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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b3708 b3008 b3752 b0871 b2925 b2097 b2407 b1238 b1004 b3713 b1109 b0046 b3236 b1779 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b1033 b2799 b3945 b1602 b2913 b4381 b2406 b3915 b0452 b2366 b2492 b0904 b1533 b1380 b4141 b1798 b1518 b0606 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.353712 (mmol/gDw/h)
  Minimum Production Rate : 0.384131 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.673802
  EX_o2_e : 279.780704
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.205344
  EX_pi_e : 0.725287
  EX_so4_e : 0.089072
  EX_k_e : 0.069042
  EX_mg2_e : 0.003068
  EX_ca2_e : 0.001841
  EX_cl_e : 0.001841
  EX_cu2_e : 0.000251
  EX_mn2_e : 0.000244
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994318
  EX_h2o_e : 543.633325
  EX_co2_e : 28.839857
  EX_pyr_e : 4.301090
  Auxiliary production reaction : 0.384094
  EX_acald_e : 0.139895
  EX_ade_e : 0.000238
  EX_mththf_e : 0.000158
  DM_5drib_c : 0.000080
  DM_4crsol_c : 0.000079

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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