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Conserved domains on  [gi|927091359|gb|ALD83176|]
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ribosomal S4 protein, partial (chloroplast) [Bulbophyllum bicoloratum]

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
 1-179 2.05e-123

ribosomal protein S4; Reviewed


:

Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 345.66  E-value: 2.05e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359   1 MSRYRGPRFKKIRRLGALPGLTSKRPRSRSDLQTQLRSGKRSQYRIRLEEKQKLRFHYGLTERQLLKYVHIAGKAKGSTG 80
Cdd:CHL00113   1 MSRYRGPRLKIIRRLGALPGLTSKTPRPGSDLRNQSRSGKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359  81 QVLLQLLEMRLDNILFRLGMASTIPGARQLVNHRHILVNGRIVDIPSYRCKPRDIITTKDKERSKALIQNHLVSSPHGEL 160
Cdd:CHL00113  81 QVLLQLLEMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREEL 160

                        170
                 ....*....|....*....
gi 927091359 161 PNHLTIDSLQYKGFVNKII 179
Cdd:CHL00113 161 PNHLTLDKLQYKGLVNQII 179
 
Name Accession Description Interval E-value
rps4 CHL00113
ribosomal protein S4; Reviewed
 1-179 2.05e-123

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 345.66  E-value: 2.05e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359   1 MSRYRGPRFKKIRRLGALPGLTSKRPRSRSDLQTQLRSGKRSQYRIRLEEKQKLRFHYGLTERQLLKYVHIAGKAKGSTG 80
Cdd:CHL00113   1 MSRYRGPRLKIIRRLGALPGLTSKTPRPGSDLRNQSRSGKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359  81 QVLLQLLEMRLDNILFRLGMASTIPGARQLVNHRHILVNGRIVDIPSYRCKPRDIITTKDKERSKALIQNHLVSSPHGEL 160
Cdd:CHL00113  81 QVLLQLLEMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREEL 160

                        170
                 ....*....|....*....
gi 927091359 161 PNHLTIDSLQYKGFVNKII 179
Cdd:CHL00113 161 PNHLTLDKLQYKGLVNQII 179
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 1-178 3.09e-70

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: 211.47  E-value: 3.09e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359   1 MSRYRGPRFKKIRRLG-ALPGLTS------KRPRSRSdlQTQLRSGKRSQYRIRLEEKQKLRFHYGLTERQLLKYVHIAG 73
Cdd:COG0522    1 MARYTGPKCKLCRREGvKLFLKGErkcaleRRPYPPG--QHGQRRKKLSDYGLQLREKQKLRRIYGVLEKQFRRYFEEAA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359  74 KAKGSTGQVLLQLLEMRLDNILFRLGMASTIPGARQLVNHRHILVNGRIVDIPSYRCKPRDIITTKDKERSKALIQNHLV 153
Cdd:COG0522   79 RRKGNTGENLLQLLERRLDNVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVKPGDVIEVREKSKKLPRIKEALE 158

                        170       180
                 ....*....|....*....|....*
gi 927091359 154 SSPHGELPNHLTIDSLQYKGFVNKI 178
Cdd:COG0522  159 SAEQRGVPEWLEVDAEKLSGTVVRL 183
rpsD_bact TIGR01017
ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and ...
 3-176 5.35e-63

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: 192.90  E-value: 5.35e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359    3 RYRGPRFKKIRRLGALPGLTSKRP---RSRSDLQTQLRSGKRSQYRIRLEEKQKLRFHYGLTERQLLKYVHIAGKAKGST 79
Cdd:TIGR01017   1 RYTGPKFKLSRRLGVNLFGKSRKLllkRKYPPGQHGQRRKKLSDYGLQLQEKQKLKFMYGITEKQFRKYFKEAKKLKGNT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359   80 GQVLLQLLEMRLDNILFRLGMASTIPGARQLVNHRHILVNGRIVDIPSYRCKPRDIITTKDKERSKALIQNHLVSSPHGE 159
Cdd:TIGR01017  81 GENLLRLLESRLDNVVYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQRN 160

                         170
                  ....*....|....*..
gi 927091359  160 LPNHLTIDSLQYKGFVN 176
Cdd:TIGR01017 161 IPSWLEVDKKTLEGKVL 177
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 3-88 4.27e-19

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: 77.59  E-value: 4.27e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359    3 RYRGPRFKKIRRLGALPGLTS------KRPRSRSDL---QTQLRSG-KRSQYRIRLEEKQKLRFHYGLTERQLLKYVHIA 72
Cdd:pfam00163   1 RYKGPEQKLLRRVGFKLWKKGrchrelKVAQNRREYpkyPGQHGKIrKLSEYLLQLREKQKVRRKYGLLEKQLRKLYDMG 80

                          90
                  ....*....|....*.
gi 927091359   73 GKAKGSTGQVLLQLLE 88
Cdd:pfam00163  81 LKLKGVTGENLLQLLE 96
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 89-148 1.09e-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: 75.75  E-value: 1.09e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359  89 MRLDNILFRLGMASTIPGARQLVNHRHILVNGRIVDIPSYRCKPRDIITTKDKERSKALI 148
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIV 60
S4 smart00363
S4 RNA-binding domain;
89-144 7.35e-15

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 65.31  E-value: 7.35e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 927091359    89 MRLDNILFRLGMASTIPGARQLVNHRHILVNGRIVDIPSYRCKPRDIITTKDKERS 144
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELK 56
 
Name Accession Description Interval E-value
rps4 CHL00113
ribosomal protein S4; Reviewed
 1-179 2.05e-123

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 345.66  E-value: 2.05e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359   1 MSRYRGPRFKKIRRLGALPGLTSKRPRSRSDLQTQLRSGKRSQYRIRLEEKQKLRFHYGLTERQLLKYVHIAGKAKGSTG 80
Cdd:CHL00113   1 MSRYRGPRLKIIRRLGALPGLTSKTPRPGSDLRNQSRSGKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359  81 QVLLQLLEMRLDNILFRLGMASTIPGARQLVNHRHILVNGRIVDIPSYRCKPRDIITTKDKERSKALIQNHLVSSPHGEL 160
Cdd:CHL00113  81 QVLLQLLEMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREEL 160

                        170
                 ....*....|....*....
gi 927091359 161 PNHLTIDSLQYKGFVNKII 179
Cdd:CHL00113 161 PNHLTLDKLQYKGLVNQII 179
rpsD PRK05327
30S ribosomal protein S4; Validated
 1-178 2.37e-74

30S ribosomal protein S4; Validated


Pssm-ID: 235411 [Multi-domain]  Cd Length: 203  Bit Score: 221.90  E-value: 2.37e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359   1 MSRYRGPRFKKIRRLGALPGLTSKRPRSRS----DLQTQLRSGKRSQYRIRLEEKQKLRFHYGLTERQLLKYVHIAGKAK 76
Cdd:PRK05327   1 MARYTGPKCKLSRRLGVDLFKSGKRCLKRKyppgQHGQRRRKPKLSDYGLQLREKQKLRRIYGVLEKQFRRYFKEAARRK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359  77 GSTGQVLLQLLEMRLDNILFRLGMASTIPGARQLVNHRHILVNGRIVDIPSYRCKPRDIITTKDKERSKALIQNHLVSSP 156
Cdd:PRK05327  81 GNTGENLLQLLESRLDNVVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVREKSKKLPRIKEALELAE 160

                        170       180
                 ....*....|....*....|..
gi 927091359 157 HGELPNHLTIDSLQYKGFVNKI 178
Cdd:PRK05327 161 RRGVPDWLEVDAEKLEGTFKRL 182
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 1-178 3.09e-70

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: 211.47  E-value: 3.09e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359   1 MSRYRGPRFKKIRRLG-ALPGLTS------KRPRSRSdlQTQLRSGKRSQYRIRLEEKQKLRFHYGLTERQLLKYVHIAG 73
Cdd:COG0522    1 MARYTGPKCKLCRREGvKLFLKGErkcaleRRPYPPG--QHGQRRKKLSDYGLQLREKQKLRRIYGVLEKQFRRYFEEAA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359  74 KAKGSTGQVLLQLLEMRLDNILFRLGMASTIPGARQLVNHRHILVNGRIVDIPSYRCKPRDIITTKDKERSKALIQNHLV 153
Cdd:COG0522   79 RRKGNTGENLLQLLERRLDNVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVKPGDVIEVREKSKKLPRIKEALE 158

                        170       180
                 ....*....|....*....|....*
gi 927091359 154 SSPHGELPNHLTIDSLQYKGFVNKI 178
Cdd:COG0522  159 SAEQRGVPEWLEVDAEKLSGTVVRL 183
rpsD_bact TIGR01017
ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and ...
 3-176 5.35e-63

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: 192.90  E-value: 5.35e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359    3 RYRGPRFKKIRRLGALPGLTSKRP---RSRSDLQTQLRSGKRSQYRIRLEEKQKLRFHYGLTERQLLKYVHIAGKAKGST 79
Cdd:TIGR01017   1 RYTGPKFKLSRRLGVNLFGKSRKLllkRKYPPGQHGQRRKKLSDYGLQLQEKQKLKFMYGITEKQFRKYFKEAKKLKGNT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359   80 GQVLLQLLEMRLDNILFRLGMASTIPGARQLVNHRHILVNGRIVDIPSYRCKPRDIITTKDKERSKALIQNHLVSSPHGE 159
Cdd:TIGR01017  81 GENLLRLLESRLDNVVYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQRN 160

                         170
                  ....*....|....*..
gi 927091359  160 LPNHLTIDSLQYKGFVN 176
Cdd:TIGR01017 161 IPSWLEVDKKTLEGKVL 177
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 3-88 4.27e-19

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: 77.59  E-value: 4.27e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359    3 RYRGPRFKKIRRLGALPGLTS------KRPRSRSDL---QTQLRSG-KRSQYRIRLEEKQKLRFHYGLTERQLLKYVHIA 72
Cdd:pfam00163   1 RYKGPEQKLLRRVGFKLWKKGrchrelKVAQNRREYpkyPGQHGKIrKLSEYLLQLREKQKVRRKYGLLEKQLRKLYDMG 80

                          90
                  ....*....|....*.
gi 927091359   73 GKAKGSTGQVLLQLLE 88
Cdd:pfam00163  81 LKLKGVTGENLLQLLE 96
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 89-148 1.09e-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: 75.75  E-value: 1.09e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359  89 MRLDNILFRLGMASTIPGARQLVNHRHILVNGRIVDIPSYRCKPRDIITTKDKERSKALI 148
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIV 60
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 89-136 4.02e-16

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: 68.29  E-value: 4.02e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 927091359   89 MRLDNILFRLGMASTIPGARQLVNHRHILVNGRIVDIPSYRCKPRDII 136
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
S4 smart00363
S4 RNA-binding domain;
89-144 7.35e-15

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 65.31  E-value: 7.35e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 927091359    89 MRLDNILFRLGMASTIPGARQLVNHRHILVNGRIVDIPSYRCKPRDIITTKDKERS 144
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELK 56
rps4p PRK04051
30S ribosomal protein S4P; Validated
 85-128 6.98e-12

30S ribosomal protein S4P; Validated


Pssm-ID: 179730 [Multi-domain]  Cd Length: 177  Bit Score: 60.65  E-value: 6.98e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 927091359  85 QLLEMRLDNILFRLGMASTIPGARQLVNHRHILVNGRIVDIPSY 128
Cdd:PRK04051  99 DILERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSY 142
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 87-128 1.92e-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: 56.66  E-value: 1.92e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 927091359   87 LEMRLDNILFRLGMASTIPGARQLVNHRHILVNGRIVDIPSY 128
Cdd:TIGR01018 102 LERRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSY 143
PLN00189 PLN00189
40S ribosomal protein S9; Provisional
 85-128 3.59e-08

40S ribosomal protein S9; Provisional


Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 50.90  E-value: 3.59e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 927091359  85 QLLEMRLDNILFRLGMASTIPGARQLVNHRHILVNGRIVDIPSY 128
Cdd:PLN00189 105 NFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSF 148
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 49-128 1.46e-07

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 48.92  E-value: 1.46e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 927091359  49 EEKQKLRFHYGLTERQLLkyvhiagkakgstgqvllqllEMRLDNILFRLGMASTIPGARQLVNHRHILVNGRIVDIPSY 128
Cdd:PTZ00155  88 EDERKLDYVLGLTVEKLL---------------------ERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSF 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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