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 : 6hmhptpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2744 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b1982 b4139 b1033 b0675 b2361 b4014 b0261 b2976 b2799 b3945 b1602 b0507 b2913 b4381 b3915 b0452 b0755 b3612 b0529 b2492 b0904 b2954 b1380 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.441727 (mmol/gDw/h)
  Minimum Production Rate : 0.274095 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.152237
  EX_o2_e : 288.900328
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.446748
  EX_pi_e : 0.974282
  EX_so4_e : 0.111236
  EX_k_e : 0.086222
  EX_mg2_e : 0.003832
  EX_ca2_e : 0.002299
  EX_cl_e : 0.002299
  EX_cu2_e : 0.000313
  EX_mn2_e : 0.000305
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992905
  EX_h2o_e : 554.323092
  EX_co2_e : 39.006789
  EX_ac_e : 0.379866
  Auxiliary production reaction : 0.274095
  EX_urea_e : 0.122698
  EX_ade_e : 0.012053
  DM_5drib_c : 0.000296
  DM_4crsol_c : 0.000099

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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