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 : imp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b3942 b1732 b0474 b2518 b1241 b0351 b4069 b2502 b2744 b3708 b2297 b2458 b2779 b3617 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0114 b1539 b2492 b0904 b1533 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.396869 (mmol/gDw/h)
  Minimum Production Rate : 0.592776 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.393604
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.658807
  EX_pi_e : 0.975598
  EX_so4_e : 0.099940
  EX_k_e : 0.077466
  EX_fe2_e : 0.006374
  EX_mg2_e : 0.003443
  EX_ca2_e : 0.002066
  EX_cl_e : 0.002066
  EX_cu2_e : 0.000281
  EX_mn2_e : 0.000274
  EX_zn2_e : 0.000135
  EX_ni2_e : 0.000128

Product: (mmol/gDw/h)
  EX_h2o_e : 51.760209
  EX_co2_e : 34.756357
  EX_h_e : 7.528707
  EX_ac_e : 1.507913
  Auxiliary production reaction : 0.592776
  DM_oxam_c : 0.001549
  DM_mththf_c : 0.001283
  DM_5drib_c : 0.000266
  DM_4crsol_c : 0.000089

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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