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Conserved domains on  [gi|516478451|ref|WP_017866895|]
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S1 domain-containing RNA-binding protein [Ligilactobacillus pobuzihii]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK08582 super family cl35719
RNA-binding protein S1;
1-160 6.39e-59

RNA-binding protein S1;


The actual alignment was detected with superfamily member PRK08582:

Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 179.84  E-value: 6.39e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   1 MSIEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDDGKIALSIRKAKESH 80
Cdd:PRK08582   1 MSIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451  81 QnhghqghshsehGPKSRPHNNSGKSFNdrsnnhnnnkkrsysshkNESHKKDDFDSLLAGFMKQSDERLTSLKRNTEGK 160
Cdd:PRK08582  81 K------------RQHDRPRHEDNRGGG------------------NDVAPKEDFEQKMSRFLKDSEDRLTSIKRNTESK 130
 
Name Accession Description Interval E-value
PRK08582 PRK08582
RNA-binding protein S1;
1-160 6.39e-59

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 179.84  E-value: 6.39e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   1 MSIEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDDGKIALSIRKAKESH 80
Cdd:PRK08582   1 MSIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451  81 QnhghqghshsehGPKSRPHNNSGKSFNdrsnnhnnnkkrsysshkNESHKKDDFDSLLAGFMKQSDERLTSLKRNTEGK 160
Cdd:PRK08582  81 K------------RQHDRPRHEDNRGGG------------------NDVAPKEDFEQKMSRFLKDSEDRLTSIKRNTESK 130
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 1-160 2.60e-53

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 165.35  E-value: 2.60e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   1 MSIEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDDGKIALSIRKAKESH 80
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGKISLSIKQAEEKP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451  81 QnhghqghshsehgPKSRPHNNSgksfndrsnnhnnnkkrsysshkNESHKKDDFDSLLAGFMKQSDERLTSLKRNTEGK 160
Cdd:COG1098   81 K-------------RPPRPRRNS-----------------------RPKAGFESFEDKLSKFLKDSDERLSDLKKRTESK 124
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 3-108 2.44e-37

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: 124.08  E-value: 2.44e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   3 IEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSV-SDDGKIALSIRkAKESHQ 81
Cdd:NF040579   1 YKIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIdEYTGKISLSLR-ALEEAP 79

                         90       100
                 ....*....|....*....|....*..
gi 516478451  82 NHGHQGHSHsehgPKSRPHNNSGksFN 108
Cdd:NF040579  80 EKHRKRRKH----RWTNKRLKIG--FN 100
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-74 1.14e-26

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: 95.82  E-value: 1.14e-26
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516478451   6 GSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDDGKIALSIR 74
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
4-74 5.38e-22

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 83.81  E-value: 5.38e-22
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516478451     4 EVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSV-SDDGKIALSIR 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 4.86e-17

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: 71.16  E-value: 4.86e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 516478451    4 EVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDD-GKIALSI 73
Cdd:pfam00575   2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDrRRIILSI 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 5-78 9.98e-15

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: 70.53  E-value: 9.98e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516478451    5 VGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEIS-DGFVKDIHDVLSVGDEVTVKVLSVS-DDGKIALSIRKAKE 78
Cdd:TIGR00717 272 VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDpERRRLSLGLKQCKA 347
 
Name Accession Description Interval E-value
PRK08582 PRK08582
RNA-binding protein S1;
1-160 6.39e-59

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 179.84  E-value: 6.39e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   1 MSIEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDDGKIALSIRKAKESH 80
Cdd:PRK08582   1 MSIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451  81 QnhghqghshsehGPKSRPHNNSGKSFNdrsnnhnnnkkrsysshkNESHKKDDFDSLLAGFMKQSDERLTSLKRNTEGK 160
Cdd:PRK08582  81 K------------RQHDRPRHEDNRGGG------------------NDVAPKEDFEQKMSRFLKDSEDRLTSIKRNTESK 130
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 1-160 2.60e-53

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 165.35  E-value: 2.60e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   1 MSIEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDDGKIALSIRKAKESH 80
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGKISLSIKQAEEKP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451  81 QnhghqghshsehgPKSRPHNNSgksfndrsnnhnnnkkrsysshkNESHKKDDFDSLLAGFMKQSDERLTSLKRNTEGK 160
Cdd:COG1098   81 K-------------RPPRPRRNS-----------------------RPKAGFESFEDKLSKFLKDSDERLSDLKKRTESK 124
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 3-108 2.44e-37

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: 124.08  E-value: 2.44e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   3 IEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSV-SDDGKIALSIRkAKESHQ 81
Cdd:NF040579   1 YKIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIdEYTGKISLSLR-ALEEAP 79

                         90       100
                 ....*....|....*....|....*..
gi 516478451  82 NHGHQGHSHsehgPKSRPHNNSGksFN 108
Cdd:NF040579  80 EKHRKRRKH----RWTNKRLKIG--FN 100
PRK08059 PRK08059
general stress protein 13; Validated
 3-88 3.59e-31

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 108.98  E-value: 3.59e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   3 IEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDD-GKIALSIRKAKESHQ 81
Cdd:PRK08059   5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEkGKISLSIRATEEAPE 84


                 ....*..
gi 516478451  82 NHGHQGH 88
Cdd:PRK08059  85 AKRKKGK 91
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
1-78 1.44e-29

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 113.20  E-value: 1.44e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   1 MSIE---VGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVsdD---GKIALSIR 74
Cdd:COG2183  634 LKIEdlkPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEV--DlkrKRISLSMK 711


                 ....
gi 516478451  75 KAKE 78
Cdd:COG2183  712 LDDE 715
PRK05807 PRK05807
RNA-binding protein S1;
1-160 1.03e-27

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 100.59  E-value: 1.03e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   1 MSIEVGSKVTGKVSGITNFGAFIDLgEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDDGKIALSIRKAKesh 80
Cdd:PRK05807   1 MTLKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQAM--- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451  81 qnhghqghshsehgpksrPHNNSGKSfndrsnnhnnnKKRSYSSHKNeSHKKDDFDSLLAGFMKQSDERLTSLKRNTEGK 160
Cdd:PRK05807  77 ------------------KQKKSVKP-----------AEIDWQKEKN-KNNNGNFEDRLSKFLKDSEERFQDLKKHQDSK 126
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-74 1.14e-26

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: 95.82  E-value: 1.14e-26
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516478451   6 GSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDDGKIALSIR 74
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 3-76 1.61e-26

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


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 104.70  E-value: 1.61e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516478451   3 IEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDDGKIALSiRKA 76
Cdd:COG1185  614 PEVGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEIDDQGRIKLS-RKA 686
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 3-76 9.73e-25

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 99.35  E-value: 9.73e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516478451   3 IEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDDGKIALSIRKA 76
Cdd:PRK11824 619 PEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKAV 692
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 2-78 3.62e-24

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: 96.27  E-value: 3.62e-24
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516478451   2 SIEVGSKVTGKVSGITNFGAFIDLGEHkNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDD-GKIALSIRKAKE 78
Cdd:COG0539  186 KLEEGDVVEGTVKNITDFGAFVDLGGV-DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREkERISLSLKQLQP 262
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 2-74 4.76e-24

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 96.48  E-value: 4.76e-24
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516478451   2 SIEVGSKVTGKVSGITNFGAFIDLGEhKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDD-GKIALSIR 74
Cdd:PRK06676 189 SLKEGDVVEGTVARLTDFGAFVDIGG-VDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWEtERISLSLK 261
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 6-72 1.87e-22

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: 84.98  E-value: 1.87e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516478451   6 GSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVS-DDGKIALS 72
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDeERGRISLS 68
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
4-74 5.38e-22

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 83.81  E-value: 5.38e-22
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516478451     4 EVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSV-SDDGKIALSIR 74
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVdEEKGRIILSLK 72
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 10-73 8.49e-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: 83.36  E-value: 8.49e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516478451  10 TGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDDGKIALSI 73
Cdd:cd04472    5 EGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLSR 68
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 3-77 1.59e-21

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: 88.95  E-value: 1.59e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 516478451   3 IEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEIS-DGFVKDIHDVLSVGDEVTVKVLSV-SDDGKIALSIRKAK 77
Cdd:COG0539  272 YPVGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIdPEERRISLSIKQLA 348
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
5-78 1.64e-19

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 84.61  E-value: 1.64e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516478451   5 VGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDDGK-IALSIRKAKE 78
Cdd:PRK00087 562 VGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKrIRLSIKEVEE 636
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 5-78 1.86e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 81.07  E-value: 1.86e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516478451   5 VGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSV-SDDGKIALSIRKAKE 78
Cdd:PRK06676 277 EGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVnEEEKRISLSIKALEE 351
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 4-78 2.25e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 80.98  E-value: 2.25e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 516478451   4 EVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEIS-DGFVKDIHDVLSVGDEVTVKVLSV-SDDGKIALSIRKAKE 78
Cdd:PRK06299 285 PVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEIdEEKRRISLGLKQCKE 361
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
3-93 9.90e-18

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 74.35  E-value: 9.90e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   3 IEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSD-DGKIALSIRK-AKESH 80
Cdd:PRK07252   1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEyTGKASLSLRTlEEEKQ 80

                         90
                 ....*....|...
gi 516478451  81 QNHGHQGHSHSEH 93
Cdd:PRK07252  81 HFPHRHRFSNSRH 93
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
2-79 3.95e-17

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 77.68  E-value: 3.95e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516478451   2 SIEVGSKVTGKVSGITNFGAFIDLGEHKnGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVS-DDGKIALSIRKAKES 79
Cdd:PRK00087 474 SLEEGDVVEGEVKRLTDFGAFVDIGGVD-GLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDkENKKLSLSLKKLLPD 551
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 4-73 4.86e-17

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: 71.16  E-value: 4.86e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 516478451    4 EVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDD-GKIALSI 73
Cdd:pfam00575   2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDrRRIILSI 72
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 9-72 6.45e-17

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: 70.49  E-value: 6.45e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516478451   9 VTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSD-DGKIALS 72
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPeKGRISLS 65
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 4-81 1.18e-16

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 74.48  E-value: 1.18e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   4 EVGSKVTGKVSGITNFGAFIDLGEH--KNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDD-GKIALSIRKAKEsH 80
Cdd:PRK03987   7 EEGELVVGTVKEVKDFGAFVTLDEYpgKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRkGHIDLSLKRVNE-H 85


                 .
gi 516478451  81 Q 81
Cdd:PRK03987  86 Q 86
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 2-80 1.21e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 75.97  E-value: 1.21e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   2 SIEVGSKVTGKVSGITNFGAFIDLGEhKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDD-GKIALSIrKAKESH 80
Cdd:PRK06299 198 NLEEGQVVEGVVKNITDYGAFVDLGG-VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEkKRVSLGL-KQLGED 275
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 5-72 2.42e-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: 69.19  E-value: 2.42e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516478451   5 VGSKVTGKVSGITNFGAFIDLGEhKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVS-DDGKIALS 72
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDLGG-VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDkERKRISLG 68
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 5-79 6.62e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 74.05  E-value: 6.62e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 516478451   5 VGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEIS-DGFVKDIHDVLSVGDEVTVKVLSV-SDDGKIALSIRKAKES 79
Cdd:PRK06299 373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVdVEKERISLGIKQLEED 449
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 5-78 7.36e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 74.05  E-value: 7.36e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516478451   5 VGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVS-DDGKIALSIrKAKE 78
Cdd:PRK06299 460 KGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDrKNRRISLSI-KALD 533
rpsA PRK13806
30S ribosomal protein S1; Provisional
 3-78 2.38e-15

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 72.45  E-value: 2.38e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   3 IEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDDGK-----IALSIRKAK 77
Cdd:PRK13806 200 VKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglrISLSIKQAG 279


                 .
gi 516478451  78 E 78
Cdd:PRK13806 280 G 280
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 5-78 9.98e-15

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: 70.53  E-value: 9.98e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516478451    5 VGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEIS-DGFVKDIHDVLSVGDEVTVKVLSVS-DDGKIALSIRKAKE 78
Cdd:TIGR00717 272 VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDpERRRLSLGLKQCKA 347
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 10-84 2.21e-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: 64.57  E-value: 2.21e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516478451  10 TGKVSGITNFGAFIDL---GEHKNGLVHISEIS-DGFVKDIHDVLSVGDEVTVKVLSVSdDGKIALSIrkaKESHQNHG 84
Cdd:cd05684    5 KGKVTSIMDFGCFVQLeglKGRKEGLVHISQLSfEGRVANPSDVVKRGQKVKVKVISIQ-NGKISLSM---KDVDQDTG 79
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 4-75 4.75e-14

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: 63.37  E-value: 4.75e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516478451   4 EVGSKVTGKVSGITNFGAFIDLGEHKN--GLVHISEISDGFVKDIHDVLSVGDEVTVKVLSV-SDDGKIALSIRK 75
Cdd:cd04452    2 EEGELVVVTVKSIADMGAYVSLLEYGNieGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVdKEKGYIDLSKKR 76
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 11-73 6.05e-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: 63.27  E-value: 6.05e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516478451  11 GKVSGITNFGAFIDL-GEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDDGKIALSI 73
Cdd:cd05686    9 GEVASVTEYGAFVKIpGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 5-74 6.25e-14

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: 68.22  E-value: 6.25e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 516478451    5 VGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVS-DDGKIALSIR 74
Cdd:TIGR00717 446 VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDkKNRKVSLSVK 516
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 11-78 9.69e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 67.76  E-value: 9.69e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516478451  11 GKVSGITNFGAFIDLGeHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSV-SDDGKIALSIRKAKE 78
Cdd:PRK07899 214 GVVSSIVNFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVdMDRERVSLSLKATQE 281
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 5-79 1.58e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 66.99  E-value: 1.58e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516478451   5 VGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVS-DDGKIALSIRKAKES 79
Cdd:PRK07899 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDlERRRISLSLKQANEG 368
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 3-71 1.78e-13

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: 67.17  E-value: 1.78e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516478451   3 IEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFvkdihdvlSVGDEVTVKVLSVSDDGKIAL 71
Cdd:COG1107   37 LEPGRYYRGTVDGVADFGVFVDLNDHVTGLLHRSELDQDW--------EVGDEVFVQVKEVRDNGNVDL 97
rpsA PRK13806
30S ribosomal protein S1; Provisional
 3-76 3.27e-13

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 66.29  E-value: 3.27e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516478451   3 IEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISdgFVKDIH---DVLSVGDEVTVKVLSV-SDDGKIALSIRKA 76
Cdd:PRK13806 290 LKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMS--WTRRVNkpeDVVAPGDAVAVKIKDIdPAKRRISLSLRDA 365
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 3-72 4.22e-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: 61.08  E-value: 4.22e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   3 IEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFvkdihdvlSVGDEVTVKVLSVSDDGKIALS 72
Cdd:cd04473   14 LEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDY--------EVGDEVIVQVTDIPENGNIDLI 75
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 3-75 5.56e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 65.21  E-value: 5.56e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516478451   3 IEVGSKVTGKVSGITNFGAFIDLGeHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSV-SDDGKIALSIRK 75
Cdd:PRK07400 194 LEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLdAERGRISLSTKQ 266
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 2-78 1.09e-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: 64.76  E-value: 1.09e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516478451    2 SIEVGSKVTGKVSGITNFGAFIDLGEhKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSV-SDDGKIALSIRKAKE 78
Cdd:TIGR00717 184 NLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFdKEKGRISLSLKQLGE 260
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 1.68e-12

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: 59.47  E-value: 1.68e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   6 GSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSD-DGKIALSIR 74
Cdd:cd05687    1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDeEGNVVLSKR 70
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 4-74 1.76e-12

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: 59.65  E-value: 1.76e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 516478451   4 EVGSKVTGKVSGITNFGAFIDL-GEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSV-SDDGKIALSIR 74
Cdd:cd05708    1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIdAEKKRISLGLK 73
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 2-78 4.25e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 62.97  E-value: 4.25e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   2 SIEVGSKVTGKVSGITNFGAFIDLGEHK-NGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDDG------KIALSIR 74
Cdd:PRK06676  14 EVEVGDVVTGEVLKVEDKQVFVNIEGYKvEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEgnlllsKRRLEAE 93


                 ....
gi 516478451  75 KAKE 78
Cdd:PRK06676  94 KAWD 97
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-78 1.10e-11

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: 57.28  E-value: 1.10e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516478451   6 GSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVsdDGK---IALSIrKAKE 78
Cdd:cd05691    1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNV--DRKnrkISLSI-KAKE 73
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
2-76 6.70e-11

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 59.58  E-value: 6.70e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516478451   2 SIEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSD-DGKIALSIRKA 76
Cdd:PRK00087 299 QIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDeDGYVVLSKKEA 374
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-66 8.14e-11

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: 54.89  E-value: 8.14e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 516478451   6 GSKVTGKVSGITNFGAFIDLGEHKNGLVHISEIsDGFVKDIH--DVLSVGDEVTVKVLSVSDD 66
Cdd:cd05689    4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEM-DWTNKNIHpsKVVSLGDEVEVMVLDIDEE 65
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 2-78 9.24e-11

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: 58.90  E-value: 9.24e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516478451   2 SIEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDgfvKDIHDVLSVGDEVTVKVLSVSD-DGKIALSIRKAKE 78
Cdd:COG0539   15 ELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSD---EPGELEVKVGDEVEVYVEKVEDgEGEIVLSKKKADR 89
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 5-73 2.86e-10

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: 53.94  E-value: 2.86e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   5 VGSKVTGKVSGITNFGAFIDLGEHK-NGLVHISEISDGFVkdIHD-------------VLSVGDEVTVKVLSVS-DDGKI 69
Cdd:cd04471    1 VGEEFDGVISGVTSFGLFVELDNLTvEGLVHVSTLGDDYY--EFDeenhalvgertgkVFRLGDKVKVRVVRVDlDRRKI 78


                 ....
gi 516478451  70 ALSI 73
Cdd:cd04471   79 DFEL 82
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 3-66 3.52e-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: 53.75  E-value: 3.52e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516478451   3 IEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDD 66
Cdd:cd04461   12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEE 75
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 5-79 4.38e-10

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: 57.05  E-value: 4.38e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 516478451    5 VGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEIS-DGFVKDIHDVLSVGDEVTVKVLSVSDDGK-IALSIRKAKES 79
Cdd:TIGR00717 359 VGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKrISLGVKQLTEN 435
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 13-141 6.64e-10

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 56.83  E-value: 6.64e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451  13 VSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDDGKIALSIRK-AKESHQnhghQGHSHS 91
Cdd:PLN00207 762 IKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQLRLSRRAlLPEANS----EKSSQK 837

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 516478451  92 EHGPKSRPHNNSGKSFNDRSNNHNNNKKRSYSSHKNESHKKDDFDSLLAG 141
Cdd:PLN00207 838 QQGGSTKDKAPQKKYVNTSSRPRRAAQAEKNSAENAAVPKKKDYKRATSG 887
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 9-74 4.16e-09

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 52.91  E-value: 4.16e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   9 VTGKVSGITNFGAFIDLGEhKNGLVHISEISDGFV-----------KDIHDVLSVGDEVTVKVLSVS------DDGKIAL 71
Cdd:PRK08563  85 VEGEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYIsydpkngrligKESKRVLKVGDVVRARIVAVSlkerrpRGSKIGL 163


                 ...
gi 516478451  72 SIR 74
Cdd:PRK08563 164 TMR 166
VacB COG0557
Exoribonuclease R [Transcription];
5-73 9.61e-09

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 53.19  E-value: 9.61e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   5 VGSKVTGKVSGITNFGAFIDLGEHK-NGLVHISEISDGFVkdIHD-------------VLSVGDEVTVKVLSVS-DDGKI 69
Cdd:COG0557  622 VGEEFEGVISGVTSFGLFVELDELGvEGLVHVSSLGDDYY--EYDerrqalvgertgkRYRLGDRVEVRVVRVDlDRRQI 699


                 ....
gi 516478451  70 ALSI 73
Cdd:COG0557  700 DFEL 703
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-63 4.26e-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: 4.26e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 516478451   6 GSKVTGKVSGITNFGAFIDLGEHKNGLVHISEIS-DGFVKDIHDVLSVGDEVTVKVLSV 63
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNI 59
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 9-76 5.73e-08

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: 48.05  E-value: 5.73e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   9 VTGKVSGITNFGAFIDLGEhKNGLVHISEISDGFV-----------KDIHDVLSVGDEVTVKVLSVS------DDGKIAL 71
Cdd:cd04460    3 VEGEVVEVVDFGAFVRIGP-VDGLLHISQIMDDYIsydpknkrligEETKRVLKVGDVVRARIVAVSlkerrpRESKIGL 81


                 ....*
gi 516478451  72 SIRKA 76
Cdd:cd04460   82 TMRQP 86
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 6-72 8.14e-08

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: 46.90  E-value: 8.14e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516478451   6 GSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVS-DDGKIALS 72
Cdd:cd05707    1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDpDNGRIEMT 68
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 5-75 7.49e-07

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 47.78  E-value: 7.49e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516478451   5 VGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISdgFVKDI---HDVLSVGDEVTVKVLSVS-DDGKIALSIRK 75
Cdd:PRK12269 578 VNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFS--WVKKTskpSDMVKIGDEVECMILGYDiQAGRVSLGLKQ 650
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 8.06e-07

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: 44.52  E-value: 8.06e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   6 GSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSV-SDDGKIALSIR 74
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCdPEQQRLLLSCK 70
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 3-74 4.92e-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: 42.24  E-value: 4.92e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 516478451   3 IEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSV-SDDGKIALSIR 74
Cdd:cd05706    1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVdVPNKKIALSLR 73
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 3-77 7.50e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 44.77  E-value: 7.50e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516478451   3 IEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDgfvKDIHDVLSVGDEVTVKVLSVSD-DGKIALSIRKAK 77
Cdd:PRK06299  28 TREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKN---EQGELEVKVGDEVEVYVERIEDgFGETVLSREKAK 100
rpsA PRK13806
30S ribosomal protein S1; Provisional
 5-104 1.05e-05

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 44.33  E-value: 1.05e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   5 VGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVS-DDGKIALSIRKAKESHQNH 83
Cdd:PRK13806 379 PGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDtAKRKISLAPAGAAGSGADD 458

                         90       100
                 ....*....|....*....|.
gi 516478451  84 GhqghSHSEHGPKSRPHNNSG 104
Cdd:PRK13806 459 D----DWKQFAPKKSAPASGG 475
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 2-74 1.09e-05

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 44.70  E-value: 1.09e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516478451   2 SIEVGSKVTGKVSGITNFGAFIDLGEHkNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSD-DGKIALSIR 74
Cdd:PRK12269 490 SVHIEDSVSGVVKSFTSFGAFIDLGGF-DGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQaEKRINLSLK 562
rpsA PRK13806
30S ribosomal protein S1; Provisional
 3-72 1.43e-05

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 43.94  E-value: 1.43e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   3 IEVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDgfvKDIHDVLSVGDEVTVKVLSVSDDgKIALS 72
Cdd:PRK13806  32 LRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLD---ADGELTVAVGDEVELYVVSVNGQ-EIRLS 97
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 4-74 1.52e-05

S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 240215 [Multi-domain]  Cd Length: 86  Bit Score: 41.38  E-value: 1.52e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516478451   4 EVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEI----SDGFVKDIHDVLSVGDEVTVKVLSVSDDGKIALSIR 74
Cdd:cd05789    5 EVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVnlprTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTR 79
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 2-74 2.21e-05

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 42.65  E-value: 2.21e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   2 SIEVGSKVTGKVSGITNFGAFI----------DLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDdgKIAL 71
Cdd:PRK09521  61 LLKKGDIVYGRVVDVKEQRALVrivsiegserELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYTD--PLQL 138


                 ...
gi 516478451  72 SIR 74
Cdd:PRK09521 139 STK 141
S1_RNase_E cd04453
S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential ...
 8-60 3.74e-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: 40.27  E-value: 3.74e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 516478451   8 KVTGKVSGITnfGAFIDLGEHKNGLVHISEISDGF---VKDIHDVLSVGDEVTVKV 60
Cdd:cd04453   14 RVKKIVPGLQ--AAFVDIGLGKNGFLHLSDILPAYfkkHKKIAKLLKEGQEILVQV 67
S1_2 pfam13509
S1 domain; The S1 domain was originally identified as a repeat motif in the ribosomal S1 ...
 5-70 1.25e-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: 38.28  E-value: 1.25e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516478451    5 VGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGfvkdihdvLSVGDEVTVKVLSVSDDGKIA 70
Cdd:pfam13509   1 IGKINTLKVIRETDFGYFLDGGEGGEVLLPKREVPEE--------LEIGDEVEVFLYTDSEDRLVA 58
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 5-81 1.43e-04

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 41.24  E-value: 1.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   5 VGSKVTGKVSGITNFGAFIDLGEHKNGLV---HISEISDGFVKDIHDVLSVGDEVTVKVLSVS-DDGKIALSIRKAKESH 80
Cdd:PRK12269 752 VGSTVEGEVSSVTDFGIFVRVPGGVEGLVrkqHLVENRDGDPGEALRKYAVGDRVKAVIVDMNvKDRKVAFSVRDYQRKV 831


                 .
gi 516478451  81 Q 81
Cdd:PRK12269 832 Q 832
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 4-74 3.15e-04

S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 239901 [Multi-domain]  Cd Length: 82  Bit Score: 37.91  E-value: 3.15e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 516478451   4 EVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSVSDDGKIALSIR 74
Cdd:cd04454    5 DVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDMNVLLTTA 75
PRK11642 PRK11642
ribonuclease R;
1-105 1.06e-03

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 38.57  E-value: 1.06e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   1 MSIEVGSKVTGKVSGITNFGAFIDLGE-HKNGLVHISEISDGFVKdiHD-------------VLSVGDEVTVKVLSVS-D 65
Cdd:PRK11642 639 MLDQVGNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDNDYYR--FDqvgqrligessgqTYRLGDRVEVRVEAVNmD 716

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 516478451  66 DGKIALSIRKAKESHQNhghQGHSHSEHGPKSRPHNNSGK 105
Cdd:PRK11642 717 ERKIDFSLISSERAPRN---VGKTAREKAKKGDAGKKGGK 753
PTZ00248 PTZ00248
eukaryotic translation initiation factor 2 subunit 1; Provisional
 4-75 1.74e-03

eukaryotic translation initiation factor 2 subunit 1; Provisional


Pssm-ID: 240329 [Multi-domain]  Cd Length: 319  Bit Score: 37.72  E-value: 1.74e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516478451   4 EVGSKVTGKVSGITNFGAFIDLGEHKN--GLVHISEISDGFVKDIHDVLSVGDEVTVKVLSV-SDDGKIALSIRK 75
Cdd:PTZ00248  16 EEDDLVMVKVVRITEMGAYVSLLEYDDieGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVdKEKGYIDLSKKR 90
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 6-66 2.17e-03

S1_Rrp5_repeat_hs11_sc8: 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 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 35.26  E-value: 2.17e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516478451   6 GSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDgFVKDIHDVLS---VGDEVTVKVLSVSDD 66
Cdd:cd05702    1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFD-EWPDGKNPLSkfkIGQKIKARVIGGHDA 63
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 6-63 2.44e-03

S1_Rrp5_repeat_hs5: 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 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 34.91  E-value: 2.44e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 516478451   6 GSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLSV 63
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSV 58
CafA COG1530
Ribonuclease G or E [Translation, ribosomal structure and biogenesis];
21-60 2.49e-03

Ribonuclease G or E [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441139 [Multi-domain]  Cd Length: 490  Bit Score: 37.44  E-value: 2.49e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 516478451  21 AFIDLGEHKNGLVHISEIS----------DGFVKDIHDVLSVGDEVTVKV 60
Cdd:COG1530   54 AFVDIGLERHGFLHVKDISpeyfslgkedSGKRPNIQDVLKEGQEVLVQV 103
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 6-75 2.64e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 37.09  E-value: 2.64e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 516478451   6 GSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVKDIHDVLSVGDEVTVKVLS-VSDDGKIALSIRK 75
Cdd:PRK07400  32 GDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSdENEDGQLTLSIRR 102
PRK04163 PRK04163
exosome complex protein Rrp4;
4-74 3.41e-03

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 36.79  E-value: 3.41e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516478451   4 EVGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFV----KDIHDVLSVGDEVTVKVLSVSDDGKIALSIR 74
Cdd:PRK04163  62 KVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVnvegTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLK 136
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 4.55e-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: 34.89  E-value: 4.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516478451   5 VGSKVTGKVSGITNFGAFIDLGEHKNGLVHISEISDGFVK-------------------DIHDVLSVGDEVTVKVLSVSD 65
Cdd:cd05693    3 EGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTErleeldeeseeeddeeelpDLEDLFSVGQLVRCKVVSLDK 82

                         90
                 ....*....|...
gi 516478451  66 DG----KIALSIR 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.
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