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 (84 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b3553 b3399 b3942 b1732 b4069 b2744 b3708 b3008 b0871 b3115 b1849 b2296 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b2883 b2690 b1982 b2797 b3117 b1814 b4471 b2210 b1033 b4374 b0675 b2361 b0261 b0411 b3945 b4381 b2406 b0452 b0114 b0509 b3125 b2366 b0755 b3612 b0529 b2492 b0904 b2578 b1533 b3927 b1380 b0594 b3662 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.333239 (mmol/gDw/h)
  Minimum Production Rate : 0.396333 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.065721
  EX_o2_e : 279.890210
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.797045
  EX_pi_e : 1.114110
  EX_so4_e : 0.083916
  EX_k_e : 0.065046
  EX_mg2_e : 0.002891
  EX_ca2_e : 0.001735
  EX_cl_e : 0.001735
  EX_cu2_e : 0.000236
  EX_mn2_e : 0.000230
  EX_zn2_e : 0.000114
  EX_ni2_e : 0.000108

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994648
  EX_h2o_e : 545.006285
  EX_co2_e : 27.761722
  EX_pyr_e : 4.862135
  Auxiliary production reaction : 0.396333
  EX_ac_e : 0.194007
  DM_oxam_c : 0.009092
  DM_5drib_c : 0.000224
  DM_4crsol_c : 0.000074

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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