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 : coa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b4467 b1478 b3399 b4382 b1241 b4069 b2744 b3708 b2297 b2458 b2926 b1004 b3713 b1109 b0046 b3236 b2883 b2797 b3117 b1814 b4471 b3449 b1623 b3665 b0411 b2799 b3945 b1602 b4381 b2239 b2406 b3915 b3654 b3714 b3664 b2366 b2492 b0904 b1533 b1380 b2660 b4141 b1798 b1518 b0606 b0221 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.418236 (mmol/gDw/h)
  Minimum Production Rate : 0.194015 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.780545
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.950049
  EX_pi_e : 1.016847
  EX_so4_e : 0.299307
  EX_k_e : 0.081637
  EX_fe3_e : 0.006719
  EX_mg2_e : 0.003628
  EX_ca2_e : 0.002177
  EX_cl_e : 0.002177
  EX_cu2_e : 0.000297
  EX_mn2_e : 0.000289
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000135
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 51.463323
  EX_co2_e : 36.606540
  EX_h_e : 5.413985
  EX_glyclt_e : 0.532591
  EX_ac_e : 0.437478
  Auxiliary production reaction : 0.193986
  EX_g3pe_e : 0.031457
  EX_hxan_e : 0.010944
  DM_mththf_c : 0.000187
  DM_5drib_c : 0.000094
  DM_4crsol_c : 0.000093

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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