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 : dnad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b4467 b3399 b3942 b1732 b4069 b4384 b2744 b2297 b2458 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1779 b0937 b1982 b1623 b3551 b0261 b0411 b2799 b3945 b1602 b4219 b1832 b1778 b4381 b1727 b0114 b0529 b2492 b0904 b2954 b3927 b1380 b1710 b2480 b3662 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.392531 (mmol/gDw/h)
  Minimum Production Rate : 0.355346 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.627629
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.373575
  EX_pi_e : 1.089330
  EX_so4_e : 0.098847
  EX_k_e : 0.076619
  EX_fe2_e : 0.006304
  EX_mg2_e : 0.003405
  EX_cl_e : 0.002043
  EX_ca2_e : 0.002043
  EX_cu2_e : 0.000278
  EX_mn2_e : 0.000271
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 51.875224
  EX_co2_e : 34.920837
  EX_h_e : 5.258839
  EX_etoh_e : 0.522587
  Auxiliary production reaction : 0.355346
  EX_ac_e : 0.228526
  EX_ade_e : 0.000439
  DM_5drib_c : 0.000263
  DM_4crsol_c : 0.000088

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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