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 (78 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b4467 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b2502 b2744 b0871 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b3908 b1656 b0937 b1982 b4139 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b2913 b2975 b3603 b1297 b0509 b3125 b0529 b2492 b0904 b2954 b1380 b0508 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.465960 (mmol/gDw/h)
  Minimum Production Rate : 0.706522 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.284349
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.034418
  EX_pi_e : 1.155990
  EX_so4_e : 0.117338
  EX_k_e : 0.090952
  EX_mg2_e : 0.004042
  EX_fe2_e : 0.003846
  EX_fe3_e : 0.003638
  EX_cl_e : 0.002425
  EX_ca2_e : 0.002425
  EX_cu2_e : 0.000330
  EX_mn2_e : 0.000322
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 48.939287
  EX_co2_e : 36.631689
  EX_h_e : 4.287154
  Auxiliary production reaction : 0.706522
  EX_hxan_e : 0.000521
  DM_5drib_c : 0.000313
  DM_4crsol_c : 0.000104

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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