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 : unagamuf_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b4152 b2297 b2458 b2779 b3617 b1612 b1611 b2883 b4122 b4138 b4123 b0621 b2913 b4381 b2406 b4064 b4464 b0114 b0529 b2492 b0904 b3662 b1518 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.299979 (mmol/gDw/h)
  Minimum Production Rate : 0.143533 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.979223
  EX_o2_e : 279.159267
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.101659
  EX_pi_e : 0.576428
  EX_so4_e : 0.075541
  EX_k_e : 0.058554
  EX_mg2_e : 0.002602
  EX_ca2_e : 0.001561
  EX_cl_e : 0.001561
  EX_cu2_e : 0.000213
  EX_mn2_e : 0.000207
  EX_zn2_e : 0.000102
  EX_ni2_e : 0.000097

Product: (mmol/gDw/h)
  EX_fe3_e : 999.995182
  EX_h2o_e : 544.874446
  EX_co2_e : 32.404655
  EX_ac_e : 0.909767
  EX_succ_e : 0.315158
  EX_ura_e : 0.215072
  Auxiliary production reaction : 0.143533
  DM_oxam_c : 0.001171
  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.

Last updated: 21-Sep-2023
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