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 : imacp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (93 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4382 b2066 b4069 b4384 b3708 b3008 b0910 b2297 b2458 b2925 b2097 b0030 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b2498 b0261 b3945 b0507 b2913 b2239 b2406 b0112 b3453 b2975 b0114 b3603 b2366 b0755 b3612 b0529 b2492 b0904 b2578 b1533 b3927 b2835 b0594 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.585603 (mmol/gDw/h)
  Minimum Production Rate : 0.744180 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.645588
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.025470
  EX_pi_e : 1.309056
  EX_so4_e : 0.147467
  EX_k_e : 0.114306
  EX_fe2_e : 0.009405
  EX_mg2_e : 0.005080
  EX_ca2_e : 0.003048
  EX_cl_e : 0.003048
  EX_cu2_e : 0.000415
  EX_mn2_e : 0.000405
  EX_zn2_e : 0.000200
  EX_ni2_e : 0.000189
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.823868
  EX_co2_e : 27.363341
  EX_h_e : 8.936749
  EX_ac_e : 1.854332
  Auxiliary production reaction : 0.744180
  EX_ura_e : 0.105996
  DM_oxam_c : 0.000655
  DM_5drib_c : 0.000393
  DM_4crsol_c : 0.000131

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