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 : 6hmhpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 71
  Gene deletion: b3399 b4382 b4269 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b2502 b3073 b2744 b3708 b3008 b1479 b2930 b4232 b3697 b3925 b0871 b3236 b1779 b2690 b3962 b0593 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b1746 b4267 b2265 b0675 b2361 b1014 b0261 b0822 b1907 b2913 b4381 b2406 b0112 b2868 b1727 b0837 b0124 b2975 b0114 b3603 b0509 b3125 b2366 b0306 b3605 b2492 b0904 b1533 b3821 b1380 b1912 b0325 b2413 b0508 b3715 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.283000 (mmol/gDw/h)
  Minimum Production Rate : 0.054071 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.062326
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.664216
  EX_so4_e : 0.377866
  EX_pi_e : 0.272983
  EX_k_e : 0.055240
  EX_fe2_e : 0.004545
  EX_mg2_e : 0.002455
  EX_ca2_e : 0.001473
  EX_cl_e : 0.001473
  EX_cu2_e : 0.000201
  EX_mn2_e : 0.000196
  EX_zn2_e : 0.000097
  EX_ni2_e : 0.000091

Product: (mmol/gDw/h)
  EX_h2o_e : 42.127074
  EX_co2_e : 27.919677
  EX_h_e : 8.159965
  EX_pyr_e : 5.510749
  EX_acald_e : 0.855097
  EX_met__L_e : 0.306601
  EX_dxylnt_e : 0.054261
  Auxiliary production reaction : 0.054071
  EX_xan_e : 0.007405
  EX_hxan_e : 0.000317
  DM_5drib_c : 0.000190
  DM_4crsol_c : 0.000063

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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