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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b1478 b3399 b1241 b0351 b4069 b2744 b3708 b0871 b3115 b1849 b2296 b2925 b2097 b3617 b0160 b2690 b2797 b3117 b1814 b4471 b1623 b3665 b4374 b0675 b2361 b2291 b0261 b0822 b2406 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.428664 (mmol/gDw/h)
  Minimum Production Rate : 1.283684 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.483587
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.196898
  EX_pi_e : 2.980859
  EX_so4_e : 0.107946
  EX_k_e : 0.083672
  EX_fe2_e : 0.006885
  EX_mg2_e : 0.003719
  EX_ca2_e : 0.002231
  EX_cl_e : 0.002231
  EX_cu2_e : 0.000304
  EX_mn2_e : 0.000296
  EX_zn2_e : 0.000146
  EX_ni2_e : 0.000138
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.256759
  EX_co2_e : 25.561893
  EX_h_e : 7.314769
  Auxiliary production reaction : 1.283684
  EX_pyr_e : 1.105575
  EX_ac_e : 0.986778
  DM_5drib_c : 0.000096
  DM_4crsol_c : 0.000096

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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