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 : sbt6p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b0238 b0125 b0474 b1241 b3831 b0871 b2779 b1004 b3713 b1109 b0046 b3236 b0477 b1033 b4015 b2799 b3945 b1602 b2913 b3915 b2492 b0904 b1380 b1511 b0606 b0221 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.494890 (mmol/gDw/h)
  Minimum Production Rate : 0.292339 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.727961
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.344773
  EX_pi_e : 0.769661
  EX_so4_e : 0.124624
  EX_k_e : 0.096599
  EX_fe3_e : 0.007950
  EX_mg2_e : 0.004293
  EX_ca2_e : 0.002576
  EX_cl_e : 0.002576
  EX_cu2_e : 0.000351
  EX_mn2_e : 0.000342
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.996908
  EX_co2_e : 37.932200
  EX_h_e : 4.555200
  Auxiliary production reaction : 0.292287
  DM_mththf_c : 0.000222
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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