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 : nac_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b0474 b2518 b3831 b3752 b2221 b2930 b4232 b3697 b3925 b4152 b0871 b2297 b2458 b2926 b1238 b1612 b1611 b4122 b2690 b4161 b0675 b4014 b2976 b0822 b0614 b4138 b4123 b0621 b1727 b0529 b1912 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.470467 (mmol/gDw/h)
  Minimum Production Rate : 0.248475 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.350374
  EX_o2_e : 281.644698
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.499788
  EX_pi_e : 0.453815
  EX_so4_e : 0.118473
  EX_k_e : 0.091832
  EX_mg2_e : 0.004081
  EX_ca2_e : 0.002449
  EX_cl_e : 0.002449
  EX_cu2_e : 0.000334
  EX_mn2_e : 0.000325
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992444
  EX_h2o_e : 547.331221
  EX_co2_e : 31.554083
  EX_succ_e : 1.689037
  EX_ac_e : 0.273899
  Auxiliary production reaction : 0.248475
  EX_ura_e : 0.085156
  DM_5drib_c : 0.000106
  DM_4crsol_c : 0.000105

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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