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Conserved domains on  [gi|1732218440|gb|QEJ66277|]
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ribosomal protein S4, partial (chloroplast) [Oncophorus virens]

Protein Classification

30S ribosomal protein S4( domain architecture ID 11414071)

30S ribosomal protein S4 binds directly to 16S rRNA and plays an important role in translational accuracy

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rps4 CHL00113
ribosomal protein S4; Reviewed
 1-187 9.00e-123

ribosomal protein S4; Reviewed


:

Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 344.51  E-value: 9.00e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732218440   1 GTLPGLTNKTPQLKSSSINQSTSnKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGQVLLQLLEMRLDNI 80
Cdd:CHL00113   16 GALPGLTSKTPRPGSDLRNQSRS-GKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTGQVLLQLLEMRLDNI 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732218440  81 IFRLGMAPTIPGARQLVNHKHILVNDHIVNIPSYRCKPQDFITVKNRQKSQAMVIKNVDFSQKANVPNHLTFNSLEKKGL 160
Cdd:CHL00113   95 LFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREELPNHLTLDKLQYKGL 174

                         170       180
                  ....*....|....*....|....*..
gi 1732218440 161 VNQILDQESIGLKINELLVVEYYSRQA 187
Cdd:CHL00113  175 VNQIIDRKWVGLKINELLVVEYYSRQT 201
 
Name Accession Description Interval E-value
rps4 CHL00113
ribosomal protein S4; Reviewed
 1-187 9.00e-123

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 344.51  E-value: 9.00e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732218440   1 GTLPGLTNKTPQLKSSSINQSTSnKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGQVLLQLLEMRLDNI 80
Cdd:CHL00113   16 GALPGLTSKTPRPGSDLRNQSRS-GKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTGQVLLQLLEMRLDNI 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732218440  81 IFRLGMAPTIPGARQLVNHKHILVNDHIVNIPSYRCKPQDFITVKNRQKSQAMVIKNVDFSQKANVPNHLTFNSLEKKGL 160
Cdd:CHL00113   95 LFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREELPNHLTLDKLQYKGL 174

                         170       180
                  ....*....|....*....|....*..
gi 1732218440 161 VNQILDQESIGLKINELLVVEYYSRQA 187
Cdd:CHL00113  175 VNQIIDRKWVGLKINELLVVEYYSRQT 201
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 25-185 2.03e-77

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: 229.96  E-value: 2.03e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732218440  25 KKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGQVLLQLLEMRLDNIIFRLGMAPTIPGARQLVNHKHILV 104
Cdd:COG0522    44 KKLSDYGLQLREKQKLRRIYGVLEKQFRRYFEEAARRKGNTGENLLQLLERRLDNVVYRLGFAPTRAQARQLVSHGHILV 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732218440 105 NDHIVNIPSYRCKPQDFITVKNRQKSQAMVIKNVDFSQKANVPNHLTFNSLEKKGLVNQILDQESIGLKINELLVVEYYS 184
Cdd:COG0522   124 NGKKVNIPSYQVKPGDVIEVREKSKKLPRIKEALESAEQRGVPEWLEVDAEKLSGTVVRLPEREEIPVPINEQLIVELYS 203


                  .
gi 1732218440 185 R 185
Cdd:COG0522   204 R 204
rpsD_bact TIGR01017
ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and ...
 24-185 7.48e-69

ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 200066 [Multi-domain]  Cd Length: 200  Bit Score: 207.93  E-value: 7.48e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732218440  24 NKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGQVLLQLLEMRLDNIIFRLGMAPTIPGARQLVNHKHIL 103
Cdd:TIGR01017  39 RKKLSDYGLQLQEKQKLKFMYGITEKQFRKYFKEAKKLKGNTGENLLRLLESRLDNVVYRLGFAPTRFAARQLVSHGHIL 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732218440 104 VNDHIVNIPSYRCKPQDFITVKNRQKSQAMVIKNVDFSQKANVPNHLTFNSLEKKGLVNQILDQESIGLKINELLVVEYY 183
Cdd:TIGR01017 119 VNGKKVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQRNIPSWLEVDKKTLEGKVLRVPERSQLPLPINESLVVEYY 198


                  ..
gi 1732218440 184 SR 185
Cdd:TIGR01017 199 SR 200
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 75-137 4.81e-18

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: 74.21  E-value: 4.81e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1732218440  75 MRLDNIIFRLGMAPTIPGARQLVNHKHILVNDHIVNIPSYRCKPQDFITVKNRQKSQAMVIKN 137
Cdd:cd00165     1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYED 63
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 20-74 2.48e-17

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: 72.97  E-value: 2.48e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1732218440  20 QSTSNKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGQVLLQLLE 74
Cdd:pfam00163  42 QHGKIRKLSEYLLQLREKQKVRRKYGLLEKQLRKLYDMGLKLKGVTGENLLQLLE 96
S4 smart00363
S4 RNA-binding domain;
75-130 6.17e-13

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 60.68  E-value: 6.17e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1732218440   75 MRLDNIIFRLGMAPTIPGARQLVNHKHILVNDHIVNIPSYRCKPQDFITVKNRQKS 130
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELK 56
 
Name Accession Description Interval E-value
rps4 CHL00113
ribosomal protein S4; Reviewed
 1-187 9.00e-123

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 344.51  E-value: 9.00e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732218440   1 GTLPGLTNKTPQLKSSSINQSTSnKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGQVLLQLLEMRLDNI 80
Cdd:CHL00113   16 GALPGLTSKTPRPGSDLRNQSRS-GKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTGQVLLQLLEMRLDNI 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732218440  81 IFRLGMAPTIPGARQLVNHKHILVNDHIVNIPSYRCKPQDFITVKNRQKSQAMVIKNVDFSQKANVPNHLTFNSLEKKGL 160
Cdd:CHL00113   95 LFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREELPNHLTLDKLQYKGL 174

                         170       180
                  ....*....|....*....|....*..
gi 1732218440 161 VNQILDQESIGLKINELLVVEYYSRQA 187
Cdd:CHL00113  175 VNQIIDRKWVGLKINELLVVEYYSRQT 201
rpsD PRK05327
30S ribosomal protein S4; Validated
 20-185 1.72e-79

30S ribosomal protein S4; Validated


Pssm-ID: 235411 [Multi-domain]  Cd Length: 203  Bit Score: 235.00  E-value: 1.72e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732218440  20 QSTSNKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGQVLLQLLEMRLDNIIFRLGMAPTIPGARQLVNH 99
Cdd:PRK05327   38 QRRRKPKLSDYGLQLREKQKLRRIYGVLEKQFRRYFKEAARRKGNTGENLLQLLESRLDNVVYRLGFAPTRRQARQLVSH 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732218440 100 KHILVNDHIVNIPSYRCKPQDFITVKNRQKSQAMVIKNVDFSQKANVPNHLTFNSLEKKGLVNQILDQESIGLKINELLV 179
Cdd:PRK05327  118 GHILVNGKKVNIPSYRVKPGDVIEVREKSKKLPRIKEALELAERRGVPDWLEVDAEKLEGTFKRLPEREEIPVPINEQLI 197


                  ....*.
gi 1732218440 180 VEYYSR 185
Cdd:PRK05327  198 VELYSK 203
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 25-185 2.03e-77

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: 229.96  E-value: 2.03e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732218440  25 KKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGQVLLQLLEMRLDNIIFRLGMAPTIPGARQLVNHKHILV 104
Cdd:COG0522    44 KKLSDYGLQLREKQKLRRIYGVLEKQFRRYFEEAARRKGNTGENLLQLLERRLDNVVYRLGFAPTRAQARQLVSHGHILV 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732218440 105 NDHIVNIPSYRCKPQDFITVKNRQKSQAMVIKNVDFSQKANVPNHLTFNSLEKKGLVNQILDQESIGLKINELLVVEYYS 184
Cdd:COG0522   124 NGKKVNIPSYQVKPGDVIEVREKSKKLPRIKEALESAEQRGVPEWLEVDAEKLSGTVVRLPEREEIPVPINEQLIVELYS 203


                  .
gi 1732218440 185 R 185
Cdd:COG0522   204 R 204
rpsD_bact TIGR01017
ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and ...
 24-185 7.48e-69

ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 200066 [Multi-domain]  Cd Length: 200  Bit Score: 207.93  E-value: 7.48e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732218440  24 NKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGQVLLQLLEMRLDNIIFRLGMAPTIPGARQLVNHKHIL 103
Cdd:TIGR01017  39 RKKLSDYGLQLQEKQKLKFMYGITEKQFRKYFKEAKKLKGNTGENLLRLLESRLDNVVYRLGFAPTRFAARQLVSHGHIL 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732218440 104 VNDHIVNIPSYRCKPQDFITVKNRQKSQAMVIKNVDFSQKANVPNHLTFNSLEKKGLVNQILDQESIGLKINELLVVEYY 183
Cdd:TIGR01017 119 VNGKKVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQRNIPSWLEVDKKTLEGKVLRVPERSQLPLPINESLVVEYY 198


                  ..
gi 1732218440 184 SR 185
Cdd:TIGR01017 199 SR 200
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 75-137 4.81e-18

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: 74.21  E-value: 4.81e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1732218440  75 MRLDNIIFRLGMAPTIPGARQLVNHKHILVNDHIVNIPSYRCKPQDFITVKNRQKSQAMVIKN 137
Cdd:cd00165     1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYED 63
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 20-74 2.48e-17

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: 72.97  E-value: 2.48e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1732218440  20 QSTSNKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGQVLLQLLE 74
Cdd:pfam00163  42 QHGKIRKLSEYLLQLREKQKVRRKYGLLEKQLRKLYDMGLKLKGVTGENLLQLLE 96
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 75-122 1.56e-14

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: 64.44  E-value: 1.56e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1732218440  75 MRLDNIIFRLGMAPTIPGARQLVNHKHILVNDHIVNIPSYRCKPQDFI 122
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
S4 smart00363
S4 RNA-binding domain;
75-130 6.17e-13

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 60.68  E-value: 6.17e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1732218440   75 MRLDNIIFRLGMAPTIPGARQLVNHKHILVNDHIVNIPSYRCKPQDFITVKNRQKS 130
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELK 56
rps4p PRK04051
30S ribosomal protein S4P; Validated
 33-114 2.07e-10

30S ribosomal protein S4P; Validated


Pssm-ID: 179730 [Multi-domain]  Cd Length: 177  Bit Score: 56.80  E-value: 2.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732218440  33 RLEEKQKLRFHYG--------ITERQLLNYVRIARKAKGSTGQV----------------LL---------------QLL 73
Cdd:PRK04051   22 RIAEERELLGKYGlrnkrelwKAQSILRKYRRQARSLLALPPEErakeeeqllgklkrygILkenatlddvlsltveDIL 101

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1732218440  74 EMRLDNIIFRLGMAPTIPGARQLVNHKHILVNDHIVNIPSY 114
Cdd:PRK04051  102 ERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSY 142
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 73-114 8.27e-10

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: 55.12  E-value: 8.27e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1732218440  73 LEMRLDNIIFRLGMAPTIPGARQLVNHKHILVNDHIVNIPSY 114
Cdd:TIGR01018 102 LERRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSY 143
PLN00189 PLN00189
40S ribosomal protein S9; Provisional
 71-122 8.44e-10

40S ribosomal protein S9; Provisional


Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 55.53  E-value: 8.44e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1732218440  71 QLLEMRLDNIIFRLGMAPTIPGARQLVNHKHILVNDHIVNIPSY--RCKPQDFI 122
Cdd:PLN00189  105 NFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFmvRVDSQKHI 158
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 72-114 8.22e-08

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 49.69  E-value: 8.22e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1732218440  72 LLEMRLDNIIFRLGMAPTIPGARQLVNHKHILVNDHIVNIPSY 114
Cdd:PTZ00155  104 LLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSF 146
 
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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