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 : uacmamu_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3831 b2744 b3614 b0910 b3752 b4152 b2781 b1612 b1611 b4122 b1759 b2440 b4374 b2361 b2291 b0411 b4138 b4123 b0621 b2913 b2239 b2197 b3918 b1912 b1206 b1378   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.694419 (mmol/gDw/h)
  Minimum Production Rate : 0.032533 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.509305
  EX_o2_e : 273.851277
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.851315
  EX_pi_e : 1.069128
  EX_so4_e : 0.174869
  EX_k_e : 0.135546
  EX_mg2_e : 0.006024
  EX_ca2_e : 0.003614
  EX_cl_e : 0.003614
  EX_cu2_e : 0.000492
  EX_mn2_e : 0.000480
  EX_zn2_e : 0.000237
  EX_ni2_e : 0.000224
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988847
  EX_h2o_e : 546.617355
  EX_co2_e : 24.536921
  EX_succ_e : 0.724135
  EX_ura_e : 0.459913
  EX_g3pe_e : 0.334221
  Auxiliary production reaction : 0.032533
  DM_5drib_c : 0.000156
  DM_4crsol_c : 0.000155

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