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 : ametam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4382 b4384 b2744 b3708 b3008 b0871 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b3665 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b2835 b0494 b4141 b1798 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.784317 (mmol/gDw/h)
  Minimum Production Rate : 0.090248 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.597647
  EX_o2_e : 274.773680
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.014688
  EX_pi_e : 0.756557
  EX_so4_e : 0.287755
  EX_k_e : 0.153093
  EX_mg2_e : 0.006804
  EX_ca2_e : 0.004082
  EX_cl_e : 0.004082
  EX_cu2_e : 0.000556
  EX_mn2_e : 0.000542
  EX_zn2_e : 0.000267
  EX_ni2_e : 0.000253
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987403
  EX_h2o_e : 548.423363
  EX_co2_e : 26.539507
  Auxiliary production reaction : 0.090248
  EX_ade_e : 0.000528
  DM_mththf_c : 0.000351
  DM_5drib_c : 0.000176
  DM_4crsol_c : 0.000175

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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