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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (27 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b2502 b4384 b2744 b3708 b3115 b1849 b2296 b2407 b2797 b3117 b1814 b4471 b3616 b3589 b3665 b0675 b2361 b2406 b0112 b0452 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.539813 (mmol/gDw/h)
  Minimum Production Rate : 1.616690 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.037420
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.446630
  EX_pi_e : 2.137397
  EX_so4_e : 0.135936
  EX_k_e : 0.105368
  EX_fe2_e : 0.008670
  EX_mg2_e : 0.004683
  EX_ca2_e : 0.002810
  EX_cl_e : 0.002810
  EX_cu2_e : 0.000383
  EX_mn2_e : 0.000373
  EX_zn2_e : 0.000184
  EX_ni2_e : 0.000174
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 39.911135
  EX_co2_e : 20.806083
  EX_h_e : 9.436219
  Auxiliary production reaction : 1.616690
  EX_ac_e : 1.242817
  DM_mththf_c : 0.000242
  DM_5drib_c : 0.000121
  DM_4crsol_c : 0.000120

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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