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 : thmnp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b3399 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b2926 b0160 b2407 b1982 b3616 b3589 b1033 b0675 b2361 b0261 b0112 b0114 b0509 b3125 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.484366 (mmol/gDw/h)
  Minimum Production Rate : 0.573911 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.560359
  EX_nh4_e : 10.102505
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.467222
  EX_so4_e : 0.121973
  EX_k_e : 0.094545
  EX_fe2_e : 0.007779
  EX_mg2_e : 0.004202
  EX_ca2_e : 0.002521
  EX_cl_e : 0.002521
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000335
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 48.906095
  EX_co2_e : 24.945156
  EX_h_e : 9.322483
  EX_thymd_e : 1.000648
  Auxiliary production reaction : 0.573911
  DM_oxam_c : 0.000542
  DM_5drib_c : 0.000325
  DM_4crsol_c : 0.000108

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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