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 (86 of 119: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b0474 b2518 b4384 b2744 b4152 b2779 b2781 b1612 b1611 b4122 b1779 b1759 b4374 b4161 b0675 b4138 b4123 b0621 b2406 b0452 b3918 b1912 b1206 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.609809 (mmol/gDw/h)
  Minimum Production Rate : 0.321466 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.893268
  EX_o2_e : 276.823431
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.450779
  EX_pi_e : 1.231158
  EX_so4_e : 0.153562
  EX_k_e : 0.119031
  EX_mg2_e : 0.005290
  EX_ca2_e : 0.003174
  EX_cl_e : 0.003174
  EX_cu2_e : 0.000432
  EX_mn2_e : 0.000421
  EX_zn2_e : 0.000208
  EX_ni2_e : 0.000197
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990206
  EX_h2o_e : 547.343079
  EX_co2_e : 27.160605
  EX_succ_e : 0.635904
  Auxiliary production reaction : 0.321466
  EX_ura_e : 0.110979
  DM_5drib_c : 0.000137
  DM_4crsol_c : 0.000136

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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