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 : pe141_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 69: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3831 b2744 b1278 b3614 b0910 b4152 b2297 b2458 b2925 b2097 b2781 b0030 b3844 b1612 b1611 b4122 b0651 b2162 b2690 b1759 b4374 b2361 b2291 b0411 b3945 b4138 b4123 b0621 b2943 b0452 b0529 b2197 b3825 b3918 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.631206 (mmol/gDw/h)
  Minimum Production Rate : 0.008273 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 993.509246
  EX_h_e : 985.128464
  EX_o2_e : 276.589651
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.720476
  EX_pi_e : 0.617137
  EX_so4_e : 0.158950
  EX_k_e : 0.123207
  EX_mg2_e : 0.005476
  EX_ca2_e : 0.003285
  EX_cl_e : 0.003285
  EX_cu2_e : 0.000448
  EX_mn2_e : 0.000436
  EX_zn2_e : 0.000215
  EX_ni2_e : 0.000204
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 993.499109
  EX_h2o_e : 545.016236
  EX_co2_e : 28.660616
  EX_succ_e : 0.658216
  EX_ura_e : 0.447618
  EX_ac_e : 0.367479
  Auxiliary production reaction : 0.008273
  DM_5drib_c : 0.000142
  DM_4crsol_c : 0.000141

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