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 : accoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b3553 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b3752 b0871 b2779 b2926 b2407 b3236 b0121 b3962 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b3665 b0261 b2799 b2239 b2406 b0112 b3453 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3825 b4266 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.386648 (mmol/gDw/h)
  Minimum Production Rate : 0.310654 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.630619
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.352315
  EX_pi_e : 1.304860
  EX_so4_e : 0.407988
  EX_k_e : 0.075471
  EX_fe2_e : 0.006212
  EX_mg2_e : 0.003354
  EX_ca2_e : 0.002013
  EX_cl_e : 0.002013
  EX_cu2_e : 0.000274
  EX_mn2_e : 0.000267
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 50.835767
  EX_co2_e : 34.408662
  EX_h_e : 4.486805
  EX_acald_e : 1.286666
  Auxiliary production reaction : 0.310622
  EX_ade_e : 0.000433
  DM_5drib_c : 0.000259
  EX_glyc__R_e : 0.000129
  DM_4crsol_c : 0.000086
  EX_g3pe_e : 0.000031

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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