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 : aconm_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (95 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b4269 b0493 b3588 b3003 b3011 b4384 b2930 b4232 b3697 b3925 b0871 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b3908 b1656 b1982 b4139 b1033 b0261 b3945 b1602 b2913 b4381 b2406 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.372416 (mmol/gDw/h)
  Minimum Production Rate : 0.074697 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.214945
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.022061
  EX_pi_e : 0.359235
  EX_so4_e : 0.093782
  EX_k_e : 0.072693
  EX_fe2_e : 0.005981
  EX_mg2_e : 0.003231
  EX_ca2_e : 0.001938
  EX_cl_e : 0.001938
  EX_cu2_e : 0.000264
  EX_mn2_e : 0.000257
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 43.644692
  EX_co2_e : 28.284024
  EX_h_e : 8.873401
  EX_pyr_e : 5.302101
  Auxiliary production reaction : 0.074697
  DM_5drib_c : 0.000250
  DM_4crsol_c : 0.000083

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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