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 : succoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (25 of 28: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 54
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2744 b3708 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b2926 b3617 b0160 b1004 b3713 b1109 b0046 b3124 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b3449 b1033 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b2239 b2789 b3127 b1727 b0114 b2366 b2492 b0904 b1533 b1380 b2660 b0514 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.303521 (mmol/gDw/h)
  Minimum Production Rate : 0.022841 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.763966
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.958425
  EX_pi_e : 0.361301
  EX_so4_e : 0.099274
  EX_k_e : 0.059245
  EX_fe3_e : 0.004875
  EX_mg2_e : 0.002633
  EX_ca2_e : 0.001580
  EX_cl_e : 0.001580
  EX_cu2_e : 0.000215
  EX_mn2_e : 0.000210
  EX_zn2_e : 0.000104
  EX_ni2_e : 0.000098

Product: (mmol/gDw/h)
  EX_h2o_e : 44.366111
  EX_co2_e : 26.903529
  EX_h_e : 10.102209
  EX_pyr_e : 4.497014
  EX_his__L_e : 0.839727
  EX_etoh_e : 0.568220
  EX_ac_e : 0.199547
  Auxiliary production reaction : 0.022841
  EX_hxan_e : 0.000340
  DM_5drib_c : 0.000204
  DM_4crsol_c : 0.000068

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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