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Conserved domains on  [gi|656325158|ref|WP_029256216|]
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MULTISPECIES: RNA-binding S4 domain-containing protein [Rhodococcus]

Protein Classification

RNA-binding S4 domain-containing protein( domain architecture ID 10003114)

RNA-binding S4 domain-containing protein

Gene Ontology:  GO:0003723
PubMed:  10093218

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HslR COG1188
Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal ...
 11-127 4.36e-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: 4.36e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 656325158  11 SVRVDSWTWAVRLFKTRSQAATACRSGHVRVNGTSAKAAQQVKAGDEVRVRVSGIERIVVVVKPITKRVSAVLAADCLQD 90
Cdd:COG1188    4 RMRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSERRGPAPEAQLLYEE 83

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 656325158  91 NSPPPPPPELIASIPRRDRGAGRPTKRERRDLEKLRG 127
Cdd:COG1188   84 LTPSPAPREEAAAAAPRPRGAGRPTKKDRRELDRFRG 120
 
Name Accession Description Interval E-value
HslR COG1188
Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal ...
 11-127 4.36e-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: 4.36e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 656325158  11 SVRVDSWTWAVRLFKTRSQAATACRSGHVRVNGTSAKAAQQVKAGDEVRVRVSGIERIVVVVKPITKRVSAVLAADCLQD 90
Cdd:COG1188    4 RMRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSERRGPAPEAQLLYEE 83

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 656325158  91 NSPPPPPPELIASIPRRDRGAGRPTKRERRDLEKLRG 127
Cdd:COG1188   84 LTPSPAPREEAAAAAPRPRGAGRPTKKDRRELDRFRG 120
PRK10348 PRK10348
ribosome-associated heat shock protein Hsp15; Provisional
 6-126 8.67e-13

ribosome-associated heat shock protein Hsp15; Provisional


Pssm-ID: 182397  Cd Length: 133  Bit Score: 60.81  E-value: 8.67e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 656325158   6 PSDaiSVRVDSWTWAVRLFKTRSQAATACRSGHVRVNGTSAKAAQQVKAGDEVRVRVSGIERIVVVVKPITKRVSAVLAA 85
Cdd:PRK10348   5 PAV--EVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAA 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 656325158  86 DCLQDNSPPPPPPELIA--------SIPRRDRgagRPTKRERRDLEKLR 126
Cdd:PRK10348  83 LLYEETAESVEKREKMAlarklnalTMPHPDR---RPDKKERRDLLRFK 128
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 12-79 6.39e-08

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: 46.47  E-value: 6.39e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 656325158  12 VRVDSWTWAVRLFKTRSQAATACRSGHVRVNGTSA-KAAQQVKAGDEVRVRVSGIERIVVVVKPITKRV 79
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVtKPSYKVKPGDVIEVDGKSIEEDIVYEDKKLLVV 69
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 12-58 1.15e-06

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: 42.48  E-value: 1.15e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 656325158   12 VRVDSWTWAVRLFKTRSQAATACRSGHVRVNGTSAK-AAQQVKAGDEV 58
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKdPSYRVKPGDEI 48
S4 smart00363
S4 RNA-binding domain;
12-68 3.71e-06

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 41.42  E-value: 3.71e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 656325158    12 VRVDSWTWAVRLFKTRSQAATACRSGHVRVNGTSA-KAAQQVKAGDEVRVRVSGIERI 68
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVtKPSYIVKPGDVISVRGKELKRL 58
 
Name Accession Description Interval E-value
HslR COG1188
Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal ...
 11-127 4.36e-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: 4.36e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 656325158  11 SVRVDSWTWAVRLFKTRSQAATACRSGHVRVNGTSAKAAQQVKAGDEVRVRVSGIERIVVVVKPITKRVSAVLAADCLQD 90
Cdd:COG1188    4 RMRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSERRGPAPEAQLLYEE 83

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 656325158  91 NSPPPPPPELIASIPRRDRGAGRPTKRERRDLEKLRG 127
Cdd:COG1188   84 LTPSPAPREEAAAAAPRPRGAGRPTKKDRRELDRFRG 120
PRK10348 PRK10348
ribosome-associated heat shock protein Hsp15; Provisional
 6-126 8.67e-13

ribosome-associated heat shock protein Hsp15; Provisional


Pssm-ID: 182397  Cd Length: 133  Bit Score: 60.81  E-value: 8.67e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 656325158   6 PSDaiSVRVDSWTWAVRLFKTRSQAATACRSGHVRVNGTSAKAAQQVKAGDEVRVRVSGIERIVVVVKPITKRVSAVLAA 85
Cdd:PRK10348   5 PAV--EVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAA 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 656325158  86 DCLQDNSPPPPPPELIA--------SIPRRDRgagRPTKRERRDLEKLR 126
Cdd:PRK10348  83 LLYEETAESVEKREKMAlarklnalTMPHPDR---RPDKKERRDLLRFK 128
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 12-79 6.39e-08

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: 46.47  E-value: 6.39e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 656325158  12 VRVDSWTWAVRLFKTRSQAATACRSGHVRVNGTSA-KAAQQVKAGDEVRVRVSGIERIVVVVKPITKRV 79
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVtKPSYKVKPGDVIEVDGKSIEEDIVYEDKKLLVV 69
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 12-58 1.15e-06

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: 42.48  E-value: 1.15e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 656325158   12 VRVDSWTWAVRLFKTRSQAATACRSGHVRVNGTSAK-AAQQVKAGDEV 58
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKdPSYRVKPGDEI 48
S4 smart00363
S4 RNA-binding domain;
12-68 3.71e-06

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 41.42  E-value: 3.71e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 656325158    12 VRVDSWTWAVRLFKTRSQAATACRSGHVRVNGTSA-KAAQQVKAGDEVRVRVSGIERI 68
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVtKPSYIVKPGDVISVRGKELKRL 58
YbbJ COG1585
Membrane protein implicated in regulation of membrane protease activity [Posttranslational ...
 36-76 9.90e-03

Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441193  Cd Length: 143  Bit Score: 34.02  E-value: 9.90e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 656325158  36 SGHVRVNGT--SAKAAQQVKAGDevRVRVSGIERIVVVVKPIT 76
Cdd:COG1585  103 RGRVKLGGEewRARSEDDLPAGT--RVRVVAVEGNTLIVEPVE 143
 
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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