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 : dhmptp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b4467 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b2744 b0871 b2779 b2926 b1238 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b3908 b1656 b1982 b4139 b0675 b2361 b4014 b0261 b2976 b2799 b3945 b1602 b4388 b4381 b2789 b3127 b3915 b0452 b4064 b4464 b2975 b3603 b0529 b2492 b0904 b1300 b2954 b1380 b1600 b2660 b3662 b1985 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.386390 (mmol/gDw/h)
  Minimum Production Rate : 0.642091 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 39.138716
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.385595
  EX_pi_e : 2.298984
  EX_so4_e : 0.097302
  EX_k_e : 0.075421
  EX_fe3_e : 0.006207
  EX_mg2_e : 0.003352
  EX_ca2_e : 0.002011
  EX_cl_e : 0.002011
  EX_cu2_e : 0.000274
  EX_mn2_e : 0.000267
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 56.910507
  EX_co2_e : 38.358615
  EX_h_e : 5.484949
  Auxiliary production reaction : 0.642090
  EX_ade_e : 0.000432
  DM_5drib_c : 0.000259
  DM_4crsol_c : 0.000086

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
Contact