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 (103 of 106: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b1241 b0351 b3831 b4152 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b2690 b1033 b1602 b4138 b4123 b0621 b1727 b1539 b1380 b2660 b1206 b0606 b2285 b1008 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.465207 (mmol/gDw/h)
  Minimum Production Rate : 0.329901 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.758092
  EX_o2_e : 278.797652
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.354095
  EX_pi_e : 0.448741
  EX_so4_e : 0.117148
  EX_k_e : 0.090805
  EX_mg2_e : 0.004036
  EX_cl_e : 0.002421
  EX_ca2_e : 0.002421
  EX_cu2_e : 0.000330
  EX_mn2_e : 0.000321
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992528
  EX_h2o_e : 543.800482
  EX_co2_e : 30.955063
  EX_12ppd__R_e : 1.900190
  EX_succ_e : 0.485114
  Auxiliary production reaction : 0.329901
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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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