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 : quln_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (105 of 106: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 54
  Gene deletion: b2242 b3553 b1478 b0469 b4382 b1241 b0351 b3831 b4069 b4384 b3708 b3614 b0910 b3752 b2297 b2458 b2407 b0583 b1612 b1611 b4122 b1779 b3962 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b3665 b1415 b1014 b2799 b3945 b4138 b4123 b0621 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b3028 b3821 b1380 b4266 b3662 b2842 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.355257 (mmol/gDw/h)
  Minimum Production Rate : 0.589315 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.727545
  EX_o2_e : 284.244453
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.328169
  EX_pi_e : 0.342683
  EX_so4_e : 0.089461
  EX_k_e : 0.069344
  EX_mg2_e : 0.003082
  EX_ca2_e : 0.001849
  EX_cl_e : 0.001849
  EX_cu2_e : 0.000252
  EX_mn2_e : 0.000245
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994294
  EX_h2o_e : 550.459554
  EX_co2_e : 32.596782
  EX_ac_e : 1.172497
  EX_succ_e : 1.079859
  Auxiliary production reaction : 0.589315
  EX_ade_e : 0.354700
  EX_ura_e : 0.064303
  EX_dxylnt_e : 0.000238
  DM_5drib_c : 0.000080
  DM_4crsol_c : 0.000079

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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