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 : dimp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3553 b1478 b3399 b1241 b0351 b2744 b0871 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b1033 b4374 b0675 b2361 b2291 b2799 b3945 b1602 b2913 b3915 b0529 b2492 b0904 b3927 b1380 b1517 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.509032 (mmol/gDw/h)
  Minimum Production Rate : 0.013826 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.905642
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.554176
  EX_pi_e : 0.504841
  EX_so4_e : 0.128184
  EX_k_e : 0.099359
  EX_fe3_e : 0.008176
  EX_mg2_e : 0.004416
  EX_ca2_e : 0.002650
  EX_cl_e : 0.002650
  EX_cu2_e : 0.000361
  EX_mn2_e : 0.000352
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.558670
  EX_co2_e : 38.965463
  EX_h_e : 4.742038
  Auxiliary production reaction : 0.013826
  EX_hxan_e : 0.000343
  DM_mththf_c : 0.000228
  DM_5drib_c : 0.000115
  DM_4crsol_c : 0.000114

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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