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 : pe120_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (97 of 104: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b2242 b3831 b2744 b1278 b3614 b0910 b3752 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b4374 b2361 b2291 b1415 b0411 b1701 b1805 b4138 b4123 b0621 b2492 b0904 b2197 b3028 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.491365 (mmol/gDw/h)
  Minimum Production Rate : 0.259512 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.738156
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.263115
  EX_pi_e : 0.733486
  EX_so4_e : 0.123736
  EX_k_e : 0.095911
  EX_fe2_e : 0.007892
  EX_mg2_e : 0.004263
  EX_ca2_e : 0.002558
  EX_cl_e : 0.002558
  EX_cu2_e : 0.000348
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 44.871276
  EX_co2_e : 28.862500
  EX_h_e : 5.977031
  EX_succ_e : 0.512392
  EX_ura_e : 0.348451
  Auxiliary production reaction : 0.259512
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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