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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b4069 b2744 b3708 b2297 b2458 b2883 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b4381 b0114 b2366 b2492 b0904 b1533 b3927 b2835 b0494 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.575039 (mmol/gDw/h)
  Minimum Production Rate : 0.098092 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.654793
  EX_o2_e : 283.704560
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.814351
  EX_pi_e : 0.554686
  EX_so4_e : 0.144806
  EX_k_e : 0.112243
  EX_mg2_e : 0.004988
  EX_ca2_e : 0.002993
  EX_cl_e : 0.002993
  EX_cu2_e : 0.000408
  EX_mn2_e : 0.000397
  EX_zn2_e : 0.000196
  EX_ni2_e : 0.000186
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990764
  EX_h2o_e : 551.005115
  EX_co2_e : 34.518496
  EX_ac_e : 0.334779
  DM_oxam_c : 0.113525
  Auxiliary production reaction : 0.098092
  DM_mththf_c : 0.000258
  DM_5drib_c : 0.000129
  DM_4crsol_c : 0.000128

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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