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 : 2agpg160_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 55: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b0474 b2518 b3831 b2744 b3752 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b4161 b2361 b2291 b0411 b4138 b4123 b0621 b2197 b2835 b3918 b4042 b0494 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.630498 (mmol/gDw/h)
  Minimum Production Rate : 0.332994 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.320409
  EX_o2_e : 269.364119
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.703560
  EX_pi_e : 0.941177
  EX_so4_e : 0.158772
  EX_k_e : 0.123069
  EX_mg2_e : 0.005470
  EX_ca2_e : 0.003282
  EX_cl_e : 0.003282
  EX_cu2_e : 0.000447
  EX_mn2_e : 0.000436
  EX_zn2_e : 0.000215
  EX_ni2_e : 0.000204
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989874
  EX_h2o_e : 542.247394
  EX_co2_e : 22.376688
  EX_succ_e : 0.657478
  EX_ura_e : 0.447117
  Auxiliary production reaction : 0.332994
  DM_5drib_c : 0.000142
  DM_4crsol_c : 0.000141

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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