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 : ipdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2436 b4382 b3831 b4384 b1278 b3614 b0910 b3752 b4152 b2297 b2458 b2781 b1612 b1611 b4122 b1759 b4388 b4138 b4123 b0621 b2406 b2943 b3825 b3918 b0418 b1206 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.702635 (mmol/gDw/h)
  Minimum Production Rate : 0.031231 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.692839
  EX_o2_e : 274.809187
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.584945
  EX_pi_e : 0.740228
  EX_so4_e : 0.176938
  EX_k_e : 0.137149
  EX_mg2_e : 0.006095
  EX_ca2_e : 0.003657
  EX_cl_e : 0.003657
  EX_cu2_e : 0.000498
  EX_mn2_e : 0.000486
  EX_zn2_e : 0.000240
  EX_ni2_e : 0.000227
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988715
  EX_h2o_e : 547.095841
  EX_co2_e : 25.260304
  EX_succ_e : 0.732702
  EX_ura_e : 0.498272
  EX_ac_e : 0.409064
  Auxiliary production reaction : 0.031231
  DM_5drib_c : 0.000471
  DM_4crsol_c : 0.000157

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
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