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 : ade_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (113 of 133: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3708 b0512 b2297 b2458 b2797 b3117 b1814 b4471 b3616 b3589 b1623 b3665 b0675 b2361 b0261 b4381 b0511 b0114 b1539 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.658953 (mmol/gDw/h)
  Minimum Production Rate : 0.969414 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.081668
  EX_nh4_e : 12.032671
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.635630
  EX_so4_e : 0.165937
  EX_k_e : 0.128623
  EX_fe2_e : 0.010583
  EX_mg2_e : 0.005716
  EX_cl_e : 0.003430
  EX_ca2_e : 0.003430
  EX_cu2_e : 0.000467
  EX_mn2_e : 0.000455
  EX_zn2_e : 0.000225
  EX_ni2_e : 0.000213
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 50.263063
  EX_co2_e : 23.012626
  EX_h_e : 13.474314
  EX_ac_e : 2.503556
  EX_ade_e : 0.969414
  EX_xan_e : 0.017242
  DM_5drib_c : 0.000148
  DM_4crsol_c : 0.000147

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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