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 : dgdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b3708 b3752 b2297 b2458 b2926 b2407 b1238 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b2440 b0261 b0411 b2799 b3945 b1602 b2913 b4381 b2406 b3915 b1539 b2492 b0904 b1533 b1380 b4141 b1798 b0606 b0221 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.444462 (mmol/gDw/h)
  Minimum Production Rate : 0.320280 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.626624
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.437358
  EX_pi_e : 1.069246
  EX_so4_e : 0.111925
  EX_k_e : 0.086756
  EX_fe3_e : 0.007140
  EX_mg2_e : 0.003856
  EX_ca2_e : 0.002313
  EX_cl_e : 0.002313
  EX_cu2_e : 0.000315
  EX_mn2_e : 0.000307
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.302061
  EX_co2_e : 36.400294
  EX_h_e : 6.416384
  EX_glyclt_e : 0.783071
  Auxiliary production reaction : 0.320257
  EX_ac_e : 0.258761
  EX_etha_e : 0.033430
  EX_ade_e : 0.000497
  DM_5drib_c : 0.000298
  DM_4crsol_c : 0.000099

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.

Last updated: 21-Sep-2023
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