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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b2836 b3553 b4069 b4384 b2744 b3708 b3008 b3614 b0910 b2297 b2458 b2781 b0030 b2407 b1759 b1982 b2797 b3117 b1814 b4471 b1033 b2440 b4374 b0675 b0261 b3709 b4381 b2406 b3161 b0112 b0114 b0509 b3125 b1539 b2492 b0904 b0591 b2578 b1533 b3927 b3918 b1473 b3447 b4141 b1798 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.529413 (mmol/gDw/h)
  Minimum Production Rate : 0.115364 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.677719
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.948264
  EX_pi_e : 0.856767
  EX_so4_e : 0.248681
  EX_k_e : 0.103338
  EX_fe2_e : 0.008503
  EX_mg2_e : 0.004593
  EX_cl_e : 0.002756
  EX_ca2_e : 0.002756
  EX_cu2_e : 0.000375
  EX_mn2_e : 0.000366
  EX_zn2_e : 0.000181
  EX_ni2_e : 0.000171
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 51.055842
  EX_co2_e : 33.595516
  EX_h_e : 6.173144
  EX_ac_e : 0.423581
  EX_thym_e : 0.211232
  Auxiliary production reaction : 0.115364
  DM_oxam_c : 0.000592
  DM_5drib_c : 0.000355
  DM_4crsol_c : 0.000118
  EX_etha_e : 0.000043

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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