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Conserved domains on  [gi|503471755|ref|WP_013706416|]
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30S ribosomal protein S3 [Desulfobacca acetoxidans]

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 ...
 1-215 1.50e-137

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: 384.06  E-value: 1.50e-137
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755   1 MGQKVHPVGFRLGSYRRWHSYWFAR-KNYSDLLLEDQKIRKFIKneKELQGAGIAAIDIERAANKVKMKIHTSRPGIVIG 79
Cdd:COG0092    1 MGQKVNPIGFRLGIIKDWDSRWYADkKDYADLLHEDLKIRKYLK--KKLKNAGISKIEIERTANRVRVTIHTARPGIVIG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755  80 QKGKKIEELRQKLQRLIGRELIVDIHEVRKPELNAQLVAENIALQLERRVAFRRAMKKAVGQAMKFGAQGIKVRVAGRLG 159
Cdd:COG0092   79 KKGAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLG 158

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 503471755 160 GAEMARREWYREGRVPLHTLRADIDYGVAEARTTYGVIGIKAWIFKGEILSEDRLN 215
Cdd:COG0092  159 GAEIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEA 214
 
Name Accession Description Interval E-value
RpsC COG0092
Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3 ...
 1-215 1.50e-137

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: 384.06  E-value: 1.50e-137
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755   1 MGQKVHPVGFRLGSYRRWHSYWFAR-KNYSDLLLEDQKIRKFIKneKELQGAGIAAIDIERAANKVKMKIHTSRPGIVIG 79
Cdd:COG0092    1 MGQKVNPIGFRLGIIKDWDSRWYADkKDYADLLHEDLKIRKYLK--KKLKNAGISKIEIERTANRVRVTIHTARPGIVIG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755  80 QKGKKIEELRQKLQRLIGRELIVDIHEVRKPELNAQLVAENIALQLERRVAFRRAMKKAVGQAMKFGAQGIKVRVAGRLG 159
Cdd:COG0092   79 KKGAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLG 158

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 503471755 160 GAEMARREWYREGRVPLHTLRADIDYGVAEARTTYGVIGIKAWIFKGEILSEDRLN 215
Cdd:COG0092  159 GAEIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEA 214
rpsC_bact TIGR01009
ribosomal protein S3, bacterial type; This model describes the bacterial type of ribosomal ...
 1-209 9.41e-113

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: 320.80  E-value: 9.41e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755    1 MGQKVHPVGFRLGSYRRWHSYWFA-RKNYSDLLLEDQKIRKFIKneKELQGAGIAAIDIERAANKVKMKIHTSRPGIVIG 79
Cdd:TIGR01009   1 MGQKVNPIGFRLGITKDWKSRWYAnPKEYAKLLHEDLKIRNYIK--KELSNAGISDVEIERPADKIRVTIHTARPGIVIG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755   80 QKGKKIEELRQKLQRLIGRELIVDIHEVRKPELNAQLVAENIALQLERRVAFRRAMKKAVGQAMKFGAQGIKVRVAGRLG 159
Cdd:TIGR01009  79 KKGSEIEKLRKDLQKLTGKEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLG 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 503471755  160 GAEMARREWYREGRVPLHTLRADIDYGVAEARTTYGVIGIKAWIFKGEIL 209
Cdd:TIGR01009 159 GAEIARTEWYKEGRVPLHTLRADIDYATAEAHTTYGIIGVKVWIFKGEVL 208
rps3 CHL00048
ribosomal protein S3
 1-208 7.09e-97

ribosomal protein S3


Pssm-ID: 214348 [Multi-domain]  Cd Length: 214  Bit Score: 280.94  E-value: 7.09e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755   1 MGQKVHPVGFRLGSYRRWHSYWFA-RKNYSDLLLEDQKIRKFIKN--EKELQGAGIAAIDIERAANKVKMKIHTSRPGIV 77
Cdd:CHL00048   1 MGQKINPLGFRLGTTQKHHSLWFAqPKNYSEGLQEDKKIRDCIKNyvQKNIKYEGIARIEIQRKIDLIQVIIYTGFPKLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755  78 IGQKGKKIEELRQKLQRLIG---RELIVDIHEVRKPELNAQLVAENIALQLERRVAFRRAMKKAVGQAMKFGAQGIKVRV 154
Cdd:CHL00048  81 IERKGRGIEELQINLQKELNsvnRKLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 503471755 155 AGRLGGAEMARREWYREGRVPLHTLRADIDYGVAEARTTYGVIGIKAWIFKGEI 208
Cdd:CHL00048 161 SGRLNGAEIARVEWIREGRVPLQTLRAKIDYCSYPARTIYGVLGIKIWIFKDEE 214
Ribosomal_S3_C pfam00189
Ribosomal protein S3, C-terminal domain; This family contains a central domain pfam00013, ...
 121-203 7.84e-50

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: 156.75  E-value: 7.84e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755  121 IALQLERRVAFRRAMKKAVGQAMKFGAQGIKVRVAGRLGGAEMARREWYREGRVPLHTLRADIDYGVAEARTTYGVIGIK 200
Cdd:pfam00189   1 IAQQLEKRVSFRRAMKQAIRRAMRAGAKGIKIIISGRLGGAERARSEKYREGRVPLHTLRADIDYAFAEALTKYGVIGVK 80


                  ...
gi 503471755  201 AWI 203
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 ...
 2-110 3.48e-49

type II K-homology (KH) RNA-binding domain found in 30S ribosomal protein S3 and similar proteins; 30S ribosomal protein S3, also called small ribosomal subunit protein uS3, is part of the head region of the 30S ribosomal subunit and binds to the lower part of the 30S subunit head. It may also bind mRNA in the 70S ribosome, positioning it for translation. S3 protein is believed to interact with mRNA as it threads its way from the latch into the channel. Members of this family contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid).


Pssm-ID: 411783  Cd Length: 108  Bit Score: 156.06  E-value: 3.48e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755   2 GQKVHPVGFRLGSYRRWHSYWFAR-KNYSDLLLEDQKIRKFIKneKELQGAGIAAIDIERAANKVKMKIHTSRPGIVIGQ 80
Cdd:cd02412    1 GQKVNPLGFRLGITKDWDSRWYADkKDYAKLLLEDLKIRKYIK--KKLKKAGISRIEIERKADKIRVTIHTARPGIVIGK 78

                         90       100       110
                 ....*....|....*....|....*....|
gi 503471755  81 KGKKIEELRQKLQRLIGRELIVDIHEVRKP 110
Cdd:cd02412   79 KGAEIEKLRKELEKLTGKKVNINVVEVKKP 108
KH smart00322
K homology RNA-binding domain;
64-125 1.49e-07

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 46.90  E-value: 1.49e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 503471755    64 KVKMKIHTSRPGIVIGQKGKKIEELRQKLQ---RLIGRELIVDIHEVRKPELNAQLVAENIALQL 125
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 1.50e-137

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: 384.06  E-value: 1.50e-137
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755   1 MGQKVHPVGFRLGSYRRWHSYWFAR-KNYSDLLLEDQKIRKFIKneKELQGAGIAAIDIERAANKVKMKIHTSRPGIVIG 79
Cdd:COG0092    1 MGQKVNPIGFRLGIIKDWDSRWYADkKDYADLLHEDLKIRKYLK--KKLKNAGISKIEIERTANRVRVTIHTARPGIVIG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755  80 QKGKKIEELRQKLQRLIGRELIVDIHEVRKPELNAQLVAENIALQLERRVAFRRAMKKAVGQAMKFGAQGIKVRVAGRLG 159
Cdd:COG0092   79 KKGAEIEKLRKELEKLTGKEVQINIVEVKKPELDAQLVAENIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLG 158

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 503471755 160 GAEMARREWYREGRVPLHTLRADIDYGVAEARTTYGVIGIKAWIFKGEILSEDRLN 215
Cdd:COG0092  159 GAEIARTEWYREGRVPLHTLRADIDYGFAEAHTTYGVIGVKVWIYKGEVLPKKEEA 214
rpsC_bact TIGR01009
ribosomal protein S3, bacterial type; This model describes the bacterial type of ribosomal ...
 1-209 9.41e-113

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: 320.80  E-value: 9.41e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755    1 MGQKVHPVGFRLGSYRRWHSYWFA-RKNYSDLLLEDQKIRKFIKneKELQGAGIAAIDIERAANKVKMKIHTSRPGIVIG 79
Cdd:TIGR01009   1 MGQKVNPIGFRLGITKDWKSRWYAnPKEYAKLLHEDLKIRNYIK--KELSNAGISDVEIERPADKIRVTIHTARPGIVIG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755   80 QKGKKIEELRQKLQRLIGRELIVDIHEVRKPELNAQLVAENIALQLERRVAFRRAMKKAVGQAMKFGAQGIKVRVAGRLG 159
Cdd:TIGR01009  79 KKGSEIEKLRKDLQKLTGKEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLG 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 503471755  160 GAEMARREWYREGRVPLHTLRADIDYGVAEARTTYGVIGIKAWIFKGEIL 209
Cdd:TIGR01009 159 GAEIARTEWYKEGRVPLHTLRADIDYATAEAHTTYGIIGVKVWIFKGEVL 208
rps3 CHL00048
ribosomal protein S3
 1-208 7.09e-97

ribosomal protein S3


Pssm-ID: 214348 [Multi-domain]  Cd Length: 214  Bit Score: 280.94  E-value: 7.09e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755   1 MGQKVHPVGFRLGSYRRWHSYWFA-RKNYSDLLLEDQKIRKFIKN--EKELQGAGIAAIDIERAANKVKMKIHTSRPGIV 77
Cdd:CHL00048   1 MGQKINPLGFRLGTTQKHHSLWFAqPKNYSEGLQEDKKIRDCIKNyvQKNIKYEGIARIEIQRKIDLIQVIIYTGFPKLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755  78 IGQKGKKIEELRQKLQRLIG---RELIVDIHEVRKPELNAQLVAENIALQLERRVAFRRAMKKAVGQAMKFGAQGIKVRV 154
Cdd:CHL00048  81 IERKGRGIEELQINLQKELNsvnRKLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 503471755 155 AGRLGGAEMARREWYREGRVPLHTLRADIDYGVAEARTTYGVIGIKAWIFKGEI 208
Cdd:CHL00048 161 SGRLNGAEIARVEWIREGRVPLQTLRAKIDYCSYPARTIYGVLGIKIWIFKDEE 214
Ribosomal_S3_C pfam00189
Ribosomal protein S3, C-terminal domain; This family contains a central domain pfam00013, ...
 121-203 7.84e-50

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: 156.75  E-value: 7.84e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755  121 IALQLERRVAFRRAMKKAVGQAMKFGAQGIKVRVAGRLGGAEMARREWYREGRVPLHTLRADIDYGVAEARTTYGVIGIK 200
Cdd:pfam00189   1 IAQQLEKRVSFRRAMKQAIRRAMRAGAKGIKIIISGRLGGAERARSEKYREGRVPLHTLRADIDYAFAEALTKYGVIGVK 80


                  ...
gi 503471755  201 AWI 203
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 ...
 2-110 3.48e-49

type II K-homology (KH) RNA-binding domain found in 30S ribosomal protein S3 and similar proteins; 30S ribosomal protein S3, also called small ribosomal subunit protein uS3, is part of the head region of the 30S ribosomal subunit and binds to the lower part of the 30S subunit head. It may also bind mRNA in the 70S ribosome, positioning it for translation. S3 protein is believed to interact with mRNA as it threads its way from the latch into the channel. Members of this family contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid).


Pssm-ID: 411783  Cd Length: 108  Bit Score: 156.06  E-value: 3.48e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755   2 GQKVHPVGFRLGSYRRWHSYWFAR-KNYSDLLLEDQKIRKFIKneKELQGAGIAAIDIERAANKVKMKIHTSRPGIVIGQ 80
Cdd:cd02412    1 GQKVNPLGFRLGITKDWDSRWYADkKDYAKLLLEDLKIRKYIK--KKLKKAGISRIEIERKADKIRVTIHTARPGIVIGK 78

                         90       100       110
                 ....*....|....*....|....*....|
gi 503471755  81 KGKKIEELRQKLQRLIGRELIVDIHEVRKP 110
Cdd:cd02412   79 KGAEIEKLRKELEKLTGKKVNINVVEVKKP 108
rps3p PRK04191
30S ribosomal protein S3P; Reviewed
 39-214 2.03e-28

30S ribosomal protein S3P; Reviewed


Pssm-ID: 235247 [Multi-domain]  Cd Length: 207  Bit Score: 106.10  E-value: 2.03e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755  39 RKFIKN-----------EKELQGAGIAAIDIERAANKVKMKIHTSRPGIVIGQKGKKIEELRQKLQRLIGRELI-VDIHE 106
Cdd:PRK04191   5 KKFVEEglkkvmideylAKELYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNIRELTEILEKKFGLENPqIDVKE 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755 107 VRKPELNAQLVAENIALQLERRVAFRRAMKKAVGQAMKFGAQGIKVRVAGRLGGaEMARREWYREGRV-----PLHTLra 181
Cdd:PRK04191  85 VENPELNARVVAFRLANALERGWHFRRAAHSAIRRIMEAGALGVEIIISGKLTG-ERARTEKFTEGYIkksgePAEEL-- 161

                        170       180       190
                 ....*....|....*....|....*....|...
gi 503471755 182 dIDYGVAEARTTYGVIGIKAWIFKGEILSEDRL 214
Cdd:PRK04191 162 -VDRGFAIAKLKLGIIGVEVRIMPPDAKLPDEI 193
uS3_euk_arch TIGR01008
ribosomal protein uS3, eukaryotic/archaeal type; This model describes ribosomal protein S3 of ...
 45-205 1.58e-27

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: 103.27  E-value: 1.58e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755   45 EKELQGAGIAAIDIERAANKVKMKIHTSRPGIVIGQKGKKIEELRQKLQRLIGRELI-VDIHEVRKPELNAQLVAENIAL 123
Cdd:TIGR01008  20 EKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIRELTEKLQKKFGLENPqIYVEEVENPELNAKVQAERIAR 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755  124 QLERRVAFRRAMKKAVGQAMKFGAQGIKVRVAGRLGGaEMARREWYREGRV-----PLHTLradIDYGVAEARTTYGVIG 198
Cdd:TIGR01008 100 ALERGLHFRRAAYAAVRRIMEAGAKGVEVTISGKLTG-ERAKTEKFAAGYLkhsgePAEEL---VDKGFAIALLKLGVLG 175


                  ....*..
gi 503471755  199 IKAWIFK 205
Cdd:TIGR01008 176 VKVKIMP 182
KH_2 pfam07650
KH domain;
37-112 4.27e-16

KH domain;


Pssm-ID: 429574 [Multi-domain]  Cd Length: 78  Bit Score: 70.27  E-value: 4.27e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755   37 KIRKFIKneKELQGAGIAAIDIERAANKVKMKIHTSRPGIVIGQKGKKIEELRQKLQRLI----GRELIVDIHEVRKPEL 112
Cdd:pfam07650   1 EIPYSLA--VELKFAGVSKVEIERTPNAVIVVIRASQPGIVIGKGGSRIKKIGKELRKDIekllGKKVYLNIVKVKKPWL 78
PTZ00084 PTZ00084
40S ribosomal protein S3; Provisional
 37-203 7.70e-12

40S ribosomal protein S3; Provisional


Pssm-ID: 240260 [Multi-domain]  Cd Length: 220  Bit Score: 61.99  E-value: 7.70e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755  37 KIRKFIK--------NE---KELQGAGIAAIDIERAANKVKMKIHTSRPGIVIGQKGKKIEELRQKLQRLIGR-----EL 100
Cdd:PTZ00084   7 KKRKFVAdgvfyaelNEflsRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRIRELTSLLQKRFGFpegkvEL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755 101 IVDIHEVRKpeLNAQLVAENIALQLERRVAFRRAMKKAVGQAMKFGAQGIKVRVAGRLgGAEMARREWYREGRV--PLHT 178
Cdd:PTZ00084  87 FAERVENRG--LCAMAQAESLRYKLLEGLPVRRAAYGVLRHVMESGAKGCEVIVSGKL-RAQRAKSMKFRDGYMisTGQP 163

                        170       180
                 ....*....|....*....|....*
gi 503471755 179 LRADIDYGVAEARTTYGVIGIKAWI 203
Cdd:PTZ00084 164 KKDFVDSAVRHVLMRQGVIGVKVKI 188
KH smart00322
K homology RNA-binding domain;
64-125 1.49e-07

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 46.90  E-value: 1.49e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 503471755    64 KVKMKIHTSRPGIVIGQKGKKIEELRQKLQ---RLIGRELIVDIHEVRKPELNAQLVAENIALQL 125
Cdd:smart00322   4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGvkiDIPGPGSEERVVEITGPPENVEKAAELILEIL 68
KH-II_30S_S3_arch cd02411
type II K-homology (KH) RNA-binding domain found in archaeal 30S ribosomal protein S3 and ...
 37-110 4.47e-07

type II K-homology (KH) RNA-binding domain found in archaeal 30S ribosomal protein S3 and similar proteins; 30S ribosomal protein S3, also called small ribosomal subunit protein uS3, is part of the head region of the 30S ribosomal subunit and binds to the lower part of the 30S subunit head. It is believed to interact with mRNA as it threads its way from the latch into the channel. Members of this family are mainly from archaea and contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid).


Pssm-ID: 411782  Cd Length: 87  Bit Score: 46.43  E-value: 4.47e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 503471755  37 KIRKFIknEKELQGAGIAAIDIERAANKVKMKIHTSRPGIVIGQKGKKIEELRQKLQRLIGRELI-VDIHEVRKP 110
Cdd:cd02411   15 KIDEYL--AKELERAGYGGMELKKTPLGTKVIIYAERPGMVIGRGGRNIRRLTEILEEEFGLENPqIEVKEVENP 87
KH-II_SF cd02409
type II K-homology (KH) RNA-binding domain superfamily; The K-homology (KH) domain binds ...
 45-101 5.72e-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: 36.97  E-value: 5.72e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 503471755  45 EKELQGA-GIAAIDIERAANKVKMKIHTSR--PGIVIGQKGKKIEELRQKLQRLIGRELI 101
Cdd:cd02409    5 EKLFPAAvTISDVEVEETPDGIRVIIAVEEgdPGIVIGKGGQRIRELRKELGKLGGGVEI 64
KH-II_40S_S3 cd02413
type II K-homology (KH) RNA-binding domain found in 40S ribosomal protein S3 and similar ...
 35-94 1.04e-03

type II K-homology (KH) RNA-binding domain found in 40S ribosomal protein S3 and similar proteins; 40S ribosomal protein S3, also called small ribosomal subunit protein uS3, is part of the head region of the 40S ribosomal subunit and is involved in translation. It is believed to interact with mRNA as it threads its way from the latch into the channel. 40S ribosomal protein S3 has endonuclease activity and plays a role in repair of damaged DNA. It cleaves phosphodiester bonds of DNAs containing altered bases with broad specificity and cleaves supercoiled DNA more efficiently than relaxed DNA. Members of this family are mainly from prokaryotes 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: 411784  Cd Length: 91  Bit Score: 37.12  E-value: 1.04e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503471755  35 DQKIRKFIKN-----------EKELQGAGIAAIDIERAANKVKMKIHTSRPGIVIGQKGKKIEELRQKLQR 94
Cdd:cd02413    1 ISKKRKFVADgvfyaelneflTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQK 71
KH-I_HNRNPK_rpt2 cd22433
second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 65-96 2.64e-03

second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411861 [Multi-domain]  Cd Length: 70  Bit Score: 35.31  E-value: 2.64e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 503471755  65 VKMKIHTSRPGIVIGQKGKKIEELRQKLQRLI 96
Cdd:cd22433    4 LRLLVHQSQAGCIIGRAGFKIKELREKTGATI 35
 
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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