Gapfilled Metabolic Model of Strain Pseudomonas sp. GM17
Jia Wang
Generated April 3, 2023

Formation and interaction network of a constructed microbial community in a nutrient-rich environment

This narrative was used to generate metabolic model of strain Pseudomonas sp. GM17 gapfilled by R2A medium environment. The metabolic model of strain GM17 (GM17_ReSeq_MetabolicModel_R2A004Gapfilled) was further used for dynamic flux balance analysis (dFBA) simulation by Computation of Microbial Ecosystems in Time and Space (COMETS) tool.

Import Media file (TSV/Excel) from Staging Area
Import a Media file (in TSV or Excel format) from your staging area into your Narrative
This app completed without errors in 1m 13s.
Summary
Import Finished Media Object Name: R2A_edition_004 Imported File: R2A_edition_004.xlsx
Annotate Genome/Assembly with RASTtk - v1.073
Annotate or re-annotate genome/assembly using RASTtk (Rapid Annotations using Subsystems Technology toolkit).
This app completed without errors in 9m 27s.
Objects
Created Object Name Type Description
GM17_ReSeq_Annotation_01 Genome RAST re-annotated genome
Report
Summary
The RAST algorithm was applied to annotating a genome sequence comprised of 1 contigs containing 6866808 nucleotides. No initial gene calls were provided. Standard features were called using: glimmer3; prodigal. A scan was conducted for the following additional feature types: rRNA; tRNA; selenoproteins; pyrrolysoproteins; repeat regions; crispr. The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity. In addition to the remaining original 0 coding features and 0 non-coding features, 6355 new features were called, of which 157 are non-coding. Output genome has the following feature types: Coding gene 6198 Non-coding repeat 74 Non-coding rna 83 The number of distinct functions can exceed the number of genes because some genes have multiple functions.
Links
Build Metabolic Model
Construct a draft metabolic model based on an annotated genome.
This app completed without errors in 5m 56s.
Objects
Created Object Name Type Description
GM17_ReSeq_MetabolicModel_R2A004Gapfilled FBAModel FBAModel-14 GM17_ReSeq_MetabolicModel_R2A004Gapfilled
GM17_ReSeq_MetabolicModel_R2A004Gapfilled.gf.1 FBA FBA-13 GM17_ReSeq_MetabolicModel_R2A004Gapfilled.gf.1
Report
Summary
RefGlucoseMinimal media.
Output from Build Metabolic Model
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/117918
Run Flux Balance Analysis
Predict metabolite fluxes in a metabolic model of an organism grown on a given media using flux balance analysis (FBA).
This app completed without errors in 1m 12s.
Objects
Created Object Name Type Description
GM17_ReSeq_FBA_R2A004Gapfilled_Carbon60 FBA FBA-13 GM17_ReSeq_FBA_R2A004Gapfilled_Carbon60
Report
Summary
A flux balance analysis (FBA) was performed on the metabolic model 117918/7/1 growing in 117918/3/1 media.
Output from Run Flux Balance Analysis
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/117918

Apps

  1. Annotate Genome/Assembly with RASTtk - v1.073
    • [1] Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics. 2008;9: 75. doi:10.1186/1471-2164-9-75
    • [2] Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42: D206 D214. doi:10.1093/nar/gkt1226
    • [3] Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, et al. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015;5. doi:10.1038/srep08365
    • [4] Kent WJ. BLAT The BLAST-Like Alignment Tool. Genome Res. 2002;12: 656 664. doi:10.1101/gr.229202
    • [5] Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25: 3389-3402. doi:10.1093/nar/25.17.3389
    • [6] Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25: 955 964.
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    • [9] van Belkum A, Sluijuter M, de Groot R, Verbrugh H, Hermans PW. Novel BOX repeat PCR assay for high-resolution typing of Streptococcus pneumoniae strains. J Clin Microbiol. 1996;34: 1176 1179.
    • [10] Croucher NJ, Vernikos GS, Parkhill J, Bentley SD. Identification, variation and transcription of pneumococcal repeat sequences. BMC Genomics. 2011;12: 120. doi:10.1186/1471-2164-12-120
    • [11] Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11: 119. doi:10.1186/1471-2105-11-119
    • [12] Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23: 673 679. doi:10.1093/bioinformatics/btm009
    • [13] Akhter S, Aziz RK, Edwards RA. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res. 2012;40: e126. doi:10.1093/nar/gks406
  2. Build Metabolic Model
    • [1] Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol. 2010;28: 977 982. doi:10.1038/nbt.1672
    • [2] Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42: D206 D214. doi:10.1093/nar/gkt1226
    • [3] Latendresse M. Efficiently gap-filling reaction networks. BMC Bioinformatics. 2014;15: 225. doi:10.1186/1471-2105-15-225
    • [4] Dreyfuss JM, Zucker JD, Hood HM, Ocasio LR, Sachs MS, Galagan JE. Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM. PLOS Computational Biology. 2013;9: e1003126. doi:10.1371/journal.pcbi.1003126
    • [5] Mahadevan R, Schilling CH. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng. 2003;5: 264 276.
  3. Import Media file (TSV/Excel) from Staging Area
    no citations
  4. Run Flux Balance Analysis
    • Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol. 2010;28: 977 982. doi:10.1038/nbt.1672
    • Orth JD, Thiele I, Palsson B . What is flux balance analysis? Nature Biotechnology. 2010;28: 245 248. doi:10.1038/nbt.1614