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 : xtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b3752 b0871 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3124 b3236 b1638 b3908 b1656 b0937 b1982 b4139 b1033 b1623 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b2789 b3127 b0529 b2492 b0904 b2954 b1298 b1380 b0514 b3662 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.448019 (mmol/gDw/h)
  Minimum Production Rate : 0.339659 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.194398
  EX_o2_e : 288.273011
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.199716
  EX_pi_e : 1.451140
  EX_so4_e : 0.112820
  EX_k_e : 0.087450
  EX_mg2_e : 0.003887
  EX_ca2_e : 0.002332
  EX_cl_e : 0.002332
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000310
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992804
  EX_h2o_e : 554.458703
  EX_co2_e : 38.210761
  Auxiliary production reaction : 0.339659
  EX_ade_e : 0.000501
  DM_5drib_c : 0.000301
  DM_4crsol_c : 0.000100

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.

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Last updated: 21-Sep-2023
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