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 : 2tpr3dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (97 of 106: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b3553 b1478 b1241 b4069 b4384 b2744 b3708 b2297 b2458 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b2361 b2291 b0261 b0411 b2799 b3945 b1602 b2913 b3915 b0755 b3612 b1539 b2492 b0904 b1533 b3821 b1380 b4141 b1798 b0606 b0221 b2285 b1008 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.427146 (mmol/gDw/h)
  Minimum Production Rate : 0.142396 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.569543
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.181321
  EX_pi_e : 1.123969
  EX_so4_e : 0.249953
  EX_k_e : 0.083376
  EX_fe3_e : 0.006862
  EX_mg2_e : 0.003705
  EX_cl_e : 0.002223
  EX_ca2_e : 0.002223
  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 : 52.962762
  EX_co2_e : 37.268115
  EX_h_e : 5.036568
  EX_ac_e : 0.391067
  EX_hxan_e : 0.142866
  Auxiliary production reaction : 0.142388
  DM_5drib_c : 0.000287
  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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