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 : orot5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (112 of 112: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 75
  Gene deletion: b4467 b2242 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b3614 b0910 b2930 b4232 b3697 b3925 b0871 b2779 b2781 b3617 b3124 b1612 b1611 b2883 b4122 b1779 b2690 b1759 b3962 b0104 b4267 b4374 b0675 b1415 b3551 b1014 b3945 b1907 b4138 b4123 b0621 b4219 b1832 b1778 b4381 b2406 b0112 b2868 b4265 b4064 b4464 b0114 b0529 b1539 b2492 b0904 b3927 b3028 b1380 b3918 b1912 b0325 b1710 b2480 b0508 b1473 b0514 b4266 b3662 b1517 b1206 b0221 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.246427 (mmol/gDw/h)
  Minimum Production Rate : 0.354132 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.954422
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.539143
  EX_pi_e : 0.591837
  EX_so4_e : 0.062055
  EX_k_e : 0.048101
  EX_mg2_e : 0.002138
  EX_fe2_e : 0.002034
  EX_fe3_e : 0.001924
  EX_ca2_e : 0.001283
  EX_cl_e : 0.001283
  EX_cu2_e : 0.000175
  EX_mn2_e : 0.000170
  EX_zn2_e : 0.000084
  EX_ni2_e : 0.000080

Product: (mmol/gDw/h)
  EX_h2o_e : 44.302435
  EX_co2_e : 25.591599
  EX_h_e : 11.544659
  EX_pyr_e : 3.954315
  EX_acald_e : 1.124343
  EX_succ_e : 1.058708
  EX_ade_e : 0.400868
  Auxiliary production reaction : 0.354132
  EX_thym_e : 0.069918
  EX_etha_e : 0.025314
  EX_dxylnt_e : 0.000165
  EX_mththf_e : 0.000110
  DM_5drib_c : 0.000055
  DM_4crsol_c : 0.000055

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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