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 : q8_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 : 52
  Gene deletion: b2242 b3553 b1478 b3846 b2341 b0474 b2518 b1241 b0351 b3831 b3708 b3752 b2926 b2781 b3617 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b3908 b1656 b1759 b1033 b4161 b4014 b2976 b2799 b3945 b1602 b4138 b4123 b0621 b4381 b3915 b0529 b1539 b3028 b1380 b3918 b1301 b4042 b2660 b1206 b2285 b1008 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.481903 (mmol/gDw/h)
  Minimum Production Rate : 0.001304 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.363971
  EX_o2_e : 287.101350
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.399832
  EX_pi_e : 0.464847
  EX_so4_e : 0.121354
  EX_k_e : 0.094064
  EX_mg2_e : 0.004181
  EX_ca2_e : 0.002508
  EX_cl_e : 0.002508
  EX_cu2_e : 0.000342
  EX_mn2_e : 0.000333
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992258
  EX_h2o_e : 551.483778
  EX_co2_e : 37.755446
  EX_succ_e : 0.502525
  EX_ura_e : 0.097659
  Auxiliary production reaction : 0.001304
  DM_5drib_c : 0.000108
  DM_4crsol_c : 0.000107

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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