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 (66 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 54
  Gene deletion: b3553 b4382 b1241 b0351 b4069 b4384 b3708 b1479 b3752 b2297 b2458 b2926 b2407 b3236 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b0596 b0675 b1415 b1014 b4014 b0261 b2976 b0822 b3709 b1907 b2406 b3161 b0112 b2868 b0114 b0509 b3125 b2366 b2492 b0904 b1533 b3821 b1380 b0325 b4042 b1473 b4266 b3662 b2842   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.276885 (mmol/gDw/h)
  Minimum Production Rate : 0.294358 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.528580
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.291911
  EX_pi_e : 1.150160
  EX_so4_e : 0.603912
  EX_k_e : 0.054046
  EX_fe2_e : 0.004447
  EX_mg2_e : 0.002402
  EX_ca2_e : 0.001441
  EX_cl_e : 0.001441
  EX_cu2_e : 0.000196
  EX_mn2_e : 0.000191
  EX_zn2_e : 0.000094
  EX_ni2_e : 0.000089

Product: (mmol/gDw/h)
  EX_h2o_e : 49.460114
  EX_co2_e : 34.012583
  EX_h_e : 5.483587
  EX_ac_e : 2.000428
  Auxiliary production reaction : 0.294358
  EX_met__L_e : 0.239829
  EX_hxan_e : 0.000310
  DM_5drib_c : 0.000186
  EX_dxylnt_e : 0.000185
  DM_4crsol_c : 0.000062

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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