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 : dgdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b4467 b1478 b3399 b4382 b1241 b0351 b4069 b2502 b4384 b2744 b3708 b2297 b2458 b2779 b3617 b0030 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b0207 b3012 b1982 b4139 b2797 b3117 b1814 b4471 b1623 b2361 b2291 b4015 b0261 b2799 b1602 b2406 b3915 b0452 b1539 b2492 b0904 b2954 b1781 b3001 b1380 b0325 b2660 b0515 b1771 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.473492 (mmol/gDw/h)
  Minimum Production Rate : 0.097807 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.059283
  EX_o2_e : 286.439736
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.605330
  EX_pi_e : 0.652335
  EX_so4_e : 0.119236
  EX_k_e : 0.092422
  EX_mg2_e : 0.004108
  EX_ca2_e : 0.002465
  EX_cl_e : 0.002465
  EX_cu2_e : 0.000336
  EX_mn2_e : 0.000327
  EX_zn2_e : 0.000161
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992393
  EX_h2o_e : 550.982889
  EX_co2_e : 37.206360
  EX_ac_e : 1.188622
  Auxiliary production reaction : 0.097801
  EX_ade_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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