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 : nadhx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b4382 b1241 b0351 b4384 b0871 b2926 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b2920 b1982 b1033 b2440 b0261 b0411 b2799 b3945 b1602 b2913 b1727 b0728 b0529 b2492 b0904 b3927 b1380 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.474227 (mmol/gDw/h)
  Minimum Production Rate : 0.095069 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.761906
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.789211
  EX_pi_e : 0.647579
  EX_so4_e : 0.119420
  EX_k_e : 0.092566
  EX_fe2_e : 0.007617
  EX_mg2_e : 0.004114
  EX_ca2_e : 0.002468
  EX_cl_e : 0.002468
  EX_cu2_e : 0.000336
  EX_mn2_e : 0.000328
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.869118
  EX_co2_e : 38.535022
  EX_h_e : 4.834850
  Auxiliary production reaction : 0.095069
  EX_hxan_e : 0.000531
  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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