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Conserved domains on  [gi|7294919|gb|AAF50249|]
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ribosomal protein S9, isoform A [Drosophila melanogaster]

Protein Classification

40S ribosomal protein S9( domain architecture ID 11488137)

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
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 4-182 4.37e-108

40S ribosomal protein S9; Provisional


:

Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 307.01  E-value: 4.37e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7294919     4 GRIPSVFSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKDEKRLFQGNALLRRLV 83
Cdd:PTZ00155   2 GRNYRNHSKTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRMH 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7294919    84 RIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFVVRLDSQKHIDFSLK 163
Cdd:PTZ00155  82 RLGLLDEDERKLDYVLGLTVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFADT 161

                        170
                 ....*....|....*....
gi 7294919   164 SPFGGGRPGRVKRKNLKKN 182
Cdd:PTZ00155 162 SPFGNGRPGRVKRKAAKAA 180
 
Name Accession Description Interval E-value
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 4-182 4.37e-108

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 307.01  E-value: 4.37e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7294919     4 GRIPSVFSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKDEKRLFQGNALLRRLV 83
Cdd:PTZ00155   2 GRNYRNHSKTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRMH 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7294919    84 RIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFVVRLDSQKHIDFSLK 163
Cdd:PTZ00155  82 RLGLLDEDERKLDYVLGLTVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFADT 161

                        170
                 ....*....|....*....
gi 7294919   164 SPFGGGRPGRVKRKNLKKN 182
Cdd:PTZ00155 162 SPFGNGRPGRVKRKAAKAA 180
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 12-167 4.86e-75

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: 222.69  E-value: 4.86e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7294919     12 KTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDekDEKRLFQGNALLRRLVRIGVLDES 91
Cdd:TIGR01018   9 KKYETPRHPWIKERLDRELKLMGKYGLRNKKEVWKAETTLRKYRRAARELLTLD--DEQRLFEGNQLLRRLVRLGILDEE 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 7294919     92 RMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFVVRLDSQKHIDFSLKSPFG 167
Cdd:TIGR01018  87 NAKLDDVLGLTVEDFLERRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSYIVRLEEEKKIDFALSSPFG 162
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 11-108 1.32e-11

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: 58.33  E-value: 1.32e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7294919     11 SKTYVTPRR----PYEKARLDQELKIIgeyglRNKREVWRVKYALAKIRKAARELLTLDEKDEKRLFQG--NALLRRLVR 84
Cdd:pfam00163   4 GPEQKLLRRvgfkLWKKGRCHRELKVA-----QNRREYPKYPGQHGKIRKLSEYLLQLREKQKVRRKYGllEKQLRKLYD 78

                          90       100
                  ....*....|....*....|....
gi 7294919     85 IGvldesrMKLDYVLGLKIEDFLE 108
Cdd:pfam00163  79 MG------LKLKGVTGENLLQLLE 96
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 107-151 7.57e-09

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: 53.16  E-value: 7.57e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 7294919  107 LERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFVVR 151
Cdd:COG0522  92 LERRLDNVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVK 136
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 109-151 6.92e-06

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: 42.24  E-value: 6.92e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 7294919  109 RRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFVVR 151
Cdd:cd00165   1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVK 43
S4 smart00363
S4 RNA-binding domain;
109-150 2.26e-04

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 37.96  E-value: 2.26e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 7294919     109 RRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFVV 150
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIV 42
 
Name Accession Description Interval E-value
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 4-182 4.37e-108

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 307.01  E-value: 4.37e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7294919     4 GRIPSVFSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKDEKRLFQGNALLRRLV 83
Cdd:PTZ00155   2 GRNYRNHSKTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRMH 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7294919    84 RIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFVVRLDSQKHIDFSLK 163
Cdd:PTZ00155  82 RLGLLDEDERKLDYVLGLTVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFADT 161

                        170
                 ....*....|....*....
gi 7294919   164 SPFGGGRPGRVKRKNLKKN 182
Cdd:PTZ00155 162 SPFGNGRPGRVKRKAAKAA 180
PLN00189 PLN00189
40S ribosomal protein S9; Provisional
 1-182 6.56e-101

40S ribosomal protein S9; Provisional


Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 289.34  E-value: 6.56e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7294919     1 MVNGRIPSVFSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKDEKRLFQGNALLR 80
Cdd:PLN00189   1 MVHVSFYRNYGKTFKKPRRPYEKERLDAELKLVGEYGLRNKRELWRVQYALSRIRNAARMLLTLDEKNPRRIFEGEALLR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7294919    81 RLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFVVRLDSQKHIDF 160
Cdd:PLN00189  81 RMNRYGLLDESQNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDF 160

                        170       180
                 ....*....|....*....|..
gi 7294919   161 SLKSPFGGGRPGRVKRKNLKKN 182
Cdd:PLN00189 161 SLTSPLGGGRPGRVKRKNQKAA 182
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 12-167 4.86e-75

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: 222.69  E-value: 4.86e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7294919     12 KTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDekDEKRLFQGNALLRRLVRIGVLDES 91
Cdd:TIGR01018   9 KKYETPRHPWIKERLDRELKLMGKYGLRNKKEVWKAETTLRKYRRAARELLTLD--DEQRLFEGNQLLRRLVRLGILDEE 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 7294919     92 RMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFVVRLDSQKHIDFSLKSPFG 167
Cdd:TIGR01018  87 NAKLDDVLGLTVEDFLERRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSYIVRLEEEKKIDFALSSPFG 162
rps4p PRK04051
30S ribosomal protein S4P; Validated
 12-166 2.47e-53

30S ribosomal protein S4P; Validated


Pssm-ID: 179730 [Multi-domain]  Cd Length: 177  Bit Score: 168.12  E-value: 2.47e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7294919    12 KTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKDEKRlfQGNALLRRLVRIGVLDES 91
Cdd:PRK04051   9 KKYETPNHPWQKERIAEERELLGKYGLRNKRELWKAQSILRKYRRQARSLLALPPEERAK--EEEQLLGKLKRYGILKEN 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 7294919    92 rMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFVVRLDSQKHIDFSLKSPF 166
Cdd:PRK04051  87 -ATLDDVLSLTVEDILERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPTSPL 160
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 11-108 1.32e-11

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: 58.33  E-value: 1.32e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7294919     11 SKTYVTPRR----PYEKARLDQELKIIgeyglRNKREVWRVKYALAKIRKAARELLTLDEKDEKRLFQG--NALLRRLVR 84
Cdd:pfam00163   4 GPEQKLLRRvgfkLWKKGRCHRELKVA-----QNRREYPKYPGQHGKIRKLSEYLLQLREKQKVRRKYGllEKQLRKLYD 78

                          90       100
                  ....*....|....*....|....
gi 7294919     85 IGvldesrMKLDYVLGLKIEDFLE 108
Cdd:pfam00163  79 MG------LKLKGVTGENLLQLLE 96
rpsD PRK05327
30S ribosomal protein S4; Validated
 107-151 5.67e-09

30S ribosomal protein S4; Validated


Pssm-ID: 235411 [Multi-domain]  Cd Length: 203  Bit Score: 53.57  E-value: 5.67e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 7294919   107 LERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFVVR 151
Cdd:PRK05327  91 LESRLDNVVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVK 135
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 107-151 7.57e-09

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: 53.16  E-value: 7.57e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 7294919  107 LERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFVVR 151
Cdd:COG0522  92 LERRLDNVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVK 136
rps4 CHL00113
ribosomal protein S4; Reviewed
 106-148 2.97e-08

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 51.37  E-value: 2.97e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 7294919   106 FLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSF 148
Cdd:CHL00113  86 LLEMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSY 128
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 109-151 1.20e-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: 46.33  E-value: 1.20e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 7294919    109 RRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFVVR 151
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVK 43
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 109-151 6.92e-06

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: 42.24  E-value: 6.92e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 7294919  109 RRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFVVR 151
Cdd:cd00165   1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVK 43
S4 smart00363
S4 RNA-binding domain;
109-150 2.26e-04

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 37.96  E-value: 2.26e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 7294919     109 RRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFVV 150
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIV 42
 
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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