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 : pe180_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1054 b0474 b2518 b2744 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b2361 b2291 b4138 b4123 b0621 b0452 b2197 b3918 b0789 b1249 b1206 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.543401 (mmol/gDw/h)
  Minimum Production Rate : 0.286995 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 16.943878
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.926387
  EX_pi_e : 0.811163
  EX_so4_e : 0.136839
  EX_k_e : 0.106068
  EX_fe2_e : 0.008728
  EX_mg2_e : 0.004714
  EX_ca2_e : 0.002828
  EX_cl_e : 0.002828
  EX_cu2_e : 0.000385
  EX_mn2_e : 0.000375
  EX_zn2_e : 0.000185
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 39.825188
  EX_co2_e : 22.121062
  EX_h_e : 6.610007
  EX_succ_e : 0.566655
  EX_ura_e : 0.385352
  Auxiliary production reaction : 0.286995
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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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