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 : 2h3oppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3708 b0871 b3115 b1849 b2296 b2925 b2097 b0030 b2407 b3236 b2690 b2797 b3117 b1814 b4471 b3945 b4381 b2868 b0114 b2366 b0529 b2492 b0904 b1533 b3825   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.779150 (mmol/gDw/h)
  Minimum Production Rate : 0.293628 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.330389
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.133615
  EX_pi_e : 0.751573
  EX_so4_e : 0.196206
  EX_k_e : 0.152085
  EX_fe2_e : 0.012514
  EX_mg2_e : 0.006759
  EX_ca2_e : 0.004055
  EX_cl_e : 0.004055
  EX_cu2_e : 0.000552
  EX_mn2_e : 0.000538
  EX_zn2_e : 0.000266
  EX_ni2_e : 0.000252
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.726267
  EX_co2_e : 26.240005
  EX_h_e : 8.171629
  Auxiliary production reaction : 0.293628
  EX_hxan_e : 0.159327
  EX_xan_e : 0.020387
  DM_5drib_c : 0.000175
  DM_4crsol_c : 0.000174

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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