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 : 5pg35pg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (83 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 56
  Gene deletion: b4467 b1478 b1241 b0351 b4069 b4384 b2744 b3708 b2297 b2458 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b0477 b4139 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b0411 b2799 b3945 b1602 b0507 b0153 b2975 b3603 b0584 b2366 b0755 b3612 b2492 b0904 b1300 b2954 b1533 b3825 b3029 b1380 b2660 b4141 b1798 b3662 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.492169 (mmol/gDw/h)
  Minimum Production Rate : 0.058342 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.355022
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.901010
  EX_pi_e : 0.591434
  EX_so4_e : 0.123938
  EX_k_e : 0.096068
  EX_mg2_e : 0.004270
  EX_fe2_e : 0.004062
  EX_fe3_e : 0.003843
  EX_ca2_e : 0.002562
  EX_cl_e : 0.002562
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.513376
  EX_co2_e : 38.054960
  EX_h_e : 5.339906
  EX_ac_e : 0.286534
  Auxiliary production reaction : 0.058342
  EX_hxan_e : 0.000551
  DM_5drib_c : 0.000330
  DM_4crsol_c : 0.000110

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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