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 : pyr_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (109 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4467 b1478 b1241 b0351 b0871 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b3946 b2210 b0825 b1493 b3517 b2799 b3945 b1602 b2913 b2975 b3603 b0755 b3612 b2492 b0904 b1380 b0514 b0606 b0221 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.396538 (mmol/gDw/h)
  Minimum Production Rate : 3.853311 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.242829
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.282581
  EX_pi_e : 0.382503
  EX_so4_e : 0.099856
  EX_k_e : 0.077402
  EX_fe3_e : 0.006369
  EX_mg2_e : 0.003440
  EX_ca2_e : 0.002064
  EX_cl_e : 0.002064
  EX_cu2_e : 0.000281
  EX_mn2_e : 0.000274
  EX_zn2_e : 0.000135
  EX_ni2_e : 0.000128

Product: (mmol/gDw/h)
  EX_h2o_e : 46.485597
  EX_co2_e : 32.163987
  EX_h_e : 7.503233
  EX_pyr_e : 3.853311
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000088

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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