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 : xdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3399 b4382 b4384 b2744 b1278 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b0160 b2690 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0822 b4381 b0452 b2868 b1727 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b3447 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.772359 (mmol/gDw/h)
  Minimum Production Rate : 0.177619 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.155351
  EX_o2_e : 274.900409
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.054484
  EX_pi_e : 1.100260
  EX_so4_e : 0.194495
  EX_k_e : 0.150759
  EX_mg2_e : 0.006700
  EX_ca2_e : 0.004020
  EX_cl_e : 0.004020
  EX_cu2_e : 0.000548
  EX_mn2_e : 0.000534
  EX_zn2_e : 0.000263
  EX_ni2_e : 0.000249
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987595
  EX_h2o_e : 548.643889
  EX_co2_e : 25.917560
  EX_pyr_e : 0.200048
  Auxiliary production reaction : 0.177619
  EX_ade_e : 0.000520
  EX_mththf_e : 0.000346
  DM_5drib_c : 0.000174
  DM_4crsol_c : 0.000172

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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