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 : dmpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b4152 b0871 b3617 b1612 b1611 b4122 b4138 b4123 b0621 b2913 b4381 b2868 b0114 b0529 b2492 b0904 b1518 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.532055 (mmol/gDw/h)
  Minimum Production Rate : 1.731011 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.969481
  EX_o2_e : 268.766219
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.500755
  EX_pi_e : 3.975246
  EX_so4_e : 0.133982
  EX_k_e : 0.103853
  EX_mg2_e : 0.004616
  EX_ca2_e : 0.002769
  EX_cl_e : 0.002769
  EX_cu2_e : 0.000377
  EX_mn2_e : 0.000368
  EX_zn2_e : 0.000181
  EX_ni2_e : 0.000172
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991455
  EX_h2o_e : 543.122498
  EX_co2_e : 23.173308
  Auxiliary production reaction : 1.731011
  EX_acald_e : 1.301768
  EX_succ_e : 0.554822
  EX_ura_e : 0.377305
  DM_mththf_c : 0.000238
  DM_5drib_c : 0.000120
  DM_4crsol_c : 0.000119

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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