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 : didp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b3399 b3942 b1732 b2744 b0871 b2297 b2458 b2779 b2925 b2097 b1004 b3713 b1109 b0046 b2690 b2210 b1033 b3945 b1602 b4381 b1727 b0114 b0529 b2492 b0904 b1380 b1517 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.364776 (mmol/gDw/h)
  Minimum Production Rate : 0.066169 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.026455
  EX_o2_e : 280.271772
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.253174
  EX_pi_e : 0.484202
  EX_so4_e : 0.091858
  EX_k_e : 0.071202
  EX_mg2_e : 0.003164
  EX_ca2_e : 0.001899
  EX_cl_e : 0.001899
  EX_cu2_e : 0.000259
  EX_mn2_e : 0.000252
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994141
  EX_h2o_e : 544.100842
  EX_co2_e : 28.210601
  EX_pyr_e : 5.368524
  Auxiliary production reaction : 0.066169
  EX_ade_e : 0.009790
  EX_mththf_e : 0.000163
  DM_5drib_c : 0.000082
  DM_4crsol_c : 0.000081

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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