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Conserved domains on  [gi|21914154|gb|AAM81299|]
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ribosomal protein subunit 4, partial (chloroplast) [Ptychostomum archangelicum]

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
 10-197 3.70e-117

ribosomal protein S4; Reviewed


:

Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 330.64  E-value: 3.70e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21914154   10 LGALPGLTNKTPQLKTNSINQSISnKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLEMRLDN 89
Cdd:CHL00113  15 LGALPGLTSKTPRPGSDLRNQSRS-GKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTGQVLLQLLEMRLDN 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21914154   90 VIFRLGMAPTIPGARQLVNHRHILVNDRIVNIPSYRCKPEDSITIKDRQKSQAIISKNLNLYQKYKTPNHLTYNFLKKKG 169
Cdd:CHL00113  94 ILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREELPNHLTLDKLQYKG 173

                        170       180
                 ....*....|....*....|....*...
gi 21914154  170 LVNQILDRESIGLKINELLVVEYYSRQA 197
Cdd:CHL00113 174 LVNQIIDRKWVGLKINELLVVEYYSRQT 201
 
Name Accession Description Interval E-value
rps4 CHL00113
ribosomal protein S4; Reviewed
 10-197 3.70e-117

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 330.64  E-value: 3.70e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21914154   10 LGALPGLTNKTPQLKTNSINQSISnKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLEMRLDN 89
Cdd:CHL00113  15 LGALPGLTSKTPRPGSDLRNQSRS-GKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTGQVLLQLLEMRLDN 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21914154   90 VIFRLGMAPTIPGARQLVNHRHILVNDRIVNIPSYRCKPEDSITIKDRQKSQAIISKNLNLYQKYKTPNHLTYNFLKKKG 169
Cdd:CHL00113  94 ILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREELPNHLTLDKLQYKG 173

                        170       180
                 ....*....|....*....|....*...
gi 21914154  170 LVNQILDRESIGLKINELLVVEYYSRQA 197
Cdd:CHL00113 174 LVNQIIDRKWVGLKINELLVVEYYSRQT 201
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 35-195 2.95e-79

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: 234.97  E-value: 2.95e-79
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21914154  35 KKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLEMRLDNVIFRLGMAPTIPGARQLVNHRHILV 114
Cdd:COG0522  44 KKLSDYGLQLREKQKLRRIYGVLEKQFRRYFEEAARRKGNTGENLLQLLERRLDNVVYRLGFAPTRAQARQLVSHGHILV 123

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21914154 115 NDRIVNIPSYRCKPEDSITIKDRQKSQAIISKNLNLYQKYKTPNHLTYNFLKKKGLVNQILDRESIGLKINELLVVEYYS 194
Cdd:COG0522 124 NGKKVNIPSYQVKPGDVIEVREKSKKLPRIKEALESAEQRGVPEWLEVDAEKLSGTVVRLPEREEIPVPINEQLIVELYS 203


                .
gi 21914154 195 R 195
Cdd:COG0522 204 R 204
rpsD_bact TIGR01017
ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and ...
 34-195 3.11e-67

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: 204.46  E-value: 3.11e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21914154    34 NKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLEMRLDNVIFRLGMAPTIPGARQLVNHRHIL 113
Cdd:TIGR01017  39 RKKLSDYGLQLQEKQKLKFMYGITEKQFRKYFKEAKKLKGNTGENLLRLLESRLDNVVYRLGFAPTRFAARQLVSHGHIL 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21914154   114 VNDRIVNIPSYRCKPEDSITIKDRQKSQAIISKNLNLYQKYKTPNHLTYNFLKKKGLVNQILDRESIGLKINELLVVEYY 193
Cdd:TIGR01017 119 VNGKKVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQRNIPSWLEVDKKTLEGKVLRVPERSQLPLPINESLVVEYY 198


                  ..
gi 21914154   194 SR 195
Cdd:TIGR01017 199 SR 200
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 85-151 8.49e-19

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: 76.52  E-value: 8.49e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 21914154  85 MRLDNVIFRLGMAPTIPGARQLVNHRHILVNDRIVNIPSYRCKPEDSITIKDRQKSQAIISKNLNLY 151
Cdd:cd00165   1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYEDKKLL 67
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 35-84 2.92e-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: 70.65  E-value: 2.92e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 21914154    35 KKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLE 84
Cdd:pfam00163  47 RKLSEYLLQLREKQKVRRKYGLLEKQLRKLYDMGLKLKGVTGENLLQLLE 96
S4 smart00363
S4 RNA-binding domain;
85-140 1.83e-13

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 62.23  E-value: 1.83e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 21914154     85 MRLDNVIFRLGMAPTIPGARQLVNHRHILVNDRIVNIPSYRCKPEDSITIKDRQKS 140
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELK 56
 
Name Accession Description Interval E-value
rps4 CHL00113
ribosomal protein S4; Reviewed
 10-197 3.70e-117

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 330.64  E-value: 3.70e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21914154   10 LGALPGLTNKTPQLKTNSINQSISnKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLEMRLDN 89
Cdd:CHL00113  15 LGALPGLTSKTPRPGSDLRNQSRS-GKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTGQVLLQLLEMRLDN 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21914154   90 VIFRLGMAPTIPGARQLVNHRHILVNDRIVNIPSYRCKPEDSITIKDRQKSQAIISKNLNLYQKYKTPNHLTYNFLKKKG 169
Cdd:CHL00113  94 ILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREELPNHLTLDKLQYKG 173

                        170       180
                 ....*....|....*....|....*...
gi 21914154  170 LVNQILDRESIGLKINELLVVEYYSRQA 197
Cdd:CHL00113 174 LVNQIIDRKWVGLKINELLVVEYYSRQT 201
rpsD PRK05327
30S ribosomal protein S4; Validated
 35-195 6.24e-80

30S ribosomal protein S4; Validated


Pssm-ID: 235411 [Multi-domain]  Cd Length: 203  Bit Score: 236.54  E-value: 6.24e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21914154   35 KKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLEMRLDNVIFRLGMAPTIPGARQLVNHRHILV 114
Cdd:PRK05327  43 PKLSDYGLQLREKQKLRRIYGVLEKQFRRYFKEAARRKGNTGENLLQLLESRLDNVVYRLGFAPTRRQARQLVSHGHILV 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21914154  115 NDRIVNIPSYRCKPEDSITIKDRQKSQAIISKNLNLYQKYKTPNHLTYNFLKKKGLVNQILDRESIGLKINELLVVEYYS 194
Cdd:PRK05327 123 NGKKVNIPSYRVKPGDVIEVREKSKKLPRIKEALELAERRGVPDWLEVDAEKLEGTFKRLPEREEIPVPINEQLIVELYS 202


                 .
gi 21914154  195 R 195
Cdd:PRK05327 203 K 203
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 35-195 2.95e-79

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: 234.97  E-value: 2.95e-79
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21914154  35 KKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLEMRLDNVIFRLGMAPTIPGARQLVNHRHILV 114
Cdd:COG0522  44 KKLSDYGLQLREKQKLRRIYGVLEKQFRRYFEEAARRKGNTGENLLQLLERRLDNVVYRLGFAPTRAQARQLVSHGHILV 123

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21914154 115 NDRIVNIPSYRCKPEDSITIKDRQKSQAIISKNLNLYQKYKTPNHLTYNFLKKKGLVNQILDRESIGLKINELLVVEYYS 194
Cdd:COG0522 124 NGKKVNIPSYQVKPGDVIEVREKSKKLPRIKEALESAEQRGVPEWLEVDAEKLSGTVVRLPEREEIPVPINEQLIVELYS 203


                .
gi 21914154 195 R 195
Cdd:COG0522 204 R 204
rpsD_bact TIGR01017
ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and ...
 34-195 3.11e-67

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: 204.46  E-value: 3.11e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21914154    34 NKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLEMRLDNVIFRLGMAPTIPGARQLVNHRHIL 113
Cdd:TIGR01017  39 RKKLSDYGLQLQEKQKLKFMYGITEKQFRKYFKEAKKLKGNTGENLLRLLESRLDNVVYRLGFAPTRFAARQLVSHGHIL 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21914154   114 VNDRIVNIPSYRCKPEDSITIKDRQKSQAIISKNLNLYQKYKTPNHLTYNFLKKKGLVNQILDRESIGLKINELLVVEYY 193
Cdd:TIGR01017 119 VNGKKVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQRNIPSWLEVDKKTLEGKVLRVPERSQLPLPINESLVVEYY 198


                  ..
gi 21914154   194 SR 195
Cdd:TIGR01017 199 SR 200
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 85-151 8.49e-19

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: 76.52  E-value: 8.49e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 21914154  85 MRLDNVIFRLGMAPTIPGARQLVNHRHILVNDRIVNIPSYRCKPEDSITIKDRQKSQAIISKNLNLY 151
Cdd:cd00165   1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYEDKKLL 67
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 35-84 2.92e-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: 70.65  E-value: 2.92e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 21914154    35 KKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLE 84
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 ...
 85-132 6.45e-15

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: 65.59  E-value: 6.45e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 21914154    85 MRLDNVIFRLGMAPTIPGARQLVNHRHILVNDRIVNIPSYRCKPEDSI 132
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
S4 smart00363
S4 RNA-binding domain;
85-140 1.83e-13

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 62.23  E-value: 1.83e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 21914154     85 MRLDNVIFRLGMAPTIPGARQLVNHRHILVNDRIVNIPSYRCKPEDSITIKDRQKS 140
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELK 56
rps4p PRK04051
30S ribosomal protein S4P; Validated
 43-133 1.66e-11

30S ribosomal protein S4P; Validated


Pssm-ID: 179730 [Multi-domain]  Cd Length: 177  Bit Score: 59.88  E-value: 1.66e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21914154   43 RLEEKQKLRFHYG--------ITERQLLNYVRIARKAKGSTGEV----------------LL---------------QLL 83
Cdd:PRK04051  22 RIAEERELLGKYGlrnkrelwKAQSILRKYRRQARSLLALPPEErakeeeqllgklkrygILkenatlddvlsltveDIL 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 21914154   84 EMRLDNVIFRLGMAPTIPGARQLVNHRHILVNDRIVNIPSYRCK--PEDSIT 133
Cdd:PRK04051 102 ERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSveEEDLID 153
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 83-134 3.04e-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: 56.28  E-value: 3.04e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 21914154    83 LEMRLDNVIFRLGMAPTIPGARQLVNHRHILVNDRIVNIPSYRCKPEDSITI 134
Cdd:TIGR01018 102 LERRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSYIVRLEEEKKI 153
PLN00189 PLN00189
40S ribosomal protein S9; Provisional
 81-134 6.45e-09

40S ribosomal protein S9; Provisional


Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 53.21  E-value: 6.45e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 21914154   81 QLLEMRLDNVIFRLGMAPTIPGARQLVNHRHILVNDRIVNIPSYRCKPEDSITI 134
Cdd:PLN00189 105 NFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHI 158
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 82-124 7.09e-08

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 50.08  E-value: 7.09e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 21914154   82 LLEMRLDNVIFRLGMAPTIPGARQLVNHRHILVNDRIVNIPSY 124
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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