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 : dhgly_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b3553 b3399 b4382 b4384 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b0160 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b0675 b2361 b2291 b0261 b0822 b1602 b0507 b2913 b2406 b0452 b1727 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b1380 b2413 b3447 b1771 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.361928 (mmol/gDw/h)
  Minimum Production Rate : 0.083077 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.926327
  EX_o2_e : 280.018058
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.409269
  EX_pi_e : 0.349118
  EX_so4_e : 0.091142
  EX_k_e : 0.070646
  EX_mg2_e : 0.003140
  EX_ca2_e : 0.001884
  EX_cl_e : 0.001884
  EX_cu2_e : 0.000257
  EX_mn2_e : 0.000250
  EX_zn2_e : 0.000123
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994186
  EX_h2o_e : 544.050507
  EX_co2_e : 28.086947
  EX_pyr_e : 5.158768
  EX_ade_e : 0.083480
  DM_5drib_c : 0.083318
  DM_4crsol_c : 0.083156
  Auxiliary production reaction : 0.083075

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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