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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b4069 b4384 b2744 b3708 b3008 b3115 b1849 b2296 b2779 b0030 b1238 b2883 b1982 b2797 b3117 b1814 b4471 b0261 b3709 b4381 b2406 b3161 b0112 b2789 b3127 b2868 b4064 b4464 b2975 b0114 b3603 b0755 b3612 b1539 b2492 b0904 b0591 b2578 b1533 b3927 b3821 b1473 b3447 b0514 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.621149 (mmol/gDw/h)
  Minimum Production Rate : 0.197338 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.321874
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.093190
  EX_pi_e : 1.191177
  EX_so4_e : 0.353755
  EX_k_e : 0.121244
  EX_fe2_e : 0.009976
  EX_mg2_e : 0.005388
  EX_ca2_e : 0.003233
  EX_cl_e : 0.003233
  EX_cu2_e : 0.000440
  EX_mn2_e : 0.000429
  EX_zn2_e : 0.000212
  EX_ni2_e : 0.000201
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 49.199675
  EX_co2_e : 28.645818
  EX_h_e : 7.059148
  EX_ac_e : 0.558962
  Auxiliary production reaction : 0.197338
  EX_ade_e : 0.000695
  DM_5drib_c : 0.000417
  DM_4crsol_c : 0.000139

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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