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 : ins_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (15 of 37: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3752 b0871 b3617 b2407 b3236 b0517 b1982 b2210 b0411 b0507 b2406 b0114 b0529 b2492 b0904 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.600977 (mmol/gDw/h)
  Minimum Production Rate : 0.975278 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.557431
  EX_o2_e : 272.953954
  EX_nh4_e : 10.400999
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.579706
  EX_so4_e : 0.151338
  EX_k_e : 0.117307
  EX_mg2_e : 0.005213
  EX_ca2_e : 0.003128
  EX_cl_e : 0.003128
  EX_cu2_e : 0.000426
  EX_mn2_e : 0.000415
  EX_zn2_e : 0.000205
  EX_ni2_e : 0.000194
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990348
  EX_h2o_e : 548.181099
  EX_co2_e : 22.546577
  EX_acald_e : 1.506023
  Auxiliary production reaction : 0.975278
  EX_alltn_e : 0.002346
  EX_mththf_e : 0.001943
  DM_5drib_c : 0.000403
  EX_glyclt_e : 0.000402
  DM_4crsol_c : 0.000134

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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