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 (62 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 56
  Gene deletion: b3553 b1478 b3399 b4382 b1241 b4069 b2502 b2744 b3708 b3115 b1849 b2296 b2779 b2926 b1004 b3713 b1109 b0046 b3236 b0120 b1982 b2797 b3117 b1814 b4471 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b3709 b2913 b4381 b2406 b3161 b0112 b2789 b3127 b3915 b2366 b2492 b0904 b1533 b3825 b1380 b1473 b0494 b4141 b1798 b0606 b0221 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.293027 (mmol/gDw/h)
  Minimum Production Rate : 0.428989 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.097391
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.207548
  EX_pi_e : 1.569615
  EX_so4_e : 0.502777
  EX_k_e : 0.057197
  EX_fe3_e : 0.004707
  EX_mg2_e : 0.002542
  EX_ca2_e : 0.001525
  EX_cl_e : 0.001525
  EX_cu2_e : 0.000208
  EX_mn2_e : 0.000202
  EX_zn2_e : 0.000100
  EX_ni2_e : 0.000095

Product: (mmol/gDw/h)
  EX_h2o_e : 50.957306
  EX_co2_e : 34.132959
  EX_h_e : 5.561261
  EX_ac_e : 1.537169
  Auxiliary production reaction : 0.428986
  EX_ade_e : 0.007995
  DM_5drib_c : 0.000197
  DM_4crsol_c : 0.000065

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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