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 : pg120_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b3831 b3614 b0910 b4152 b2926 b2781 b0030 b3844 b1612 b1611 b4122 b0651 b2162 b1759 b4138 b4123 b0621 b4381 b2406 b3915 b2197 b3918 b4042 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.518150 (mmol/gDw/h)
  Minimum Production Rate : 0.273201 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.688368
  EX_o2_e : 273.613505
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.330872
  EX_pi_e : 0.773012
  EX_so4_e : 0.130481
  EX_k_e : 0.101139
  EX_mg2_e : 0.004495
  EX_cl_e : 0.002697
  EX_ca2_e : 0.002697
  EX_cu2_e : 0.000367
  EX_mn2_e : 0.000358
  EX_zn2_e : 0.000177
  EX_ni2_e : 0.000167
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991678
  EX_h2o_e : 543.507919
  EX_co2_e : 26.905207
  EX_succ_e : 0.540323
  EX_ura_e : 0.367445
  Auxiliary production reaction : 0.273201
  DM_5drib_c : 0.000117
  DM_4crsol_c : 0.000116

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