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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b3708 b2297 b2458 b2779 b0030 b2407 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b0937 b2797 b3117 b1814 b4471 b3665 b0261 b2799 b3945 b1602 b3709 b2913 b4381 b2406 b3161 b0112 b3654 b3714 b3664 b1539 b2492 b0904 b1533 b3821 b1380 b1473 b4141 b1798 b3662 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.356250 (mmol/gDw/h)
  Minimum Production Rate : 0.271372 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.704513
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.747072
  EX_pi_e : 1.157756
  EX_so4_e : 0.361082
  EX_k_e : 0.069538
  EX_fe2_e : 0.005722
  EX_mg2_e : 0.003090
  EX_cl_e : 0.001854
  EX_ca2_e : 0.001854
  EX_cu2_e : 0.000253
  EX_mn2_e : 0.000246
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 52.470742
  EX_co2_e : 35.736130
  EX_h_e : 4.566258
  EX_ac_e : 0.478775
  Auxiliary production reaction : 0.271372
  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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