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 : uri_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b1241 b0351 b3831 b3614 b0910 b3752 b4152 b0871 b2297 b2458 b2925 b2097 b2926 b2781 b3236 b1612 b1611 b4122 b2690 b1759 b2210 b0411 b0614 b3945 b4138 b4123 b0621 b2913 b0452 b1539 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.449544 (mmol/gDw/h)
  Minimum Production Rate : 0.237424 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.938151
  EX_o2_e : 280.849430
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.492620
  EX_pi_e : 0.433633
  EX_so4_e : 0.113204
  EX_k_e : 0.087748
  EX_mg2_e : 0.003900
  EX_cl_e : 0.002340
  EX_ca2_e : 0.002340
  EX_cu2_e : 0.000319
  EX_mn2_e : 0.000311
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992780
  EX_h2o_e : 545.850659
  EX_co2_e : 30.513089
  EX_succ_e : 1.638583
  EX_ac_e : 1.009290
  Auxiliary production reaction : 0.237424
  EX_ura_e : 0.081369
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

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