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Conserved domains on  [gi|446452081|ref|WP_000529936|]
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MULTISPECIES: 30S ribosomal protein S3 [Terrabacteria group]

Protein Classification

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 ...
 1-212 1.63e-147

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: 409.48  E-value: 1.63e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081   1 MGQKVHPIGMRVGIIRDWDAKWYAE-KEYADYLHEDLAIRKFVQKELADAAVSTIEIERAVNKVNVSLHTAKPGMVIGKG 79
Cdd:COG0092    1 MGQKVNPIGFRLGIIKDWDSRWYADkKDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081  80 GANVDALRAKLNKLTGKQVHINIIEIKQPDLDAHLVGEGIARQLEQRVAFRRAQKQAIQRAMRAGAKGIKTQVSGRLNGA 159
Cdd:COG0092   81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGA 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446452081 160 DIARAEGYSEGTVPLHTLRADIDYAWEEADTTYGKLGVKVWIYRGEVLPARKN 212
Cdd:COG0092  161 EIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEE 213
 
Name Accession Description Interval E-value
RpsC COG0092
Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3 ...
 1-212 1.63e-147

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: 409.48  E-value: 1.63e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081   1 MGQKVHPIGMRVGIIRDWDAKWYAE-KEYADYLHEDLAIRKFVQKELADAAVSTIEIERAVNKVNVSLHTAKPGMVIGKG 79
Cdd:COG0092    1 MGQKVNPIGFRLGIIKDWDSRWYADkKDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081  80 GANVDALRAKLNKLTGKQVHINIIEIKQPDLDAHLVGEGIARQLEQRVAFRRAQKQAIQRAMRAGAKGIKTQVSGRLNGA 159
Cdd:COG0092   81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGA 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446452081 160 DIARAEGYSEGTVPLHTLRADIDYAWEEADTTYGKLGVKVWIYRGEVLPARKN 212
Cdd:COG0092  161 EIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEE 213
rpsC_bact TIGR01009
ribosomal protein S3, bacterial type; This model describes the bacterial type of ribosomal ...
 1-208 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 446452081    1 MGQKVHPIGMRVGIIRDWDAKWYA-EKEYADYLHEDLAIRKFVQKELADAAVSTIEIERAVNKVNVSLHTAKPGMVIGKG 79
Cdd:TIGR01009   1 MGQKVNPIGFRLGITKDWKSRWYAnPKEYAKLLHEDLKIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081   80 GANVDALRAKLNKLTGKQVHINIIEIKQPDLDAHLVGEGIARQLEQRVAFRRAQKQAIQRAMRAGAKGIKTQVSGRLNGA 159
Cdd:TIGR01009  81 GSEIEKLRKDLQKLTGKEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLGGA 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 446452081  160 DIARAEGYSEGTVPLHTLRADIDYAWEEADTTYGKLGVKVWIYRGEVLP 208
Cdd:TIGR01009 161 EIARTEWYKEGRVPLHTLRADIDYATAEAHTTYGIIGVKVWIFKGEVLG 209
rps3 CHL00048
ribosomal protein S3
 1-205 1.36e-85

ribosomal protein S3


Pssm-ID: 214348 [Multi-domain]  Cd Length: 214  Bit Score: 252.05  E-value: 1.36e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081   1 MGQKVHPIGMRVGIIRDWDAKWYAE-KEYADYLHEDLAIRKF----VQKELADAAVSTIEIERAVNKVNVSLHTAKPGMV 75
Cdd:CHL00048   1 MGQKINPLGFRLGTTQKHHSLWFAQpKNYSEGLQEDKKIRDCiknyVQKNIKYEGIARIEIQRKIDLIQVIIYTGFPKLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081  76 IGKGGANVDALRAKLNKLTGK---QVHINIIEIKQPDLDAHLVGEGIARQLEQRVAFRRAQKQAIQRAMRAGAKGIKTQV 152
Cdd:CHL00048  81 IERKGRGIEELQINLQKELNSvnrKLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446452081 153 SGRLNGADIARAEGYSEGTVPLHTLRADIDYAWEEADTTYGKLGVKVWIYRGE 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 3.51e-55

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: 171.09  E-value: 3.51e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081   2 GQKVHPIGMRVGIIRDWDAKWYAE-KEYADYLHEDLAIRKFVQKELADAAVSTIEIERAVNKVNVSLHTAKPGMVIGKGG 80
Cdd:cd02412    1 GQKVNPLGFRLGITKDWDSRWYADkKDYAKLLLEDLKIRKYIKKKLKKAGISRIEIERKADKIRVTIHTARPGIVIGKKG 80

                         90       100
                 ....*....|....*....|....*...
gi 446452081  81 ANVDALRAKLNKLTGKQVHINIIEIKQP 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 1.12e-49

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: 156.37  E-value: 1.12e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081  119 IARQLEQRVAFRRAQKQAIQRAMRAGAKGIKTQVSGRLNGADIARAEGYSEGTVPLHTLRADIDYAWEEADTTYGKLGVK 198
Cdd:pfam00189   1 IAQQLEKRVSFRRAMKQAIRRAMRAGAKGIKIIISGRLGGAERARSEKYREGRVPLHTLRADIDYAFAEALTKYGVIGVK 80


                  ...
gi 446452081  199 VWI 201
Cdd:pfam00189  81 VWI 83
KH smart00322
K homology RNA-binding domain;
62-123 5.03e-07

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 45.75  E-value: 5.03e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446452081    62 KVNVSLHTAKPGMVIGKGGANVDALRAKLN---KLTGKQVHINIIEIKQPDLDAHLVGEGIARQL 123
Cdd:smart00322   4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGvkiDIPGPGSEERVVEITGPPENVEKAAELILEIL 68
 
Name Accession Description Interval E-value
RpsC COG0092
Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3 ...
 1-212 1.63e-147

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: 409.48  E-value: 1.63e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081   1 MGQKVHPIGMRVGIIRDWDAKWYAE-KEYADYLHEDLAIRKFVQKELADAAVSTIEIERAVNKVNVSLHTAKPGMVIGKG 79
Cdd:COG0092    1 MGQKVNPIGFRLGIIKDWDSRWYADkKDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081  80 GANVDALRAKLNKLTGKQVHINIIEIKQPDLDAHLVGEGIARQLEQRVAFRRAQKQAIQRAMRAGAKGIKTQVSGRLNGA 159
Cdd:COG0092   81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGA 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446452081 160 DIARAEGYSEGTVPLHTLRADIDYAWEEADTTYGKLGVKVWIYRGEVLPARKN 212
Cdd:COG0092  161 EIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEE 213
rpsC_bact TIGR01009
ribosomal protein S3, bacterial type; This model describes the bacterial type of ribosomal ...
 1-208 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 446452081    1 MGQKVHPIGMRVGIIRDWDAKWYA-EKEYADYLHEDLAIRKFVQKELADAAVSTIEIERAVNKVNVSLHTAKPGMVIGKG 79
Cdd:TIGR01009   1 MGQKVNPIGFRLGITKDWKSRWYAnPKEYAKLLHEDLKIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081   80 GANVDALRAKLNKLTGKQVHINIIEIKQPDLDAHLVGEGIARQLEQRVAFRRAQKQAIQRAMRAGAKGIKTQVSGRLNGA 159
Cdd:TIGR01009  81 GSEIEKLRKDLQKLTGKEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLGGA 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 446452081  160 DIARAEGYSEGTVPLHTLRADIDYAWEEADTTYGKLGVKVWIYRGEVLP 208
Cdd:TIGR01009 161 EIARTEWYKEGRVPLHTLRADIDYATAEAHTTYGIIGVKVWIFKGEVLG 209
rps3 CHL00048
ribosomal protein S3
 1-205 1.36e-85

ribosomal protein S3


Pssm-ID: 214348 [Multi-domain]  Cd Length: 214  Bit Score: 252.05  E-value: 1.36e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081   1 MGQKVHPIGMRVGIIRDWDAKWYAE-KEYADYLHEDLAIRKF----VQKELADAAVSTIEIERAVNKVNVSLHTAKPGMV 75
Cdd:CHL00048   1 MGQKINPLGFRLGTTQKHHSLWFAQpKNYSEGLQEDKKIRDCiknyVQKNIKYEGIARIEIQRKIDLIQVIIYTGFPKLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081  76 IGKGGANVDALRAKLNKLTGK---QVHINIIEIKQPDLDAHLVGEGIARQLEQRVAFRRAQKQAIQRAMRAGAKGIKTQV 152
Cdd:CHL00048  81 IERKGRGIEELQINLQKELNSvnrKLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446452081 153 SGRLNGADIARAEGYSEGTVPLHTLRADIDYAWEEADTTYGKLGVKVWIYRGE 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 3.51e-55

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: 171.09  E-value: 3.51e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081   2 GQKVHPIGMRVGIIRDWDAKWYAE-KEYADYLHEDLAIRKFVQKELADAAVSTIEIERAVNKVNVSLHTAKPGMVIGKGG 80
Cdd:cd02412    1 GQKVNPLGFRLGITKDWDSRWYADkKDYAKLLLEDLKIRKYIKKKLKKAGISRIEIERKADKIRVTIHTARPGIVIGKKG 80

                         90       100
                 ....*....|....*....|....*...
gi 446452081  81 ANVDALRAKLNKLTGKQVHINIIEIKQP 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 1.12e-49

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: 156.37  E-value: 1.12e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081  119 IARQLEQRVAFRRAQKQAIQRAMRAGAKGIKTQVSGRLNGADIARAEGYSEGTVPLHTLRADIDYAWEEADTTYGKLGVK 198
Cdd:pfam00189   1 IAQQLEKRVSFRRAMKQAIRRAMRAGAKGIKIIISGRLGGAERARSEKYREGRVPLHTLRADIDYAFAEALTKYGVIGVK 80


                  ...
gi 446452081  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 ...
 36-208 1.54e-26

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: 100.96  E-value: 1.54e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081   36 LAIRKFVQKELADAAVSTIEIERAVNKVNVSLHTAKPGMVIGKGGANVDALRAKLNKLTG-KQVHINIIEIKQPDLDAHL 114
Cdd:TIGR01008  13 TLIDEFLEKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIRELTEKLQKKFGlENPQIYVEEVENPELNAKV 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081  115 VGEGIARQLEQRVAFRRAQKQAIQRAMRAGAKGIKTQVSGRLNGADiARAEGYSEGTV-----PLHTLradIDYAWEEAD 189
Cdd:TIGR01008  93 QAERIARALERGLHFRRAAYAAVRRIMEAGAKGVEVTISGKLTGER-AKTEKFAAGYLkhsgePAEEL---VDKGFAIAL 168

                         170
                  ....*....|....*....
gi 446452081  190 TTYGKLGVKVWIYRGEVLP 208
Cdd:TIGR01008 169 LKLGVLGVKVKIMPPDAKL 187
rps3p PRK04191
30S ribosomal protein S3P; Reviewed
 38-208 5.52e-25

30S ribosomal protein S3P; Reviewed


Pssm-ID: 235247 [Multi-domain]  Cd Length: 207  Bit Score: 96.86  E-value: 5.52e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081  38 IRKFVQKELADAAVSTIEIERAVNKVNVSLHTAKPGMVIGKGGANVDALRAKLNKLTG-KQVHINIIEIKQPDLDAHLVG 116
Cdd:PRK04191  17 IDEYLAKELYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNIRELTEILEKKFGlENPQIDVKEVENPELNARVVA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081 117 EGIARQLEQRVAFRRAQKQAIQRAMRAGAKGIKTQVSGRLNGADiARAEGYSEGTV-----PLHTLradIDYAWEEADTT 191
Cdd:PRK04191  97 FRLANALERGWHFRRAAHSAIRRIMEAGALGVEIIISGKLTGER-ARTEKFTEGYIkksgePAEEL---VDRGFAIAKLK 172

                        170
                 ....*....|....*...
gi 446452081 192 YGKLGVKVWIYRGEV-LP 208
Cdd:PRK04191 173 LGIIGVEVRIMPPDAkLP 190
KH_2 pfam07650
KH domain;
38-110 1.22e-19

KH domain;


Pssm-ID: 429574 [Multi-domain]  Cd Length: 78  Bit Score: 79.52  E-value: 1.22e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446452081   38 IRKFVQKELADAAVSTIEIERAVNKVNVSLHTAKPGMVIGKGGANVDALRAKLNKLT----GKQVHINIIEIKQPDL 110
Cdd:pfam07650   2 IPYSLAVELKFAGVSKVEIERTPNAVIVVIRASQPGIVIGKGGSRIKKIGKELRKDIekllGKKVYLNIVKVKKPWL 78
KH-II_30S_S3_arch cd02411
type II K-homology (KH) RNA-binding domain found in archaeal 30S ribosomal protein S3 and ...
 24-108 6.15e-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: 54.13  E-value: 6.15e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081  24 AEKEYADYLHEDLAIRKFVQKELADAAVSTIEIERAVNKVNVSLHTAKPGMVIGKGGANVDALRAKLNKLTG-KQVHINI 102
Cdd:cd02411    2 IEKKFIEEGLKRMKIDEYLAKELERAGYGGMELKKTPLGTKVIIYAERPGMVIGRGGRNIRRLTEILEEEFGlENPQIEV 81


                 ....*.
gi 446452081 103 IEIKQP 108
Cdd:cd02411   82 KEVENP 87
PTZ00084 PTZ00084
40S ribosomal protein S3; Provisional
 4-203 2.53e-09

40S ribosomal protein S3; Provisional


Pssm-ID: 240260 [Multi-domain]  Cd Length: 220  Bit Score: 55.05  E-value: 2.53e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081   4 KVHPIGMRVGIIRDwdAKWYAEkeyadyLHEdlairkFVQKELADAAVSTIEIERAVNKVNVSLHTAKPGMVIGKGGANV 83
Cdd:PTZ00084   1 SMGQISKKRKFVAD--GVFYAE------LNE------FLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRI 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446452081  84 DALRAKLNKLTG---KQVHINIIEIKQPDLDAHLVGEGIARQLEQRVAFRRAQKQAIQRAMRAGAKGIKTQVSGRLnGAD 160
Cdd:PTZ00084  67 RELTSLLQKRFGfpeGKVELFAERVENRGLCAMAQAESLRYKLLEGLPVRRAAYGVLRHVMESGAKGCEVIVSGKL-RAQ 145

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 446452081 161 IARA----EGY--SEGtvplHTLRADIDYAWEEADTTYGKLGVKVWIYR 203
Cdd:PTZ00084 146 RAKSmkfrDGYmiSTG----QPKKDFVDSAVRHVLMRQGVIGVKVKIML 190
KH smart00322
K homology RNA-binding domain;
62-123 5.03e-07

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 45.75  E-value: 5.03e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446452081    62 KVNVSLHTAKPGMVIGKGGANVDALRAKLN---KLTGKQVHINIIEIKQPDLDAHLVGEGIARQL 123
Cdd:smart00322   4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGvkiDIPGPGSEERVVEITGPPENVEKAAELILEIL 68
KH_4 pfam13083
KH domain;
38-102 2.07e-03

KH domain;


Pssm-ID: 463779  Cd Length: 73  Bit Score: 35.53  E-value: 2.07e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446452081   38 IRKFVQK--ELADAAVSTIEIERAVNKVNVSLHTAKPGMVIGKGGANVDALR----AKLNKlTGKQVHINI 102
Cdd:pfam13083   4 VEDILKAlvDDPEEVSVTEEEEEKTVVLELNVAGEDMGKVIGKQGRTLDALRtlvsAAANK-DGKRVRVEI 73
Jag COG1847
Predicted RNA-binding protein Jag (SpoIIIJ-associated), conains KH and R3H domains [General ...
 53-102 2.08e-03

Predicted RNA-binding protein Jag (SpoIIIJ-associated), conains KH and R3H domains [General function prediction only];


Pssm-ID: 441452 [Multi-domain]  Cd Length: 143  Bit Score: 37.01  E-value: 2.08e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446452081  53 TIEIERAVNKVNVSLHTAKPGMVIGKGGANVDAL----RAKLNKLTGKQVHINI 102
Cdd:COG1847   17 DIEIEVEGDRLTVDISGEDLGLLIGRRGETLDALqyltNLAVNRKTGERSRVIL 70
KH-II_Jag cd02414
type II K-homology (KH) RNA-binding domain found in protein Jag and similar proteins; Protein ...
 53-100 6.25e-03

type II K-homology (KH) RNA-binding domain found in protein Jag and similar proteins; Protein Jag, also called SpoIIIJ-associated protein, is associated with SpoIIIJ and is necessary for the third stage of sporulation. Members of this family are mainly from bacteria 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: 411785  Cd Length: 79  Bit Score: 34.42  E-value: 6.25e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446452081  53 TIEIERAVNKVNVSLHTAKPGMVIGKGGANVDAL----RAKLNKLTGKQVHI 100
Cdd:cd02414   18 EVEVEEEEGTVKLNIDGEDPGLLIGKHGETLDALqylaNLVLNKEFGKRVRV 69
KH-II_SF cd02409
type II K-homology (KH) RNA-binding domain superfamily; The K-homology (KH) domain binds ...
 39-103 6.35e-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: 34.27  E-value: 6.35e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446452081  39 RKFVQKELADAA-VSTIEIERAVNKVNVSLHTAK--PGMVIGKGGANVDALRAKLNKLtGKQVHINII 103
Cdd:cd02409    1 AEILEKLFPAAVtISDVEVEETPDGIRVIIAVEEgdPGIVIGKGGQRIRELRKELGKL-GGGVEIDVV 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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