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 : ppcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (102 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3399 b4069 b2744 b3708 b3008 b2297 b2458 b0160 b0593 b1982 b2688 b2797 b3117 b1814 b4471 b2265 b4374 b0675 b2361 b2291 b0261 b3709 b3161 b0112 b3915 b0452 b0114 b0509 b3125 b2366 b2492 b0904 b2578 b1533 b3927 b0508 b4141 b1798 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.709603 (mmol/gDw/h)
  Minimum Production Rate : 0.179932 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.580403
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.923967
  EX_pi_e : 1.224282
  EX_so4_e : 0.358624
  EX_k_e : 0.138510
  EX_fe3_e : 0.011397
  EX_mg2_e : 0.006156
  EX_cl_e : 0.003693
  EX_ca2_e : 0.003693
  EX_cu2_e : 0.000503
  EX_mn2_e : 0.000490
  EX_zn2_e : 0.000242
  EX_ni2_e : 0.000229
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.699598
  EX_co2_e : 25.366424
  EX_h_e : 7.665948
  EX_ac_e : 0.593052
  Auxiliary production reaction : 0.179932
  DM_oxam_c : 0.000794
  DM_5drib_c : 0.000476
  DM_4crsol_c : 0.000158

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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