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 : gdptp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b4069 b2744 b3708 b3008 b2297 b2458 b0160 b1982 b2797 b3117 b1814 b4471 b2440 b0675 b2361 b0261 b4381 b2406 b0452 b0114 b1539 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.744300 (mmol/gDw/h)
  Minimum Production Rate : 0.295768 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.922565
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.517276
  EX_pi_e : 2.196797
  EX_so4_e : 0.187430
  EX_k_e : 0.145282
  EX_fe2_e : 0.011954
  EX_mg2_e : 0.006457
  EX_ca2_e : 0.003874
  EX_cl_e : 0.003874
  EX_cu2_e : 0.000528
  EX_mn2_e : 0.000514
  EX_zn2_e : 0.000254
  EX_ni2_e : 0.000240
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 50.010998
  EX_co2_e : 25.623808
  EX_h_e : 7.863781
  EX_ac_e : 0.433321
  Auxiliary production reaction : 0.295768
  DM_5drib_c : 0.000499
  DM_4crsol_c : 0.000166
  EX_etha_e : 0.000060

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
Contact