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 : prbamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b4382 b1241 b0351 b4384 b3708 b3008 b3752 b0871 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b0261 b0411 b2799 b3945 b1602 b0153 b2406 b0452 b1727 b0584 b0529 b1539 b2492 b0904 b1533 b3927 b1380 b2660 b0606 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.497983 (mmol/gDw/h)
  Minimum Production Rate : 0.034552 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 38.062884
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.553715
  EX_pi_e : 0.549460
  EX_so4_e : 0.125402
  EX_k_e : 0.097203
  EX_fe2_e : 0.007998
  EX_mg2_e : 0.004320
  EX_cl_e : 0.002592
  EX_ca2_e : 0.002592
  EX_cu2_e : 0.000353
  EX_mn2_e : 0.000344
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.677569
  EX_co2_e : 39.037928
  EX_h_e : 4.751208
  Auxiliary production reaction : 0.034552
  EX_ade_e : 0.000557
  DM_5drib_c : 0.000334
  DM_4crsol_c : 0.000111

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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