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 : 4fe4s_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (16 of 16: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b2744 b3708 b3008 b0871 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b2797 b3117 b1814 b4471 b1033 b4374 b2361 b2291 b2799 b1602 b3915 b2366 b2492 b0904 b1781 b3001 b1380 b0325 b2660 b1771 b4141 b1798 b1518 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.490997 (mmol/gDw/h)
  Minimum Production Rate : 0.076301 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.468091
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.304373
  EX_pi_e : 0.473618
  EX_so4_e : 0.428838
  EX_fe3_e : 0.313082
  EX_k_e : 0.095839
  EX_mg2_e : 0.004259
  EX_cl_e : 0.002556
  EX_ca2_e : 0.002556
  EX_cu2_e : 0.000348
  EX_mn2_e : 0.000339
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.190200
  EX_co2_e : 39.301277
  EX_h_e : 4.673609
  EX_acald_e : 0.271409
  Auxiliary production reaction : 0.076298
  EX_ade_e : 0.000330
  DM_mththf_c : 0.000220
  DM_5drib_c : 0.000110
  DM_4crsol_c : 0.000109

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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