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 : ppgpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b4467 b1478 b3399 b1241 b4069 b4384 b2744 b3115 b1849 b2296 b2926 b0030 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b1982 b4139 b1623 b0261 b0411 b2799 b3945 b1602 b2913 b4381 b3915 b2975 b3603 b0509 b3125 b0529 b2492 b0904 b2954 b3927 b3029 b1380 b0508 b3662 b0221 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.418486 (mmol/gDw/h)
  Minimum Production Rate : 0.438055 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.587918
  EX_o2_e : 288.372475
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.712232
  EX_pi_e : 2.155896
  EX_so4_e : 0.105383
  EX_k_e : 0.081686
  EX_mg2_e : 0.003630
  EX_ca2_e : 0.002178
  EX_cl_e : 0.002178
  EX_cu2_e : 0.000297
  EX_mn2_e : 0.000289
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000135
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993279
  EX_h2o_e : 555.575181
  EX_co2_e : 37.951970
  Auxiliary production reaction : 0.438055
  EX_ac_e : 0.243637
  EX_ade_e : 0.000468
  DM_5drib_c : 0.000281
  DM_4crsol_c : 0.000093

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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