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 : camp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4069 b4384 b3708 b3752 b2297 b2458 b2779 b2407 b1982 b2797 b3117 b1814 b4471 b2440 b0261 b4381 b2406 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.477806 (mmol/gDw/h)
  Minimum Production Rate : 0.202397 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.292840
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.172788
  EX_pi_e : 0.663292
  EX_so4_e : 0.120321
  EX_k_e : 0.093264
  EX_fe2_e : 0.007674
  EX_mg2_e : 0.004145
  EX_cl_e : 0.002487
  EX_ca2_e : 0.002487
  EX_cu2_e : 0.000339
  EX_mn2_e : 0.000330
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000154
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.055574
  EX_co2_e : 37.805799
  EX_h_e : 5.479105
  EX_ac_e : 0.278172
  Auxiliary production reaction : 0.202397
  DM_oxam_c : 0.000535
  DM_5drib_c : 0.000321
  DM_4crsol_c : 0.000107

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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