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 (68 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b0910 b4152 b0871 b3115 b1849 b2296 b2925 b2097 b3617 b1612 b1611 b4122 b1779 b3946 b0825 b4374 b0675 b2361 b2291 b4138 b4123 b0621 b0114 b2492 b0904 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.542802 (mmol/gDw/h)
  Minimum Production Rate : 0.286678 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.336285
  EX_o2_e : 275.273227
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.632075
  EX_pi_e : 1.096947
  EX_so4_e : 0.136689
  EX_k_e : 0.105951
  EX_mg2_e : 0.004709
  EX_cl_e : 0.002825
  EX_ca2_e : 0.002825
  EX_cu2_e : 0.000385
  EX_mn2_e : 0.000375
  EX_zn2_e : 0.000185
  EX_ni2_e : 0.000175
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991282
  EX_h2o_e : 543.772257
  EX_co2_e : 25.914737
  EX_ac_e : 2.588331
  EX_succ_e : 0.566030
  EX_pyr_e : 0.463944
  EX_ura_e : 0.384927
  Auxiliary production reaction : 0.286678
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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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