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 : dmpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4382 b4384 b3708 b3008 b3752 b0512 b0871 b2925 b2097 b2407 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b3945 b0114 b1539 b2492 b0904 b1533 b3927 b3821 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.643942 (mmol/gDw/h)
  Minimum Production Rate : 0.444572 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.360372
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.956248
  EX_pi_e : 1.510294
  EX_so4_e : 0.162157
  EX_k_e : 0.125693
  EX_fe2_e : 0.010342
  EX_mg2_e : 0.005586
  EX_ca2_e : 0.003352
  EX_cl_e : 0.003352
  EX_cu2_e : 0.000457
  EX_mn2_e : 0.000445
  EX_zn2_e : 0.000220
  EX_ni2_e : 0.000208
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 47.063439
  EX_co2_e : 28.078257
  EX_h_e : 6.562241
  EX_pyr_e : 1.088288
  Auxiliary production reaction : 0.444572
  EX_alltn_e : 0.000433
  DM_mththf_c : 0.000288
  DM_5drib_c : 0.000145
  DM_4crsol_c : 0.000144

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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