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 : fum_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (7 of 8: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b3942 b1732 b3831 b4069 b4384 b3926 b2297 b2458 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b2463 b2498 b2210 b3551 b1602 b4138 b4123 b0621 b4219 b1832 b1778 b3915 b0114 b0529 b2492 b0904 b1380 b1710 b2480 b1771 b1517 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.468480 (mmol/gDw/h)
  Minimum Production Rate : 0.245184 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.756468
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.444242
  EX_pi_e : 0.451898
  EX_so4_e : 0.117973
  EX_k_e : 0.091444
  EX_fe3_e : 0.007524
  EX_mg2_e : 0.004064
  EX_cl_e : 0.002438
  EX_ca2_e : 0.002438
  EX_cu2_e : 0.000332
  EX_mn2_e : 0.000324
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.793998
  EX_co2_e : 36.474386
  EX_h_e : 6.459914
  EX_ura_e : 0.692350
  EX_ac_e : 0.272742
  EX_fum_e : 0.245184
  DM_mththf_c : 0.000210
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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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