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Conserved domains on  [gi|2020259076|gb|QTI57342|]
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small ribosomal protein 4, partial (chloroplast) [Lewinskya hookeri]

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
 1-176 1.22e-110

ribosomal protein S4; Reviewed


:

Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 313.30  E-value: 1.22e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020259076   1 PQLKSSSVNQSTSnKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLEMRLDNVIFRLGMAPTI 80
Cdd:CHL00113   26 PRPGSDLRNQSRS-GKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTGQVLLQLLEMRLDNILFRLGMAPTI 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020259076  81 PGARQLVNHRHIIVNHRIVDIPSYRCKPQDFITIKNRQKSQDIITKNIDFYQKSKIPNHLTYNSLEKKGFVNQILDRELI 160
Cdd:CHL00113  105 PAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREELPNHLTLDKLQYKGLVNQIIDRKWV 184

                         170
                  ....*....|....*.
gi 2020259076 161 GLKINELLVVEYYSRQ 176
Cdd:CHL00113  185 GLKINELLVVEYYSRQ 200
 
Name Accession Description Interval E-value
rps4 CHL00113
ribosomal protein S4; Reviewed
 1-176 1.22e-110

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 313.30  E-value: 1.22e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020259076   1 PQLKSSSVNQSTSnKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLEMRLDNVIFRLGMAPTI 80
Cdd:CHL00113   26 PRPGSDLRNQSRS-GKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTGQVLLQLLEMRLDNILFRLGMAPTI 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020259076  81 PGARQLVNHRHIIVNHRIVDIPSYRCKPQDFITIKNRQKSQDIITKNIDFYQKSKIPNHLTYNSLEKKGFVNQILDRELI 160
Cdd:CHL00113  105 PAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREELPNHLTLDKLQYKGLVNQIIDRKWV 184

                         170
                  ....*....|....*.
gi 2020259076 161 GLKINELLVVEYYSRQ 176
Cdd:CHL00113  185 GLKINELLVVEYYSRQ 200
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 15-175 3.07e-75

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: 223.80  E-value: 3.07e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020259076  15 KKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLEMRLDNVIFRLGMAPTIPGARQLVNHRHIIV 94
Cdd:COG0522    44 KKLSDYGLQLREKQKLRRIYGVLEKQFRRYFEEAARRKGNTGENLLQLLERRLDNVVYRLGFAPTRAQARQLVSHGHILV 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020259076  95 NHRIVDIPSYRCKPQDFITIKNRQKSQDIITKNIDFYQKSKIPNHLTYNSLEKKGFVNQILDRELIGLKINELLVVEYYS 174
Cdd:COG0522   124 NGKKVNIPSYQVKPGDVIEVREKSKKLPRIKEALESAEQRGVPEWLEVDAEKLSGTVVRLPEREEIPVPINEQLIVELYS 203


                  .
gi 2020259076 175 R 175
Cdd:COG0522   204 R 204
rpsD_bact TIGR01017
ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and ...
 14-175 4.65e-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: 200.61  E-value: 4.65e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020259076  14 NKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLEMRLDNVIFRLGMAPTIPGARQLVNHRHII 93
Cdd:TIGR01017  39 RKKLSDYGLQLQEKQKLKFMYGITEKQFRKYFKEAKKLKGNTGENLLRLLESRLDNVVYRLGFAPTRFAARQLVSHGHIL 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020259076  94 VNHRIVDIPSYRCKPQDFITIKNRQKSQDIITKNIDFYQKSKIPNHLTYNSLEKKGFVNQILDRELIGLKINELLVVEYY 173
Cdd:TIGR01017 119 VNGKKVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQRNIPSWLEVDKKTLEGKVLRVPERSQLPLPINESLVVEYY 198


                  ..
gi 2020259076 174 SR 175
Cdd:TIGR01017 199 SR 200
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 65-131 2.63e-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: 74.59  E-value: 2.63e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2020259076  65 MRLDNVIFRLGMAPTIPGARQLVNHRHIIVNHRIVDIPSYRCKPQDFITIKNRQKSQDIITKNIDFY 131
Cdd:cd00165     1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYEDKKLL 67
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 10-64 5.03e-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: 72.19  E-value: 5.03e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2020259076  10 QSTSNKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLE 64
Cdd:pfam00163  42 QHGKIRKLSEYLLQLREKQKVRRKYGLLEKQLRKLYDMGLKLKGVTGENLLQLLE 96
S4 smart00363
S4 RNA-binding domain;
65-120 1.02e-11

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 57.22  E-value: 1.02e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2020259076   65 MRLDNVIFRLGMAPTIPGARQLVNHRHIIVNHRIVDIPSYRCKPQDFITIKNRQKS 120
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELK 56
 
Name Accession Description Interval E-value
rps4 CHL00113
ribosomal protein S4; Reviewed
 1-176 1.22e-110

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 313.30  E-value: 1.22e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020259076   1 PQLKSSSVNQSTSnKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLEMRLDNVIFRLGMAPTI 80
Cdd:CHL00113   26 PRPGSDLRNQSRS-GKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTGQVLLQLLEMRLDNILFRLGMAPTI 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020259076  81 PGARQLVNHRHIIVNHRIVDIPSYRCKPQDFITIKNRQKSQDIITKNIDFYQKSKIPNHLTYNSLEKKGFVNQILDRELI 160
Cdd:CHL00113  105 PAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREELPNHLTLDKLQYKGLVNQIIDRKWV 184

                         170
                  ....*....|....*.
gi 2020259076 161 GLKINELLVVEYYSRQ 176
Cdd:CHL00113  185 GLKINELLVVEYYSRQ 200
rpsD PRK05327
30S ribosomal protein S4; Validated
 10-175 5.01e-76

30S ribosomal protein S4; Validated


Pssm-ID: 235411 [Multi-domain]  Cd Length: 203  Bit Score: 225.75  E-value: 5.01e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020259076  10 QSTSNKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLEMRLDNVIFRLGMAPTIPGARQLVNH 89
Cdd:PRK05327   38 QRRRKPKLSDYGLQLREKQKLRRIYGVLEKQFRRYFKEAARRKGNTGENLLQLLESRLDNVVYRLGFAPTRRQARQLVSH 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020259076  90 RHIIVNHRIVDIPSYRCKPQDFITIKNRQKSQDIITKNIDFYQKSKIPNHLTYNSLEKKGFVNQILDRELIGLKINELLV 169
Cdd:PRK05327  118 GHILVNGKKVNIPSYRVKPGDVIEVREKSKKLPRIKEALELAERRGVPDWLEVDAEKLEGTFKRLPEREEIPVPINEQLI 197


                  ....*.
gi 2020259076 170 VEYYSR 175
Cdd:PRK05327  198 VELYSK 203
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 15-175 3.07e-75

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: 223.80  E-value: 3.07e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020259076  15 KKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLEMRLDNVIFRLGMAPTIPGARQLVNHRHIIV 94
Cdd:COG0522    44 KKLSDYGLQLREKQKLRRIYGVLEKQFRRYFEEAARRKGNTGENLLQLLERRLDNVVYRLGFAPTRAQARQLVSHGHILV 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020259076  95 NHRIVDIPSYRCKPQDFITIKNRQKSQDIITKNIDFYQKSKIPNHLTYNSLEKKGFVNQILDRELIGLKINELLVVEYYS 174
Cdd:COG0522   124 NGKKVNIPSYQVKPGDVIEVREKSKKLPRIKEALESAEQRGVPEWLEVDAEKLSGTVVRLPEREEIPVPINEQLIVELYS 203


                  .
gi 2020259076 175 R 175
Cdd:COG0522   204 R 204
rpsD_bact TIGR01017
ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and ...
 14-175 4.65e-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: 200.61  E-value: 4.65e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020259076  14 NKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLEMRLDNVIFRLGMAPTIPGARQLVNHRHII 93
Cdd:TIGR01017  39 RKKLSDYGLQLQEKQKLKFMYGITEKQFRKYFKEAKKLKGNTGENLLRLLESRLDNVVYRLGFAPTRFAARQLVSHGHIL 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020259076  94 VNHRIVDIPSYRCKPQDFITIKNRQKSQDIITKNIDFYQKSKIPNHLTYNSLEKKGFVNQILDRELIGLKINELLVVEYY 173
Cdd:TIGR01017 119 VNGKKVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQRNIPSWLEVDKKTLEGKVLRVPERSQLPLPINESLVVEYY 198


                  ..
gi 2020259076 174 SR 175
Cdd:TIGR01017 199 SR 200
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 65-131 2.63e-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: 74.59  E-value: 2.63e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2020259076  65 MRLDNVIFRLGMAPTIPGARQLVNHRHIIVNHRIVDIPSYRCKPQDFITIKNRQKSQDIITKNIDFY 131
Cdd:cd00165     1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYEDKKLL 67
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 10-64 5.03e-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: 72.19  E-value: 5.03e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2020259076  10 QSTSNKKISQYRIRLEEKQKLRFHYGITERQLLNYVRIARKAKGSTGEVLLQLLE 64
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 ...
 65-112 3.56e-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: 63.28  E-value: 3.56e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2020259076  65 MRLDNVIFRLGMAPTIPGARQLVNHRHIIVNHRIVDIPSYRCKPQDFI 112
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
S4 smart00363
S4 RNA-binding domain;
65-120 1.02e-11

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 57.22  E-value: 1.02e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2020259076   65 MRLDNVIFRLGMAPTIPGARQLVNHRHIIVNHRIVDIPSYRCKPQDFITIKNRQKS 120
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELK 56
rps4p PRK04051
30S ribosomal protein S4P; Validated
 23-104 1.85e-10

30S ribosomal protein S4P; Validated


Pssm-ID: 179730 [Multi-domain]  Cd Length: 177  Bit Score: 56.80  E-value: 1.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020259076  23 RLEEKQKLRFHYG--------ITERQLLNYVRIARKAKGSTGEV----------------LL---------------QLL 63
Cdd:PRK04051   22 RIAEERELLGKYGlrnkrelwKAQSILRKYRRQARSLLALPPEErakeeeqllgklkrygILkenatlddvlsltveDIL 101

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2020259076  64 EMRLDNVIFRLGMAPTIPGARQLVNHRHIIVNHRIVDIPSY 104
Cdd:PRK04051  102 ERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSY 142
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 63-104 6.95e-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: 54.74  E-value: 6.95e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2020259076  63 LEMRLDNVIFRLGMAPTIPGARQLVNHRHIIVNHRIVDIPSY 104
Cdd:TIGR01018 102 LERRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSY 143
PLN00189 PLN00189
40S ribosomal protein S9; Provisional
 61-112 6.50e-09

40S ribosomal protein S9; Provisional


Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 52.83  E-value: 6.50e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2020259076  61 QLLEMRLDNVIFRLGMAPTIPGARQLVNHRHIIVNHRIVDIPSY--RCKPQDFI 112
Cdd:PLN00189  105 NFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFmvRVDSQKHI 158
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 62-104 7.72e-08

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 49.69  E-value: 7.72e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2020259076  62 LLEMRLDNVIFRLGMAPTIPGARQLVNHRHIIVNHRIVDIPSY 104
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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