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 (117 of 119: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 62
  Gene deletion: b4467 b2242 b0469 b1241 b0351 b3831 b4069 b4384 b3708 b3614 b0910 b3752 b2297 b2458 b2926 b2781 b2407 b1612 b1611 b4122 b1759 b3962 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b0675 b1415 b1014 b0822 b2799 b1907 b4138 b4123 b0621 b2913 b4381 b2406 b0112 b0452 b2868 b4265 b0114 b2366 b2492 b0904 b3035 b1533 b3028 b1380 b3918 b1912 b0508 b1473 b4266 b3662 b1206 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.323722 (mmol/gDw/h)
  Minimum Production Rate : 0.497940 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.445729
  EX_o2_e : 282.898757
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.127653
  EX_pi_e : 1.308144
  EX_so4_e : 0.081520
  EX_k_e : 0.063188
  EX_mg2_e : 0.002808
  EX_ca2_e : 0.001685
  EX_cl_e : 0.001685
  EX_cu2_e : 0.000230
  EX_mn2_e : 0.000224
  EX_zn2_e : 0.000110
  EX_ni2_e : 0.000105

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994801
  EX_h2o_e : 548.855800
  EX_co2_e : 31.553598
  EX_ac_e : 1.048886
  EX_succ_e : 0.944940
  Auxiliary production reaction : 0.497940
  EX_ade_e : 0.303682
  EX_thym_e : 0.058595
  EX_dxylnt_e : 0.000217
  DM_5drib_c : 0.000073
  DM_4crsol_c : 0.000072

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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