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 : uacmam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3916 b3831 b1278 b3614 b0910 b4152 b2779 b2781 b1850 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b1200 b1701 b1805 b4138 b4123 b0621 b2913 b4381 b2406 b1723 b3918 b1517 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.612690 (mmol/gDw/h)
  Minimum Production Rate : 0.108055 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.106247
  EX_o2_e : 276.640144
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.450342
  EX_pi_e : 0.807115
  EX_so4_e : 0.154288
  EX_k_e : 0.119593
  EX_mg2_e : 0.005315
  EX_ca2_e : 0.003189
  EX_cl_e : 0.003189
  EX_cu2_e : 0.000434
  EX_mn2_e : 0.000423
  EX_zn2_e : 0.000209
  EX_ni2_e : 0.000198
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.918315
  EX_h2o_e : 547.744675
  EX_co2_e : 27.571630
  EX_succ_e : 0.638908
  EX_ura_e : 0.110899
  Auxiliary production reaction : 0.108055
  EX_pheme_e : 0.071845
  DM_mththf_c : 0.000274
  DM_5drib_c : 0.000138
  DM_4crsol_c : 0.000137

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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