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 : hemeO_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b1478 b1241 b4069 b4384 b3752 b2297 b2458 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b1982 b1033 b4014 b0261 b2976 b2799 b3945 b1602 b0507 b2913 b4381 b2406 b3915 b0529 b2492 b0904 b3029 b1380 b1695 b3662 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.205184 (mmol/gDw/h)
  Minimum Production Rate : 0.224297 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.798433
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.357275
  EX_fe3_e : 0.227592
  EX_pi_e : 0.197922
  EX_so4_e : 0.051669
  EX_k_e : 0.040051
  EX_mg2_e : 0.001780
  EX_ca2_e : 0.001068
  EX_cl_e : 0.001068
  EX_cu2_e : 0.000145
  EX_mn2_e : 0.000142
  EX_zn2_e : 0.000070
  EX_ni2_e : 0.000066

Product: (mmol/gDw/h)
  EX_h2o_e : 49.038117
  EX_co2_e : 31.414692
  EX_h_e : 8.494074
  EX_fum_e : 1.111611
  EX_ade_e : 0.448823
  DM_5drib_c : 0.448731
  Auxiliary production reaction : 0.224297
  EX_ac_e : 0.119455
  DM_4crsol_c : 0.000046

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.

Last updated: 21-Sep-2023
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