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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b3399 b4269 b0493 b3588 b3003 b3011 b2502 b2744 b0871 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b1033 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b4381 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b2660 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.418397 (mmol/gDw/h)
  Minimum Production Rate : 0.704089 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.193691
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.633265
  EX_pi_e : 1.811767
  EX_so4_e : 0.105361
  EX_k_e : 0.081668
  EX_fe2_e : 0.006720
  EX_mg2_e : 0.003630
  EX_ca2_e : 0.002178
  EX_cl_e : 0.002178
  EX_cu2_e : 0.000297
  EX_mn2_e : 0.000289
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000135
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 52.771598
  EX_co2_e : 35.749806
  EX_h_e : 5.254922
  Auxiliary production reaction : 0.704089
  EX_etoh_e : 0.368412
  EX_ade_e : 0.000468
  DM_5drib_c : 0.000281
  DM_4crsol_c : 0.000093

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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