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 : nadhx__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b4384 b3115 b1849 b2296 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b3665 b0411 b2799 b3945 b1602 b3654 b3714 b3664 b0529 b2492 b0904 b1380 b2660 b1517 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.384148 (mmol/gDw/h)
  Minimum Production Rate : 0.403128 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.506710
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.970657
  EX_pi_e : 1.176807
  EX_so4_e : 0.096736
  EX_k_e : 0.074983
  EX_fe2_e : 0.006170
  EX_mg2_e : 0.003332
  EX_ca2_e : 0.001999
  EX_cl_e : 0.001999
  EX_cu2_e : 0.000272
  EX_mn2_e : 0.000265
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_h2o_e : 53.122375
  EX_co2_e : 35.318668
  EX_h_e : 5.768986
  Auxiliary production reaction : 0.403128
  EX_ac_e : 0.223645
  DM_mththf_c : 0.000172
  DM_5drib_c : 0.000086
  DM_4crsol_c : 0.000086

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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