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 (83 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b2836 b3553 b1478 b4382 b0238 b0125 b1241 b0351 b4384 b2744 b3708 b3008 b3752 b0871 b1004 b3713 b1109 b0046 b3236 b2883 b1779 b2920 b1982 b0477 b2797 b3117 b1814 b4471 b1033 b0261 b2799 b3945 b1602 b2913 b2406 b3915 b2868 b4064 b4464 b0728 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b1380 b3662 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.502438 (mmol/gDw/h)
  Minimum Production Rate : 0.041490 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.678011
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.678039
  EX_pi_e : 0.484655
  EX_so4_e : 0.168014
  EX_k_e : 0.098072
  EX_fe3_e : 0.008070
  EX_mg2_e : 0.004359
  EX_ca2_e : 0.002615
  EX_cl_e : 0.002615
  EX_cu2_e : 0.000356
  EX_mn2_e : 0.000347
  EX_zn2_e : 0.000171
  EX_ni2_e : 0.000162
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.601393
  EX_co2_e : 38.792437
  EX_h_e : 4.710461
  Auxiliary production reaction : 0.041490
  EX_ade_e : 0.000562
  DM_5drib_c : 0.000337
  DM_4crsol_c : 0.000112

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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