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 (44 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b3617 b0030 b3124 b2883 b1982 b1623 b0261 b0411 b4381 b0112 b0114 b0529 b2492 b0904 b0514 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.516255 (mmol/gDw/h)
  Minimum Production Rate : 0.253991 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.085305
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.009693
  EX_pi_e : 0.497982
  EX_so4_e : 0.130003
  EX_k_e : 0.100769
  EX_fe2_e : 0.008292
  EX_mg2_e : 0.004479
  EX_ca2_e : 0.002687
  EX_cl_e : 0.002687
  EX_cu2_e : 0.000366
  EX_mn2_e : 0.000357
  EX_zn2_e : 0.000176
  EX_ni2_e : 0.000167
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 42.909640
  EX_co2_e : 20.704845
  EX_h_e : 8.240847
  EX_thymd_e : 0.962813
  DM_oxam_c : 0.508560
  DM_5drib_c : 0.508328
  DM_4crsol_c : 0.508097
  EX_ac_e : 0.300556
  Auxiliary production reaction : 0.253991

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.

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Last updated: 21-Sep-2023
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