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 : nadphx__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (18 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b2297 b2458 b3617 b0160 b1779 b1982 b0675 b2361 b2291 b0261 b0507 b2913 b4381 b0112 b2975 b0114 b3603 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.400924 (mmol/gDw/h)
  Minimum Production Rate : 0.768361 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.505589
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.708922
  EX_pi_e : 2.691816
  EX_so4_e : 0.100961
  EX_k_e : 0.078258
  EX_fe2_e : 0.006439
  EX_mg2_e : 0.003478
  EX_ca2_e : 0.002087
  EX_cl_e : 0.002087
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000129
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 49.395099
  EX_co2_e : 23.439685
  EX_h_e : 9.509977
  EX_ac_e : 1.983424
  Auxiliary production reaction : 0.768361
  DM_oxam_c : 0.000449
  DM_5drib_c : 0.000269
  DM_4crsol_c : 0.000089

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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