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 : nmn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2744 b3614 b0910 b4152 b2779 b2925 b2097 b2781 b1612 b1611 b4122 b1779 b2690 b1759 b4374 b0675 b3945 b4138 b4123 b0621 b4381 b3821 b3918 b4042 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.618766 (mmol/gDw/h)
  Minimum Production Rate : 0.104620 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.018955
  EX_o2_e : 276.846959
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.412093
  EX_pi_e : 0.701485
  EX_so4_e : 0.155818
  EX_k_e : 0.120779
  EX_mg2_e : 0.005368
  EX_ca2_e : 0.003221
  EX_cl_e : 0.003221
  EX_cu2_e : 0.000439
  EX_mn2_e : 0.000428
  EX_zn2_e : 0.000211
  EX_ni2_e : 0.000200
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.916003
  EX_h2o_e : 547.948154
  EX_co2_e : 27.904695
  EX_succ_e : 0.645244
  EX_ura_e : 0.111998
  Auxiliary production reaction : 0.104620
  EX_pheme_e : 0.074059
  DM_5drib_c : 0.000139
  DM_4crsol_c : 0.000138

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