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 : ins_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 37: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3942 b1732 b0474 b2518 b2744 b3708 b3008 b1479 b0871 b2779 b3236 b2883 b2463 b2797 b3117 b1814 b4471 b2210 b3551 b0411 b4219 b1832 b1778 b4381 b2868 b4064 b4464 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b1710 b2480 b1511 b4141 b1798 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.476327 (mmol/gDw/h)
  Minimum Production Rate : 0.109617 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.786648
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.584361
  EX_pi_e : 0.459468
  EX_so4_e : 0.119949
  EX_k_e : 0.092976
  EX_mg2_e : 0.004132
  EX_fe2_e : 0.003931
  EX_fe3_e : 0.003719
  EX_ca2_e : 0.002479
  EX_cl_e : 0.002479
  EX_cu2_e : 0.000338
  EX_mn2_e : 0.000329
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000154
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.205218
  EX_co2_e : 36.922256
  EX_h_e : 6.034409
  EX_mal__L_e : 0.606968
  Auxiliary production reaction : 0.109617
  EX_ade_e : 0.000321
  DM_mththf_c : 0.000213
  DM_5drib_c : 0.000107
  DM_4crsol_c : 0.000106

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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