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 : 2ombzl_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b0238 b0125 b4069 b2744 b3708 b0871 b2297 b2458 b2925 b2097 b1612 b1611 b2883 b4122 b0477 b2797 b3117 b1814 b4471 b3449 b3946 b0825 b4374 b2361 b2291 b2868 b4064 b4464 b0114 b2366 b0755 b3612 b2492 b0904 b1533 b3927 b0494 b3662 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.605833 (mmol/gDw/h)
  Minimum Production Rate : 0.059284 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.115179
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.841404
  EX_pi_e : 0.584390
  EX_so4_e : 0.152561
  EX_k_e : 0.118254
  EX_fe2_e : 0.009730
  EX_mg2_e : 0.005256
  EX_cl_e : 0.003153
  EX_ca2_e : 0.003153
  EX_cu2_e : 0.000430
  EX_mn2_e : 0.000419
  EX_zn2_e : 0.000207
  EX_ni2_e : 0.000196
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.406100
  EX_co2_e : 27.315326
  EX_h_e : 8.061155
  EX_fum_e : 0.751142
  EX_ac_e : 0.352707
  EX_pyr_e : 0.341068
  EX_ade_e : 0.059692
  Auxiliary production reaction : 0.059284
  DM_5drib_c : 0.000136
  DM_4crsol_c : 0.000135

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.

Last updated: 21-Sep-2023
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