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 (32 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b4384 b2744 b3752 b2297 b2458 b3617 b3124 b2883 b1982 b1033 b1623 b0261 b0411 b4381 b2406 b0112 b2789 b3127 b0114 b0529 b2492 b0904 b0514 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.461739 (mmol/gDw/h)
  Minimum Production Rate : 0.872829 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.786714
  EX_nh4_e : 11.109139
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.191053
  EX_so4_e : 0.116275
  EX_k_e : 0.090128
  EX_fe2_e : 0.007416
  EX_mg2_e : 0.004006
  EX_cl_e : 0.002403
  EX_ca2_e : 0.002403
  EX_cu2_e : 0.000327
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 48.373240
  EX_co2_e : 19.571053
  EX_h_e : 10.192511
  EX_ac_e : 1.560221
  Auxiliary production reaction : 0.872829
  DM_oxam_c : 0.012599
  DM_5drib_c : 0.000310
  EX_glyclt_e : 0.000309
  DM_4crsol_c : 0.000103

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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