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 : dhpmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (88 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b3708 b2297 b2458 b2407 b1779 b2797 b3117 b1814 b4471 b3616 b3589 b3665 b4374 b0675 b2361 b2291 b0112 b0452 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b1511 b3662 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.443610 (mmol/gDw/h)
  Minimum Production Rate : 1.328641 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.508377
  EX_nh4_e : 11.434151
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.756549
  EX_so4_e : 0.111710
  EX_k_e : 0.086590
  EX_fe2_e : 0.007125
  EX_mg2_e : 0.003848
  EX_cl_e : 0.002309
  EX_ca2_e : 0.002309
  EX_cu2_e : 0.000315
  EX_mn2_e : 0.000307
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.463003
  EX_co2_e : 25.133448
  EX_h_e : 13.069091
  EX_ac_e : 2.349824
  Auxiliary production reaction : 1.328641
  EX_mththf_e : 0.000199
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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