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 : gtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b1478 b3399 b4382 b1241 b4069 b2502 b4384 b2744 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b4117 b3908 b1656 b1982 b4139 b1033 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b3915 b0509 b3125 b0529 b2492 b0904 b2954 b2938 b1380 b2660 b1695 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445579 (mmol/gDw/h)
  Minimum Production Rate : 0.376033 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.604974
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.694874
  EX_pi_e : 1.557908
  EX_so4_e : 0.112206
  EX_k_e : 0.086974
  EX_fe3_e : 0.007156
  EX_mg2_e : 0.003865
  EX_ca2_e : 0.002319
  EX_cl_e : 0.002319
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 54.460772
  EX_co2_e : 37.428391
  EX_h_e : 5.491316
  Auxiliary production reaction : 0.376033
  EX_ac_e : 0.259410
  EX_ade_e : 0.000499
  DM_5drib_c : 0.000299
  DM_4crsol_c : 0.000099

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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