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 : ocdca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b2744 b3614 b0910 b4152 b3115 b1849 b2296 b2781 b0767 b1612 b1611 b4122 b1759 b4374 b0675 b4138 b4123 b0621 b4381 b2406 b0452 b0529 b2197 b3918 b1912 b1206 b2285 b1378 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.412074 (mmol/gDw/h)
  Minimum Production Rate : 0.217228 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.071746
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.034810
  EX_pi_e : 0.397489
  EX_so4_e : 0.103769
  EX_k_e : 0.080434
  EX_fe3_e : 0.006618
  EX_mg2_e : 0.003575
  EX_cl_e : 0.002145
  EX_ca2_e : 0.002145
  EX_cu2_e : 0.000292
  EX_mn2_e : 0.000285
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 36.857470
  EX_co2_e : 20.278834
  EX_h_e : 13.312688
  EX_succ_e : 4.239096
  EX_thym_e : 0.292222
  EX_ac_e : 0.239904
  Auxiliary production reaction : 0.217228
  DM_5drib_c : 0.000093
  DM_4crsol_c : 0.000092

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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