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Conserved domains on  [gi|6325176|ref|NP_015244|]
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ribosomal 40S subunit protein S9A [Saccharomyces cerevisiae S288C]

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
 1-181 1.76e-105

40S ribosomal protein S9; Provisional


:

Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 300.46  E-value: 1.76e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325176     1 MPRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLTRDEKDPKRLFEGNALIRRL 80
Cdd:PTZ00155   1 MGRNYRNHSKTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRM 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325176    81 VRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAP 160
Cdd:PTZ00155  81 HRLGLLDEDERKLDYVLGLTVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFAD 160

                        170       180
                 ....*....|....*....|.
gi 6325176   161 TSPFGGARPGRVARRNAARKA 181
Cdd:PTZ00155 161 TSPFGNGRPGRVKRKAAKAAK 181
 
Name Accession Description Interval E-value
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 1-181 1.76e-105

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 300.46  E-value: 1.76e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325176     1 MPRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLTRDEKDPKRLFEGNALIRRL 80
Cdd:PTZ00155   1 MGRNYRNHSKTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRM 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325176    81 VRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAP 160
Cdd:PTZ00155  81 HRLGLLDEDERKLDYVLGLTVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFAD 160

                        170       180
                 ....*....|....*....|.
gi 6325176   161 TSPFGGARPGRVARRNAARKA 181
Cdd:PTZ00155 161 TSPFGNGRPGRVKRKAAKAAK 181
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 4-165 4.40e-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: 223.07  E-value: 4.40e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325176      4 APRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLTRDekDPKRLFEGNALIRRLVRV 83
Cdd:TIGR01018   3 DPRRQRKKYETPRHPWIKERLDRELKLMGKYGLRNKKEVWKAETTLRKYRRAARELLTLD--DEQRLFEGNQLLRRLVRL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325176     84 GVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSP 163
Cdd:TIGR01018  81 GILDEENAKLDDVLGLTVEDFLERRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSYIVRLEEEKKIDFALSSP 160


                  ..
gi 6325176    164 FG 165
Cdd:TIGR01018 161 FG 162
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 6-106 8.75e-10

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: 53.71  E-value: 8.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325176      6 RTYSKTYSTPKR----PYESSRLDAELKLAgefglKNKKEIYRISFQLSKIRRAARDLLTRDEKDPKRLFEG--NALIRR 79
Cdd:pfam00163   1 RYKGPEQKLLRRvgfkLWKKGRCHRELKVA-----QNRREYPKYPGQHGKIRKLSEYLLQLREKQKVRRKYGllEKQLRK 75

                          90       100
                  ....*....|....*....|....*..
gi 6325176     80 LVRVGvlsedkKKLDYVLALKVEDFLE 106
Cdd:pfam00163  76 LYDMG------LKLKGVTGENLLQLLE 96
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 105-149 3.76e-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: 53.93  E-value: 3.76e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 6325176  105 LERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVR 149
Cdd:COG0522  92 LERRLDNVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVK 136
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 107-149 7.90e-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: 7.90e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 6325176  107 RRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVR 149
Cdd:cd00165   1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVK 43
S4 smart00363
S4 RNA-binding domain;
107-148 2.52e-04

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 37.57  E-value: 2.52e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 6325176     107 RRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMV 148
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIV 42
 
Name Accession Description Interval E-value
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 1-181 1.76e-105

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 300.46  E-value: 1.76e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325176     1 MPRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLTRDEKDPKRLFEGNALIRRL 80
Cdd:PTZ00155   1 MGRNYRNHSKTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRM 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325176    81 VRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAP 160
Cdd:PTZ00155  81 HRLGLLDEDERKLDYVLGLTVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFAD 160

                        170       180
                 ....*....|....*....|.
gi 6325176   161 TSPFGGARPGRVARRNAARKA 181
Cdd:PTZ00155 161 TSPFGNGRPGRVKRKAAKAAK 181
PLN00189 PLN00189
40S ribosomal protein S9; Provisional
 6-185 2.71e-96

40S ribosomal protein S9; Provisional


Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 277.79  E-value: 2.71e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325176     6 RTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLTRDEKDPKRLFEGNALIRRLVRVGV 85
Cdd:PLN00189   8 RNYGKTFKKPRRPYEKERLDAELKLVGEYGLRNKRELWRVQYALSRIRNAARMLLTLDEKNPRRIFEGEALLRRMNRYGL 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325176    86 LSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFG 165
Cdd:PLN00189  88 LDESQNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFSLTSPLG 167

                        170       180
                 ....*....|....*....|
gi 6325176   166 GARPGRVARRNAarKAEASG 185
Cdd:PLN00189 168 GGRPGRVKRKNQ--KAASGG 185
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 4-165 4.40e-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: 223.07  E-value: 4.40e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325176      4 APRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLTRDekDPKRLFEGNALIRRLVRV 83
Cdd:TIGR01018   3 DPRRQRKKYETPRHPWIKERLDRELKLMGKYGLRNKKEVWKAETTLRKYRRAARELLTLD--DEQRLFEGNQLLRRLVRL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325176     84 GVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSP 163
Cdd:TIGR01018  81 GILDEENAKLDDVLGLTVEDFLERRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSYIVRLEEEKKIDFALSSP 160


                  ..
gi 6325176    164 FG 165
Cdd:TIGR01018 161 FG 162
rps4p PRK04051
30S ribosomal protein S4P; Validated
 5-164 4.92e-62

30S ribosomal protein S4P; Validated


Pssm-ID: 179730 [Multi-domain]  Cd Length: 177  Bit Score: 190.47  E-value: 4.92e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325176     5 PRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLTRDEKDPKRlfEGNALIRRLVRVG 84
Cdd:PRK04051   4 PKKPRKKYETPNHPWQKERIAEERELLGKYGLRNKRELWKAQSILRKYRRQARSLLALPPEERAK--EEEQLLGKLKRYG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325176    85 VLSEDKKkLDYVLALKVEDFLERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPF 164
Cdd:PRK04051  82 ILKENAT-LDDVLSLTVEDILERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPTSPL 160
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 6-106 8.75e-10

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: 53.71  E-value: 8.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325176      6 RTYSKTYSTPKR----PYESSRLDAELKLAgefglKNKKEIYRISFQLSKIRRAARDLLTRDEKDPKRLFEG--NALIRR 79
Cdd:pfam00163   1 RYKGPEQKLLRRvgfkLWKKGRCHRELKVA-----QNRREYPKYPGQHGKIRKLSEYLLQLREKQKVRRKYGllEKQLRK 75

                          90       100
                  ....*....|....*....|....*..
gi 6325176     80 LVRVGvlsedkKKLDYVLALKVEDFLE 106
Cdd:pfam00163  76 LYDMG------LKLKGVTGENLLQLLE 96
rpsD PRK05327
30S ribosomal protein S4; Validated
 105-149 2.92e-09

30S ribosomal protein S4; Validated


Pssm-ID: 235411 [Multi-domain]  Cd Length: 203  Bit Score: 54.34  E-value: 2.92e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 6325176   105 LERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVR 149
Cdd:PRK05327  91 LESRLDNVVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVK 135
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 105-149 3.76e-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: 53.93  E-value: 3.76e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 6325176  105 LERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVR 149
Cdd:COG0522  92 LERRLDNVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVK 136
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 107-149 1.33e-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: 49.03  E-value: 1.33e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 6325176    107 RRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVR 149
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVK 43
rps4 CHL00113
ribosomal protein S4; Reviewed
 104-147 5.18e-08

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 50.98  E-value: 5.18e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 6325176   104 FLERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFM 147
Cdd:CHL00113  86 LLEMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYR 129
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 107-149 7.90e-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: 7.90e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 6325176  107 RRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVR 149
Cdd:cd00165   1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVK 43
S4 smart00363
S4 RNA-binding domain;
107-148 2.52e-04

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 37.57  E-value: 2.52e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 6325176     107 RRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMV 148
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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