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 : dump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4382 b4069 b4384 b3708 b3008 b3752 b2297 b2458 b2779 b2925 b2097 b2407 b3844 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0596 b3665 b0261 b0507 b3709 b0153 b2406 b3161 b0112 b0452 b2975 b0114 b3603 b0584 b0886 b2366 b0529 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 : 0.579080 (mmol/gDw/h)
  Minimum Production Rate : 0.735610 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.880775
  EX_o2_e : 275.987363
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.728475
  EX_pi_e : 1.294194
  EX_so4_e : 0.145824
  EX_k_e : 0.113032
  EX_mg2_e : 0.005024
  EX_ca2_e : 0.003014
  EX_cl_e : 0.003014
  EX_cu2_e : 0.000411
  EX_mn2_e : 0.000400
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990699
  EX_h2o_e : 546.442601
  EX_co2_e : 25.999599
  EX_glyc__R_e : 0.977514
  Auxiliary production reaction : 0.735610
  EX_ac_e : 0.337132
  EX_ade_e : 0.000648
  DM_5drib_c : 0.000389
  DM_4crsol_c : 0.000129

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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