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 : rhcys_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (4 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4069 b4384 b3708 b3008 b2297 b2458 b0030 b2407 b2687 b1982 b2797 b3117 b1814 b4471 b2440 b4381 b2406 b0452 b0114 b1539 b2492 b0904 b1533 b3927 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.731149 (mmol/gDw/h)
  Minimum Production Rate : 0.002364 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.923624
  EX_o2_e : 273.398513
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.819650
  EX_pi_e : 0.705271
  EX_so4_e : 0.186482
  EX_k_e : 0.142715
  EX_mg2_e : 0.006343
  EX_ca2_e : 0.003806
  EX_cl_e : 0.003806
  EX_cu2_e : 0.000518
  EX_mn2_e : 0.000505
  EX_zn2_e : 0.000249
  EX_ni2_e : 0.000236
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988257
  EX_h2o_e : 545.656823
  EX_co2_e : 24.506218
  EX_acser_e : 0.920876
  EX_ac_e : 0.428029
  Auxiliary production reaction : 0.002364
  DM_5drib_c : 0.000491
  DM_4crsol_c : 0.000163
  EX_etha_e : 0.000059

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