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 : prpncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (5 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4384 b3708 b3008 b3752 b0871 b2407 b1982 b2797 b3117 b1814 b4471 b2440 b0261 b4381 b2406 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b0494 b0515 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.772265 (mmol/gDw/h)
  Minimum Production Rate : 0.042844 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.439432
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.966784
  EX_pi_e : 1.005448
  EX_so4_e : 0.283461
  EX_k_e : 0.150741
  EX_fe2_e : 0.012403
  EX_mg2_e : 0.006699
  EX_ca2_e : 0.004020
  EX_cl_e : 0.004020
  EX_cu2_e : 0.000548
  EX_mn2_e : 0.000534
  EX_zn2_e : 0.000263
  EX_ni2_e : 0.000249
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.420746
  EX_co2_e : 26.176182
  EX_h_e : 7.364157
  Auxiliary production reaction : 0.086839
  EX_alltn_e : 0.003015
  EX_5mtr_e : 0.002151
  EX_spmd_e : 0.002151
  DM_5drib_c : 0.000518
  DM_4crsol_c : 0.000172

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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