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 : bmoco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (127 of 137: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b3553 b1478 b4382 b1241 b3831 b4069 b4384 b3708 b0910 b3115 b1849 b2296 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b2143 b2797 b3117 b1814 b4471 b2498 b1033 b0261 b2799 b3945 b1602 b0153 b2913 b2406 b2366 b2492 b0904 b0591 b1533 b1380 b4141 b1798 b3662 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.425643 (mmol/gDw/h)
  Minimum Production Rate : 0.092501 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.030887
  EX_o2_e : 287.506289
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.140415
  EX_pi_e : 0.688081
  EX_so4_e : 0.477191
  EX_mobd_e : 0.092504
  EX_k_e : 0.083082
  EX_mg2_e : 0.003692
  EX_ca2_e : 0.002215
  EX_cl_e : 0.002215
  EX_cu2_e : 0.000302
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993164
  EX_h2o_e : 553.903352
  EX_co2_e : 38.207167
  EX_ac_e : 0.617808
  Auxiliary production reaction : 0.092501
  EX_ura_e : 0.077043
  EX_hxan_e : 0.000476
  DM_5drib_c : 0.000286
  DM_4crsol_c : 0.000095

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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