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 : gua_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b4467 b2836 b1478 b3399 b4382 b0238 b0125 b1241 b4069 b4384 b2744 b3708 b3752 b2297 b2458 b2779 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b1982 b0477 b4139 b2797 b3117 b1814 b4471 b1623 b4015 b0411 b2799 b3945 b1602 b2913 b3915 b2366 b2492 b0904 b2954 b3029 b1380 b1517 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.496848 (mmol/gDw/h)
  Minimum Production Rate : 0.102996 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.758763
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.880896
  EX_pi_e : 0.479263
  EX_so4_e : 0.125116
  EX_k_e : 0.096981
  EX_fe3_e : 0.007980
  EX_mg2_e : 0.004310
  EX_ca2_e : 0.002586
  EX_cl_e : 0.002586
  EX_cu2_e : 0.000352
  EX_mn2_e : 0.000343
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.658409
  EX_co2_e : 38.512056
  EX_h_e : 5.377456
  EX_ac_e : 0.289258
  Auxiliary production reaction : 0.102996
  DM_mththf_c : 0.000223
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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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