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 : hemeO_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2744 b3614 b0910 b3115 b1849 b2296 b2779 b2781 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b1759 b1982 b4139 b1033 b4374 b0675 b2361 b4014 b0261 b2976 b2799 b3945 b1602 b4381 b3915 b0452 b1297 b0509 b3125 b0529 b2492 b0904 b2954 b3029 b1380 b3918 b1912 b2660 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.414953 (mmol/gDw/h)
  Minimum Production Rate : 0.044829 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.235381
  EX_o2_e : 286.726424
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.861611
  EX_pi_e : 0.400266
  EX_so4_e : 0.104494
  EX_k_e : 0.080996
  EX_mg2_e : 0.003600
  EX_ca2_e : 0.002160
  EX_cl_e : 0.002160
  EX_cu2_e : 0.000294
  EX_mn2_e : 0.000287
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.948506
  EX_h2o_e : 552.198171
  EX_co2_e : 37.544911
  EX_ac_e : 0.241580
  EX_ade_e : 0.200399
  EX_thymd_e : 0.099418
  EX_3hpp_e : 0.099320
  DM_5drib_c : 0.089937
  Auxiliary production reaction : 0.044829
  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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