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 : 25aics_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3553 b1241 b0351 b4069 b4384 b2744 b3752 b2297 b2458 b2779 b2926 b3617 b2407 b1982 b1033 b4374 b2361 b2291 b0261 b0411 b4388 b0112 b2789 b3127 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.371020 (mmol/gDw/h)
  Minimum Production Rate : 1.422101 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.664471
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.695810
  EX_pi_e : 1.779990
  EX_so4_e : 0.093430
  EX_k_e : 0.072421
  EX_fe2_e : 0.005959
  EX_mg2_e : 0.003219
  EX_ca2_e : 0.001931
  EX_cl_e : 0.001931
  EX_cu2_e : 0.000263
  EX_mn2_e : 0.000256
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 46.630837
  EX_co2_e : 21.189268
  EX_h_e : 14.489059
  EX_ac_e : 2.546288
  Auxiliary production reaction : 1.422101
  DM_oxam_c : 0.000415
  DM_5drib_c : 0.000249
  EX_glyclt_e : 0.000248
  DM_4crsol_c : 0.000083

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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