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 : coa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 56
  Gene deletion: b3553 b1478 b4382 b3942 b1732 b1241 b0351 b4069 b3708 b3115 b1849 b2296 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b2797 b3117 b1814 b4471 b1033 b3551 b0261 b0411 b2799 b3945 b1602 b4219 b1832 b1778 b4381 b2406 b3915 b3654 b3714 b3664 b4064 b4464 b1539 b2492 b0904 b1533 b2835 b1380 b1710 b2480 b0723 b0494 b4141 b1798 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.425806 (mmol/gDw/h)
  Minimum Production Rate : 0.004094 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.010888
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.153095
  EX_pi_e : 0.423013
  EX_so4_e : 0.111320
  EX_k_e : 0.083114
  EX_fe3_e : 0.006841
  EX_mg2_e : 0.003694
  EX_ca2_e : 0.002216
  EX_cl_e : 0.002216
  EX_cu2_e : 0.000302
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000138
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.032737
  EX_co2_e : 36.031037
  EX_h_e : 8.081581
  EX_ac_e : 1.624209
  EX_xan_e : 0.631445
  Auxiliary production reaction : 0.004093
  DM_5drib_c : 0.000096
  DM_4crsol_c : 0.000095

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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