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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3399 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b3708 b3008 b0871 b2779 b2926 b3617 b0160 b0121 b1982 b2797 b3117 b1814 b4471 b3449 b0675 b2361 b0261 b4381 b2406 b0112 b2789 b3127 b2975 b0114 b3603 b0886 b1539 b2492 b0904 b2578 b1533 b0494 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.489968 (mmol/gDw/h)
  Minimum Production Rate : 0.385098 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.527015
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.000633
  EX_pi_e : 1.627903
  EX_so4_e : 0.508477
  EX_k_e : 0.095638
  EX_fe2_e : 0.007871
  EX_mg2_e : 0.004250
  EX_ca2_e : 0.002550
  EX_cl_e : 0.002550
  EX_cu2_e : 0.000347
  EX_mn2_e : 0.000339
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 48.418329
  EX_co2_e : 27.365940
  EX_h_e : 6.069132
  EX_acald_e : 1.626530
  Auxiliary production reaction : 0.385092
  DM_oxam_c : 0.013369
  DM_5drib_c : 0.000329
  DM_4crsol_c : 0.000109

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