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 : xmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3553 b3399 b4069 b2744 b3115 b1849 b2296 b0160 b1238 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b3908 b1656 b1982 b4139 b1033 b0675 b2361 b0261 b1602 b4381 b3915 b1727 b0114 b0529 b2492 b0904 b2954 b1380 b2660 b1771 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.486438 (mmol/gDw/h)
  Minimum Production Rate : 0.083562 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.841419
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.587734
  EX_pi_e : 0.552782
  EX_so4_e : 0.122495
  EX_k_e : 0.094949
  EX_fe3_e : 0.007813
  EX_mg2_e : 0.004220
  EX_ca2_e : 0.002532
  EX_cl_e : 0.002532
  EX_cu2_e : 0.000345
  EX_mn2_e : 0.000336
  EX_zn2_e : 0.000166
  EX_ni2_e : 0.000157
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.391615
  EX_co2_e : 38.630865
  EX_h_e : 5.094842
  EX_ac_e : 0.283197
  Auxiliary production reaction : 0.083562
  DM_5drib_c : 0.000326
  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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