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 : ins_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (106 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3942 b1732 b0474 b2518 b3708 b3008 b1479 b3752 b0871 b2925 b2097 b2407 b3844 b3236 b2883 b2463 b2797 b3117 b1814 b4471 b3449 b3946 b2210 b0825 b3551 b4219 b1832 b1778 b4381 b2239 b2406 b2868 b4064 b4464 b0114 b2366 b0755 b3612 b2492 b0904 b2578 b1533 b3927 b1710 b2480 b1511 b1813 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.362241 (mmol/gDw/h)
  Minimum Production Rate : 0.083363 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.992794
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.246845
  EX_pi_e : 0.349420
  EX_so4_e : 0.091220
  EX_k_e : 0.070707
  EX_fe2_e : 0.005818
  EX_mg2_e : 0.003142
  EX_ca2_e : 0.001885
  EX_cl_e : 0.001885
  EX_cu2_e : 0.000257
  EX_mn2_e : 0.000250
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_h2o_e : 43.430395
  EX_co2_e : 27.624897
  EX_h_e : 9.526908
  EX_pyr_e : 4.943464
  EX_mal__L_e : 0.460178
  EX_ins_e : 0.083363
  EX_ade_e : 0.000244
  DM_mththf_c : 0.000162
  DM_5drib_c : 0.000082
  DM_4crsol_c : 0.000081

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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