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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 57
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b1479 b2297 b2458 b2779 b2926 b0030 b2407 b3124 b3236 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b0596 b0675 b1014 b4014 b0261 b2976 b0822 b0507 b3709 b2406 b3161 b0112 b0452 b4265 b2975 b0114 b3603 b2366 b0306 b3605 b2492 b0904 b1533 b1380 b0325 b0508 b4042 b1473 b0514 b4266 b3662 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.299119 (mmol/gDw/h)
  Minimum Production Rate : 0.317493 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.188799
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.713330
  EX_pi_e : 1.241010
  EX_so4_e : 0.652908
  EX_k_e : 0.058386
  EX_fe2_e : 0.004804
  EX_mg2_e : 0.002595
  EX_ca2_e : 0.001557
  EX_cl_e : 0.001557
  EX_cu2_e : 0.000212
  EX_mn2_e : 0.000207
  EX_zn2_e : 0.000102
  EX_ni2_e : 0.000097

Product: (mmol/gDw/h)
  EX_h2o_e : 49.563910
  EX_co2_e : 34.476815
  EX_h_e : 5.920732
  EX_ac_e : 2.161561
  Auxiliary production reaction : 0.317493
  EX_met__L_e : 0.260091
  DM_oxam_c : 0.000335
  DM_5drib_c : 0.000201
  EX_dxylnt_e : 0.000200
  DM_4crsol_c : 0.000067

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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