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 : dhpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (112 of 115: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b2836 b3553 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b0910 b0871 b0030 b2407 b0517 b0121 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b3449 b1033 b0596 b0261 b0507 b3709 b2239 b2406 b3161 b0112 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.441592 (mmol/gDw/h)
  Minimum Production Rate : 1.064490 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 987.418869
  EX_o2_e : 272.531947
  EX_nh4_e : 11.156875
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.425998
  EX_so4_e : 0.111202
  EX_k_e : 0.086196
  EX_mg2_e : 0.003831
  EX_ca2_e : 0.002298
  EX_cl_e : 0.002298
  EX_cu2_e : 0.000313
  EX_mn2_e : 0.000305
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992906
  EX_h2o_e : 549.883592
  EX_co2_e : 21.193869
  EX_acald_e : 1.824265
  EX_glyclt_e : 1.064580
  Auxiliary production reaction : 1.064285
  EX_alltn_e : 0.000494
  DM_5drib_c : 0.000296
  DM_4crsol_c : 0.000098
  EX_g3pe_e : 0.000036

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