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 : malcoame_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b4382 b4384 b2744 b3708 b3008 b0871 b2925 b2097 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b3945 b0452 b0114 b2366 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.775525 (mmol/gDw/h)
  Minimum Production Rate : 0.028942 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.487106
  EX_o2_e : 274.728613
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.836168
  EX_pi_e : 0.834903
  EX_so4_e : 0.224235
  EX_k_e : 0.151377
  EX_mg2_e : 0.006728
  EX_ca2_e : 0.004037
  EX_cl_e : 0.004037
  EX_cu2_e : 0.000550
  EX_mn2_e : 0.000536
  EX_zn2_e : 0.000264
  EX_ni2_e : 0.000250
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987544
  EX_h2o_e : 547.839527
  EX_co2_e : 26.242560
  EX_acser_e : 0.228161
  DM_oxam_c : 0.029810
  Auxiliary production reaction : 0.028942
  DM_5drib_c : 0.000520
  DM_4crsol_c : 0.000173

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
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