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 : mnl1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b1478 b0238 b0125 b1241 b4069 b2744 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b0477 b2210 b4374 b2361 b2291 b2799 b3945 b1602 b2223 b3915 b0755 b3612 b0529 b2492 b0904 b2954 b1380 b2660 b1511 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.485235 (mmol/gDw/h)
  Minimum Production Rate : 0.015862 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.352983
  EX_o2_e : 287.815320
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.138690
  EX_pi_e : 0.483923
  EX_so4_e : 0.122192
  EX_k_e : 0.094715
  EX_mg2_e : 0.004209
  EX_ca2_e : 0.002526
  EX_cl_e : 0.002526
  EX_cu2_e : 0.000344
  EX_mn2_e : 0.000335
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000157
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992207
  EX_h2o_e : 553.130086
  EX_co2_e : 38.299332
  EX_ac_e : 0.282497
  EX_hxan_e : 0.224548
  Auxiliary production reaction : 0.015862
  DM_mththf_c : 0.000217
  DM_5drib_c : 0.000109
  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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