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 : udpgalfur_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b2436 b4467 b2242 b4382 b0474 b2518 b3831 b4384 b3752 b2781 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1759 b3449 b4161 b1415 b4015 b4138 b4123 b0621 b2239 b2406 b0114 b3028 b1380 b3918 b1912 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.524134 (mmol/gDw/h)
  Minimum Production Rate : 0.276819 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.892769
  EX_o2_e : 281.477627
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.403975
  EX_pi_e : 1.059220
  EX_so4_e : 0.131987
  EX_k_e : 0.102307
  EX_mg2_e : 0.004547
  EX_ca2_e : 0.002728
  EX_cl_e : 0.002728
  EX_cu2_e : 0.000372
  EX_mn2_e : 0.000362
  EX_zn2_e : 0.000179
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991582
  EX_h2o_e : 549.116536
  EX_co2_e : 31.767546
  EX_succ_e : 0.546562
  Auxiliary production reaction : 0.276819
  EX_ura_e : 0.094870
  DM_5drib_c : 0.000352
  DM_4crsol_c : 0.000117

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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