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 : dcyt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b0030 b2407 b1238 b3236 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b2210 b0675 b0822 b4381 b2406 b1727 b0114 b1539 b2492 b0904 b1533 b4042 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.312554 (mmol/gDw/h)
  Minimum Production Rate : 0.753734 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.977269
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.636964
  EX_pi_e : 0.301491
  EX_so4_e : 0.078707
  EX_k_e : 0.061008
  EX_fe2_e : 0.005020
  EX_mg2_e : 0.002711
  EX_ca2_e : 0.001627
  EX_cl_e : 0.001627
  EX_cu2_e : 0.000222
  EX_mn2_e : 0.000216
  EX_zn2_e : 0.000107
  EX_ni2_e : 0.000101

Product: (mmol/gDw/h)
  EX_h2o_e : 44.719683
  EX_co2_e : 27.128721
  EX_h_e : 9.194217
  EX_pyr_e : 4.060728
  Auxiliary production reaction : 0.753734
  EX_acald_e : 0.537740
  DM_oxam_c : 0.000210
  DM_mththf_c : 0.000140
  DM_5drib_c : 0.000070
  DM_4crsol_c : 0.000070

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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