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Conserved domains on  [gi|489327778|ref|WP_003235068|]
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MULTISPECIES: 30S ribosomal protein S3 [Bacillus]

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 ...
 1-215 1.80e-154

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: 426.82  E-value: 1.80e-154
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778   1 MGQKVNPVGLRIGVIRDWESKWYA-GKDYADFLHEDLKIREYISKRLSDASVSKVEIERAANRVNITIHTAKPGMVIGKG 79
Cdd:COG0092    1 MGQKVNPIGFRLGIIKDWDSRWYAdKKDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778  80 GSEVEALRKALNSLTGKRVHINILEIKRADLDAQLVADNIARQLENRVSFRRAQKQQIQRTMRAGAQGVKTMVSGRLGGA 159
Cdd:COG0092   81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGA 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 489327778 160 DIARSEYYSEGTVPLHTLRADIDYATSEADTTYGKLGVKVWIYRGEVLPTKKKNEE 215
Cdd:COG0092  161 EIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEAAA 216
 
Name Accession Description Interval E-value
RpsC COG0092
Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3 ...
 1-215 1.80e-154

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: 426.82  E-value: 1.80e-154
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778   1 MGQKVNPVGLRIGVIRDWESKWYA-GKDYADFLHEDLKIREYISKRLSDASVSKVEIERAANRVNITIHTAKPGMVIGKG 79
Cdd:COG0092    1 MGQKVNPIGFRLGIIKDWDSRWYAdKKDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778  80 GSEVEALRKALNSLTGKRVHINILEIKRADLDAQLVADNIARQLENRVSFRRAQKQQIQRTMRAGAQGVKTMVSGRLGGA 159
Cdd:COG0092   81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGA 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 489327778 160 DIARSEYYSEGTVPLHTLRADIDYATSEADTTYGKLGVKVWIYRGEVLPTKKKNEE 215
Cdd:COG0092  161 EIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEAAA 216
rpsC_bact TIGR01009
ribosomal protein S3, bacterial type; This model describes the bacterial type of ribosomal ...
 1-210 7.51e-131

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: 366.64  E-value: 7.51e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778    1 MGQKVNPVGLRIGVIRDWESKWYAG-KDYADFLHEDLKIREYISKRLSDASVSKVEIERAANRVNITIHTAKPGMVIGKG 79
Cdd:TIGR01009   1 MGQKVNPIGFRLGITKDWKSRWYANpKEYAKLLHEDLKIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778   80 GSEVEALRKALNSLTGKRVHINILEIKRADLDAQLVADNIARQLENRVSFRRAQKQQIQRTMRAGAQGVKTMVSGRLGGA 159
Cdd:TIGR01009  81 GSEIEKLRKDLQKLTGKEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLGGA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 489327778  160 DIARSEYYSEGTVPLHTLRADIDYATSEADTTYGKLGVKVWIYRGEVLPTK 210
Cdd:TIGR01009 161 EIARTEWYKEGRVPLHTLRADIDYATAEAHTTYGIIGVKVWIFKGEVLGGG 211
rps3 CHL00048
ribosomal protein S3
 1-205 1.68e-82

ribosomal protein S3


Pssm-ID: 214348 [Multi-domain]  Cd Length: 214  Bit Score: 244.35  E-value: 1.68e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778   1 MGQKVNPVGLRIGVIRDWESKWYAG-KDYADFLHEDLKIRE----YISKRLSDASVSKVEIERAANRVNITIHTAKPGMV 75
Cdd:CHL00048   1 MGQKINPLGFRLGTTQKHHSLWFAQpKNYSEGLQEDKKIRDciknYVQKNIKYEGIARIEIQRKIDLIQVIIYTGFPKLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778  76 IGKGGSEVEALR----KALNSLTgKRVHINILEIKRADLDAQLVADNIARQLENRVSFRRAQKQQIQRTMRAGAQGVKTM 151
Cdd:CHL00048  81 IERKGRGIEELQinlqKELNSVN-RKLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQ 159

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 489327778 152 VSGRLGGADIARSEYYSEGTVPLHTLRADIDYATSEADTTYGKLGVKVWIYRGE 205
Cdd:CHL00048 160 ISGRLNGAEIARVEWIREGRVPLQTLRAKIDYCSYPARTIYGVLGIKIWIFKDE 213
KH-II_30S_S3 cd02412
type II K-homology (KH) RNA-binding domain found in 30S ribosomal protein S3 and similar ...
 2-107 1.39e-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: 177.25  E-value: 1.39e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778   2 GQKVNPVGLRIGVIRDWESKWYA-GKDYADFLHEDLKIREYISKRLSDASVSKVEIERAANRVNITIHTAKPGMVIGKGG 80
Cdd:cd02412    1 GQKVNPLGFRLGITKDWDSRWYAdKKDYAKLLLEDLKIRKYIKKKLKKAGISRIEIERKADKIRVTIHTARPGIVIGKKG 80

                         90       100
                 ....*....|....*....|....*..
gi 489327778  81 SEVEALRKALNSLTGKRVHINILEIKR 107
Cdd:cd02412   81 AEIEKLRKELEKLTGKKVNINVVEVKK 107
Ribosomal_S3_C pfam00189
Ribosomal protein S3, C-terminal domain; This family contains a central domain pfam00013, ...
 119-201 1.84e-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: 155.98  E-value: 1.84e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778  119 IARQLENRVSFRRAQKQQIQRTMRAGAQGVKTMVSGRLGGADIARSEYYSEGTVPLHTLRADIDYATSEADTTYGKLGVK 198
Cdd:pfam00189   1 IAQQLEKRVSFRRAMKQAIRRAMRAGAKGIKIIISGRLGGAERARSEKYREGRVPLHTLRADIDYAFAEALTKYGVIGVK 80


                  ...
gi 489327778  199 VWI 201
Cdd:pfam00189  81 VWI 83
KH smart00322
K homology RNA-binding domain;
62-123 1.01e-07

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 47.68  E-value: 1.01e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489327778    62 RVNITIHTAKPGMVIGKGGSEVEALRKALN---SLTGKRVHINILEIKRADLDAQLVADNIARQL 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 ...
 1-215 1.80e-154

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: 426.82  E-value: 1.80e-154
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778   1 MGQKVNPVGLRIGVIRDWESKWYA-GKDYADFLHEDLKIREYISKRLSDASVSKVEIERAANRVNITIHTAKPGMVIGKG 79
Cdd:COG0092    1 MGQKVNPIGFRLGIIKDWDSRWYAdKKDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778  80 GSEVEALRKALNSLTGKRVHINILEIKRADLDAQLVADNIARQLENRVSFRRAQKQQIQRTMRAGAQGVKTMVSGRLGGA 159
Cdd:COG0092   81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGA 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 489327778 160 DIARSEYYSEGTVPLHTLRADIDYATSEADTTYGKLGVKVWIYRGEVLPTKKKNEE 215
Cdd:COG0092  161 EIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEAAA 216
rpsC_bact TIGR01009
ribosomal protein S3, bacterial type; This model describes the bacterial type of ribosomal ...
 1-210 7.51e-131

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: 366.64  E-value: 7.51e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778    1 MGQKVNPVGLRIGVIRDWESKWYAG-KDYADFLHEDLKIREYISKRLSDASVSKVEIERAANRVNITIHTAKPGMVIGKG 79
Cdd:TIGR01009   1 MGQKVNPIGFRLGITKDWKSRWYANpKEYAKLLHEDLKIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778   80 GSEVEALRKALNSLTGKRVHINILEIKRADLDAQLVADNIARQLENRVSFRRAQKQQIQRTMRAGAQGVKTMVSGRLGGA 159
Cdd:TIGR01009  81 GSEIEKLRKDLQKLTGKEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLGGA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 489327778  160 DIARSEYYSEGTVPLHTLRADIDYATSEADTTYGKLGVKVWIYRGEVLPTK 210
Cdd:TIGR01009 161 EIARTEWYKEGRVPLHTLRADIDYATAEAHTTYGIIGVKVWIFKGEVLGGG 211
rps3 CHL00048
ribosomal protein S3
 1-205 1.68e-82

ribosomal protein S3


Pssm-ID: 214348 [Multi-domain]  Cd Length: 214  Bit Score: 244.35  E-value: 1.68e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778   1 MGQKVNPVGLRIGVIRDWESKWYAG-KDYADFLHEDLKIRE----YISKRLSDASVSKVEIERAANRVNITIHTAKPGMV 75
Cdd:CHL00048   1 MGQKINPLGFRLGTTQKHHSLWFAQpKNYSEGLQEDKKIRDciknYVQKNIKYEGIARIEIQRKIDLIQVIIYTGFPKLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778  76 IGKGGSEVEALR----KALNSLTgKRVHINILEIKRADLDAQLVADNIARQLENRVSFRRAQKQQIQRTMRAGAQGVKTM 151
Cdd:CHL00048  81 IERKGRGIEELQinlqKELNSVN-RKLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQ 159

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 489327778 152 VSGRLGGADIARSEYYSEGTVPLHTLRADIDYATSEADTTYGKLGVKVWIYRGE 205
Cdd:CHL00048 160 ISGRLNGAEIARVEWIREGRVPLQTLRAKIDYCSYPARTIYGVLGIKIWIFKDE 213
KH-II_30S_S3 cd02412
type II K-homology (KH) RNA-binding domain found in 30S ribosomal protein S3 and similar ...
 2-107 1.39e-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: 177.25  E-value: 1.39e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778   2 GQKVNPVGLRIGVIRDWESKWYA-GKDYADFLHEDLKIREYISKRLSDASVSKVEIERAANRVNITIHTAKPGMVIGKGG 80
Cdd:cd02412    1 GQKVNPLGFRLGITKDWDSRWYAdKKDYAKLLLEDLKIRKYIKKKLKKAGISRIEIERKADKIRVTIHTARPGIVIGKKG 80

                         90       100
                 ....*....|....*....|....*..
gi 489327778  81 SEVEALRKALNSLTGKRVHINILEIKR 107
Cdd:cd02412   81 AEIEKLRKELEKLTGKKVNINVVEVKK 107
Ribosomal_S3_C pfam00189
Ribosomal protein S3, C-terminal domain; This family contains a central domain pfam00013, ...
 119-201 1.84e-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: 155.98  E-value: 1.84e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778  119 IARQLENRVSFRRAQKQQIQRTMRAGAQGVKTMVSGRLGGADIARSEYYSEGTVPLHTLRADIDYATSEADTTYGKLGVK 198
Cdd:pfam00189   1 IAQQLEKRVSFRRAMKQAIRRAMRAGAKGIKIIISGRLGGAERARSEKYREGRVPLHTLRADIDYAFAEALTKYGVIGVK 80


                  ...
gi 489327778  199 VWI 201
Cdd:pfam00189  81 VWI 83
rps3p PRK04191
30S ribosomal protein S3P; Reviewed
 26-208 9.06e-30

30S ribosomal protein S3P; Reviewed


Pssm-ID: 235247 [Multi-domain]  Cd Length: 207  Bit Score: 109.57  E-value: 9.06e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778  26 KDYADFLHEDLK---IREYISKRLSDASVSKVEIERAANRVNITIHTAKPGMVIGKGGSEVEALRKALNSLTG-KRVHIN 101
Cdd:PRK04191   2 AIEKKFVEEGLKkvmIDEYLAKELYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNIRELTEILEKKFGlENPQID 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778 102 ILEIKRADLDAQLVADNIARQLENRVSFRRAQKQQIQRTMRAGAQGVKTMVSGRLGGADiARSEYYSEGTV-----PLHT 176
Cdd:PRK04191  82 VKEVENPELNARVVAFRLANALERGWHFRRAAHSAIRRIMEAGALGVEIIISGKLTGER-ARTEKFTEGYIkksgePAEE 160

                        170       180       190
                 ....*....|....*....|....*....|...
gi 489327778 177 LradIDYATSEADTTYGKLGVKVWIYRGEV-LP 208
Cdd:PRK04191 161 L---VDRGFAIAKLKLGIIGVEVRIMPPDAkLP 190
KH_2 pfam07650
KH domain;
37-110 2.62e-21

KH domain;


Pssm-ID: 429574 [Multi-domain]  Cd Length: 78  Bit Score: 83.76  E-value: 2.62e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489327778   37 KIREYISKRLSDASVSKVEIERAANRVNITIHTAKPGMVIGKGGSEVEALRKALNSLT----GKRVHINILEIKRADL 110
Cdd:pfam07650   1 EIPYSLAVELKFAGVSKVEIERTPNAVIVVIRASQPGIVIGKGGSRIKKIGKELRKDIekllGKKVYLNIVKVKKPWL 78
PTZ00084 PTZ00084
40S ribosomal protein S3; Provisional
 40-218 8.81e-11

40S ribosomal protein S3; Provisional


Pssm-ID: 240260 [Multi-domain]  Cd Length: 220  Bit Score: 59.29  E-value: 8.81e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778  40 EYISKRLSDASVSKVEIERAANRVNITIHTAKPGMVIGKGGSEVealrKALNSLTGKR-------VHINILEIKRADLDA 112
Cdd:PTZ00084  23 EFLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRI----RELTSLLQKRfgfpegkVELFAERVENRGLCA 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778 113 QLVADNIARQLENRVSFRRAQKQQIQRTMRAGAQGVKTMVSGRLgGADIARSEYYSEGTV--PLHTLRADIDYATSEADT 190
Cdd:PTZ00084  99 MAQAESLRYKLLEGLPVRRAAYGVLRHVMESGAKGCEVIVSGKL-RAQRAKSMKFRDGYMisTGQPKKDFVDSAVRHVLM 177

                        170       180
                 ....*....|....*....|....*...
gi 489327778 191 TYGKLGVKVWIYrgevLPTKKKNEEGGK 218
Cdd:PTZ00084 178 RQGVIGVKVKIM----LPYDPSGKNGPS 201
KH-II_30S_S3_arch cd02411
type II K-homology (KH) RNA-binding domain found in archaeal 30S ribosomal protein S3 and ...
 36-107 1.28e-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: 56.06  E-value: 1.28e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489327778  36 LKIREYISKRLSDASVSKVEIERAANRVNITIHTAKPGMVIGKGGSEVEALRKALNSLTG-KRVHINILEIKR 107
Cdd:cd02411   14 MKIDEYLAKELERAGYGGMELKKTPLGTKVIIYAERPGMVIGRGGRNIRRLTEILEEEFGlENPQIEVKEVEN 86
KH smart00322
K homology RNA-binding domain;
62-123 1.01e-07

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 47.68  E-value: 1.01e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489327778    62 RVNITIHTAKPGMVIGKGGSEVEALRKALN---SLTGKRVHINILEIKRADLDAQLVADNIARQL 123
Cdd:smart00322   4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGvkiDIPGPGSEERVVEITGPPENVEKAAELILEIL 68
YlqC COG1837
Predicted RNA-binding protein YlqC, contains KH domain, UPF0109 family [General function ...
 53-104 1.53e-04

Predicted RNA-binding protein YlqC, contains KH domain, UPF0109 family [General function prediction only];


Pssm-ID: 441442  Cd Length: 76  Bit Score: 38.88  E-value: 1.53e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489327778  53 KVEIERAANRVNITIHTAKP--GMVIGKGGSEVEALR---KALNSLTGKRVHINILE 104
Cdd:COG1837   20 SVTEEEGERTVVLELRVAPEdlGKVIGKQGRTAKAIRtvlSAAAAKEGKRVRLEIVD 76
KH-II_YlqC-like cd22533
type II K-homology (KH) RNA-binding domain found in Bacillus subtilis UPF0109 protein YlqC and ...
 40-103 2.44e-04

type II K-homology (KH) RNA-binding domain found in Bacillus subtilis UPF0109 protein YlqC and similar proteins; The family includes a group of uncharacterized proteins which show sequence similarity to Bacillus subtilis UPF0109 protein YlqC. They are mainly found in 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: 411790  Cd Length: 75  Bit Score: 38.22  E-value: 2.44e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489327778  40 EYISKRL----SDASVSKVEIERAanrVNITIHTAKP--GMVIGKGGSEVEALRKALNSL---TGKRVHINIL 103
Cdd:cd22533    6 EYIAKSLvdhpESVRVSEIEGEKT---TVYELRVAPEdvGRVIGKQGRTAKAIRTLVSAAaakDGKRVRLEIL 75
VAR1 pfam05316
Mitochondrial ribosomal protein (VAR1); This family consists of the yeast mitochondrial ...
 52-201 1.07e-03

Mitochondrial ribosomal protein (VAR1); This family consists of the yeast mitochondrial ribosomal proteins VAR1. Mitochondria possess their own ribosomes responsible for the synthesis of a small number of proteins encoded by the mitochondrial genome. In yeast the two ribosomal RNAs and a single ribosomal protein, VAR1, are products of mitochondrial genes, and the remaining approximately 80 ribosomal proteins are encoded in the nucleus. VAR1 along with 15S rRNA are necessary for the formation of mature 37S subunits.


Pssm-ID: 461621  Cd Length: 197  Bit Score: 38.55  E-value: 1.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778   52 SKVEIERAANRVNITIHTAKPGMVIGKGGSE-----------VEALRKALNSLTGKRVHINILEIKRADLDAQLVADNIA 120
Cdd:pfam05316   4 SKPIFQHSTNKVNIQLYYYNPDIINNNNNNKennyymlmqnkLNNLSKLLSKLYNKKVNIELIKLHYPYLNSDILAQYLA 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489327778  121 ------------RQLENRVSFRR----------AQKQQIQRTMRAGAQGVKTMVSGRLGG-ADIARSE--YYSEGTVPLH 175
Cdd:pfam05316  84 indnkknfngltRALFNNMPLLNdnnisknyinNINKYMNLLLPKYLQGIKIQLSGRLGLnKGIPRTTvtNKSIGTFNNN 163

                         170       180       190
                  ....*....|....*....|....*....|.
gi 489327778  176 -----TLRADIDYATSEADTTYGKLGVKVWI 201
Cdd:pfam05316 164 snlnnNYKNNIDYGKNTNKNKNGAYTIKVWL 194
KH-II_SF cd02409
type II K-homology (KH) RNA-binding domain superfamily; The K-homology (KH) domain binds ...
 47-102 2.32e-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: 35.43  E-value: 2.32e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489327778  47 SDASVSKVEIERAANRVNITIHTAK--PGMVIGKGGSEVEALRKALnSLTGKRVHINI 102
Cdd:cd02409   10 AAVTISDVEVEETPDGIRVIIAVEEgdPGIVIGKGGQRIRELRKEL-GKLGGGVEIDV 66
era PRK00089
GTPase Era; Reviewed
 38-102 3.44e-03

GTPase Era; Reviewed


Pssm-ID: 234624 [Multi-domain]  Cd Length: 292  Bit Score: 37.72  E-value: 3.44e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489327778  38 IREYISKRLSDA---SVSkVEIE----RAANRVNITIHTAKP---GMVIGKGGS---EV-EALRKALNSLTGKRVHINI 102
Cdd:PRK00089 195 IREKLLRLLGDElpySVA-VEIEkfeeRGLVRIEATIYVERDsqkGIIIGKGGAmlkKIgTEARKDIEKLLGKKVFLEL 272
KH-II_Jag cd02414
type II K-homology (KH) RNA-binding domain found in protein Jag and similar proteins; Protein ...
 53-100 3.58e-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: 35.19  E-value: 3.58e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489327778  53 KVEIERAANRVNITIHTAKPGMVIGKGGSEVEAL----RKALNSLTGKRVHI 100
Cdd:cd02414   18 EVEVEEEEGTVKLNIDGEDPGLLIGKHGETLDALqylaNLVLNKEFGKRVRV 69
 
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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