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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b2297 b2458 b3617 b0030 b2407 b3124 b3236 b1982 b2797 b3117 b1814 b4471 b2210 b0596 b0261 b3709 b2406 b3161 b0112 b2789 b3127 b2975 b0114 b3603 b1539 b2492 b0904 b1533 b3821 b1473 b0514 b0515 b4141 b1798 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.313941 (mmol/gDw/h)
  Minimum Production Rate : 0.469715 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.677688
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.679949
  EX_pi_e : 1.711976
  EX_so4_e : 0.548772
  EX_k_e : 0.061279
  EX_fe2_e : 0.005042
  EX_mg2_e : 0.002723
  EX_ca2_e : 0.001634
  EX_cl_e : 0.001634
  EX_cu2_e : 0.000223
  EX_mn2_e : 0.000217
  EX_zn2_e : 0.000107
  EX_ni2_e : 0.000101

Product: (mmol/gDw/h)
  EX_h2o_e : 48.791464
  EX_co2_e : 27.816376
  EX_h_e : 6.427562
  EX_ac_e : 2.132395
  Auxiliary production reaction : 0.469715
  EX_alltn_e : 0.000351
  DM_5drib_c : 0.000211
  DM_4crsol_c : 0.000070

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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