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Conserved domains on  [gi|1012282576|ref|NP_001308630|]
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small ribosomal subunit protein uS4 isoform a [Homo sapiens]

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
 11-177 6.03e-105

40S ribosomal protein S9; Provisional


:

Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 298.92  E-value: 6.03e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012282576  11 KTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRRLFEGNALLRRLVRIGVLDEG 90
Cdd:PTZ00155   10 KTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRMHRLGLLDED 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012282576  91 KMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRP 170
Cdd:PTZ00155   90 ERKLDYVLGLTVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFADTSPFGNGRP 169


                  ....*..
gi 1012282576 171 GRVKRKN 177
Cdd:PTZ00155  170 GRVKRKA 176
 
Name Accession Description Interval E-value
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 11-177 6.03e-105

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 298.92  E-value: 6.03e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012282576  11 KTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRRLFEGNALLRRLVRIGVLDEG 90
Cdd:PTZ00155   10 KTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRMHRLGLLDED 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012282576  91 KMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRP 170
Cdd:PTZ00155   90 ERKLDYVLGLTVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFADTSPFGNGRP 169


                  ....*..
gi 1012282576 171 GRVKRKN 177
Cdd:PTZ00155  170 GRVKRKA 176
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 1-166 5.73e-79

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: 232.70  E-value: 5.73e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012282576   1 MPVARSwvCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDekDPRRLFEGNALLRR 80
Cdd:TIGR01018   1 MGDPRR--QRKKYETPRHPWIKERLDRELKLMGKYGLRNKKEVWKAETTLRKYRRAARELLTLD--DEQRLFEGNQLLRR 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012282576  81 LVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFS 160
Cdd:TIGR01018  77 LVRLGILDEENAKLDDVLGLTVEDFLERRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSYIVRLEEEKKIDFA 156


                  ....*.
gi 1012282576 161 LRSPYG 166
Cdd:TIGR01018 157 LSSPFG 162
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 10-107 2.61e-12

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: 60.25  E-value: 2.61e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012282576  10 RKTYVTPRR----PFEKSRLDQELKLIgeyglRNKREVWRVKFTLAKIRKAARELLTLDEKDPRRLFEG--NALLRRLVR 83
Cdd:pfam00163   4 GPEQKLLRRvgfkLWKKGRCHRELKVA-----QNRREYPKYPGQHGKIRKLSEYLLQLREKQKVRRKYGllEKQLRKLYD 78

                          90       100
                  ....*....|....*....|....
gi 1012282576  84 IGvldegkMKLDYILGLKIEDFLE 107
Cdd:pfam00163  79 MG------LKLKGVTGENLLQLLE 96
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 106-150 2.75e-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: 54.31  E-value: 2.75e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1012282576 106 LERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVR 150
Cdd:COG0522    92 LERRLDNVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVK 136
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 108-150 1.26e-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: 44.16  E-value: 1.26e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1012282576 108 RRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVR 150
Cdd:cd00165     1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVK 43
S4 smart00363
S4 RNA-binding domain;
108-149 1.72e-05

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 41.04  E-value: 1.72e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1012282576  108 RRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIV 149
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIV 42
 
Name Accession Description Interval E-value
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 11-177 6.03e-105

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 298.92  E-value: 6.03e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012282576  11 KTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRRLFEGNALLRRLVRIGVLDEG 90
Cdd:PTZ00155   10 KTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRMHRLGLLDED 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012282576  91 KMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRP 170
Cdd:PTZ00155   90 ERKLDYVLGLTVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFADTSPFGNGRP 169


                  ....*..
gi 1012282576 171 GRVKRKN 177
Cdd:PTZ00155  170 GRVKRKA 176
PLN00189 PLN00189
40S ribosomal protein S9; Provisional
 11-193 3.12e-99

40S ribosomal protein S9; Provisional


Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 285.10  E-value: 3.12e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012282576  11 KTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRRLFEGNALLRRLVRIGVLDEG 90
Cdd:PLN00189   12 KTFKKPRRPYEKERLDAELKLVGEYGLRNKRELWRVQYALSRIRNAARMLLTLDEKNPRRIFEGEALLRRMNRYGLLDES 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012282576  91 KMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRP 170
Cdd:PLN00189   92 QNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFSLTSPLGGGRP 171

                         170       180
                  ....*....|....*....|...
gi 1012282576 171 GRVKRKNAKKGQGGAGAGDDEEE 193
Cdd:PLN00189  172 GRVKRKNQKAASGGGDGDEEDEE 194
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 1-166 5.73e-79

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: 232.70  E-value: 5.73e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012282576   1 MPVARSwvCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDekDPRRLFEGNALLRR 80
Cdd:TIGR01018   1 MGDPRR--QRKKYETPRHPWIKERLDRELKLMGKYGLRNKKEVWKAETTLRKYRRAARELLTLD--DEQRLFEGNQLLRR 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012282576  81 LVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFS 160
Cdd:TIGR01018  77 LVRLGILDEENAKLDDVLGLTVEDFLERRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSYIVRLEEEKKIDFA 156


                  ....*.
gi 1012282576 161 LRSPYG 166
Cdd:TIGR01018 157 LSSPFG 162
rps4p PRK04051
30S ribosomal protein S4P; Validated
 10-165 1.68e-54

30S ribosomal protein S4P; Validated


Pssm-ID: 179730 [Multi-domain]  Cd Length: 177  Bit Score: 171.21  E-value: 1.68e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012282576  10 RKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRRlfEGNALLRRLVRIGVLDE 89
Cdd:PRK04051    8 RKKYETPNHPWQKERIAEERELLGKYGLRNKRELWKAQSILRKYRRQARSLLALPPEERAK--EEEQLLGKLKRYGILKE 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1012282576  90 GKmKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPY 165
Cdd:PRK04051   86 NA-TLDDVLSLTVEDILERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPTSPL 160
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 10-107 2.61e-12

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: 60.25  E-value: 2.61e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012282576  10 RKTYVTPRR----PFEKSRLDQELKLIgeyglRNKREVWRVKFTLAKIRKAARELLTLDEKDPRRLFEG--NALLRRLVR 83
Cdd:pfam00163   4 GPEQKLLRRvgfkLWKKGRCHRELKVA-----QNRREYPKYPGQHGKIRKLSEYLLQLREKQKVRRKYGllEKQLRKLYD 78

                          90       100
                  ....*....|....*....|....
gi 1012282576  84 IGvldegkMKLDYILGLKIEDFLE 107
Cdd:pfam00163  79 MG------LKLKGVTGENLLQLLE 96
rpsD PRK05327
30S ribosomal protein S4; Validated
 106-150 1.95e-09

30S ribosomal protein S4; Validated


Pssm-ID: 235411 [Multi-domain]  Cd Length: 203  Bit Score: 54.73  E-value: 1.95e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1012282576 106 LERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVR 150
Cdd:PRK05327   91 LESRLDNVVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVK 135
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 106-150 2.75e-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: 54.31  E-value: 2.75e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1012282576 106 LERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVR 150
Cdd:COG0522    92 LERRLDNVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVK 136
rps4 CHL00113
ribosomal protein S4; Reviewed
 105-148 7.97e-09

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 52.91  E-value: 7.97e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1012282576 105 FLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFI 148
Cdd:CHL00113   86 LLEMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYR 129
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 108-150 1.60e-08

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: 48.64  E-value: 1.60e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1012282576 108 RRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVR 150
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVK 43
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 108-150 1.26e-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: 44.16  E-value: 1.26e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1012282576 108 RRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVR 150
Cdd:cd00165     1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVK 43
S4 smart00363
S4 RNA-binding domain;
108-149 1.72e-05

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 41.04  E-value: 1.72e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1012282576  108 RRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIV 149
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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