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 : mal__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (16 of 29: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3553 b3942 b1732 b1241 b0351 b0871 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b2463 b3946 b2210 b0825 b1033 b3551 b1602 b4219 b1832 b1778 b1727 b2492 b0904 b1380 b1710 b2480 b1771 b1206 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.427162 (mmol/gDw/h)
  Minimum Production Rate : 0.445441 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.994638
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.613312
  EX_pi_e : 0.412043
  EX_so4_e : 0.107568
  EX_k_e : 0.083379
  EX_mg2_e : 0.003706
  EX_fe2_e : 0.003525
  EX_fe3_e : 0.003335
  EX_ca2_e : 0.002223
  EX_cl_e : 0.002223
  EX_cu2_e : 0.000303
  EX_mn2_e : 0.000295
  EX_zn2_e : 0.000146
  EX_ni2_e : 0.000138
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 43.991442
  EX_co2_e : 32.267503
  EX_h_e : 6.222101
  EX_hxa_e : 1.402950
  Auxiliary production reaction : 0.445441
  DM_5drib_c : 0.000096
  DM_4crsol_c : 0.000095

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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