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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b3752 b0871 b3617 b2407 b0120 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b2406 b0112 b0114 b0886 b0509 b3125 b2366 b2492 b0904 b2578 b1533 b3821 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.549065 (mmol/gDw/h)
  Minimum Production Rate : 0.441117 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.134863
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.018286
  EX_pi_e : 1.852983
  EX_so4_e : 0.579383
  EX_k_e : 0.107174
  EX_fe2_e : 0.008819
  EX_mg2_e : 0.004763
  EX_ca2_e : 0.002858
  EX_cl_e : 0.002858
  EX_cu2_e : 0.000389
  EX_mn2_e : 0.000379
  EX_zn2_e : 0.000187
  EX_ni2_e : 0.000177
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 46.983128
  EX_co2_e : 23.219160
  EX_h_e : 6.811089
  EX_acald_e : 1.827130
  Auxiliary production reaction : 0.441117
  DM_oxam_c : 0.000614
  DM_5drib_c : 0.000368
  EX_glyclt_e : 0.000367
  DM_4crsol_c : 0.000122

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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