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Conserved domains on  [gi|493324487|ref|WP_006281751|]
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MULTISPECIES: RNA-binding S4 domain-containing protein [Segatella]

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 ...
 1-122 3.78e-45

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


:

Pssm-ID: 440801  Cd Length: 120  Bit Score: 143.05  E-value: 3.78e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493324487   1 MADTARIDKWLWAARIFKTRSIAADACKNSRVTINGSNVKPSHMIKRGEIIHVKKPPITYSFRVLDCIEKRVGAKLLINV 80
Cdd:COG1188    1 AAERMRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSERRGPAPEAQLL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 493324487  81 YENVTDPKQYELLEMSRISgfidRARGTGRPTKKDRRAIDAF 122
Cdd:COG1188   81 YEELTPSPAPREEAAAAAP----RPRGAGRPTKKDRRELDRF 118
 
Name Accession Description Interval E-value
HslR COG1188
Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal ...
 1-122 3.78e-45

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


Pssm-ID: 440801  Cd Length: 120  Bit Score: 143.05  E-value: 3.78e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493324487   1 MADTARIDKWLWAARIFKTRSIAADACKNSRVTINGSNVKPSHMIKRGEIIHVKKPPITYSFRVLDCIEKRVGAKLLINV 80
Cdd:COG1188    1 AAERMRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSERRGPAPEAQLL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 493324487  81 YENVTDPKQYELLEMSRISgfidRARGTGRPTKKDRRAIDAF 122
Cdd:COG1188   81 YEELTPSPAPREEAAAAAP----RPRGAGRPTKKDRRELDRF 118
PRK10348 PRK10348
ribosome-associated heat shock protein Hsp15; Provisional
 2-122 3.72e-15

ribosome-associated heat shock protein Hsp15; Provisional


Pssm-ID: 182397  Cd Length: 133  Bit Score: 67.36  E-value: 3.72e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493324487   2 ADTARIDKWLWAARIFKTRSIAADACKNSRVTINGSNVKPSHMIKRGEIIHVKKPPITYSFRVLDCIEKRVGAKLLINVY 81
Cdd:PRK10348   6 AVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALLY 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 493324487  82 ENVTDP-KQYELLEMSRISGFIDRARGTGRPTKKDRRAIDAF 122
Cdd:PRK10348  86 EETAESvEKREKMALARKLNALTMPHPDRRPDKKERRDLLRF 127
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 6-61 8.91e-09

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: 48.78  E-value: 8.91e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 493324487   6 RIDKWLWAARIFKTRSIAADACKNSRVTINGSNV-KPSHMIKRGEIIHVKKPPITYS 61
Cdd:cd00165    2 RLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVtKPSYKVKPGDVIEVDGKSIEED 58
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 6-51 9.64e-07

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: 42.86  E-value: 9.64e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 493324487    6 RIDKWLWAARIFKTRSIAADACKNSRVTINGSNVK-PSHMIKRGEII 51
Cdd:pfam01479   2 RLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKdPSYRVKPGDEI 48
S4 smart00363
S4 RNA-binding domain;
6-55 1.83e-05

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 39.88  E-value: 1.83e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 493324487     6 RIDKWLWAARIFKTRSIAADACKNSRVTINGSNV-KPSHMIKRGEIIHVKK 55
Cdd:smart00363   2 RLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVtKPSYIVKPGDVISVRG 52
 
Name Accession Description Interval E-value
HslR COG1188
Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal ...
 1-122 3.78e-45

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


Pssm-ID: 440801  Cd Length: 120  Bit Score: 143.05  E-value: 3.78e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493324487   1 MADTARIDKWLWAARIFKTRSIAADACKNSRVTINGSNVKPSHMIKRGEIIHVKKPPITYSFRVLDCIEKRVGAKLLINV 80
Cdd:COG1188    1 AAERMRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSERRGPAPEAQLL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 493324487  81 YENVTDPKQYELLEMSRISgfidRARGTGRPTKKDRRAIDAF 122
Cdd:COG1188   81 YEELTPSPAPREEAAAAAP----RPRGAGRPTKKDRRELDRF 118
PRK10348 PRK10348
ribosome-associated heat shock protein Hsp15; Provisional
 2-122 3.72e-15

ribosome-associated heat shock protein Hsp15; Provisional


Pssm-ID: 182397  Cd Length: 133  Bit Score: 67.36  E-value: 3.72e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493324487   2 ADTARIDKWLWAARIFKTRSIAADACKNSRVTINGSNVKPSHMIKRGEIIHVKKPPITYSFRVLDCIEKRVGAKLLINVY 81
Cdd:PRK10348   6 AVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALLY 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 493324487  82 ENVTDP-KQYELLEMSRISGFIDRARGTGRPTKKDRRAIDAF 122
Cdd:PRK10348  86 EETAESvEKREKMALARKLNALTMPHPDRRPDKKERRDLLRF 127
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 6-61 8.91e-09

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: 48.78  E-value: 8.91e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 493324487   6 RIDKWLWAARIFKTRSIAADACKNSRVTINGSNV-KPSHMIKRGEIIHVKKPPITYS 61
Cdd:cd00165    2 RLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVtKPSYKVKPGDVIEVDGKSIEED 58
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 6-51 9.64e-07

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: 42.86  E-value: 9.64e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 493324487    6 RIDKWLWAARIFKTRSIAADACKNSRVTINGSNVK-PSHMIKRGEII 51
Cdd:pfam01479   2 RLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKdPSYRVKPGDEI 48
S4 smart00363
S4 RNA-binding domain;
6-55 1.83e-05

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 39.88  E-value: 1.83e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 493324487     6 RIDKWLWAARIFKTRSIAADACKNSRVTINGSNV-KPSHMIKRGEIIHVKK 55
Cdd:smart00363   2 RLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVtKPSYIVKPGDVISVRG 52
 
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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