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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b2836 b3399 b4382 b2502 b4384 b2744 b3708 b3008 b0871 b0583 b0121 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b2291 b0261 b0507 b3709 b2406 b3161 b0112 b3915 b2975 b0114 b3603 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b1473 b4141 b1798 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.747034 (mmol/gDw/h)
  Minimum Production Rate : 0.102661 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.350424
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.787370
  EX_pi_e : 1.028578
  EX_so4_e : 0.290779
  EX_k_e : 0.145816
  EX_fe3_e : 0.011998
  EX_mg2_e : 0.006481
  EX_ca2_e : 0.003888
  EX_cl_e : 0.003888
  EX_cu2_e : 0.000530
  EX_mn2_e : 0.000516
  EX_zn2_e : 0.000255
  EX_ni2_e : 0.000241
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.543816
  EX_co2_e : 26.049183
  EX_h_e : 7.185701
  Auxiliary production reaction : 0.102661
  DM_oxam_c : 0.000836
  DM_5drib_c : 0.000501
  DM_4crsol_c : 0.000167

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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