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 (97 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 64
  Gene deletion: b3553 b1478 b3399 b1241 b0351 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b2926 b0160 b1004 b3713 b1109 b0046 b3236 b2690 b0207 b3012 b1982 b2797 b3117 b1814 b4471 b1033 b0675 b2361 b0261 b2799 b1602 b4381 b2406 b3915 b0886 b0509 b3125 b2366 b0529 b2492 b0904 b1781 b3001 b2578 b1533 b3927 b2835 b1380 b2965 b0693 b0325 b0494 b2660 b1771 b4141 b1798 b0606 b0221 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.365813 (mmol/gDw/h)
  Minimum Production Rate : 0.010177 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.420475
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.142961
  EX_pi_e : 0.352866
  EX_so4_e : 0.092120
  EX_k_e : 0.071404
  EX_fe3_e : 0.016041
  EX_mg2_e : 0.003173
  EX_ca2_e : 0.001904
  EX_cl_e : 0.001904
  EX_cu2_e : 0.000259
  EX_mn2_e : 0.000253
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 44.044842
  EX_co2_e : 28.636812
  EX_h_e : 8.808867
  EX_pyr_e : 5.198722
  EX_ade_e : 0.030310
  DM_5drib_c : 0.020574
  Auxiliary production reaction : 0.010164
  DM_4crsol_c : 0.000082

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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