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 : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 61
  Gene deletion: b1478 b4382 b1241 b0351 b4069 b4384 b3708 b3115 b1849 b2296 b0030 b2407 b3124 b2937 b3962 b1982 b0477 b4139 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b3665 b1415 b1014 b4014 b0261 b2976 b3945 b3709 b2406 b3161 b0112 b2789 b3127 b2975 b0114 b3603 b0509 b3125 b2366 b0755 b3612 b2492 b0904 b2954 b0591 b1533 b3821 b1380 b0325 b1473 b0514 b4266 b3662 b2842 b1985   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.301526 (mmol/gDw/h)
  Minimum Production Rate : 0.108668 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.984946
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.812437
  EX_so4_e : 0.978212
  EX_pi_e : 0.616859
  EX_k_e : 0.058856
  EX_fe2_e : 0.004843
  EX_mg2_e : 0.002616
  EX_ca2_e : 0.001569
  EX_cl_e : 0.001569
  EX_cu2_e : 0.000214
  EX_mn2_e : 0.000208
  EX_zn2_e : 0.000103
  EX_ni2_e : 0.000097

Product: (mmol/gDw/h)
  EX_h2o_e : 47.555344
  EX_co2_e : 35.720232
  EX_h_e : 4.912503
  EX_ac_e : 2.607678
  EX_met__L_e : 0.793613
  Auxiliary production reaction : 0.108668
  EX_ade_e : 0.000337
  DM_5drib_c : 0.000202
  EX_dxylnt_e : 0.000202
  DM_4crsol_c : 0.000067

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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