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 : hdca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b4382 b0474 b2518 b4384 b2744 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b4138 b4123 b0621 b2406 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 : 0.576817 (mmol/gDw/h)
  Minimum Production Rate : 0.609286 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.060328
  EX_o2_e : 267.949610
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.047671
  EX_pi_e : 0.556401
  EX_so4_e : 0.145254
  EX_k_e : 0.112591
  EX_mg2_e : 0.005004
  EX_ca2_e : 0.003002
  EX_cl_e : 0.003002
  EX_cu2_e : 0.000409
  EX_mn2_e : 0.000399
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000186
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990736
  EX_h2o_e : 540.407795
  EX_co2_e : 22.533544
  Auxiliary production reaction : 0.609286
  EX_succ_e : 0.601500
  EX_ura_e : 0.409049
  DM_5drib_c : 0.000130
  DM_4crsol_c : 0.000129

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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