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Conserved domains on  [gi|510824614|ref|WP_016197786|]
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30S ribosomal protein S3 [Elizabethkingia meningoseptica]

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 ...
 1-225 1.87e-141

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: 395.23  E-value: 1.87e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614   1 MGQKTNPIGNRLGIIRGWDSNWF-GGNDFGDRIAEDYKIRRYLEARLAKGGISRIYIERTLKLVTVTITTARPGLIIGKG 79
Cdd:COG0092    1 MGQKVNPIGFRLGIIKDWDSRWYaDKKDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614  80 GQEVDKLKEELKKITKKDIQINIFEIKRPELDAILVAESIAKQIENRISYRRAVKMAISSTMRMGAEGIKVQISGRLNGA 159
Cdd:COG0092   81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGA 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 510824614 160 EMARSESFKEGRIPLSTFRADIDYHWAEAHTTYGRLGVKVWIMKGEVYGKRELSPLVGQQQKKGSG 225
Cdd:COG0092  161 EIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEAAAAEAAEGGKPR 226
 
Name Accession Description Interval E-value
RpsC COG0092
Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3 ...
 1-225 1.87e-141

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: 395.23  E-value: 1.87e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614   1 MGQKTNPIGNRLGIIRGWDSNWF-GGNDFGDRIAEDYKIRRYLEARLAKGGISRIYIERTLKLVTVTITTARPGLIIGKG 79
Cdd:COG0092    1 MGQKVNPIGFRLGIIKDWDSRWYaDKKDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614  80 GQEVDKLKEELKKITKKDIQINIFEIKRPELDAILVAESIAKQIENRISYRRAVKMAISSTMRMGAEGIKVQISGRLNGA 159
Cdd:COG0092   81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGA 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 510824614 160 EMARSESFKEGRIPLSTFRADIDYHWAEAHTTYGRLGVKVWIMKGEVYGKRELSPLVGQQQKKGSG 225
Cdd:COG0092  161 EIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEAAAAEAAEGGKPR 226
rpsC_bact TIGR01009
ribosomal protein S3, bacterial type; This model describes the bacterial type of ribosomal ...
 1-210 7.13e-106

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: 304.62  E-value: 7.13e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614    1 MGQKTNPIGNRLGIIRGWDSNWFGGN-DFGDRIAEDYKIRRYLEARLAKGGISRIYIERTLKLVTVTITTARPGLIIGKG 79
Cdd:TIGR01009   1 MGQKVNPIGFRLGITKDWKSRWYANPkEYAKLLHEDLKIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614   80 GQEVDKLKEELKKITKKDIQINIFEIKRPELDAILVAESIAKQIENRISYRRAVKMAISSTMRMGAEGIKVQISGRLNGA 159
Cdd:TIGR01009  81 GSEIEKLRKDLQKLTGKEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLGGA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 510824614  160 EMARSESFKEGRIPLSTFRADIDYHWAEAHTTYGRLGVKVWIMKGEVYGKR 210
Cdd:TIGR01009 161 EIARTEWYKEGRVPLHTLRADIDYATAEAHTTYGIIGVKVWIFKGEVLGGG 211
rps3 CHL00048
ribosomal protein S3
 1-205 1.44e-78

ribosomal protein S3


Pssm-ID: 214348 [Multi-domain]  Cd Length: 214  Bit Score: 235.49  E-value: 1.44e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614   1 MGQKTNPIGNRLGIIRGWDSNWFGG-NDFGDRIAEDYKIRRYLEARLAK----GGISRIYIERTLKLVTVTITTARPGLI 75
Cdd:CHL00048   1 MGQKINPLGFRLGTTQKHHSLWFAQpKNYSEGLQEDKKIRDCIKNYVQKnikyEGIARIEIQRKIDLIQVIIYTGFPKLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614  76 IGKGGQEVDKLKEELKKITKKD---IQINIFEIKRPELDAILVAESIAKQIENRISYRRAVKMAISSTMRMGAEGIKVQI 152
Cdd:CHL00048  81 IERKGRGIEELQINLQKELNSVnrkLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 510824614 153 SGRLNGAEMARSESFKEGRIPLSTFRADIDYHWAEAHTTYGRLGVKVWIMKGE 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 8.67e-49

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: 156.06  E-value: 8.67e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614   2 GQKTNPIGNRLGIIRGWDSNWFG-GNDFGDRIAEDYKIRRYLEARLAKGGISRIYIERTLKLVTVTITTARPGLIIGKGG 80
Cdd:cd02412    1 GQKVNPLGFRLGITKDWDSRWYAdKKDYAKLLLEDLKIRKYIKKKLKKAGISRIEIERKADKIRVTIHTARPGIVIGKKG 80

                         90       100
                 ....*....|....*....|....*...
gi 510824614  81 QEVDKLKEELKKITKKDIQINIFEIKRP 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 4.50e-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: 150.59  E-value: 4.50e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614  119 IAKQIENRISYRRAVKMAISSTMRMGAEGIKVQISGRLNGAEMARSESFKEGRIPLSTFRADIDYHWAEAHTTYGRLGVK 198
Cdd:pfam00189   1 IAQQLEKRVSFRRAMKQAIRRAMRAGAKGIKIIISGRLGGAERARSEKYREGRVPLHTLRADIDYAFAEALTKYGVIGVK 80


                  ...
gi 510824614  199 VWI 201
Cdd:pfam00189  81 VWI 83
KH smart00322
K homology RNA-binding domain;
63-123 4.31e-08

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 48.83  E-value: 4.31e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 510824614    63 VTVTITTARPGLIIGKGGQEVDKLKEELK---KITKKDIQINIFEIKRPELDAILVAESIAKQI 123
Cdd:smart00322   5 IEVLIPADKVGLIIGKGGSTIKKIEEETGvkiDIPGPGSEERVVEITGPPENVEKAAELILEIL 68
 
Name Accession Description Interval E-value
RpsC COG0092
Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3 ...
 1-225 1.87e-141

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: 395.23  E-value: 1.87e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614   1 MGQKTNPIGNRLGIIRGWDSNWF-GGNDFGDRIAEDYKIRRYLEARLAKGGISRIYIERTLKLVTVTITTARPGLIIGKG 79
Cdd:COG0092    1 MGQKVNPIGFRLGIIKDWDSRWYaDKKDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614  80 GQEVDKLKEELKKITKKDIQINIFEIKRPELDAILVAESIAKQIENRISYRRAVKMAISSTMRMGAEGIKVQISGRLNGA 159
Cdd:COG0092   81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGA 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 510824614 160 EMARSESFKEGRIPLSTFRADIDYHWAEAHTTYGRLGVKVWIMKGEVYGKRELSPLVGQQQKKGSG 225
Cdd:COG0092  161 EIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEAAAAEAAEGGKPR 226
rpsC_bact TIGR01009
ribosomal protein S3, bacterial type; This model describes the bacterial type of ribosomal ...
 1-210 7.13e-106

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: 304.62  E-value: 7.13e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614    1 MGQKTNPIGNRLGIIRGWDSNWFGGN-DFGDRIAEDYKIRRYLEARLAKGGISRIYIERTLKLVTVTITTARPGLIIGKG 79
Cdd:TIGR01009   1 MGQKVNPIGFRLGITKDWKSRWYANPkEYAKLLHEDLKIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614   80 GQEVDKLKEELKKITKKDIQINIFEIKRPELDAILVAESIAKQIENRISYRRAVKMAISSTMRMGAEGIKVQISGRLNGA 159
Cdd:TIGR01009  81 GSEIEKLRKDLQKLTGKEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLGGA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 510824614  160 EMARSESFKEGRIPLSTFRADIDYHWAEAHTTYGRLGVKVWIMKGEVYGKR 210
Cdd:TIGR01009 161 EIARTEWYKEGRVPLHTLRADIDYATAEAHTTYGIIGVKVWIFKGEVLGGG 211
rps3 CHL00048
ribosomal protein S3
 1-205 1.44e-78

ribosomal protein S3


Pssm-ID: 214348 [Multi-domain]  Cd Length: 214  Bit Score: 235.49  E-value: 1.44e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614   1 MGQKTNPIGNRLGIIRGWDSNWFGG-NDFGDRIAEDYKIRRYLEARLAK----GGISRIYIERTLKLVTVTITTARPGLI 75
Cdd:CHL00048   1 MGQKINPLGFRLGTTQKHHSLWFAQpKNYSEGLQEDKKIRDCIKNYVQKnikyEGIARIEIQRKIDLIQVIIYTGFPKLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614  76 IGKGGQEVDKLKEELKKITKKD---IQINIFEIKRPELDAILVAESIAKQIENRISYRRAVKMAISSTMRMGAEGIKVQI 152
Cdd:CHL00048  81 IERKGRGIEELQINLQKELNSVnrkLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 510824614 153 SGRLNGAEMARSESFKEGRIPLSTFRADIDYHWAEAHTTYGRLGVKVWIMKGE 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 8.67e-49

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: 156.06  E-value: 8.67e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614   2 GQKTNPIGNRLGIIRGWDSNWFG-GNDFGDRIAEDYKIRRYLEARLAKGGISRIYIERTLKLVTVTITTARPGLIIGKGG 80
Cdd:cd02412    1 GQKVNPLGFRLGITKDWDSRWYAdKKDYAKLLLEDLKIRKYIKKKLKKAGISRIEIERKADKIRVTIHTARPGIVIGKKG 80

                         90       100
                 ....*....|....*....|....*...
gi 510824614  81 QEVDKLKEELKKITKKDIQINIFEIKRP 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 4.50e-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: 150.59  E-value: 4.50e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614  119 IAKQIENRISYRRAVKMAISSTMRMGAEGIKVQISGRLNGAEMARSESFKEGRIPLSTFRADIDYHWAEAHTTYGRLGVK 198
Cdd:pfam00189   1 IAQQLEKRVSFRRAMKQAIRRAMRAGAKGIKIIISGRLGGAERARSEKYREGRVPLHTLRADIDYAFAEALTKYGVIGVK 80


                  ...
gi 510824614  199 VWI 201
Cdd:pfam00189  81 VWI 83
uS3_euk_arch TIGR01008
ribosomal protein uS3, eukaryotic/archaeal type; This model describes ribosomal protein S3 of ...
 37-206 3.88e-28

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: 105.58  E-value: 3.88e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614   37 KIRRYLEARLAKGGISRIYIERTLKLVTVTITTARPGLIIGKGGQEVDKLKEEL-KKITKKDIQINIFEIKRPELDAILV 115
Cdd:TIGR01008  14 LIDEFLEKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIRELTEKLqKKFGLENPQIYVEEVENPELNAKVQ 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614  116 AESIAKQIENRISYRRAVKMAISSTMRMGAEGIKVQISGRLNGaEMARSESFKEGRIPLSTFRAD--IDYHWAEAHTTYG 193
Cdd:TIGR01008  94 AERIARALERGLHFRRAAYAAVRRIMEAGAKGVEVTISGKLTG-ERAKTEKFAAGYLKHSGEPAEelVDKGFAIALLKLG 172

                         170
                  ....*....|...
gi 510824614  194 RLGVKVWIMKGEV 206
Cdd:TIGR01008 173 VLGVKVKIMPPDA 185
rps3p PRK04191
30S ribosomal protein S3P; Reviewed
 37-206 8.71e-26

30S ribosomal protein S3P; Reviewed


Pssm-ID: 235247 [Multi-domain]  Cd Length: 207  Bit Score: 99.94  E-value: 8.71e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614  37 KIRRYLEARLAKGGISRIYIERTLKLVTVTITTARPGLIIGKGGQEVDKLKEELKKITK-KDIQINIFEIKRPELDAILV 115
Cdd:PRK04191  16 MIDEYLAKELYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNIRELTEILEKKFGlENPQIDVKEVENPELNARVV 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614 116 AESIAKQIENRISYRRAVKMAISSTMRMGAEGIKVQISGRLNGaEMARSESFKEGRIPLSTFRAD--IDYHWAEAHTTYG 193
Cdd:PRK04191  96 AFRLANALERGWHFRRAAHSAIRRIMEAGALGVEIIISGKLTG-ERARTEKFTEGYIKKSGEPAEelVDRGFAIAKLKLG 174

                        170
                 ....*....|...
gi 510824614 194 RLGVKVWIMKGEV 206
Cdd:PRK04191 175 IIGVEVRIMPPDA 187
KH_2 pfam07650
KH domain;
37-110 3.50e-17

KH domain;


Pssm-ID: 429574 [Multi-domain]  Cd Length: 78  Bit Score: 73.36  E-value: 3.50e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 510824614   37 KIRRYLEARLAKGGISRIYIERTLKLVTVTITTARPGLIIGKGGQEVDKLKEELKKIT----KKDIQINIFEIKRPEL 110
Cdd:pfam07650   1 EIPYSLAVELKFAGVSKVEIERTPNAVIVVIRASQPGIVIGKGGSRIKKIGKELRKDIekllGKKVYLNIVKVKKPWL 78
PTZ00084 PTZ00084
40S ribosomal protein S3; Provisional
 41-202 6.63e-09

40S ribosomal protein S3; Provisional


Pssm-ID: 240260 [Multi-domain]  Cd Length: 220  Bit Score: 54.28  E-value: 6.63e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614  41 YLEARLAKGGISRIYIERTLKLVTVTITTARPGLIIGKGGQEVDKLKEELKK---ITKKDIQINIFEIKRPELDAILVAE 117
Cdd:PTZ00084  24 FLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRIRELTSLLQKrfgFPEGKVELFAERVENRGLCAMAQAE 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 510824614 118 SIAKQIENRISYRRAVKMAISSTMRMGAEGIKVQISGRLnGAEMARSESFKEGRIpLST---FRADIDYHWAEAHTTYGR 194
Cdd:PTZ00084 104 SLRYKLLEGLPVRRAAYGVLRHVMESGAKGCEVIVSGKL-RAQRAKSMKFRDGYM-ISTgqpKKDFVDSAVRHVLMRQGV 181


                 ....*...
gi 510824614 195 LGVKVWIM 202
Cdd:PTZ00084 182 IGVKVKIM 189
KH smart00322
K homology RNA-binding domain;
63-123 4.31e-08

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 48.83  E-value: 4.31e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 510824614    63 VTVTITTARPGLIIGKGGQEVDKLKEELK---KITKKDIQINIFEIKRPELDAILVAESIAKQI 123
Cdd:smart00322   5 IEVLIPADKVGLIIGKGGSTIKKIEEETGvkiDIPGPGSEERVVEITGPPENVEKAAELILEIL 68
KH-II_30S_S3_arch cd02411
type II K-homology (KH) RNA-binding domain found in archaeal 30S ribosomal protein S3 and ...
 37-108 4.86e-07

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: 46.43  E-value: 4.86e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 510824614  37 KIRRYLEARLAKGGISRIYIERTLKLVTVTITTARPGLIIGKGGQEVDKLKEELKKITK-KDIQINIFEIKRP 108
Cdd:cd02411   15 KIDEYLAKELERAGYGGMELKKTPLGTKVIIYAERPGMVIGRGGRNIRRLTEILEEEFGlENPQIEVKEVENP 87
KH-II_SF cd02409
type II K-homology (KH) RNA-binding domain superfamily; The K-homology (KH) domain binds ...
 50-103 3.92e-03

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: 35.04  E-value: 3.92e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 510824614  50 GISRIYIERTLKLVTVTITTAR--PGLIIGKGGQEVDKLKEELKKITKKdIQINIF 103
Cdd:cd02409   13 TISDVEVEETPDGIRVIIAVEEgdPGIVIGKGGQRIRELRKELGKLGGG-VEIDVV 67
 
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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