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 : forcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (17 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b2407 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b3449 b1033 b0261 b0507 b2406 b0112 b0114 b1539 b2492 b0904 b1533 b0494 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.510947 (mmol/gDw/h)
  Minimum Production Rate : 0.509649 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.037720
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.086300
  EX_pi_e : 2.021810
  EX_so4_e : 0.638316
  EX_k_e : 0.099733
  EX_fe2_e : 0.008206
  EX_mg2_e : 0.004432
  EX_ca2_e : 0.002659
  EX_cl_e : 0.002659
  EX_cu2_e : 0.000362
  EX_mn2_e : 0.000353
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.068826
  EX_co2_e : 21.382001
  EX_h_e : 9.440579
  EX_ac_e : 3.215361
  Auxiliary production reaction : 0.509649
  DM_oxam_c : 0.000572
  DM_5drib_c : 0.000343
  EX_glyclt_e : 0.000342
  DM_4crsol_c : 0.000114

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.

Last updated: 21-Sep-2023
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