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 : apg120_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (24 of 34: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YPO3371 YPO1384 YPO4078 YPO3825 YPO3937 YPO0918 YPO3949 YPO3428 YPO0348 YPO0253 YPO3202 YPO0465 YPO1964 YPO1109 YPO0670 YPO2303 YPO3914 YPO0440 YPO3376 YPO1851 YPO3418 YPO2370 YPO0442 YPO2567 YPO1171   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.123979 (mmol/gDw/h)
  Minimum Production Rate : 0.086496 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_h_e : 9.654437
  EX_cit_e : 7.400000
  EX_o2_e : 4.076470
  EX_gly_e : 2.200000
  EX_cys__L_e : 1.000000
  EX_glc__D_e : 0.401559
  EX_pi_e : 0.324854
  EX_fe2_e : 0.033840
  EX_lys__L_e : 0.030995
  EX_phe__L_e : 0.023556
  EX_met__L_e : 0.017357
  EX_tyr__L_e : 0.016117

Product: (mmol/gDw/h)
  EX_co2_e : 14.883991
  EX_succ_e : 6.975299
  EX_h2o_e : 6.374657
  EX_nh4_e : 1.665506
  EX_h2s_e : 0.990942
  EX_ac_e : 0.410000
  EX_g3pg_e : 0.136854
  EX_glyald_e : 0.087149
  Auxiliary production reaction : 0.086496
  EX_pheme_e : 0.033840

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.

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Last updated: 27-Sep-2023
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