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 : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3708 b3115 b1849 b2296 b3617 b0160 b0583 b0121 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b4014 b0261 b2976 b0507 b3709 b3161 b0112 b2975 b0114 b3603 b1539 b2492 b0904 b1533 b3821 b1473 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.300652 (mmol/gDw/h)
  Minimum Production Rate : 0.054611 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.645325
  EX_nh4_e : 11.235112
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.143950
  EX_so4_e : 0.130321
  EX_k_e : 0.058685
  EX_fe2_e : 0.004829
  EX_mg2_e : 0.002608
  EX_cl_e : 0.001565
  EX_ca2_e : 0.001565
  EX_cu2_e : 0.000213
  EX_mn2_e : 0.000208
  EX_zn2_e : 0.000103
  EX_ni2_e : 0.000097

Product: (mmol/gDw/h)
  EX_h2o_e : 50.286746
  EX_co2_e : 18.383405
  EX_h_e : 11.388967
  EX_ac_e : 2.546574
  EX_fad_e : 0.845054
  Auxiliary production reaction : 0.054611
  DM_oxam_c : 0.000336
  DM_5drib_c : 0.000202
  DM_4crsol_c : 0.000067

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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