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 : his__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b0871 b2779 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b2406 b0112 b0511 b0114 b2366 b2492 b0904 b1533 b2413 b0515 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.563624 (mmol/gDw/h)
  Minimum Production Rate : 1.359199 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.733029
  EX_o2_e : 276.438500
  EX_nh4_e : 10.166208
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.543675
  EX_so4_e : 0.141932
  EX_k_e : 0.110015
  EX_mg2_e : 0.004889
  EX_cl_e : 0.002934
  EX_ca2_e : 0.002934
  EX_cu2_e : 0.000400
  EX_mn2_e : 0.000389
  EX_zn2_e : 0.000192
  EX_ni2_e : 0.000182
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990948
  EX_h2o_e : 549.805901
  EX_co2_e : 26.768062
  Auxiliary production reaction : 1.359199
  EX_acald_e : 0.969700
  EX_xan_e : 0.000379
  DM_mththf_c : 0.000253
  DM_5drib_c : 0.000127
  DM_4crsol_c : 0.000126

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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