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 : hemeO_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (88 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b3553 b1478 b3399 b0474 b2518 b1241 b4069 b2744 b3115 b1849 b2296 b2781 b0160 b1004 b3713 b1109 b0046 b3124 b3236 b1638 b1779 b1759 b1982 b4139 b1033 b4374 b4161 b0675 b2361 b2291 b4014 b0261 b2976 b2799 b3945 b1602 b2913 b2789 b3127 b3915 b0452 b0529 b2492 b0904 b1300 b2954 b3029 b1380 b3918 b4042 b0514 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.408628 (mmol/gDw/h)
  Minimum Production Rate : 0.061521 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.501800
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.153232
  EX_pi_e : 0.394165
  EX_so4_e : 0.102901
  EX_k_e : 0.079761
  EX_fe3_e : 0.068084
  EX_mg2_e : 0.003545
  EX_ca2_e : 0.002127
  EX_cl_e : 0.002127
  EX_cu2_e : 0.000290
  EX_mn2_e : 0.000282
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 51.134381
  EX_co2_e : 37.728157
  EX_h_e : 5.305315
  EX_3hpp_e : 0.258527
  EX_ac_e : 0.237897
  EX_hxan_e : 0.123500
  DM_5drib_c : 0.123317
  Auxiliary production reaction : 0.061521
  DM_4crsol_c : 0.000091

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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