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 : 5mthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b2836 b3553 b4382 b4069 b4384 b3708 b3008 b2297 b2458 b0030 b2407 b0593 b1982 b2688 b2797 b3117 b1814 b4471 b2265 b1033 b2440 b0261 b0507 b3709 b2406 b3161 b0112 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b2413 b1473 b4141 b1798 b3662 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.690732 (mmol/gDw/h)
  Minimum Production Rate : 0.115004 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.898065
  EX_o2_e : 274.099339
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.508560
  EX_pi_e : 0.666284
  EX_so4_e : 0.173940
  EX_k_e : 0.134826
  EX_mg2_e : 0.005992
  EX_ca2_e : 0.003595
  EX_cl_e : 0.003595
  EX_cu2_e : 0.000490
  EX_mn2_e : 0.000477
  EX_zn2_e : 0.000236
  EX_ni2_e : 0.000223
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988906
  EX_h2o_e : 548.492371
  EX_co2_e : 24.990061
  EX_ac_e : 0.402134
  Auxiliary production reaction : 0.292555
  DM_oxam_c : 0.000773
  DM_5drib_c : 0.000463
  DM_4crsol_c : 0.000154
  EX_etha_e : 0.000056

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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