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 : sbzcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b2836 b3553 b3399 b4069 b2744 b3708 b3008 b0871 b2297 b2458 b2925 b2097 b0160 b1238 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b2440 b0595 b0675 b2361 b4014 b0261 b2976 b3945 b0507 b3709 b4381 b2406 b3161 b0112 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b1473 b3447 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.690640 (mmol/gDw/h)
  Minimum Production Rate : 0.023263 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.458731
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.407023
  EX_so4_e : 0.981677
  EX_pi_e : 0.735985
  EX_k_e : 0.134808
  EX_fe2_e : 0.011092
  EX_mg2_e : 0.005991
  EX_cl_e : 0.003595
  EX_ca2_e : 0.003595
  EX_cu2_e : 0.000490
  EX_mn2_e : 0.000477
  EX_zn2_e : 0.000236
  EX_ni2_e : 0.000223
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 46.544881
  EX_co2_e : 26.131602
  EX_h_e : 6.865821
  EX_ac_e : 1.209841
  EX_cys__L_e : 0.784497
  Auxiliary production reaction : 0.023263
  DM_oxam_c : 0.000773
  DM_5drib_c : 0.000463
  DM_4crsol_c : 0.000154
  EX_etha_e : 0.000056

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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