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 : dhgly_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b0030 b2407 b1982 b3616 b3589 b0261 b0411 b0507 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.550798 (mmol/gDw/h)
  Minimum Production Rate : 0.435083 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.728115
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.660049
  EX_pi_e : 0.531303
  EX_so4_e : 0.138702
  EX_k_e : 0.107512
  EX_fe2_e : 0.008846
  EX_mg2_e : 0.004778
  EX_ca2_e : 0.002867
  EX_cl_e : 0.002867
  EX_cu2_e : 0.000391
  EX_mn2_e : 0.000381
  EX_zn2_e : 0.000188
  EX_ni2_e : 0.000178
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 44.338962
  EX_co2_e : 21.225012
  EX_h_e : 8.643211
  EX_thymd_e : 0.920347
  DM_oxam_c : 0.435699
  DM_5drib_c : 0.435452
  DM_4crsol_c : 0.435206
  Auxiliary production reaction : 0.435083

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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