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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4384 b2744 b3708 b3008 b3752 b0871 b2925 b2097 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b2440 b4374 b2361 b2291 b0261 b0411 b3945 b0452 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b2413 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.768078 (mmol/gDw/h)
  Minimum Production Rate : 0.143741 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.769446
  EX_o2_e : 274.429131
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.568162
  EX_pi_e : 0.740892
  EX_so4_e : 0.321805
  EX_k_e : 0.149923
  EX_mg2_e : 0.006663
  EX_ca2_e : 0.003998
  EX_cl_e : 0.003998
  EX_cu2_e : 0.000545
  EX_mn2_e : 0.000531
  EX_zn2_e : 0.000262
  EX_ni2_e : 0.000248
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987664
  EX_h2o_e : 547.357517
  EX_co2_e : 26.534900
  Auxiliary production reaction : 0.143741
  EX_met__L_e : 0.128387
  DM_oxam_c : 0.000859
  DM_5drib_c : 0.000515
  DM_4crsol_c : 0.000171

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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