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 : ugmd_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4382 b0474 b2518 b3831 b4384 b3752 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b3449 b4161 b4138 b4123 b0621 b2913 b2406 b0452 b2197 b3918 b0789 b1249 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.521760 (mmol/gDw/h)
  Minimum Production Rate : 0.275104 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.248610
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.750496
  EX_pi_e : 1.053501
  EX_so4_e : 0.131390
  EX_k_e : 0.101844
  EX_fe3_e : 0.008380
  EX_mg2_e : 0.004526
  EX_ca2_e : 0.002716
  EX_cl_e : 0.002716
  EX_cu2_e : 0.000370
  EX_mn2_e : 0.000361
  EX_zn2_e : 0.000178
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 46.969379
  EX_co2_e : 26.399548
  EX_h_e : 8.006226
  EX_succ_e : 0.544087
  Auxiliary production reaction : 0.275104
  EX_ura_e : 0.094901
  DM_5drib_c : 0.000117
  DM_4crsol_c : 0.000116

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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