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 : xan_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (87 of 94: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b3942 b1732 b4069 b4384 b2744 b3708 b2297 b2458 b0160 b3124 b0517 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b2789 b3127 b0452 b0511 b0114 b1539 b2492 b0904 b1533 b0514   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.774159 (mmol/gDw/h)
  Minimum Production Rate : 0.243613 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.179101
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.335300
  EX_pi_e : 0.746758
  EX_so4_e : 0.194949
  EX_k_e : 0.151110
  EX_fe2_e : 0.012434
  EX_mg2_e : 0.006716
  EX_ca2_e : 0.004029
  EX_cl_e : 0.004029
  EX_cu2_e : 0.000549
  EX_mn2_e : 0.000535
  EX_zn2_e : 0.000264
  EX_ni2_e : 0.000250
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.734729
  EX_co2_e : 26.098822
  EX_h_e : 8.541457
  EX_ac_e : 0.450704
  EX_xan_e : 0.243613
  EX_glyclt_e : 0.003022
  DM_5drib_c : 0.000174
  DM_4crsol_c : 0.000173

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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