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 : accoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b2836 b3399 b4382 b4069 b2502 b2744 b3708 b3008 b2297 b2458 b2779 b1982 b2797 b3117 b1814 b4471 b2440 b0675 b2361 b0261 b3709 b4381 b2406 b3161 b0112 b2789 b3127 b2975 b0114 b3603 b2366 b0755 b3612 b2492 b0904 b2947 b3035 b2578 b1533 b3927 b1473 b0514 b4141 b1798 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.453130 (mmol/gDw/h)
  Minimum Production Rate : 0.134521 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.398977
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.848854
  EX_pi_e : 0.840646
  EX_so4_e : 0.248626
  EX_k_e : 0.088448
  EX_fe2_e : 0.007280
  EX_mg2_e : 0.003931
  EX_ca2_e : 0.002359
  EX_cl_e : 0.002359
  EX_cu2_e : 0.000321
  EX_mn2_e : 0.000313
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.163594
  EX_co2_e : 37.482589
  EX_h_e : 4.990148
  EX_ac_e : 0.398325
  Auxiliary production reaction : 0.134518
  DM_oxam_c : 0.012364
  EX_etha_e : 0.001096
  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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