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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 56
  Gene deletion: b3553 b3399 b4382 b3942 b1732 b0238 b0125 b4069 b4384 b2744 b3708 b3008 b3752 b3926 b3115 b1849 b2296 b2925 b2097 b2926 b3844 b1004 b3713 b1109 b0046 b2883 b2690 b1982 b0477 b2797 b3117 b1814 b4471 b2210 b1033 b1623 b0261 b0411 b3945 b1602 b2406 b0452 b0114 b2366 b2492 b0904 b2954 b0591 b2578 b1533 b3927 b1380 b2413 b3662 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.371161 (mmol/gDw/h)
  Minimum Production Rate : 0.471489 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.333370
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.953144
  EX_pi_e : 1.301001
  EX_so4_e : 0.093466
  EX_k_e : 0.072448
  EX_fe2_e : 0.005961
  EX_mg2_e : 0.003220
  EX_ca2_e : 0.001932
  EX_cl_e : 0.001932
  EX_cu2_e : 0.000263
  EX_mn2_e : 0.000256
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 45.229970
  EX_co2_e : 31.652991
  EX_h_e : 8.316653
  EX_ac_e : 4.433129
  Auxiliary production reaction : 0.471489
  EX_hxan_e : 0.000415
  DM_5drib_c : 0.000249
  DM_4crsol_c : 0.000083

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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