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 : duri_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 50: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b1478 b2066 b1241 b4069 b3708 b0910 b3115 b1849 b2296 b2926 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b2797 b3117 b1814 b4471 b2498 b4015 b2799 b3945 b1602 b0153 b2913 b4381 b0590 b1539 b2492 b0904 b1380 b1517 b0606 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.466631 (mmol/gDw/h)
  Minimum Production Rate : 0.084462 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.988399
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.461808
  EX_pi_e : 0.450115
  EX_so4_e : 0.117507
  EX_k_e : 0.091083
  EX_fe2_e : 0.007495
  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_h2o_e : 52.765569
  EX_co2_e : 37.116419
  EX_h_e : 6.411167
  EX_ac_e : 0.701343
  EX_hxan_e : 0.313327
  Auxiliary production reaction : 0.084462
  DM_mththf_c : 0.000209
  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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