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 : 25drapp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b0160 b3236 b1638 b3908 b1656 b1982 b4139 b2797 b3117 b1814 b4471 b3449 b4374 b0675 b2361 b2291 b0261 b2913 b0452 b2868 b0114 b0886 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.758835 (mmol/gDw/h)
  Minimum Production Rate : 0.123836 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.425003
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.817936
  EX_pi_e : 0.855813
  EX_so4_e : 0.191090
  EX_k_e : 0.148119
  EX_fe2_e : 0.012188
  EX_mg2_e : 0.006583
  EX_ca2_e : 0.003950
  EX_cl_e : 0.003950
  EX_cu2_e : 0.000538
  EX_mn2_e : 0.000524
  EX_zn2_e : 0.000259
  EX_ni2_e : 0.000245
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 49.017579
  EX_co2_e : 27.732829
  EX_h_e : 7.595060
  Auxiliary production reaction : 0.123836
  EX_hxan_e : 0.000849
  DM_5drib_c : 0.000509
  DM_4crsol_c : 0.000169

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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