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 : ncam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (110 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b0474 b2518 b1241 b0351 b3831 b3752 b2221 b2930 b4232 b3697 b3925 b4152 b0871 b3115 b1849 b2296 b3617 b1612 b1611 b4122 b1779 b2690 b1525 b4161 b2661 b4014 b2976 b0614 b0726 b3945 b4388 b4138 b4123 b0621 b1380 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.594369 (mmol/gDw/h)
  Minimum Production Rate : 0.185846 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.112120
  EX_o2_e : 277.883647
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.262121
  EX_pi_e : 0.573331
  EX_so4_e : 0.149674
  EX_k_e : 0.116017
  EX_mg2_e : 0.005156
  EX_ca2_e : 0.003094
  EX_cl_e : 0.003094
  EX_cu2_e : 0.000421
  EX_mn2_e : 0.000411
  EX_zn2_e : 0.000203
  EX_ni2_e : 0.000192
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990454
  EX_h2o_e : 547.002114
  EX_co2_e : 28.398130
  EX_ac_e : 1.334442
  EX_succ_e : 0.619803
  EX_ura_e : 0.235649
  Auxiliary production reaction : 0.185846
  DM_5drib_c : 0.000134
  DM_4crsol_c : 0.000133

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