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 (87 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b2779 b2926 b0160 b0517 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b4381 b2406 b2789 b3127 b0511 b2975 b0114 b3603 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b3821 b4141 b1798 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.498153 (mmol/gDw/h)
  Minimum Production Rate : 0.050655 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.169933
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.788963
  EX_pi_e : 0.632485
  EX_so4_e : 0.176099
  EX_k_e : 0.097236
  EX_fe2_e : 0.008001
  EX_mg2_e : 0.004321
  EX_ca2_e : 0.002593
  EX_cl_e : 0.002593
  EX_cu2_e : 0.000353
  EX_mn2_e : 0.000344
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.558587
  EX_co2_e : 38.268319
  EX_h_e : 4.783563
  Auxiliary production reaction : 0.050655
  EX_xan_e : 0.013592
  DM_5drib_c : 0.000334
  DM_4crsol_c : 0.000111

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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