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 : 5mthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (116 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 61
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b2502 b2744 b3708 b1479 b2297 b2458 b3236 b1779 b2690 b0120 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b0675 b2361 b1415 b1014 b4014 b0261 b2976 b0822 b2799 b0507 b3709 b1907 b4381 b2406 b3161 b0112 b0837 b0124 b2975 b0114 b3603 b0509 b3125 b1539 b2492 b0904 b0591 b1533 b3821 b1380 b4042 b1473 b3715 b4266 b1985 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.247252 (mmol/gDw/h)
  Minimum Production Rate : 0.492533 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.404556
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.359183
  EX_so4_e : 0.296664
  EX_pi_e : 0.238501
  EX_k_e : 0.048262
  EX_fe2_e : 0.003971
  EX_mg2_e : 0.002145
  EX_ca2_e : 0.001287
  EX_cl_e : 0.001287
  EX_cu2_e : 0.000175
  EX_mn2_e : 0.000171
  EX_zn2_e : 0.000084
  EX_ni2_e : 0.000080

Product: (mmol/gDw/h)
  EX_h2o_e : 49.153861
  EX_co2_e : 33.276720
  EX_h_e : 8.021161
  EX_ac_e : 1.537252
  EX_dxylnt_e : 0.492699
  Auxiliary production reaction : 0.492533
  EX_met__L_e : 0.234401
  DM_oxam_c : 0.006746
  DM_5drib_c : 0.000166
  DM_4crsol_c : 0.000055

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.

Last updated: 21-Sep-2023
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