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 : nad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b3399 b1241 b0351 b2502 b2744 b0871 b2925 b2097 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b0207 b3012 b0937 b1982 b1033 b4374 b0675 b2361 b2291 b0261 b2799 b1602 b2913 b0452 b1727 b0529 b2492 b0904 b1781 b3001 b3927 b1380 b0325 b1771 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.367969 (mmol/gDw/h)
  Minimum Production Rate : 0.032503 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.361970
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.203612
  EX_pi_e : 0.419951
  EX_so4_e : 0.092662
  EX_k_e : 0.071825
  EX_fe2_e : 0.005910
  EX_mg2_e : 0.003192
  EX_ca2_e : 0.001915
  EX_cl_e : 0.001915
  EX_cu2_e : 0.000261
  EX_mn2_e : 0.000254
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 44.084959
  EX_co2_e : 28.416295
  EX_h_e : 8.778059
  EX_pyr_e : 5.264944
  Auxiliary production reaction : 0.032503
  EX_ade_e : 0.000412
  DM_5drib_c : 0.000247
  DM_4crsol_c : 0.000082

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