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 : gmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 102: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b1479 b0871 b3236 b2883 b2463 b1982 b3616 b3589 b2210 b0675 b2361 b2291 b0411 b4381 b0114 b0529 b2492 b0904 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.588965 (mmol/gDw/h)
  Minimum Production Rate : 0.425070 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.173910
  EX_nh4_e : 11.149203
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.525806
  EX_so4_e : 0.148313
  EX_k_e : 0.114962
  EX_fe2_e : 0.009459
  EX_mg2_e : 0.005109
  EX_cl_e : 0.003066
  EX_ca2_e : 0.003066
  EX_cu2_e : 0.000418
  EX_mn2_e : 0.000407
  EX_zn2_e : 0.000201
  EX_ni2_e : 0.000190
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 50.340845
  EX_co2_e : 23.295674
  EX_h_e : 10.200077
  EX_acald_e : 1.475920
  Auxiliary production reaction : 0.957687
  DM_mththf_c : 0.000264
  DM_5drib_c : 0.000133
  DM_4crsol_c : 0.000131

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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