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 : sbzcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 63
  Gene deletion: b3553 b1241 b0351 b4069 b4384 b1278 b3708 b1479 b3752 b0512 b2297 b2458 b2779 b2407 b3844 b1238 b3236 b2690 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b3449 b4267 b1033 b0675 b1415 b1014 b4014 b0261 b2976 b0822 b2799 b0507 b3709 b1907 b0153 b2913 b4381 b0590 b2406 b3161 b0112 b0837 b0124 b0114 b1539 b2492 b0904 b1533 b1380 b0418 b1473 b0494 b0594 b3715 b4266 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.281927 (mmol/gDw/h)
  Minimum Production Rate : 0.166433 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.161420
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.721830
  EX_pi_e : 0.771235
  EX_so4_e : 0.748201
  EX_k_e : 0.055030
  EX_fe2_e : 0.004529
  EX_mg2_e : 0.002446
  EX_ca2_e : 0.001467
  EX_cl_e : 0.001467
  EX_cu2_e : 0.000200
  EX_mn2_e : 0.000195
  EX_zn2_e : 0.000096
  EX_ni2_e : 0.000091

Product: (mmol/gDw/h)
  EX_h2o_e : 49.001277
  EX_co2_e : 36.205451
  EX_h_e : 4.916997
  EX_ac_e : 2.170148
  EX_met__L_e : 0.510776
  Auxiliary production reaction : 0.166429
  EX_alltn_e : 0.000315
  DM_5drib_c : 0.000189
  EX_dxylnt_e : 0.000189
  DM_4crsol_c : 0.000063

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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