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 : dhgly_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (88 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 56
  Gene deletion: b3553 b1478 b1241 b0351 b4069 b4384 b3708 b3115 b1849 b2296 b2779 b2925 b2097 b0030 b2407 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b0937 b1982 b0477 b4139 b2797 b3117 b1814 b4471 b3616 b3589 b1033 b2440 b0261 b2799 b3945 b1602 b0507 b4381 b2239 b2406 b0114 b1539 b2492 b0904 b2954 b1533 b3029 b1380 b2660 b3662 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.319265 (mmol/gDw/h)
  Minimum Production Rate : 0.050461 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.227539
  EX_o2_e : 281.123533
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.265080
  EX_pi_e : 0.307964
  EX_so4_e : 0.080397
  EX_k_e : 0.062318
  EX_mg2_e : 0.002770
  EX_ca2_e : 0.001662
  EX_cl_e : 0.001662
  EX_cu2_e : 0.000226
  EX_mn2_e : 0.000221
  EX_zn2_e : 0.000109
  EX_ni2_e : 0.000103

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994872
  EX_h2o_e : 545.139813
  EX_co2_e : 30.875180
  EX_ac_e : 4.966292
  EX_his__L_e : 0.854438
  EX_hxan_e : 0.050819
  DM_5drib_c : 0.050676
  DM_4crsol_c : 0.050533
  Auxiliary production reaction : 0.050461

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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