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 (77 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b3399 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3708 b3008 b1479 b0910 b0871 b2779 b0160 b3236 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b0675 b2361 b2291 b1415 b1014 b0261 b0822 b2913 b2406 b0112 b2789 b3127 b2975 b0114 b3603 b2366 b2492 b0904 b1533 b3821 b1380 b0325 b0508 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.408975 (mmol/gDw/h)
  Minimum Production Rate : 0.015249 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.398519
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.910212
  EX_so4_e : 0.565346
  EX_pi_e : 0.394500
  EX_k_e : 0.079829
  EX_fe2_e : 0.006570
  EX_mg2_e : 0.003548
  EX_ca2_e : 0.002129
  EX_cl_e : 0.002129
  EX_cu2_e : 0.000290
  EX_mn2_e : 0.000283
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 49.910431
  EX_co2_e : 38.032402
  EX_h_e : 3.372907
  EX_acald_e : 1.196669
  EX_met__L_e : 0.462357
  DM_oxam_c : 0.030956
  DM_5drib_c : 0.030772
  DM_4crsol_c : 0.030589
  Auxiliary production reaction : 0.015249
  EX_dxylnt_e : 0.000274

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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