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 (64 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3553 b1478 b4382 b3846 b1241 b0351 b4069 b4384 b3115 b1849 b2296 b2779 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b1033 b0261 b0411 b2799 b3945 b1602 b3915 b0529 b2492 b0904 b1380 b2660 b1695 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.310518 (mmol/gDw/h)
  Minimum Production Rate : 0.015392 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.171776
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.584717
  EX_pi_e : 0.299527
  EX_so4_e : 0.078195
  EX_k_e : 0.060611
  EX_fe3_e : 0.020378
  EX_mg2_e : 0.002694
  EX_ca2_e : 0.001616
  EX_cl_e : 0.001616
  EX_cu2_e : 0.000220
  EX_mn2_e : 0.000215
  EX_zn2_e : 0.000106
  EX_ni2_e : 0.000100

Product: (mmol/gDw/h)
  EX_h2o_e : 50.314975
  EX_co2_e : 33.592949
  EX_h_e : 7.312208
  EX_ac_e : 1.087924
  EX_ade_e : 0.633919
  DM_5drib_c : 0.633780
  DM_4crsol_c : 0.602863
  EX_glyc__R_e : 0.058036
  Auxiliary production reaction : 0.015389

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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