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 (104 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b4467 b2836 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b2744 b3708 b3008 b0871 b2779 b0030 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b0121 b1982 b2797 b3117 b1814 b4471 b1623 b0261 b2799 b3945 b1602 b0507 b2913 b4381 b2406 b3915 b2975 b3603 b2366 b2492 b0904 b1533 b1380 b2413 b4141 b1798 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.453195 (mmol/gDw/h)
  Minimum Production Rate : 0.163477 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.041347
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.040592
  EX_pi_e : 0.437154
  EX_so4_e : 0.114124
  EX_k_e : 0.088460
  EX_fe3_e : 0.007281
  EX_mg2_e : 0.003931
  EX_ca2_e : 0.002359
  EX_cl_e : 0.002359
  EX_cu2_e : 0.000321
  EX_mn2_e : 0.000313
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.681123
  EX_co2_e : 37.771408
  EX_h_e : 5.480912
  EX_acald_e : 0.178040
  Auxiliary production reaction : 0.163370
  EX_ade_e : 0.000507
  DM_5drib_c : 0.000304
  DM_4crsol_c : 0.000101

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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