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 : amp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b1478 b3399 b4382 b1241 b2502 b4384 b2744 b3708 b3008 b0871 b2925 b2097 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b2291 b0261 b0822 b0114 b2366 b2492 b0904 b1533 b3927 b3821 b1912   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.640071 (mmol/gDw/h)
  Minimum Production Rate : 0.146919 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.560720
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.648027
  EX_pi_e : 0.764336
  EX_so4_e : 0.161183
  EX_k_e : 0.124937
  EX_fe2_e : 0.010280
  EX_mg2_e : 0.005553
  EX_ca2_e : 0.003332
  EX_cl_e : 0.003332
  EX_cu2_e : 0.000454
  EX_mn2_e : 0.000442
  EX_zn2_e : 0.000218
  EX_ni2_e : 0.000207
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 47.164900
  EX_co2_e : 26.618907
  EX_h_e : 8.496277
  EX_pyr_e : 1.879018
  Auxiliary production reaction : 0.146919
  DM_oxam_c : 0.000716
  DM_5drib_c : 0.000429
  DM_4crsol_c : 0.000143

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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