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 : nad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 58
  Gene deletion: b4467 b3399 b3942 b1732 b4069 b2502 b4384 b2744 b3708 b3008 b3752 b0871 b2297 b2458 b2779 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b0583 b2883 b2690 b1982 b2797 b3117 b1814 b4471 b2210 b4374 b2361 b2291 b0261 b0411 b3945 b0507 b0452 b2868 b4064 b4464 b2975 b0114 b3603 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b1380 b3662 b1813 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.331296 (mmol/gDw/h)
  Minimum Production Rate : 0.140009 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.985583
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.559893
  EX_pi_e : 0.599589
  EX_so4_e : 0.083427
  EX_k_e : 0.064667
  EX_fe3_e : 0.005321
  EX_mg2_e : 0.002874
  EX_ca2_e : 0.001724
  EX_cl_e : 0.001724
  EX_cu2_e : 0.000235
  EX_mn2_e : 0.000229
  EX_zn2_e : 0.000113
  EX_ni2_e : 0.000107

Product: (mmol/gDw/h)
  EX_h2o_e : 44.522940
  EX_co2_e : 27.712978
  EX_h_e : 8.924266
  EX_pyr_e : 5.120094
  EX_ac_e : 0.192876
  Auxiliary production reaction : 0.140009
  EX_ade_e : 0.000371
  DM_5drib_c : 0.000222
  DM_4crsol_c : 0.000074

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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