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 : ppcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (111 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b4467 b1478 b2066 b1241 b4069 b4384 b2744 b3708 b0910 b2297 b2458 b2926 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b0411 b2799 b3945 b1602 b2239 b3453 b2975 b3603 b2366 b2492 b0904 b1533 b2835 b1380 b2660 b4141 b1798 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.404151 (mmol/gDw/h)
  Minimum Production Rate : 0.204938 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.418312
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.801167
  EX_pi_e : 1.004660
  EX_so4_e : 0.306711
  EX_k_e : 0.078887
  EX_fe2_e : 0.006491
  EX_mg2_e : 0.003506
  EX_ca2_e : 0.002104
  EX_cl_e : 0.002104
  EX_cu2_e : 0.000287
  EX_mn2_e : 0.000279
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 51.362474
  EX_co2_e : 36.587144
  EX_h_e : 5.281448
  EX_ac_e : 0.951328
  Auxiliary production reaction : 0.204938
  EX_hxan_e : 0.000452
  DM_5drib_c : 0.000271
  DM_4crsol_c : 0.000090

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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