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 : 5mthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b4384 b3708 b3008 b3752 b0871 b2925 b2097 b2407 b1238 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b2440 b0261 b3945 b0507 b3709 b4381 b2406 b3161 b0112 b0452 b0114 b0886 b2366 b2492 b0904 b3035 b2578 b1533 b3927 b1473 b1600 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.744460 (mmol/gDw/h)
  Minimum Production Rate : 0.149789 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.698215
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.121094
  EX_pi_e : 0.718110
  EX_so4_e : 0.187470
  EX_k_e : 0.145313
  EX_fe2_e : 0.011957
  EX_mg2_e : 0.006458
  EX_ca2_e : 0.003875
  EX_cl_e : 0.003875
  EX_cu2_e : 0.000528
  EX_mn2_e : 0.000514
  EX_zn2_e : 0.000254
  EX_ni2_e : 0.000240
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.516933
  EX_co2_e : 26.002062
  EX_h_e : 8.103523
  Auxiliary production reaction : 0.149789
  DM_oxam_c : 0.032409
  DM_5drib_c : 0.032075
  DM_4crsol_c : 0.031742
  EX_etha_e : 0.000060

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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