NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|491320527|ref|WP_005178493|]
View 

MULTISPECIES: RNA-binding S4 domain-containing protein [Acinetobacter]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
HslR COG1188
Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal ...
 9-131 1.00e-54

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


:

Pssm-ID: 440801  Cd Length: 120  Bit Score: 167.70  E-value: 1.00e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491320527   9 AVESMRIDKWLWAARFFKTRSIAKAAIEGGKVHHNGERVKVSKEIRVGMELTVQQGFDRKTVKVLSLSAVRGPAPVAQQL 88
Cdd:COG1188    1 AAERMRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSERRGPAPEAQLL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 491320527  89 YEETEVSIARRELIAsqrKLHNLARPDHRPSKKDRRQISKFKQ 131
Cdd:COG1188   81 YEELTPSPAPREEAA---AAAPRPRGAGRPTKKDRRELDRFRG 120
 
Name Accession Description Interval E-value
HslR COG1188
Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal ...
 9-131 1.00e-54

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


Pssm-ID: 440801  Cd Length: 120  Bit Score: 167.70  E-value: 1.00e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491320527   9 AVESMRIDKWLWAARFFKTRSIAKAAIEGGKVHHNGERVKVSKEIRVGMELTVQQGFDRKTVKVLSLSAVRGPAPVAQQL 88
Cdd:COG1188    1 AAERMRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSERRGPAPEAQLL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 491320527  89 YEETEVSIARRELIAsqrKLHNLARPDHRPSKKDRRQISKFKQ 131
Cdd:COG1188   81 YEELTPSPAPREEAA---AAAPRPRGAGRPTKKDRRELDRFRG 120
PRK10348 PRK10348
ribosome-associated heat shock protein Hsp15; Provisional
 11-130 7.52e-40

ribosome-associated heat shock protein Hsp15; Provisional


Pssm-ID: 182397  Cd Length: 133  Bit Score: 130.53  E-value: 7.52e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491320527  11 ESMRIDKWLWAARFFKTRSIAKAAIEGGKVHHNGERVKVSKEIRVGMELTVQQGFDRKTVKVLSLSAVRGPAPVAQQLYE 90
Cdd:PRK10348   7 VEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALLYE 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 491320527  91 ETEVSIARRELIASQRKLHNLA--RPDHRPSKKDRRQISKFK 130
Cdd:PRK10348  87 ETAESVEKREKMALARKLNALTmpHPDRRPDKKERRDLLRFK 128
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 13-59 3.36e-09

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: 49.41  E-value: 3.36e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 491320527   13 MRIDKWLWAARFFKTRSIAKAAIEGGKVHHNGERVK-VSKEIRVGMEL 59
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKdPSYRVKPGDEI 48
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 13-62 6.69e-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: 49.56  E-value: 6.69e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 491320527  13 MRIDKWLWAARFFKTRSIAKAAIEGGKVHHNGERV-KVSKEIRVGMELTVQ 62
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVtKPSYKVKPGDVIEVD 51
S4 smart00363
S4 RNA-binding domain;
13-64 7.05e-08

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 46.43  E-value: 7.05e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 491320527    13 MRIDKWLWAARFFKTRSIAKAAIEGGKVHHNGERV-KVSKEIRVGMELTVQQG 64
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVtKPSYIVKPGDVISVRGK 53
 
Name Accession Description Interval E-value
HslR COG1188
Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal ...
 9-131 1.00e-54

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


Pssm-ID: 440801  Cd Length: 120  Bit Score: 167.70  E-value: 1.00e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491320527   9 AVESMRIDKWLWAARFFKTRSIAKAAIEGGKVHHNGERVKVSKEIRVGMELTVQQGFDRKTVKVLSLSAVRGPAPVAQQL 88
Cdd:COG1188    1 AAERMRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSERRGPAPEAQLL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 491320527  89 YEETEVSIARRELIAsqrKLHNLARPDHRPSKKDRRQISKFKQ 131
Cdd:COG1188   81 YEELTPSPAPREEAA---AAAPRPRGAGRPTKKDRRELDRFRG 120
PRK10348 PRK10348
ribosome-associated heat shock protein Hsp15; Provisional
 11-130 7.52e-40

ribosome-associated heat shock protein Hsp15; Provisional


Pssm-ID: 182397  Cd Length: 133  Bit Score: 130.53  E-value: 7.52e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491320527  11 ESMRIDKWLWAARFFKTRSIAKAAIEGGKVHHNGERVKVSKEIRVGMELTVQQGFDRKTVKVLSLSAVRGPAPVAQQLYE 90
Cdd:PRK10348   7 VEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALLYE 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 491320527  91 ETEVSIARRELIASQRKLHNLA--RPDHRPSKKDRRQISKFK 130
Cdd:PRK10348  87 ETAESVEKREKMALARKLNALTmpHPDRRPDKKERRDLLRFK 128
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 13-59 3.36e-09

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: 49.41  E-value: 3.36e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 491320527   13 MRIDKWLWAARFFKTRSIAKAAIEGGKVHHNGERVK-VSKEIRVGMEL 59
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKdPSYRVKPGDEI 48
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 13-62 6.69e-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: 49.56  E-value: 6.69e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 491320527  13 MRIDKWLWAARFFKTRSIAKAAIEGGKVHHNGERV-KVSKEIRVGMELTVQ 62
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVtKPSYKVKPGDVIEVD 51
S4 smart00363
S4 RNA-binding domain;
13-64 7.05e-08

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 46.43  E-value: 7.05e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 491320527    13 MRIDKWLWAARFFKTRSIAKAAIEGGKVHHNGERV-KVSKEIRVGMELTVQQG 64
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVtKPSYIVKPGDVISVRGK 53
 
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