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 : nadph_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b2836 b3553 b4069 b4384 b2744 b3708 b3008 b3752 b2297 b2458 b2779 b2407 b1982 b2688 b2797 b3117 b1814 b4471 b1033 b4374 b2361 b2291 b0261 b0411 b2342 b3845 b3709 b3161 b0112 b2789 b3127 b0114 b2366 b0755 b3612 b2492 b0904 b3035 b2578 b1533 b3927 b1473 b0514 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.622168 (mmol/gDw/h)
  Minimum Production Rate : 0.263549 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.533181
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.564899
  EX_pi_e : 1.390793
  EX_so4_e : 0.156674
  EX_k_e : 0.121443
  EX_fe2_e : 0.009993
  EX_mg2_e : 0.005397
  EX_ca2_e : 0.003238
  EX_cl_e : 0.003238
  EX_cu2_e : 0.000441
  EX_mn2_e : 0.000430
  EX_zn2_e : 0.000212
  EX_ni2_e : 0.000201
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 50.166776
  EX_co2_e : 28.201123
  EX_h_e : 7.398082
  EX_ac_e : 0.362218
  Auxiliary production reaction : 0.263549
  DM_oxam_c : 0.000696
  DM_5drib_c : 0.000417
  DM_4crsol_c : 0.000139

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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