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 : hpyr_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b2779 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b1302 b2662 b4139 b1033 b1623 b4014 b2976 b3945 b1602 b3915 b0509 b3125 b3029 b1380 b2660 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.600352 (mmol/gDw/h)
  Minimum Production Rate : 0.241843 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.591047
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.483751
  EX_pi_e : 0.579103
  EX_so4_e : 0.151181
  EX_k_e : 0.117185
  EX_fe3_e : 0.009642
  EX_mg2_e : 0.005208
  EX_ca2_e : 0.003125
  EX_cl_e : 0.003125
  EX_cu2_e : 0.000426
  EX_mn2_e : 0.000415
  EX_zn2_e : 0.000205
  EX_ni2_e : 0.000194
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 50.723437
  EX_co2_e : 34.632778
  EX_h_e : 5.767759
  Auxiliary production reaction : 0.241843
  DM_5drib_c : 0.000135
  DM_4crsol_c : 0.000134

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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