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 : dtdp4d6dg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3916 b4382 b3831 b4384 b3614 b0910 b3752 b4152 b2779 b2781 b1850 b2407 b1612 b1611 b4122 b1759 b1200 b2440 b4138 b4123 b0621 b2406 b1723 b3918 b1912 b0494 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.636892 (mmol/gDw/h)
  Minimum Production Rate : 0.336371 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.578905
  EX_o2_e : 274.670359
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.781678
  EX_pi_e : 1.287092
  EX_so4_e : 0.160382
  EX_k_e : 0.124317
  EX_mg2_e : 0.005525
  EX_ca2_e : 0.003315
  EX_cl_e : 0.003315
  EX_cu2_e : 0.000452
  EX_mn2_e : 0.000440
  EX_zn2_e : 0.000217
  EX_ni2_e : 0.000206
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989771
  EX_h2o_e : 546.776570
  EX_co2_e : 25.358879
  EX_succ_e : 0.664146
  Auxiliary production reaction : 0.336371
  EX_ura_e : 0.115279
  DM_5drib_c : 0.000143
  DM_4crsol_c : 0.000142

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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