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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b1478 b1241 b4069 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b2210 b2799 b3945 b1602 b2913 b4381 b2406 b3915 b3654 b3714 b3664 b4064 b4464 b0755 b3612 b0529 b2492 b0904 b1380 b0516 b3662 b1518 b0606 b0221 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.365388 (mmol/gDw/h)
  Minimum Production Rate : 1.148523 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 996.424076
  EX_o2_e : 284.606835
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.243206
  EX_pi_e : 3.798024
  EX_so4_e : 0.092012
  EX_k_e : 0.071321
  EX_mg2_e : 0.003170
  EX_ca2_e : 0.001902
  EX_cl_e : 0.001902
  EX_cu2_e : 0.000259
  EX_mn2_e : 0.000252
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994132
  EX_h2o_e : 554.222186
  EX_co2_e : 34.239525
  Auxiliary production reaction : 1.148523
  EX_ac_e : 0.212724
  DM_mththf_c : 0.000164
  DM_5drib_c : 0.000082
  DM_4crsol_c : 0.000081

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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