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 : nicrnt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3831 b2744 b3614 b0910 b3752 b3926 b4152 b2297 b2458 b2925 b2097 b2926 b2781 b1612 b1611 b4122 b2690 b1759 b4374 b2361 b2291 b0411 b3945 b4138 b4123 b0621 b0529 b3927 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.478170 (mmol/gDw/h)
  Minimum Production Rate : 0.252543 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.877729
  EX_o2_e : 280.141560
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.589834
  EX_pi_e : 0.713788
  EX_so4_e : 0.120413
  EX_k_e : 0.093335
  EX_mg2_e : 0.004148
  EX_ca2_e : 0.002489
  EX_cl_e : 0.002489
  EX_cu2_e : 0.000339
  EX_mn2_e : 0.000330
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000154
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992320
  EX_h2o_e : 545.980971
  EX_co2_e : 30.658492
  EX_ac_e : 2.298072
  EX_succ_e : 0.498631
  Auxiliary production reaction : 0.252543
  EX_ura_e : 0.086550
  DM_5drib_c : 0.000108
  DM_4crsol_c : 0.000107

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