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 : 10fthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 46: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b3831 b4384 b1278 b3708 b3008 b3614 b0910 b0871 b2781 b0030 b2407 b3124 b0651 b2162 b1759 b1982 b2797 b3117 b1814 b4471 b0261 b3709 b4381 b2406 b3161 b0112 b2789 b3127 b2975 b0114 b3603 b0886 b1539 b2492 b0904 b3035 b2578 b1533 b3927 b3821 b2965 b0693 b3918 b1473 b0514 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.756064 (mmol/gDw/h)
  Minimum Production Rate : 0.127927 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.614107
  EX_o2_e : 274.626126
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.335459
  EX_pi_e : 0.729304
  EX_so4_e : 0.190392
  EX_k_e : 0.147578
  EX_mg2_e : 0.006559
  EX_ca2_e : 0.003935
  EX_cl_e : 0.003935
  EX_cu2_e : 0.000536
  EX_mn2_e : 0.000522
  EX_zn2_e : 0.000258
  EX_ni2_e : 0.000244
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987857
  EX_h2o_e : 548.796923
  EX_co2_e : 25.720887
  EX_thym_e : 0.136850
  Auxiliary production reaction : 0.127927
  DM_oxam_c : 0.000846
  DM_5drib_c : 0.000507
  DM_4crsol_c : 0.000169

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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