Tag: InterPro

Awasthi MK, Singh E, Binod P, Sindhu R, Sarsaiya S, Kumar A, et al. Biotechnological strategies for bio-transforming biosolid into resources toward circular bio-economy: a review. Renew Sustain Energy Rev. 2022;156:111987. Article  CAS  Google Scholar  Diamantis V, Eftaxias A, Stamatelatou K, Noutsopoulos C, Vlachokostas C, Aivasidis A. Bioenergy in the…

Yang, Q. L., Gao, T. X. & Miao, Z. Q. Differentiation between populations of Japanese grenadier anchovy (Coilia nasus) in Northwestern Pacific based on ISSR markers: Implications for biogeography. Biochem Syst and Ecol 39, 286–296 (2011). CAS  Google Scholar  Shen, H. S. et al. In-depth transcriptome analysis of Coilia ectenes,…

From Wikipedia, the free encyclopedia Summary DescriptionLINE-1 Retrotransposon ORF2p.png English: www.ebi.ac.uk/interpro/protein/reviewed/O00370/ Has reverse transcriptase activity required for target-primed reverse transcription of the LINE-1 element mRNA, a crucial step in LINE-1 retrotransposition. Date 24 May 2023 Source alphafold.ebi.ac.uk/entry/O00370 Author Jumper, J et al. Highly accurate protein structure prediction with AlphaFold. Nature…

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…

Hunt, T. et al. A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science 318, 1913–1916 (2007). Article  ADS  CAS  PubMed  Google Scholar  Crowson, R. A. The phylogeny of coleoptera. Annu. Rev. Entomol. 5, 111–134 (1960). Article  Google Scholar  Darwin, C. The Descent of Man, and Selection…

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…

Mutant collection development We mutagenized 2,700 seeds of the wheat–Th. elongatum introgression line RWG34 containing Sr43 (ref. 29). Dry seeds were incubated for 16 h with 200 ml of a 0.8% (w/v) EMS solution with constant shaking on a Roller Mixer (Model SRT1, Stuart Scientific) to ensure maximum homogenous exposure of the…

Get protein information from ensemblbacteria using interpro 1 So I am trying to access protein information using interpro ids on ensemblbacteria. I have written a MySQL code in R however, I can’t quite figure out how to get protein information using the ids using programming language. I have put in…

Elmore, S. Apoptosis: A review of programmed cell death. Toxicol. Pathol. 35, 495–516 (2007). Article  CAS  PubMed  PubMed Central  Google Scholar  Shi, Y. Caspase activation, inhibition, and reactivation: A mechanistic view. Protein Sci. 13, 1979–1987 (2004). Article  CAS  PubMed  PubMed Central  Google Scholar  Alberts, B., Johnson, A. & Lewis, J….

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…

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;…

Ethics statement All animal experimental procedures were approved by the Biomedical Ethics Committee of Qufu Normal University (approval number: 2022001). Sampling and sequening The experimental sample is a wounded male duck found during the wild bird survey in Jiangsu, China, which died unexpectedly during rescue. We dissected the sample and…

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…

FAO. Faostat: FAO Statistical Databases. (Food & Agriculture Organization of the United Nations (FAO), 2000). The war in Ukraine is exposing gaps in the world’s food-systems research. Nature 604, 217–218 (2022). Chapman, M. A., He, Y. & Zhou, M. Beyond a reference genome: pangenomes and population genomics of underutilized and…

Hello, I am using the standalone interproscan-5.15-54.0. I could run the given test_proteins file sucessfully however, when I am trying to run my protein sequences, it gives same errors. This is the sam question in biostar (Problem running interproscan-5.14-53.0 for protein sequences), but I can’t find any useful information. Please…

how to get pfam id of proteins belonging to a particular family along with sequences in that family? 1 Hello, i am a newbie in bioinformatics I am trying to get protein sequences of a particular species e.g homo sapiens along with the pfam id of the family to which…

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….

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…

Gicquel, C., El-Osta, A. & Le Bouc, Y. Epigenetic regulation and fetal programming. Best Pract. Res. Clin. Endocrinol. Metab. 22, 1–16 (2008). CAS  Google Scholar  Godfrey, K. M. & Barker, D. J. Fetal programming and adult health. Public Health Nutr. 4, 611–624 (2001). CAS  Google Scholar  Encinias, H. B., Lardy,…

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 collection Metagenomic project information was collected from the MGnify metagenomic database31. Currently (September 2021), microbiome data (sequence, taxonomic, and functional information, etc.) of 325,323 environmental samples can be found in this database. Often, microbes from similar ecological communities have been studied by different groups at different times and locations….

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…

Dear colleagues, Data on sequence level mapping through the SIFTS process www.ebi.ac.uk/pdbe/docs/sifts/ can now be retrieved directly from updated mmCIF files, available on PDBe entry pages. These files now contain residue-level mapping between UniProt and PDB entries, including coordinate numbering for UniProt accessions and mapping to a host of other…

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;…

Hallam, S. J., Goncharov, A., McEwen, J., Baran, R. & Jin, Y. Syd-1, a presynaptic protein with PDZ, C2 and rhoGAP-like domains specifies axon identity in C. elegans. Nat. Neurosci. 5, 1137–1146 (2002). CAS  PubMed  Google Scholar  Xu, Y. & Quinn, C. C. SYD-1 promotes multiple developmental steps leading to…

INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…

ID A0A1S3QEZ7_SALSA Unreviewed; 104 AA. AC A0A1S3QEZ7; DT 12-APR-2017, integrated into UniProtKB/TrEMBL. DT 12-APR-2017, sequence version 1. DT 02-JUN-2021, entry version 11. DE SubName: Full=lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog isoform X2 {ECO:0000313|RefSeq:XP_014038412.1}; GN Name=LOC106591717 {ECO:0000313|RefSeq:XP_014038412.1}; OS Salmo salar (Atlantic salmon). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Actinopterygii;…

1. Dunbar, C. E. et al. Gene therapy comes of age. Science 359, eaan4672 (2018). PubMed Google Scholar  2. Wang, D., Tai, P. W. L. & Gao, G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat. Rev. Drug Discov. 18, 358–378 (2019). CAS PubMed PubMed Central Google Scholar  3. Eid, A.,…

Batch conversion of InterPro IDs to GO IDS for TopGO analysis 0 Hi all, I have a list of about two thousand InterPro IDs that I would like to convert to their corresponding GO IDs for subsequent enrichment analyses in TopGO. I initially used the Interpro2go batch text file to…

Using protein domains for annotation validation 0 I am trying to develop a procedure for assessing the reliability of proteins derived from a genome annotation analysis. One thing I’d like to do is search the annotated protein for protein domains, with the idea being that proteins containing known domains are…

I have an S4 object named ‘res’ which I got while using an R package called RDAVIDWebService. I can’t seem to find a way to convert this object into a dataframe in R. I tried using the function ‘as.data.frame(res)’ but it throws this error: > as.data.frame(res) Error in as.data.frame.default(res) :…