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 : 5mthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b4384 b3708 b2297 b2458 b2926 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b0261 b2799 b3945 b1602 b2913 b2406 b3915 b0452 b2366 b2492 b0904 b1533 b1380 b4141 b1798 b3662 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.424940 (mmol/gDw/h)
  Minimum Production Rate : 0.235627 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.660709
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.240605
  EX_pi_e : 0.409900
  EX_so4_e : 0.107009
  EX_k_e : 0.082945
  EX_fe3_e : 0.006827
  EX_mg2_e : 0.003686
  EX_ca2_e : 0.002212
  EX_cl_e : 0.002212
  EX_cu2_e : 0.000301
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.477000
  EX_co2_e : 37.013361
  EX_h_e : 6.212734
  EX_ac_e : 0.247395
  Auxiliary production reaction : 0.235627
  EX_glyclt_e : 0.167078
  EX_hxan_e : 0.000476
  DM_5drib_c : 0.000285
  DM_4crsol_c : 0.000095

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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