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 : ppcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b2502 b2744 b3708 b3008 b0871 b2925 b2097 b2690 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b3945 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.772705 (mmol/gDw/h)
  Minimum Production Rate : 0.038800 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.535934
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.857047
  EX_pi_e : 0.861757
  EX_so4_e : 0.293240
  EX_k_e : 0.150827
  EX_fe2_e : 0.012410
  EX_mg2_e : 0.006703
  EX_cl_e : 0.004022
  EX_ca2_e : 0.004022
  EX_cu2_e : 0.000548
  EX_mn2_e : 0.000534
  EX_zn2_e : 0.000263
  EX_ni2_e : 0.000250
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 47.933511
  EX_co2_e : 26.451480
  EX_h_e : 7.218054
  DM_oxam_c : 0.060722
  EX_5mtr_e : 0.059857
  EX_spmd_e : 0.059857
  Auxiliary production reaction : 0.038800
  DM_5drib_c : 0.000518
  DM_4crsol_c : 0.000172

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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