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 : hxan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b1478 b0238 b0125 b1241 b4069 b4384 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2926 b1004 b3713 b1109 b0046 b3236 b1638 b0477 b1302 b2662 b4139 b3946 b0825 b1033 b4015 b2799 b3945 b1602 b3915 b4064 b4464 b2492 b0904 b2954 b3029 b1380 b2660 b0221 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.411065 (mmol/gDw/h)
  Minimum Production Rate : 0.043397 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.341357
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.614158
  EX_pi_e : 0.396515
  EX_so4_e : 0.103514
  EX_k_e : 0.080237
  EX_fe3_e : 0.006602
  EX_mg2_e : 0.003566
  EX_ca2_e : 0.002140
  EX_cl_e : 0.002140
  EX_cu2_e : 0.000291
  EX_mn2_e : 0.000284
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 44.355886
  EX_co2_e : 33.111044
  EX_h_e : 8.857459
  EX_ac_e : 4.899136
  Auxiliary production reaction : 0.043674
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000092

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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