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 : sbt6p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b1478 b1241 b3831 b4069 b4384 b3115 b1849 b2296 b2779 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b1982 b2498 b2799 b1602 b2913 b3915 b0529 b2492 b0904 b1781 b3001 b1380 b0325 b1771 b1518 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.484060 (mmol/gDw/h)
  Minimum Production Rate : 0.127663 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.590339
  EX_o2_e : 286.862501
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.900144
  EX_pi_e : 0.594590
  EX_so4_e : 0.121896
  EX_k_e : 0.094485
  EX_mg2_e : 0.004199
  EX_ca2_e : 0.002520
  EX_cl_e : 0.002520
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992226
  EX_h2o_e : 551.916495
  EX_co2_e : 37.457179
  EX_ura_e : 0.335517
  EX_ac_e : 0.281813
  Auxiliary production reaction : 0.127663
  EX_hxan_e : 0.000326
  DM_mththf_c : 0.000217
  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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