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 (88 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 57
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2502 b2744 b3708 b2297 b2458 b2926 b3844 b1004 b3713 b1109 b0046 b3124 b3236 b1638 b0907 b0937 b1982 b4139 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b2291 b4014 b0261 b2976 b2799 b3945 b1602 b2789 b3127 b0452 b1297 b2366 b0755 b3612 b2492 b0904 b2954 b1533 b3029 b1380 b1600 b2660 b4141 b1798 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.470327 (mmol/gDw/h)
  Minimum Production Rate : 0.294107 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.198501
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.375706
  EX_pi_e : 0.747788
  EX_so4_e : 0.118438
  EX_k_e : 0.091805
  EX_mg2_e : 0.004080
  EX_fe2_e : 0.003882
  EX_fe3_e : 0.003672
  EX_cl_e : 0.002448
  EX_ca2_e : 0.002448
  EX_cu2_e : 0.000333
  EX_mn2_e : 0.000325
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.801162
  EX_co2_e : 37.495898
  EX_h_e : 5.189574
  Auxiliary production reaction : 0.294107
  EX_ac_e : 0.273818
  EX_hxan_e : 0.000526
  DM_5drib_c : 0.000316
  EX_dxylnt_e : 0.000210
  DM_4crsol_c : 0.000105

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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