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 : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 56
  Gene deletion: b3553 b1478 b1241 b0351 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b2926 b2407 b1238 b0120 b3962 b1982 b0477 b4139 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b1415 b1014 b4014 b0261 b2976 b3945 b3709 b4381 b2406 b3161 b0112 b4265 b0114 b0509 b3125 b1539 b2492 b0904 b2954 b3035 b1533 b3821 b1380 b0325 b1473 b4266 b3662 b1985   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.301595 (mmol/gDw/h)
  Minimum Production Rate : 0.108356 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.084228
  EX_o2_e : 282.985140
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.810165
  EX_so4_e : 0.978436
  EX_pi_e : 0.615988
  EX_k_e : 0.058869
  EX_mg2_e : 0.002616
  EX_ca2_e : 0.001570
  EX_cl_e : 0.001570
  EX_cu2_e : 0.000214
  EX_mn2_e : 0.000208
  EX_zn2_e : 0.000103
  EX_ni2_e : 0.000097

Product: (mmol/gDw/h)
  EX_fe3_e : 999.995156
  EX_h2o_e : 547.549397
  EX_co2_e : 35.723108
  EX_ac_e : 2.607938
  EX_met__L_e : 0.794132
  Auxiliary production reaction : 0.108356
  DM_oxam_c : 0.000337
  DM_5drib_c : 0.000202
  EX_dxylnt_e : 0.000202
  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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