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 : ametam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b4467 b2836 b4382 b1241 b0351 b4069 b4384 b3708 b3008 b3752 b3115 b1849 b2296 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b2797 b3117 b1814 b4471 b0261 b0335 b2799 b3945 b1602 b2406 b1727 b0728 b1539 b2492 b0904 b1533 b3927 b1380 b2660 b3662 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.449017 (mmol/gDw/h)
  Minimum Production Rate : 0.112228 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.266938
  EX_o2_e : 285.184204
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.524721
  EX_pi_e : 0.433124
  EX_so4_e : 0.225299
  EX_k_e : 0.087645
  EX_mg2_e : 0.003895
  EX_ca2_e : 0.002337
  EX_cl_e : 0.002337
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000310
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992788
  EX_h2o_e : 549.572461
  EX_co2_e : 37.252840
  EX_etoh_e : 0.997550
  EX_ac_e : 0.373639
  Auxiliary production reaction : 0.112228
  EX_hxan_e : 0.000502
  DM_5drib_c : 0.000301
  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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