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 : glyc__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2502 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b3617 b3124 b2690 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b0822 b0112 b2789 b3127 b0452 b1727 b0114 b1539 b2492 b0904 b1533 b1912 b0514 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.587561 (mmol/gDw/h)
  Minimum Production Rate : 0.042075 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.828861
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.678152
  EX_so4_e : 1.395700
  EX_pi_e : 0.566764
  EX_k_e : 0.114688
  EX_fe2_e : 0.009437
  EX_mg2_e : 0.005097
  EX_cl_e : 0.003058
  EX_ca2_e : 0.003058
  EX_cu2_e : 0.000417
  EX_mn2_e : 0.000406
  EX_zn2_e : 0.000200
  EX_ni2_e : 0.000190
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 44.579331
  EX_co2_e : 26.145936
  EX_h_e : 4.363082
  EX_acald_e : 2.343224
  EX_cys__L_e : 1.247741
  DM_oxam_c : 0.084807
  DM_5drib_c : 0.084544
  DM_4crsol_c : 0.084281
  Auxiliary production reaction : 0.042075
  EX_glyclt_e : 0.000393

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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