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 : quln_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (106 of 106: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 57
  Gene deletion: b2242 b3553 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3708 b3008 b0871 b2925 b2097 b3617 b2407 b1612 b1611 b4122 b1779 b3962 b0104 b2797 b3117 b1814 b4471 b3946 b0825 b4267 b1033 b4374 b2361 b2291 b1415 b1014 b3945 b4138 b4123 b0621 b0112 b2868 b0114 b1539 b2492 b0904 b1533 b3927 b3028 b1380 b0325 b4266 b1517 b1206 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.299417 (mmol/gDw/h)
  Minimum Production Rate : 0.247038 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.565602
  EX_o2_e : 279.675189
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.898854
  EX_pi_e : 0.288819
  EX_so4_e : 0.075399
  EX_k_e : 0.058444
  EX_mg2_e : 0.002597
  EX_ca2_e : 0.001558
  EX_cl_e : 0.001558
  EX_cu2_e : 0.000212
  EX_mn2_e : 0.000207
  EX_zn2_e : 0.000102
  EX_ni2_e : 0.000097

Product: (mmol/gDw/h)
  EX_fe3_e : 999.995191
  EX_h2o_e : 544.493260
  EX_co2_e : 27.090417
  EX_pyr_e : 4.225605
  EX_acald_e : 0.889552
  EX_succ_e : 0.660071
  EX_hxan_e : 0.347841
  Auxiliary production reaction : 0.247038
  EX_etha_e : 0.026774
  EX_dxylnt_e : 0.000200
  DM_mththf_c : 0.000134
  DM_5drib_c : 0.000067
  DM_4crsol_c : 0.000067

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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