NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|488285050|ref|WP_002356258|]
View 

MULTISPECIES: S1 domain-containing RNA-binding protein [Enterococcus]

Protein Classification

RNA-binding protein S1( domain architecture ID 11483364)

RNA-binding protein S1 contains an RNA-binding domain first identified in ribosomal protein S1.

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK08582 PRK08582
RNA-binding protein S1;
1-148 5.77e-67

RNA-binding protein S1;


:

Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 199.87  E-value: 5.77e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   1 MSIEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDDGKIGLSIRKAQEPA 80
Cdd:PRK08582   1 MSIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRP 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488285050  81 EGQQPKrefqrrennyenrdrnPRAGGKKPFNKPQAnnnnNKQDFDSLMSSFLKDSDDRLSSLKRNTE 148
Cdd:PRK08582  81 KRQHDR----------------PRHEDNRGGGNDVA----PKEDFEQKMSRFLKDSEDRLTSIKRNTE 128
 
Name Accession Description Interval E-value
PRK08582 PRK08582
RNA-binding protein S1;
1-148 5.77e-67

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 199.87  E-value: 5.77e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   1 MSIEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDDGKIGLSIRKAQEPA 80
Cdd:PRK08582   1 MSIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRP 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488285050  81 EGQQPKrefqrrennyenrdrnPRAGGKKPFNKPQAnnnnNKQDFDSLMSSFLKDSDDRLSSLKRNTE 148
Cdd:PRK08582  81 KRQHDR----------------PRHEDNRGGGNDVA----PKEDFEQKMSRFLKDSEDRLTSIKRNTE 128
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 1-148 2.08e-57

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 175.37  E-value: 2.08e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   1 MSIEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDDGKIGLSIRKAQEPA 80
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGKISLSIKQAEEKP 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488285050  81 EGQqpkrefqrrenNYENRDRNPRAGgkkpfnkpqannnnnKQDFDSLMSSFLKDSDDRLSSLKRNTE 148
Cdd:COG1098   81 KRP-----------PRPRRNSRPKAG---------------FESFEDKLSKFLKDSDERLSDLKKRTE 122
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 3-98 2.74e-35

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator.


Pssm-ID: 468553 [Multi-domain]  Cd Length: 113  Bit Score: 118.68  E-value: 2.74e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   3 IEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDD-GKIGLSIRkAQEPAE 81
Cdd:NF040579   1 YKIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYtGKISLSLR-ALEEAP 79

                         90
                 ....*....|....*..
gi 488285050  82 GQQPKREFQRRENNYEN 98
Cdd:NF040579  80 EKHRKRRKHRWTNKRLK 96
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-74 2.37e-27

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 96.97  E-value: 2.37e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488285050   6 GAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDDGKIGLSIR 74
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
4-74 1.31e-20

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 79.96  E-value: 1.31e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488285050     4 EVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSV-GDDGKIGLSIR 74
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVdEEKGRIILSLK 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 4-73 1.10e-16

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 70.01  E-value: 1.10e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488285050    4 EVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDD-GKIGLSI 73
Cdd:pfam00575   2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDrRRIILSI 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 5-74 4.08e-13

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 65.53  E-value: 4.08e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488285050    5 VGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVG-DDGKIGLSIR 74
Cdd:TIGR00717 446 VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDkKNRKVSLSVK 516
 
Name Accession Description Interval E-value
PRK08582 PRK08582
RNA-binding protein S1;
1-148 5.77e-67

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 199.87  E-value: 5.77e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   1 MSIEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDDGKIGLSIRKAQEPA 80
Cdd:PRK08582   1 MSIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRP 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488285050  81 EGQQPKrefqrrennyenrdrnPRAGGKKPFNKPQAnnnnNKQDFDSLMSSFLKDSDDRLSSLKRNTE 148
Cdd:PRK08582  81 KRQHDR----------------PRHEDNRGGGNDVA----PKEDFEQKMSRFLKDSEDRLTSIKRNTE 128
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 1-148 2.08e-57

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 175.37  E-value: 2.08e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   1 MSIEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDDGKIGLSIRKAQEPA 80
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGKISLSIKQAEEKP 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488285050  81 EGQqpkrefqrrenNYENRDRNPRAGgkkpfnkpqannnnnKQDFDSLMSSFLKDSDDRLSSLKRNTE 148
Cdd:COG1098   81 KRP-----------PRPRRNSRPKAG---------------FESFEDKLSKFLKDSDERLSDLKKRTE 122
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 3-98 2.74e-35

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator.


Pssm-ID: 468553 [Multi-domain]  Cd Length: 113  Bit Score: 118.68  E-value: 2.74e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   3 IEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDD-GKIGLSIRkAQEPAE 81
Cdd:NF040579   1 YKIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYtGKISLSLR-ALEEAP 79

                         90
                 ....*....|....*..
gi 488285050  82 GQQPKREFQRRENNYEN 98
Cdd:NF040579  80 EKHRKRRKHRWTNKRLK 96
PRK05807 PRK05807
RNA-binding protein S1;
1-148 4.28e-35

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 119.08  E-value: 4.28e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   1 MSIEVGAKLPGKVSGITNFGAFIDLgEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDDGKIGLSIRKAQEPA 80
Cdd:PRK05807   1 MTLKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQAMKQK 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488285050  81 EGQQPKREFQRRENNYENrdrnpraggkkpfnkpqannnnnKQDFDSLMSSFLKDSDDRLSSLKRNTE 148
Cdd:PRK05807  80 KSVKPAEIDWQKEKNKNN-----------------------NGNFEDRLSKFLKDSEERFQDLKKHQD 124
PRK08059 PRK08059
general stress protein 13; Validated
 3-87 3.79e-32

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 110.91  E-value: 3.79e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   3 IEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDD-GKIGLSIRKAQEPAE 81
Cdd:PRK08059   5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEkGKISLSIRATEEAPE 84


                 ....*.
gi 488285050  82 GQQPKR 87
Cdd:PRK08059  85 AKRKKG 90
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-74 2.37e-27

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 96.97  E-value: 2.37e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488285050   6 GAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDDGKIGLSIR 74
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 3-76 1.13e-25

Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 101.62  E-value: 1.13e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488285050   3 IEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDDGKIGLSiRKA 76
Cdd:COG1185  614 PEVGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEIDDQGRIKLS-RKA 686
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
4-82 1.36e-25

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 101.64  E-value: 1.36e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   4 EVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVgdD---GKIGLSIRKAQEPA 80
Cdd:COG2183  640 KPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEV--DlkrKRISLSMKLDDEAG 717


                 ..
gi 488285050  81 EG 82
Cdd:COG2183  718 AA 719
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 3-76 5.32e-24

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 97.04  E-value: 5.32e-24
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488285050   3 IEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDDGKIGLSIRKA 76
Cdd:PRK11824 619 PEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKAV 692
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 11-73 1.04e-22

S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 85.29  E-value: 1.04e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488285050  11 GKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDDGKIGLSI 73
Cdd:cd04472    6 GKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLSR 68
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 2-78 1.30e-22

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 91.64  E-value: 1.30e-22
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488285050   2 SIEVGAKLPGKVSGITNFGAFIDLGeGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDD-GKIGLSIRKAQE 78
Cdd:COG0539  186 KLEEGDVVEGTVKNITDFGAFVDLG-GVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREkERISLSLKQLQP 262
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 2-78 2.29e-21

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 88.78  E-value: 2.29e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488285050   2 SIEVGAKLPGKVSGITNFGAFIDLGeGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDD-GKIGLSIRKAQE 78
Cdd:PRK06676 189 SLKEGDVVEGTVARLTDFGAFVDIG-GVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWEtERISLSLKDTLP 265
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 6-72 9.49e-21

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 80.35  E-value: 9.49e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488285050   6 GAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVG-DDGKIGLS 72
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDeERGRISLS 68
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
4-74 1.31e-20

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 79.96  E-value: 1.31e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488285050     4 EVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSV-GDDGKIGLSIR 74
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVdEEKGRIILSLK 72
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
3-96 6.67e-20

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 79.75  E-value: 6.67e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   3 IEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGD-DGKIGLSIRKAQEPAE 81
Cdd:PRK07252   1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEyTGKASLSLRTLEEEKQ 80

                         90
                 ....*....|....*
gi 488285050  82 GQQPKREFQRRENNY 96
Cdd:PRK07252  81 HFPHRHRFSNSRHKI 95
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 3-77 1.41e-19

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 83.17  E-value: 1.41e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488285050   3 IEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVS-NGFVKDIHDVLTVGDEVTVKVTSV-GDDGKIGLSIRKAQ 77
Cdd:COG0539  272 YPVGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIdPEERRISLSIKQLA 348
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
5-81 1.13e-17

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 78.84  E-value: 1.13e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488285050   5 VGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSV-GDDGKIGLSIRKAQEPAE 81
Cdd:PRK00087 562 VGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVdPEEKRIRLSIKEVEEEPG 639
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 5-99 3.20e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 77.22  E-value: 3.20e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   5 VGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDDGK-IGLSIRKAQE-PAEG 82
Cdd:PRK06676 277 EGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKrISLSIKALEEaPAEE 356

                         90
                 ....*....|....*..
gi 488285050  83 QQPKREFQRRENNYENR 99
Cdd:PRK06676 357 EDRREEYRQYELPEEET 373
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 4-73 1.10e-16

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 70.01  E-value: 1.10e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488285050    4 EVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDD-GKIGLSI 73
Cdd:pfam00575   2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDrRRIILSI 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 5-98 2.26e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 74.82  E-value: 2.26e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   5 VGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVG-DDGKIGLSIrKAQEPAEGQ 83
Cdd:PRK06299 460 KGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDrKNRRISLSI-KALDEAEEK 538

                         90
                 ....*....|....*
gi 488285050  84 QPKREFQRRENNYEN 98
Cdd:PRK06299 539 EAIAEYNSASDSKTT 553
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 5-72 3.31e-16

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 68.42  E-value: 3.31e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488285050   5 VGAKLPGKVSGITNFGAFIDLGeGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSV-GDDGKIGLS 72
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIdKERKRISLG 68
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 9-72 3.36e-16

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 68.56  E-value: 3.36e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488285050   9 LPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGD-DGKIGLS 72
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPeKGRISLS 65
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 4-78 6.16e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 73.66  E-value: 6.16e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   4 EVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVS--NgfvKDIH--DVLTVGDEVTVKVTSV-GDDGKIGLSIRKAQE 78
Cdd:PRK06299 285 PVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSwtK---KNKHpsKVVSVGQEVEVMVLEIdEEKRRISLGLKQCKE 361
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
2-75 1.18e-15

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 73.06  E-value: 1.18e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488285050   2 SIEVGAKLPGKVSGITNFGAFIDLGeGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVG-DDGKIGLSIRK 75
Cdd:PRK00087 474 SLEEGDVVEGEVKRLTDFGAFVDIG-GVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDkENKKLSLSLKK 547
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 4-93 4.51e-15

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 69.85  E-value: 4.51e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   4 EVGAKLPGKVSGITNFGAFIDLGE--GKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDD-GKIGLSIRKAqepa 80
Cdd:PRK03987   7 EEGELVVGTVKEVKDFGAFVTLDEypGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRkGHIDLSLKRV---- 82

                         90
                 ....*....|...
gi 488285050  81 egqqpkREFQRRE 93
Cdd:PRK03987  83 ------NEHQRRE 89
rpsA PRK13806
30S ribosomal protein S1; Provisional
 3-78 1.01e-14

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 70.14  E-value: 1.01e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   3 IEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDDGK-----IGLSIRKAQ 77
Cdd:PRK13806 200 VKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglrISLSIKQAG 279


                 .
gi 488285050  78 E 78
Cdd:PRK13806 280 G 280
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 10-91 1.09e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 70.07  E-value: 1.09e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050  10 PGKVSGITNFGAFIDLGeGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVG-DDGKIGLSIRKAQEpaegqQPKRE 88
Cdd:PRK07899 213 KGVVSSIVNFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDmDRERVSLSLKATQE-----DPWQQ 286


                 ...
gi 488285050  89 FQR 91
Cdd:PRK07899 287 FAR 289
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 11-74 1.11e-14

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 64.95  E-value: 1.11e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488285050  11 GKVSGITNFGAFIDL---GEGKTGLVHISEVS-NGFVKDIHDVLTVGDEVTVKVTSVgDDGKIGLSIR 74
Cdd:cd05684    6 GKVTSIMDFGCFVQLeglKGRKEGLVHISQLSfEGRVANPSDVVKRGQKVKVKVISI-QNGKISLSMK 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 2-78 1.16e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 70.19  E-value: 1.16e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488285050   2 SIEVGAKLPGKVSGITNFGAFIDLGeGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDD-GKIGLSIRKAQE 78
Cdd:PRK06299 198 NLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEkKRVSLGLKQLGE 274
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 11-73 3.77e-14

S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.


Pssm-ID: 240191 [Multi-domain]  Cd Length: 73  Bit Score: 63.65  E-value: 3.77e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488285050  11 GKVSGITNFGAFIDL-GEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDDGKIGLSI 73
Cdd:cd05686    9 GEVASVTEYGAFVKIpGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL 72
rpsA PRK13806
30S ribosomal protein S1; Provisional
 3-77 6.15e-14

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 67.83  E-value: 6.15e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488285050   3 IEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSngFVKDIH---DVLTVGDEVTVKVTSVGDDGK-IGLSIRKAQ 77
Cdd:PRK13806 290 LKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMS--WTRRVNkpeDVVAPGDAVAVKIKDIDPAKRrISLSLRDAE 366
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 5-78 9.61e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 67.38  E-value: 9.61e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488285050   5 VGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVG-DDGKIGLSIRKAQE 78
Cdd:PRK07899 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDlERRRISLSLKQANE 367
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 5-74 4.08e-13

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 65.53  E-value: 4.08e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488285050    5 VGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVG-DDGKIGLSIR 74
Cdd:TIGR00717 446 VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDkKNRKVSLSVK 516
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 3-72 4.34e-13

S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.


Pssm-ID: 239919 [Multi-domain]  Cd Length: 77  Bit Score: 60.70  E-value: 4.34e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   3 IEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVkdihdvltVGDEVTVKVTSVGDDGKIGLS 72
Cdd:cd04473   14 LEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDYE--------VGDEVIVQVTDIPENGNIDLI 75
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 3-93 5.65e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 64.82  E-value: 5.65e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   3 IEVGAKLPGKVSGITNFGAFIDLGeGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSV-GDDGKIGLSIrKAQEPAE 81
Cdd:PRK07400 194 LEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLdAERGRISLST-KQLEPEP 271

                         90
                 ....*....|....*
gi 488285050  82 G---QQPKREFQRRE 93
Cdd:PRK07400 272 GdmlKDPQKVFDKAE 286
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 3-87 1.58e-12

Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, recombination and repair];


Pssm-ID: 440724 [Multi-domain]  Cd Length: 626  Bit Score: 64.09  E-value: 1.58e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   3 IEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVkdihdvltVGDEVTVKVTSVGDDGKIGL---SIRKAQEP 79
Cdd:COG1107   37 LEPGRYYRGTVDGVADFGVFVDLNDHVTGLLHRSELDQDWE--------VGDEVFVQVKEVRDNGNVDLgwvSIDSYETV 108


                 ....*...
gi 488285050  80 AEGQQPKR 87
Cdd:COG1107  109 EVEKELPR 116
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 5-78 2.01e-12

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 63.60  E-value: 2.01e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488285050    5 VGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVS-NGFVKDIHDVLTVGDEVTVKVTSVG-DDGKIGLSIRKAQE 78
Cdd:TIGR00717 272 VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDpERRRLSLGLKQCKA 347
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 5-74 8.65e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 61.72  E-value: 8.65e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488285050   5 VGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVS-NGFVKDIHDVLTVGDEVTVKVTSVG-DDGKIGLSIR 74
Cdd:PRK06299 373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDvEKERISLGIK 444
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 13-131 1.82e-11

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 61.06  E-value: 1.82e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050  13 VSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDDGKIGLSIRKAQEPAEGQQPKREFQR- 91
Cdd:PLN00207 762 IKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQLRLSRRALLPEANSEKSSQKQQGg 841

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 488285050  92 ------RENNYENRDRNPRAGGKKPFNKPQANNNNNKQDFDSLMSS 131
Cdd:PLN00207 842 stkdkaPQKKYVNTSSRPRRAAQAEKNSAENAAVPKKKDYKRATSG 887
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 4-75 3.24e-11

S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein.


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 56.05  E-value: 3.24e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488285050   4 EVGAKLPGKVSGITNFGAFIDLGE--GKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDD-GKIGLSIRK 75
Cdd:cd04452    2 EEGELVVVTVKSIADMGAYVSLLEygNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEkGYIDLSKKR 76
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 2-78 3.70e-11

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 60.13  E-value: 3.70e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488285050    2 SIEVGAKLPGKVSGITNFGAFIDLGeGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDD-GKIGLSIRKAQE 78
Cdd:TIGR00717 184 NLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEkGRISLSLKQLGE 260
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 3-63 4.30e-10

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 52.98  E-value: 4.30e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488285050   3 IEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSV 63
Cdd:cd04461   12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSV 72
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 2-78 1.38e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 55.27  E-value: 1.38e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488285050   2 SIEVGAKLPGKVSGITNFGAFIDLGEGKT-GLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSV-GDDGKIGLSIRKAQE 78
Cdd:PRK06676  14 EVEVGDVVTGEVLKVEDKQVFVNIEGYKVeGVIPISELSNDHIEDINDVVKVGDELEVYVLKVeDGEGNLLLSKRRLEA 92
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-66 1.75e-09

S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240194 [Multi-domain]  Cd Length: 72  Bit Score: 51.42  E-value: 1.75e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488285050   6 GAKLPGKVSGITNFGAFIDLGEGKTGLVHISEV--SNgfvKDIH--DVLTVGDEVTVKVTSVGDD 66
Cdd:cd05689    4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMdwTN---KNIHpsKVVSLGDEVEVMVLDIDEE 65
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 4-74 2.15e-09

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 51.18  E-value: 2.15e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488285050   4 EVGAKLPGKVSGITNFGAFIDL-GEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDD-GKIGLSIR 74
Cdd:cd05708    1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEkKRISLGLK 73
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-74 7.30e-09

S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 49.45  E-value: 7.30e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   6 GAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGD-DGKIGLSIR 74
Cdd:cd05687    1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDeEGNVVLSKR 70
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
2-78 7.64e-09

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 53.41  E-value: 7.64e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488285050   2 SIEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGD-DGKIGLSIRKAQE 78
Cdd:PRK00087 299 QIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDeDGYVVLSKKEADR 376
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 5-74 1.71e-08

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 52.43  E-value: 1.71e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488285050    5 VGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVS-NGFVKDIHDVLTVGDEVTVKVTSVGDDGK-IGLSIR 74
Cdd:TIGR00717 359 VGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKrISLGVK 430
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 2-78 3.37e-08

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 51.20  E-value: 3.37e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488285050   2 SIEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNgfvKDIHDVLTVGDEVTVKVTSVGD-DGKIGLSIRKAQE 78
Cdd:COG0539   15 ELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSD---EPGELEVKVGDEVEVYVEKVEDgEGEIVLSKKKADR 89
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-78 3.38e-08

S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 48.04  E-value: 3.38e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488285050   6 GAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVgdDGK---IGLSIrKAQE 78
Cdd:cd05691    1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNV--DRKnrkISLSI-KAKE 73
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-63 3.89e-08

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 47.87  E-value: 3.89e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488285050   6 GAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVS-NGFVKDIHDVLTVGDEVTVKVTSV 63
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNI 59
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 5-69 4.86e-08

S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.


Pssm-ID: 239917 [Multi-domain]  Cd Length: 83  Bit Score: 47.78  E-value: 4.86e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   5 VGAKLPGKVSGITNFGAFIDLGEGKT-GLVHISEVSNGFVkdIHD-------------VLTVGDEVTVKVTSVG-DDGKI 69
Cdd:cd04471    1 VGEEFDGVISGVTSFGLFVELDNLTVeGLVHVSTLGDDYY--EFDeenhalvgertgkVFRLGDKVKVRVVRVDlDRRKI 78
VacB COG0557
Exoribonuclease R [Transcription];
5-73 2.69e-07

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 48.95  E-value: 2.69e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   5 VGAKLPGKVSGITNFGAFIDLGEGKT-GLVHISEVSNGFVkdIHD-------------VLTVGDEVTVKVTSV-GDDGKI 69
Cdd:COG0557  622 VGEEFEGVISGVTSFGLFVELDELGVeGLVHVSSLGDDYY--EYDerrqalvgertgkRYRLGDRVEVRVVRVdLDRRQI 699


                 ....
gi 488285050  70 GLSI 73
Cdd:COG0557  700 DFEL 703
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 3-74 1.09e-06

S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240211 [Multi-domain]  Cd Length: 73  Bit Score: 43.78  E-value: 1.09e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488285050   3 IEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVG-DDGKIGLSIR 74
Cdd:cd05706    1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDvPNKKIALSLR 73
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 11-92 1.25e-06

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 47.01  E-value: 1.25e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050  11 GKVSGITNFGAFIDLGEGKTGLVHISEVSngFVKDI---HDVLTVGDEVTVKVtsVGDD---GKIGLSIRKAQ----EPA 80
Cdd:PRK12269 584 GRVTKIADFGAFIELAEGIEGLAHISEFS--WVKKTskpSDMVKIGDEVECMI--LGYDiqaGRVSLGLKQVTanpwEEI 659

                         90
                 ....*....|...
gi 488285050  81 EGQQP-KREFQRR 92
Cdd:PRK12269 660 EARYPvGARFTRR 672
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 6-74 1.54e-06

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 43.37  E-value: 1.54e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   6 GAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVG-DDGKIGLSIR 74
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDpEQQRLLLSCK 70
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 11-74 3.26e-06

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 44.82  E-value: 3.26e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050  11 GKVSGITNFGAFIDLGEgKTGLVHISEVSNGFV-----------KDIHDVLTVGDEVTVKVTSV------GDDGKIGLSI 73
Cdd:PRK08563  87 GEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYIsydpkngrligKESKRVLKVGDVVRARIVAVslkerrPRGSKIGLTM 165


                 .
gi 488285050  74 R 74
Cdd:PRK08563 166 R 166
rpsA PRK13806
30S ribosomal protein S1; Provisional
 5-94 1.17e-05

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 43.94  E-value: 1.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   5 VGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVG-DDGKIGLSIRKAQEPAEGQ 83
Cdd:PRK13806 379 PGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDtAKRKISLAPAGAAGSGADD 458

                         90
                 ....*....|.
gi 488285050  84 QPKREFQRREN 94
Cdd:PRK13806 459 DDWKQFAPKKS 469
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 6-72 1.53e-05

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 40.74  E-value: 1.53e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488285050   6 GAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVG-DDGKIGLS 72
Cdd:cd05707    1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDpDNGRIEMT 68
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 2-92 2.26e-05

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 43.16  E-value: 2.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   2 SIEVGAKLPGKVSGITNFGAFIDLGeGKTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGD-DGKIGLSIRKAQEpa 80
Cdd:PRK12269 490 SVHIEDSVSGVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQaEKRINLSLKHFQP-- 566

                         90
                 ....*....|..
gi 488285050  81 egqQPKREFQRR 92
Cdd:PRK12269 567 ---DPWLEFENK 575
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 11-76 7.22e-05

S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.


Pssm-ID: 239907 [Multi-domain]  Cd Length: 99  Bit Score: 39.58  E-value: 7.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050  11 GKVSGITNFGAFIDLGEgKTGLVHISEVSNGFV-----------KDIHDVLTVGDEVTVKVTSV------GDDGKIGLSI 73
Cdd:cd04460    5 GEVVEVVDFGAFVRIGP-VDGLLHISQIMDDYIsydpknkrligEETKRVLKVGDVVRARIVAVslkerrPRESKIGLTM 83


                 ...
gi 488285050  74 RKA 76
Cdd:cd04460   84 RQP 86
S1_RNase_E cd04453
S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential ...
 20-61 8.48e-05

S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain that is highly homologous to that of RNase E. RNase G not only shares sequence similarity with RNase E, but also functionally overlaps with RNase E. In Escherichia coli, RNase G is involved in the maturation of the 5' end of the 16S rRNA. RNase G plays a secondary role in mRNA decay.


Pssm-ID: 239900 [Multi-domain]  Cd Length: 88  Bit Score: 39.11  E-value: 8.48e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 488285050  20 GAFIDLGEGKTGLVHISEVSNGF---VKDIHDVLTVGDEVTVKVT 61
Cdd:cd04453   24 AAFVDIGLGKNGFLHLSDILPAYfkkHKKIAKLLKEGQEILVQVV 68
PRK11642 PRK11642
ribonuclease R;
1-124 4.46e-04

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 39.34  E-value: 4.46e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   1 MSIEVGAKLPGKVSGITNFGAFIDLGE-GKTGLVHISEVSNGFVKdiHD-------------VLTVGDEVTVKVTSVG-D 65
Cdd:PRK11642 639 MLDQVGNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDNDYYR--FDqvgqrligessgqTYRLGDRVEVRVEAVNmD 716

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050  66 DGKIGLSIRKAQEPAEGQ-QPKREFQRRENNYENRDRNPRAGGKKPFNKPQANNNNNKQD 124
Cdd:PRK11642 717 ERKIDFSLISSERAPRNVgKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAK 776
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 29-74 4.49e-04

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 38.80  E-value: 4.49e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 488285050  29 KTGLVHISEVSNGFVKDIHDVLTVGDEVTVKVTSVGDdgKIGLSIR 74
Cdd:PRK09521  98 KLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYTD--PLQLSTK 141
S1_2 pfam13509
S1 domain; The S1 domain was originally identified as a repeat motif in the ribosomal S1 ...
 11-58 6.17e-04

S1 domain; The S1 domain was originally identified as a repeat motif in the ribosomal S1 protein. It was later identified in a wide range of proteins. The S1 domain has an OB-fold structure. The S1 domain is involved in nucleic acid binding.


Pssm-ID: 433267 [Multi-domain]  Cd Length: 61  Bit Score: 36.36  E-value: 6.17e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 488285050   11 GKVSGITNFGAFIDLGEGKTGLVHISEVSNGfvkdihdvLTVGDEVTV 58
Cdd:pfam13509   7 LKVIRETDFGYFLDGGEGGEVLLPKREVPEE--------LEIGDEVEV 46
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 5-87 7.52e-04

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 38.92  E-value: 7.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   5 VGAKLPGKVSGITNFGAFIDLGEGKTGLV---HISEVSNGFVKDIHDVLTVGDEVTVKVTSVG-DDGKIGLSIRKAQEPA 80
Cdd:PRK12269 752 VGSTVEGEVSSVTDFGIFVRVPGGVEGLVrkqHLVENRDGDPGEALRKYAVGDRVKAVIVDMNvKDRKVAFSVRDYQRKV 831


                 ....*..
gi 488285050  81 EGQQPKR 87
Cdd:PRK12269 832 QRDELSR 838
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 3-76 9.76e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 38.22  E-value: 9.76e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488285050   3 IEVGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNgfvKDIHDVLTVGDEVTVKVTSVGD-DGKIGLSIRKA 76
Cdd:PRK06299  28 TREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKN---EQGELEVKVGDEVEVYVERIEDgFGETVLSREKA 99
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 5-74 2.75e-03

S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 35.27  E-value: 2.75e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488285050   5 VGAKLPGKVSGITNFGAFIDLGEGKTGLVHISEVSNGFVK-------------------DIHDVLTVGDEVTVKVTSVGD 65
Cdd:cd05693    3 EGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTErleeldeeseeeddeeelpDLEDLFSVGQLVRCKVVSLDK 82

                         90
                 ....*....|...
gi 488285050  66 DG----KIGLSIR 74
Cdd:cd05693   83 SKsgkkRIELSLE 95
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH