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 : glyc__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3399 b0586 b4069 b2502 b2744 b1278 b3708 b3008 b3115 b1849 b2296 b2779 b2925 b2097 b2690 b1982 b2797 b3117 b1814 b4471 b3449 b4374 b0675 b2361 b2291 b0261 b0822 b2789 b3127 b0452 b1727 b0114 b2366 b2492 b0904 b2578 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.606098 (mmol/gDw/h)
  Minimum Production Rate : 0.116755 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.072684
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.779995
  EX_pi_e : 0.584646
  EX_so4_e : 0.152628
  EX_k_e : 0.118306
  EX_fe2_e : 0.009735
  EX_mg2_e : 0.005258
  EX_ca2_e : 0.003155
  EX_cl_e : 0.003155
  EX_cu2_e : 0.000430
  EX_mn2_e : 0.000419
  EX_zn2_e : 0.000207
  EX_ni2_e : 0.000196
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 45.597883
  EX_co2_e : 28.423604
  EX_h_e : 7.692573
  EX_ac_e : 1.538371
  DM_oxam_c : 0.234189
  DM_5drib_c : 0.233917
  DM_4crsol_c : 0.233646
  Auxiliary production reaction : 0.116755

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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