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 : nadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b3553 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b2744 b0871 b0160 b1004 b3713 b1109 b0046 b3124 b3236 b1638 b1779 b1982 b4139 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b4381 b2406 b2789 b3127 b3915 b0529 b2492 b0904 b2954 b3029 b1380 b1301 b2660 b0514 b1695 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.483449 (mmol/gDw/h)
  Minimum Production Rate : 0.096785 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.346724
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.964657
  EX_pi_e : 0.756694
  EX_so4_e : 0.121742
  EX_k_e : 0.094366
  EX_fe3_e : 0.007765
  EX_mg2_e : 0.004194
  EX_cl_e : 0.002516
  EX_ca2_e : 0.002516
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.080976
  EX_co2_e : 38.057128
  EX_h_e : 4.902980
  Auxiliary production reaction : 0.096785
  EX_ade_e : 0.013191
  DM_5drib_c : 0.000324
  DM_4crsol_c : 0.000108

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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