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 : preq0_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b3617 b0030 b2407 b1982 b4374 b2361 b2291 b0261 b2406 b0112 b2975 b0114 b3603 b0509 b3125 b0529 b2492 b0904 b0508 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.461252 (mmol/gDw/h)
  Minimum Production Rate : 1.767956 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.588542
  EX_nh4_e : 13.821779
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.444927
  EX_so4_e : 0.116153
  EX_k_e : 0.090033
  EX_fe2_e : 0.007408
  EX_mg2_e : 0.004001
  EX_ca2_e : 0.002401
  EX_cl_e : 0.002401
  EX_cu2_e : 0.000327
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.665222
  EX_co2_e : 20.268325
  EX_h_e : 17.289799
  EX_ac_e : 4.210819
  Auxiliary production reaction : 1.767956
  DM_oxam_c : 0.000516
  DM_5drib_c : 0.000310
  DM_4crsol_c : 0.000103

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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