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 : trp__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b2836 b1241 b0351 b4069 b4384 b2744 b3708 b3115 b1849 b2296 b3617 b0030 b2407 b3124 b1982 b2797 b3117 b1814 b4471 b0596 b4374 b2361 b2291 b0261 b0411 b0112 b2789 b3127 b2975 b0114 b3603 b1539 b2492 b0904 b1533 b0514 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.466641 (mmol/gDw/h)
  Minimum Production Rate : 1.396330 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.848608
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.832869
  EX_pi_e : 0.450125
  EX_so4_e : 0.117510
  EX_k_e : 0.091085
  EX_fe2_e : 0.007495
  EX_mg2_e : 0.004048
  EX_ca2_e : 0.002429
  EX_cl_e : 0.002429
  EX_cu2_e : 0.000331
  EX_mn2_e : 0.000322
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 44.036310
  EX_co2_e : 20.541916
  EX_h_e : 9.552833
  EX_ac_e : 2.471442
  EX_trp__L_e : 1.396330
  DM_oxam_c : 0.000522
  DM_5drib_c : 0.000313
  DM_4crsol_c : 0.000104

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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