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 : 6hmhptpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3553 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b3617 b0030 b2407 b1982 b1033 b4374 b2361 b2291 b0261 b0411 b0507 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.482947 (mmol/gDw/h)
  Minimum Production Rate : 1.569946 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 987.703602
  EX_o2_e : 274.735299
  EX_nh4_e : 13.066055
  EX_glc__D_e : 10.000000
  EX_pi_e : 3.605745
  EX_so4_e : 0.121616
  EX_k_e : 0.094268
  EX_mg2_e : 0.004190
  EX_cl_e : 0.002514
  EX_ca2_e : 0.002514
  EX_cu2_e : 0.000342
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992243
  EX_h2o_e : 553.644555
  EX_co2_e : 22.054710
  EX_acald_e : 1.995109
  EX_glyclt_e : 1.570269
  Auxiliary production reaction : 1.569946
  DM_oxam_c : 0.000540
  DM_5drib_c : 0.000324
  DM_4crsol_c : 0.000108

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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