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 : q8h2_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3752 b0871 b3617 b2407 b3665 b2406 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.536396 (mmol/gDw/h)
  Minimum Production Rate : 0.218142 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 19.168058
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.793027
  EX_pi_e : 0.517410
  EX_so4_e : 0.135075
  EX_k_e : 0.104701
  EX_fe2_e : 0.008615
  EX_mg2_e : 0.004653
  EX_cl_e : 0.002792
  EX_ca2_e : 0.002792
  EX_cu2_e : 0.000380
  EX_mn2_e : 0.000371
  EX_zn2_e : 0.000183
  EX_ni2_e : 0.000173
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 40.585432
  EX_co2_e : 24.021148
  EX_h_e : 4.928617
  DM_mththf_c : 0.654666
  Auxiliary production reaction : 0.218142
  DM_5drib_c : 0.000121
  DM_4crsol_c : 0.000120

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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