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 : ametam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b3553 b3399 b4382 b2066 b1241 b0351 b4384 b2744 b3708 b3008 b0910 b3752 b0871 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b2920 b1982 b2797 b3117 b1814 b4471 b1033 b2440 b1623 b0261 b2799 b3945 b1602 b2406 b3915 b1727 b0728 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b1380 b2660 b0606 b0221 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.505806 (mmol/gDw/h)
  Minimum Production Rate : 0.011333 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.889789
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.570970
  EX_pi_e : 0.487904
  EX_so4_e : 0.138705
  EX_k_e : 0.098730
  EX_fe3_e : 0.008124
  EX_mg2_e : 0.004388
  EX_ca2_e : 0.002633
  EX_cl_e : 0.002633
  EX_cu2_e : 0.000359
  EX_mn2_e : 0.000350
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.505578
  EX_co2_e : 39.000273
  EX_h_e : 4.680602
  EX_etha_e : 0.038044
  Auxiliary production reaction : 0.011333
  EX_hxan_e : 0.000566
  DM_5drib_c : 0.000339
  DM_4crsol_c : 0.000113

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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