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 (81 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b4384 b2744 b3708 b3115 b1849 b2296 b2407 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b2440 b0595 b0675 b2361 b4014 b0261 b2976 b0507 b3709 b2406 b3161 b0112 b0452 b2975 b0114 b3603 b2366 b2492 b0904 b1533 b1473 b4141 b1798 b3662 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.274403 (mmol/gDw/h)
  Minimum Production Rate : 0.820983 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.822925
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.710859
  EX_pi_e : 0.264691
  EX_so4_e : 0.069100
  EX_k_e : 0.053562
  EX_fe3_e : 0.004407
  EX_mg2_e : 0.002380
  EX_ca2_e : 0.001428
  EX_cl_e : 0.001428
  EX_cu2_e : 0.000195
  EX_mn2_e : 0.000190
  EX_zn2_e : 0.000094
  EX_ni2_e : 0.000089

Product: (mmol/gDw/h)
  EX_h2o_e : 49.789654
  EX_co2_e : 27.767310
  EX_h_e : 11.368481
  EX_ac_e : 2.274265
  Auxiliary production reaction : 0.820983
  DM_oxam_c : 0.000307
  DM_5drib_c : 0.000184
  EX_etha_e : 0.000135
  DM_4crsol_c : 0.000061

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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