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 : u3aga_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (92 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b2242 b3553 b4382 b3831 b4384 b1278 b3614 b0910 b3752 b2781 b3844 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b1033 b1415 b4138 b4123 b0621 b2406 b3915 b0452 b2197 b3028 b3918 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.497963 (mmol/gDw/h)
  Minimum Production Rate : 0.262117 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.933832
  EX_o2_e : 277.277191
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.346333
  EX_pi_e : 1.004570
  EX_so4_e : 0.125398
  EX_k_e : 0.097199
  EX_mg2_e : 0.004320
  EX_ca2_e : 0.002592
  EX_cl_e : 0.002592
  EX_cu2_e : 0.000353
  EX_mn2_e : 0.000344
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992000
  EX_h2o_e : 546.259723
  EX_co2_e : 28.994166
  EX_succ_e : 0.519272
  Auxiliary production reaction : 0.262116
  EX_ura_e : 0.091013
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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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