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 : dhpmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (116 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 54
  Gene deletion: b4467 b1478 b3399 b0238 b0125 b1241 b4069 b2502 b4384 b2744 b2297 b2458 b2407 b1004 b3713 b1109 b0046 b3124 b3236 b1638 b1779 b4139 b0675 b2361 b2799 b3945 b1602 b4381 b2789 b3127 b3915 b0452 b3654 b2868 b3714 b3664 b4064 b4464 b2975 b3603 b0755 b3612 b0529 b2492 b0904 b1300 b2954 b3029 b1380 b2660 b1511 b1985 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.421663 (mmol/gDw/h)
  Minimum Production Rate : 0.123425 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.267561
  EX_o2_e : 285.800273
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.159694
  EX_pi_e : 0.530128
  EX_so4_e : 0.106184
  EX_k_e : 0.082306
  EX_mg2_e : 0.003658
  EX_ca2_e : 0.002195
  EX_cl_e : 0.002195
  EX_cu2_e : 0.000299
  EX_mn2_e : 0.000291
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993226
  EX_h2o_e : 551.601448
  EX_co2_e : 36.146129
  EX_thymd_e : 0.494411
  EX_ac_e : 0.245487
  Auxiliary production reaction : 0.123389
  EX_mththf_e : 0.000189
  DM_5drib_c : 0.000095
  DM_4crsol_c : 0.000094

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