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 : 5apru_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b2297 b2458 b0160 b3124 b1982 b3616 b3589 b0675 b2361 b2291 b0261 b4381 b0112 b2789 b3127 b2975 b0114 b3603 b0529 b2492 b0904 b0514   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.506631 (mmol/gDw/h)
  Minimum Production Rate : 0.747768 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.661333
  EX_o2_e : 271.325857
  EX_nh4_e : 10.851453
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.236468
  EX_so4_e : 0.127580
  EX_k_e : 0.098891
  EX_mg2_e : 0.004395
  EX_ca2_e : 0.002637
  EX_cl_e : 0.002637
  EX_cu2_e : 0.000359
  EX_mn2_e : 0.000350
  EX_zn2_e : 0.000173
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991863
  EX_h2o_e : 547.212261
  EX_co2_e : 19.941833
  EX_thymd_e : 1.194121
  Auxiliary production reaction : 0.747768
  EX_ac_e : 0.294953
  DM_oxam_c : 0.000567
  DM_5drib_c : 0.000340
  DM_4crsol_c : 0.000113

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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