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Conserved domains on  [gi|1091062894|gb|OHP97427|]
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hypothetical protein HMPREF2649_00140 [Staphylococcus sp. HMSC063F03]

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 ...
 1-87 5.59e-30

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


:

Pssm-ID: 440801  Cd Length: 120  Bit Score: 102.60  E-value: 5.59e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091062894   1 MRLDKYLKVSRLVKRRTLAKEISDQGRVTVNGNVAKAGTDIKENDELIIRFGQKLVTVKVTGLSD-HATKENAKGMYDLI 79
Cdd:COG1188     5 MRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSErRGPAPEAQLLYEEL 84


                  ....*...
gi 1091062894  80 KEERINEE 87
Cdd:COG1188    85 TPSPAPRE 92
 
Name Accession Description Interval E-value
HslR COG1188
Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal ...
 1-87 5.59e-30

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


Pssm-ID: 440801  Cd Length: 120  Bit Score: 102.60  E-value: 5.59e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091062894   1 MRLDKYLKVSRLVKRRTLAKEISDQGRVTVNGNVAKAGTDIKENDELIIRFGQKLVTVKVTGLSD-HATKENAKGMYDLI 79
Cdd:COG1188     5 MRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSErRGPAPEAQLLYEEL 84


                  ....*...
gi 1091062894  80 KEERINEE 87
Cdd:COG1188    85 TPSPAPRE 92
PRK10348 PRK10348
ribosome-associated heat shock protein Hsp15; Provisional
 1-66 5.81e-08

ribosome-associated heat shock protein Hsp15; Provisional


Pssm-ID: 182397  Cd Length: 133  Bit Score: 46.56  E-value: 5.81e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1091062894   1 MRLDKYLKVSRLVKRRTLAKEISDQGRVTVNGNVAKAGTDIKENDELIIRFGQKLVTVKVTGLSDH 66
Cdd:PRK10348    9 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQ 74
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 1-47 1.26e-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: 43.63  E-value: 1.26e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 1091062894  1 MRLDKYLKVSRLVKRRTLAKEISDQGRVTVNGNVAK-AGTDIKENDEL 47
Cdd:pfam01479  1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKdPSYRVKPGDEI 48
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 1-59 5.12e-07

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: 42.62  E-value: 5.12e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091062894  1 MRLDKYLKVSRLVKRRTLAKEISDQGRVTVNGNVA-KAGTDIKENDELIIRFGQKLVTVK 59
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVtKPSYKVKPGDVIEVDGKSIEEDIV 60
S4 smart00363
S4 RNA-binding domain;
1-59 5.61e-07

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 42.19  E-value: 5.61e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091062894   1 MRLDKYLKVSRLVKRRTLAKEISDQGRVTVNGNVA-KAGTDIKENDELIIRFGQKLVTVK 59
Cdd:smart00363  1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVtKPSYIVKPGDVISVRGKELKRLKK 60
 
Name Accession Description Interval E-value
HslR COG1188
Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal ...
 1-87 5.59e-30

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


Pssm-ID: 440801  Cd Length: 120  Bit Score: 102.60  E-value: 5.59e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091062894   1 MRLDKYLKVSRLVKRRTLAKEISDQGRVTVNGNVAKAGTDIKENDELIIRFGQKLVTVKVTGLSD-HATKENAKGMYDLI 79
Cdd:COG1188     5 MRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSErRGPAPEAQLLYEEL 84


                  ....*...
gi 1091062894  80 KEERINEE 87
Cdd:COG1188    85 TPSPAPRE 92
YqxC COG1189
Predicted rRNA methylase YqxC, contains S4 and FtsJ domains [Translation, ribosomal structure ...
 1-50 3.25e-08

Predicted rRNA methylase YqxC, contains S4 and FtsJ domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440802 [Multi-domain]  Cd Length: 248  Bit Score: 48.52  E-value: 3.25e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1091062894   1 MRLDKYLkVSR-LVKRRTLAKEISDQGRVTVNGNVA-KAGTDIKENDELIIR 50
Cdd:COG1189     1 ERLDVLL-VERgLAESREKAQRLIMAGRVLVNGQVVdKPGTKVPEDAEIEVK 51
PRK10348 PRK10348
ribosome-associated heat shock protein Hsp15; Provisional
 1-66 5.81e-08

ribosome-associated heat shock protein Hsp15; Provisional


Pssm-ID: 182397  Cd Length: 133  Bit Score: 46.56  E-value: 5.81e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1091062894   1 MRLDKYLKVSRLVKRRTLAKEISDQGRVTVNGNVAKAGTDIKENDELIIRFGQKLVTVKVTGLSDH 66
Cdd:PRK10348    9 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQ 74
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 1-47 1.26e-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: 43.63  E-value: 1.26e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 1091062894  1 MRLDKYLKVSRLVKRRTLAKEISDQGRVTVNGNVAK-AGTDIKENDEL 47
Cdd:pfam01479  1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKdPSYRVKPGDEI 48
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 1-59 5.12e-07

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: 42.62  E-value: 5.12e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091062894  1 MRLDKYLKVSRLVKRRTLAKEISDQGRVTVNGNVA-KAGTDIKENDELIIRFGQKLVTVK 59
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVtKPSYKVKPGDVIEVDGKSIEEDIV 60
S4 smart00363
S4 RNA-binding domain;
1-59 5.61e-07

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 42.19  E-value: 5.61e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091062894   1 MRLDKYLKVSRLVKRRTLAKEISDQGRVTVNGNVA-KAGTDIKENDELIIRFGQKLVTVK 59
Cdd:smart00363  1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVtKPSYIVKPGDVISVRGKELKRLKK 60
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 1-83 2.47e-05

Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ribosomal structure and biogenesis]; Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440800 [Multi-domain]  Cd Length: 226  Bit Score: 40.40  E-value: 2.47e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091062894   1 MRLDKYLKVSRLVKRRTlAKEISDQGRVTVNGNVAK-AGTDIKENDEliIRFGQKLVTVK--------------VTGLSD 65
Cdd:COG1187     3 MRLQKFLANAGVGSRRE-AEELIEAGRVTVNGKVVTeLGTKVDPGDE--VTVDGKPLKLPeepvylllnkpagvVSTTKD 79

                          90
                  ....*....|....*...
gi 1091062894  66 HATKENAkgmYDLIKEER 83
Cdd:COG1187    80 PEGRPTV---FDLLPEAR 94
PRK10839 PRK10839
16S rRNA pseudouridine(516) synthase RsuA;
1-38 3.19e-03

16S rRNA pseudouridine(516) synthase RsuA;


Pssm-ID: 236774 [Multi-domain]  Cd Length: 232  Bit Score: 34.31  E-value: 3.19e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1091062894   1 MRLDKYLKVSRLVKRRTLAKEISDQgRVTVNGNVAKAG 38
Cdd:PRK10839    1 MRLDKFISQQLGVSRAIAGRELRAN-RVTVDGEIVKNG 37
 
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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