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 : 2h3oppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b2779 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b1982 b4139 b1033 b1623 b1493 b3517 b4014 b2976 b3945 b1602 b3915 b0452 b0509 b3125 b1300 b1380 b2660 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.599627 (mmol/gDw/h)
  Minimum Production Rate : 0.286651 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.532756
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.475917
  EX_pi_e : 0.578403
  EX_so4_e : 0.150998
  EX_k_e : 0.117043
  EX_fe3_e : 0.009631
  EX_mg2_e : 0.005202
  EX_cl_e : 0.003121
  EX_ca2_e : 0.003121
  EX_cu2_e : 0.000425
  EX_mn2_e : 0.000414
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000194
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 50.644445
  EX_co2_e : 34.528128
  EX_h_e : 5.805890
  Auxiliary production reaction : 0.286651
  DM_5drib_c : 0.000135
  DM_4crsol_c : 0.000134

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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