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Conserved domains on  [gi|1063532405|ref|WP_069395657|]
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30S ribosomal protein S3 [Mycobacterium shimoidei]

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 ...
 1-226 9.58e-146

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: 407.56  E-value: 9.58e-146
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405   1 MGQKINPHGFRLGITTDWKSRWYAD-KQYAEYVKEDVAIRRLLSSGLERAGIADVEIERTRDRVRVDIHTARPGIVIGRR 79
Cdd:COG0092     1 MGQKVNPIGFRLGIIKDWDSRWYADkKDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405  80 GTEADRIRADLEKLTGKQVQLNILEVKNPESQAQLVAQGVAEQLSNRVAFRRAMRKAIQSAMRQpNVKGIRVQCSGRLGG 159
Cdd:COG0092    81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRA-GAKGIKIQVSGRLGG 159

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063532405 160 AEMSRSEFYREGRVPLHTLRADIDYGLYEAKTTFGRIGVKVWIYKGDIVGGKRELVAPTAAGAERPR 226
Cdd:COG0092   160 AEIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEAAAAEAAEGGKPR 226
 
Name Accession Description Interval E-value
RpsC COG0092
Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3 ...
 1-226 9.58e-146

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: 407.56  E-value: 9.58e-146
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405   1 MGQKINPHGFRLGITTDWKSRWYAD-KQYAEYVKEDVAIRRLLSSGLERAGIADVEIERTRDRVRVDIHTARPGIVIGRR 79
Cdd:COG0092     1 MGQKVNPIGFRLGIIKDWDSRWYADkKDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405  80 GTEADRIRADLEKLTGKQVQLNILEVKNPESQAQLVAQGVAEQLSNRVAFRRAMRKAIQSAMRQpNVKGIRVQCSGRLGG 159
Cdd:COG0092    81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRA-GAKGIKIQVSGRLGG 159

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063532405 160 AEMSRSEFYREGRVPLHTLRADIDYGLYEAKTTFGRIGVKVWIYKGDIVGGKRELVAPTAAGAERPR 226
Cdd:COG0092   160 AEIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEAAAAEAAEGGKPR 226
rpsC_bact TIGR01009
ribosomal protein S3, bacterial type; This model describes the bacterial type of ribosomal ...
 1-211 2.19e-127

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: 360.48  E-value: 2.19e-127
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405   1 MGQKINPHGFRLGITTDWKSRWYAD-KQYAEYVKEDVAIRRLLSSGLERAGIADVEIERTRDRVRVDIHTARPGIVIGRR 79
Cdd:TIGR01009   1 MGQKVNPIGFRLGITKDWKSRWYANpKEYAKLLHEDLKIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405  80 GTEADRIRADLEKLTGKQVQLNILEVKNPESQAQLVAQGVAEQLSNRVAFRRAMRKAIQSAMRQpNVKGIRVQCSGRLGG 159
Cdd:TIGR01009  81 GSEIEKLRKDLQKLTGKEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKA-GAKGIKVQVSGRLGG 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1063532405 160 AEMSRSEFYREGRVPLHTLRADIDYGLYEAKTTFGRIGVKVWIYKGDIVGGK 211
Cdd:TIGR01009 160 AEIARTEWYKEGRVPLHTLRADIDYATAEAHTTYGIIGVKVWIFKGEVLGGG 211
rps3 CHL00048
ribosomal protein S3
 1-207 2.23e-90

ribosomal protein S3


Pssm-ID: 214348 [Multi-domain]  Cd Length: 214  Bit Score: 266.69  E-value: 2.23e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405   1 MGQKINPHGFRLGITTDWKSRWYAD-KQYAEYVKEDVAIRRLLSSGLER----AGIADVEIERTRDRVRVDIHTARPGIV 75
Cdd:CHL00048    1 MGQKINPLGFRLGTTQKHHSLWFAQpKNYSEGLQEDKKIRDCIKNYVQKnikyEGIARIEIQRKIDLIQVIIYTGFPKLL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405  76 IGRRGTEADRIRADLEKLTGK---QVQLNILEVKNPESQAQLVAQGVAEQLSNRVAFRRAMRKAIQSAMRQpNVKGIRVQ 152
Cdd:CHL00048   81 IERKGRGIEELQINLQKELNSvnrKLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKA-DIKGIKIQ 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1063532405 153 CSGRLGGAEMSRSEFYREGRVPLHTLRADIDYGLYEAKTTFGRIGVKVWIYKGDI 207
Cdd:CHL00048  160 ISGRLNGAEIARVEWIREGRVPLQTLRAKIDYCSYPARTIYGVLGIKIWIFKDEE 214
KH-II_30S_S3 cd02412
type II K-homology (KH) RNA-binding domain found in 30S ribosomal protein S3 and similar ...
 2-108 2.60e-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: 173.78  E-value: 2.60e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405   2 GQKINPHGFRLGITTDWKSRWYAD-KQYAEYVKEDVAIRRLLSSGLERAGIADVEIERTRDRVRVDIHTARPGIVIGRRG 80
Cdd:cd02412     1 GQKVNPLGFRLGITKDWDSRWYADkKDYAKLLLEDLKIRKYIKKKLKKAGISRIEIERKADKIRVTIHTARPGIVIGKKG 80

                          90       100
                  ....*....|....*....|....*...
gi 1063532405  81 TEADRIRADLEKLTGKQVQLNILEVKNP 108
Cdd:cd02412    81 AEIEKLRKELEKLTGKKVNINVVEVKKP 108
Ribosomal_S3_C pfam00189
Ribosomal protein S3, C-terminal domain; This family contains a central domain pfam00013, ...
 119-202 1.90e-44

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: 145.20  E-value: 1.90e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405 119 VAEQLSNRVAFRRAMRKAIQSAMRQpNVKGIRVQCSGRLGGAEMSRSEFYREGRVPLHTLRADIDYGLYEAKTTFGRIGV 198
Cdd:pfam00189   1 IAQQLEKRVSFRRAMKQAIRRAMRA-GAKGIKIIISGRLGGAERARSEKYREGRVPLHTLRADIDYAFAEALTKYGVIGV 79


                  ....
gi 1063532405 199 KVWI 202
Cdd:pfam00189  80 KVWI 83
KH smart00322
K homology RNA-binding domain;
59-123 5.35e-07

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 46.13  E-value: 5.35e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1063532405   59 TRDRVRVDIHTARPGIVIGRRGTeadRIRAdLEKLTGKQVQL-------NILEVKNPESQAQLVAQGVAEQL 123
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGS---TIKK-IEEETGVKIDIpgpgseeRVVEITGPPENVEKAAELILEIL 68
 
Name Accession Description Interval E-value
RpsC COG0092
Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3 ...
 1-226 9.58e-146

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: 407.56  E-value: 9.58e-146
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405   1 MGQKINPHGFRLGITTDWKSRWYAD-KQYAEYVKEDVAIRRLLSSGLERAGIADVEIERTRDRVRVDIHTARPGIVIGRR 79
Cdd:COG0092     1 MGQKVNPIGFRLGIIKDWDSRWYADkKDYADLLHEDLKIRKYLKKKLKNAGISKIEIERTANRVRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405  80 GTEADRIRADLEKLTGKQVQLNILEVKNPESQAQLVAQGVAEQLSNRVAFRRAMRKAIQSAMRQpNVKGIRVQCSGRLGG 159
Cdd:COG0092    81 GAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRA-GAKGIKIQVSGRLGG 159

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063532405 160 AEMSRSEFYREGRVPLHTLRADIDYGLYEAKTTFGRIGVKVWIYKGDIVGGKRELVAPTAAGAERPR 226
Cdd:COG0092   160 AEIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEAAAAEAAEGGKPR 226
rpsC_bact TIGR01009
ribosomal protein S3, bacterial type; This model describes the bacterial type of ribosomal ...
 1-211 2.19e-127

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: 360.48  E-value: 2.19e-127
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405   1 MGQKINPHGFRLGITTDWKSRWYAD-KQYAEYVKEDVAIRRLLSSGLERAGIADVEIERTRDRVRVDIHTARPGIVIGRR 79
Cdd:TIGR01009   1 MGQKVNPIGFRLGITKDWKSRWYANpKEYAKLLHEDLKIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405  80 GTEADRIRADLEKLTGKQVQLNILEVKNPESQAQLVAQGVAEQLSNRVAFRRAMRKAIQSAMRQpNVKGIRVQCSGRLGG 159
Cdd:TIGR01009  81 GSEIEKLRKDLQKLTGKEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKA-GAKGIKVQVSGRLGG 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1063532405 160 AEMSRSEFYREGRVPLHTLRADIDYGLYEAKTTFGRIGVKVWIYKGDIVGGK 211
Cdd:TIGR01009 160 AEIARTEWYKEGRVPLHTLRADIDYATAEAHTTYGIIGVKVWIFKGEVLGGG 211
rps3 CHL00048
ribosomal protein S3
 1-207 2.23e-90

ribosomal protein S3


Pssm-ID: 214348 [Multi-domain]  Cd Length: 214  Bit Score: 266.69  E-value: 2.23e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405   1 MGQKINPHGFRLGITTDWKSRWYAD-KQYAEYVKEDVAIRRLLSSGLER----AGIADVEIERTRDRVRVDIHTARPGIV 75
Cdd:CHL00048    1 MGQKINPLGFRLGTTQKHHSLWFAQpKNYSEGLQEDKKIRDCIKNYVQKnikyEGIARIEIQRKIDLIQVIIYTGFPKLL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405  76 IGRRGTEADRIRADLEKLTGK---QVQLNILEVKNPESQAQLVAQGVAEQLSNRVAFRRAMRKAIQSAMRQpNVKGIRVQ 152
Cdd:CHL00048   81 IERKGRGIEELQINLQKELNSvnrKLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKA-DIKGIKIQ 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1063532405 153 CSGRLGGAEMSRSEFYREGRVPLHTLRADIDYGLYEAKTTFGRIGVKVWIYKGDI 207
Cdd:CHL00048  160 ISGRLNGAEIARVEWIREGRVPLQTLRAKIDYCSYPARTIYGVLGIKIWIFKDEE 214
KH-II_30S_S3 cd02412
type II K-homology (KH) RNA-binding domain found in 30S ribosomal protein S3 and similar ...
 2-108 2.60e-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: 173.78  E-value: 2.60e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405   2 GQKINPHGFRLGITTDWKSRWYAD-KQYAEYVKEDVAIRRLLSSGLERAGIADVEIERTRDRVRVDIHTARPGIVIGRRG 80
Cdd:cd02412     1 GQKVNPLGFRLGITKDWDSRWYADkKDYAKLLLEDLKIRKYIKKKLKKAGISRIEIERKADKIRVTIHTARPGIVIGKKG 80

                          90       100
                  ....*....|....*....|....*...
gi 1063532405  81 TEADRIRADLEKLTGKQVQLNILEVKNP 108
Cdd:cd02412    81 AEIEKLRKELEKLTGKKVNINVVEVKKP 108
Ribosomal_S3_C pfam00189
Ribosomal protein S3, C-terminal domain; This family contains a central domain pfam00013, ...
 119-202 1.90e-44

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: 145.20  E-value: 1.90e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405 119 VAEQLSNRVAFRRAMRKAIQSAMRQpNVKGIRVQCSGRLGGAEMSRSEFYREGRVPLHTLRADIDYGLYEAKTTFGRIGV 198
Cdd:pfam00189   1 IAQQLEKRVSFRRAMKQAIRRAMRA-GAKGIKIIISGRLGGAERARSEKYREGRVPLHTLRADIDYAFAEALTKYGVIGV 79


                  ....
gi 1063532405 199 KVWI 202
Cdd:pfam00189  80 KVWI 83
rps3p PRK04191
30S ribosomal protein S3P; Reviewed
 46-208 2.07e-20

30S ribosomal protein S3P; Reviewed


Pssm-ID: 235247 [Multi-domain]  Cd Length: 207  Bit Score: 86.46  E-value: 2.07e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405  46 LERAGIADVEIERTRDRVRVDIHTARPGIVIGRRGTEADRIRADLEKLTG-KQVQLNILEVKNPESQAQLVAQGVAEQLS 124
Cdd:PRK04191   25 LYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNIRELTEILEKKFGlENPQIDVKEVENPELNARVVAFRLANALE 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405 125 NRVAFRRAMRKAIQSAMRQpNVKGIRVQCSGRLGGaEMSRSEFYREGRV-----PLHTLradIDYGLYEAKTTFGRIGVK 199
Cdd:PRK04191  105 RGWHFRRAAHSAIRRIMEA-GALGVEIIISGKLTG-ERARTEKFTEGYIkksgePAEEL---VDRGFAIAKLKLGIIGVE 179


                  ....*....
gi 1063532405 200 VWIYKGDIV 208
Cdd:PRK04191  180 VRIMPPDAK 188
KH_2 pfam07650
KH domain;
38-109 1.29e-18

KH domain;


Pssm-ID: 429574 [Multi-domain]  Cd Length: 78  Bit Score: 77.98  E-value: 1.29e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063532405  38 IRRLLSSGLERAGIADVEIERTRDRVRVDIHTARPGIVIGRRGTEADRIRADLEKLT----GKQVQLNILEVKNPE 109
Cdd:pfam07650   2 IPYSLAVELKFAGVSKVEIERTPNAVIVVIRASQPGIVIGKGGSRIKKIGKELRKDIekllGKKVYLNIVKVKKPW 77
uS3_euk_arch TIGR01008
ribosomal protein uS3, eukaryotic/archaeal type; This model describes ribosomal protein S3 of ...
 38-208 1.98e-17

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: 78.23  E-value: 1.98e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405  38 IRRLLSSGLERAGIADVEIERTRDRVRVDIHTARPGIVIGRRGTeadRIRADLEKLTGK----QVQLNILEVKNPESQAQ 113
Cdd:TIGR01008  15 IDEFLEKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGR---RIRELTEKLQKKfgleNPQIYVEEVENPELNAK 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405 114 LVAQGVAEQLSNRVAFRRAMRKAIQSAMrQPNVKGIRVQCSGRLGGaEMSRSEFYREGRV-----PLHTLradIDYGLYE 188
Cdd:TIGR01008  92 VQAERIARALERGLHFRRAAYAAVRRIM-EAGAKGVEVTISGKLTG-ERAKTEKFAAGYLkhsgePAEEL---VDKGFAI 166

                         170       180
                  ....*....|....*....|
gi 1063532405 189 AKTTFGRIGVKVWIYKGDIV 208
Cdd:TIGR01008 167 ALLKLGVLGVKVKIMPPDAK 186
KH-II_30S_S3_arch cd02411
type II K-homology (KH) RNA-binding domain found in archaeal 30S ribosomal protein S3 and ...
 26-108 2.96e-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: 55.67  E-value: 2.96e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405  26 KQYAEYVKEDVAIRRLLSSGLERAGIADVEIERTRDRVRVDIHTARPGIVIGRRGTEADRIRADLEKLTG-KQVQLNILE 104
Cdd:cd02411     4 KKFIEEGLKRMKIDEYLAKELERAGYGGMELKKTPLGTKVIIYAERPGMVIGRGGRNIRRLTEILEEEFGlENPQIEVKE 83


                  ....
gi 1063532405 105 VKNP 108
Cdd:cd02411    84 VENP 87
KH smart00322
K homology RNA-binding domain;
59-123 5.35e-07

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 46.13  E-value: 5.35e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1063532405   59 TRDRVRVDIHTARPGIVIGRRGTeadRIRAdLEKLTGKQVQL-------NILEVKNPESQAQLVAQGVAEQL 123
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGS---TIKK-IEEETGVKIDIpgpgseeRVVEITGPPENVEKAAELILEIL 68
PTZ00084 PTZ00084
40S ribosomal protein S3; Provisional
 41-217 1.48e-06

40S ribosomal protein S3; Provisional


Pssm-ID: 240260 [Multi-domain]  Cd Length: 220  Bit Score: 48.12  E-value: 1.48e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405  41 LLSSGLERAGIADVEIERTRDRVRVDIHTARPGIVIGRRGTEADRIRADLEKLTG---KQVQLNILEVKNPESQAQLVAQ 117
Cdd:PTZ00084   24 FLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRIRELTSLLQKRFGfpeGKVELFAERVENRGLCAMAQAE 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532405 118 GVAEQLSNRVAFRRAMRKAIQSAMRQpNVKGIRVQCSGRLgGAEMSRSEFYREGRV--PLHTLRADIDYGLYEAKTTFGR 195
Cdd:PTZ00084  104 SLRYKLLEGLPVRRAAYGVLRHVMES-GAKGCEVIVSGKL-RAQRAKSMKFRDGYMisTGQPKKDFVDSAVRHVLMRQGV 181

                         170       180
                  ....*....|....*....|..
gi 1063532405 196 IGVKVWIYKGDIVGGKRELVAP 217
Cdd:PTZ00084  182 IGVKVKIMLPYDPSGKNGPSAP 203
Era COG1159
GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis];
54-106 2.55e-05

GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440773 [Multi-domain]  Cd Length: 290  Bit Score: 44.59  E-value: 2.55e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063532405  54 VEIER-----TRDRVRVDIHTARP---GIVIGRRG-------TEAdriRADLEKLTGKQVQLNiLEVK 106
Cdd:COG1159   210 VEIEEfeereGLLRIRATIYVERDsqkGIIIGKGGsmlkkigTEA---RKDIEKLLGKKVFLE-LWVK 273
KH-II_SF cd02409
type II K-homology (KH) RNA-binding domain superfamily; The K-homology (KH) domain binds ...
 50-102 1.98e-04

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


Pssm-ID: 411780 [Multi-domain]  Cd Length: 67  Bit Score: 38.90  E-value: 1.98e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1063532405  50 GIADVEIERTRDRVRVDIHTAR--PGIVIGRRGTEADRIRADLEKLtGKQVQLNI 102
Cdd:cd02409    13 TISDVEVEETPDGIRVIIAVEEgdPGIVIGKGGQRIRELRKELGKL-GGGVEIDV 66
KH-II_Jag cd02414
type II K-homology (KH) RNA-binding domain found in protein Jag and similar proteins; Protein ...
 38-80 2.00e-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: 36.35  E-value: 2.00e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1063532405  38 IRRLLSSGLERAGI-ADVEIERTRDRVRVDIHTARPGIVIGRRG 80
Cdd:cd02414     2 AKEFLEELLDAMGIeAEVEVEEEEGTVKLNIDGEDPGLLIGKHG 45
 
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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