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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3752 b2930 b4232 b3697 b3925 b0871 b2926 b3617 b2407 b3236 b1982 b3946 b2210 b0825 b4388 b4381 b0112 b0114 b0529 b2492 b0904 b0516 b3662 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.283525 (mmol/gDw/h)
  Minimum Production Rate : 0.922053 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.861859
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.828969
  EX_pi_e : 2.117595
  EX_so4_e : 0.071397
  EX_k_e : 0.055342
  EX_fe2_e : 0.004554
  EX_mg2_e : 0.002460
  EX_ca2_e : 0.001476
  EX_cl_e : 0.001476
  EX_cu2_e : 0.000201
  EX_mn2_e : 0.000196
  EX_zn2_e : 0.000097
  EX_ni2_e : 0.000092

Product: (mmol/gDw/h)
  EX_h2o_e : 46.634897
  EX_co2_e : 26.934482
  EX_h_e : 8.363500
  EX_pyr_e : 3.913488
  Auxiliary production reaction : 0.922053
  EX_acald_e : 0.693887
  EX_alltn_e : 0.000191
  DM_mththf_c : 0.000127
  DM_5drib_c : 0.000064
  DM_4crsol_c : 0.000063

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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