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 : ump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (91 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b4467 b2242 b1478 b4382 b0474 b2518 b1241 b3831 b4069 b4384 b3752 b2297 b2458 b2926 b2781 b2407 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b1759 b4161 b0411 b2799 b3945 b1602 b4138 b4123 b0621 b3915 b0529 b2492 b0904 b3029 b3028 b1380 b3918 b4042 b2660 b1517 b1206 b0221 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.286280 (mmol/gDw/h)
  Minimum Production Rate : 1.029592 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.525879
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.297685
  EX_pi_e : 1.305740
  EX_so4_e : 0.072091
  EX_k_e : 0.055880
  EX_fe3_e : 0.004598
  EX_mg2_e : 0.002483
  EX_ca2_e : 0.001490
  EX_cl_e : 0.001490
  EX_cu2_e : 0.000203
  EX_mn2_e : 0.000198
  EX_zn2_e : 0.000098
  EX_ni2_e : 0.000092

Product: (mmol/gDw/h)
  EX_h2o_e : 47.989090
  EX_co2_e : 31.659822
  EX_h_e : 8.355600
  EX_succ_e : 1.197805
  Auxiliary production reaction : 1.029592
  EX_ac_e : 0.669413
  EX_glyclt_e : 0.449637
  EX_ura_e : 0.073350
  DM_mththf_c : 0.000128
  DM_5drib_c : 0.000064
  DM_4crsol_c : 0.000064

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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