Tag: mg1655

Antibiotic resistance genes are spread more widely between bacteria than previously thought

Plasmid transfer from the Escherichia coli MG1655 donor strain to bacterial community extracted from a hospital wastewater treatment plant. (A) Transconjugants formed in the absence of NaClO. The green fluorescence indicates successful acquisition of the gfp-expressing plasmid. (B) Transconjugants formed in the presence of 40 mg/L NaClO. (C) Transconjugants formed…

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Common analysis of direct RNA sequencinG CUrrently leads to misidentification of m5C at GCU motifs

Introduction Oxford Nanopore Technologies (ONT) direct RNA sequencing (Fig 1A) enables detection of RNA modifications. A modified base produces an altered electrical current and/or dwell time relative to a canonical base that can be detected with algorithms (Garalde et al, 2018; Smith et al, 2019; Workman et al, 2019). Figure…

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Sequence-Based Classification and Identification | SpringerLink

Adékambi T, Drancourt M, Raoult D (2009) The rpoB gene as a tool for clinical microbiologists. Trends Microbiol 17:37–45 CrossRef  PubMed  Google Scholar  Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 CrossRef  CAS  PubMed  Google Scholar  Arahal DR,…

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Detection of Electroporation in Microbial Cells: Techniques and Procedures

Alvarez-Ordóñez A, Mouwen DJM, López M, Prieto M (2011) Fourier transform infrared spectroscopy as a tool to characterize molecular composition and stress response in foodborne pathogenic bacteria. J Microbiol Methods 84:369–378 CrossRef  Google Scholar  Aronsson K, Rönner U, Borch E (2005) Inactivation of Escherichia coli, Listeria innocua and Saccharomyces cerevisiae…

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Deep learning and single-cell phenotyping for rapid antimicrobial susceptibility detection in Escherichia coli

Detecting antibiotic susceptibility based on deep learning of single-cell subcellular phenotypes We designed a method that takes as an input bacterial cultures grown in rich medium to a consistent optical density and then treated with an antibiotic of choice for a time sufficient to produce distinct, antibiotic-specific, cellular phenotypic changes…

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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 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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Solved 2. Post the residue number of the catalytic Lysine

Transcribed image text: 2. Post the residue number of the catalytic Lysine (Lys, K) in CadA of E. coli K-12 MG1655? (For example: If the lysine was at position 11 along the amino acid sequence, then you would provide: K11) 3. Show an alignment (MSA) of the family that you…

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Solved Using the NCBI website, find the exact nucleotide

Using the NCBI website, find the exact nucleotide position of the folE gene start and stop in E. coli K-12 MG1655. Hint: make sure to search the “gene” database Is the gene on the + or – strand ? Find the names of the genes located before and after the…

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Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655.

Abstract Three transcription factors (TFs), OxyR, SoxR, and SoxS, play a critical role in transcriptional regulation of the defense system for oxidative stress in bacteria. However, their full genome-wide regulatory potential is unknown. Here, we perform a genome-scale reconstruction of the OxyR, SoxR, and SoxS regulons in Escherichia coli K-12…

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Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol.

Abstract Laboratory adaptive evolution studies can provide key information to address a wide range of issues in evolutionary biology. Such studies have been limited thus far by the inability of workers to readily detect mutations in evolved microbial strains on a genome scale. This limitation has now been overcome by…

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Distribution of phage T5 adsorption on E. coli MG1655.

(a) GFP channel of an epifluorescence microscopy image showing the appearance of fluorescent T5 phages (coated with Pb10-GFP fusions) adsorbing to E. coli MG1655. (b) Comparison of phage adsorption distribution between untreated, ciprofloxacin, and ceftazidime-treated cultures; percentages to the right of the dashed lanes indicate the fraction of cells with…

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Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection

Bacterial strains and growth conditions for eBW1 B. subtilis 168 and E. coli (MG1655) were streaked out from a frozen glycerol stock onto an LB plate and grown overnight at 37 °C. Following a night of growth, a single colony was picked and inoculated into 5 ml of LB broth and grown…

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Highly Effective Salt-Activated Alcohol-Based Disinfectants with Enhanced Antimicrobial Activity

journal contribution posted on 2023-08-28, 18:09 authored by Euna Oh, Seung Joon Choi, Sumin Han, Kyu Hyoung Lee, Hyo-Jick Choi Surfaces contaminated with pathogens raise concerns about the increased risk of disease transmission and infection. To clean biocontaminated surfaces, alcohol-based disinfectants have been predominantly used for disinfecting high-touch areas in…

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Reply to: Antibiotics and hexagonal order in the bacterial outer membrane

replying to G. Benn et al. Nature Communications doi.org/10.1038/s41467-023-40275-0 (2023) Benn et al. comment that the hexagonal lattices observed in outer membrane (OM) patches upon the addition of polymyxin might be formed by outer membrane proteins (OMPs). They assume that lipopolysaccharides (LPS) protrude above the OMPs, which might hide the…

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Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants

Klepzig KD, Adams AS, Handelsman J, Raffa KF. Symbioses: a key driver of insect physiological processes, ecological interactions, evolutionary diversification, and impacts on humans. Environ Entomol. 2009;38:67–77. CAS  PubMed  Google Scholar  Dale C, Moran NA. Molecular interactions between bacterial symbionts and their hosts. Cell. 2006;126:453–65. CAS  PubMed  Google Scholar  Salem…

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E. coli K-12 substr. MG1655

E. coli K-12 substr. MG1655 1 Hi all, I was wondering if E. coli K-12 substr. MG1655, which is usually used as a reference genome for E. coli, also contain the plasmid genes. I would appreciate it if someone can help me with that, please? Thanks Escherichia_coli E._coli plasmid microbe…

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Solved E. coli MG1655 and E. coli DA1 were grown in

E. coli MG1655 and E. coli DA1 were grown in deuterated minimal medium supplemented with hydrogenated (D-M9) (closed symbols) or deuterated (DD-M9) (open symbols) glycerol. Circles represent the reference strain MG1655 and squares the DA1 strain. Rank the growth rate of strain-medium pairs from highest to lowest. In which medium…

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KEGG T00007: b0720

Entry b0720             CDS       T00007                                  Symbol gltA Name (RefSeq) citrate synthase   KO K01647   citrate synthase [EC:2.3.3.1] Organism eco  Escherichia coli K-12 MG1655 Pathway eco00020   Citrate cycle (TCA cycle) eco00630   Glyoxylate and dicarboxylate metabolism eco01100   Metabolic pathways eco01110   Biosynthesis of secondary metabolites eco01120   Microbial metabolism in diverse environments eco01200   Carbon metabolism eco01210   2-Oxocarboxylic acid metabolism…

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GREs

Escherichia coli K-12 MG1655 eco_1 1502 True 0.0051 Escherichia coli K-12 MG1655 eco_2 435 True 0.0028 Escherichia coli K-12 MG1655 eco_3 420 False 0.0379 Escherichia coli K-12 MG1655 eco_4 331 True 0.0037 Escherichia coli K-12 MG1655 eco_5 320 False 0.0191 Escherichia coli K-12 MG1655 eco_6 317 False 0.089 Escherichia coli…

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Previously uncharacterized rectangular bacterial structures in the dolphin mouth

To maximize reproducibility, a list of the reagents and resources used in this study, as well as their source and identifier, is provided in Supplementary Table 5. Experimental model and subject details Oral swab samples were obtained from bottlenose dolphins (Tursiops truncatus) managed by the U.S. Navy MMP Biosciences Division, Space…

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The benefit of redundancy in biological systems

Genetic redundancy in translational components is costly under nutrient poor conditions, but beneficial under nutrient rich conditions. Credit: Max Planck Society When viewed from an engineer’s perspective, biology is often messy and imperfect. For example, redundancy is a common feature of biological systems, with the job of one biological component…

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

[ Pathway menu | Organism menu | Pathway entry | Download | Help ] Option Scale: 100% Image resolution: High Search ID search Color KGML Image (png) file 1x Read more here: Source link

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KEGG PATHWAY: Bacterial secretion system

KEGG PATHWAY: Bacterial secretion system – Escherichia coli K-12 MG1655 [ | | Pathway entry | Show description | | Help ] Gram-negative bacteria secrete a wide range of proteins whose functions include biogenesis of organelles, such as pilli and flagella, nutrient acquisition, virulence, and efflux of drugs and other…

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yeiB – 511145_v2020_sRDB19_eStrong – Abasy Atlas

Escherichia coli str. K-12 substr. MG1655 [2020, RDB19, Strong] yeiB – Module M39.6 kout: 0, kin: 1, Clustering: 0 Locus tag – b2152 UniProt ID – P25747 NCBI GeneID – 949044 Synonyms – JW2139 Biological function Product function – conserved inner membrane protein GO terms GO:0005886 – Plasma membrane…

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Comparative Analysis of Transcriptomic Response of Escherichia coli K-12 MG1655 to Nine Representative Classes of Antibiotics

The use of antibiotics leads to strong stresses to bacteria, leading to profound impact on cellular physiology. Elucidating how bacteria respond to antibiotic stresses not only helps us to decipher bacteria’s strategies to resistant antibiotics but also assists in proposing targets for antibiotic development. In this work, a comprehensive comparative…

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Module M3 – 511145_v2020_s13-RDB19 – Abasy Atlas

Home Browse Downloads Help About Contact Escherichia coli str. K-12 substr. MG1655 [2020, 13-RDB19, Weak + Strong] Module M3     Global regulators  Intermodulars  Weak interactions  Disconnected nodes  | HD quality  Interaction tooltips  | Layout:  Animate | Flash:  | Selection mode …

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Module M39.13 – 511145_v2020_sRDB19_eStrong – Abasy Atlas

Home Browse Downloads Help About Contact Escherichia coli str. K-12 substr. MG1655 [2020, RDB19, Strong] Module M39.13     Global regulators  Intermodulars  Weak interactions  Disconnected nodes  | HD quality  Interaction tooltips  | Layout:  Animate | Flash:  | Selection mode …

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Team:INSA Toulouse/contenu/lab practice/notebook/calendar/MG1655 – 2013.igem.org

Week 9 (5-11 August)In order to use this strain for light sensors characterization, we need to delete the envZ gene. For this we did a transduction of the strain with phages previously mixed with the del(EnvZ) strain from the Keio collection. The strains from this collection have individual kan cassette…

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Module M25 – 511145_v2011_sRDB11 – Abasy Atlas

Home Browse Downloads Help About Contact Escherichia coli str. K-12 substr. MG1655 [2011, RDB11, Weak + Strong] Module M25     Global regulators  Intermodulars  Weak interactions  Disconnected nodes  | HD quality  Interaction tooltips  | Layout:  Animate | Flash:  | Selection mode …

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When editing bacteria with CRISPR, less is more

The outcome of chromosomal targeting in E. coli depends on gRNA format and abundance. a Schematic of the experimental setup for chromosomal targeting and editing. b Genome targeting assay in E. coli and E. coli ΔrecA. c Northern blot analysis of whole RNA isolated from E. coli ΔlacI-Z with pCas9…

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Have model organisms evolved too far?

Genome comparison of different E. coli K-12 strains. The figure shows the comparison of the WG1 chromosome (contig 1) and F plasmid (contig 2) with the genomes of EMG2, MG1655 (NC_000913.3) and W3110 (NC_007779.1), using the Proksee Server (19). The outer two rings display the genes and features of the…

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Antidepressants linked to antibiotic resistance: E. coli study

The widespread use of antibiotics has long been implicated in the rise of drug-resistant infections. Now, scientists wonder whether unrelated drugs play a role too. In a new study, antidepressants — designed to regulate the brain chemistry of patients with mental illness — were also linked to Escherichia coli (E. coli)…

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a database of DNA repair pathways

Protein FULL name: CPD photolyase, DNA photolyase Phr (Escherichia coli strain K-12 substr. MG1655) is product of expression of phr gene. Phr is involved in: DDS in Escherichia coli strain K-12 substr. MG1655 DRR in Escherichia coli strain K-12 substr. MG1655 Keywords: FUNCTION: Involved in repair of UV radiation-induced DNA…

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Escherichia coli K-12 substr. MG1655 gntK

BioCyc ID:TU0-42512 Local Context (not to scale — see Genome Browser for correct scale) Transcription Unit Notes: Click on a binding site (if any) to navigate to the page for its transcription factor. Click on a gene to navigate to its gene page. Key to regulator colors: Green: activator; Magenta:…

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Bash script to automate htseq-count

Hi everyone- I am trying to write a script to automate htseq-count on a large number of samples. The script runs but then throws the following error: “Please provide 2 arguments”. Does anyone see something obvious I am missing: #!/bin/bash for samples in *.sam do gtf = “Galaxy135-\[Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.29.gtf\].gtf” echo $sample …

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Construction of robust Escherichia coli strains for large-scale production

  Universität Stuttgart OPUS – Online Publikationen der Universität Stuttgart Autor(en):  Ziegler, Martin Titel:  Construction of robust Escherichia coli strains for large-scale production Sonstige Titel:  Konstruktion robuster Escherichia coli Stämme für die Produktion in großvolumigen Reaktoren Erscheinungsdatum:  2022 Dokumentart:  Dissertation URI:  nbn-resolving.de/urn:nbn:de:bsz:93-opus-ds-123019elib.uni-stuttgart.de/handle/11682/12301dx.doi.org/10.18419/opus-12284 Zusammenfassung:  The biotechnical production of many fine chemicals,…

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Guiqiu E.Coli K-12 mg1655 – ECHEMI

28  Upvotes · 10 Comments 27  Upvotes · 10 Comments 26  Upvotes · 7 Comments 26  Upvotes · 4 Comments 24  Upvotes · 1 Comments 23  Upvotes · 3 Comments 22  Upvotes · 1 Comments Read more here: Source link

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Alpha Fold Working

AlphaFold: The making of a scientific breakthrough The inside story of the DeepMind team of scientists and engineers who created AlphaFold, an AI system that is recognised as a solution to “protein folding”, a grand scientific challenge for more than 50…

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Escherichia coli K-12 substr. MG1655 sdsN

BioCyc ID:TU0-42620 Local Context (not to scale — see Genome Browser for correct scale) Transcription Unit Notes: Click on a binding site (if any) to navigate to the page for its transcription factor. Click on a gene to navigate to its gene page. Roll the mouse over any element in…

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Escherichia coli K-12 substr. MG1655 EC 2.7.1.180

BioCyc ID: RXN-14461 EC Number: 2.7.1.180 Enzymes and Genes: FAD:protein FMN transferase: ftp Reaction Locations: periplasmic space The reaction direction shown is in accordance with the direction in which it was curated. Mass balance status: Balanced. Enzyme Commission Primary Name: FAD:protein FMN transferase Enzyme Commission Synonyms: flavin transferase, apbE (gene…

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Summary of Escherichia coli K-12 substr. MG1655, version 26.0

Summary of Escherichia coli, Strain K-12 substr. MG1655, version 26.0 Tier 1 Highly Curated Database Authors: Peter D. Karp1, Ingrid Keseler1, Carol Fulcher1, Anamika Kothari1, Suzanne Paley1, Markus Krummenacker1, Ian Paulsen2, Amanda Mackie2, Julio Collado-Vides3, Cesar Bonavides-Martinez3, Socorro Gama-Castro3, Alberto Santos-Zavaleta3, Victor H Tierrafria3 1SRI International, 2Macquarie University, 3Centro de…

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Escherichia coli K-12 substr. MG1655 GO:0033468

Escherichia coli K-12 substr. MG1655 Gene-Ontology-Terms Class: GO:0033468 – CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process Synonyms: CMP-KDO biosynthesis, CMP-KDO biosynthetic process, CMP-keto-3-deoxy-D-manno-octulosonic acid anabolism, CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthesis, CMP-keto-3-deoxy-D-manno-octulosonic acid formation, CMP-keto-3-deoxy-D-manno-octulosonic acid synthesis Definition: The chemical reactions and pathways resulting in the formation of CMP-keto-3-deoxy-D-manno-octulosonic acid, a substance composed of the acidic…

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Escherichia coli K-12 substr. MG1655 ackA-pta

BioCyc ID:TU0-8301 Local Context (not to scale — see Genome Browser for correct scale) Transcription Unit Notes: Click on a binding site (if any) to navigate to the page for its transcription factor. Click on a gene to navigate to its gene page. Key to regulator colors: Green: activator; Magenta:…

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Extensively drug resistant E. coli LZ00114

Introduction Escherichia coli is a common Gram-negative opportunistic pathogen that causes invasive host infections through virulence factors such as flagella, toxin secretion, and adhesins. According to the source of the infection, pathogenic E. coli can be classified as intestinal (diarrheagenic) and extraintestinal (ExPEC). Uropathogenic E. coli (UPEC) is the most…

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Escherichia coli K-12 substr. MG1655 purA

BioCyc ID:TU00094 Synonyms: OP00133 Local Context (not to scale — see Genome Browser for correct scale) Transcription Unit Notes: Click on a binding site (if any) to navigate to the page for its transcription factor. Click on a gene to navigate to its gene page. Key to regulator colors: Green:…

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Escherichia coli K-12 substr. MG1655 EC 7.2.2.8

BioCyc ID: RXN-14455 EC Number: 7.2.2.8 Transporters and Genes: Cu+ exporting P-type ATPase: copA Supersedes EC number: 3.6.3.54 Reaction Locations: inner membrane 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….

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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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Download mRNA fasta sequence for all proteins in the escherichia coli mg1655 genome

Download mRNA fasta sequence for all proteins in the escherichia coli mg1655 genome 2 Hi, I am looking for a way to download the fasta sequence of all protein coding mRNA in the escherichia coli genome. Does anyone know a simple way to do this. I would be most comfortable…

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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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