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 (116 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 58
  Gene deletion: b4467 b1478 b3399 b1241 b4069 b2744 b3708 b2297 b2458 b2926 b0160 b1238 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b4139 b2797 b3117 b1814 b4471 b0675 b2361 b4014 b0261 b2976 b2799 b3945 b1602 b2913 b4381 b2406 b3915 b3453 b2975 b3603 b0509 b3125 b1539 b2492 b0904 b1300 b2954 b1533 b2835 b3029 b1380 b2240 b0508 b1600 b4141 b1798 b0221 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.483253 (mmol/gDw/h)
  Minimum Production Rate : 0.009464 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.230064
  EX_o2_e : 287.645011
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.287951
  EX_pi_e : 0.683454
  EX_so4_e : 0.131145
  EX_k_e : 0.094328
  EX_mg2_e : 0.004192
  EX_ca2_e : 0.002515
  EX_cl_e : 0.002515
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992237
  EX_h2o_e : 551.737553
  EX_co2_e : 38.785634
  EX_ac_e : 0.290795
  EX_glyc3p_e : 0.188953
  Auxiliary production reaction : 0.009451
  EX_ade_e : 0.000541
  DM_5drib_c : 0.000324
  DM_4crsol_c : 0.000108

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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