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 : udpgal_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (119 of 119: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 85
  Gene deletion: b2836 b2242 b3553 b1478 b3399 b4382 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b3831 b4384 b2744 b3708 b3008 b3614 b0910 b3752 b0871 b2779 b2781 b3617 b0160 b3844 b1612 b1611 b4122 b1759 b3962 b0104 b2797 b3117 b1814 b4471 b4267 b1033 b0595 b0675 b2361 b2291 b3551 b1014 b3945 b1907 b4138 b4123 b0621 b2913 b4219 b1832 b1778 b2406 b0112 b3915 b2868 b1444 b2975 b0114 b3603 b0886 b0529 b0306 b1539 b3605 b2492 b0904 b2578 b1533 b3028 b1380 b3918 b1912 b0325 b1710 b2480 b1473 b4266 b2842 b1518 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.277346 (mmol/gDw/h)
  Minimum Production Rate : 0.570729 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.989010
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.493600
  EX_pi_e : 1.408849
  EX_so4_e : 0.069842
  EX_k_e : 0.054136
  EX_fe3_e : 0.004456
  EX_mg2_e : 0.002406
  EX_ca2_e : 0.001444
  EX_cl_e : 0.001444
  EX_cu2_e : 0.000197
  EX_mn2_e : 0.000192
  EX_zn2_e : 0.000095
  EX_ni2_e : 0.000090

Product: (mmol/gDw/h)
  EX_h2o_e : 48.920688
  EX_co2_e : 30.507601
  EX_h_e : 7.292727
  EX_succ_e : 1.191546
  EX_acald_e : 1.161765
  Auxiliary production reaction : 0.570660
  EX_ade_e : 0.451166
  EX_ura_e : 0.050446
  EX_etha_e : 0.000245
  DM_mththf_c : 0.000124
  EX_glyc__R_e : 0.000093
  DM_5drib_c : 0.000062
  DM_4crsol_c : 0.000062

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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