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 : ppgpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b4467 b4069 b4384 b2744 b3708 b2297 b2458 b2925 b2097 b2926 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b1982 b4139 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b1602 b2913 b2406 b1727 b0114 b1539 b2492 b0904 b1533 b3927 b3029 b3821 b1380 b1771 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.413126 (mmol/gDw/h)
  Minimum Production Rate : 0.174999 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 38.762638
  EX_glc__D_e : 10.000000
  EX_fe3_e : 6.764372
  EX_nh4_e : 5.336719
  EX_pi_e : 1.098500
  EX_so4_e : 0.104033
  EX_k_e : 0.080639
  EX_mg2_e : 0.003584
  EX_ca2_e : 0.002150
  EX_cl_e : 0.002150
  EX_cu2_e : 0.000293
  EX_mn2_e : 0.000285
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 50.962524
  EX_co2_e : 40.810214
  EX_h_e : 11.326312
  EX_fe2_e : 6.757736
  EX_ac_e : 0.240516
  Auxiliary production reaction : 0.174999
  EX_glyclt_e : 0.000462
  DM_5drib_c : 0.000277
  DM_4crsol_c : 0.000092

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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