markmuir87/Lactobacillus_reuteri_MM41A_GEM

Genome-scale Insights into the Metabolic Versatility of Limosilactobacillus reuteri

Lactobacillus_reuteri_MM41A_GEM: The generic genome-scale metabolic model of Lactobacillus reuteri ATCC PTA 6475 & core/pan GEM

Description

GEM for Lactobacillus reuteri ATCC PTA 6475/MM4-1A Taxonomy ID: 548485

Citation

Genome-scale Insights into the Metabolic Versatility of Limosilactobacillus reuteri

Requirements

• Prokka
• Blast+ or
• Diamond
• Biopython
• cobrapy

Notice

Please add ./ComplementaryScripts/My_def to sys.path to ues functions
- import sys
- sys.path.extend(['./Projects/Project_Lreuteri/Lactobacillus_reuteri_MM41A_GEM/ComplementaryScripts/My_def'])

Structure

• ComplementaryData/
  

  • Initial data/
    

    • Sequences of L.reuteri ,
      • Lreuteri_refseq_v01, Genbank , FTP ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/ASSEMBLY_BACTERIA/Lactobacillus_reuteri/GCF_000159475/
      • Lreuteri_refseq_v02, Genbank , ACCESSION NZ_ACGX02000007,FTP ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/159/475/GCF_000159475.2_ASM15947v2/
      • Lreuteri_biogaia_v03, Biogaia company, raw genome Lreuteri_biogaia_v03_Complete_sequence.fas annotated by Prokka
    • Template models informations,

      • iNF517, Lactococcus lactisMG1363, BiGG

        • seq, GenBank, GCF_000009425.1
        • 2006,
        • Journal of Biological Chemistry
        • Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model

      • iBT721, Lactobacillus plantarumWCFS1, BioModels,

        • seq, GenBank, GCF_000203855.3
        • 2013,
        • Applied Microbiology and Biotechnology,
        • Genome-scale metabolic model for Lactococcus lactisMG1363 and its application to the analysis of flavor formation

      • iML1515, Escherichia coli str. K-12 substr. MG1655, , BiGG

        • seq, GenBank, NC_000913.3
        • 2017
        • Nature Biotechnology
        • iML1515, a knowledgebase that computes Escherichia coli traits

      • Potential template models, Streptococcus thermophilus LMG18311 iMP429 biomodels, Bacillus subtilis subsp. subtilis str. 168 iYO844 bigg,

  • Database/
    

    • BiGG
    • MetaNetX
    • COG

  • Step_01_Sequences_analysis/
    

    • process sequences
    • three versions of L.reuteri seqs, V3 from BioGaia
    • figs

  • Step_02_DraftModels/
    

    • pan/core seqs
      • .faa/.fna/.gbff
      • info Table_1: Genomes info
    • processed template models
      • map ids
    • other method draft(RAVEN/Carveme/SEED)
      • back up to compare

  • Step_03_Compare_Refine/
    

    • refine model
    • simulate

  • Step_04_SimulationStep_01/
    

    • seqs from different source
    • models

  • ComplementaryScripts/

    • Step_01_Sequences_analysis/
      
    • Step_02_DraftModels/
      
    • Step_03_Compare_Refine/
      
    • Step_04_SimulationStep_01/
      

  • ModelFiles/

    • model files .xml/.json/.mat/.yml/.txt
    • the MEMOTE report