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 : dadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b0871 b2779 b2925 b2097 b3617 b0517 b3946 b0825 b4388 b4381 b2789 b3127 b0114 b0529 b2492 b0904 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.315303 (mmol/gDw/h)
  Minimum Production Rate : 0.341120 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.372846
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.115773
  EX_pi_e : 0.986384
  EX_so4_e : 0.079400
  EX_k_e : 0.061545
  EX_fe2_e : 0.005064
  EX_mg2_e : 0.002735
  EX_cl_e : 0.001641
  EX_ca2_e : 0.001641
  EX_cu2_e : 0.000224
  EX_mn2_e : 0.000218
  EX_zn2_e : 0.000108
  EX_ni2_e : 0.000102

Product: (mmol/gDw/h)
  EX_h2o_e : 44.985403
  EX_co2_e : 27.617204
  EX_h_e : 8.865480
  EX_pyr_e : 4.598732
  EX_acald_e : 1.113798
  Auxiliary production reaction : 0.341120
  EX_alltn_e : 0.001231
  EX_glyclt_e : 0.000211
  DM_mththf_c : 0.000141
  DM_5drib_c : 0.000071
  DM_4crsol_c : 0.000070

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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