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 : accoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b3752 b0871 b2407 b3124 b0120 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0261 b2406 b0112 b2868 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3821 b0514 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.550565 (mmol/gDw/h)
  Minimum Production Rate : 0.442323 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.027538
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.044773
  EX_pi_e : 1.858045
  EX_so4_e : 0.580966
  EX_k_e : 0.107466
  EX_fe2_e : 0.008843
  EX_mg2_e : 0.004776
  EX_ca2_e : 0.002866
  EX_cl_e : 0.002866
  EX_cu2_e : 0.000390
  EX_mn2_e : 0.000380
  EX_zn2_e : 0.000188
  EX_ni2_e : 0.000178
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 46.950213
  EX_co2_e : 23.559329
  EX_h_e : 6.388423
  EX_acald_e : 1.832122
  Auxiliary production reaction : 0.442323
  EX_hxan_e : 0.000616
  DM_5drib_c : 0.000369
  EX_glyc__R_e : 0.000184
  DM_4crsol_c : 0.000123

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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