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 : udp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b0474 b2518 b2744 b3614 b0910 b3926 b4152 b2925 b2097 b2781 b1232 b1612 b1611 b4122 b1779 b1759 b3946 b0825 b4374 b0675 b4138 b4123 b0621 b4381 b3918 b1206 b2285 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.443253 (mmol/gDw/h)
  Minimum Production Rate : 0.234102 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.921822
  EX_o2_e : 281.926148
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.415763
  EX_pi_e : 0.895769
  EX_so4_e : 0.111620
  EX_k_e : 0.086520
  EX_mg2_e : 0.003845
  EX_cl_e : 0.002307
  EX_ca2_e : 0.002307
  EX_cu2_e : 0.000314
  EX_mn2_e : 0.000306
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992881
  EX_h2o_e : 546.608955
  EX_co2_e : 32.171231
  EX_ac_e : 2.679266
  EX_succ_e : 0.462221
  Auxiliary production reaction : 0.234102
  EX_ura_e : 0.080230
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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