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 : trp__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (14 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b0160 b1982 b2797 b3117 b1814 b4471 b0595 b4374 b0675 b2361 b2291 b0261 b1701 b1805 b0507 b3709 b3161 b0112 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b2965 b0693 b1473 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.761423 (mmol/gDw/h)
  Minimum Production Rate : 0.258979 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.465491
  EX_o2_e : 274.104662
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.744232
  EX_pi_e : 0.734473
  EX_so4_e : 0.191741
  EX_k_e : 0.148624
  EX_mg2_e : 0.006605
  EX_ca2_e : 0.003963
  EX_cl_e : 0.003963
  EX_cu2_e : 0.000540
  EX_mn2_e : 0.000526
  EX_zn2_e : 0.000260
  EX_ni2_e : 0.000246
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987771
  EX_h2o_e : 548.046087
  EX_co2_e : 25.860992
  Auxiliary production reaction : 0.258979
  DM_oxam_c : 0.002973
  DM_5drib_c : 0.002631
  DM_4crsol_c : 0.002290
  EX_glyclt_e : 0.002121

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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