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 : ncam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (112 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b2242 b3553 b0474 b2518 b3831 b0871 b2925 b2097 b0030 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b0651 b2162 b1779 b2690 b1033 b4161 b3945 b4138 b4123 b0621 b4381 b2406 b0114 b0529 b0306 b3605 b2492 b0904 b3028 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.343876 (mmol/gDw/h)
  Minimum Production Rate : 0.181156 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.578881
  EX_o2_e : 280.113354
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.200628
  EX_pi_e : 0.331705
  EX_so4_e : 0.086595
  EX_k_e : 0.067122
  EX_mg2_e : 0.002983
  EX_ca2_e : 0.001790
  EX_cl_e : 0.001790
  EX_cu2_e : 0.000244
  EX_mn2_e : 0.000238
  EX_zn2_e : 0.000117
  EX_ni2_e : 0.000111

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994477
  EX_h2o_e : 543.846099
  EX_co2_e : 27.959361
  EX_pyr_e : 5.051948
  EX_succ_e : 0.358591
  Auxiliary production reaction : 0.181156
  EX_ura_e : 0.062243
  DM_5drib_c : 0.000077
  DM_4crsol_c : 0.000077

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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