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 : dgtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b4382 b0238 b0125 b4384 b2744 b3708 b3008 b0871 b2883 b1982 b0477 b2797 b3117 b1814 b4471 b2440 b0675 b2361 b0261 b2868 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b3927 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.789964 (mmol/gDw/h)
  Minimum Production Rate : 0.136258 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.866527
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.215496
  EX_pi_e : 1.170778
  EX_so4_e : 0.198929
  EX_k_e : 0.154196
  EX_fe2_e : 0.012688
  EX_mg2_e : 0.006853
  EX_ca2_e : 0.004112
  EX_cl_e : 0.004112
  EX_cu2_e : 0.000560
  EX_mn2_e : 0.000546
  EX_zn2_e : 0.000269
  EX_ni2_e : 0.000255
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_h2o_e : 48.984055
  EX_co2_e : 26.210354
  EX_h_e : 7.669940
  Auxiliary production reaction : 0.136258
  EX_ade_e : 0.000532
  DM_5drib_c : 0.000178
  DM_4crsol_c : 0.000176

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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