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__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b4467 b1478 b3399 b3942 b1732 b3846 b1241 b0351 b2744 b0871 b1004 b3713 b1109 b0046 b3236 b1779 b2920 b1623 b3665 b3551 b4015 b0411 b2799 b3945 b1602 b4219 b1832 b1778 b4381 b3915 b3654 b3714 b3664 b0728 b0529 b2492 b0904 b3927 b1380 b1710 b2480 b1695 b1511 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.480602 (mmol/gDw/h)
  Minimum Production Rate : 0.034974 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.566484
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.485557
  EX_pi_e : 0.533534
  EX_so4_e : 0.121026
  EX_k_e : 0.093810
  EX_fe3_e : 0.007721
  EX_mg2_e : 0.004169
  EX_ca2_e : 0.002502
  EX_cl_e : 0.002502
  EX_cu2_e : 0.000341
  EX_mn2_e : 0.000332
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.940294
  EX_co2_e : 39.475163
  EX_h_e : 4.648838
  Auxiliary production reaction : 0.034971
  EX_hxan_e : 0.012575
  EX_mththf_e : 0.000215
  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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