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 : dadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (94 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3553 b1478 b0238 b0125 b1241 b4069 b0512 b3115 b1849 b2296 b2926 b1004 b3713 b1109 b0046 b3124 b3236 b1638 b3908 b1656 b0477 b4139 b1033 b0261 b1602 b4381 b3915 b3654 b3714 b3664 b4064 b4464 b0529 b2492 b0904 b2954 b1380 b2660 b0514 b1771 b0221 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.476161 (mmol/gDw/h)
  Minimum Production Rate : 0.199797 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.540788
  EX_o2_e : 287.284907
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.141489
  EX_pi_e : 0.858903
  EX_so4_e : 0.119907
  EX_k_e : 0.092943
  EX_mg2_e : 0.004131
  EX_ca2_e : 0.002478
  EX_cl_e : 0.002478
  EX_cu2_e : 0.000338
  EX_mn2_e : 0.000329
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000154
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992352
  EX_h2o_e : 553.071008
  EX_co2_e : 37.903362
  EX_ac_e : 0.277214
  Auxiliary production reaction : 0.199797
  DM_5drib_c : 0.000107
  DM_4crsol_c : 0.000106

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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