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Conserved domains on  [gi|209870351|pdb|3BBU|A]
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Chain A, Heat Shock Protein 15

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, ...
 1-104 7.44e-67

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 PRK10348:

Pssm-ID: 447867  Cd Length: 133  Bit Score: 197.17  E-value: 7.44e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3BBU_A         1 PAVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALL 80
Cdd:PRK10348   5 PAVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALL 84

                         90       100
                 ....*....|....*....|....
3BBU_A        81 YEETAESVEKREKMALARKLNALT 104
Cdd:PRK10348  85 YEETAESVEKREKMALARKLNALT 108
 
Name Accession Description Interval E-value
PRK10348 PRK10348
ribosome-associated heat shock protein Hsp15; Provisional
 1-104 7.44e-67

ribosome-associated heat shock protein Hsp15; Provisional


Pssm-ID: 182397  Cd Length: 133  Bit Score: 197.17  E-value: 7.44e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3BBU_A         1 PAVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALL 80
Cdd:PRK10348   5 PAVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALL 84

                         90       100
                 ....*....|....*....|....
3BBU_A        81 YEETAESVEKREKMALARKLNALT 104
Cdd:PRK10348  85 YEETAESVEKREKMALARKLNALT 108
HslR COG1188
Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal ...
 5-97 1.36e-43

Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440801  Cd Length: 120  Bit Score: 137.66  E-value: 1.36e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3BBU_A        5 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALLYEET 84
Cdd:COG1188   5 MRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSERRGPAPEAQLLYEEL 84

                        90
                ....*....|...
3BBU_A       85 AESVEKREKMALA 97
Cdd:COG1188  85 TPSPAPREEAAAA 97
S4 smart00363
S4 RNA-binding domain;
5-60 1.43e-11

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 54.52  E-value: 1.43e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
3BBU_A           5 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQGNDER 60
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKvTKPSYIVKPGDVISVRGKELKR 57
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 5-65 1.72e-11

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: 54.95  E-value: 1.72e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
3BBU_A        5 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQGNDERTVIVK 65
Cdd:cd00165   1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVvTKPSYKVKPGDVIEVDGKSIEEDIVYE 62
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 5-51 2.58e-10

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, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA.


Pssm-ID: 396182 [Multi-domain]  Cd Length: 48  Bit Score: 51.34  E-value: 2.58e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
3BBU_A          5 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATL 51
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVvKDPSYRVKPGDEI 48
 
Name Accession Description Interval E-value
PRK10348 PRK10348
ribosome-associated heat shock protein Hsp15; Provisional
 1-104 7.44e-67

ribosome-associated heat shock protein Hsp15; Provisional


Pssm-ID: 182397  Cd Length: 133  Bit Score: 197.17  E-value: 7.44e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3BBU_A         1 PAVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALL 80
Cdd:PRK10348   5 PAVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALL 84

                         90       100
                 ....*....|....*....|....
3BBU_A        81 YEETAESVEKREKMALARKLNALT 104
Cdd:PRK10348  85 YEETAESVEKREKMALARKLNALT 108
HslR COG1188
Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal ...
 5-97 1.36e-43

Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440801  Cd Length: 120  Bit Score: 137.66  E-value: 1.36e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3BBU_A        5 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALLYEET 84
Cdd:COG1188   5 MRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSERRGPAPEAQLLYEEL 84

                        90
                ....*....|...
3BBU_A       85 AESVEKREKMALA 97
Cdd:COG1188  85 TPSPAPREEAAAA 97
S4 smart00363
S4 RNA-binding domain;
5-60 1.43e-11

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 54.52  E-value: 1.43e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
3BBU_A           5 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQGNDER 60
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKvTKPSYIVKPGDVISVRGKELKR 57
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 5-65 1.72e-11

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: 54.95  E-value: 1.72e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
3BBU_A        5 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQGNDERTVIVK 65
Cdd:cd00165   1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVvTKPSYKVKPGDVIEVDGKSIEEDIVYE 62
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 5-51 2.58e-10

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, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA.


Pssm-ID: 396182 [Multi-domain]  Cd Length: 48  Bit Score: 51.34  E-value: 2.58e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
3BBU_A          5 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATL 51
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVvKDPSYRVKPGDEI 48
 
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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