MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iPC815 [2].
Target metabolite : apg141_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (28 of 34: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: YPO3371 YPO1384 YPO4078 YPO3825 YPO3937 YPO2157 YPO3949 YPO3428 YPO0348 YPO0253 YPO3992 YPO0347 YPO3319 YPO1207 YPO3202 YPO3516 YPO0670 YPO2303 YPO3914 YPO3868 YPO3270 YPO0440 YPO3376 YPO1851 YPO3418 YPO2567 YPO1171   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.096500 (mmol/gDw/h)
  Minimum Production Rate : 0.081447 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_h_e : 9.230333
  EX_cit_e : 7.400000
  EX_o2_e : 4.508966
  EX_gly_e : 2.200000
  EX_cys__L_e : 1.000000
  EX_glc__D_e : 0.227215
  EX_pi_e : 0.160452
  EX_lys__L_e : 0.024125
  EX_phe__L_e : 0.018335
  EX_met__L_e : 0.013510
  EX_tyr__L_e : 0.012545

Product: (mmol/gDw/h)
  EX_co2_e : 14.899998
  EX_succ_e : 7.400000
  EX_h2o_e : 5.717071
  EX_nh4_e : 2.110989
  EX_h2s_e : 0.992950
  EX_ac_e : 0.410000
  EX_glyald_e : 0.081955
  Auxiliary production reaction : 0.081447

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 27-Sep-2023
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