MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : STM_v1_0 [2].
Target metabolite : phe__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: STM2927 STM4482 STM1749 STM2463 STM2285 STM2009 STM3526 STM1886 STM3512 STM3541 STM4326 STM1511 STM2952 STM2947 STM3068 STM2141 STM1620 STM0141 STM0370 STM3597 STM4408 STM1291 STM0150 STM0518 STM4184 STM4484 STM0568 STM2317 STM3179 STM1480 STM4126 STM4578 STM2338 STM2466 STM1937 STM3103 STM1124 STM4467 STM2196 STM3240 STM0007 STM2473 STM0402 STM0608 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.061825 (mmol/gDw/h)
  Minimum Production Rate : 0.042471 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.635990
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.723780
  EX_pi_e : 0.054826
  EX_k_e : 0.010980
  EX_so4_e : 0.007541
  EX_mg2_e : 0.000488
  EX_fe2_e : 0.000453
  EX_ca2_e : 0.000293
  EX_cl_e : 0.000293
  EX_cobalt2_e : 0.000195
  EX_cu2_e : 0.000195
  EX_mn2_e : 0.000195
  EX_mobd_e : 0.000195
  EX_zn2_e : 0.000195

Product: (mmol/gDw/h)
  EX_h2o_e : 12.007860
  EX_co2_e : 10.091123
  EX_dha_e : 4.923747
  EX_h_e : 0.886220
  EX_acald_e : 0.862309
  EX_ac_e : 0.316537
  Auxiliary production reaction : 0.042471
  EX_glyclt_e : 0.003091
  DM_hmfurn_c : 0.000028

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

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: 27-Sep-2023
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