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 : trp__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (6 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4382 b4384 b3708 b3008 b0871 b0030 b2407 b0120 b1982 b2797 b3117 b1814 b4471 b3665 b0261 b2342 b3845 b3709 b2406 b3161 b0112 b0452 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b1473 b0594 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.756527 (mmol/gDw/h)
  Minimum Production Rate : 0.260475 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.334147
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.695615
  EX_pi_e : 0.729751
  EX_so4_e : 0.190509
  EX_k_e : 0.147669
  EX_fe2_e : 0.012151
  EX_mg2_e : 0.006563
  EX_ca2_e : 0.003938
  EX_cl_e : 0.003938
  EX_cu2_e : 0.000536
  EX_mn2_e : 0.000523
  EX_zn2_e : 0.000258
  EX_ni2_e : 0.000244
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.146943
  EX_co2_e : 26.076881
  EX_h_e : 7.476458
  Auxiliary production reaction : 0.260475
  EX_ade_e : 0.000847
  DM_5drib_c : 0.000508
  DM_4crsol_c : 0.000169

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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