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 : 6hmhptpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (95 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b4382 b0586 b1241 b0351 b4069 b4384 b3708 b1479 b3752 b2297 b2458 b2779 b2407 b3124 b3236 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b0675 b1415 b1014 b0261 b0822 b2799 b3709 b2406 b3161 b0112 b2789 b3127 b2975 b0114 b3603 b2366 b2492 b0904 b1533 b3821 b1380 b0508 b1473 b0514 b0516 b4266 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.315630 (mmol/gDw/h)
  Minimum Production Rate : 0.335195 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.745793
  EX_o2_e : 284.220136
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.695446
  EX_pi_e : 0.974847
  EX_so4_e : 0.688771
  EX_k_e : 0.061609
  EX_mg2_e : 0.002738
  EX_ca2_e : 0.001643
  EX_cl_e : 0.001643
  EX_cu2_e : 0.000224
  EX_mn2_e : 0.000218
  EX_zn2_e : 0.000108
  EX_ni2_e : 0.000102

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994931
  EX_h2o_e : 548.987260
  EX_co2_e : 35.411507
  EX_ac_e : 2.280700
  EX_met__L_e : 0.609289
  EX_dxylnt_e : 0.335406
  Auxiliary production reaction : 0.335195
  EX_alltn_e : 0.000353
  DM_5drib_c : 0.000212
  DM_4crsol_c : 0.000070

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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