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Conserved domains on  [gi|488285047|ref|WP_002356255|]
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MULTISPECIES: RNA-binding S4 domain-containing protein [Lactobacillales]

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 6.77e-33

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


:

Pssm-ID: 440801  Cd Length: 120  Bit Score: 109.92  E-value: 6.77e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285047   1 MRLDKFLKVSRIIKRRTVAKEVADKGRIQINGVLAKSSSTVKIGDLVKIQFGNRILEVEVLQLNDS-TKKEDATKMYEIK 79
Cdd:COG1188    5 MRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSERrGPAPEAQLLYEEL 84


                 ....*...
gi 488285047  80 SETRVSEE 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 6.77e-33

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


Pssm-ID: 440801  Cd Length: 120  Bit Score: 109.92  E-value: 6.77e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285047   1 MRLDKFLKVSRIIKRRTVAKEVADKGRIQINGVLAKSSSTVKIGDLVKIQFGNRILEVEVLQLNDS-TKKEDATKMYEIK 79
Cdd:COG1188    5 MRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSERrGPAPEAQLLYEEL 84


                 ....*...
gi 488285047  80 SETRVSEE 87
Cdd:COG1188   85 TPSPAPRE 92
PRK10348 PRK10348
ribosome-associated heat shock protein Hsp15; Provisional
 1-82 3.42e-06

ribosome-associated heat shock protein Hsp15; Provisional


Pssm-ID: 182397  Cd Length: 133  Bit Score: 41.94  E-value: 3.42e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285047   1 MRLDKFLKVSRIIKRRTVAKEVADKGRIQINGVLAKSSSTVKIGDLVKIQFGNRILEVEVLQLNDSTK-KEDATKMYEIK 79
Cdd:PRK10348   9 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRpASEAALLYEET 88


                 ...
gi 488285047  80 SET 82
Cdd:PRK10348  89 AES 91
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 1-47 6.50e-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: 39.40  E-value: 6.50e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 488285047   1 MRLDKFLKVSRIIKRRTVAKEVADKGRIQINGVLAKSSS-TVKIGDLV 47
Cdd:pfam01479  1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSyRVKPGDEI 48
S4 smart00363
S4 RNA-binding domain;
1-54 2.51e-05

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 38.34  E-value: 2.51e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 488285047    1 MRLDKFLKVSRIIKRRTVAKEVADKGRIQINGVLAKSSST-VKIGDLVKIQFGNR 54
Cdd:smart00363  1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYiVKPGDVISVRGKEL 55
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 1-58 3.74e-05

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: 38.00  E-value: 3.74e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 488285047  1 MRLDKFLKVSRIIKRRTVAKEVADKGRIQINGVLAKSSST-VKIGDLVKIQFGNRILEV 58
Cdd:cd00165   1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYkVKPGDVIEVDGKSIEEDI 59
 
Name Accession Description Interval E-value
HslR COG1188
Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal ...
 1-87 6.77e-33

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


Pssm-ID: 440801  Cd Length: 120  Bit Score: 109.92  E-value: 6.77e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285047   1 MRLDKFLKVSRIIKRRTVAKEVADKGRIQINGVLAKSSSTVKIGDLVKIQFGNRILEVEVLQLNDS-TKKEDATKMYEIK 79
Cdd:COG1188    5 MRLDKWLWAARFFKTRSLAAEACDGGRVRVNGQRAKPSREVKVGDVLTIRQGGRERVVRVLALSERrGPAPEAQLLYEEL 84


                 ....*...
gi 488285047  80 SETRVSEE 87
Cdd:COG1188   85 TPSPAPRE 92
PRK10348 PRK10348
ribosome-associated heat shock protein Hsp15; Provisional
 1-82 3.42e-06

ribosome-associated heat shock protein Hsp15; Provisional


Pssm-ID: 182397  Cd Length: 133  Bit Score: 41.94  E-value: 3.42e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285047   1 MRLDKFLKVSRIIKRRTVAKEVADKGRIQINGVLAKSSSTVKIGDLVKIQFGNRILEVEVLQLNDSTK-KEDATKMYEIK 79
Cdd:PRK10348   9 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRpASEAALLYEET 88


                 ...
gi 488285047  80 SET 82
Cdd:PRK10348  89 AES 91
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 1-47 6.50e-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: 39.40  E-value: 6.50e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 488285047   1 MRLDKFLKVSRIIKRRTVAKEVADKGRIQINGVLAKSSS-TVKIGDLV 47
Cdd:pfam01479  1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSyRVKPGDEI 48
S4 smart00363
S4 RNA-binding domain;
1-54 2.51e-05

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 38.34  E-value: 2.51e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 488285047    1 MRLDKFLKVSRIIKRRTVAKEVADKGRIQINGVLAKSSST-VKIGDLVKIQFGNR 54
Cdd:smart00363  1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYiVKPGDVISVRGKEL 55
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 1-58 3.74e-05

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: 38.00  E-value: 3.74e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 488285047  1 MRLDKFLKVSRIIKRRTVAKEVADKGRIQINGVLAKSSST-VKIGDLVKIQFGNRILEV 58
Cdd:cd00165   1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYkVKPGDVIEVDGKSIEEDI 59
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 1-55 8.84e-03

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: 33.08  E-value: 8.84e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 488285047   1 MRLDKFLKVSRIIKRRtVAKEVADKGRIQINGVLAKSSST-VKIGDLVKIQfGNRI 55
Cdd:COG1187    3 MRLQKFLANAGVGSRR-EAEELIEAGRVTVNGKVVTELGTkVDPGDEVTVD-GKPL 56
 
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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