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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3553 b3399 b4382 b1241 b0351 b4384 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b3617 b0160 b3236 b2690 b3962 b2797 b3117 b1814 b4471 b3449 b4267 b1033 b3665 b0675 b2361 b2291 b2799 b3945 b2239 b2406 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b2413 b4266 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.551883 (mmol/gDw/h)
  Minimum Production Rate : 0.382130 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.177999
  EX_o2_e : 277.400360
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.342423
  EX_pi_e : 0.914480
  EX_so4_e : 0.138975
  EX_k_e : 0.107724
  EX_mg2_e : 0.004788
  EX_ca2_e : 0.002873
  EX_cl_e : 0.002873
  EX_cu2_e : 0.000391
  EX_mn2_e : 0.000381
  EX_zn2_e : 0.000188
  EX_ni2_e : 0.000178
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991136
  EX_h2o_e : 545.667084
  EX_co2_e : 27.973460
  EX_pyr_e : 1.977953
  Auxiliary production reaction : 0.382130
  EX_mththf_e : 0.000247
  DM_5drib_c : 0.000124
  DM_4crsol_c : 0.000123

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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