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 : didp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b1478 b4382 b0238 b0125 b1241 b4069 b4384 b3752 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b1982 b0477 b4139 b4015 b0411 b1602 b2913 b3915 b2868 b4064 b4464 b0529 b1539 b2492 b0904 b2954 b3029 b1380 b1771 b1511 b0221 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.465261 (mmol/gDw/h)
  Minimum Production Rate : 0.161244 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.399491
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.671321
  EX_pi_e : 0.771281
  EX_so4_e : 0.117162
  EX_k_e : 0.090816
  EX_fe3_e : 0.007473
  EX_mg2_e : 0.004036
  EX_ca2_e : 0.002422
  EX_cl_e : 0.002422
  EX_cu2_e : 0.000330
  EX_mn2_e : 0.000321
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.291544
  EX_co2_e : 38.239821
  EX_h_e : 5.038642
  EX_ac_e : 0.270868
  EX_12ppd__S_e : 0.168856
  Auxiliary production reaction : 0.161244
  EX_ade_e : 0.000313
  DM_mththf_c : 0.000208
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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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