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 : udpgalfur_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 64
  Gene deletion: b4467 b2242 b1241 b0351 b4069 b4384 b2744 b1278 b3708 b3614 b0910 b3752 b3115 b1849 b2296 b2926 b2781 b2407 b1612 b1611 b4122 b1759 b3962 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b0595 b4374 b0675 b2361 b2291 b1415 b1014 b0261 b0822 b1907 b4138 b4123 b0621 b2913 b0112 b0511 b4265 b0114 b2366 b2492 b0904 b1533 b3028 b3821 b1380 b3918 b0325 b0508 b1473 b0515 b4266 b3662 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.317748 (mmol/gDw/h)
  Minimum Production Rate : 0.368362 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.284008
  EX_o2_e : 283.304854
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.186475
  EX_pi_e : 1.043225
  EX_so4_e : 0.080015
  EX_k_e : 0.062022
  EX_mg2_e : 0.002756
  EX_ca2_e : 0.001654
  EX_cl_e : 0.001654
  EX_cu2_e : 0.000225
  EX_mn2_e : 0.000220
  EX_zn2_e : 0.000108
  EX_ni2_e : 0.000103

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994897
  EX_h2o_e : 548.832463
  EX_co2_e : 31.276550
  EX_succ_e : 1.282880
  EX_ac_e : 1.207220
  EX_xan_e : 0.475767
  Auxiliary production reaction : 0.368362
  EX_ura_e : 0.057513
  EX_dxylnt_e : 0.000213
  DM_5drib_c : 0.000071
  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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