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 : cdigmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b4467 b4269 b0493 b3588 b3003 b3011 b4384 b2744 b0871 b2925 b2097 b2926 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b2690 b3908 b1656 b1982 b4139 b1623 b0261 b0411 b2799 b3945 b1602 b2913 b4381 b2868 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b3662 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.349724 (mmol/gDw/h)
  Minimum Production Rate : 0.046763 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.417652
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.246583
  EX_pi_e : 0.430873
  EX_so4_e : 0.088068
  EX_k_e : 0.068264
  EX_mg2_e : 0.003034
  EX_fe2_e : 0.002886
  EX_fe3_e : 0.002731
  EX_ca2_e : 0.001820
  EX_cl_e : 0.001820
  EX_cu2_e : 0.000248
  EX_mn2_e : 0.000242
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000113

Product: (mmol/gDw/h)
  EX_h2o_e : 44.101669
  EX_co2_e : 28.118322
  EX_h_e : 9.121901
  EX_pyr_e : 5.529701
  Auxiliary production reaction : 0.046763
  EX_ade_e : 0.000391
  DM_5drib_c : 0.000235
  DM_4crsol_c : 0.000078

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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