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 : hemeO_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b3553 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b2744 b3752 b0871 b0160 b1004 b3713 b1109 b0046 b3236 b2883 b1779 b1982 b1033 b1623 b4374 b2361 b2291 b0261 b0411 b2799 b3945 b1602 b0507 b2913 b2223 b3915 b0529 b2492 b0904 b1380 b4042 b3662 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.441170 (mmol/gDw/h)
  Minimum Production Rate : 0.065883 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.817291
  EX_o2_e : 286.021729
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.557164
  EX_pi_e : 0.425556
  EX_so4_e : 0.111096
  EX_k_e : 0.086113
  EX_mg2_e : 0.003827
  EX_ca2_e : 0.002296
  EX_cl_e : 0.002296
  EX_cu2_e : 0.000313
  EX_mn2_e : 0.000305
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.927030
  EX_h2o_e : 551.793641
  EX_co2_e : 37.342656
  EX_hxan_e : 0.132258
  DM_5drib_c : 0.132060
  Auxiliary production reaction : 0.065882
  DM_4crsol_c : 0.000098

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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