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Conserved domains on  [gi|491683223|ref|WP_005539361|]
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30S ribosomal protein S3 [Aggregatibacter actinomycetemcomitans]

Protein Classification

30S ribosomal protein S3( domain architecture ID 11490079)

30S ribosomal protein S3 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 ...
 1-226 1.64e-157

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: 435.29  E-value: 1.64e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223   1 MGQKVHPHGIRLGIVKPWSSTWFANTQDFADNLEGDFKVRKFLNKELANASVSRITIERPAKSIRVTIHTARPGIVIGKK 80
Cdd:COG0092    1 MGQKVNPIGFRLGIIKDWDSRWYADKKDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223  81 GEDVEKLRNAVAKIAGVPAQINIAEVKKPELDAKLVADSIASQLERRVMFRRAMKKAVQNAMRLGAKGIKVEVSGRLGGA 160
Cdd:COG0092   81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGA 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 491683223 161 EIARSEWYREGRVPLHTLRADIDYNTAEAHTTYGVIGVKVWIFKGEILGGMAALTQPEQQPADKPK 226
Cdd:COG0092  161 EIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEAAAAEAAEGGKPR 226
 
Name Accession Description Interval E-value
RpsC COG0092
Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3 ...
 1-226 1.64e-157

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: 435.29  E-value: 1.64e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223   1 MGQKVHPHGIRLGIVKPWSSTWFANTQDFADNLEGDFKVRKFLNKELANASVSRITIERPAKSIRVTIHTARPGIVIGKK 80
Cdd:COG0092    1 MGQKVNPIGFRLGIIKDWDSRWYADKKDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223  81 GEDVEKLRNAVAKIAGVPAQINIAEVKKPELDAKLVADSIASQLERRVMFRRAMKKAVQNAMRLGAKGIKVEVSGRLGGA 160
Cdd:COG0092   81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGA 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 491683223 161 EIARSEWYREGRVPLHTLRADIDYNTAEAHTTYGVIGVKVWIFKGEILGGMAALTQPEQQPADKPK 226
Cdd:COG0092  161 EIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEAAAAEAAEGGKPR 226
rpsC_bact TIGR01009
ribosomal protein S3, bacterial type; This model describes the bacterial type of ribosomal ...
 1-211 2.48e-137

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: 383.98  E-value: 2.48e-137
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223    1 MGQKVHPHGIRLGIVKPWSSTWFANTQDFADNLEGDFKVRKFLNKELANASVSRITIERPAKSIRVTIHTARPGIVIGKK 80
Cdd:TIGR01009   1 MGQKVNPIGFRLGITKDWKSRWYANPKEYAKLLHEDLKIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223   81 GEDVEKLRNAVAKIAGVPAQINIAEVKKPELDAKLVADSIASQLERRVMFRRAMKKAVQNAMRLGAKGIKVEVSGRLGGA 160
Cdd:TIGR01009  81 GSEIEKLRKDLQKLTGKEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLGGA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 491683223  161 EIARSEWYREGRVPLHTLRADIDYNTAEAHTTYGVIGVKVWIFKGEILGGM 211
Cdd:TIGR01009 161 EIARTEWYKEGRVPLHTLRADIDYATAEAHTTYGIIGVKVWIFKGEVLGGG 211
rps3 CHL00048
ribosomal protein S3
 1-207 4.43e-96

ribosomal protein S3


Pssm-ID: 214348 [Multi-domain]  Cd Length: 214  Bit Score: 279.40  E-value: 4.43e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223   1 MGQKVHPHGIRLGIVKPWSSTWFANTQDFADNLEGDFKVRKFLN----KELANASVSRITIERPAKSIRVTIHTARPGIV 76
Cdd:CHL00048   1 MGQKINPLGFRLGTTQKHHSLWFAQPKNYSEGLQEDKKIRDCIKnyvqKNIKYEGIARIEIQRKIDLIQVIIYTGFPKLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223  77 IGKKGEDVEKLRNAVAKIAG-VPAQINIA--EVKKPELDAKLVADSIASQLERRVMFRRAMKKAVQNAMRLGAKGIKVEV 153
Cdd:CHL00048  81 IERKGRGIEELQINLQKELNsVNRKLNINitEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 491683223 154 SGRLGGAEIARSEWYREGRVPLHTLRADIDYNTAEAHTTYGVIGVKVWIFKGEI 207
Cdd:CHL00048 161 SGRLNGAEIARVEWIREGRVPLQTLRAKIDYCSYPARTIYGVLGIKIWIFKDEE 214
Ribosomal_S3_C pfam00189
Ribosomal protein S3, C-terminal domain; This family contains a central domain pfam00013, ...
 120-202 3.14e-54

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: 168.70  E-value: 3.14e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223  120 IASQLERRVMFRRAMKKAVQNAMRLGAKGIKVEVSGRLGGAEIARSEWYREGRVPLHTLRADIDYNTAEAHTTYGVIGVK 199
Cdd:pfam00189   1 IAQQLEKRVSFRRAMKQAIRRAMRAGAKGIKIIISGRLGGAERARSEKYREGRVPLHTLRADIDYAFAEALTKYGVIGVK 80


                  ...
gi 491683223  200 VWI 202
Cdd:pfam00189  81 VWI 83
KH-II_30S_S3 cd02412
type II K-homology (KH) RNA-binding domain found in 30S ribosomal protein S3 and similar ...
 2-109 1.71e-53

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: 167.62  E-value: 1.71e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223   2 GQKVHPHGIRLGIVKPWSSTWFANTQDFADNLEGDFKVRKFLNKELANASVSRITIERPAKSIRVTIHTARPGIVIGKKG 81
Cdd:cd02412    1 GQKVNPLGFRLGITKDWDSRWYADKKDYAKLLLEDLKIRKYIKKKLKKAGISRIEIERKADKIRVTIHTARPGIVIGKKG 80

                         90       100
                 ....*....|....*....|....*...
gi 491683223  82 EDVEKLRNAVAKIAGVPAQINIAEVKKP 109
Cdd:cd02412   81 AEIEKLRKELEKLTGKKVNINVVEVKKP 108
KH smart00322
K homology RNA-binding domain;
62-124 3.23e-07

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 46.52  E-value: 3.23e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 491683223    62 KSIRVTIHTARPGIVIGKKGEDVEKLR---NAVAKIAGVPAQINIAEVKKPELDAKLVADSIASQL 124
Cdd:smart00322   3 VTIEVLIPADKVGLIIGKGGSTIKKIEeetGVKIDIPGPGSEERVVEITGPPENVEKAAELILEIL 68
 
Name Accession Description Interval E-value
RpsC COG0092
Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3 ...
 1-226 1.64e-157

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: 435.29  E-value: 1.64e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223   1 MGQKVHPHGIRLGIVKPWSSTWFANTQDFADNLEGDFKVRKFLNKELANASVSRITIERPAKSIRVTIHTARPGIVIGKK 80
Cdd:COG0092    1 MGQKVNPIGFRLGIIKDWDSRWYADKKDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223  81 GEDVEKLRNAVAKIAGVPAQINIAEVKKPELDAKLVADSIASQLERRVMFRRAMKKAVQNAMRLGAKGIKVEVSGRLGGA 160
Cdd:COG0092   81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGA 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 491683223 161 EIARSEWYREGRVPLHTLRADIDYNTAEAHTTYGVIGVKVWIFKGEILGGMAALTQPEQQPADKPK 226
Cdd:COG0092  161 EIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEAAAAEAAEGGKPR 226
rpsC_bact TIGR01009
ribosomal protein S3, bacterial type; This model describes the bacterial type of ribosomal ...
 1-211 2.48e-137

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: 383.98  E-value: 2.48e-137
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223    1 MGQKVHPHGIRLGIVKPWSSTWFANTQDFADNLEGDFKVRKFLNKELANASVSRITIERPAKSIRVTIHTARPGIVIGKK 80
Cdd:TIGR01009   1 MGQKVNPIGFRLGITKDWKSRWYANPKEYAKLLHEDLKIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223   81 GEDVEKLRNAVAKIAGVPAQINIAEVKKPELDAKLVADSIASQLERRVMFRRAMKKAVQNAMRLGAKGIKVEVSGRLGGA 160
Cdd:TIGR01009  81 GSEIEKLRKDLQKLTGKEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLGGA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 491683223  161 EIARSEWYREGRVPLHTLRADIDYNTAEAHTTYGVIGVKVWIFKGEILGGM 211
Cdd:TIGR01009 161 EIARTEWYKEGRVPLHTLRADIDYATAEAHTTYGIIGVKVWIFKGEVLGGG 211
rps3 CHL00048
ribosomal protein S3
 1-207 4.43e-96

ribosomal protein S3


Pssm-ID: 214348 [Multi-domain]  Cd Length: 214  Bit Score: 279.40  E-value: 4.43e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223   1 MGQKVHPHGIRLGIVKPWSSTWFANTQDFADNLEGDFKVRKFLN----KELANASVSRITIERPAKSIRVTIHTARPGIV 76
Cdd:CHL00048   1 MGQKINPLGFRLGTTQKHHSLWFAQPKNYSEGLQEDKKIRDCIKnyvqKNIKYEGIARIEIQRKIDLIQVIIYTGFPKLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223  77 IGKKGEDVEKLRNAVAKIAG-VPAQINIA--EVKKPELDAKLVADSIASQLERRVMFRRAMKKAVQNAMRLGAKGIKVEV 153
Cdd:CHL00048  81 IERKGRGIEELQINLQKELNsVNRKLNINitEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 491683223 154 SGRLGGAEIARSEWYREGRVPLHTLRADIDYNTAEAHTTYGVIGVKVWIFKGEI 207
Cdd:CHL00048 161 SGRLNGAEIARVEWIREGRVPLQTLRAKIDYCSYPARTIYGVLGIKIWIFKDEE 214
Ribosomal_S3_C pfam00189
Ribosomal protein S3, C-terminal domain; This family contains a central domain pfam00013, ...
 120-202 3.14e-54

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: 168.70  E-value: 3.14e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223  120 IASQLERRVMFRRAMKKAVQNAMRLGAKGIKVEVSGRLGGAEIARSEWYREGRVPLHTLRADIDYNTAEAHTTYGVIGVK 199
Cdd:pfam00189   1 IAQQLEKRVSFRRAMKQAIRRAMRAGAKGIKIIISGRLGGAERARSEKYREGRVPLHTLRADIDYAFAEALTKYGVIGVK 80


                  ...
gi 491683223  200 VWI 202
Cdd:pfam00189  81 VWI 83
KH-II_30S_S3 cd02412
type II K-homology (KH) RNA-binding domain found in 30S ribosomal protein S3 and similar ...
 2-109 1.71e-53

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: 167.62  E-value: 1.71e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223   2 GQKVHPHGIRLGIVKPWSSTWFANTQDFADNLEGDFKVRKFLNKELANASVSRITIERPAKSIRVTIHTARPGIVIGKKG 81
Cdd:cd02412    1 GQKVNPLGFRLGITKDWDSRWYADKKDYAKLLLEDLKIRKYIKKKLKKAGISRIEIERKADKIRVTIHTARPGIVIGKKG 80

                         90       100
                 ....*....|....*....|....*...
gi 491683223  82 EDVEKLRNAVAKIAGVPAQINIAEVKKP 109
Cdd:cd02412   81 AEIEKLRKELEKLTGKKVNINVVEVKKP 108
rps3p PRK04191
30S ribosomal protein S3P; Reviewed
 38-204 1.22e-30

30S ribosomal protein S3P; Reviewed


Pssm-ID: 235247 [Multi-domain]  Cd Length: 207  Bit Score: 112.27  E-value: 1.22e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223  38 KVRKFLNKELANASVSRITIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRNAVAKIAGVP-AQINIAEVKKPELDAKLV 116
Cdd:PRK04191  16 MIDEYLAKELYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNIRELTEILEKKFGLEnPQIDVKEVENPELNARVV 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223 117 ADSIASQLERRVMFRRAMKKAVQNAMRLGAKGIKVEVSGRLGGaEIARSEWYREGRV-----PLHTLradIDYNTAEAHT 191
Cdd:PRK04191  96 AFRLANALERGWHFRRAAHSAIRRIMEAGALGVEIIISGKLTG-ERARTEKFTEGYIkksgePAEEL---VDRGFAIAKL 171

                        170
                 ....*....|...
gi 491683223 192 TYGVIGVKVWIFK 204
Cdd:PRK04191 172 KLGIIGVEVRIMP 184
uS3_euk_arch TIGR01008
ribosomal protein uS3, eukaryotic/archaeal type; This model describes ribosomal protein S3 of ...
 38-204 1.95e-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: 106.35  E-value: 1.95e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223   38 KVRKFLNKELANASVSRITIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRNAVAKIAGVP-AQINIAEVKKPELDAKLV 116
Cdd:TIGR01008  14 LIDEFLEKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIRELTEKLQKKFGLEnPQIYVEEVENPELNAKVQ 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223  117 ADSIASQLERRVMFRRAMKKAVQNAMRLGAKGIKVEVSGRLGGAEiARSEWYREGRV-----PLHTLradIDYNTAEAHT 191
Cdd:TIGR01008  94 AERIARALERGLHFRRAAYAAVRRIMEAGAKGVEVTISGKLTGER-AKTEKFAAGYLkhsgePAEEL---VDKGFAIALL 169

                         170
                  ....*....|...
gi 491683223  192 TYGVIGVKVWIFK 204
Cdd:TIGR01008 170 KLGVLGVKVKIMP 182
KH_2 pfam07650
KH domain;
38-111 1.99e-20

KH domain;


Pssm-ID: 429574 [Multi-domain]  Cd Length: 78  Bit Score: 81.83  E-value: 1.99e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491683223   38 KVRKFLNKELANASVSRITIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRNAVAK----IAGVPAQINIAEVKKPEL 111
Cdd:pfam07650   1 EIPYSLAVELKFAGVSKVEIERTPNAVIVVIRASQPGIVIGKGGSRIKKIGKELRKdiekLLGKKVYLNIVKVKKPWL 78
PTZ00084 PTZ00084
40S ribosomal protein S3; Provisional
 42-202 1.04e-12

40S ribosomal protein S3; Provisional


Pssm-ID: 240260 [Multi-domain]  Cd Length: 220  Bit Score: 65.07  E-value: 1.04e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223  42 FLNKELANASVSRITIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRNAVAKIAGVPA---QINIAEVKKPELDAKLVAD 118
Cdd:PTZ00084  24 FLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRIRELTSLLQKRFGFPEgkvELFAERVENRGLCAMAQAE 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491683223 119 SIASQLERRVMFRRAMKKAVQNAMRLGAKGIKVEVSGRLgGAEIARSEWYREGRV--PLHTLRADIDYNTAEAHTTYGVI 196
Cdd:PTZ00084 104 SLRYKLLEGLPVRRAAYGVLRHVMESGAKGCEVIVSGKL-RAQRAKSMKFRDGYMisTGQPKKDFVDSAVRHVLMRQGVI 182


                 ....*.
gi 491683223 197 GVKVWI 202
Cdd:PTZ00084 183 GVKVKI 188
KH-II_30S_S3_arch cd02411
type II K-homology (KH) RNA-binding domain found in archaeal 30S ribosomal protein S3 and ...
 38-109 4.93e-10

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: 54.52  E-value: 4.93e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491683223  38 KVRKFLNKELANASVSRITIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRNAVAKIAGVP-AQINIAEVKKP 109
Cdd:cd02411   15 KIDEYLAKELERAGYGGMELKKTPLGTKVIIYAERPGMVIGRGGRNIRRLTEILEEEFGLEnPQIEVKEVENP 87
KH smart00322
K homology RNA-binding domain;
62-124 3.23e-07

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 46.52  E-value: 3.23e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 491683223    62 KSIRVTIHTARPGIVIGKKGEDVEKLR---NAVAKIAGVPAQINIAEVKKPELDAKLVADSIASQL 124
Cdd:smart00322   3 VTIEVLIPADKVGLIIGKGGSTIKKIEeetGVKIDIPGPGSEERVVEITGPPENVEKAAELILEIL 68
KH-II_SF cd02409
type II K-homology (KH) RNA-binding domain superfamily; The K-homology (KH) domain binds ...
 40-103 2.62e-06

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: 43.90  E-value: 2.62e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 491683223  40 RKFLNKELANAS-VSRITIERPAKSIRVTIHTAR--PGIVIGKKGEDVEKLRNAVAKIaGVPAQINI 103
Cdd:cd02409    1 AEILEKLFPAAVtISDVEVEETPDGIRVIIAVEEgdPGIVIGKGGQRIRELRKELGKL-GGGVEIDV 66
KH-I_PCBP1_2_rpt1 cd22515
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 63-110 1.70e-03

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411943  Cd Length: 70  Bit Score: 36.14  E-value: 1.70e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 491683223  63 SIRVTIHTARPGIVIGKKGEDVEKLRNAVAkiagvpAQINIAEVKKPE 110
Cdd:cd22515    3 TIRLLMHGKEVGSIIGKKGESVKKMREESG------ARINISEGNCPE 44
KH-I_PCBP4_rpt1 cd22517
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 63-110 5.87e-03

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411945  Cd Length: 70  Bit Score: 34.62  E-value: 5.87e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 491683223  63 SIRVTIHTARPGIVIGKKGEDVEKLRNAVAkiagvpAQINIAEVKKPE 110
Cdd:cd22517    3 TLRLLMHGKEVGSIIGKKGETVKRIREESS------ARITISEGSCPE 44
KH-I_PCBP3_rpt1 cd22516
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 63-110 6.94e-03

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411944  Cd Length: 77  Bit Score: 34.69  E-value: 6.94e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 491683223  63 SIRVTIHTARPGIVIGKKGEDVEKLRNAVAkiagvpAQINIAEVKKPE 110
Cdd:cd22516   10 TIRLLMHGKEVGSIIGKKGETVKKMREESG------ARINISEGNCPE 51
 
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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