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 : ps180_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b1054 b4382 b4384 b2744 b1278 b3614 b0910 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b4374 b0675 b4138 b4123 b0621 b0153 b2406 b0452 b0584 b2197 b3918 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.543970 (mmol/gDw/h)
  Minimum Production Rate : 0.287207 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 16.903938
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.933543
  EX_pi_e : 0.811923
  EX_so4_e : 0.136982
  EX_k_e : 0.106179
  EX_fe2_e : 0.008737
  EX_mg2_e : 0.004719
  EX_cl_e : 0.002831
  EX_ca2_e : 0.002831
  EX_cu2_e : 0.000386
  EX_mn2_e : 0.000376
  EX_zn2_e : 0.000185
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 39.807422
  EX_co2_e : 21.797838
  EX_h_e : 6.904214
  EX_succ_e : 0.567247
  EX_ura_e : 0.385755
  Auxiliary production reaction : 0.287207
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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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