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 : urdglyc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b4467 b1478 b0238 b0125 b1241 b3831 b4069 b2744 b2297 b2458 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b0937 b0477 b4139 b2498 b2361 b2291 b4014 b0261 b2976 b3945 b1602 b2913 b3654 b3714 b3664 b0511 b4064 b4464 b2975 b3603 b0509 b3125 b0529 b2492 b0904 b2954 b1380 b0508 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.469404 (mmol/gDw/h)
  Minimum Production Rate : 0.130417 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.670025
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.330357
  EX_pi_e : 0.452790
  EX_so4_e : 0.118205
  EX_k_e : 0.091624
  EX_mg2_e : 0.004072
  EX_fe2_e : 0.003874
  EX_fe3_e : 0.003665
  EX_ca2_e : 0.002443
  EX_cl_e : 0.002443
  EX_cu2_e : 0.000333
  EX_mn2_e : 0.000324
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.196902
  EX_co2_e : 38.007696
  EX_h_e : 4.981268
  EX_12ppd__S_e : 0.595873
  EX_ac_e : 0.273280
  Auxiliary production reaction : 0.130417
  DM_5drib_c : 0.000106
  DM_4crsol_c : 0.000105

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.

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Last updated: 21-Sep-2023
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