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Conserved domains on  [gi|90111146|ref|NP_415061|]
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putative RNA-binding protein YbcJ [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

RluA family pseudouridine synthase; rRNA pseudouridine synthase( domain architecture ID 10013817)

RluA family pseudouridine synthase catalyzes the isomerization of specific uridines in rRNA or tRNA to pseudouridines| rRNA pseudouridine synthase catalyzes the formation of pseudouridine at position 516 in 16S or position 2605 in 23S rRNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11507 PRK11507
ribosome-associated protein YbcJ;
1-70 7.05e-44

ribosome-associated protein YbcJ;


:

Pssm-ID: 183166  Cd Length: 70  Bit Score: 135.40  E-value: 7.05e-44
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111146   1 MATFSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVVA 70
Cdd:PRK11507  1 MATFSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVVA 70
 
Name Accession Description Interval E-value
PRK11507 PRK11507
ribosome-associated protein YbcJ;
1-70 7.05e-44

ribosome-associated protein YbcJ;


Pssm-ID: 183166  Cd Length: 70  Bit Score: 135.40  E-value: 7.05e-44
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111146   1 MATFSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVVA 70
Cdd:PRK11507  1 MATFSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVVA 70
YbcJ COG2501
Ribosome-associated protein YbcJ, S4-like RNA-binding protein [Translation, ribosomal ...
 10-70 4.29e-28

Ribosome-associated protein YbcJ, S4-like RNA-binding protein [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441995 [Multi-domain]  Cd Length: 61  Bit Score: 95.09  E-value: 4.29e-28
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 90111146 10 PHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVVA 70
Cdd:COG2501  1 EYITLGQLLKLAGLVESGGEAKALIAEGEVKVNGEVETRRGRKLRPGDVVEVGGETIRVVA 61
S4_2 pfam13275
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 10-69 2.97e-27

S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4.


Pssm-ID: 433078 [Multi-domain]  Cd Length: 65  Bit Score: 93.27  E-value: 2.97e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111146   10 PHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVV 69
Cdd:pfam13275  6 EYITLGQLLKLAGLVESGGEAKWFIAEGEVLVNGEVETRRGKKLRAGDVVEFDGETIEVV 65
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 26-68 1.67e-03

S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.


Pssm-ID: 238095 [Multi-domain]  Cd Length: 70  Bit Score: 32.99  E-value: 1.67e-03
                       10        20        30        40
               ....*....|....*....|....*....|....*....|...
gi 90111146 26 SGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQV 68
Cdd:cd00165 15 SRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEE 57
 
Name Accession Description Interval E-value
PRK11507 PRK11507
ribosome-associated protein YbcJ;
1-70 7.05e-44

ribosome-associated protein YbcJ;


Pssm-ID: 183166  Cd Length: 70  Bit Score: 135.40  E-value: 7.05e-44
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111146   1 MATFSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVVA 70
Cdd:PRK11507  1 MATFSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVVA 70
YbcJ COG2501
Ribosome-associated protein YbcJ, S4-like RNA-binding protein [Translation, ribosomal ...
 10-70 4.29e-28

Ribosome-associated protein YbcJ, S4-like RNA-binding protein [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441995 [Multi-domain]  Cd Length: 61  Bit Score: 95.09  E-value: 4.29e-28
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 90111146 10 PHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVVA 70
Cdd:COG2501  1 EYITLGQLLKLAGLVESGGEAKALIAEGEVKVNGEVETRRGRKLRPGDVVEVGGETIRVVA 61
S4_2 pfam13275
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 10-69 2.97e-27

S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4.


Pssm-ID: 433078 [Multi-domain]  Cd Length: 65  Bit Score: 93.27  E-value: 2.97e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111146   10 PHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVV 69
Cdd:pfam13275  6 EYITLGQLLKLAGLVESGGEAKWFIAEGEVLVNGEVETRRGKKLRAGDVVEFDGETIEVV 65
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 26-68 1.67e-03

S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.


Pssm-ID: 238095 [Multi-domain]  Cd Length: 70  Bit Score: 32.99  E-value: 1.67e-03
                       10        20        30        40
               ....*....|....*....|....*....|....*....|...
gi 90111146 26 SGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQV 68
Cdd:cd00165 15 SRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEE 57
 
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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