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 : datp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (95 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3553 b3399 b4069 b2744 b3926 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b4139 b1033 b1623 b3665 b0505 b1602 b2913 b4381 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b3029 b1380 b1695 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.471603 (mmol/gDw/h)
  Minimum Production Rate : 0.105250 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.634985
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.668885
  EX_pi_e : 0.770662
  EX_so4_e : 0.118759
  EX_k_e : 0.092054
  EX_fe3_e : 0.007574
  EX_mg2_e : 0.004091
  EX_ca2_e : 0.002455
  EX_cl_e : 0.002455
  EX_cu2_e : 0.000334
  EX_mn2_e : 0.000326
  EX_zn2_e : 0.000161
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.436450
  EX_co2_e : 38.546074
  EX_h_e : 4.980524
  EX_ac_e : 0.274561
  EX_12ppd__R_e : 0.144134
  Auxiliary production reaction : 0.105250
  EX_hxan_e : 0.012340
  DM_mththf_c : 0.000211
  DM_5drib_c : 0.000106
  DM_4crsol_c : 0.000105

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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