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 : dnad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 65
  Gene deletion: b4382 b4269 b0493 b3588 b0586 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b1479 b0871 b2925 b2097 b0030 b2407 b1744 b3124 b3236 b2690 b3962 b1982 b1302 b2662 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b2440 b1415 b1014 b0261 b3945 b1907 b2913 b2406 b0112 b2789 b3127 b2868 b4265 b2975 b0114 b3603 b2366 b0755 b3612 b2492 b0904 b2578 b1533 b3927 b1380 b0325 b0508 b1473 b4266 b3662 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.304626 (mmol/gDw/h)
  Minimum Production Rate : 0.025014 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.605900
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.799460
  EX_so4_e : 0.403154
  EX_pi_e : 0.343873
  EX_k_e : 0.059461
  EX_fe2_e : 0.004893
  EX_mg2_e : 0.002643
  EX_ca2_e : 0.001586
  EX_cl_e : 0.001586
  EX_cu2_e : 0.000216
  EX_mn2_e : 0.000210
  EX_zn2_e : 0.000104
  EX_ni2_e : 0.000098

Product: (mmol/gDw/h)
  EX_h2o_e : 42.264951
  EX_co2_e : 27.866549
  EX_h_e : 7.772040
  EX_pyr_e : 5.197493
  EX_acald_e : 0.906987
  EX_met__L_e : 0.326443
  EX_etha_e : 0.031293
  Auxiliary production reaction : 0.025014
  EX_ade_e : 0.000341
  DM_5drib_c : 0.000204
  EX_dxylnt_e : 0.000204
  DM_4crsol_c : 0.000068

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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