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 : dhmptp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b0160 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b4374 b0675 b2361 b2291 b0261 b0507 b0112 b0452 b2975 b0114 b3603 b2366 b0755 b3612 b2492 b0904 b1533 b2835   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.473095 (mmol/gDw/h)
  Minimum Production Rate : 1.230723 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.261648
  EX_o2_e : 274.893497
  EX_nh4_e : 11.448449
  EX_glc__D_e : 10.000000
  EX_pi_e : 4.148520
  EX_so4_e : 0.119135
  EX_k_e : 0.092345
  EX_mg2_e : 0.004104
  EX_ca2_e : 0.002462
  EX_cl_e : 0.002462
  EX_cu2_e : 0.000335
  EX_mn2_e : 0.000327
  EX_zn2_e : 0.000161
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992402
  EX_h2o_e : 552.426796
  EX_co2_e : 22.642576
  EX_ac_e : 2.505622
  Auxiliary production reaction : 1.230723
  EX_enter_e : 0.061639
  DM_oxam_c : 0.000529
  DM_5drib_c : 0.000317
  DM_4crsol_c : 0.000106

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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