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 (78 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b1478 b4382 b1241 b4069 b4384 b2744 b2297 b2458 b2926 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b0937 b1982 b4139 b1033 b1623 b4014 b0261 b2976 b0411 b2799 b3945 b1602 b2913 b0509 b3125 b0529 b2492 b0904 b2954 b1380 b1301 b3662 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.414466 (mmol/gDw/h)
  Minimum Production Rate : 0.289913 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.202440
  EX_o2_e : 286.543707
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.927612
  EX_pi_e : 0.399796
  EX_so4_e : 0.104371
  EX_k_e : 0.080901
  EX_mg2_e : 0.003595
  EX_ca2_e : 0.002157
  EX_cl_e : 0.002157
  EX_cu2_e : 0.000294
  EX_mn2_e : 0.000286
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993343
  EX_h2o_e : 551.998428
  EX_co2_e : 36.993913
  EX_hxan_e : 0.290377
  DM_5drib_c : 0.290191
  DM_4crsol_c : 0.290005
  Auxiliary production reaction : 0.289913
  EX_ac_e : 0.241296

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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