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 : dhmptp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b3553 b4269 b0493 b3588 b3003 b3011 b4384 b2744 b3752 b0871 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b0477 b4139 b1033 b4014 b0261 b2976 b0411 b2799 b3945 b1602 b0507 b2342 b3845 b2913 b4381 b3915 b1727 b0114 b0529 b2492 b0904 b2954 b3927 b3029 b1380 b3662 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.435011 (mmol/gDw/h)
  Minimum Production Rate : 0.357316 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.922118
  EX_o2_e : 287.793239
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.486514
  EX_pi_e : 1.491505
  EX_so4_e : 0.109545
  EX_k_e : 0.084911
  EX_mg2_e : 0.003774
  EX_ca2_e : 0.002264
  EX_cl_e : 0.002264
  EX_cu2_e : 0.000308
  EX_mn2_e : 0.000301
  EX_zn2_e : 0.000148
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993012
  EX_h2o_e : 553.962135
  EX_co2_e : 38.194538
  EX_etoh_e : 0.365589
  Auxiliary production reaction : 0.357297
  EX_hxan_e : 0.000487
  DM_5drib_c : 0.000292
  DM_4crsol_c : 0.000097

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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