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 : ppgpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b4467 b4269 b0493 b3588 b3003 b3011 b0238 b0125 b2744 b0871 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b1779 b2690 b0477 b4139 b4374 b2361 b2291 b0411 b2799 b3945 b1602 b0452 b3654 b2868 b3714 b3664 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b3927 b3029 b1380 b2660 b3662 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.345947 (mmol/gDw/h)
  Minimum Production Rate : 0.092956 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.368217
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.200976
  EX_pi_e : 0.705525
  EX_so4_e : 0.087116
  EX_k_e : 0.067526
  EX_fe3_e : 0.005556
  EX_mg2_e : 0.003001
  EX_ca2_e : 0.001801
  EX_cl_e : 0.001801
  EX_cu2_e : 0.000245
  EX_mn2_e : 0.000239
  EX_zn2_e : 0.000118
  EX_ni2_e : 0.000112

Product: (mmol/gDw/h)
  EX_h2o_e : 44.047082
  EX_co2_e : 28.137972
  EX_h_e : 9.040509
  EX_pyr_e : 5.382049
  EX_3hpp_e : 0.195338
  Auxiliary production reaction : 0.092956
  DM_mththf_c : 0.000155
  DM_5drib_c : 0.000078
  DM_4crsol_c : 0.000077

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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