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 : dump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 64
  Gene deletion: b4467 b1478 b3399 b4382 b4269 b0493 b3846 b3588 b3003 b3011 b1241 b4384 b2744 b3708 b3008 b0871 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b4139 b2797 b3117 b1814 b4471 b3449 b1623 b3665 b2799 b3945 b1602 b0507 b0153 b2913 b2239 b2406 b3654 b3714 b3664 b2975 b3603 b1297 b0886 b1539 b2492 b0904 b2954 b3035 b2578 b1533 b3927 b3029 b1380 b1511 b4141 b1798 b3662 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.513419 (mmol/gDw/h)
  Minimum Production Rate : 0.024301 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.634298
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.593484
  EX_pi_e : 0.519548
  EX_so4_e : 0.129289
  EX_k_e : 0.100216
  EX_mg2_e : 0.004454
  EX_fe2_e : 0.004237
  EX_fe3_e : 0.004009
  EX_ca2_e : 0.002672
  EX_cl_e : 0.002672
  EX_cu2_e : 0.000364
  EX_mn2_e : 0.000355
  EX_zn2_e : 0.000175
  EX_ni2_e : 0.000166
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.432727
  EX_co2_e : 38.706646
  EX_h_e : 4.770110
  Auxiliary production reaction : 0.024301
  EX_mththf_e : 0.000230
  DM_5drib_c : 0.000116
  DM_4crsol_c : 0.000114

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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