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 : trp__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (15 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3399 b4382 b2744 b3708 b3008 b0871 b0160 b0120 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b1701 b1805 b3709 b4381 b2406 b3161 b0112 b2868 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b1473 b0594 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.765471 (mmol/gDw/h)
  Minimum Production Rate : 0.233510 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.217979
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.817580
  EX_pi_e : 0.738378
  EX_so4_e : 0.192761
  EX_k_e : 0.149414
  EX_fe2_e : 0.012294
  EX_mg2_e : 0.006640
  EX_cl_e : 0.003984
  EX_ca2_e : 0.003984
  EX_cu2_e : 0.000543
  EX_mn2_e : 0.000529
  EX_zn2_e : 0.000261
  EX_ni2_e : 0.000247
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.176218
  EX_co2_e : 25.906205
  EX_h_e : 7.584012
  Auxiliary production reaction : 0.233510
  EX_xan_e : 0.020029
  EX_hxan_e : 0.000857
  DM_5drib_c : 0.000514
  DM_4crsol_c : 0.000171

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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