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 : mmcoa__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 57
  Gene deletion: b2836 b3553 b1478 b3399 b1241 b4069 b2744 b3708 b3115 b1849 b2296 b2926 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b2937 b3908 b1656 b0937 b4139 b2797 b3117 b1814 b4471 b1033 b1623 b3665 b4374 b2361 b2291 b4015 b0411 b2799 b3945 b1602 b2913 b3654 b3714 b3664 b1539 b2492 b0904 b2954 b1533 b1380 b4141 b1798 b3662 b1517 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.473216 (mmol/gDw/h)
  Minimum Production Rate : 0.074465 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.966024
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.631950
  EX_pi_e : 0.679862
  EX_so4_e : 0.193630
  EX_k_e : 0.092368
  EX_mg2_e : 0.004105
  EX_fe2_e : 0.003905
  EX_fe3_e : 0.003695
  EX_ca2_e : 0.002463
  EX_cl_e : 0.002463
  EX_cu2_e : 0.000336
  EX_mn2_e : 0.000327
  EX_zn2_e : 0.000161
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.072283
  EX_co2_e : 38.014033
  EX_h_e : 4.999619
  EX_ac_e : 0.349965
  Auxiliary production reaction : 0.074465
  DM_mththf_c : 0.000212
  DM_5drib_c : 0.000106
  DM_4crsol_c : 0.000106

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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