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

Gene deletion strategy (39 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3553 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b0871 b0030 b2407 b1982 b3616 b3589 b1033 b0261 b0507 b4381 b2406 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 : 0.491632 (mmol/gDw/h)
  Minimum Production Rate : 1.598179 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.103092
  EX_nh4_e : 13.301028
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.474231
  EX_so4_e : 0.123803
  EX_k_e : 0.095963
  EX_fe2_e : 0.007896
  EX_mg2_e : 0.004265
  EX_ca2_e : 0.002559
  EX_cl_e : 0.002559
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.337854
  EX_co2_e : 21.372323
  EX_h_e : 14.107812
  EX_acald_e : 2.030988
  EX_glyclt_e : 1.598507
  Auxiliary production reaction : 1.598179
  DM_oxam_c : 0.000550
  DM_5drib_c : 0.000330
  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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