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 : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4382 b4384 b3708 b3008 b3752 b0871 b2407 b0121 b1982 b2797 b3117 b1814 b4471 b0596 b3665 b0261 b0507 b3709 b2406 b3161 b0112 b2975 b0114 b3603 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.738011 (mmol/gDw/h)
  Minimum Production Rate : 0.508199 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.063631
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.499185
  EX_pi_e : 2.236487
  EX_so4_e : 0.185846
  EX_k_e : 0.144055
  EX_fe2_e : 0.011853
  EX_mg2_e : 0.006402
  EX_ca2_e : 0.003841
  EX_cl_e : 0.003841
  EX_cu2_e : 0.000523
  EX_mn2_e : 0.000510
  EX_zn2_e : 0.000252
  EX_ni2_e : 0.000238
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 49.707548
  EX_co2_e : 25.128463
  EX_h_e : 7.293470
  Auxiliary production reaction : 0.508199
  EX_ade_e : 0.000826
  DM_5drib_c : 0.000495
  DM_4crsol_c : 0.000165

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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