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 : dhgly_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2744 b2297 b2458 b0160 b1982 b3616 b3589 b1033 b4374 b0675 b2361 b2291 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 : 0.492736 (mmol/gDw/h)
  Minimum Production Rate : 0.944316 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.755134
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.210693
  EX_pi_e : 0.475296
  EX_so4_e : 0.124081
  EX_k_e : 0.096179
  EX_fe2_e : 0.007914
  EX_mg2_e : 0.004274
  EX_ca2_e : 0.002565
  EX_cl_e : 0.002565
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 40.956719
  EX_co2_e : 21.333603
  EX_h_e : 9.971114
  EX_ac_e : 1.664961
  DM_oxam_c : 0.944867
  DM_5drib_c : 0.944647
  DM_4crsol_c : 0.944426
  Auxiliary production reaction : 0.944316
  EX_glyclt_e : 0.000330

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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