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 : udpgal_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (115 of 119: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b0474 b2518 b1241 b0351 b3831 b3708 b3752 b2930 b4232 b3697 b3925 b4152 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b0907 b1779 b2690 b1759 b2210 b4161 b0411 b3945 b1602 b4138 b4123 b0621 b4381 b1727 b0529 b2197 b1380 b3918 b1912 b1695 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.437678 (mmol/gDw/h)
  Minimum Production Rate : 0.019635 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.581688
  EX_o2_e : 279.546626
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.347640
  EX_pi_e : 0.884501
  EX_so4_e : 0.110216
  EX_k_e : 0.085432
  EX_mg2_e : 0.003797
  EX_ca2_e : 0.002278
  EX_cl_e : 0.002278
  EX_cu2_e : 0.000310
  EX_mn2_e : 0.000302
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992970
  EX_h2o_e : 544.275802
  EX_co2_e : 29.788528
  EX_ac_e : 3.318273
  EX_succ_e : 0.456407
  Auxiliary production reaction : 0.231157
  EX_ura_e : 0.079221
  EX_glyclt_e : 0.000195
  DM_5drib_c : 0.000098
  DM_4crsol_c : 0.000098

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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