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 : adn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4467 b4382 b3942 b1732 b1241 b0351 b4384 b0871 b2779 b2925 b2097 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b3551 b2799 b3945 b1602 b2342 b3845 b4219 b1832 b1778 b3915 b1727 b0529 b2492 b0904 b3927 b1380 b1710 b2480 b1511 b3662 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.459541 (mmol/gDw/h)
  Minimum Production Rate : 0.040205 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 39.852206
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.165508
  EX_pi_e : 0.443276
  EX_so4_e : 0.115722
  EX_k_e : 0.089699
  EX_fe3_e : 0.007383
  EX_mg2_e : 0.003987
  EX_ca2_e : 0.002392
  EX_cl_e : 0.002392
  EX_cu2_e : 0.000326
  EX_mn2_e : 0.000318
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.310183
  EX_co2_e : 40.733469
  EX_h_e : 4.432333
  EX_adn_e : 0.040192
  EX_ade_e : 0.000309
  EX_mththf_e : 0.000206
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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