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Conserved domains on  [gi|1469361728|ref|WP_117698349|]
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MULTISPECIES: 30S ribosomal protein S3 [unclassified Roseburia]

Protein Classification

small ribosomal subunit protein uS3( domain architecture ID 17564983)

small ribosomal subunit protein uS3, also called 30S ribosomal protein S3 in bacteria, forms a complex with S10 and S14; it binds the lower part of the 30S subunit head and the mRNA in the complete ribosome

CATH:  3.30.300.20|3.30.1140.32
Gene Ontology:  GO:0003735|GO:0006412
PubMed:  12900959|24524803
SCOP:  4001203|4001200

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpsC COG0092
Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3 ...
 1-214 3.42e-148

Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3 is part of the Pathway/BioSystem: Ribosome 30S subunit


:

Pssm-ID: 439862 [Multi-domain]  Cd Length: 226  Bit Score: 411.02  E-value: 3.42e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728   1 MGQKVNPHGLRVGVIKDWDSKWYAES-DFADFLVEDYNIRTFLKKKLYAAGVSKIEIERASDRVKVILYTAKPGVVIGKG 79
Cdd:COG0092     1 MGQKVNPIGFRLGIIKDWDSRWYADKkDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728  80 GAEIEKVKAELQKFTDKKLVVDIKEVKRPDKDAQLVAENIALQLENRVSFRRAMKSCMGRCMKAGAKGIKASVSGRLGGA 159
Cdd:COG0092    81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1469361728 160 DMARTEFYSEGTIPLQTLRADIEYGFAEADTTYGKVGVKVWIYKGEVLPTKGNKE 214
Cdd:COG0092   161 EIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEAA 215
 
Name Accession Description Interval E-value
RpsC COG0092
Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3 ...
 1-214 3.42e-148

Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 439862 [Multi-domain]  Cd Length: 226  Bit Score: 411.02  E-value: 3.42e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728   1 MGQKVNPHGLRVGVIKDWDSKWYAES-DFADFLVEDYNIRTFLKKKLYAAGVSKIEIERASDRVKVILYTAKPGVVIGKG 79
Cdd:COG0092     1 MGQKVNPIGFRLGIIKDWDSRWYADKkDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728  80 GAEIEKVKAELQKFTDKKLVVDIKEVKRPDKDAQLVAENIALQLENRVSFRRAMKSCMGRCMKAGAKGIKASVSGRLGGA 159
Cdd:COG0092    81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1469361728 160 DMARTEFYSEGTIPLQTLRADIEYGFAEADTTYGKVGVKVWIYKGEVLPTKGNKE 214
Cdd:COG0092   161 EIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEAA 215
rpsC_bact TIGR01009
ribosomal protein S3, bacterial type; This model describes the bacterial type of ribosomal ...
 1-210 2.03e-118

ribosomal protein S3, bacterial type; This model describes the bacterial type of ribosomal protein S3. Chloroplast and mitochondrial forms have large, variable inserts between conserved N-terminal and C-terminal domains. This model recognizes all bacterial forms and many chloroplast forms above the trusted cutoff score. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 130082 [Multi-domain]  Cd Length: 211  Bit Score: 335.44  E-value: 2.03e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728   1 MGQKVNPHGLRVGVIKDWDSKWYAES-DFADFLVEDYNIRTFLKKKLYAAGVSKIEIERASDRVKVILYTAKPGVVIGKG 79
Cdd:TIGR01009   1 MGQKVNPIGFRLGITKDWKSRWYANPkEYAKLLHEDLKIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728  80 GAEIEKVKAELQKFTDKKLVVDIKEVKRPDKDAQLVAENIALQLENRVSFRRAMKSCMGRCMKAGAKGIKASVSGRLGGA 159
Cdd:TIGR01009  81 GSEIEKLRKDLQKLTGKEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLGGA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1469361728 160 DMARTEFYSEGTIPLQTLRADIEYGFAEADTTYGKVGVKVWIYKGEVLPTK 210
Cdd:TIGR01009 161 EIARTEWYKEGRVPLHTLRADIDYATAEAHTTYGIIGVKVWIFKGEVLGGG 211
rps3 CHL00048
ribosomal protein S3
 1-205 4.20e-82

ribosomal protein S3


Pssm-ID: 214348 [Multi-domain]  Cd Length: 214  Bit Score: 243.58  E-value: 4.20e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728   1 MGQKVNPHGLRVGVIKDWDSKWYAES-DFADFLVEDYNIRTFLK----KKLYAAGVSKIEIERASDRVKVILYTAKPGVV 75
Cdd:CHL00048    1 MGQKINPLGFRLGTTQKHHSLWFAQPkNYSEGLQEDKKIRDCIKnyvqKNIKYEGIARIEIQRKIDLIQVIIYTGFPKLL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728  76 IGKGGAEIEKVKAELQK---FTDKKLVVDIKEVKRPDKDAQLVAENIALQLENRVSFRRAMKSCMGRCMKAGAKGIKASV 152
Cdd:CHL00048   81 IERKGRGIEELQINLQKelnSVNRKLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQI 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1469361728 153 SGRLGGADMARTEFYSEGTIPLQTLRADIEYGFAEADTTYGKVGVKVWIYKGE 205
Cdd:CHL00048  161 SGRLNGAEIARVEWIREGRVPLQTLRAKIDYCSYPARTIYGVLGIKIWIFKDE 213
KH-II_30S_S3 cd02412
type II K-homology (KH) RNA-binding domain found in 30S ribosomal protein S3 and similar ...
 2-108 2.34e-57

type II K-homology (KH) RNA-binding domain found in 30S ribosomal protein S3 and similar proteins; 30S ribosomal protein S3, also called small ribosomal subunit protein uS3, is part of the head region of the 30S ribosomal subunit and binds to the lower part of the 30S subunit head. It may also bind mRNA in the 70S ribosome, positioning it for translation. S3 protein is believed to interact with mRNA as it threads its way from the latch into the channel. Members of this family contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid).


Pssm-ID: 411783  Cd Length: 108  Bit Score: 176.87  E-value: 2.34e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728   2 GQKVNPHGLRVGVIKDWDSKWYAE-SDFADFLVEDYNIRTFLKKKLYAAGVSKIEIERASDRVKVILYTAKPGVVIGKGG 80
Cdd:cd02412     1 GQKVNPLGFRLGITKDWDSRWYADkKDYAKLLLEDLKIRKYIKKKLKKAGISRIEIERKADKIRVTIHTARPGIVIGKKG 80

                          90       100
                  ....*....|....*....|....*...
gi 1469361728  81 AEIEKVKAELQKFTDKKLVVDIKEVKRP 108
Cdd:cd02412    81 AEIEKLRKELEKLTGKKVNINVVEVKKP 108
Ribosomal_S3_C pfam00189
Ribosomal protein S3, C-terminal domain; This family contains a central domain pfam00013, ...
 119-201 1.52e-47

Ribosomal protein S3, C-terminal domain; This family contains a central domain pfam00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer.


Pssm-ID: 425514 [Multi-domain]  Cd Length: 83  Bit Score: 150.98  E-value: 1.52e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728 119 IALQLENRVSFRRAMKSCMGRCMKAGAKGIKASVSGRLGGADMARTEFYSEGTIPLQTLRADIEYGFAEADTTYGKVGVK 198
Cdd:pfam00189   1 IAQQLEKRVSFRRAMKQAIRRAMRAGAKGIKIIISGRLGGAERARSEKYREGRVPLHTLRADIDYAFAEALTKYGVIGVK 80


                  ...
gi 1469361728 199 VWI 201
Cdd:pfam00189  81 VWI 83
KH smart00322
K homology RNA-binding domain;
59-123 2.38e-07

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 46.52  E-value: 2.38e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1469361728   59 ASDRVKVILYTAKPGVVIGKGGAEIEKVKAELQ---KFTDKKLVVDIKEVKRPDKDAQLVAENIALQL 123
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGvkiDIPGPGSEERVVEITGPPENVEKAAELILEIL 68
 
Name Accession Description Interval E-value
RpsC COG0092
Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3 ...
 1-214 3.42e-148

Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 439862 [Multi-domain]  Cd Length: 226  Bit Score: 411.02  E-value: 3.42e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728   1 MGQKVNPHGLRVGVIKDWDSKWYAES-DFADFLVEDYNIRTFLKKKLYAAGVSKIEIERASDRVKVILYTAKPGVVIGKG 79
Cdd:COG0092     1 MGQKVNPIGFRLGIIKDWDSRWYADKkDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728  80 GAEIEKVKAELQKFTDKKLVVDIKEVKRPDKDAQLVAENIALQLENRVSFRRAMKSCMGRCMKAGAKGIKASVSGRLGGA 159
Cdd:COG0092    81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1469361728 160 DMARTEFYSEGTIPLQTLRADIEYGFAEADTTYGKVGVKVWIYKGEVLPTKGNKE 214
Cdd:COG0092   161 EIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEAA 215
rpsC_bact TIGR01009
ribosomal protein S3, bacterial type; This model describes the bacterial type of ribosomal ...
 1-210 2.03e-118

ribosomal protein S3, bacterial type; This model describes the bacterial type of ribosomal protein S3. Chloroplast and mitochondrial forms have large, variable inserts between conserved N-terminal and C-terminal domains. This model recognizes all bacterial forms and many chloroplast forms above the trusted cutoff score. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 130082 [Multi-domain]  Cd Length: 211  Bit Score: 335.44  E-value: 2.03e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728   1 MGQKVNPHGLRVGVIKDWDSKWYAES-DFADFLVEDYNIRTFLKKKLYAAGVSKIEIERASDRVKVILYTAKPGVVIGKG 79
Cdd:TIGR01009   1 MGQKVNPIGFRLGITKDWKSRWYANPkEYAKLLHEDLKIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728  80 GAEIEKVKAELQKFTDKKLVVDIKEVKRPDKDAQLVAENIALQLENRVSFRRAMKSCMGRCMKAGAKGIKASVSGRLGGA 159
Cdd:TIGR01009  81 GSEIEKLRKDLQKLTGKEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLGGA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1469361728 160 DMARTEFYSEGTIPLQTLRADIEYGFAEADTTYGKVGVKVWIYKGEVLPTK 210
Cdd:TIGR01009 161 EIARTEWYKEGRVPLHTLRADIDYATAEAHTTYGIIGVKVWIFKGEVLGGG 211
rps3 CHL00048
ribosomal protein S3
 1-205 4.20e-82

ribosomal protein S3


Pssm-ID: 214348 [Multi-domain]  Cd Length: 214  Bit Score: 243.58  E-value: 4.20e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728   1 MGQKVNPHGLRVGVIKDWDSKWYAES-DFADFLVEDYNIRTFLK----KKLYAAGVSKIEIERASDRVKVILYTAKPGVV 75
Cdd:CHL00048    1 MGQKINPLGFRLGTTQKHHSLWFAQPkNYSEGLQEDKKIRDCIKnyvqKNIKYEGIARIEIQRKIDLIQVIIYTGFPKLL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728  76 IGKGGAEIEKVKAELQK---FTDKKLVVDIKEVKRPDKDAQLVAENIALQLENRVSFRRAMKSCMGRCMKAGAKGIKASV 152
Cdd:CHL00048   81 IERKGRGIEELQINLQKelnSVNRKLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQI 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1469361728 153 SGRLGGADMARTEFYSEGTIPLQTLRADIEYGFAEADTTYGKVGVKVWIYKGE 205
Cdd:CHL00048  161 SGRLNGAEIARVEWIREGRVPLQTLRAKIDYCSYPARTIYGVLGIKIWIFKDE 213
KH-II_30S_S3 cd02412
type II K-homology (KH) RNA-binding domain found in 30S ribosomal protein S3 and similar ...
 2-108 2.34e-57

type II K-homology (KH) RNA-binding domain found in 30S ribosomal protein S3 and similar proteins; 30S ribosomal protein S3, also called small ribosomal subunit protein uS3, is part of the head region of the 30S ribosomal subunit and binds to the lower part of the 30S subunit head. It may also bind mRNA in the 70S ribosome, positioning it for translation. S3 protein is believed to interact with mRNA as it threads its way from the latch into the channel. Members of this family contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid).


Pssm-ID: 411783  Cd Length: 108  Bit Score: 176.87  E-value: 2.34e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728   2 GQKVNPHGLRVGVIKDWDSKWYAE-SDFADFLVEDYNIRTFLKKKLYAAGVSKIEIERASDRVKVILYTAKPGVVIGKGG 80
Cdd:cd02412     1 GQKVNPLGFRLGITKDWDSRWYADkKDYAKLLLEDLKIRKYIKKKLKKAGISRIEIERKADKIRVTIHTARPGIVIGKKG 80

                          90       100
                  ....*....|....*....|....*...
gi 1469361728  81 AEIEKVKAELQKFTDKKLVVDIKEVKRP 108
Cdd:cd02412    81 AEIEKLRKELEKLTGKKVNINVVEVKKP 108
Ribosomal_S3_C pfam00189
Ribosomal protein S3, C-terminal domain; This family contains a central domain pfam00013, ...
 119-201 1.52e-47

Ribosomal protein S3, C-terminal domain; This family contains a central domain pfam00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer.


Pssm-ID: 425514 [Multi-domain]  Cd Length: 83  Bit Score: 150.98  E-value: 1.52e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728 119 IALQLENRVSFRRAMKSCMGRCMKAGAKGIKASVSGRLGGADMARTEFYSEGTIPLQTLRADIEYGFAEADTTYGKVGVK 198
Cdd:pfam00189   1 IAQQLEKRVSFRRAMKQAIRRAMRAGAKGIKIIISGRLGGAERARSEKYREGRVPLHTLRADIDYAFAEALTKYGVIGVK 80


                  ...
gi 1469361728 199 VWI 201
Cdd:pfam00189  81 VWI 83
rps3p PRK04191
30S ribosomal protein S3P; Reviewed
 38-208 5.16e-31

30S ribosomal protein S3P; Reviewed


Pssm-ID: 235247 [Multi-domain]  Cd Length: 207  Bit Score: 112.65  E-value: 5.16e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728  38 IRTFLKKKLYAAGVSKIEIERASDRVKVILYTAKPGVVIGKGGAEIEKVKAELQ-KFTDKKLVVDIKEVKRPDKDAQLVA 116
Cdd:PRK04191   17 IDEYLAKELYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNIRELTEILEkKFGLENPQIDVKEVENPELNARVVA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728 117 ENIALQLENRVSFRRAMKSCMGRCMKAGAKGIKASVSGRLGGAdMARTEFYSEGTI-----PLQTLradIEYGFAEADTT 191
Cdd:PRK04191   97 FRLANALERGWHFRRAAHSAIRRIMEAGALGVEIIISGKLTGE-RARTEKFTEGYIkksgePAEEL---VDRGFAIAKLK 172

                         170
                  ....*....|....*...
gi 1469361728 192 YGKVGVKVWIYKGEV-LP 208
Cdd:PRK04191  173 LGIIGVEVRIMPPDAkLP 190
uS3_euk_arch TIGR01008
ribosomal protein uS3, eukaryotic/archaeal type; This model describes ribosomal protein S3 of ...
 38-208 6.90e-31

ribosomal protein uS3, eukaryotic/archaeal type; This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273393 [Multi-domain]  Cd Length: 195  Bit Score: 112.13  E-value: 6.90e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728  38 IRTFLKKKLYAAGVSKIEIERASDRVKVILYTAKPGVVIGKGGAEIEKVKAELQK-FTDKKLVVDIKEVKRPDKDAQLVA 116
Cdd:TIGR01008  15 IDEFLEKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIRELTEKLQKkFGLENPQIYVEEVENPELNAKVQA 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728 117 ENIALQLENRVSFRRAMKSCMGRCMKAGAKGIKASVSGRLGGAdMARTEFYSEGTI-----PLQTLradIEYGFAEADTT 191
Cdd:TIGR01008  95 ERIARALERGLHFRRAAYAAVRRIMEAGAKGVEVTISGKLTGE-RAKTEKFAAGYLkhsgePAEEL---VDKGFAIALLK 170

                         170
                  ....*....|....*..
gi 1469361728 192 YGKVGVKVWIYKGEVLP 208
Cdd:TIGR01008 171 LGVLGVKVKIMPPDAKL 187
KH_2 pfam07650
KH domain;
38-109 1.09e-19

KH domain;


Pssm-ID: 429574 [Multi-domain]  Cd Length: 78  Bit Score: 79.52  E-value: 1.09e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1469361728  38 IRTFLKKKLYAAGVSKIEIERASDRVKVILYTAKPGVVIGKGGAEIEKVKAELQK----FTDKKLVVDIKEVKRPD 109
Cdd:pfam07650   2 IPYSLAVELKFAGVSKVEIERTPNAVIVVIRASQPGIVIGKGGSRIKKIGKELRKdiekLLGKKVYLNIVKVKKPW 77
PTZ00084 PTZ00084
40S ribosomal protein S3; Provisional
 41-170 1.11e-11

40S ribosomal protein S3; Provisional


Pssm-ID: 240260 [Multi-domain]  Cd Length: 220  Bit Score: 61.60  E-value: 1.11e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728  41 FLKKKLYAAGVSKIEIERASDRVKVILYTAKPGVVIGKGGAEIEKVKAELQK---FTDKKLVVDIKEVKRPDKDAQLVAE 117
Cdd:PTZ00084   24 FLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRIRELTSLLQKrfgFPEGKVELFAERVENRGLCAMAQAE 103

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1469361728 118 NIALQLENRVSFRRAMKSCMGRCMKAGAKGIKASVSGRLgGADMARTEFYSEG 170
Cdd:PTZ00084  104 SLRYKLLEGLPVRRAAYGVLRHVMESGAKGCEVIVSGKL-RAQRAKSMKFRDG 155
KH-II_30S_S3_arch cd02411
type II K-homology (KH) RNA-binding domain found in archaeal 30S ribosomal protein S3 and ...
 38-108 1.48e-11

type II K-homology (KH) RNA-binding domain found in archaeal 30S ribosomal protein S3 and similar proteins; 30S ribosomal protein S3, also called small ribosomal subunit protein uS3, is part of the head region of the 30S ribosomal subunit and binds to the lower part of the 30S subunit head. It is believed to interact with mRNA as it threads its way from the latch into the channel. Members of this family are mainly from archaea and contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid).


Pssm-ID: 411782  Cd Length: 87  Bit Score: 58.37  E-value: 1.48e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1469361728  38 IRTFLKKKLYAAGVSKIEIERASDRVKVILYTAKPGVVIGKGGAEIEKVKAELQKFTDKKLV-VDIKEVKRP 108
Cdd:cd02411    16 IDEYLAKELERAGYGGMELKKTPLGTKVIIYAERPGMVIGRGGRNIRRLTEILEEEFGLENPqIEVKEVENP 87
KH smart00322
K homology RNA-binding domain;
59-123 2.38e-07

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 46.52  E-value: 2.38e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1469361728   59 ASDRVKVILYTAKPGVVIGKGGAEIEKVKAELQ---KFTDKKLVVDIKEVKRPDKDAQLVAENIALQL 123
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGvkiDIPGPGSEERVVEITGPPENVEKAAELILEIL 68
KH-II_SF cd02409
type II K-homology (KH) RNA-binding domain superfamily; The K-homology (KH) domain binds ...
 41-92 2.27e-04

type II K-homology (KH) RNA-binding domain superfamily; The K-homology (KH) domain binds single-stranded RNA or DNA, and is found in a wide variety of proteins including ribosomal proteins, transcription factors, and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but share a single "minimal KH motif" which is folded into a beta-alpha-alpha-beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension while type I KH domains (e.g. hnRNP K) contain a C-terminal extension, connected to the KH motif by variable loops that are different in different KH domains, whether they are type I or type II. KH-II superfamily members contain one or two KH domains, most of which are canonical type II KH domains that have the signature motif GXXG (where X represents any amino acid). The first KH domain found in archaeal cleavage and polyadenylation specificity factors (CPSFs) is a non-canonical type II KH domain that lacks the GXXG motif. Some others have mutated GXXG motifs which may or may not have nucleic acid binding ability.


Pssm-ID: 411780 [Multi-domain]  Cd Length: 67  Bit Score: 38.13  E-value: 2.27e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1469361728  41 FLKKKLYAA-GVSKIEIERASDRVKVILYTAK--PGVVIGKGGAEIEKVKAELQK 92
Cdd:cd02409     3 ILEKLFPAAvTISDVEVEETPDGIRVIIAVEEgdPGIVIGKGGQRIRELRKELGK 57
KH-II_40S_S3 cd02413
type II K-homology (KH) RNA-binding domain found in 40S ribosomal protein S3 and similar ...
 41-107 4.78e-03

type II K-homology (KH) RNA-binding domain found in 40S ribosomal protein S3 and similar proteins; 40S ribosomal protein S3, also called small ribosomal subunit protein uS3, is part of the head region of the 40S ribosomal subunit and is involved in translation. It is believed to interact with mRNA as it threads its way from the latch into the channel. 40S ribosomal protein S3 has endonuclease activity and plays a role in repair of damaged DNA. It cleaves phosphodiester bonds of DNAs containing altered bases with broad specificity and cleaves supercoiled DNA more efficiently than relaxed DNA. Members of this family are mainly from prokaryotes and contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid).


Pssm-ID: 411784  Cd Length: 91  Bit Score: 35.19  E-value: 4.78e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469361728  41 FLKKKLYAAGVSKIEIERASDRVKVILYTAKPGVVIGKGGAEIEKVKAELQK---FTDKKLVVDIKEVKR 107
Cdd:cd02413    20 FLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKrfgFPEGSVELYAEKVAN 89
KH-II_NusA_arch_rpt2 cd22531
second type II K-homology (KH) RNA-binding domain found in archaeal probable transcription ...
 39-87 5.85e-03

second type II K-homology (KH) RNA-binding domain found in archaeal probable transcription termination protein NusA and similar proteins; NusA, also called N utilization substance protein A, is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. It participates in both transcription termination and antitermination. NusA homologs consisting of only the two type II K-homology (KH) domains are widely conserved in archaea. Although their function remains unclear, it has been found that Aeropyrum pernix NusA strongly binds to a certain CU-rich sequence near a termination signal. Archaeal NusA may have retained some functions of bacterial NusA, including ssRNA-binding ability. This model corresponds to the second KH domain of NusA mainly found in archaea.


Pssm-ID: 411788 [Multi-domain]  Cd Length: 67  Bit Score: 34.14  E-value: 5.85e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1469361728  39 RTFLKKKLYAAGVSKIEIERASDRVKVILYTA--KPGVVIGKGGAEIEKVK 87
Cdd:cd22531     2 EEFIKNIFAPAKVQNVKVKEKNGKKVAIVEVPpkDKGIAIGKNGKNIERAK 52
 
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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