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 : uri_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b1054 b2242 b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b3831 b3614 b0910 b3926 b0871 b2779 b2781 b0030 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b0651 b2162 b1759 b1033 b0261 b2799 b3945 b1602 b4138 b4123 b0621 b2913 b2223 b4381 b3915 b0529 b2492 b0904 b3029 b3028 b1380 b3918 b1206 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445935 (mmol/gDw/h)
  Minimum Production Rate : 0.319819 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.223505
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.617129
  EX_pi_e : 0.430152
  EX_so4_e : 0.112296
  EX_k_e : 0.087043
  EX_fe3_e : 0.007164
  EX_mg2_e : 0.003868
  EX_ca2_e : 0.002321
  EX_cl_e : 0.002321
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.945102
  EX_co2_e : 36.301983
  EX_h_e : 6.002263
  EX_succ_e : 0.548301
  EX_uri_e : 0.319817
  EX_ura_e : 0.080716
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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