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 : coa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b0945 b3553 b1478 b1241 b3831 b4069 b4384 b3708 b3752 b2297 b2458 b2779 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b0477 b4139 b2797 b3117 b1814 b4471 b2498 b1033 b3665 b0261 b2799 b3945 b1602 b2913 b2406 b3654 b3714 b3664 b1539 b2492 b0904 b2954 b1533 b2835 b1380 b0723 b4141 b1798 b3662 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.455007 (mmol/gDw/h)
  Minimum Production Rate : 0.006455 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.688278
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.633052
  EX_pi_e : 0.458266
  EX_so4_e : 0.121034
  EX_k_e : 0.088814
  EX_fe2_e : 0.007308
  EX_mg2_e : 0.003947
  EX_ca2_e : 0.002368
  EX_cl_e : 0.002368
  EX_cu2_e : 0.000323
  EX_mn2_e : 0.000314
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.395200
  EX_co2_e : 36.085116
  EX_h_e : 6.583388
  EX_ac_e : 0.734631
  EX_succ_e : 0.487387
  EX_thym_e : 0.336917
  Auxiliary production reaction : 0.006455
  DM_5drib_c : 0.000102
  DM_4crsol_c : 0.000101

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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