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 : dgdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2502 b2744 b3708 b2297 b2458 b2779 b3844 b1004 b3713 b1109 b0046 b3124 b3236 b1638 b0937 b1982 b4139 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b2913 b2789 b3127 b1539 b2492 b0904 b2954 b1533 b3029 b1380 b0514 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.498966 (mmol/gDw/h)
  Minimum Production Rate : 0.078864 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.798544
  EX_o2_e : 287.277832
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.785907
  EX_pi_e : 0.639035
  EX_so4_e : 0.125650
  EX_k_e : 0.097395
  EX_mg2_e : 0.004329
  EX_ca2_e : 0.002597
  EX_cl_e : 0.002597
  EX_cu2_e : 0.000354
  EX_mn2_e : 0.000345
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991986
  EX_h2o_e : 552.349328
  EX_co2_e : 38.146194
  EX_ac_e : 0.290491
  Auxiliary production reaction : 0.078864
  EX_ade_e : 0.000558
  DM_5drib_c : 0.000335
  DM_4crsol_c : 0.000111

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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