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 : 12ppd__S_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (27 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4467 b1241 b0351 b2297 b2458 b2779 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b1302 b2662 b4015 b3945 b1602 b2342 b3845 b1727 b1539 b1380 b2660 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.541610 (mmol/gDw/h)
  Minimum Production Rate : 0.194449 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.502044
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.849344
  EX_pi_e : 0.522440
  EX_so4_e : 0.136388
  EX_k_e : 0.105719
  EX_fe2_e : 0.008699
  EX_mg2_e : 0.004698
  EX_ca2_e : 0.002819
  EX_cl_e : 0.002819
  EX_cu2_e : 0.000384
  EX_mn2_e : 0.000374
  EX_zn2_e : 0.000185
  EX_ni2_e : 0.000175
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 47.960278
  EX_co2_e : 34.753337
  EX_h_e : 5.291848
  EX_etoh_e : 0.901037
  EX_ac_e : 0.315318
  EX_12ppd__S_e : 0.194449
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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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