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 : hemeO_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (95 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 58
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b4384 b3708 b3115 b1849 b2296 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b0120 b0937 b1982 b2797 b3117 b1814 b4471 b3449 b4014 b0261 b2976 b2799 b3945 b1602 b0507 b3709 b2913 b2406 b3161 b0112 b2975 b3603 b2366 b2492 b0904 b1533 b3029 b1380 b1473 b0494 b4141 b1798 b3662 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.252630 (mmol/gDw/h)
  Minimum Production Rate : 0.191897 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.404465
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.032282
  EX_pi_e : 0.243689
  EX_fe2_e : 0.193982
  EX_so4_e : 0.063617
  EX_k_e : 0.049312
  EX_mg2_e : 0.002192
  EX_fe3_e : 0.001973
  EX_ca2_e : 0.001315
  EX_cl_e : 0.001315
  EX_cu2_e : 0.000179
  EX_mn2_e : 0.000175
  EX_zn2_e : 0.000086
  EX_ni2_e : 0.000082

Product: (mmol/gDw/h)
  EX_h2o_e : 48.954862
  EX_co2_e : 31.967266
  EX_h_e : 7.604995
  EX_fum_e : 1.031595
  EX_hxan_e : 0.384077
  DM_5drib_c : 0.383964
  Auxiliary production reaction : 0.191897
  EX_ac_e : 0.147078
  DM_4crsol_c : 0.000056

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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