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Conserved domains on  [gi|332541822|gb|AEE69486|]
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small ribosomal protein subunit 4, partial (chloroplast) [Anoectangium aestivum]

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

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
rps4 CHL00113
ribosomal protein S4; Reviewed
 1-195 2.68e-120

ribosomal protein S4; Reviewed


:

Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 338.73  E-value: 2.68e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332541822   1 RVRIIRRLGTLPGLSNKTPHLKSSSTNQSSSnKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGLILLQL 80
Cdd:CHL00113   8 RLKIIRRLGALPGLTSKTPRPGSDLRNQSRS-GKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTGQVLLQL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332541822  81 LEMRLDNVIFRLGMAPTIPGARQLVNHRHILVNNCIVNIPSYRCKPQDFITIKNRQKSQVMITKNIDFSQKSKIPNHLTF 160
Cdd:CHL00113  87 LEMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREELPNHLTL 166

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 332541822 161 NSLEKKGLVNQILDQESIGLKINELLVVEYYSRQA 195
Cdd:CHL00113 167 DKLQYKGLVNQIIDRKWVGLKINELLVVEYYSRQT 201
 
Name Accession Description Interval E-value
rps4 CHL00113
ribosomal protein S4; Reviewed
 1-195 2.68e-120

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 338.73  E-value: 2.68e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332541822   1 RVRIIRRLGTLPGLSNKTPHLKSSSTNQSSSnKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGLILLQL 80
Cdd:CHL00113   8 RLKIIRRLGALPGLTSKTPRPGSDLRNQSRS-GKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTGQVLLQL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332541822  81 LEMRLDNVIFRLGMAPTIPGARQLVNHRHILVNNCIVNIPSYRCKPQDFITIKNRQKSQVMITKNIDFSQKSKIPNHLTF 160
Cdd:CHL00113  87 LEMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREELPNHLTL 166

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 332541822 161 NSLEKKGLVNQILDQESIGLKINELLVVEYYSRQA 195
Cdd:CHL00113 167 DKLQYKGLVNQIIDRKWVGLKINELLVVEYYSRQT 201
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 33-193 4.61e-74

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: 221.87  E-value: 4.61e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332541822  33 KKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGLILLQLLEMRLDNVIFRLGMAPTIPGARQLVNHRHILV 112
Cdd:COG0522   44 KKLSDYGLQLREKQKLRRIYGVLEKQFRRYFEEAARRKGNTGENLLQLLERRLDNVVYRLGFAPTRAQARQLVSHGHILV 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332541822 113 NNCIVNIPSYRCKPQDFITIKNRQKSQVMITKNIDFSQKSKIPNHLTFNSLEKKGLVNQILDQESIGLKINELLVVEYYS 192
Cdd:COG0522  124 NGKKVNIPSYQVKPGDVIEVREKSKKLPRIKEALESAEQRGVPEWLEVDAEKLSGTVVRLPEREEIPVPINEQLIVELYS 203


                 .
gi 332541822 193 R 193
Cdd:COG0522  204 R 204
rpsD_bact TIGR01017
ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and ...
 1-193 1.22e-66

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: 202.92  E-value: 1.22e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332541822    1 RVRIIRRLGT-LPGLSNK-TPHLKSSSTNQSSSNKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGLILL 78
Cdd:TIGR01017   6 KFKLSRRLGVnLFGKSRKlLLKRKYPPGQHGQRRKKLSDYGLQLQEKQKLKFMYGITEKQFRKYFKEAKKLKGNTGENLL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332541822   79 QLLEMRLDNVIFRLGMAPTIPGARQLVNHRHILVNNCIVNIPSYRCKPQDFITIKNRQKSQVMITKNIDFSQKSKIPNHL 158
Cdd:TIGR01017  86 RLLESRLDNVVYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQRNIPSWL 165

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 332541822  159 TFNSLEKKGLVNQILDQESIGLKINELLVVEYYSR 193
Cdd:TIGR01017 166 EVDKKTLEGKVLRVPERSQLPLPINESLVVEYYSR 200
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 83-148 2.73e-16

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: 69.97  E-value: 2.73e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 332541822  83 MRLDNVIFRLGMAPTIPGARQLVNHRHILVNNCIVNIPSYRCKPQDFITIKNRQKSQVMITKNIDF 148
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYEDKKL 66
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 33-82 9.06e-16

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: 69.11  E-value: 9.06e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 332541822   33 KKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGLILLQLLE 82
Cdd:pfam00163  47 RKLSEYLLQLREKQKVRRKYGLLEKQLRKLYDMGLKLKGVTGENLLQLLE 96
S4 smart00363
S4 RNA-binding domain;
83-138 2.68e-11

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 56.45  E-value: 2.68e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 332541822    83 MRLDNVIFRLGMAPTIPGARQLVNHRHILVNNCIVNIPSYRCKPQDFITIKNRQKS 138
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELK 56
 
Name Accession Description Interval E-value
rps4 CHL00113
ribosomal protein S4; Reviewed
 1-195 2.68e-120

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 338.73  E-value: 2.68e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332541822   1 RVRIIRRLGTLPGLSNKTPHLKSSSTNQSSSnKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGLILLQL 80
Cdd:CHL00113   8 RLKIIRRLGALPGLTSKTPRPGSDLRNQSRS-GKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTGQVLLQL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332541822  81 LEMRLDNVIFRLGMAPTIPGARQLVNHRHILVNNCIVNIPSYRCKPQDFITIKNRQKSQVMITKNIDFSQKSKIPNHLTF 160
Cdd:CHL00113  87 LEMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREELPNHLTL 166

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 332541822 161 NSLEKKGLVNQILDQESIGLKINELLVVEYYSRQA 195
Cdd:CHL00113 167 DKLQYKGLVNQIIDRKWVGLKINELLVVEYYSRQT 201
rpsD PRK05327
30S ribosomal protein S4; Validated
 1-193 4.63e-76

30S ribosomal protein S4; Validated


Pssm-ID: 235411 [Multi-domain]  Cd Length: 203  Bit Score: 226.91  E-value: 4.63e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332541822   1 RVRIIRRLGT-LPGLSNKT--------PHlkssstNQSSSNKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKG 71
Cdd:PRK05327   8 KCKLSRRLGVdLFKSGKRClkrkyppgQH------GQRRRKPKLSDYGLQLREKQKLRRIYGVLEKQFRRYFKEAARRKG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332541822  72 STGLILLQLLEMRLDNVIFRLGMAPTIPGARQLVNHRHILVNNCIVNIPSYRCKPQDFITIKNRQKSQVMITKNIDFSQK 151
Cdd:PRK05327  82 NTGENLLQLLESRLDNVVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVREKSKKLPRIKEALELAER 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 332541822 152 SKIPNHLTFNSLEKKGLVNQILDQESIGLKINELLVVEYYSR 193
Cdd:PRK05327 162 RGVPDWLEVDAEKLEGTFKRLPEREEIPVPINEQLIVELYSK 203
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 33-193 4.61e-74

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: 221.87  E-value: 4.61e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332541822  33 KKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGLILLQLLEMRLDNVIFRLGMAPTIPGARQLVNHRHILV 112
Cdd:COG0522   44 KKLSDYGLQLREKQKLRRIYGVLEKQFRRYFEEAARRKGNTGENLLQLLERRLDNVVYRLGFAPTRAQARQLVSHGHILV 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332541822 113 NNCIVNIPSYRCKPQDFITIKNRQKSQVMITKNIDFSQKSKIPNHLTFNSLEKKGLVNQILDQESIGLKINELLVVEYYS 192
Cdd:COG0522  124 NGKKVNIPSYQVKPGDVIEVREKSKKLPRIKEALESAEQRGVPEWLEVDAEKLSGTVVRLPEREEIPVPINEQLIVELYS 203


                 .
gi 332541822 193 R 193
Cdd:COG0522  204 R 204
rpsD_bact TIGR01017
ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and ...
 1-193 1.22e-66

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: 202.92  E-value: 1.22e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332541822    1 RVRIIRRLGT-LPGLSNK-TPHLKSSSTNQSSSNKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGLILL 78
Cdd:TIGR01017   6 KFKLSRRLGVnLFGKSRKlLLKRKYPPGQHGQRRKKLSDYGLQLQEKQKLKFMYGITEKQFRKYFKEAKKLKGNTGENLL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332541822   79 QLLEMRLDNVIFRLGMAPTIPGARQLVNHRHILVNNCIVNIPSYRCKPQDFITIKNRQKSQVMITKNIDFSQKSKIPNHL 158
Cdd:TIGR01017  86 RLLESRLDNVVYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQRNIPSWL 165

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 332541822  159 TFNSLEKKGLVNQILDQESIGLKINELLVVEYYSR 193
Cdd:TIGR01017 166 EVDKKTLEGKVLRVPERSQLPLPINESLVVEYYSR 200
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 83-148 2.73e-16

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: 69.97  E-value: 2.73e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 332541822  83 MRLDNVIFRLGMAPTIPGARQLVNHRHILVNNCIVNIPSYRCKPQDFITIKNRQKSQVMITKNIDF 148
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYEDKKL 66
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 33-82 9.06e-16

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: 69.11  E-value: 9.06e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 332541822   33 KKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGLILLQLLE 82
Cdd:pfam00163  47 RKLSEYLLQLREKQKVRRKYGLLEKQLRKLYDMGLKLKGVTGENLLQLLE 96
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 83-130 2.78e-13

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: 61.35  E-value: 2.78e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 332541822   83 MRLDNVIFRLGMAPTIPGARQLVNHRHILVNNCIVNIPSYRCKPQDFI 130
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
S4 smart00363
S4 RNA-binding domain;
83-138 2.68e-11

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 56.45  E-value: 2.68e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 332541822    83 MRLDNVIFRLGMAPTIPGARQLVNHRHILVNNCIVNIPSYRCKPQDFITIKNRQKS 138
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELK 56
PLN00189 PLN00189
40S ribosomal protein S9; Provisional
 75-130 3.49e-09

40S ribosomal protein S9; Provisional


Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 53.99  E-value: 3.49e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 332541822  75 LILLQLLEMRLDNVIFRLGMAPTIPGARQLVNHRHILVNNCIVNIPSY--RCKPQDFI 130
Cdd:PLN00189 101 LTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFmvRVDSQKHI 158
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 74-122 8.28e-09

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: 52.43  E-value: 8.28e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 332541822   74 GLILLQLLEMRLDNVIFRLGMAPTIPGARQLVNHRHILVNNCIVNIPSY 122
Cdd:TIGR01018  95 GLTVEDFLERRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSY 143
rps4p PRK04051
30S ribosomal protein S4P; Validated
 79-122 8.44e-09

30S ribosomal protein S4P; Validated


Pssm-ID: 179730 [Multi-domain]  Cd Length: 177  Bit Score: 52.57  E-value: 8.44e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 332541822  79 QLLEMRLDNVIFRLGMAPTIPGARQLVNHRHILVNNCIVNIPSY 122
Cdd:PRK04051  99 DILERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSY 142
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 56-122 9.53e-08

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 49.69  E-value: 9.53e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 332541822  56 ERQLLNYVriarkakgsTGLILLQLLEMRLDNVIFRLGMAPTIPGARQLVNHRHILVNNCIVNIPSY 122
Cdd:PTZ00155  89 DERKLDYV---------LGLTVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSF 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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