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 : gdpfuc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3399 b0474 b2518 b2502 b2744 b3708 b3008 b0871 b2925 b2097 b2926 b2690 b1982 b2797 b3117 b1814 b4471 b0596 b1623 b3665 b0675 b2361 b0261 b3945 b4381 b2406 b0114 b0886 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b1380   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.575845 (mmol/gDw/h)
  Minimum Production Rate : 0.117109 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.064166
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.822916
  EX_pi_e : 0.789682
  EX_so4_e : 0.145009
  EX_k_e : 0.112401
  EX_fe2_e : 0.009249
  EX_mg2_e : 0.004995
  EX_ca2_e : 0.002997
  EX_cl_e : 0.002997
  EX_cu2_e : 0.000408
  EX_mn2_e : 0.000398
  EX_zn2_e : 0.000196
  EX_ni2_e : 0.000186
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 46.154693
  EX_co2_e : 26.680249
  EX_h_e : 8.267633
  EX_pyr_e : 2.591852
  Auxiliary production reaction : 0.117109
  DM_oxam_c : 0.015068
  EX_ade_e : 0.000644
  DM_5drib_c : 0.000386
  DM_4crsol_c : 0.000128

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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