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 : fum_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (6 of 7: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3553 b1478 b3942 b1732 b1241 b4069 b4384 b2297 b2458 b3844 b1004 b3713 b1109 b0046 b1779 b2463 b2210 b1033 b3551 b2799 b3945 b1602 b4219 b1832 b1778 b3915 b2492 b0904 b1380 b1710 b2480 b1206 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.478480 (mmol/gDw/h)
  Minimum Production Rate : 0.917482 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.028029
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.167539
  EX_pi_e : 0.461544
  EX_so4_e : 0.120491
  EX_k_e : 0.093396
  EX_fe3_e : 0.007685
  EX_mg2_e : 0.004151
  EX_ca2_e : 0.002490
  EX_cl_e : 0.002490
  EX_cu2_e : 0.000339
  EX_mn2_e : 0.000331
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.599999
  EX_co2_e : 36.133553
  EX_h_e : 6.517675
  Auxiliary production reaction : 0.917482
  EX_ac_e : 0.278564
  DM_5drib_c : 0.000108
  DM_4crsol_c : 0.000107

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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