Tag: mg1655

KEGG T00007: b1542

Entry b4323             CDS       T00007                                  Symbol uxuB Name (RefSeq) D-mannonate oxidoreductase   KO K00040   fructuronate reductase [EC:1.1.1.57] Organism eco  Escherichia coli K-12 MG1655 Pathway eco00040   Pentose and glucuronate interconversions eco01100   Metabolic pathways Module eco_M00061   D-Glucuronate degradation, D-glucuronate => pyruvate + D-glyceraldehyde 3P Brite KEGG Orthology (KO) [BR:eco00001] 09100 Metabolism  09101 Carbohydrate metabolism   00040 Pentose and glucuronate interconversions    b4323 (uxuB)Enzymes…

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Convert list of Accession Numbers to Full Taxonomy

Using NCBI Entrez direct. $ esearch -db assembly -query “GCA_000005845” | elink -target taxonomy | efetch -format native -mode xml | grep ScientificName | awk -F “>|<” ‘BEGIN{ORS=”, “;}{print $3;}’ Escherichia coli str. K-12 substr. MG1655, cellular organisms, Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacterales, Enterobacteriaceae, Escherichia, Escherichia coli, Escherichia coli K-12, If…

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Rockhopper’s alignment issue

Rockhopper’s alignment issue 0 Hi everyone, I’m trying to identify the operons with the Rockhopper tool but at the end of the alignment something strange happens: Aligning sequencing reads from file: SRR6757591_1.sorted.bam Total reads: 10209877 Successfully aligned reads: 9358027 92% (>NC_000913.3 Escherichia coli str. K-12 substr. MG1655, complete genome) Aligning…

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Escherichia coli K-12 substr. MG1655 GO:0042781

Escherichia coli K-12 substr. MG1655 Gene-Ontology-Terms Class: GO:0042781 – 3′-tRNA processing endoribonuclease activity Synonyms: 3′ tRNA processing endoribonuclease activity, 3′ tRNase activity, tRNA 3′ endonuclease activity Definition: Catalysis of the endonucleolytic cleavage of RNA, removing extra 3′ nucleotides from tRNA precursor, generating 3′ termini of tRNAs. A 3′-hydroxy group is…

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Escherichia coli K-12 substr. MG1655 EC 1.1.1.282

BioCyc ID: RXN-11174 EC Number: 1.1.1.282 Enzymes and Genes: shikimate dehydrogenase: ydiB The reaction direction shown is in accordance with the direction in which it was curated. Most BioCyc compounds have been protonated to a reference pH value of 7.3. Please see the PGDB Concepts Guide for more information. Mass…

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Escherichia coli K-12 substr. MG1655 Chemical Reactions

Summary: Chemical Reactions are those for which at least one substrate molecule is chemically modified, meaning that either a chemical bond (covalent, ionic or coodination) is formed and/or broken, or that a redox modification has occurred. Parent Classes: Simple Reactions Child classes: Protein-Modification Reactions (429), Group Translocation (23), Transport Energized…

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KEGG PATHWAY: Fluorobenzoate degradation – Escherichia coli K-12 MG1655

[ Pathway menu | Pathway entry | Download KGML | Image (png) file | Help ] Option Scale: 100% Search ID search Color Read more here: Source link

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KEGG PATHWAY: DNA replication – Escherichia coli K-12 MG1655

KEGG PATHWAY: DNA replication – Escherichia coli K-12 MG1655 [ | Pathway entry | Download KGML | Show description | Image (png) file | Help ] A complex network of interacting proteins and enzymes is required for DNA replication. Generally, DNA replication follows a multistep enzymatic pathway. At the DNA…

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rosetta fold vs alphafold 2

S. Both AlphaFold and Xu use simple folding engines L-BFGS (L- Broyden–Fletcher–Goldfarb– Shanno (BFGS)) and CNS (Crystallography and NMR System), respectively, i.e., improvements come from a better energy potential using distributional information. The phase problem is a problem, to the point that in the past decade, several structures, such as M-PMV…

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The LpoA activator is required to stimulate the peptidoglycan polymerase activity of its cognate cell wall synthase PBP1a

Significance Class A penicillin-binding proteins (aPBPs) assemble the bacterial cell wall and are the targets of penicillin and related β-lactam antibiotics. In gram-negative bacteria, the aPBPs require outer membrane lipoproteins to function. However, little is known about how these proteins promote the activity of their cognate synthases in cells. Here,…

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Limiting The Genes Associated With a Pathway to a Certain Species

Hello everyone! I am currently trying to establish a metabolic pathway analysis pipeline for my lab, using complete genomes. The final goal is to be able to see the primary metabolic pathways from a complete/draft genome. As a test, I am using the sequence of the complete genome of E….

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