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 : hemeO_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b1478 b3399 b1241 b4069 b2744 b2297 b2458 b2779 b0160 b1004 b3713 b1109 b0046 b3236 b1982 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b0507 b2913 b3915 b2975 b3603 b0529 b2492 b0904 b1380 b1695 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.225785 (mmol/gDw/h)
  Minimum Production Rate : 0.247002 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.522358
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.897747
  EX_fe3_e : 0.250628
  EX_pi_e : 0.217793
  EX_so4_e : 0.056857
  EX_k_e : 0.044072
  EX_mg2_e : 0.001959
  EX_ca2_e : 0.001175
  EX_cl_e : 0.001175
  EX_cu2_e : 0.000160
  EX_mn2_e : 0.000156
  EX_zn2_e : 0.000077
  EX_ni2_e : 0.000073

Product: (mmol/gDw/h)
  EX_h2o_e : 50.379425
  EX_co2_e : 33.424774
  EX_h_e : 6.903976
  EX_ade_e : 0.494256
  DM_5drib_c : 0.494155
  Auxiliary production reaction : 0.247002
  EX_ac_e : 0.131449
  DM_4crsol_c : 0.000050

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