Tag: Pfam

KEGG T01015: 4329963

Entry 4332822           CDS       T01015                                  Name (RefSeq) LOW QUALITY PROTEIN: nuclear cap-binding protein subunit 1-like   KO K12882   nuclear cap-binding protein subunit 1 Organism osa  Oryza sativa japonica (Japanese rice) (RefSeq) Pathway osa03013   Nucleocytoplasmic transport osa03015   mRNA surveillance pathway osa03040   Spliceosome Brite KEGG Orthology (KO) [BR:osa00001] 09120 Genetic Information Processing  09121 Transcription   03040 Spliceosome    4332822  09122 Translation   03013 Nucleocytoplasmic transport    4332822   03015 mRNA…

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KEGG T01710: 100306272

Entry 100782702         CDS       T01710                                  Symbol COX2 Name (RefSeq) cytochrome c oxidase subunit 2, mitochondrial   KO K02261   cytochrome c oxidase subunit 2 Organism gmx  Glycine max (soybean) Pathway gmx00190   Oxidative phosphorylation gmx01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:gmx00001] 09100 Metabolism  09102 Energy metabolism   00190 Oxidative phosphorylation    100782702 (COX2) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03029 Mitochondrial biogenesis…

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KEGG T08053: IA203_01755

Entry IA203_01755       CDS       T08053                                  Name (GenBank) UDP-N-acetylmuramate dehydrogenase   KO K00075   UDP-N-acetylmuramate dehydrogenase [EC:1.3.1.98] Organism cwk  Corynebacterium wankanglinii Pathway cwk00520   Amino sugar and nucleotide sugar metabolism cwk00550   Peptidoglycan biosynthesis cwk01100   Metabolic pathways cwk01250   Biosynthesis of nucleotide sugars Brite KEGG Orthology (KO) [BR:cwk00001] 09100 Metabolism  09101 Carbohydrate metabolism   00520 Amino sugar and nucleotide sugar metabolism    IA203_01755  09107 Glycan biosynthesis and…

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KEGG T09148: BWI76_09435

Entry BWI76_09435       CDS       T09148                                  Name (GenBank) glutaredoxin, GrxA family   KO K03674   glutaredoxin 1 Organism klm  Klebsiella sp. M5al Brite KEGG Orthology (KO) [BR:klm00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03110 Chaperones and folding catalysts [BR:klm03110]    BWI76_09435Chaperones and folding catalysts [BR:klm03110] Protein folding catalysts  Protein disulfide isomerase   BWI76_09435 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam:  Glutaredoxin Glrx-like Thioredoxin_3…

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A super-pangenome of the North American wild grape species | Genome Biology

Alston JM, Sambucci O. Grapes in the world economy. In: Cantu D, Walker MA, editors. The grape genome. Springer International Publishing; 2019. p. 1–24. Google Scholar  Rahemi A, Dodson Peterson JC, Lund KT. Grape rootstocks and related species. Cham: Springer International Publishing; 2022. Walker MA, Heinitz C, Riaz S, Uretsky…

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How to filter hmmer output and get needed enzymes

How to filter hmmer output and get needed enzymes 0 This is a part of my file. You can see the output for KI0314_NODE_20043_length_7522_cov_1.691954_4. Glyco_hydro_43 PF04616.18 KI0314_NODE_20043_length_7522_cov_1.691954_4 – 2.3e-43 148.8 4.0 3.5e-43 148.2 4.0 1.3 1 0 0 1 1 1 1 Glycosyl hydrolases family 43 GH43_C2 PF17851.5 KI0314_NODE_20043_length_7522_cov_1.691954_4 –…

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Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa)

Identification of the AP2/ERF transcription factors in lettuce genome To identify AP2/ERF family genes in lettuce, we queried the lettuce genomic protein database (version 8) using the Pfam model (PF00847) of the AP2 domain. This search led us to discover 223 genes that showed a significant match with the AP2…

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Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome

Zachos, J., Pagani, H., Sloan, L., Thomas, E. & Billups, K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292, 686–693 (2001). Article  ADS  CAS  PubMed  Google Scholar  Favre, A. et al. The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan…

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Genome sequence and characterization of a novel Pseudomonas putida phage, MiCath

Bacterial strains We used P. putida strains S12, DOT-T1E, F1 (kindly gifted by Grant Rybnicky), ATCC 12633 (purchased from ATCC), JUb85 (kindly provided by Samuel Buck), EM383 (kindly gifted by Huseyin Tas), p106 (kindly provided by Carey-Ann Burnham), and KT2440 (obtained from lab stocks). An overnight culture of each P….

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Human hg38 chr6:31,165,200-31,165,800 UCSC Genome Browser v457

     Custom Tracks ac4C-RIP-seq peaks, hESC CTL-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC CTL-2hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-2hidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull p14 Fix Patcheshidedensesquishpackfull p14 Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19…

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Curated model organism gene functional annotations

Curated model organism gene functional annotations 0 Hi, I’m working with a model organism for the first time – C. elegans nematodes – and have created a list of differential expressed genes from some RNAseq data the lab had. One of the things I like to do is look for…

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Comparative genomics and proteomics analysis of phages infecting multi-drug resistant Escherichia coli O177 isolated from cattle faeces

Batinovic, S. et al. Bacteriophages in natural and artificial environments. Pathogens 8, 100. doi.org/10.3390/pathogens8030100 (2019). Article  PubMed  PubMed Central  Google Scholar  Mushegian, A. R. Are there 10^31 virus particles on earth, or more, or fewer?. J. Bacteriol. 202(9), 2020. doi.org/10.1128/JB.00052-20 (2020). Article  Google Scholar  Kutter, E. & Sulakvelidze, A. Bacteriophages:…

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Page not found at /GeneAnnotation/?id=Ash020296&type=Apostasia

Page not found at /GeneAnnotation/?id=Ash020296&type=Apostasia Using the URLconf defined in orchidbase6.urls, Django tried these URL patterns, in this order: ^admin/ ^home/ ^ ^tools/ [name=”tools”] ^ ^help/ [name=”Help”] ^ ^download/ [name=”download”] ^ ^Phalaenopsis_home/ [name=”Phalaenopsis_2020″] ^ ^Dendrobium_home/ [name=”Dendrobium_2020″] ^ ^Apostasia_home/ [name=”Apostasia_2020″] ^ ^Vpompona_home/ [name=”Vpompona_2020″] ^ ^Vshenzhenica_home/ [name=”Vshenzhenica_2020″] ^ ^Pguangdongensis_home/ [name=”Pguangdongensis_2020″] ^ ^Pzijinensis_home/…

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A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera

Jiao, Y. N. et al. Ancestral polyploidy in seed plants and angiosperms. Nature 473, 97–100 (2011). Article  PubMed  Google Scholar  Levin, D. A. Polyploidy and novelty in flowering plants. Am. Nat. 122, 1–25 (1983). Article  Google Scholar  Soltis, P. S. & Soltis, D. E. Ancient WGD events as drivers of…

Continue Reading A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera

Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses

Honegger, R. The lichen symbiosis: What is so spectacular about it?. Lichenologist 30, 193–212 (1998). Article  Google Scholar  Grube, M. & Berg, G. Microbial consortia of bacteria and fungi with focus on the lichen symbiosis. Fung. Biol. Rev. 23, 72–85 (2009). Article  Google Scholar  Spribille, T. et al. Basidiomycete yeasts…

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KEGG T01005: 473325

Entry 473325            CDS       T01005                                  Symbol RNASE2 Name (RefSeq) non-secretory ribonuclease precursor   KO K01168   pancreatic ribonuclease [EC:4.6.1.18] Organism ptr  Pan troglodytes (chimpanzee) Brite KEGG Orthology (KO) [BR:ptr00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03019 Messenger RNA biogenesis [BR:ptr03019]    473325 (RNASE2)   04131 Membrane trafficking [BR:ptr04131]    473325 (RNASE2)Enzymes [BR:ptr01000] 4. Lyases  4.6  Phosphorus-oxygen lyases   4.6.1  Phosphorus-oxygen lyases (only sub-subclass identified to date)    4.6.1.18  pancreatic ribonuclease     473325 (RNASE2)Messenger…

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How to get multiple protein domain database domain name from id’s

How to get multiple protein domain database domain name from id’s 0 Hello i got a blast2go output with a column with id’s from multiple databases suported by interpro but i need the domain names so i can filter the data someone know how can i do it? My data…

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KEGG T01007: 415125

Entry 415125            CDS       T01007                                  Symbol FGFR2 Name (RefSeq) fibroblast growth factor receptor 2 precursor   KO K05093   fibroblast growth factor receptor 2 [EC:2.7.10.1] Organism cfa  Canis lupus familiaris (dog) Pathway cfa01521   EGFR tyrosine kinase inhibitor resistance cfa04010   MAPK signaling pathway cfa04014   Ras signaling pathway cfa04015   Rap1 signaling pathway cfa04020   Calcium signaling pathway cfa04144   Endocytosis…

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KEGG T02994: 18601618

Entry 18601618          CDS       T02994                                  Name (RefSeq) alpha-glucan phosphorylase 1   KO K00688   glycogen phosphorylase [EC:2.4.1.1] Organism tcc  Theobroma cacao (cacao) Pathway tcc00500   Starch and sucrose metabolism tcc01100   Metabolic pathways tcc01110   Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:tcc00001] 09100 Metabolism  09101 Carbohydrate metabolism   00500 Starch and sucrose metabolism    18601618Enzymes [BR:tcc01000] 2. Transferases  2.4  Glycosyltransferases   2.4.1  Hexosyltransferases    2.4.1.1  glycogen phosphorylase     18601618 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT…

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KEGG T00196: STH138

Entry STH138            CDS       T00196                                  Name (GenBank) putative N-acetyl-mannosamine transferase   KO K05946   N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase [EC:2.4.1.187] Organism sth  Symbiobacterium thermophilum Pathway sth00552   Teichoic acid biosynthesis Brite KEGG Orthology (KO) [BR:sth00001] 09100 Metabolism  09107 Glycan biosynthesis and metabolism   00552 Teichoic acid biosynthesis    STH138 09180 Brite Hierarchies  09181 Protein families: metabolism   01003 Glycosyltransferases [BR:sth01003]    STH138Enzymes [BR:sth01000] 2. Transferases  2.4  Glycosyltransferases   2.4.1  Hexosyltransferases    2.4.1.187  N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase     STH138Glycosyltransferases [BR:sth01003] Polysaccharide  Bacterial polysaccharide (excluding LPS)   STH138 BRITE hierarchy SSDB…

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Whole genome sequencing provides evidence for Bacillus velezensis SH-1471 as a beneficial rhizosphere bacterium in plants

Inhibition effect of strain SH-1471 on plant pathogenic fungi The results of the plate confrontation experiment showed that B. velezensis SH-1471 had good inhibitory effects on various pathogenic microorganisms (Fig. 1). Specifically, our experiment showed that its inhibition rates on Sclerotinia scrotiorum, Phoma mateuciicola, and Fusarium oxysporum were 93.5%, 90.3%, and…

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KEGG T02920: 102247935

Entry 102247935         CDS       T02920                                  Symbol TRMT44 Name (RefSeq) tRNA methyltransferase 44 homolog (S. cerevisiae)   KO K15447   tRNASer (uridine44-2′-O)-methyltransferase [EC:2.1.1.211] Organism myb  Myotis brandtii (Brandt’s bat) Brite KEGG Orthology (KO) [BR:myb00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03016 Transfer RNA biogenesis [BR:myb03016]    102247935 (TRMT44)Enzymes [BR:myb01000] 2. Transferases  2.1  Transferring one-carbon groups   2.1.1  Methyltransferases    2.1.1.211  tRNASer (uridine44-2′-O)-methyltransferase     102247935 (TRMT44)Transfer RNA biogenesis [BR:myb03016] Eukaryotic type  tRNA modification…

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KEGG T03531: KR75_11080

Entry KR75_11080        CDS       T03531                                  Name (GenBank) xylose isomerase   KO K01805   xylose isomerase [EC:5.3.1.5] Organism kvd  Klebsiella variicola DX120E Pathway kvd00040   Pentose and glucuronate interconversions kvd00051   Fructose and mannose metabolism kvd01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:kvd00001] 09100 Metabolism  09101 Carbohydrate metabolism   00040 Pentose and glucuronate interconversions    KR75_11080   00051 Fructose and mannose metabolism    KR75_11080Enzymes [BR:kvd01000] 5. Isomerases  5.3  Intramolecular oxidoreductases   5.3.1  Interconverting aldoses and…

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KEGG T01001: 1474

Entry 1474              CDS       T01001                                  Symbol CST6, ECTD15 Name (RefSeq) cystatin E/M   KO K13902   cystatin-M Organism hsa  Homo sapiens (human) Disease H00651   Hypohidrotic ectodermal dysplasia Brite KEGG Orthology (KO) [BR:hsa00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:hsa01002]    1474 (CST6)Peptidases and inhibitors [BR:hsa01002] Peptidase inhibitors  Family I25: cystatin family   1474 (CST6) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif…

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KEGG T01001: 637

Entry 637               CDS       T01001                                  Symbol BID, FP497 Name (RefSeq) BH3 interacting domain death agonist   KO K04726   BH3 interacting domain death agonist Organism hsa  Homo sapiens (human) Pathway hsa01524   Platinum drug resistance hsa04071   Sphingolipid signaling pathway hsa04115   p53 signaling pathway hsa04210   Apoptosis hsa04215   Apoptosis – multiple species hsa04217   Necroptosis hsa04650   Natural killer cell mediated…

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The Rauvolfia tetraphylla genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids

Genome sequencing and assembly of R. tetraphylla After DNA extraction from young leaves and sequencing, the R. tetraphylla genome was first assembled into 1008 contigs with an N50 of 3.7 Mb. After haplotigs removal and a final pilon polishing, the 364,945,498 bp final assembly was distributed across 76 scaffolds with an N50…

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Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

Soltis, D. E. et al. Polyploidy and angiosperm diversification. Am. J. Bot. 96, 336–348 (2009). Article  PubMed  Google Scholar  Van de Peer, Y., Mizrachi, E. & Marchal, K. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424 (2017). Article  PubMed  Google Scholar  Amborella Genome Project et al. The Amborella…

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The Mla system of diderm Firmicute Veillonella parvula reveals an ancestral transenvelope bridge for phospholipid trafficking

Bacterial strains and growth conditions Veillonella parvula SKV38 was grown in SK medium (10 g/L tryptone [Difco], 10 g/L yeast extract [Difco], 0.4 g/L disodium phosphate, 2 g/L sodium chloride, and 10 ml/L 60% [wt/vol] sodium DL-lactate; described in ref. 51. Cultures were incubated at 37 °C in anaerobic conditions, either in anaerobic bags (GENbag anaero;…

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Taxonomic and environmental distribution of bacterial amino acid auxotrophies

Tripp, H. J. et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452, 741–744 (2008). Article  ADS  CAS  PubMed  Google Scholar  Yu, X. J., Walker, D. H., Liu, Y. & Zhang, L. Amino acid biosynthesis deficiency in bacteria associated with human and animal hosts. Infect. Genet. Evol….

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KEGG T00046: PM0721

Entry PM0721            CDS       T00046                                  Symbol ttrA Name (GenBank) TtrA   KO K08357   tetrathionate reductase subunit A Organism pmu  Pasteurella multocida subsp. multocida Pm70 Pathway pmu00920   Sulfur metabolism pmu01100   Metabolic pathways pmu01120   Microbial metabolism in diverse environments pmu02020   Two-component system Brite KEGG Orthology (KO) [BR:pmu00001] 09100 Metabolism  09102 Energy metabolism   00920 Sulfur metabolism    PM0721 (ttrA) 09130 Environmental Information Processing  09132 Signal…

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EMDB < EMD-14025

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…

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EMDB < EMD-16930

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…

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KEGG T06063: 106511269

Entry 106522761         CDS       T06063                                  Symbol pak1 Name (RefSeq) serine/threonine-protein kinase PAK 1   KO K04409   p21-activated kinase 1 [EC:2.7.11.1] Organism alim  Austrofundulus limnaeus (annual killifish) Pathway alim04010   MAPK signaling pathway alim04012   ErbB signaling pathway alim04510   Focal adhesion alim04625   C-type lectin receptor signaling pathway alim04810   Regulation of actin cytoskeleton alim05132   Salmonella infection Brite KEGG Orthology…

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KEGG T00183: SAS2563

Entry SAS2563           CDS       T00183                                  Name (GenBank) putative histidinol dehydrogenase   KO K00013   histidinol dehydrogenase [EC:1.1.1.23] Organism sas  Staphylococcus aureus subsp. aureus MSSA476 (MSSA) Pathway sas00340   Histidine metabolism sas01100   Metabolic pathways sas01110   Biosynthesis of secondary metabolites sas01230   Biosynthesis of amino acids Brite KEGG Orthology (KO) [BR:sas00001] 09100 Metabolism  09105 Amino acid metabolism   00340 Histidine metabolism    SAS2563Enzymes [BR:sas01000] 1. Oxidoreductases  1.1  Acting on…

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KEGG T00918: Mlut_12280

Entry Mlut_12280        CDS       T00918                                  Name (GenBank) Undecaprenyl pyrophosphate synthetase   KO K00806   undecaprenyl diphosphate synthase [EC:2.5.1.31] Organism mlu  Micrococcus luteus Pathway mlu00550   Peptidoglycan biosynthesis mlu00900   Terpenoid backbone biosynthesis mlu01110   Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:mlu00001] 09100 Metabolism  09107 Glycan biosynthesis and metabolism   00550 Peptidoglycan biosynthesis    Mlut_12280  09109 Metabolism of terpenoids and polyketides   00900 Terpenoid backbone biosynthesis    Mlut_12280 09180 Brite…

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Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2’-fucosyllactose utilization can be facilitated by coexisting species

Stewart, C. J. et al. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature 562, 583–588 (2018). Article  CAS  ADS  PubMed  PubMed Central  Google Scholar  Tamburini, S., Shen, N., Wu, H. C. & Clemente, J. C. The microbiome in early life: implications for health outcomes….

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KEGG T00139: BP3287

Entry BP3287            CDS       T00139                                  Symbol atpG Name (GenBank) ATP synthase gamma chain   KO K02115   F-type H+-transporting ATPase subunit gamma Organism bpe  Bordetella pertussis Tohama I Pathway bpe00190   Oxidative phosphorylation bpe01100   Metabolic pathways Module bpe_M00157   F-type ATPase, prokaryotes and chloroplasts Brite KEGG Orthology (KO) [BR:bpe00001] 09100 Metabolism  09102 Energy metabolism   00190 Oxidative phosphorylation    BP3287 (atpG) 09180 Brite Hierarchies  09181 Protein…

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KEGG T01028: 706234

Entry 706234            CDS       T01028                                  Symbol TRAP1 Name (RefSeq) heat shock protein 75 kDa, mitochondrial   KO K09488   TNF receptor-associated protein 1 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc05012   Parkinson disease mcc05022   Pathways of neurodegeneration – multiple diseases Brite KEGG Orthology (KO) [BR:mcc00001] 09160 Human Diseases  09164 Neurodegenerative disease   05012 Parkinson disease    706234 (TRAP1)   05022 Pathways of neurodegeneration –…

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KEGG T03271: 103675060

Entry 103675060         CDS       T03271                                  Symbol APPL1 Name (RefSeq) DCC-interacting protein 13-alpha   KO K08733   DCC-interacting protein 13 alpha Organism umr  Ursus maritimus (polar bear) Pathway umr04211   Longevity regulating pathway umr05200   Pathways in cancer umr05210   Colorectal cancer Brite KEGG Orthology (KO) [BR:umr00001] 09150 Organismal Systems  09149 Aging   04211 Longevity regulating pathway    103675060 (APPL1) 09160 Human Diseases  09161 Cancer: overview   05200 Pathways in…

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Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years

Egan, E. S., Fogel, M. A. & Waldor, M. K. Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol. Microbiol. 56, 1129–1138 (2005). Article  CAS  PubMed  Google Scholar  Harrison, P. W., Lower, R. P., Kim, N. K. & Young, J. P. Introducing the bacterial ‘chromid’: not a…

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KEGG T01001: 257194

Entry 257194            CDS       T01001                                  Symbol NEGR1, DMML2433, IGLON4, KILON, Ntra Name (RefSeq) neuronal growth regulator 1   KO K06775   neuronal growth regulator 1 Organism hsa  Homo sapiens (human) Pathway hsa04514   Cell adhesion molecules Brite KEGG Orthology (KO) [BR:hsa00001] 09130 Environmental Information Processing  09133 Signaling molecules and interaction   04514 Cell adhesion molecules    257194 (NEGR1) 09180 Brite Hierarchies  09183 Protein families: signaling…

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KEGG T08541: 104528229

Entry 104528229         CDS       T08541                                  Symbol SLC15A4 Name (RefSeq) solute carrier family 15 member 4   KO K14638   solute carrier family 15 (peptide/histidine transporter), member 3/4 Organism acar  Antrostomus carolinensis (chuck-will’s-widow) Brite KEGG Orthology (KO) [BR:acar00001] 09180 Brite Hierarchies  09183 Protein families: signaling and cellular processes   02000 Transporters [BR:acar02000]    104528229 (SLC15A4)Transporters [BR:acar02000] Solute carrier family (SLC)  SLC15: Proton oligopeptide cotransporter   104528229 (SLC15A4)…

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KEGG T01011: 100038077

Entry 100038077         CDS       T01011                                  Symbol nkx2-2 Name (RefSeq) homeobox protein Nkx-2.2 isoform X1   KO K08029   homeobox protein Nkx-2.2 Organism xtr  Xenopus tropicalis (tropical clawed frog) Brite KEGG Orthology (KO) [BR:xtr00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03000 Transcription factors [BR:xtr03000]    100038077 (nkx2-2)Transcription factors [BR:xtr03000] Eukaryotic type  Helix-turn-helix   Homeo domain ANTP: NKL    100038077 (nkx2-2) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT…

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KEGG T09424: 118385109

Entry 118385109         CDS       T09424                                  Name (RefSeq) adenylosuccinate synthetase isozyme 2-like   KO K01939   adenylosuccinate synthase [EC:6.3.4.4] Organism oke  Oncorhynchus keta (chum salmon) Pathway oke00230   Purine metabolism oke00250   Alanine, aspartate and glutamate metabolism oke01100   Metabolic pathways oke01232   Nucleotide metabolism oke01240   Biosynthesis of cofactors Module oke_M00049   Adenine ribonucleotide biosynthesis, IMP => ADP,ATP Brite KEGG Orthology (KO)…

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KEGG T08782: 127423656

Entry 127423656         CDS       T08782                                  Name (RefSeq) heparan sulfate glucosamine 3-O-sulfotransferase 3B1-like   KO K07809   [heparan sulfate]-glucosamine 3-sulfotransferase 3 [EC:2.8.2.30] Organism masi  Myxocyprinus asiaticus (Chinese sucker) Pathway masi00534   Glycosaminoglycan biosynthesis – heparan sulfate / heparin Brite KEGG Orthology (KO) [BR:masi00001] 09100 Metabolism  09107 Glycan biosynthesis and metabolism   00534 Glycosaminoglycan biosynthesis – heparan sulfate / heparin    127423656 09180 Brite Hierarchies  09181 Protein…

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When will RNA get its AlphaFold moment? | Nucleic Acids Research

Abstract The protein structure prediction problem has been solved for many types of proteins by AlphaFold. Recently, there has been considerable excitement to build off the success of AlphaFold and predict the 3D structures of RNAs. RNA prediction methods use a variety of techniques, from physics-based to machine learning approaches….

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KEGG T00186: ECA0055

Entry ECA0055           CDS       T00186                                  Symbol prlC Name (GenBank) oligopeptidase A   KO K01414   oligopeptidase A [EC:3.4.24.70] Organism eca  Pectobacterium atrosepticum SCRI1043 Brite KEGG Orthology (KO) [BR:eca00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:eca01002]    ECA0055 (prlC)Enzymes [BR:eca01000] 3. Hydrolases  3.4  Acting on peptide bonds (peptidases)   3.4.24  Metalloendopeptidases    3.4.24.70  oligopeptidase A     ECA0055 (prlC)Peptidases and inhibitors [BR:eca01002] Metallo peptidases  Family M3   ECA0055 (prlC) BRITE hierarchy SSDB OrthologParalogGene…

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KEGG T00644: APJL_0327

Entry APJL_0327         CDS       T00644                                  Symbol rumA Name (GenBank) 23S rRNA (Uracil-5-)-methyltransferase   KO K03215   23S rRNA (uracil1939-C5)-methyltransferase [EC:2.1.1.190] Organism apj  Actinobacillus pleuropneumoniae JL03 (serotype 3) Brite KEGG Orthology (KO) [BR:apj00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03009 Ribosome biogenesis [BR:apj03009]    APJL_0327 (rumA)Enzymes [BR:apj01000] 2. Transferases  2.1  Transferring one-carbon groups   2.1.1  Methyltransferases    2.1.1.190  23S rRNA (uracil1939-C5)-methyltransferase     APJL_0327 (rumA)Ribosome biogenesis [BR:apj03009] Prokaryotic type  rRNA modification factors   23S rRNA…

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Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae

Sheridan, P. O. et al. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat. Commun. 11, 1–12 (2020). Article  Google Scholar  Sheridan, P. O., Meng, Y., Williams, T. A. & Gubry-Rangin, C. Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota. Nat. Commun. 13, 1–13…

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KEGG T00186: ECA2422

Entry ECA2422           CDS       T00186                                  Symbol thrS Name (GenBank) threonyl-tRNA synthetase   KO K01868   threonyl-tRNA synthetase [EC:6.1.1.3] Organism eca  Pectobacterium atrosepticum SCRI1043 Pathway eca00970   Aminoacyl-tRNA biosynthesis Brite KEGG Orthology (KO) [BR:eca00001] 09120 Genetic Information Processing  09122 Translation   00970 Aminoacyl-tRNA biosynthesis    ECA2422 (thrS) 09180 Brite Hierarchies  09181 Protein families: metabolism   01007 Amino acid related enzymes [BR:eca01007]    ECA2422 (thrS)  09182 Protein families: genetic information processing   03016 Transfer…

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KEGG T01028: 701915

Entry 701915            CDS       T01028                                  Symbol KRT25 Name (RefSeq) keratin, type I cytoskeletal 25   KO K07604   type I keratin, acidic Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc04915   Estrogen signaling pathway mcc05150   Staphylococcus aureus infection Brite KEGG Orthology (KO) [BR:mcc00001] 09150 Organismal Systems  09152 Endocrine system   04915 Estrogen signaling pathway    701915 (KRT25) 09160 Human Diseases  09171 Infectious disease: bacterial   05150 Staphylococcus…

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KEGG T05390: C3V38_02785

Entry C3V38_14330       CDS       T05390                                  Name (GenBank) GTP pyrophosphokinase   KO K01139   GTP diphosphokinase / guanosine-3′,5′-bis(diphosphate) 3′-diphosphatase [EC:2.7.6.5 3.1.7.2] Organism dit  Dietzia sp. oral taxon 368 Pathway dit00230   Purine metabolism dit01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:dit00001] 09100 Metabolism  09104 Nucleotide metabolism   00230 Purine metabolism    C3V38_14330 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03009 Ribosome biogenesis [BR:dit03009]    C3V38_14330Enzymes [BR:dit01000] 2. Transferases  2.7  Transferring…

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KEGG T01028: 698365

Entry 698365            CDS       T01028                                  Symbol AMACR Name (RefSeq) alpha-methylacyl-CoA racemase   KO K01796   alpha-methylacyl-CoA racemase [EC:5.1.99.4] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00120   Primary bile acid biosynthesis mcc01100   Metabolic pathways mcc04146   Peroxisome Module mcc_M00104   Bile acid biosynthesis, cholesterol => cholate/chenodeoxycholate Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09103 Lipid metabolism   00120 Primary bile acid biosynthesis    698365 (AMACR) 09140…

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EMDB < Search results

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…

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KEGG T01028: 703937

Entry 703937            CDS       T01028                                  Symbol PTPRG Name (RefSeq) receptor-type tyrosine-protein phosphatase gamma isoform X2   KO K16667   receptor-type tyrosine-protein phosphatase gamma [EC:3.1.3.48] Organism mcc  Macaca mulatta (rhesus monkey) Brite KEGG Orthology (KO) [BR:mcc00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01009 Protein phosphatases and associated proteins [BR:mcc01009]    703937 (PTPRG)Enzymes [BR:mcc01000] 3. Hydrolases  3.1  Acting on ester bonds   3.1.3  Phosphoric-monoester hydrolases    3.1.3.48  protein-tyrosine-phosphatase     703937 (PTPRG)Protein phosphatases and…

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KEGG T07278: 119316072

Entry 119322531         CDS       T07278                                  Name (RefSeq) porphobilinogen deaminase, chloroplastic-like   KO K01749   hydroxymethylbilane synthase [EC:2.5.1.61] Organism tdc  Triticum dicoccoides (wild emmer wheat) Pathway tdc00860   Porphyrin metabolism tdc01100   Metabolic pathways tdc01110   Biosynthesis of secondary metabolites tdc01240   Biosynthesis of cofactors Module tdc_M00121   Heme biosynthesis, plants and bacteria, glutamate => heme Brite KEGG Orthology (KO) [BR:tdc00001] 09100 Metabolism  09108…

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KEGG T01028: 704242

Entry 704242            CDS       T01028                                  Symbol CYP39A1 Name (RefSeq) 24-hydroxycholesterol 7-alpha-hydroxylase   KO K07439   24-hydroxycholesterol 7alpha-hydroxylase [EC:1.14.14.26] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00120   Primary bile acid biosynthesis Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09103 Lipid metabolism   00120 Primary bile acid biosynthesis    704242 (CYP39A1) 09180 Brite Hierarchies  09181 Protein families: metabolism   00199 Cytochrome P450 [BR:mcc00199]    704242 (CYP39A1)Enzymes [BR:mcc01000] 1. Oxidoreductases  1.14  Acting on paired…

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UniProt: A0A8U0V2F9_MUSPF

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…

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KEGG T01028: 694719

Entry 694719            CDS       T01028                                  Symbol RPL23 Name (RefSeq) 60S ribosomal protein L23   KO K02894   large subunit ribosomal protein L23e Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc03010   Ribosome mcc05171   Coronavirus disease – COVID-19 Brite KEGG Orthology (KO) [BR:mcc00001] 09120 Genetic Information Processing  09122 Translation   03010 Ribosome    694719 (RPL23) 09160 Human Diseases  09172 Infectious disease: viral   05171 Coronavirus disease – COVID-19    694719…

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Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis

Identification of CH cases from WGS in ISL and UKB We used WGS from 45,510 Icelanders and 130,709 British ancestry participants from the UKB17,18. Average sequencing depth was 33× for UKB and 38× for ISL. Participants with prior diagnoses of hematological disorders or grossly abnormal hematology measurements on entry were…

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KEGG T08540: 104459063

Entry 104463828         CDS       T08540                                  Symbol ACOX3 Name (RefSeq) peroxisomal acyl-coenzyme A oxidase 3   KO K00232   acyl-CoA oxidase [EC:1.3.3.6] Organism pguu  Pterocles gutturalis (yellow-throated sandgrouse) Pathway pguu00071   Fatty acid degradation pguu00410   beta-Alanine metabolism pguu00592   alpha-Linolenic acid metabolism pguu00640   Propanoate metabolism pguu01040   Biosynthesis of unsaturated fatty acids pguu01100   Metabolic pathways pguu01200   Carbon metabolism pguu01212   Fatty…

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KEGG T01028: 704366

Entry 704366            CDS       T01028                                  Symbol ZDHHC15 Name (RefSeq) palmitoyltransferase ZDHHC15   KO K20028   palmitoyltransferase ZDHHC2/15/20 [EC:2.3.1.225] Organism mcc  Macaca mulatta (rhesus monkey) Brite KEGG Orthology (KO) [BR:mcc00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking [BR:mcc04131]    704366 (ZDHHC15)Enzymes [BR:mcc01000] 2. Transferases  2.3  Acyltransferases   2.3.1  Transferring groups other than aminoacyl groups    2.3.1.225  protein S-acyltransferase     704366 (ZDHHC15)Membrane trafficking [BR:mcc04131] SNARE  SNARE associated proteins   Palmitoyltransferases    704366 (ZDHHC15) BRITE hierarchy…

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KEGG T05489: A6B45_00495

Entry A6B45_05465       CDS       T05489                                  Name (GenBank) diacetyl reductase   KO K03366   meso-butanediol dehydrogenase / (S,S)-butanediol dehydrogenase / diacetyl reductase [EC:1.1.1.- 1.1.1.76 1.1.1.304] Organism lsu  Leuconostoc suionicum Pathway lsu00650   Butanoate metabolism lsu01110   Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:lsu00001] 09100 Metabolism  09101 Carbohydrate metabolism   00650 Butanoate metabolism    A6B45_05465Enzymes [BR:lsu01000] 1. Oxidoreductases  1.1  Acting on the CH-OH group of donors   1.1.1  With NAD+…

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KEGG T01028: 695442

Entry 695442            CDS       T01028                                  Symbol RPLP1 Name (RefSeq) 60S acidic ribosomal protein P1   KO K02942   large subunit ribosomal protein LP1 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc03010   Ribosome mcc05171   Coronavirus disease – COVID-19 Brite KEGG Orthology (KO) [BR:mcc00001] 09120 Genetic Information Processing  09122 Translation   03010 Ribosome    695442 (RPLP1) 09160 Human Diseases  09172 Infectious disease: viral   05171 Coronavirus disease –…

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KEGG T01028: 717682

Entry 717682            CDS       T01028                                  Symbol SEPTIN2 Name (RefSeq) septin-2 isoform X1   KO K16942   septin 2 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc05100   Bacterial invasion of epithelial cells Brite KEGG Orthology (KO) [BR:mcc00001] 09160 Human Diseases  09171 Infectious disease: bacterial   05100 Bacterial invasion of epithelial cells    717682 (SEPTIN2) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking…

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KEGG T01028: 699325

Entry 699325            CDS       T01028                                  Symbol OSBP Name (RefSeq) oxysterol-binding protein 1   KO K20456   oxysterol-binding protein 1 Organism mcc  Macaca mulatta (rhesus monkey) Brite KEGG Orthology (KO) [BR:mcc00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking [BR:mcc04131]    699325 (OSBP)Membrane trafficking [BR:mcc04131] Endoplasmic reticulum (ER) – Golgi transport  Others   Oxysterol-binding proteins    699325 (OSBP) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif…

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KEGG T04128: 106346836

Entry 111199314         CDS       T04128                                  Name (RefSeq) GDP-L-fucose synthase 1 isoform X2   KO K02377   GDP-L-fucose synthase [EC:1.1.1.271] Organism bna  Brassica napus (rape) Pathway bna00051   Fructose and mannose metabolism bna00520   Amino sugar and nucleotide sugar metabolism bna01100   Metabolic pathways bna01250   Biosynthesis of nucleotide sugars Brite KEGG Orthology (KO) [BR:bna00001] 09100 Metabolism  09101 Carbohydrate metabolism   00051 Fructose and mannose…

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KEGG T01028: 706713

Entry 706713            CDS       T01028                                  Symbol HNMT Name (RefSeq) histamine N-methyltransferase   KO K00546   histamine N-methyltransferase [EC:2.1.1.8] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00340   Histidine metabolism mcc01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09105 Amino acid metabolism   00340 Histidine metabolism    706713 (HNMT) 09180 Brite Hierarchies  09183 Protein families: signaling and cellular processes   04147 Exosome [BR:mcc04147]    706713 (HNMT)Enzymes [BR:mcc01000] 2. Transferases  2.1  Transferring…

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KEGG T01028: 694392

Entry 694392            CDS       T01028                                  Symbol WEE2 Name (RefSeq) wee1-like protein kinase 2   KO K06632   wee1-like protein kinase [EC:2.7.11.1] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc04110   Cell cycle mcc05170   Human immunodeficiency virus 1 infection Brite KEGG Orthology (KO) [BR:mcc00001] 09140 Cellular Processes  09143 Cell growth and death   04110 Cell cycle    694392 (WEE2) 09160 Human Diseases  09172 Infectious disease: viral   05170…

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KEGG T02386: 101070831

Entry 101070831         CDS       T02386                                  Symbol cldn3d Name (RefSeq) claudin-4   KO K06087   claudin Organism tru  Takifugu rubripes (torafugu) Pathway tru04514   Cell adhesion molecules tru04530   Tight junction Brite KEGG Orthology (KO) [BR:tru00001] 09130 Environmental Information Processing  09133 Signaling molecules and interaction   04514 Cell adhesion molecules    101070831 (cldn3d) 09140 Cellular Processes  09144 Cellular community – eukaryotes   04530 Tight junction    101070831 (cldn3d) 09180 Brite Hierarchies  09183 Protein…

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KEGG T01028: 693999

Entry 693999            CDS       T01028                                  Symbol POLI Name (RefSeq) DNA polymerase iota isoform X1   KO K03510   DNA polymerase iota [EC:2.7.7.7] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc03460   Fanconi anemia pathway Brite KEGG Orthology (KO) [BR:mcc00001] 09120 Genetic Information Processing  09124 Replication and repair   03460 Fanconi anemia pathway    693999 (POLI) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03400 DNA…

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KEGG T02994: 18603710

Entry 18603710          CDS       T02994                                  Name (RefSeq) gibberellin 2-beta-dioxygenase 2   KO K04125   gibberellin 2beta-dioxygenase [EC:1.14.11.13] Organism tcc  Theobroma cacao (cacao) Pathway tcc00904   Diterpenoid biosynthesis tcc01110   Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:tcc00001] 09100 Metabolism  09109 Metabolism of terpenoids and polyketides   00904 Diterpenoid biosynthesis    18603710Enzymes [BR:tcc01000] 1. Oxidoreductases  1.14  Acting on paired donors, with incorporation or reduction of molecular oxygen   1.14.11  With…

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KEGG T00186: ECA4130

Entry ECA4130           CDS       T00186                                  Name (GenBank) alkaline phosphatase   KO K01077   alkaline phosphatase [EC:3.1.3.1] Organism eca  Pectobacterium atrosepticum SCRI1043 Pathway eca00730   Thiamine metabolism eca00790   Folate biosynthesis eca01100   Metabolic pathways eca01240   Biosynthesis of cofactors eca02020   Two-component system Module eca_M00126   Tetrahydrofolate biosynthesis, GTP => THF Brite KEGG Orthology (KO) [BR:eca00001] 09100 Metabolism  09108 Metabolism of cofactors and vitamins   00730…

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KEGG T01028: 712850

Entry 712850            CDS       T01028                                  Symbol PDE4A Name (RefSeq) cAMP-specific 3′,5′-cyclic phosphodiesterase 4A isoform X1   KO K13293   cAMP-specific phosphodiesterase 4 [EC:3.1.4.53] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00230   Purine metabolism mcc01100   Metabolic pathways mcc04024   cAMP signaling pathway mcc04928   Parathyroid hormone synthesis, secretion and action mcc05032   Morphine addiction Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09104…

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KEGG T01892: HMPREF4655_20621

Entry HMPREF4655_20621  CDS       T01892                                  Symbol pssA Name (GenBank) CDP-diacylglycerol-serine O-phosphatidyltransferase   KO K17103   CDP-diacylglycerol—serine O-phosphatidyltransferase [EC:2.7.8.8] Organism hpo  Helicobacter pylori 35A Pathway hpo00260   Glycine, serine and threonine metabolism hpo00564   Glycerophospholipid metabolism hpo01100   Metabolic pathways hpo01110   Biosynthesis of secondary metabolites Module hpo_M00093   Phosphatidylethanolamine (PE) biosynthesis, PA => PS => PE Brite KEGG Orthology (KO) [BR:hpo00001] 09100…

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Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria

Isolation of phyllosphere isolates All bacterial strains were isolated in June 2021 from the flag leaves of four wheat cultivars (Sheriff, Heerup, Rembrandt and Kvium) grown in an experimental field in Høje Taastrup, near Copenhagen, Denmark. Wheat flag leaves were picked, pooled, and either washed or blended prior to dilution…

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KEGG T01028: 701317

Entry 701317            CDS       T01028                                  Symbol HIPK4 Name (RefSeq) homeodomain-interacting protein kinase 4   KO K08826   homeodomain interacting protein kinase [EC:2.7.11.1] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc04218   Cellular senescence Brite KEGG Orthology (KO) [BR:mcc00001] 09140 Cellular Processes  09143 Cell growth and death   04218 Cellular senescence    701317 (HIPK4) 09180 Brite Hierarchies  09181 Protein families: metabolism   01001 Protein kinases [BR:mcc01001]    701317 (HIPK4)Enzymes [BR:mcc01000] 2….

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KEGG T01028: 717212

Entry 717212            CDS       T01028                                  Symbol PPT2 Name (RefSeq) lysosomal thioesterase PPT2 isoform X1   KO K01074   palmitoyl-protein thioesterase [EC:3.1.2.22] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00062   Fatty acid elongation mcc01100   Metabolic pathways mcc01212   Fatty acid metabolism mcc04142   Lysosome Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09103 Lipid metabolism   00062 Fatty acid elongation    717212 (PPT2) 09140 Cellular Processes  09141 Transport…

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KEGG T01028: 715211

Entry 715211            CDS       T01028                                  Symbol CYB5RL Name (RefSeq) NADH-cytochrome b5 reductase-like isoform X1   KO K00326   cytochrome-b5 reductase [EC:1.6.2.2] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00520   Amino sugar and nucleotide sugar metabolism Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09101 Carbohydrate metabolism   00520 Amino sugar and nucleotide sugar metabolism    715211 (CYB5RL)Enzymes [BR:mcc01000] 1. Oxidoreductases  1.6  Acting on NADH or NADPH   1.6.2  With…

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KEGG T01028: 705628

Entry 705628            CDS       T01028                                  Symbol NUP85 Name (RefSeq) nuclear pore complex protein Nup85 isoform X1   KO K14304   nuclear pore complex protein Nup85 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc03013   Nucleocytoplasmic transport mcc05014   Amyotrophic lateral sclerosis Brite KEGG Orthology (KO) [BR:mcc00001] 09120 Genetic Information Processing  09122 Translation   03013 Nucleocytoplasmic transport    705628 (NUP85) 09160 Human Diseases  09164 Neurodegenerative disease   05014 Amyotrophic…

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KEGG T01028: 717394

Entry 717394            CDS       T01028                                  Symbol VPS35 Name (RefSeq) vacuolar protein sorting-associated protein 35 isoform X1   KO K18468   vacuolar protein sorting-associated protein 35 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc04144   Endocytosis Brite KEGG Orthology (KO) [BR:mcc00001] 09140 Cellular Processes  09141 Transport and catabolism   04144 Endocytosis    717394 (VPS35) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking [BR:mcc04131]    717394…

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EMDB < EMD-40454

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…

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Mouse mm10 chr4:22,481,383-22,489,763 UCSC Genome Browser v455

     Custom Tracks Adiposehidedensesquishpackfull Cerebellumhidedensesquishpackfull Cortexhidedensesquishpackfull Liverhidedensesquishpackfull Lunghidedensesquishpackfull Sintesthidedensesquishpackfull Spleenhidedensesquishpackfull    mouse_7_core ATAC Adipose Rep1hidedensefull ATAC Adipose Rep2hidedensefull ATAC Cerebellum Rep1hidedensefull ATAC Cerebellum Rep2hidedensefull ATAC Colon Rep1hidedensefull ATAC Colon Rep2hidedensefull ATAC Cortex Rep1hidedensefull ATAC Cortex Rep2hidedensefull ATAC Heart Rep1hidedensefull ATAC Heart Rep2hidedensefull ATAC Liver Rep1hidedensefull ATAC Liver Rep2hidedensefull ATAC…

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The Age of Aquarius – RNA, the Epicenter of Genetic Information

The veil on genetic information was lifted by the advent of gene cloning and sequencing technologies in the 1970s. The discovery and purification of bacterial nucleases capable of cutting DNA at specific sequences and ligases capable of joining them enabled DNA from any species – or mRNAs converted to complementary…

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EMDB < EMD-25228

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…

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Distantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps

de Jonge, P. A., Nobrega, F. L., Brouns, S. J. J. & Dutilh, B. E. Molecular and evolutionary determinants of bacteriophage host range. Trends Microbiol. 27, 51–63 (2019). Article  PubMed  Google Scholar  Cambillau, C. Bacteriophage module reshuffling results in adaptive host range as exemplified by the baseplate model of listerial…

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Plastid-localized xanthorhodopsin increases diatom biomass and ecosystem productivity in iron-limited surface oceans

Protein sequence and prediction analysis The amino acid sequence of FcR was deduced from the F. cylindrus genome sequence33. Protein alignments with characterized microbial rhodopsins were performed using the MUSCLE algorithm implemented in Geneious (v.5.6)69. Predictions of subcellular location were performed with SignalP v.4.0 and TargetP (v.1.1)70. Putative transmembrane domains…

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EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets | BMC Bioinformatics

EasyCGTree was implemented in Perl programming languages (www.perl.org/) and was built using a collection of published reputable tools, including Clustal Omega version 1.2.4 [12]; consense from PHYLIP version 3.698 [13]; FastTree version 2.1 [14]; hmmbuild and hmmsearch from HMMER version 3.0 (hmmer.org/); IQ-TREE version 2.1.1 [15]; trimAl version 1.2 [16];…

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Widespread occurrence of chitinase-encoding genes suggests the Endozoicomonadaceae family as a key player in chitin processing in the marine benthos

Genes coding for endo-chitinases (EC 3.2.1.14), the enzymes that cleave chitin polymers into oligomers [16], were found on 32 of 42 Endozoicomonadaceae genomes (Fig. 1 and Table S1), including representatives of all formally described genera and all Candidatus Gorgonimonas MAGs. Several genomes harbored more than one endo-chitinase encoding gene, resulting in…

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KEGG T00007: b1676

Entry b1676             CDS       T00007                                  Symbol pykF Name (RefSeq) pyruvate kinase I   KO K00873   pyruvate kinase [EC:2.7.1.40] Organism eco  Escherichia coli K-12 MG1655 Pathway eco00010   Glycolysis / Gluconeogenesis eco00620   Pyruvate metabolism eco01100   Metabolic pathways eco01110   Biosynthesis of secondary metabolites eco01120   Microbial metabolism in diverse environments eco01200   Carbon metabolism eco01230   Biosynthesis of amino acids Module…

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KEGG T01028: 717963

Entry 717963            CDS       T01028                                  Symbol STIM1 Name (RefSeq) stromal interaction molecule 1 precursor   KO K16059   stromal interaction molecule 1 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc04020   Calcium signaling pathway mcc04611   Platelet activation Brite KEGG Orthology (KO) [BR:mcc00001] 09130 Environmental Information Processing  09132 Signal transduction   04020 Calcium signaling pathway    717963 (STIM1) 09150 Organismal Systems  09151 Immune system   04611 Platelet activation    717963…

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KEGG T05149: 103473078

Entry 103473078         CDS       T05149                                  Symbol ppt1 Name (RefSeq) palmitoyl-protein thioesterase 1 isoform X1   KO K01074   palmitoyl-protein thioesterase [EC:3.1.2.22] Organism pret  Poecilia reticulata (guppy) Pathway pret00062   Fatty acid elongation pret01100   Metabolic pathways pret01212   Fatty acid metabolism pret04142   Lysosome Brite KEGG Orthology (KO) [BR:pret00001] 09100 Metabolism  09103 Lipid metabolism   00062 Fatty acid elongation    103473078 (ppt1) 09140 Cellular Processes  09141 Transport and…

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KEGG T05897: 110480856

Entry 110480856         CDS       T05897                                  Symbol AGA Name (RefSeq) N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase   KO K01444   N4-(beta-N-acetylglucosaminyl)-L-asparaginase [EC:3.5.1.26] Organism lsr  Lonchura striata domestica (Bengalese finch) Pathway lsr00511   Other glycan degradation lsr04142   Lysosome Brite KEGG Orthology (KO) [BR:lsr00001] 09100 Metabolism  09107 Glycan biosynthesis and metabolism   00511 Other glycan degradation    110480856 (AGA) 09140 Cellular Processes  09141 Transport and catabolism   04142 Lysosome    110480856 (AGA)Enzymes [BR:lsr01000] 3. Hydrolases  3.5  Acting on carbon-nitrogen bonds,…

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KEGG T02867: BN877_I0744

Entry BN877_I0744       CDS       T02867                                  Symbol coxB1 Name (GenBank) cytochrome c oxidase, subunit II   KO K02275   cytochrome c oxidase subunit II [EC:7.1.1.9] Organism rir  Agrobacterium pusense IRBG74 Pathway rir00190   Oxidative phosphorylation rir01100   Metabolic pathways Module rir_M00155   Cytochrome c oxidase, prokaryotes Brite KEGG Orthology (KO) [BR:rir00001] 09100 Metabolism  09102 Energy metabolism   00190 Oxidative phosphorylation    BN877_I0744 (coxB1)Enzymes [BR:rir01000] 7. Translocases  7.1  Catalysing the…

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KEGG T08832: 125909104

Entry 125925080         CDS       T08832                                  Name (RefSeq) adenylosuccinate synthetase isozyme 2 isoform X1   KO K01939   adenylosuccinate synthase [EC:6.3.4.4] Organism puc  Panthera uncia (snow leopard) Pathway puc00230   Purine metabolism puc00250   Alanine, aspartate and glutamate metabolism puc01100   Metabolic pathways puc01232   Nucleotide metabolism puc01240   Biosynthesis of cofactors Module puc_M00049   Adenine ribonucleotide biosynthesis, IMP => ADP,ATP Brite KEGG…

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KEGG T00061: RC0581

Entry RC0582            CDS       T00061                                  Symbol pheT Name (GenBank) phenylalanyl-tRNA synthetase beta chain   KO K01890   phenylalanyl-tRNA synthetase beta chain [EC:6.1.1.20] Organism rco  Rickettsia conorii Pathway rco00970   Aminoacyl-tRNA biosynthesis Brite KEGG Orthology (KO) [BR:rco00001] 09120 Genetic Information Processing  09122 Translation   00970 Aminoacyl-tRNA biosynthesis    RC0582 (pheT) 09180 Brite Hierarchies  09181 Protein families: metabolism   01007 Amino acid related enzymes [BR:rco01007]    RC0582 (pheT)  09182 Protein families: genetic…

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KEGG T00123: EF1761

Entry EF1761            CDS       T00123                                  Symbol ftsE Name (RefSeq) cell division ATP-binding protein FtsE   KO K09812   cell division transport system ATP-binding protein Organism efa  Enterococcus faecalis V583 Pathway efa02010   ABC transporters Brite KEGG Orthology (KO) [BR:efa00001] 09130 Environmental Information Processing  09131 Membrane transport   02010 ABC transporters    EF1761 (ftsE) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03036 Chromosome and associated…

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The blackcap (Sylvia atricapilla) genome reveals a recent accumulation of LTR retrotransposons

The genome assembly was performed with the pipeline v1.5 of the Vertebrate Genomes Project (VGP) and can be found under NCBI BioProject PRJNA558064, accession number GCA_009819655.1, for further details on the sample collection and assembly see Ishigohoka et al.9. In brief, a female blackcap from mainland Spain was caught to…

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KEGG T00835: Ccel_0126

Entry Ccel_0126         CDS       T00835                                  Name (GenBank) 3-isopropylmalate dehydratase, large subunit   KO K01703   3-isopropylmalate/(R)-2-methylmalate dehydratase large subunit [EC:4.2.1.33 4.2.1.35] Organism cce  Ruminiclostridium cellulolyticum Pathway cce00290   Valine, leucine and isoleucine biosynthesis cce00660   C5-Branched dibasic acid metabolism cce01100   Metabolic pathways cce01110   Biosynthesis of secondary metabolites cce01210   2-Oxocarboxylic acid metabolism cce01230   Biosynthesis of amino acids Module cce_M00432  …

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KEGG T01028: 713306

Entry 713306            CDS       T01028                                  Symbol GATM Name (RefSeq) glycine amidinotransferase, mitochondrial   KO K00613   glycine amidinotransferase [EC:2.1.4.1] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00260   Glycine, serine and threonine metabolism mcc00330   Arginine and proline metabolism mcc01100   Metabolic pathways Module mcc_M00047   Creatine pathway Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09105 Amino acid metabolism   00260 Glycine, serine and…

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