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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (6 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b0871 b2297 b2458 b2925 b2097 b3617 b2407 b3236 b2690 b2797 b3117 b1814 b4471 b2210 b3945 b4381 b2406 b2868 b0114 b1539 b2492 b0904 b1533 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.459471 (mmol/gDw/h)
  Minimum Production Rate : 0.921147 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.559503
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.110787
  EX_pi_e : 0.443208
  EX_so4_e : 0.115704
  EX_k_e : 0.089685
  EX_fe2_e : 0.007380
  EX_mg2_e : 0.003986
  EX_ca2_e : 0.002392
  EX_cl_e : 0.002392
  EX_cu2_e : 0.000326
  EX_mn2_e : 0.000317
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 43.119000
  EX_co2_e : 28.688565
  EX_h_e : 7.576580
  Auxiliary production reaction : 1.148543
  EX_ac_e : 1.057695
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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