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Conserved domains on  [gi|186523035|ref|NP_001119227|]
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Ribosomal protein S4 [Arabidopsis thaliana]

Protein Classification

40S ribosomal protein S9( domain architecture ID 11476450)

40S ribosomal protein S9 plays a critical role in ribosome biogenesis and directly binds to ribosomal RNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN00189 PLN00189
40S ribosomal protein S9; Provisional
 1-156 1.92e-99

40S ribosomal protein S9; Provisional


:

Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 283.95  E-value: 1.92e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523035   1 MVHVCYYRNYGKTFKGPRRPYEKERLDSELKLVGEYGLRNKRELWRVQYSLSRIRNAARDLLTLDEKSPRRIFEGEALLR 80
Cdd:PLN00189   1 MVHVSFYRNYGKTFKKPRRPYEKERLDAELKLVGEYGLRNKRELWRVQYALSRIRNAARMLLTLDEKNPRRIFEGEALLR 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 186523035  81 RMNRYGLLDESQNKLDYVLALTVENFLERRLQTIVFKSGMAKSIHHSRVLIRQRHIRY---CISSIYLCLCMNYLCYIN 156
Cdd:PLN00189  81 RMNRYGLLDESQNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVgkqIVNVPSFMVRVDSQKHID 159
 
Name Accession Description Interval E-value
PLN00189 PLN00189
40S ribosomal protein S9; Provisional
 1-156 1.92e-99

40S ribosomal protein S9; Provisional


Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 283.95  E-value: 1.92e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523035   1 MVHVCYYRNYGKTFKGPRRPYEKERLDSELKLVGEYGLRNKRELWRVQYSLSRIRNAARDLLTLDEKSPRRIFEGEALLR 80
Cdd:PLN00189   1 MVHVSFYRNYGKTFKKPRRPYEKERLDAELKLVGEYGLRNKRELWRVQYALSRIRNAARMLLTLDEKNPRRIFEGEALLR 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 186523035  81 RMNRYGLLDESQNKLDYVLALTVENFLERRLQTIVFKSGMAKSIHHSRVLIRQRHIRY---CISSIYLCLCMNYLCYIN 156
Cdd:PLN00189  81 RMNRYGLLDESQNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVgkqIVNVPSFMVRVDSQKHID 159
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 8-137 4.27e-58

ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273397 [Multi-domain]  Cd Length: 162  Bit Score: 178.00  E-value: 4.27e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523035    8 RNYGKTFKGPRRPYEKERLDSELKLVGEYGLRNKRELWRVQYSLSRIRNAARDLLTLDekSPRRIFEGEALLRRMNRYGL 87
Cdd:TIGR01018   5 RRQRKKYETPRHPWIKERLDRELKLMGKYGLRNKKEVWKAETTLRKYRRAARELLTLD--DEQRLFEGNQLLRRLVRLGI 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 186523035   88 LDESQNKLDYVLALTVENFLERRLQTIVFKSGMAKSIHHSRVLIRQRHIR 137
Cdd:TIGR01018  83 LDEENAKLDDVLGLTVEDFLERRLQTQVYKKGLARTIHQARQLIVHGHIA 132
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 8-108 7.26e-15

Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 from prokaryotes and S16 from metazoans. This domain is predicted to bind to ribosomal RNA. This domain is composed of four helices in the known structure. However the domain is discontinuous in sequence and the alignment for this family contains only the first three helices.


Pssm-ID: 459696  Cd Length: 96  Bit Score: 65.65  E-value: 7.26e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523035    8 RNYGKTFKGPRR----PYEKERLDSELKLVgeyglRNKRELWRVQYSLSRIRNAARDLLTLDEKSPRRIFEG--EALLRR 81
Cdd:pfam00163   1 RYKGPEQKLLRRvgfkLWKKGRCHRELKVA-----QNRREYPKYPGQHGKIRKLSEYLLQLREKQKVRRKYGllEKQLRK 75

                          90       100
                  ....*....|....*....|....*..
gi 186523035   82 MNRYGLldesqnKLDYVLALTVENFLE 108
Cdd:pfam00163  76 LYDMGL------KLKGVTGENLLQLLE 96
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 79-136 1.47e-04

Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; Ribosomal protein S4 or related protein is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440288 [Multi-domain]  Cd Length: 204  Bit Score: 40.06  E-value: 1.47e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 186523035  79 LRRMnrYGLLdESQNKLDYVLAL-----TVENF---LERRLQTIVFKSGMAKSIHHSRVLIRQRHI 136
Cdd:COG0522   59 LRRI--YGVL-EKQFRRYFEEAArrkgnTGENLlqlLERRLDNVVYRLGFAPTRAQARQLVSHGHI 121
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 109-137 5.77e-03

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: 33.76  E-value: 5.77e-03
                         10        20
                 ....*....|....*....|....*....
gi 186523035 109 RRLQTIVFKSGMAKSIHHSRVLIRQRHIR 137
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVL 29
 
Name Accession Description Interval E-value
PLN00189 PLN00189
40S ribosomal protein S9; Provisional
 1-156 1.92e-99

40S ribosomal protein S9; Provisional


Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 283.95  E-value: 1.92e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523035   1 MVHVCYYRNYGKTFKGPRRPYEKERLDSELKLVGEYGLRNKRELWRVQYSLSRIRNAARDLLTLDEKSPRRIFEGEALLR 80
Cdd:PLN00189   1 MVHVSFYRNYGKTFKKPRRPYEKERLDAELKLVGEYGLRNKRELWRVQYALSRIRNAARMLLTLDEKNPRRIFEGEALLR 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 186523035  81 RMNRYGLLDESQNKLDYVLALTVENFLERRLQTIVFKSGMAKSIHHSRVLIRQRHIRY---CISSIYLCLCMNYLCYIN 156
Cdd:PLN00189  81 RMNRYGLLDESQNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVgkqIVNVPSFMVRVDSQKHID 159
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 7-137 2.17e-82

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 240.37  E-value: 2.17e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523035   7 YRNYGKTFKGPRRPYEKERLDSELKLVGEYGLRNKRELWRVQYSLSRIRNAARDLLTLDEKSPRRIFEGEALLRRMNRYG 86
Cdd:PTZ00155   5 YRNHSKTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRMHRLG 84

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 186523035  87 LLDESQNKLDYVLALTVENFLERRLQTIVFKSGMAKSIHHSRVLIRQRHIR 137
Cdd:PTZ00155  85 LLDEDERKLDYVLGLTVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIR 135
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 8-137 4.27e-58

ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273397 [Multi-domain]  Cd Length: 162  Bit Score: 178.00  E-value: 4.27e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523035    8 RNYGKTFKGPRRPYEKERLDSELKLVGEYGLRNKRELWRVQYSLSRIRNAARDLLTLDekSPRRIFEGEALLRRMNRYGL 87
Cdd:TIGR01018   5 RRQRKKYETPRHPWIKERLDRELKLMGKYGLRNKKEVWKAETTLRKYRRAARELLTLD--DEQRLFEGNQLLRRLVRLGI 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 186523035   88 LDESQNKLDYVLALTVENFLERRLQTIVFKSGMAKSIHHSRVLIRQRHIR 137
Cdd:TIGR01018  83 LDEENAKLDDVLGLTVEDFLERRLQTQVYKKGLARTIHQARQLIVHGHIA 132
rps4p PRK04051
30S ribosomal protein S4P; Validated
 12-136 1.08e-48

30S ribosomal protein S4P; Validated


Pssm-ID: 179730 [Multi-domain]  Cd Length: 177  Bit Score: 154.64  E-value: 1.08e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523035  12 KTFKGPRRPYEKERLDSELKLVGEYGLRNKRELWRVQYSLSRIRNAARDLLTLDEksPRRIFEGEALLRRMNRYGLLDEs 91
Cdd:PRK04051   9 KKYETPNHPWQKERIAEERELLGKYGLRNKRELWKAQSILRKYRRQARSLLALPP--EERAKEEEQLLGKLKRYGILKE- 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 186523035  92 QNKLDYVLALTVENFLERRLQTIVFKSGMAKSIHHSRVLIRQRHI 136
Cdd:PRK04051  86 NATLDDVLSLTVEDILERRLQTIVYRKGLARTPKQARQFIVHGHI 130
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 8-108 7.26e-15

Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 from prokaryotes and S16 from metazoans. This domain is predicted to bind to ribosomal RNA. This domain is composed of four helices in the known structure. However the domain is discontinuous in sequence and the alignment for this family contains only the first three helices.


Pssm-ID: 459696  Cd Length: 96  Bit Score: 65.65  E-value: 7.26e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523035    8 RNYGKTFKGPRR----PYEKERLDSELKLVgeyglRNKRELWRVQYSLSRIRNAARDLLTLDEKSPRRIFEG--EALLRR 81
Cdd:pfam00163   1 RYKGPEQKLLRRvgfkLWKKGRCHRELKVA-----QNRREYPKYPGQHGKIRKLSEYLLQLREKQKVRRKYGllEKQLRK 75

                          90       100
                  ....*....|....*....|....*..
gi 186523035   82 MNRYGLldesqnKLDYVLALTVENFLE 108
Cdd:pfam00163  76 LYDMGL------KLKGVTGENLLQLLE 96
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 79-136 1.47e-04

Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; Ribosomal protein S4 or related protein is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440288 [Multi-domain]  Cd Length: 204  Bit Score: 40.06  E-value: 1.47e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 186523035  79 LRRMnrYGLLdESQNKLDYVLAL-----TVENF---LERRLQTIVFKSGMAKSIHHSRVLIRQRHI 136
Cdd:COG0522   59 LRRI--YGVL-EKQFRRYFEEAArrkgnTGENLlqlLERRLDNVVYRLGFAPTRAQARQLVSHGHI 121
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 109-137 2.91e-04

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: 36.70  E-value: 2.91e-04
                          10        20
                  ....*....|....*....|....*....
gi 186523035  109 RRLQTIVFKSGMAKSIHHSRVLIRQRHIR 137
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVL 29
rps4 CHL00113
ribosomal protein S4; Reviewed
 105-137 2.38e-03

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 36.73  E-value: 2.38e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 186523035 105 NFLERRLQTIVFKSGMAKSIHHSRVLIRQRHIR 137
Cdd:CHL00113  85 QLLEMRLDNILFRLGMAPTIPAARQLVNHGHIL 117
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 109-137 5.77e-03

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: 33.76  E-value: 5.77e-03
                         10        20
                 ....*....|....*....|....*....
gi 186523035 109 RRLQTIVFKSGMAKSIHHSRVLIRQRHIR 137
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVL 29
 
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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