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 : fgam_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 : 49
  Gene deletion: b3553 b3942 b1732 b3708 b3008 b1479 b0871 b2925 b2097 b0030 b2407 b3844 b3236 b2883 b2690 b2463 b2797 b3117 b1814 b4471 b2210 b1033 b2440 b3551 b3945 b4219 b1832 b1778 b4381 b2406 b2868 b4064 b4464 b0114 b0509 b3125 b0755 b3612 b1539 b2492 b0904 b2578 b1533 b3927 b1710 b2480 b1517 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.366742 (mmol/gDw/h)
  Minimum Production Rate : 0.112204 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.856268
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.234406
  EX_pi_e : 0.465965
  EX_so4_e : 0.092353
  EX_k_e : 0.071585
  EX_fe2_e : 0.005890
  EX_mg2_e : 0.003181
  EX_ca2_e : 0.001909
  EX_cl_e : 0.001909
  EX_cu2_e : 0.000260
  EX_mn2_e : 0.000253
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 43.705894
  EX_co2_e : 27.642384
  EX_h_e : 9.362812
  EX_pyr_e : 4.918037
  EX_fum_e : 0.400690
  Auxiliary production reaction : 0.112204
  EX_ade_e : 0.009843
  DM_mththf_c : 0.000164
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000082

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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