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 : 2omph_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4382 b4384 b2744 b3614 b0910 b4152 b0871 b2925 b2097 b2926 b2781 b1612 b1611 b4122 b0907 b2690 b1759 b4374 b0675 b0726 b3945 b4138 b4123 b0621 b0114 b2492 b0904 b3918 b1912 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.600451 (mmol/gDw/h)
  Minimum Production Rate : 0.024994 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.477888
  EX_o2_e : 276.166156
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.336440
  EX_pi_e : 0.579199
  EX_so4_e : 0.151206
  EX_k_e : 0.117204
  EX_mg2_e : 0.005209
  EX_ca2_e : 0.003125
  EX_cl_e : 0.003125
  EX_cu2_e : 0.000426
  EX_mn2_e : 0.000415
  EX_zn2_e : 0.000205
  EX_ni2_e : 0.000194
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990356
  EX_h2o_e : 546.484643
  EX_co2_e : 26.594538
  EX_pyr_e : 0.891373
  EX_succ_e : 0.626146
  EX_ura_e : 0.308633
  EX_thymd_e : 0.117176
  Auxiliary production reaction : 0.024994
  DM_5drib_c : 0.000135
  DM_4crsol_c : 0.000134

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