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 : gmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (100 of 102: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b3752 b0871 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b1982 b0477 b4139 b1033 b0261 b2799 b3945 b1602 b4381 b2406 b3915 b0452 b0509 b3125 b0755 b3612 b0529 b1539 b2492 b0904 b2954 b1380 b1301 b2660 b3662 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.442181 (mmol/gDw/h)
  Minimum Production Rate : 0.367401 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 38.330960
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.615000
  EX_pi_e : 0.793932
  EX_so4_e : 0.111350
  EX_k_e : 0.086311
  EX_fe3_e : 0.007102
  EX_mg2_e : 0.003836
  EX_ca2_e : 0.002302
  EX_cl_e : 0.002302
  EX_cu2_e : 0.000314
  EX_mn2_e : 0.000306
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 54.260013
  EX_co2_e : 38.173018
  EX_h_e : 5.909519
  Auxiliary production reaction : 0.367401
  EX_ade_e : 0.000495
  DM_5drib_c : 0.000297
  DM_4crsol_c : 0.000099

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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