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 : gtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b4382 b4269 b0493 b3588 b3003 b3011 b4384 b0871 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b0477 b4139 b0261 b3945 b1602 b2913 b2406 b3915 b1727 b0114 b0755 b3612 b0529 b2492 b0904 b2954 b3029 b1380 b3662 b0221 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.467069 (mmol/gDw/h)
  Minimum Production Rate : 0.089782 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.954863
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.493196
  EX_pi_e : 0.719871
  EX_so4_e : 0.117618
  EX_k_e : 0.091169
  EX_fe3_e : 0.007503
  EX_mg2_e : 0.004052
  EX_ca2_e : 0.002431
  EX_cl_e : 0.002431
  EX_cu2_e : 0.000331
  EX_mn2_e : 0.000323
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.271388
  EX_co2_e : 38.245719
  EX_h_e : 4.568454
  EX_12ppd__S_e : 0.561473
  Auxiliary production reaction : 0.089778
  DM_5drib_c : 0.000313
  DM_4crsol_c : 0.000104

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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