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 : ppgpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b4382 b3942 b1732 b1241 b0351 b4069 b4384 b1479 b3115 b1849 b2296 b2926 b0030 b2407 b3844 b3236 b2463 b3962 b0104 b3616 b3589 b2210 b4267 b3665 b1415 b3551 b1014 b2799 b3945 b2913 b4219 b1832 b1778 b2406 b0112 b0114 b0529 b2492 b0904 b1380 b1710 b2480 b0508 b4266 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.354828 (mmol/gDw/h)
  Minimum Production Rate : 0.524706 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.102583
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.234588
  EX_pi_e : 2.441093
  EX_so4_e : 0.089353
  EX_k_e : 0.069260
  EX_fe3_e : 0.005699
  EX_mg2_e : 0.003078
  EX_ca2_e : 0.001847
  EX_cl_e : 0.001847
  EX_cu2_e : 0.000252
  EX_mn2_e : 0.000245
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 54.693167
  EX_co2_e : 35.897508
  EX_h_e : 7.374523
  EX_ac_e : 1.755222
  Auxiliary production reaction : 0.524706
  EX_ade_e : 0.155789
  EX_dxylnt_e : 0.000237
  EX_mththf_e : 0.000159
  DM_5drib_c : 0.000080
  DM_4crsol_c : 0.000079

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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