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 : aps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b2925 b2097 b2883 b2690 b2688 b2797 b3117 b1814 b4471 b1623 b3665 b0675 b0822 b4381 b2406 b0452 b3654 b3714 b3664 b1727 b4064 b4464 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b1912 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.764079 (mmol/gDw/h)
  Minimum Production Rate : 0.152834 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.137191
  EX_o2_e : 275.018003
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.036157
  EX_pi_e : 0.889870
  EX_so4_e : 0.345245
  EX_k_e : 0.149143
  EX_mg2_e : 0.006628
  EX_ca2_e : 0.003977
  EX_cl_e : 0.003977
  EX_cu2_e : 0.000542
  EX_mn2_e : 0.000528
  EX_zn2_e : 0.000261
  EX_ni2_e : 0.000247
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987728
  EX_h2o_e : 548.603167
  EX_co2_e : 26.073866
  EX_pyr_e : 0.331382
  Auxiliary production reaction : 0.152834
  DM_oxam_c : 0.019993
  EX_mththf_e : 0.000342
  DM_5drib_c : 0.000172
  DM_4crsol_c : 0.000170

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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