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 : thmnp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3399 b3831 b2502 b2744 b3708 b3008 b0910 b0871 b2779 b1982 b2797 b3117 b1814 b4471 b3449 b4374 b0675 b2361 b2291 b0261 b2239 b0114 b0886 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b2965 b0693 b4141 b1798 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.486227 (mmol/gDw/h)
  Minimum Production Rate : 0.167409 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.831674
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.088799
  EX_pi_e : 0.469017
  EX_so4_e : 0.122442
  EX_k_e : 0.094908
  EX_fe2_e : 0.007809
  EX_mg2_e : 0.004218
  EX_cl_e : 0.002531
  EX_ca2_e : 0.002531
  EX_cu2_e : 0.000345
  EX_mn2_e : 0.000336
  EX_zn2_e : 0.000166
  EX_ni2_e : 0.000157
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.881444
  EX_co2_e : 38.533766
  EX_h_e : 5.305781
  Auxiliary production reaction : 0.167409
  DM_oxam_c : 0.000544
  DM_5drib_c : 0.000326
  DM_4crsol_c : 0.000108

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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