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 : pg141_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (94 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b2836 b2242 b4382 b0474 b2518 b3831 b4384 b1278 b3752 b2781 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1759 b4161 b1415 b4014 b2976 b2342 b3845 b4138 b4123 b0621 b2406 b2492 b0904 b2197 b3028 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.466665 (mmol/gDw/h)
  Minimum Production Rate : 0.246467 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.315931
  EX_o2_e : 275.979779
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.701810
  EX_pi_e : 0.696614
  EX_so4_e : 0.117516
  EX_k_e : 0.091090
  EX_mg2_e : 0.004048
  EX_ca2_e : 0.002429
  EX_cl_e : 0.002429
  EX_cu2_e : 0.000331
  EX_mn2_e : 0.000322
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992505
  EX_h2o_e : 544.642162
  EX_co2_e : 29.195407
  EX_succ_e : 0.486634
  EX_ura_e : 0.330934
  Auxiliary production reaction : 0.246467
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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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