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 : gtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b2836 b1478 b1241 b4384 b2744 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b0871 b2883 b2690 b1982 b2797 b3117 b1814 b4471 b0675 b0411 b0822 b4381 b2868 b4064 b4464 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b4042 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.763208 (mmol/gDw/h)
  Minimum Production Rate : 0.175576 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.129753
  EX_o2_e : 275.019944
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.123030
  EX_pi_e : 1.262923
  EX_so4_e : 0.192191
  EX_k_e : 0.148973
  EX_mg2_e : 0.006621
  EX_ca2_e : 0.003972
  EX_cl_e : 0.003972
  EX_cu2_e : 0.000541
  EX_mn2_e : 0.000527
  EX_zn2_e : 0.000260
  EX_ni2_e : 0.000247
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987742
  EX_h2o_e : 548.892999
  EX_co2_e : 25.965682
  EX_pyr_e : 0.316033
  Auxiliary production reaction : 0.175576
  EX_ade_e : 0.000514
  EX_mththf_e : 0.000342
  DM_5drib_c : 0.000172
  DM_4crsol_c : 0.000170

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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