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 : ckdo_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b0474 b2518 b2744 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b4138 b4123 b0621 b4381 b2406 b3453 b2197 b3918 b2240 b0789 b1249 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.693425 (mmol/gDw/h)
  Minimum Production Rate : 0.366173 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.821553
  EX_o2_e : 271.717994
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.838580
  EX_pi_e : 1.035110
  EX_so4_e : 0.174618
  EX_k_e : 0.135352
  EX_mg2_e : 0.006015
  EX_ca2_e : 0.003609
  EX_cl_e : 0.003609
  EX_cu2_e : 0.000492
  EX_mn2_e : 0.000479
  EX_zn2_e : 0.000236
  EX_ni2_e : 0.000224
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988863
  EX_h2o_e : 545.236862
  EX_co2_e : 21.918342
  EX_succ_e : 0.723098
  Auxiliary production reaction : 0.366173
  EX_ura_e : 0.125568
  DM_5drib_c : 0.000156
  DM_4crsol_c : 0.000155
  EX_glyc3p_e : 0.000056

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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