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 : bmoco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (137 of 137: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 68
  Gene deletion: b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3708 b3008 b1479 b0871 b2297 b2458 b2926 b0030 b2407 b3236 b2463 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b2210 b4267 b3665 b4374 b2361 b2291 b3551 b1014 b3945 b2913 b4219 b1832 b1778 b0112 b2975 b0114 b3603 b0509 b3125 b2366 b0306 b3605 b2492 b0904 b0591 b1533 b3927 b3821 b1380 b0325 b1710 b2480 b4266 b3662 b2842 b1517 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.389165 (mmol/gDw/h)
  Minimum Production Rate : 0.032978 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.427136
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.003245
  EX_so4_e : 0.534267
  EX_pi_e : 0.474315
  EX_k_e : 0.075962
  EX_mobd_e : 0.032978
  EX_mg2_e : 0.003376
  EX_fe2_e : 0.003213
  EX_fe3_e : 0.003039
  EX_ca2_e : 0.002026
  EX_cl_e : 0.002026
  EX_cu2_e : 0.000276
  EX_mn2_e : 0.000269
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 50.430797
  EX_co2_e : 37.082774
  EX_h_e : 4.385238
  EX_acald_e : 1.204739
  EX_fum_e : 0.505266
  EX_met__L_e : 0.304367
  Auxiliary production reaction : 0.032975
  EX_ade_e : 0.000262
  EX_mththf_e : 0.000174
  DM_5drib_c : 0.000088
  DM_4crsol_c : 0.000087

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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