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 : datp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b2502 b2744 b0871 b2779 b3617 b2883 b1623 b3665 b4374 b2361 b2291 b0411 b4388 b0114 b0529 b2492 b0904 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.400090 (mmol/gDw/h)
  Minimum Production Rate : 0.433711 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.014903
  EX_o2_e : 285.719272
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.490846
  EX_pi_e : 1.687064
  EX_so4_e : 0.100751
  EX_k_e : 0.078095
  EX_mg2_e : 0.003471
  EX_cl_e : 0.002082
  EX_ca2_e : 0.002082
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000276
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993574
  EX_h2o_e : 553.049743
  EX_co2_e : 36.413021
  EX_acald_e : 1.412874
  Auxiliary production reaction : 0.433711
  EX_ade_e : 0.000269
  DM_mththf_c : 0.000179
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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