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 : ppcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (113 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 54
  Gene deletion: b2836 b3553 b1478 b3399 b1241 b4069 b2502 b2744 b3708 b3115 b1849 b2296 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b0121 b3908 b1656 b1982 b4139 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b2291 b4014 b0261 b2976 b2799 b3945 b1602 b0507 b2913 b3915 b1539 b2492 b0904 b2954 b1533 b1380 b1301 b4141 b1798 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.473673 (mmol/gDw/h)
  Minimum Production Rate : 0.073465 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.970867
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.632001
  EX_pi_e : 0.677302
  EX_so4_e : 0.192746
  EX_k_e : 0.092458
  EX_fe3_e : 0.007610
  EX_mg2_e : 0.004109
  EX_ca2_e : 0.002465
  EX_cl_e : 0.002465
  EX_cu2_e : 0.000336
  EX_mn2_e : 0.000327
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.071231
  EX_co2_e : 38.092576
  EX_h_e : 4.931652
  EX_ac_e : 0.349232
  Auxiliary production reaction : 0.073465
  EX_hxan_e : 0.000530
  DM_5drib_c : 0.000318
  DM_4crsol_c : 0.000106

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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