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 : succoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (21 of 28: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b3553 b1478 b4382 b1241 b4069 b4384 b3708 b3752 b2297 b2458 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b0411 b2799 b3945 b1602 b2913 b2406 b3915 b0509 b3125 b1539 b2492 b0904 b1533 b3821 b1380 b1695 b4141 b1798 b0606 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.396927 (mmol/gDw/h)
  Minimum Production Rate : 0.220529 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.412800
  EX_o2_e : 285.134210
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.832227
  EX_pi_e : 1.044453
  EX_so4_e : 0.320480
  EX_k_e : 0.077477
  EX_mg2_e : 0.003443
  EX_ca2_e : 0.002066
  EX_cl_e : 0.002066
  EX_cu2_e : 0.000281
  EX_mn2_e : 0.000274
  EX_zn2_e : 0.000135
  EX_ni2_e : 0.000128

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993623
  EX_h2o_e : 551.205670
  EX_co2_e : 36.092097
  EX_ac_e : 1.049825
  Auxiliary production reaction : 0.220525
  EX_hxan_e : 0.000444
  DM_5drib_c : 0.000266
  DM_4crsol_c : 0.000089

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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