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 : nadhx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (116 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b3553 b3399 b3846 b2341 b0474 b2518 b3831 b4069 b2502 b2744 b3708 b3008 b0910 b3752 b2297 b2458 b3236 b1779 b3962 b1982 b2797 b3117 b1814 b4471 b4267 b1033 b0675 b2361 b0261 b3709 b4381 b2406 b3161 b0112 b0452 b0114 b0509 b3125 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b0325 b1473 b0594 b3447 b4266 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.483970 (mmol/gDw/h)
  Minimum Production Rate : 0.167366 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.250439
  EX_o2_e : 285.133162
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.561480
  EX_pi_e : 0.801573
  EX_so4_e : 0.121873
  EX_k_e : 0.094468
  EX_mg2_e : 0.004198
  EX_ca2_e : 0.002519
  EX_cl_e : 0.002519
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992227
  EX_h2o_e : 552.012339
  EX_co2_e : 35.654856
  EX_ac_e : 0.281761
  Auxiliary production reaction : 0.167366
  EX_thym_e : 0.074937
  DM_oxam_c : 0.013205
  DM_5drib_c : 0.000325
  DM_4crsol_c : 0.000108

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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