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 : mmcoa__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b4467 b1478 b1241 b0351 b4069 b2744 b3708 b3115 b1849 b2296 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b0937 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b4015 b0411 b2799 b3945 b1602 b2913 b4381 b3654 b3714 b3664 b4064 b4464 b1539 b2492 b0904 b1533 b3821 b1380 b4141 b1798 b1517 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.427333 (mmol/gDw/h)
  Minimum Production Rate : 0.007522 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.141779
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.667816
  EX_pi_e : 0.434775
  EX_so4_e : 0.115133
  EX_k_e : 0.083412
  EX_fe2_e : 0.006863
  EX_mg2_e : 0.003707
  EX_ca2_e : 0.002224
  EX_cl_e : 0.002224
  EX_cu2_e : 0.000303
  EX_mn2_e : 0.000295
  EX_zn2_e : 0.000146
  EX_ni2_e : 0.000138
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.185797
  EX_co2_e : 37.743147
  EX_h_e : 6.220487
  EX_ac_e : 1.635229
  EX_glyclt_e : 0.628662
  Auxiliary production reaction : 0.007522
  DM_mththf_c : 0.000191
  DM_5drib_c : 0.000096
  DM_4crsol_c : 0.000095

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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