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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b3553 b3399 b4382 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b2779 b0160 b0583 b3962 b1982 b4139 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b0675 b2361 b1415 b1014 b4014 b0261 b2976 b3945 b0507 b3709 b4381 b2406 b3161 b0112 b0114 b2366 b2492 b0904 b2954 b1533 b3927 b3821 b1380 b0325 b0508 b1473 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.319445 (mmol/gDw/h)
  Minimum Production Rate : 0.071449 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.411517
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.755128
  EX_so4_e : 0.948178
  EX_pi_e : 0.522486
  EX_k_e : 0.062353
  EX_fe2_e : 0.005131
  EX_mg2_e : 0.002771
  EX_ca2_e : 0.001663
  EX_cl_e : 0.001663
  EX_cu2_e : 0.000226
  EX_mn2_e : 0.000221
  EX_zn2_e : 0.000109
  EX_ni2_e : 0.000103

Product: (mmol/gDw/h)
  EX_h2o_e : 47.616928
  EX_co2_e : 36.070826
  EX_h_e : 4.993341
  EX_ac_e : 2.550995
  EX_met__L_e : 0.796286
  Auxiliary production reaction : 0.071449
  DM_oxam_c : 0.008716
  DM_5drib_c : 0.000214
  EX_dxylnt_e : 0.000214
  DM_4crsol_c : 0.000071

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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