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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b1478 b4382 b3942 b1732 b1241 b4069 b4384 b2297 b2458 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b2463 b0937 b1982 b2210 b3551 b2799 b3945 b1602 b4219 b1832 b1778 b0529 b2492 b0904 b1380 b1710 b2480 b3662 b1518 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.353889 (mmol/gDw/h)
  Minimum Production Rate : 1.112343 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.055054
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.047844
  EX_pi_e : 3.678393
  EX_so4_e : 0.089116
  EX_k_e : 0.069077
  EX_fe2_e : 0.005684
  EX_mg2_e : 0.003070
  EX_cl_e : 0.001842
  EX_ca2_e : 0.001842
  EX_cu2_e : 0.000251
  EX_mn2_e : 0.000245
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_h2o_e : 52.425520
  EX_co2_e : 32.327812
  EX_h_e : 4.819667
  Auxiliary production reaction : 1.112343
  EX_ac_e : 0.827789
  EX_fum_e : 0.369509
  EX_ade_e : 0.000238
  DM_mththf_c : 0.000159
  DM_5drib_c : 0.000080
  DM_4crsol_c : 0.000079

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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