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 : xtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b3399 b4069 b2744 b2297 b2458 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b3908 b1656 b0937 b1982 b4139 b1033 b4374 b0675 b2361 b0261 b0411 b3945 b1602 b2913 b4381 b2406 b1727 b0114 b0529 b2492 b0904 b2954 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.452576 (mmol/gDw/h)
  Minimum Production Rate : 0.197018 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.778218
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.675856
  EX_pi_e : 1.027613
  EX_so4_e : 0.113968
  EX_k_e : 0.088340
  EX_mg2_e : 0.003926
  EX_fe2_e : 0.003735
  EX_fe3_e : 0.003534
  EX_ca2_e : 0.002356
  EX_cl_e : 0.002356
  EX_cu2_e : 0.000321
  EX_mn2_e : 0.000313
  EX_zn2_e : 0.000154
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.664707
  EX_co2_e : 38.153954
  EX_h_e : 5.076743
  EX_ac_e : 0.263483
  EX_3hpp_e : 0.257240
  Auxiliary production reaction : 0.197018
  DM_5drib_c : 0.000304
  DM_4crsol_c : 0.000101

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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