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 : udpgalfur_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 76
  Gene deletion: b2836 b2242 b3553 b4382 b4269 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b3831 b4384 b1278 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b0871 b2781 b2407 b1612 b1611 b4122 b1779 b2690 b1759 b3962 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b3665 b4161 b1415 b1014 b0261 b2799 b3945 b1907 b4138 b4123 b0621 b2913 b2406 b0112 b1444 b0837 b0124 b0114 b0529 b1539 b2492 b0904 b3035 b1533 b3927 b3028 b1380 b3918 b1473 b0494 b3715 b4266 b3662 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.210339 (mmol/gDw/h)
  Minimum Production Rate : 0.436329 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.091742
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.931020
  EX_pi_e : 1.075551
  EX_so4_e : 0.052967
  EX_k_e : 0.041057
  EX_fe2_e : 0.003378
  EX_mg2_e : 0.001825
  EX_ca2_e : 0.001095
  EX_cl_e : 0.001095
  EX_cu2_e : 0.000149
  EX_mn2_e : 0.000145
  EX_zn2_e : 0.000072
  EX_ni2_e : 0.000068

Product: (mmol/gDw/h)
  EX_h2o_e : 43.082756
  EX_co2_e : 24.838140
  EX_h_e : 9.774788
  EX_pyr_e : 4.248106
  EX_succ_e : 0.903571
  EX_acald_e : 0.880660
  Auxiliary production reaction : 0.436329
  EX_ade_e : 0.342116
  EX_ura_e : 0.038072
  EX_dxylnt_e : 0.000141
  DM_5drib_c : 0.000047
  DM_4crsol_c : 0.000047

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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