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Conserved domains on  [gi|490305595|ref|WP_004200741|]
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MULTISPECIES: hypothetical protein, partial [Enterobacterales]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK00049 super family cl35051
elongation factor Tu; Reviewed
 1-20 3.06e-09

elongation factor Tu; Reviewed


The actual alignment was detected with superfamily member PRK00049:

Pssm-ID: 234596 [Multi-domain]  Cd Length: 396  Bit Score: 48.26  E-value: 3.06e-09
                         10        20
                 ....*....|....*....|
gi 490305595   1 RFAIREGGRTVGAGVVAKVL 20
Cdd:PRK00049 376 RFAIREGGRTVGAGVVTKII 395
 
Name Accession Description Interval E-value
PRK00049 PRK00049
elongation factor Tu; Reviewed
 1-20 3.06e-09

elongation factor Tu; Reviewed


Pssm-ID: 234596 [Multi-domain]  Cd Length: 396  Bit Score: 48.26  E-value: 3.06e-09
                         10        20
                 ....*....|....*....|
gi 490305595   1 RFAIREGGRTVGAGVVAKVL 20
Cdd:PRK00049 376 RFAIREGGRTVGAGVVTKII 395
TufA COG0050
Translation elongation factor EF-Tu, a GTPase [Translation, ribosomal structure and biogenesis] ...
 1-20 7.96e-09

Translation elongation factor EF-Tu, a GTPase [Translation, ribosomal structure and biogenesis]; Translation elongation factor EF-Tu, a GTPase is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 439820 [Multi-domain]  Cd Length: 396  Bit Score: 47.07  E-value: 7.96e-09
                         10        20
                 ....*....|....*....|
gi 490305595   1 RFAIREGGRTVGAGVVAKVL 20
Cdd:COG0050  376 RFAIREGGRTVGAGVVTKII 395
EF-Tu TIGR00485
translation elongation factor TU; This model models orthologs of translation elongation factor ...
 1-20 4.46e-07

translation elongation factor TU; This model models orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts, one of several GTP-binding translation factors found by the more general pfam model GTP_EFTU. The eukaryotic conterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this model. EF-Tu is one of the most abundant proteins in bacteria, as well as one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation. [Protein synthesis, Translation factors]


Pssm-ID: 129576 [Multi-domain]  Cd Length: 394  Bit Score: 42.07  E-value: 4.46e-07
                          10        20
                  ....*....|....*....|
gi 490305595    1 RFAIREGGRTVGAGVVAKVL 20
Cdd:TIGR00485 374 RFAIREGGRTVGAGVVSKIL 393
GTP_EFTU_D3 pfam03143
Elongation factor Tu C-terminal domain; Elongation factor Tu consists of three structural ...
 1-19 1.23e-06

Elongation factor Tu C-terminal domain; Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA and binding to EF-Ts pfam00889.


Pssm-ID: 397314 [Multi-domain]  Cd Length: 105  Bit Score: 39.56  E-value: 1.23e-06
                          10
                  ....*....|....*....
gi 490305595    1 RFAIREGGRTVGAGVVAKV 19
Cdd:pfam03143  87 RFAIREGGRTVAAGVVTEI 105
EFTU_III cd03707
Domain III of Elongation Factor (EF) Tu; EF-Tu consists of three structural domains, ...
 1-16 2.00e-06

Domain III of Elongation Factor (EF) Tu; EF-Tu consists of three structural domains, designated I, II, and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and to elongation factor Ts (EF-Ts). EF-Ts is the guanine-nucleotide-exchange factor for EF-Tu. EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Crystallographic studies revealed structural similarities ("molecular mimicry") between tertiary structures of EF-G and the EF-Tu-aminoacyl-tRNA ternary complex. Domains III, IV, and V of EF-G mimic the tRNA structure in the EF-Tu ternary complex; domains III, IV and V can be related to the acceptor stem, anticodon helix and T stem of tRNA respectively.


Pssm-ID: 294006 [Multi-domain]  Cd Length: 90  Bit Score: 38.65  E-value: 2.00e-06
                        10
                ....*....|....*.
gi 490305595  1 RFAIREGGRTVGAGVV 16
Cdd:cd03707  75 RFAIREGGRTVGAGVV 90
 
Name Accession Description Interval E-value
PRK00049 PRK00049
elongation factor Tu; Reviewed
 1-20 3.06e-09

elongation factor Tu; Reviewed


Pssm-ID: 234596 [Multi-domain]  Cd Length: 396  Bit Score: 48.26  E-value: 3.06e-09
                         10        20
                 ....*....|....*....|
gi 490305595   1 RFAIREGGRTVGAGVVAKVL 20
Cdd:PRK00049 376 RFAIREGGRTVGAGVVTKII 395
PRK12735 PRK12735
elongation factor Tu; Reviewed
 1-20 5.12e-09

elongation factor Tu; Reviewed


Pssm-ID: 183708 [Multi-domain]  Cd Length: 396  Bit Score: 47.53  E-value: 5.12e-09
                         10        20
                 ....*....|....*....|
gi 490305595   1 RFAIREGGRTVGAGVVAKVL 20
Cdd:PRK12735 376 RFAIREGGRTVGAGVVAKII 395
TufA COG0050
Translation elongation factor EF-Tu, a GTPase [Translation, ribosomal structure and biogenesis] ...
 1-20 7.96e-09

Translation elongation factor EF-Tu, a GTPase [Translation, ribosomal structure and biogenesis]; Translation elongation factor EF-Tu, a GTPase is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 439820 [Multi-domain]  Cd Length: 396  Bit Score: 47.07  E-value: 7.96e-09
                         10        20
                 ....*....|....*....|
gi 490305595   1 RFAIREGGRTVGAGVVAKVL 20
Cdd:COG0050  376 RFAIREGGRTVGAGVVTKII 395
tufA CHL00071
elongation factor Tu
 1-20 2.63e-08

elongation factor Tu


Pssm-ID: 177010 [Multi-domain]  Cd Length: 409  Bit Score: 45.33  E-value: 2.63e-08
                         10        20
                 ....*....|....*....|
gi 490305595   1 RFAIREGGRTVGAGVVAKVL 20
Cdd:CHL00071 389 RFAIREGGRTVGAGVVSKIL 408
PLN03127 PLN03127
Elongation factor Tu; Provisional
 1-21 1.20e-07

Elongation factor Tu; Provisional


Pssm-ID: 178673 [Multi-domain]  Cd Length: 447  Bit Score: 43.66  E-value: 1.20e-07
                         10        20
                 ....*....|....*....|.
gi 490305595   1 RFAIREGGRTVGAGVVAKVLG 21
Cdd:PLN03127 427 RFALREGGRTVGAGVVSKVLS 447
PRK12736 PRK12736
elongation factor Tu; Reviewed
 1-20 1.99e-07

elongation factor Tu; Reviewed


Pssm-ID: 237184 [Multi-domain]  Cd Length: 394  Bit Score: 43.01  E-value: 1.99e-07
                         10        20
                 ....*....|....*....|
gi 490305595   1 RFAIREGGRTVGAGVVAKVL 20
Cdd:PRK12736 374 KFAIREGGRTVGAGTVTEIL 393
EF-Tu TIGR00485
translation elongation factor TU; This model models orthologs of translation elongation factor ...
 1-20 4.46e-07

translation elongation factor TU; This model models orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts, one of several GTP-binding translation factors found by the more general pfam model GTP_EFTU. The eukaryotic conterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this model. EF-Tu is one of the most abundant proteins in bacteria, as well as one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation. [Protein synthesis, Translation factors]


Pssm-ID: 129576 [Multi-domain]  Cd Length: 394  Bit Score: 42.07  E-value: 4.46e-07
                          10        20
                  ....*....|....*....|
gi 490305595    1 RFAIREGGRTVGAGVVAKVL 20
Cdd:TIGR00485 374 RFAIREGGRTVGAGVVSKIL 393
GTP_EFTU_D3 pfam03143
Elongation factor Tu C-terminal domain; Elongation factor Tu consists of three structural ...
 1-19 1.23e-06

Elongation factor Tu C-terminal domain; Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA and binding to EF-Ts pfam00889.


Pssm-ID: 397314 [Multi-domain]  Cd Length: 105  Bit Score: 39.56  E-value: 1.23e-06
                          10
                  ....*....|....*....
gi 490305595    1 RFAIREGGRTVGAGVVAKV 19
Cdd:pfam03143  87 RFAIREGGRTVAAGVVTEI 105
EFTU_III cd03707
Domain III of Elongation Factor (EF) Tu; EF-Tu consists of three structural domains, ...
 1-16 2.00e-06

Domain III of Elongation Factor (EF) Tu; EF-Tu consists of three structural domains, designated I, II, and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and to elongation factor Ts (EF-Ts). EF-Ts is the guanine-nucleotide-exchange factor for EF-Tu. EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Crystallographic studies revealed structural similarities ("molecular mimicry") between tertiary structures of EF-G and the EF-Tu-aminoacyl-tRNA ternary complex. Domains III, IV, and V of EF-G mimic the tRNA structure in the EF-Tu ternary complex; domains III, IV and V can be related to the acceptor stem, anticodon helix and T stem of tRNA respectively.


Pssm-ID: 294006 [Multi-domain]  Cd Length: 90  Bit Score: 38.65  E-value: 2.00e-06
                        10
                ....*....|....*.
gi 490305595  1 RFAIREGGRTVGAGVV 16
Cdd:cd03707  75 RFAIREGGRTVGAGVV 90
PLN03126 PLN03126
Elongation factor Tu; Provisional
 1-20 4.56e-05

Elongation factor Tu; Provisional


Pssm-ID: 215592 [Multi-domain]  Cd Length: 478  Bit Score: 36.52  E-value: 4.56e-05
                         10        20
                 ....*....|....*....|
gi 490305595   1 RFAIREGGRTVGAGVVAKVL 20
Cdd:PLN03126 458 RFAIREGGKTVGAGVIQSII 477
mtEFTU_III cd03706
Domain III of mitochondrial EF-TU (mtEF-TU); mtEF-TU is highly conserved and is 55-60% ...
 1-19 2.36e-04

Domain III of mitochondrial EF-TU (mtEF-TU); mtEF-TU is highly conserved and is 55-60% identical to bacterial EF-TU. The overall structure is similar to that observed in the Escherichia coli and Thermus aquaticus EF-TU. However, compared with that observed in prokaryotic EF-TU, the nucleotide-binding domain (domain I) of mtEF-TU is in a different orientation relative to the rest of the structure. Furthermore, domain III is followed by a short 11-amino acid extension that forms one helical turn. This extension seems to be specific to the mitochondrial factors and has not been observed in any of the prokaryotic factors.


Pssm-ID: 294005 [Multi-domain]  Cd Length: 93  Bit Score: 33.36  E-value: 2.36e-04
                        10
                ....*....|....*....
gi 490305595  1 RFAIREGGRTVGAGVVAKV 19
Cdd:cd03706  75 RFTLREGGRTIGTGVVTKL 93
TEF1 COG5256
Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ...
 1-19 5.92e-04

Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]; Translation elongation factor EF-1alpha (GTPase) is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 444074 [Multi-domain]  Cd Length: 423  Bit Score: 33.37  E-value: 5.92e-04
                         10
                 ....*....|....*....
gi 490305595   1 RFAIREGGRTVGAGVVAKV 19
Cdd:COG5256  401 RFAIRDMGQTVAAGVVLDV 419
PRK12317 PRK12317
elongation factor 1-alpha; Reviewed
 1-19 1.20e-03

elongation factor 1-alpha; Reviewed


Pssm-ID: 237055 [Multi-domain]  Cd Length: 425  Bit Score: 32.21  E-value: 1.20e-03
                         10
                 ....*....|....*....
gi 490305595   1 RFAIREGGRTVGAGVVAKV 19
Cdd:PRK12317 402 RFAIRDMGQTIAAGMVIDV 420
HBS1_C_III cd04093
C-terminal domain of Hsp70 subfamily B suppressor 1 (HBS1); This model represents the ...
 1-19 4.53e-03

C-terminal domain of Hsp70 subfamily B suppressor 1 (HBS1); This model represents the C-terminal domain of Hsp70 subfamily B suppressor 1 (HBS1), which is homologous to the domain III of EF-1alpha. This group contains proteins similar to yeast Hbs1, which together with Dom34, promotes the No-go decay (NGD) of mRNA. The NGD targets mRNAs whose elongation stalled for degradation initiated by endonucleolytic cleavage in the vicinity of the stalled ribosome.


Pssm-ID: 294008 [Multi-domain]  Cd Length: 109  Bit Score: 30.21  E-value: 4.53e-03
                         10
                 ....*....|....*....
gi 490305595   1 RFAIREGGRTVGAGVVAKV 19
Cdd:cd04093   91 RFVLRRGGETIAAGIVTEI 109
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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