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 : ahcys_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 57
  Gene deletion: b4467 b1478 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b3708 b3008 b0871 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b0937 b2797 b3117 b1814 b4471 b3449 b2210 b3665 b0411 b2799 b1602 b0507 b2406 b3654 b3714 b3664 b2366 b2492 b0904 b1781 b3001 b1533 b1380 b0325 b2413 b2660 b1771 b4141 b1798 b1517 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.465488 (mmol/gDw/h)
  Minimum Production Rate : 0.146142 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.315337
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.903978
  EX_pi_e : 0.449013
  EX_so4_e : 0.263344
  EX_k_e : 0.090860
  EX_fe2_e : 0.007478
  EX_mg2_e : 0.004038
  EX_ca2_e : 0.002423
  EX_cl_e : 0.002423
  EX_cu2_e : 0.000330
  EX_mn2_e : 0.000322
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.369476
  EX_co2_e : 38.031481
  EX_h_e : 5.269903
  EX_glyclt_e : 0.408314
  Auxiliary production reaction : 0.146124
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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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