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Conserved domains on  [gi|1066946133|gb|AOP43942|]
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ribosome-associated protein YbcJ [Edwardsiella piscicida]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S4 super family cl09940
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 1-70 2.22e-36

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.


The actual alignment was detected with superfamily member PRK11507:

Pssm-ID: 447867  Cd Length: 70  Bit Score: 116.53  E-value: 2.22e-36
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066946133  1 MQTFHLDNHPHVELCDLLKLQGWCDSGAQAKNLIAEGQVKVDGAVETRKRAKIVAGQVVDFAGQQARVIA 70
Cdd:PRK11507   1 MATFSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVVA 70
 
Name Accession Description Interval E-value
PRK11507 PRK11507
ribosome-associated protein YbcJ;
1-70 2.22e-36

ribosome-associated protein YbcJ;


Pssm-ID: 183166  Cd Length: 70  Bit Score: 116.53  E-value: 2.22e-36
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066946133  1 MQTFHLDNHPHVELCDLLKLQGWCDSGAQAKNLIAEGQVKVDGAVETRKRAKIVAGQVVDFAGQQARVIA 70
Cdd:PRK11507   1 MATFSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVVA 70
YbcJ COG2501
Ribosome-associated protein YbcJ, S4-like RNA-binding protein [Translation, ribosomal ...
 10-70 2.01e-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: 95.86  E-value: 2.01e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1066946133 10 PHVELCDLLKLQGWCDSGAQAKNLIAEGQVKVDGAVETRKRAKIVAGQVVDFAGQQARVIA 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 1.35e-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: 94.04  E-value: 1.35e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066946133 10 PHVELCDLLKLQGWCDSGAQAKNLIAEGQVKVDGAVETRKRAKIVAGQVVDFAGQQARVI 69
Cdd:pfam13275  6 EYITLGQLLKLAGLVESGGEAKWFIAEGEVLVNGEVETRRGKKLRAGDVVEFDGETIEVV 65
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 24-68 8.65e-04

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: 33.76  E-value: 8.65e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 1066946133 24 CDSGAQAKNLIAEGQVKVDGAVETRKRAKIVAGQVVDFAGQQARV 68
Cdd:cd00165   13 APSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEE 57
 
Name Accession Description Interval E-value
PRK11507 PRK11507
ribosome-associated protein YbcJ;
1-70 2.22e-36

ribosome-associated protein YbcJ;


Pssm-ID: 183166  Cd Length: 70  Bit Score: 116.53  E-value: 2.22e-36
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066946133  1 MQTFHLDNHPHVELCDLLKLQGWCDSGAQAKNLIAEGQVKVDGAVETRKRAKIVAGQVVDFAGQQARVIA 70
Cdd:PRK11507   1 MATFSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVVA 70
YbcJ COG2501
Ribosome-associated protein YbcJ, S4-like RNA-binding protein [Translation, ribosomal ...
 10-70 2.01e-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: 95.86  E-value: 2.01e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1066946133 10 PHVELCDLLKLQGWCDSGAQAKNLIAEGQVKVDGAVETRKRAKIVAGQVVDFAGQQARVIA 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 1.35e-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: 94.04  E-value: 1.35e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066946133 10 PHVELCDLLKLQGWCDSGAQAKNLIAEGQVKVDGAVETRKRAKIVAGQVVDFAGQQARVI 69
Cdd:pfam13275  6 EYITLGQLLKLAGLVESGGEAKWFIAEGEVLVNGEVETRRGKKLRAGDVVEFDGETIEVV 65
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 24-68 8.65e-04

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: 33.76  E-value: 8.65e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 1066946133 24 CDSGAQAKNLIAEGQVKVDGAVETRKRAKIVAGQVVDFAGQQARV 68
Cdd:cd00165   13 APSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEE 57
TyrS COG0162
Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Tyrosyl-tRNA ...
 14-56 6.55e-03

Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Tyrosyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases


Pssm-ID: 439932 [Multi-domain]  Cd Length: 409  Bit Score: 33.08  E-value: 6.55e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1066946133  14 LCDLLKLQGWCDSGAQAKNLIAEGQVKVDGAVETRKRAKIVAG 56
Cdd:COG0162   344 LVDLLVEAGLAASKSEARRLIKQGGVSVNGEKVTDPDAVLTAG 386
 
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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