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 : dhgly_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b3399 b4382 b4269 b0493 b3846 b3588 b3003 b3011 b2502 b4384 b2744 b0871 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b4139 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b0507 b2913 b3915 b1727 b0114 b0529 b2492 b0904 b2954 b3927 b3029 b1380 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.494220 (mmol/gDw/h)
  Minimum Production Rate : 0.024162 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.279215
  EX_o2_e : 288.232817
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.485146
  EX_pi_e : 0.476727
  EX_so4_e : 0.124455
  EX_k_e : 0.096468
  EX_mg2_e : 0.004287
  EX_ca2_e : 0.002572
  EX_cl_e : 0.002572
  EX_cu2_e : 0.000350
  EX_mn2_e : 0.000342
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992060
  EX_h2o_e : 552.666655
  EX_co2_e : 39.251994
  EX_ade_e : 0.024695
  DM_5drib_c : 0.024473
  DM_4crsol_c : 0.024252
  Auxiliary production reaction : 0.024142

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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