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 : accoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b2836 b3553 b1478 b4382 b1241 b4069 b4384 b3708 b2297 b2458 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b2799 b3945 b1602 b3709 b2406 b3161 b0112 b0509 b3125 b1539 b2492 b0904 b1533 b1380 b1473 b1600 b2660 b4141 b1798 b3662 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.363467 (mmol/gDw/h)
  Minimum Production Rate : 0.303786 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.472359
  EX_o2_e : 284.474007
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.053949
  EX_pi_e : 1.261960
  EX_so4_e : 0.395314
  EX_k_e : 0.070946
  EX_mg2_e : 0.003153
  EX_cl_e : 0.001892
  EX_ca2_e : 0.001892
  EX_cu2_e : 0.000258
  EX_mn2_e : 0.000251
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994162
  EX_h2o_e : 551.228990
  EX_co2_e : 35.553963
  EX_ac_e : 1.268730
  Auxiliary production reaction : 0.303786
  EX_ade_e : 0.000407
  DM_5drib_c : 0.000244
  DM_4crsol_c : 0.000081

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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