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 : sbzcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 57
  Gene deletion: b3553 b1478 b3399 b4382 b1241 b0351 b4069 b2502 b2744 b3708 b2297 b2458 b2925 b2097 b2926 b2690 b3962 b1982 b4139 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b0675 b2361 b1415 b1014 b4014 b0261 b2976 b3945 b0507 b2342 b3845 b3709 b4381 b2406 b3161 b0112 b0452 b0114 b2366 b2492 b0904 b2954 b1533 b1380 b0325 b1473 b0594 b4266 b2842   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.263358 (mmol/gDw/h)
  Minimum Production Rate : 0.058904 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.260950
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.920236
  EX_so4_e : 0.781700
  EX_pi_e : 0.430749
  EX_k_e : 0.051406
  EX_fe2_e : 0.004230
  EX_mg2_e : 0.002285
  EX_ca2_e : 0.001371
  EX_cl_e : 0.001371
  EX_cu2_e : 0.000187
  EX_mn2_e : 0.000182
  EX_zn2_e : 0.000090
  EX_ni2_e : 0.000085

Product: (mmol/gDw/h)
  EX_h2o_e : 41.325641
  EX_co2_e : 31.512250
  EX_h_e : 8.261004
  EX_ac_e : 6.247478
  EX_met__L_e : 0.656477
  Auxiliary production reaction : 0.058904
  DM_oxam_c : 0.007186
  DM_5drib_c : 0.000177
  EX_dxylnt_e : 0.000176
  DM_4crsol_c : 0.000059

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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