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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b4467 b1478 b1241 b3831 b4069 b4384 b3708 b3614 b0910 b3752 b2297 b2458 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b2210 b0411 b2799 b3945 b1602 b4381 b2406 b3915 b4064 b4464 b1539 b2492 b0904 b1533 b1380 b2660 b1511 b4141 b1798 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.447822 (mmol/gDw/h)
  Minimum Production Rate : 0.199065 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.765087
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.393520
  EX_pi_e : 0.431972
  EX_so4_e : 0.112771
  EX_k_e : 0.087412
  EX_fe3_e : 0.007192
  EX_mg2_e : 0.003885
  EX_cl_e : 0.002331
  EX_ca2_e : 0.002331
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.106253
  EX_co2_e : 36.690759
  EX_h_e : 6.446252
  EX_glyclt_e : 0.506496
  EX_thym_e : 0.280123
  EX_ac_e : 0.260716
  Auxiliary production reaction : 0.199065
  EX_ade_e : 0.000301
  DM_mththf_c : 0.000201
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

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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