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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4069 b4384 b3708 b3115 b1849 b2296 b2779 b2925 b2097 b0030 b2407 b2690 b2797 b3117 b1814 b4471 b3665 b3945 b4381 b0452 b0114 b1539 b2492 b0904 b1533 b3927 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.400652 (mmol/gDw/h)
  Minimum Production Rate : 0.127417 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.980658
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.965439
  EX_pi_e : 0.386471
  EX_so4_e : 0.100892
  EX_k_e : 0.078204
  EX_fe2_e : 0.006435
  EX_mg2_e : 0.003476
  EX_ca2_e : 0.002085
  EX_cl_e : 0.002085
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000129
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 44.500832
  EX_co2_e : 32.516441
  EX_h_e : 9.200894
  EX_ac_e : 4.881112
  Auxiliary production reaction : 0.127417
  EX_ade_e : 0.000270
  DM_mththf_c : 0.000179
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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