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 : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b4384 b3752 b0871 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b2210 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b3915 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b3662 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.478415 (mmol/gDw/h)
  Minimum Production Rate : 0.229943 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.498585
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.859256
  EX_pi_e : 1.151224
  EX_so4_e : 0.120475
  EX_k_e : 0.093383
  EX_fe3_e : 0.007686
  EX_mg2_e : 0.004150
  EX_ca2_e : 0.002490
  EX_cl_e : 0.002490
  EX_cu2_e : 0.000339
  EX_mn2_e : 0.000331
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.224567
  EX_co2_e : 38.290309
  EX_h_e : 4.636141
  Auxiliary production reaction : 0.229914
  EX_ade_e : 0.000535
  DM_5drib_c : 0.000321
  DM_4crsol_c : 0.000107

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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