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 : dhnpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b4384 b2297 b2458 b2779 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b2937 b4139 b1623 b3665 b4015 b2799 b3945 b1602 b2342 b3845 b2913 b2406 b3915 b3654 b3714 b3664 b0529 b2492 b0904 b2954 b3029 b1380 b3662 b1985 b1517 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.355525 (mmol/gDw/h)
  Minimum Production Rate : 0.799532 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 39.035494
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.837298
  EX_pi_e : 0.342941
  EX_so4_e : 0.089528
  EX_k_e : 0.069396
  EX_fe3_e : 0.005710
  EX_mg2_e : 0.003084
  EX_ca2_e : 0.001851
  EX_cl_e : 0.001851
  EX_cu2_e : 0.000252
  EX_mn2_e : 0.000246
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 55.177682
  EX_co2_e : 37.796790
  EX_h_e : 7.477055
  Auxiliary production reaction : 0.799532
  EX_ac_e : 0.206982
  EX_mththf_e : 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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