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 : nadphx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b3399 b3846 b4069 b2502 b2744 b3115 b1849 b2296 b2779 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b1982 b4139 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b4381 b2406 b3915 b2868 b1727 b0114 b0529 b2492 b0904 b2954 b1380 b2660 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.473865 (mmol/gDw/h)
  Minimum Production Rate : 0.038429 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.485335
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.954925
  EX_pi_e : 0.572381
  EX_so4_e : 0.119329
  EX_k_e : 0.092495
  EX_fe3_e : 0.007611
  EX_mg2_e : 0.004111
  EX_ca2_e : 0.002466
  EX_cl_e : 0.002466
  EX_cu2_e : 0.000336
  EX_mn2_e : 0.000327
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.029512
  EX_co2_e : 38.118399
  EX_h_e : 5.397914
  EX_gly_e : 0.503570
  EX_ac_e : 0.275878
  Auxiliary production reaction : 0.038429
  EX_ade_e : 0.012929
  DM_5drib_c : 0.000318
  DM_4crsol_c : 0.000106

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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