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 : utp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 71
  Gene deletion: b4467 b2242 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b3614 b0910 b2930 b4232 b3697 b3925 b0871 b2779 b2781 b1612 b1611 b2883 b4122 b0907 b2690 b1759 b3962 b0104 b3616 b3589 b4267 b0595 b4374 b0675 b1014 b0822 b3945 b1907 b4138 b4123 b0621 b4381 b2406 b0112 b2868 b4265 b4064 b4464 b2975 b0114 b3603 b0509 b3125 b0529 b0306 b3605 b2492 b0904 b3028 b3821 b1380 b3918 b1912 b0325 b1473 b1511 b4266 b3662 b1813 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.239262 (mmol/gDw/h)
  Minimum Production Rate : 0.466835 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.921448
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.550360
  EX_pi_e : 1.631298
  EX_so4_e : 0.060251
  EX_k_e : 0.046702
  EX_fe2_e : 0.003843
  EX_mg2_e : 0.002076
  EX_ca2_e : 0.001245
  EX_cl_e : 0.001245
  EX_cu2_e : 0.000170
  EX_mn2_e : 0.000165
  EX_zn2_e : 0.000082
  EX_ni2_e : 0.000077

Product: (mmol/gDw/h)
  EX_h2o_e : 45.358001
  EX_co2_e : 25.719187
  EX_h_e : 10.269533
  EX_pyr_e : 3.982456
  EX_succ_e : 1.027927
  EX_acald_e : 1.017972
  Auxiliary production reaction : 0.466835
  EX_ade_e : 0.389213
  EX_thym_e : 0.043307
  DM_mththf_c : 0.000107
  EX_dxylnt_e : 0.000107
  DM_5drib_c : 0.000054
  DM_4crsol_c : 0.000053

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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