatic aldoxime dehydratase. Alternative Name(s) aliphatic aldoxime hydro-lyase. Reaction catalysed an aliphatic aldoxime <=> a nitrile + H2O Comment(s) The enzyme from Pseudomonas chlororaphis contains Ca(2+) and protoheme IX, the iron of which must be in the form iron(II) for activity. The enzyme exhibits a strong preference for…

How to extract FASTA headers in R 1 I have downloaded a reference uniprotkb FASTA file. How can I only extract the FASTA headers of each gene (raw-wise) into a CSV file using R? r bioinformatics • 26 views • link updated 1 hour ago by cfos4698 &utrif; 670 •…

Transcribed image text: Now, refine your information using the ProtScale tools at the ExPASy bioinformatics resource portal. Each of the PDB Protein Feature Views was created with a UniProt Knowledgebase ID. – For glycophorin A, the UniProtKB ID is P02724. – For myoglobin, the UniProtKB ID is P02185. – For…

Can you explain to me important aspects of this genbank Bos taurus partial gdf-8 for myostatin and promoter region GenBank: AJ438578.1 FASTA Graphics Go to: LOCUS AJ438578 1269 bp DNA linear MAM 26-JUL-2016 DEFINITION Bos taurus partial gdf-8 for myostatin and promoter region. ACCESSION AJ438578 VERSION AJ438578.1 KEYWORDS gdf-8; myostatin….

How to parse a gene’s location using biopython 0 Hi, I’m trying to extract gene location information for certain genes across multiple bacteria. Currently I’m using this set up to retrieve the gene information: from Bio import SeqIO, Entrez Entrez.email=”my@email.com” # example is E. coli K-12 reference sequence handle =…

Parsing gene location using biopython 0 Hi, I’m trying to extract gene location information for certain genes across multiple bacteria. Currently I’m using this set up to retrieve the gene information: from Bio import SeqIO, Entrez Entrez.email=”my@email.com” # example is E. coli K-12 reference sequence handle = Entrez.efetch(db=”nuccore”, id=’NC_000913′, rettype=”fasta_cds_na”,…

I am using the Python code example from www.uniprot.org/help/id_mapping to programmatically get the ID Mapping results of a list of identifiers. However the returned results are a json file. I cannot figure out how to retrieve the results as a tsv instead. import re import time import json import zlib…

NM_001184.4(ATR):c.4820G>A (p.Ser1607Asn) AND not specified Based on: 1 submission [Details] Record status: current Accession: RCV001821037.3 Allele description [Variation Report for NM_001184.4(ATR):c.4820G>A (p.Ser1607Asn)] NM_001184.4(ATR):c.4820G>A (p.Ser1607Asn) Gene: ATR:ATR serine/threonine kinase [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 3q23 Genomic location: Preferred name: NM_001184.4(ATR):c.4820G>A (p.Ser1607Asn) HGVS: NC_000003.12:g.142512292C>T NG_008951.1:g.71535G>A…

Sequence information Variant position:  156 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  337 The length of the canonical sequence. Location on the sequence:   LNRTLSKLQWVSVFMLCAGV  T LVQWKPAQATKVVVEQNPLL The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

Hi all, I am trying to count the number of reads that map to each gene using FeatureCounts. (RNA-Seq PE, linux) my input; GFF. file generated using Prokka GTF.file generated by NCBI annotation Sorted.bam files generated by bowtie2 and samtools. When I used gtf.file generated by NCBI, featurecounts run without…

genbank parsing using perl 1 I have genbank file. and want to retrieve relevant information. the problem is when the code fetches data related to product, it considers only one line information. since the while loop read data line by line. #! /usr/local/bin/perl -w open (GB,”$ARGV[0]”); open (AC, “>$ARGV[1]”); print…

How to find the difference between old and current releases in UniprotKB 2 How to find the difference between old and current releases in UniprotKB. For specific entry id, what it has changed from previous releases to current releases. How we can check. previous UniprotKB current difference releases • 30…

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

Development of the CusProSe software CustomProteinSearch (CusProSe) is a generic genome mining software, consisting of two distinct but complementary customizable programs: IterHMMBuild and ProSeCDA. IterHMMBuild is an HMM profile building tool based on an iterative learning process. ProSeCDA is a protein search and annotation tool based on user-defined domain architectures….

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

Ensembl ID mapping GRCh37 vs GRCh38 0 I currently have a large list of Ensembl protein IDs (ENSP) that are from GRCh37. I need to map these IDs to the entry name listed on the UniProt website (e.g. ‘CASPE_HUMAN’ ). I am having trouble doing this using the UniProt dataset…

Expasy is an online bioinformatics resource operated by the SIB Swiss Institute of Bioinformatics. It is an extensible and integrative portal which provides access to over 160 databases and software tools and supports a range of life science and clinical research areas, from genomics, proteomics and structural biology, to evolution…

ID A0A6I9ZUN5_ACIJB Unreviewed; 234 AA. AC A0A6I9ZUN5; DT 07-OCT-2020, integrated into UniProtKB/TrEMBL. DT 07-OCT-2020, sequence version 1. DT 25-MAY-2022, entry version 6. DE SubName: Full=tumor necrosis factor ligand superfamily member 8 {ECO:0000313|RefSeq:XP_014931799.1}; GN Name=TNFSF8 {ECO:0000313|RefSeq:XP_014931799.1}; OS Acinonyx jubatus (Cheetah). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Laurasiatheria;…

UniProtKB – Q27974 <p>An evidence describes the source of an annotation, e.g. an experiment that has been published in the scientific literature, an orthologous protein, a record from another database, etc.</p> <p><a href=”www.uniprot.org/manual/evidences”>More…</a></p>&#13; Skip Header You are using a version of browser that may not display all the features…

I need to calculate the number and percentages of polar/non-polar, aliphatic/aromatic/heterocyclic amino acids in this protein sequence that I got from UNIPROT, using BioJava. I have found in the BioJava tutorial how to read the Fasta files and implemented this code. But I have no ideas how to solve this…

Hello, I am looking to create a subset FASTA file from an existing FASTA file. The subset file should only include entries with certain accession numbers. I have created a BioIndexed File with the correct number of entries, but I am unsure how to use the getsubset function in this…

Sequence information Variant position:  755 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  1473 The length of the canonical sequence. Location on the sequence:   MAHFEEMGMCVETDMELLVC  T FCIKFSRHVKKLQLIEGRQH The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

Sequence information Variant position:  575 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  749 The length of the canonical sequence. Location on the sequence:   NLPYPLILRPQRGVDLIISF  D FSARPSDSSPPFKELLLAEK The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

Sequence information Variant position:  340 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  418 The length of the canonical sequence. Location on the sequence:   NFAASLCSDVILYPLETVLH  R LHIQGTRTIIDNTDLGYEVL The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

Sequence information Variant position:  507 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  1247 The length of the canonical sequence. Location on the sequence:   PPPSQPDPEHLDKPKLKAGG  S VESLRSSLSGQSSMSGQTVS The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

Sequence information Variant position:  95 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  290 The length of the canonical sequence. Location on the sequence:   KLRQPFFQKRSELIAKIPNF  W VTTFVNHPQVSALLGEEDEE The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

You can do this directly on UniProt: www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select “UniProtKB AC/ID” in the “From” field and “UniParc” in the “To” field I’ve also written a script, pasted below, that can do this with some useful options: $ uniprot_map.pl -h uniprot_map.pl…

Sequence information Variant position:  733 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  1333 The length of the canonical sequence. Location on the sequence:   RMEEFIGTVRGKAMKKWVES  I TKIIQRKKIARDNGPGHNIT The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

Sequence information Variant position:  28 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  230 The length of the canonical sequence. Location on the sequence:   ILLFVTELSGAHNTTVFQGV  A GQSLQVSCPYDSMKHWGRRK The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

Sequence information Variant position:  28 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  311 The length of the canonical sequence. Location on the sequence:   RALAAAAPASGKAKLTHPGK  A ILAGGLAGGIEICITFPTEY The residue change on the sequence. Unless the variant is located at the beginning or at the end of…