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 : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 57
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2744 b3708 b1479 b2297 b2458 b2926 b0160 b1238 b3236 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b0675 b2361 b1415 b1014 b4014 b0261 b2976 b0822 b0507 b3709 b1907 b4381 b2406 b3161 b0112 b4265 b0114 b1539 b2492 b0904 b1533 b3927 b3821 b1380 b2965 b0693 b0325 b4042 b1473 b0594 b4266 b1985   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.226317 (mmol/gDw/h)
  Minimum Production Rate : 0.480439 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.546836
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.004316
  EX_pi_e : 1.659622
  EX_so4_e : 0.734218
  EX_k_e : 0.044176
  EX_fe2_e : 0.003635
  EX_mg2_e : 0.001963
  EX_ca2_e : 0.001178
  EX_cl_e : 0.001178
  EX_cu2_e : 0.000160
  EX_mn2_e : 0.000156
  EX_zn2_e : 0.000077
  EX_ni2_e : 0.000073

Product: (mmol/gDw/h)
  EX_h2o_e : 49.461504
  EX_co2_e : 33.001805
  EX_h_e : 5.680801
  EX_ac_e : 2.356124
  Auxiliary production reaction : 0.480439
  EX_met__L_e : 0.196788
  DM_oxam_c : 0.000253
  DM_5drib_c : 0.000152
  EX_dxylnt_e : 0.000151
  DM_4crsol_c : 0.000050

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.

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Last updated: 21-Sep-2023
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