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 : udpgalfur_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b2836 b2242 b4382 b4384 b2744 b1278 b3614 b0910 b2297 b2458 b2781 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1759 b4374 b0675 b1415 b4015 b1602 b4138 b4123 b0621 b2406 b1727 b2492 b0904 b3028 b1380 b3918 b2660 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.460340 (mmol/gDw/h)
  Minimum Production Rate : 0.243126 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.910455
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.457889
  EX_pi_e : 0.930300
  EX_so4_e : 0.115923
  EX_k_e : 0.089855
  EX_fe2_e : 0.007394
  EX_mg2_e : 0.003993
  EX_ca2_e : 0.002396
  EX_cl_e : 0.002396
  EX_cu2_e : 0.000326
  EX_mn2_e : 0.000318
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.112614
  EX_co2_e : 35.288121
  EX_h_e : 5.273192
  EX_succ_e : 0.480039
  Auxiliary production reaction : 0.243126
  EX_3hpp_e : 0.083323
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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