MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : h2mb4p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b1478 b4382 b0474 b2518 b1241 b4069 b4384 b2744 b4152 b2297 b2458 b2779 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b2690 b0477 b1033 b4374 b4161 b0675 b3945 b1602 b4138 b4123 b0621 b2913 b0114 b0529 b2492 b0904 b1380 b1695 b1206 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.358180 (mmol/gDw/h)
  Minimum Production Rate : 0.189171 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.354885
  EX_o2_e : 281.643805
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.868309
  EX_pi_e : 0.723844
  EX_so4_e : 0.090197
  EX_k_e : 0.069914
  EX_mg2_e : 0.003107
  EX_ca2_e : 0.001864
  EX_cl_e : 0.001864
  EX_cu2_e : 0.000254
  EX_mn2_e : 0.000248
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994247
  EX_h2o_e : 542.714113
  EX_co2_e : 32.635867
  EX_ac_e : 4.536420
  EX_succ_e : 0.373507
  EX_3hpp_e : 0.254002
  Auxiliary production reaction : 0.189171
  EX_12ppd__S_e : 0.129259
  DM_5drib_c : 0.000081
  DM_4crsol_c : 0.000080

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

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: 21-Sep-2023
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