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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b3553 b3399 b3942 b1732 b1241 b0351 b4069 b2502 b2744 b3708 b2297 b2458 b2925 b2097 b3617 b1982 b2797 b3117 b1814 b4471 b3449 b3946 b0825 b1033 b4374 b0675 b2361 b2291 b0261 b3709 b3161 b0112 b0114 b0509 b3125 b1539 b2492 b0904 b3035 b1533 b1473 b0494 b0515 b4141 b1798 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.317265 (mmol/gDw/h)
  Minimum Production Rate : 0.474247 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.136286
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.751123
  EX_pi_e : 1.728778
  EX_so4_e : 0.554141
  EX_k_e : 0.061928
  EX_fe2_e : 0.005096
  EX_mg2_e : 0.002752
  EX_ca2_e : 0.001651
  EX_cl_e : 0.001651
  EX_cu2_e : 0.000225
  EX_mn2_e : 0.000219
  EX_zn2_e : 0.000108
  EX_ni2_e : 0.000102

Product: (mmol/gDw/h)
  EX_h2o_e : 48.479697
  EX_co2_e : 27.285600
  EX_h_e : 6.592826
  EX_ac_e : 2.249758
  Auxiliary production reaction : 0.474247
  EX_alltn_e : 0.001239
  DM_5drib_c : 0.001096
  DM_4crsol_c : 0.000954
  EX_glyclt_e : 0.000212

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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