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 : q8_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1054 b1478 b1241 b0351 b3708 b2779 b3617 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b3908 b1656 b2920 b4015 b2799 b3945 b1602 b2342 b3845 b2913 b3915 b0728 b0529 b1380 b2965 b0693 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.540216 (mmol/gDw/h)
  Minimum Production Rate : 0.002555 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.963471
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.834291
  EX_pi_e : 0.521096
  EX_so4_e : 0.136037
  EX_k_e : 0.105446
  EX_fe3_e : 0.008676
  EX_mg2_e : 0.004686
  EX_cl_e : 0.002812
  EX_ca2_e : 0.002812
  EX_cu2_e : 0.000383
  EX_mn2_e : 0.000373
  EX_zn2_e : 0.000184
  EX_ni2_e : 0.000174
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 50.299498
  EX_co2_e : 34.313706
  EX_h_e : 6.666249
  EX_fum_e : 0.846924
  Auxiliary production reaction : 0.002555
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000120

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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