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 : malcoame_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (88 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b4467 b4382 b3942 b1732 b4069 b4384 b3708 b3752 b2297 b2458 b2779 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b3551 b0261 b3945 b1602 b0153 b4219 b1832 b1778 b2406 b1727 b0114 b0584 b2366 b2492 b0904 b1533 b3927 b3821 b1380 b1710 b2480 b3662 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.470559 (mmol/gDw/h)
  Minimum Production Rate : 0.066443 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.764363
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.814972
  EX_pi_e : 0.653232
  EX_so4_e : 0.184939
  EX_k_e : 0.091850
  EX_fe2_e : 0.007558
  EX_mg2_e : 0.004082
  EX_ca2_e : 0.002449
  EX_cl_e : 0.002449
  EX_cu2_e : 0.000334
  EX_mn2_e : 0.000325
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.058629
  EX_co2_e : 37.634450
  EX_h_e : 5.255788
  EX_ac_e : 0.340395
  EX_3hpp_e : 0.124504
  EX_hxan_e : 0.066969
  Auxiliary production reaction : 0.066443
  DM_5drib_c : 0.000316
  DM_4crsol_c : 0.000105

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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