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 : acetol_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b1478 b3846 b2341 b1241 b0351 b0871 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b4139 b1493 b3517 b4015 b0726 b3945 b1602 b2913 b1297 b2492 b0904 b3029 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.405622 (mmol/gDw/h)
  Minimum Production Rate : 1.580297 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.802931
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.380683
  EX_pi_e : 0.391265
  EX_so4_e : 0.102144
  EX_k_e : 0.079175
  EX_fe2_e : 0.006515
  EX_mg2_e : 0.003519
  EX_ca2_e : 0.002111
  EX_cl_e : 0.002111
  EX_cu2_e : 0.000288
  EX_mn2_e : 0.000280
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 39.841817
  EX_co2_e : 28.579527
  Auxiliary production reaction : 4.372917
  EX_h_e : 4.277952
  EX_pyr_e : 0.550935
  DM_5drib_c : 0.000091
  DM_4crsol_c : 0.000090

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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