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 : nadh_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4382 b4069 b4384 b3708 b3008 b3752 b0871 b2297 b2458 b2925 b2097 b2926 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b0595 b0261 b3945 b0507 b2406 b0112 b0452 b2975 b0114 b3603 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b3662 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.340885 (mmol/gDw/h)
  Minimum Production Rate : 0.144062 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.769189
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.690338
  EX_pi_e : 0.616943
  EX_so4_e : 0.085842
  EX_k_e : 0.066538
  EX_fe3_e : 0.005475
  EX_mg2_e : 0.002957
  EX_ca2_e : 0.001774
  EX_cl_e : 0.001774
  EX_cu2_e : 0.000242
  EX_mn2_e : 0.000236
  EX_zn2_e : 0.000116
  EX_ni2_e : 0.000110

Product: (mmol/gDw/h)
  EX_h2o_e : 44.507873
  EX_co2_e : 27.647932
  EX_h_e : 9.036050
  EX_pyr_e : 4.978861
  EX_ac_e : 0.198458
  Auxiliary production reaction : 0.144062
  DM_oxam_c : 0.000381
  DM_5drib_c : 0.000229
  DM_4crsol_c : 0.000076

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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