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 : dhnpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b2407 b3616 b3589 b3665 b0675 b2361 b0261 b4381 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.542316 (mmol/gDw/h)
  Minimum Production Rate : 0.643485 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 21.754076
  EX_nh4_e : 11.315734
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.523122
  EX_so4_e : 0.136566
  EX_k_e : 0.105856
  EX_fe2_e : 0.008710
  EX_mg2_e : 0.004705
  EX_ca2_e : 0.002823
  EX_cl_e : 0.002823
  EX_cu2_e : 0.000385
  EX_mn2_e : 0.000375
  EX_zn2_e : 0.000185
  EX_ni2_e : 0.000175
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.222285
  EX_co2_e : 20.742344
  EX_h_e : 10.441782
  EX_thymd_e : 1.120670
  Auxiliary production reaction : 0.643485
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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.

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Last updated: 21-Sep-2023
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