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 (55 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b4382 b0474 b2518 b3831 b4384 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b4161 b4388 b4138 b4123 b0621 b2406 b2197 b3918 b1912 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.676641 (mmol/gDw/h)
  Minimum Production Rate : 0.357310 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.043712
  EX_o2_e : 272.644779
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.624647
  EX_pi_e : 1.010001
  EX_so4_e : 0.170392
  EX_k_e : 0.132076
  EX_mg2_e : 0.005870
  EX_ca2_e : 0.003522
  EX_cl_e : 0.003522
  EX_cu2_e : 0.000480
  EX_mn2_e : 0.000468
  EX_zn2_e : 0.000231
  EX_ni2_e : 0.000219
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989132
  EX_h2o_e : 545.594360
  EX_co2_e : 22.840251
  EX_succ_e : 0.705595
  Auxiliary production reaction : 0.357310
  EX_ura_e : 0.122529
  DM_5drib_c : 0.000152
  DM_4crsol_c : 0.000151

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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