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 : udpgalfur_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2436 b0474 b2518 b2744 b4152 b2781 b1612 b1611 b4122 b1759 b3449 b4374 b4161 b0675 b4138 b4123 b0621 b2913 b4381 b2239 b2406 b3918 b1912 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.583830 (mmol/gDw/h)
  Minimum Production Rate : 0.308347 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.197185
  EX_o2_e : 278.229069
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.133356
  EX_pi_e : 1.179859
  EX_so4_e : 0.147020
  EX_k_e : 0.113960
  EX_mg2_e : 0.005065
  EX_ca2_e : 0.003039
  EX_cl_e : 0.003039
  EX_cu2_e : 0.000414
  EX_mn2_e : 0.000403
  EX_zn2_e : 0.000199
  EX_ni2_e : 0.000189
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990623
  EX_h2o_e : 547.876963
  EX_co2_e : 28.552010
  EX_succ_e : 0.608813
  Auxiliary production reaction : 0.308347
  EX_ura_e : 0.105675
  DM_5drib_c : 0.000392
  DM_4crsol_c : 0.000130

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