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 : ser__D_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 62
  Gene deletion: b4467 b1478 b4382 b4269 b0493 b3846 b3588 b2341 b3003 b3011 b1241 b4384 b3708 b3008 b0871 b2925 b2097 b2926 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b0207 b3012 b1982 b4139 b2797 b3117 b1814 b4471 b3946 b0825 b1623 b1493 b3517 b0261 b2799 b1602 b0507 b2406 b3915 b2975 b3603 b2366 b2492 b0904 b2954 b1781 b3001 b1298 b1533 b3029 b1380 b0325 b2660 b1771 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.447439 (mmol/gDw/h)
  Minimum Production Rate : 0.016840 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 40.633780
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.851572
  EX_pi_e : 0.431602
  EX_so4_e : 0.112675
  EX_k_e : 0.087337
  EX_fe3_e : 0.007188
  EX_mg2_e : 0.003882
  EX_ca2_e : 0.002329
  EX_cl_e : 0.002329
  EX_cu2_e : 0.000317
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.414693
  EX_co2_e : 41.580888
  EX_h_e : 4.137705
  Auxiliary production reaction : 0.016765
  EX_ade_e : 0.000501
  DM_5drib_c : 0.000300
  DM_4crsol_c : 0.000100

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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