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 (92 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b3553 b3399 b1241 b0351 b2744 b3708 b3008 b0871 b2925 b2097 b2926 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b0507 b0153 b2913 b0452 b1727 b0584 b0886 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b1380 b2965 b0693 b4141 b1798 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.360660 (mmol/gDw/h)
  Minimum Production Rate : 0.018769 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.226987
  EX_o2_e : 279.898544
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.159856
  EX_pi_e : 0.347894
  EX_so4_e : 0.090822
  EX_k_e : 0.070398
  EX_mg2_e : 0.003129
  EX_cl_e : 0.001877
  EX_ca2_e : 0.001877
  EX_cu2_e : 0.000256
  EX_mn2_e : 0.000249
  EX_zn2_e : 0.000123
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_fe3_e : 999.975438
  EX_h2o_e : 543.184317
  EX_co2_e : 29.691044
  EX_pyr_e : 4.094734
  EX_etoh_e : 0.961777
  EX_ade_e : 0.037939
  DM_5drib_c : 0.037777
  Auxiliary production reaction : 0.018768
  DM_4crsol_c : 0.000080

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.

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Last updated: 21-Sep-2023
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