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 : didp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b1478 b3399 b2066 b1241 b0351 b4069 b2744 b2297 b2458 b2925 b2097 b2926 b0160 b3236 b2690 b2498 b3616 b3589 b2210 b1623 b3665 b0675 b2361 b2291 b0822 b2913 b0114 b0529 b2492 b0904 b4042 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.513936 (mmol/gDw/h)
  Minimum Production Rate : 0.656859 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.729920
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.179629
  EX_pi_e : 1.809464
  EX_so4_e : 0.129419
  EX_k_e : 0.100317
  EX_fe2_e : 0.008254
  EX_mg2_e : 0.004458
  EX_ca2_e : 0.002675
  EX_cl_e : 0.002675
  EX_cu2_e : 0.000364
  EX_mn2_e : 0.000355
  EX_zn2_e : 0.000175
  EX_ni2_e : 0.000166
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 47.969479
  EX_co2_e : 26.512087
  EX_h_e : 9.605423
  EX_ac_e : 2.910868
  Auxiliary production reaction : 0.656859
  EX_ade_e : 0.000346
  DM_mththf_c : 0.000230
  DM_5drib_c : 0.000116
  DM_4crsol_c : 0.000115

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