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 (26 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b4069 b4384 b3752 b2297 b2458 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b0261 b2799 b3945 b1602 b0153 b2913 b4381 b0590 b2406 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b3662 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.396720 (mmol/gDw/h)
  Minimum Production Rate : 0.898574 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.419945
  EX_o2_e : 284.167693
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.982039
  EX_pi_e : 0.382678
  EX_so4_e : 0.099902
  EX_k_e : 0.077437
  EX_mg2_e : 0.003442
  EX_ca2_e : 0.002065
  EX_cl_e : 0.002065
  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_fe3_e : 999.993628
  EX_h2o_e : 550.883401
  EX_co2_e : 34.465622
  Auxiliary production reaction : 0.898574
  EX_etoh_e : 0.349324
  EX_ac_e : 0.230965
  EX_hxan_e : 0.000444
  DM_5drib_c : 0.000266
  DM_4crsol_c : 0.000088

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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