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 : nadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (27 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b2779 b3617 b0160 b1982 b1033 b4374 b0675 b2361 b2291 b0261 b0112 b2789 b3127 b0114 b0755 b3612 b0529 b2492 b0904 b0514   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.434561 (mmol/gDw/h)
  Minimum Production Rate : 0.832824 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.306561
  EX_nh4_e : 10.523475
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.917653
  EX_so4_e : 0.109431
  EX_k_e : 0.084823
  EX_fe2_e : 0.006979
  EX_mg2_e : 0.003770
  EX_cl_e : 0.002262
  EX_ca2_e : 0.002262
  EX_cu2_e : 0.000308
  EX_mn2_e : 0.000300
  EX_zn2_e : 0.000148
  EX_ni2_e : 0.000140
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.533327
  EX_co2_e : 21.734672
  EX_h_e : 8.793864
  EX_ac_e : 1.468386
  Auxiliary production reaction : 0.832824
  DM_oxam_c : 0.000486
  DM_5drib_c : 0.000292
  EX_glyclt_e : 0.000291
  DM_4crsol_c : 0.000097

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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