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 : 12ppd__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3553 b4269 b0493 b3588 b3003 b3011 b4384 b3926 b0871 b2779 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1033 b1602 b2913 b2492 b0904 b1380 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.514752 (mmol/gDw/h)
  Minimum Production Rate : 0.153222 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.261983
  EX_o2_e : 287.158336
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.559281
  EX_pi_e : 0.496533
  EX_so4_e : 0.129625
  EX_k_e : 0.100476
  EX_mg2_e : 0.004465
  EX_cl_e : 0.002679
  EX_ca2_e : 0.002679
  EX_cu2_e : 0.000365
  EX_mn2_e : 0.000356
  EX_zn2_e : 0.000176
  EX_ni2_e : 0.000166
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991733
  EX_h2o_e : 551.847947
  EX_co2_e : 38.412117
  EX_12ppd__R_e : 0.153222
  DM_5drib_c : 0.000116
  DM_4crsol_c : 0.000115

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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