NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|515629890|ref|WP_017062490|]
View 

MULTISPECIES: ribosome-associated heat shock protein Hsp15 [Vibrio]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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, ...
 5-126 1.40e-58

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: 177.14  E-value: 1.40e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515629890   5 NEAVRLDKWLWAARFYKTRSIARNMVDGGKVHYNGQRSKPSKIVELGAVITLRQGNEEKTVTIEKISAHRGGAPIAQTLY 84
Cdd:PRK10348   6 AVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALLY 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 515629890  85 EETTESLAKREEFAQQRKLNAHS-PAPERRPDKKQRRDIIKFK 126
Cdd:PRK10348  86 EETAESVEKREKMALARKLNALTmPHPDRRPDKKERRDLLRFK 128
 
Name Accession Description Interval E-value
PRK10348 PRK10348
ribosome-associated heat shock protein Hsp15; Provisional
 5-126 1.40e-58

ribosome-associated heat shock protein Hsp15; Provisional


Pssm-ID: 182397  Cd Length: 133  Bit Score: 177.14  E-value: 1.40e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515629890   5 NEAVRLDKWLWAARFYKTRSIARNMVDGGKVHYNGQRSKPSKIVELGAVITLRQGNEEKTVTIEKISAHRGGAPIAQTLY 84
Cdd:PRK10348   6 AVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALLY 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 515629890  85 EETTESLAKREEFAQQRKLNAHS-PAPERRPDKKQRRDIIKFK 126
Cdd:PRK10348  86 EETAESVEKREKMALARKLNALTmPHPDRRPDKKERRDLLRFK 128
HslR COG1188
Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal ...
 4-126 2.02e-53

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


Pssm-ID: 440801  Cd Length: 120  Bit Score: 163.47  E-value: 2.02e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515629890   4 ANEAVRLDKWLWAARFYKTRSIARNMVDGGKVHYNGQRSKPSKIVELGAVITLRQGNEEKTVTIEKISAHRGGAPIAQTL 83
Cdd:COG1188    1 AAERMRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSERRGPAPEAQLL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 515629890  84 YEETTESLAKREEFAQqrklNAHSPAPERRPDKKQRRDIIKFK 126
Cdd:COG1188   81 YEELTPSPAPREEAAA----AAPRPRGAGRPTKKDRRELDRFR 119
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 8-69 3.90e-12

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: 57.26  E-value: 3.90e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 515629890   8 VRLDKWLWAARFYKTRSIARNMVDGGKVHYNGQR-SKPSKIVELGAVITLRQGNEEKTVTIEK 69
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVvTKPSYKVKPGDVIEVDGKSIEEDIVYED 63
S4 smart00363
S4 RNA-binding domain;
8-59 2.03e-10

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 52.60  E-value: 2.03e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 515629890     8 VRLDKWLWAARFYKTRSIARNMVDGGKVHYNGQR-SKPSKIVELGAVITLRQG 59
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKvTKPSYIVKPGDVISVRGK 53
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 8-54 2.13e-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: 52.11  E-value: 2.13e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 515629890    8 VRLDKWLWAARFYKTRSIARNMVDGGKVHYNGQR-SKPSKIVELGAVI 54
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVvKDPSYRVKPGDEI 48
 
Name Accession Description Interval E-value
PRK10348 PRK10348
ribosome-associated heat shock protein Hsp15; Provisional
 5-126 1.40e-58

ribosome-associated heat shock protein Hsp15; Provisional


Pssm-ID: 182397  Cd Length: 133  Bit Score: 177.14  E-value: 1.40e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515629890   5 NEAVRLDKWLWAARFYKTRSIARNMVDGGKVHYNGQRSKPSKIVELGAVITLRQGNEEKTVTIEKISAHRGGAPIAQTLY 84
Cdd:PRK10348   6 AVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALLY 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 515629890  85 EETTESLAKREEFAQQRKLNAHS-PAPERRPDKKQRRDIIKFK 126
Cdd:PRK10348  86 EETAESVEKREKMALARKLNALTmPHPDRRPDKKERRDLLRFK 128
HslR COG1188
Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal ...
 4-126 2.02e-53

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


Pssm-ID: 440801  Cd Length: 120  Bit Score: 163.47  E-value: 2.02e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515629890   4 ANEAVRLDKWLWAARFYKTRSIARNMVDGGKVHYNGQRSKPSKIVELGAVITLRQGNEEKTVTIEKISAHRGGAPIAQTL 83
Cdd:COG1188    1 AAERMRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSERRGPAPEAQLL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 515629890  84 YEETTESLAKREEFAQqrklNAHSPAPERRPDKKQRRDIIKFK 126
Cdd:COG1188   81 YEELTPSPAPREEAAA----AAPRPRGAGRPTKKDRRELDRFR 119
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 8-69 3.90e-12

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: 57.26  E-value: 3.90e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 515629890   8 VRLDKWLWAARFYKTRSIARNMVDGGKVHYNGQR-SKPSKIVELGAVITLRQGNEEKTVTIEK 69
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVvTKPSYKVKPGDVIEVDGKSIEEDIVYED 63
S4 smart00363
S4 RNA-binding domain;
8-59 2.03e-10

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 52.60  E-value: 2.03e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 515629890     8 VRLDKWLWAARFYKTRSIARNMVDGGKVHYNGQR-SKPSKIVELGAVITLRQG 59
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKvTKPSYIVKPGDVISVRGK 53
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 8-54 2.13e-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: 52.11  E-value: 2.13e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 515629890    8 VRLDKWLWAARFYKTRSIARNMVDGGKVHYNGQR-SKPSKIVELGAVI 54
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH