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 : dmpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (102 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b3399 b4069 b2502 b2744 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b4374 b2361 b2291 b0261 b3945 b1602 b2913 b3915 b1727 b0114 b0755 b3612 b0529 b2492 b0904 b3029 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.462251 (mmol/gDw/h)
  Minimum Production Rate : 0.010569 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.349161
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.992267
  EX_pi_e : 0.467027
  EX_so4_e : 0.116404
  EX_k_e : 0.090228
  EX_fe3_e : 0.007424
  EX_mg2_e : 0.004010
  EX_cl_e : 0.002406
  EX_ca2_e : 0.002406
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.275144
  EX_co2_e : 37.666256
  EX_h_e : 5.898016
  EX_fum_e : 0.692351
  EX_ac_e : 0.269116
  Auxiliary production reaction : 0.010569
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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