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 : dcamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3942 b1732 b4384 b2744 b3708 b3008 b1479 b3752 b2930 b4232 b3697 b3925 b0871 b2926 b2407 b3236 b2690 b2463 b1982 b2797 b3117 b1814 b4471 b2210 b4374 b2361 b2291 b0411 b3945 b2868 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b3821 b3447 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.609935 (mmol/gDw/h)
  Minimum Production Rate : 0.140365 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.886200
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.291120
  EX_pi_e : 0.728712
  EX_so4_e : 0.153594
  EX_k_e : 0.119055
  EX_fe2_e : 0.009796
  EX_mg2_e : 0.005291
  EX_ca2_e : 0.003175
  EX_cl_e : 0.003175
  EX_cu2_e : 0.000432
  EX_mn2_e : 0.000421
  EX_zn2_e : 0.000208
  EX_ni2_e : 0.000197
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.831602
  EX_co2_e : 26.635322
  EX_h_e : 8.709307
  EX_pyr_e : 2.120377
  Auxiliary production reaction : 0.140365
  EX_ade_e : 0.000410
  DM_mththf_c : 0.000273
  DM_5drib_c : 0.000137
  DM_4crsol_c : 0.000136

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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