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 : dump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 54
  Gene deletion: b4467 b4069 b4384 b2744 b3708 b3008 b2297 b2458 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b2797 b3117 b1814 b4471 b0595 b3665 b4374 b2361 b2291 b0411 b3709 b3161 b0112 b0452 b3654 b3714 b3664 b4265 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b3825 b1380 b4321 b3415 b4476 b2413 b1473 b3447 b4141 b1798 b3662 b1517 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.494192 (mmol/gDw/h)
  Minimum Production Rate : 0.629211 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.905193
  EX_o2_e : 283.049269
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.595553
  EX_pi_e : 1.105863
  EX_so4_e : 0.124448
  EX_k_e : 0.096463
  EX_mg2_e : 0.004287
  EX_ca2_e : 0.002572
  EX_cl_e : 0.002572
  EX_cu2_e : 0.000350
  EX_mn2_e : 0.000341
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992061
  EX_h2o_e : 550.927111
  EX_co2_e : 33.476708
  Auxiliary production reaction : 0.629162
  EX_ac_e : 0.287712
  EX_mththf_e : 0.000221
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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