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 : gdpofuc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4384 b2744 b1278 b3708 b3008 b0871 b2925 b2097 b2926 b0030 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b0411 b0822 b0507 b0452 b1727 b0114 b0529 b1539 b2492 b0904 b2947 b2578 b1533 b3927 b2835 b2413 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.360962 (mmol/gDw/h)
  Minimum Production Rate : 0.081822 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.994359
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.308863
  EX_pi_e : 0.511824
  EX_so4_e : 0.090898
  EX_k_e : 0.070457
  EX_fe2_e : 0.005799
  EX_mg2_e : 0.003131
  EX_ca2_e : 0.001879
  EX_cl_e : 0.001879
  EX_cu2_e : 0.000256
  EX_mn2_e : 0.000249
  EX_zn2_e : 0.000123
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_h2o_e : 43.951543
  EX_co2_e : 27.850942
  EX_h_e : 8.901419
  EX_pyr_e : 5.335475
  Auxiliary production reaction : 0.081819
  DM_oxam_c : 0.001409
  DM_5drib_c : 0.001247
  DM_4crsol_c : 0.001086
  EX_glyclt_e : 0.001005

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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