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Conserved domains on  [gi|2131286305|gb|UEN69385|]
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ribosomal protein small subunit 4, partial (chloroplast) [Hypodematium crenatum subsp. mehrae]

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
 1-189 5.86e-103

ribosomal protein S4; Reviewed


:

Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 294.43  E-value: 5.86e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305   1 LPGFTGKgkTPNLGEFRvaTDQSASRKISQFCVRLEAKQRLRFNYGLTER*LLKYVRIARKTRGSTGQVPLQLLEMRLDN 80
Cdd:CHL00113   18 LPGLTSK--TPRPGSDL--RNQSRSGKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTGQVLLQLLEMRLDN 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305  81 VIFHLGMASTIPAARQLVNHRHILVNNRIVDIPSYRCKPRDFINVRNRPTSHNALKG--KSPVGDKTPSHLTVSLSEGNr 158
Cdd:CHL00113   94 ILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNnlESSPREELPNHLTLDKLQYK- 172

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2131286305 159 paGLVNRIANRESVNLNINELLVVEYYSRKA 189
Cdd:CHL00113  173 --GLVNQIIDRKWVGLKINELLVVEYYSRQT 201
 
Name Accession Description Interval E-value
rps4 CHL00113
ribosomal protein S4; Reviewed
 1-189 5.86e-103

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 294.43  E-value: 5.86e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305   1 LPGFTGKgkTPNLGEFRvaTDQSASRKISQFCVRLEAKQRLRFNYGLTER*LLKYVRIARKTRGSTGQVPLQLLEMRLDN 80
Cdd:CHL00113   18 LPGLTSK--TPRPGSDL--RNQSRSGKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTGQVLLQLLEMRLDN 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305  81 VIFHLGMASTIPAARQLVNHRHILVNNRIVDIPSYRCKPRDFINVRNRPTSHNALKG--KSPVGDKTPSHLTVSLSEGNr 158
Cdd:CHL00113   94 ILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNnlESSPREELPNHLTLDKLQYK- 172

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2131286305 159 paGLVNRIANRESVNLNINELLVVEYYSRKA 189
Cdd:CHL00113  173 --GLVNQIIDRKWVGLKINELLVVEYYSRQT 201
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 26-187 3.47e-63

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: 193.75  E-value: 3.47e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305  26 RKISQFCVRLEAKQRLRFNYGLTER*LLKYVRIARKTRGSTGQVPLQLLEMRLDNVIFHLGMASTIPAARQLVNHRHILV 105
Cdd:COG0522    44 KKLSDYGLQLREKQKLRRIYGVLEKQFRRYFEEAARRKGNTGENLLQLLERRLDNVVYRLGFAPTRAQARQLVSHGHILV 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305 106 NNRIVDIPSYRCKPRDFINVRNRPTSHNALKG--KSPVGDKTPSHLTVslsEGNRPAGLVNRIANRESVNLNINELLVVE 183
Cdd:COG0522   124 NGKKVNIPSYQVKPGDVIEVREKSKKLPRIKEalESAEQRGVPEWLEV---DAEKLSGTVVRLPEREEIPVPINEQLIVE 200


                  ....
gi 2131286305 184 YYSR 187
Cdd:COG0522   201 LYSR 204
rpsD_bact TIGR01017
ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and ...
 22-187 5.50e-54

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: 170.56  E-value: 5.50e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305  22 QSASRKISQFCVRLEAKQRLRFNYGLTER*LLKYVRIARKTRGSTGQVPLQLLEMRLDNVIFHLGMASTIPAARQLVNHR 101
Cdd:TIGR01017  36 GQRRKKLSDYGLQLQEKQKLKFMYGITEKQFRKYFKEAKKLKGNTGENLLRLLESRLDNVVYRLGFAPTRFAARQLVSHG 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305 102 HILVNNRIVDIPSYRCKPRDFINVRNRPTSHNALKGKSPVGDK--TPSHLTVslsEGNRPAGLVNRIANRESVNLNINEL 179
Cdd:TIGR01017 116 HILVNGKKVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQrnIPSWLEV---DKKTLEGKVLRVPERSQLPLPINES 192


                  ....*...
gi 2131286305 180 LVVEYYSR 187
Cdd:TIGR01017 193 LVVEYYSR 200
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 76-138 6.12e-17

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: 71.51  E-value: 6.12e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2131286305  76 MRLDNVIFHLGMASTIPAARQLVNHRHILVNNRIVDIPSYRCKPRDFINVRNRPTSHNALKGK 138
Cdd:cd00165     1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYED 63
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 76-123 7.88e-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: 65.21  E-value: 7.88e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2131286305  76 MRLDNVIFHLGMASTIPAARQLVNHRHILVNNRIVDIPSYRCKPRDFI 123
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
S4 smart00363
S4 RNA-binding domain;
76-126 3.14e-12

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 58.76  E-value: 3.14e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2131286305   76 MRLDNVIFHLGMASTIPAARQLVNHRHILVNNRIVDIPSYRCKPRDFINVR 126
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVR 51
 
Name Accession Description Interval E-value
rps4 CHL00113
ribosomal protein S4; Reviewed
 1-189 5.86e-103

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 294.43  E-value: 5.86e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305   1 LPGFTGKgkTPNLGEFRvaTDQSASRKISQFCVRLEAKQRLRFNYGLTER*LLKYVRIARKTRGSTGQVPLQLLEMRLDN 80
Cdd:CHL00113   18 LPGLTSK--TPRPGSDL--RNQSRSGKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTGQVLLQLLEMRLDN 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305  81 VIFHLGMASTIPAARQLVNHRHILVNNRIVDIPSYRCKPRDFINVRNRPTSHNALKG--KSPVGDKTPSHLTVSLSEGNr 158
Cdd:CHL00113   94 ILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNnlESSPREELPNHLTLDKLQYK- 172

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2131286305 159 paGLVNRIANRESVNLNINELLVVEYYSRKA 189
Cdd:CHL00113  173 --GLVNQIIDRKWVGLKINELLVVEYYSRQT 201
rpsD PRK05327
30S ribosomal protein S4; Validated
 22-187 9.61e-64

30S ribosomal protein S4; Validated


Pssm-ID: 235411 [Multi-domain]  Cd Length: 203  Bit Score: 195.32  E-value: 9.61e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305  22 QSASRKISQFCVRLEAKQRLRFNYGLTER*LLKYVRIARKTRGSTGQVPLQLLEMRLDNVIFHLGMASTIPAARQLVNHR 101
Cdd:PRK05327   39 RRRKPKLSDYGLQLREKQKLRRIYGVLEKQFRRYFKEAARRKGNTGENLLQLLESRLDNVVYRLGFAPTRRQARQLVSHG 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305 102 HILVNNRIVDIPSYRCKPRDFINVRNRPTSHNALKG--KSPVGDKTPSHLTVSLSEGNrpaGLVNRIANRESVNLNINEL 179
Cdd:PRK05327  119 HILVNGKKVNIPSYRVKPGDVIEVREKSKKLPRIKEalELAERRGVPDWLEVDAEKLE---GTFKRLPEREEIPVPINEQ 195


                  ....*...
gi 2131286305 180 LVVEYYSR 187
Cdd:PRK05327  196 LIVELYSK 203
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 26-187 3.47e-63

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: 193.75  E-value: 3.47e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305  26 RKISQFCVRLEAKQRLRFNYGLTER*LLKYVRIARKTRGSTGQVPLQLLEMRLDNVIFHLGMASTIPAARQLVNHRHILV 105
Cdd:COG0522    44 KKLSDYGLQLREKQKLRRIYGVLEKQFRRYFEEAARRKGNTGENLLQLLERRLDNVVYRLGFAPTRAQARQLVSHGHILV 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305 106 NNRIVDIPSYRCKPRDFINVRNRPTSHNALKG--KSPVGDKTPSHLTVslsEGNRPAGLVNRIANRESVNLNINELLVVE 183
Cdd:COG0522   124 NGKKVNIPSYQVKPGDVIEVREKSKKLPRIKEalESAEQRGVPEWLEV---DAEKLSGTVVRLPEREEIPVPINEQLIVE 200


                  ....
gi 2131286305 184 YYSR 187
Cdd:COG0522   201 LYSR 204
rpsD_bact TIGR01017
ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and ...
 22-187 5.50e-54

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: 170.56  E-value: 5.50e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305  22 QSASRKISQFCVRLEAKQRLRFNYGLTER*LLKYVRIARKTRGSTGQVPLQLLEMRLDNVIFHLGMASTIPAARQLVNHR 101
Cdd:TIGR01017  36 GQRRKKLSDYGLQLQEKQKLKFMYGITEKQFRKYFKEAKKLKGNTGENLLRLLESRLDNVVYRLGFAPTRFAARQLVSHG 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305 102 HILVNNRIVDIPSYRCKPRDFINVRNRPTSHNALKGKSPVGDK--TPSHLTVslsEGNRPAGLVNRIANRESVNLNINEL 179
Cdd:TIGR01017 116 HILVNGKKVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQrnIPSWLEV---DKKTLEGKVLRVPERSQLPLPINES 192


                  ....*...
gi 2131286305 180 LVVEYYSR 187
Cdd:TIGR01017 193 LVVEYYSR 200
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 76-138 6.12e-17

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: 71.51  E-value: 6.12e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2131286305  76 MRLDNVIFHLGMASTIPAARQLVNHRHILVNNRIVDIPSYRCKPRDFINVRNRPTSHNALKGK 138
Cdd:cd00165     1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYED 63
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 76-123 7.88e-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: 65.21  E-value: 7.88e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2131286305  76 MRLDNVIFHLGMASTIPAARQLVNHRHILVNNRIVDIPSYRCKPRDFI 123
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
S4 smart00363
S4 RNA-binding domain;
76-126 3.14e-12

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 58.76  E-value: 3.14e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2131286305   76 MRLDNVIFHLGMASTIPAARQLVNHRHILVNNRIVDIPSYRCKPRDFINVR 126
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVR 51
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 26-75 5.71e-12

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: 59.10  E-value: 5.71e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2131286305  26 RKISQFCVRLEAKQRLRFNYGLTER*LLKYVRIARKTRGSTGQVPLQLLE 75
Cdd:pfam00163  47 RKLSEYLLQLREKQKVRRKYGLLEKQLRKLYDMGLKLKGVTGENLLQLLE 96
rps4p PRK04051
30S ribosomal protein S4P; Validated
 34-115 3.92e-10

30S ribosomal protein S4P; Validated


Pssm-ID: 179730 [Multi-domain]  Cd Length: 177  Bit Score: 56.03  E-value: 3.92e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305  34 RLEAKQRLRFNYGL--------TER*LLKYVRIARKTRGSTGQV----------------------PL---------QLL 74
Cdd:PRK04051   22 RIAEERELLGKYGLrnkrelwkAQSILRKYRRQARSLLALPPEErakeeeqllgklkrygilkenaTLddvlsltveDIL 101

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2131286305  75 EMRLDNVIFHLGMASTIPAARQLVNHRHILVNNRIVDIPSY 115
Cdd:PRK04051  102 ERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSY 142
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 74-115 8.49e-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: 8.49e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2131286305  74 LEMRLDNVIFHLGMASTIPAARQLVNHRHILVNNRIVDIPSY 115
Cdd:TIGR01018 102 LERRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSY 143
PLN00189 PLN00189
40S ribosomal protein S9; Provisional
 72-124 3.54e-09

40S ribosomal protein S9; Provisional


Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 53.99  E-value: 3.54e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2131286305  72 QLLEMRLDNVIFHLGMASTIPAARQLVNHRHILVNNRIVDIPSY--RCKPRDFIN 124
Cdd:PLN00189  105 NFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFmvRVDSQKHID 159
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 73-171 5.04e-09

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 53.16  E-value: 5.04e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2131286305  73 LLEMRLDNVIFHLGMASTIPAARQLVNHRHILVNNRIVDIPSYRckprdfinVRNRPTSHNALKGKSPVGdktpshltvs 152
Cdd:PTZ00155  104 LLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFL--------VRVDSEKHIDFADTSPFG---------- 165

                          90
                  ....*....|....*....
gi 2131286305 153 lseGNRPaGLVNRIANRES 171
Cdd:PTZ00155  166 ---NGRP-GRVKRKAAKAA 180
 
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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