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 (46 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b2925 b2097 b3617 b0030 b1238 b2883 b1982 b1033 b1623 b0261 b0411 b2913 b4381 b0112 b0114 b0509 b3125 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.442369 (mmol/gDw/h)
  Minimum Production Rate : 0.847789 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.836557
  EX_nh4_e : 10.712567
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.970079
  EX_so4_e : 0.111397
  EX_k_e : 0.086347
  EX_fe2_e : 0.007105
  EX_mg2_e : 0.003838
  EX_ca2_e : 0.002303
  EX_cl_e : 0.002303
  EX_cu2_e : 0.000314
  EX_mn2_e : 0.000306
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.298834
  EX_co2_e : 19.660318
  EX_h_e : 10.493057
  EX_ac_e : 2.188161
  Auxiliary production reaction : 0.847789
  DM_oxam_c : 0.000495
  DM_5drib_c : 0.000297
  EX_glyclt_e : 0.000296
  DM_4crsol_c : 0.000099

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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