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 : hisp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4467 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3926 b0871 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b3616 b3589 b0261 b1602 b4381 b2406 b0114 b0529 b2492 b0904 b1380 b2660 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.410951 (mmol/gDw/h)
  Minimum Production Rate : 1.335904 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.545607
  EX_o2_e : 283.151105
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.445952
  EX_pi_e : 1.732310
  EX_so4_e : 0.103486
  EX_k_e : 0.080215
  EX_mg2_e : 0.003565
  EX_ca2_e : 0.002139
  EX_cl_e : 0.002139
  EX_cu2_e : 0.000291
  EX_mn2_e : 0.000284
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993400
  EX_h2o_e : 552.894038
  EX_co2_e : 34.391881
  Auxiliary production reaction : 1.335904
  EX_etoh_e : 0.362057
  DM_5drib_c : 0.000276
  DM_4crsol_c : 0.000092

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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