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 : ckdo_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b4467 b2242 b0474 b2518 b1241 b0351 b3831 b4069 b3752 b2297 b2458 b2781 b3617 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b1779 b1759 b4161 b1415 b2799 b3945 b1602 b4138 b4123 b0621 b2913 b4381 b2406 b3915 b0452 b1727 b0529 b2492 b0904 b3927 b3029 b3028 b1380 b3918 b1912 b1517 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.390807 (mmol/gDw/h)
  Minimum Production Rate : 0.206404 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.670295
  EX_o2_e : 283.927437
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.839896
  EX_pi_e : 0.583378
  EX_so4_e : 0.098414
  EX_k_e : 0.076283
  EX_mg2_e : 0.003390
  EX_ca2_e : 0.002034
  EX_cl_e : 0.002034
  EX_cu2_e : 0.000277
  EX_mn2_e : 0.000270
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993722
  EX_h2o_e : 546.934994
  EX_co2_e : 35.481632
  EX_etoh_e : 1.335204
  EX_succ_e : 0.407531
  EX_ac_e : 0.227523
  Auxiliary production reaction : 0.206403
  EX_3hpp_e : 0.070737
  EX_mththf_e : 0.000175
  DM_5drib_c : 0.000088
  DM_4crsol_c : 0.000087

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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