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 : dtdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4467 b2836 b2242 b2744 b3614 b0910 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b4374 b0675 b2361 b2291 b4138 b4123 b0621 b0306 b3605 b3028 b3918 b4042 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.560607 (mmol/gDw/h)
  Minimum Production Rate : 0.086711 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.051990
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.710029
  EX_pi_e : 0.714186
  EX_so4_e : 0.141172
  EX_k_e : 0.109426
  EX_fe2_e : 0.078794
  EX_mg2_e : 0.004863
  EX_cl_e : 0.002918
  EX_ca2_e : 0.002918
  EX_cu2_e : 0.000397
  EX_mn2_e : 0.000387
  EX_zn2_e : 0.000191
  EX_ni2_e : 0.000181
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 49.198939
  EX_co2_e : 31.004054
  EX_h_e : 7.169620
  EX_succ_e : 0.584596
  EX_ura_e : 0.101471
  Auxiliary production reaction : 0.086711
  EX_pheme_e : 0.069790
  EX_for_e : 0.001375
  DM_5drib_c : 0.000126
  DM_4crsol_c : 0.000125

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