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 (55 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b1478 b4382 b1241 b0351 b4069 b4384 b1278 b3708 b3752 b0871 b3115 b1849 b2296 b2925 b2097 b3617 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b0675 b0261 b0822 b0507 b3709 b2406 b3161 b0112 b0114 b0755 b3612 b1539 b2492 b0904 b1533 b3821 b0508 b1473 b0594 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.399966 (mmol/gDw/h)
  Minimum Production Rate : 0.424681 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.143682
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.640297
  EX_pi_e : 1.659853
  EX_so4_e : 0.871773
  EX_k_e : 0.078070
  EX_fe2_e : 0.006424
  EX_mg2_e : 0.003470
  EX_ca2_e : 0.002082
  EX_cl_e : 0.002082
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000276
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_h2o_e : 46.042490
  EX_co2_e : 26.287670
  EX_h_e : 7.495171
  EX_ac_e : 2.889066
  Auxiliary production reaction : 0.424681
  EX_met__L_e : 0.346373
  DM_oxam_c : 0.001561
  DM_5drib_c : 0.001382
  DM_4crsol_c : 0.001203
  EX_glyclt_e : 0.000268

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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