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 : 2agpe141_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 63: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b0474 b2518 b4384 b2744 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b4138 b4123 b0621 b2406 b2197 b3825 b3918 b0789 b1249 b0494 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.647146 (mmol/gDw/h)
  Minimum Production Rate : 0.341787 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.117637
  EX_o2_e : 269.829210
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.248751
  EX_pi_e : 0.966028
  EX_so4_e : 0.162964
  EX_k_e : 0.126318
  EX_mg2_e : 0.005614
  EX_ca2_e : 0.003368
  EX_cl_e : 0.003368
  EX_cu2_e : 0.000459
  EX_mn2_e : 0.000447
  EX_zn2_e : 0.000221
  EX_ni2_e : 0.000209
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989606
  EX_h2o_e : 543.487589
  EX_co2_e : 22.408643
  EX_succ_e : 0.674839
  EX_ura_e : 0.458922
  Auxiliary production reaction : 0.341787
  DM_5drib_c : 0.000146
  DM_4crsol_c : 0.000144

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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