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 (104 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1478 b0469 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b0871 b2779 b1004 b3713 b1109 b0046 b3236 b0477 b2210 b2799 b3945 b1602 b0507 b4381 b3915 b0452 b1539 b2492 b0904 b1380 b2660 b0606 b2285 b1008 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.494508 (mmol/gDw/h)
  Minimum Production Rate : 0.167178 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.475452
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.340648
  EX_pi_e : 0.811284
  EX_so4_e : 0.124528
  EX_k_e : 0.096525
  EX_fe3_e : 0.007944
  EX_mg2_e : 0.004290
  EX_ca2_e : 0.002574
  EX_cl_e : 0.002574
  EX_cu2_e : 0.000351
  EX_mn2_e : 0.000342
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.255913
  EX_co2_e : 38.867009
  EX_h_e : 4.384545
  Auxiliary production reaction : 0.167139
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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