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 : orot_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (12 of 14: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b2242 b3553 b1478 b1241 b0351 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b0207 b3012 b1033 b2799 b1602 b4138 b4123 b0621 b0153 b2913 b0590 b0529 b1781 b3001 b3028 b1380 b0325 b1771 b1206 b0606 b2285 b1007 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.484818 (mmol/gDw/h)
  Minimum Production Rate : 0.010541 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.494754
  EX_o2_e : 287.268039
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.257081
  EX_pi_e : 0.467659
  EX_so4_e : 0.122087
  EX_k_e : 0.094633
  EX_mg2_e : 0.004206
  EX_ca2_e : 0.002523
  EX_cl_e : 0.002523
  EX_cu2_e : 0.000344
  EX_mn2_e : 0.000335
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000157
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992213
  EX_h2o_e : 551.393098
  EX_co2_e : 38.025462
  EX_succ_e : 0.505565
  Auxiliary production reaction : 0.010541
  DM_5drib_c : 0.000109
  DM_4crsol_c : 0.000108

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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