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 : nadh_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b4069 b4384 b2744 b3708 b3008 b3752 b2297 b2458 b2407 b3844 b2920 b1982 b2688 b2797 b3117 b1814 b4471 b1033 b2440 b0596 b4374 b2361 b2291 b0261 b0507 b3709 b2406 b3161 b0112 b0452 b0114 b0728 b1539 b2492 b0904 b2578 b1533 b3927 b1473 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.659497 (mmol/gDw/h)
  Minimum Production Rate : 0.394729 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.450795
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.886404
  EX_pi_e : 1.425612
  EX_so4_e : 0.166075
  EX_k_e : 0.128729
  EX_fe2_e : 0.010592
  EX_mg2_e : 0.005721
  EX_ca2_e : 0.003433
  EX_cl_e : 0.003433
  EX_cu2_e : 0.000468
  EX_mn2_e : 0.000456
  EX_zn2_e : 0.000225
  EX_ni2_e : 0.000213
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 49.181963
  EX_co2_e : 23.870420
  EX_h_e : 8.418791
  Auxiliary production reaction : 0.394729
  EX_ac_e : 0.383950
  DM_oxam_c : 0.000738
  DM_5drib_c : 0.000443
  DM_4crsol_c : 0.000147
  EX_etha_e : 0.000053

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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