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Conserved domains on  [gi|504045057|ref|WP_014279051|]
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MULTISPECIES: S1 domain-containing RNA-binding protein [Paenibacillus]

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

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List of domain hits

 Name Accession Description Interval E-value
PRK08582 PRK08582
RNA-binding protein S1;
1-173 3.28e-63

RNA-binding protein S1;


:

Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 191.01  E-value: 3.28e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   1 MAIEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGKIGLSIKQTIDKP 80
Cdd:PRK08582   1 MSIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057  81 ASEARPPRAPRPERTGgpgggdrfggggsgpsqgrggggggfnrdrggrsfKPAPGKPSFEDKMSRFLKDSEERISSLKK 160
Cdd:PRK08582  81 KRQHDRPRHEDNRGGG-----------------------------------NDVAPKEDFEQKMSRFLKDSEDRLTSIKR 125

                        170
                 ....*....|...
gi 504045057 161 NTEGKRGGRGAKR 173
Cdd:PRK08582 126 NTESKRGGRGARR 138
 
Name Accession Description Interval E-value
PRK08582 PRK08582
RNA-binding protein S1;
1-173 3.28e-63

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 191.01  E-value: 3.28e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   1 MAIEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGKIGLSIKQTIDKP 80
Cdd:PRK08582   1 MSIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057  81 ASEARPPRAPRPERTGgpgggdrfggggsgpsqgrggggggfnrdrggrsfKPAPGKPSFEDKMSRFLKDSEERISSLKK 160
Cdd:PRK08582  81 KRQHDRPRHEDNRGGG-----------------------------------NDVAPKEDFEQKMSRFLKDSEDRLTSIKR 125

                        170
                 ....*....|...
gi 504045057 161 NTEGKRGGRGAKR 173
Cdd:PRK08582 126 NTESKRGGRGARR 138
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 1-171 1.37e-60

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 184.23  E-value: 1.37e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   1 MAIEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGKIGLSIKQTIDKP 80
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGKISLSIKQAEEKP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057  81 ASearppraprpertggpgggdrfggggsgpsqgrggggggfnRDRGGRSFKPAPGKPSFEDKMSRFLKDSEERISSLKK 160
Cdd:COG1098   81 KR-----------------------------------------PPRPRRNSRPKAGFESFEDKLSKFLKDSDERLSDLKK 119

                        170
                 ....*....|.
gi 504045057 161 NTEGKRGGRGA 171
Cdd:COG1098  120 RTESKRGGRGR 130
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 3-80 6.91e-32

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: 110.59  E-value: 6.91e-32
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIKQTIDKP 80
Cdd:NF040579   1 YKIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYtGKISLSLRALEEAP 79
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-74 4.33e-28

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: 99.67  E-value: 4.33e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504045057   6 GTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGKIGLSIK 74
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
4-74 2.19e-20

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 79.96  E-value: 2.19e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504045057     4 EVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIK 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 1.52e-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: 1.52e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504045057    4 EVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSI 73
Cdd:pfam00575   2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDrRRIILSI 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 5-80 1.49e-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: 73.23  E-value: 1.49e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504045057    5 VGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIA-DNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIKQTIDKP 80
Cdd:TIGR00717 272 VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPErRRLSLGLKQCKANP 349
 
Name Accession Description Interval E-value
PRK08582 PRK08582
RNA-binding protein S1;
1-173 3.28e-63

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 191.01  E-value: 3.28e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   1 MAIEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGKIGLSIKQTIDKP 80
Cdd:PRK08582   1 MSIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057  81 ASEARPPRAPRPERTGgpgggdrfggggsgpsqgrggggggfnrdrggrsfKPAPGKPSFEDKMSRFLKDSEERISSLKK 160
Cdd:PRK08582  81 KRQHDRPRHEDNRGGG-----------------------------------NDVAPKEDFEQKMSRFLKDSEDRLTSIKR 125

                        170
                 ....*....|...
gi 504045057 161 NTEGKRGGRGAKR 173
Cdd:PRK08582 126 NTESKRGGRGARR 138
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 1-171 1.37e-60

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 184.23  E-value: 1.37e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   1 MAIEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGKIGLSIKQTIDKP 80
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGKISLSIKQAEEKP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057  81 ASearppraprpertggpgggdrfggggsgpsqgrggggggfnRDRGGRSFKPAPGKPSFEDKMSRFLKDSEERISSLKK 160
Cdd:COG1098   81 KR-----------------------------------------PPRPRRNSRPKAGFESFEDKLSKFLKDSDERLSDLKK 119

                        170
                 ....*....|.
gi 504045057 161 NTEGKRGGRGA 171
Cdd:COG1098  120 RTESKRGGRGR 130
PRK05807 PRK05807
RNA-binding protein S1;
1-173 2.31e-38

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 127.94  E-value: 2.31e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   1 MAIEVGTKLEGKVTGITHFGAFVDLSGGvTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGKIGLSIKQTIDKP 80
Cdd:PRK05807   1 MTLKAGSILEGTVVNITNFGAFVEVEGK-TGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQAMKQK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057  81 ASearppraprpertggpgggdrfggggsgpsqgrgggggGFNRDRGGRSFKPAPGKPSFEDKMSRFLKDSEERISSLKK 160
Cdd:PRK05807  80 KS--------------------------------------VKPAEIDWQKEKNKNNNGNFEDRLSKFLKDSEERFQDLKK 121

                        170
                 ....*....|...
gi 504045057 161 NTEGKrgGRGAKR 173
Cdd:PRK05807 122 HQDSK--GRGYKK 132
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 3-80 6.91e-32

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: 110.59  E-value: 6.91e-32
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIKQTIDKP 80
Cdd:NF040579   1 YKIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYtGKISLSLRALEEAP 79
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 3-74 1.68e-28

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


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 110.48  E-value: 1.68e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGKIGLSIK 74
Cdd:COG1185  614 PEVGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEIDDQGRIKLSRK 685
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-74 4.33e-28

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: 99.67  E-value: 4.33e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504045057   6 GTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGKIGLSIK 74
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69
PRK08059 PRK08059
general stress protein 13; Validated
 3-81 8.54e-28

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 100.51  E-value: 8.54e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVD-KDGKIGLSIKQTIDKPA 81
Cdd:PRK08059   5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDeEKGKISLSIRATEEAPE 84
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 3-74 1.51e-26

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 104.75  E-value: 1.51e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGKIGLSIK 74
Cdd:PRK11824 619 PEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRK 690
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
4-82 1.63e-26

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 104.72  E-value: 1.63e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   4 EVGTKLEGKVTGITHFGAFVDLsgGV--TGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIKQTIDKP 80
Cdd:COG2183  640 KPGMILEGTVTNVTDFGAFVDI--GVhqDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKrKRISLSMKLDDEAG 717


                 ..
gi 504045057  81 AS 82
Cdd:COG2183  718 AA 719
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 3-80 2.43e-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: 96.65  E-value: 2.43e-24
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLsGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIKQTIDKP 80
Cdd:COG0539  187 LEEGDVVEGTVKNITDFGAFVDL-GGVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREkERISLSLKQLQPDP 264
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 3-80 1.32e-22

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 92.63  E-value: 1.32e-22
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLsGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIKQTIDKP 80
Cdd:PRK06676 190 LKEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWEtERISLSLKDTLPGP 267
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 3-76 1.65e-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: 1.65e-22
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIA-DNYVKDVNDHLKINDVVTVKVINVDKDGK-IGLSIKQT 76
Cdd:COG0539  272 YPVGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERrISLSIKQL 347
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 6-73 1.06e-21

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: 82.98  E-value: 1.06e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504045057   6 GTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGKIGLSI 73
Cdd:cd04472    1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLSR 68
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
4-74 2.19e-20

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 79.96  E-value: 2.19e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504045057     4 EVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIK 74
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEkGRIILSLK 72
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 6-72 7.30e-20

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: 78.43  E-value: 7.30e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504045057   6 GTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLS 72
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEErGRISLS 68
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 4-80 9.12e-20

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 85.22  E-value: 9.12e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504045057   4 EVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIA-DNYVKDVNDHLKINDVVTVKVINVDKDG-KIGLSIKQTIDKP 80
Cdd:PRK06299 285 PVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEIDEEKrRISLGLKQCKENP 363
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 5-82 4.03e-19

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 83.29  E-value: 4.03e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   5 VGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIA-DNYVKDVNDHLKINDVVTVKVINVDKDG-KIGLSIKQTIDKPAS 82
Cdd:PRK06299 373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKeRISLGIKQLEEDPFE 452
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
3-80 4.60e-19

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 83.46  E-value: 4.60e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLsGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIKQTIDKP 80
Cdd:PRK00087 475 LEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKEnKKLSLSLKKLLPDP 552
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
3-74 1.78e-18

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 76.28  E-value: 1.78e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDK-DGKIGLSIK 74
Cdd:PRK07252   1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEyTGKASLSLR 73
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
5-81 1.88e-18

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 81.53  E-value: 1.88e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504045057   5 VGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGK-IGLSIKQTIDKPA 81
Cdd:PRK00087 562 VGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKrIRLSIKEVEEEPG 639
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 5-82 2.09e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 81.07  E-value: 2.09e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504045057   5 VGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGK-IGLSIKQTIDKPAS 82
Cdd:PRK06676 277 EGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKrISLSIKALEEAPAE 355
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 3-80 2.29e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 81.36  E-value: 2.29e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLsGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIKQTIDKP 80
Cdd:PRK06299 199 LEEGQVVEGVVKNITDYGAFVDL-GGVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEkKRVSLGLKQLGEDP 276
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 5-74 1.24e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 76.36  E-value: 1.24e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504045057   5 VGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGK-IGLSIK 74
Cdd:PRK06299 460 KGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRrISLSIK 530
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 4-73 1.52e-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: 1.52e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504045057    4 EVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSI 73
Cdd:pfam00575   2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDrRRIILSI 72
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 5-72 1.23e-15

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: 67.65  E-value: 1.23e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504045057   5 VGTKLEGKVTGITHFGAFVDLsGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLS 72
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKErKRISLG 68
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 5-80 1.49e-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: 73.23  E-value: 1.49e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504045057    5 VGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIA-DNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIKQTIDKP 80
Cdd:TIGR00717 272 VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPErRRLSLGLKQCKANP 349
SUI2 COG1093
Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure ...
 11-75 7.43e-15

Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]; Translation initiation factor 2, alpha subunit (eIF-2alpha) is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440710 [Multi-domain]  Cd Length: 259  Bit Score: 69.84  E-value: 7.43e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504045057  11 GKVTGITHFGAFVDLS--GGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIKQ 75
Cdd:COG1093   16 GTVKEVKDFGAYVTLDeyEGKEGFIHISEVASGWIKNIRDYVREGQKVVCKVLRVDPKrGHIDLSLKR 83
rpsA PRK13806
30S ribosomal protein S1; Provisional
 3-80 2.64e-14

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 69.75  E-value: 2.64e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGK-----IGLSIKQTI 77
Cdd:PRK13806 200 VKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglrISLSIKQAG 279


                 ...
gi 504045057  78 DKP 80
Cdd:PRK13806 280 GDP 282
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 9-72 2.77e-14

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: 63.94  E-value: 2.77e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 504045057   9 LEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDK-DGKIGLS 72
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPeKGRISLS 65
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 4-74 4.42e-14

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 67.93  E-value: 4.42e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 504045057   4 EVGTKLEGKVTGITHFGAFVDLS--GGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIK 74
Cdd:PRK03987   7 EEGELVVGTVKEVKDFGAFVTLDeyPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRkGHIDLSLK 80
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 3-80 8.35e-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: 8.35e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504045057    3 IEVGTKLEGKVTGITHFGAFVDLsGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIKQTIDKP 80
Cdd:TIGR00717 185 LKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEkGRISLSLKQLGEDP 262
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 5-75 1.23e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 67.76  E-value: 1.23e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504045057   5 VGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDG-KIGLSIKQ 75
Cdd:PRK07899 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERrRISLSLKQ 364
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 3-75 2.11e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 66.36  E-value: 2.11e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLsGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIKQ 75
Cdd:PRK07400 194 LEVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAErGRISLSTKQ 266
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 4-74 2.91e-13

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: 61.58  E-value: 2.91e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 504045057   4 EVGTKLEGKVTGITHFGAFVDLSG-GVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIK 74
Cdd:cd05708    1 KVGQKIDGTVRRVEDYGVFIDIDGtNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEkKRISLGLK 73
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 5-74 5.02e-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: 65.91  E-value: 5.02e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504045057    5 VGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVD-KDGKIGLSIK 74
Cdd:TIGR00717 446 VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDkKNRKVSLSVK 516
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 10-74 6.56e-13

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: 60.72  E-value: 6.56e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504045057  10 EGKVTGITHFGAFVDLSG---GVTGLVHISEI-ADNYVKDVNDHLKINDVVTVKVINVdKDGKIGLSIK 74
Cdd:cd05684    5 KGKVTSIMDFGCFVQLEGlkgRKEGLVHISQLsFEGRVANPSDVVKRGQKVKVKVISI-QNGKISLSMK 72
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 4-75 1.54e-12

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: 59.91  E-value: 1.54e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 504045057   4 EVGTKLEGKVTGITHFGAFVDLS--GGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIKQ 75
Cdd:cd04452    2 EEGELVVVTVKSIADMGAYVSLLeyGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEkGYIDLSKKR 76
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 3-66 3.22e-12

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: 59.14  E-value: 3.22e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD 66
Cdd:cd04461   12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEE 75
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 5-80 3.22e-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: 3.22e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504045057    5 VGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKI-NDVVTVKVINVDKDGK-IGLSIKQTIDKP 80
Cdd:TIGR00717 359 VGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKkGDEIEAVVLAVDKEKKrISLGVKQLTENP 436
rpsA PRK13806
30S ribosomal protein S1; Provisional
 3-74 4.17e-12

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 63.20  E-value: 4.17e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIAdnYVKDVN---DHLKINDVVTVKVINVDKDGK-IGLSIK 74
Cdd:PRK13806 290 LKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMS--WTRRVNkpeDVVAPGDAVAVKIKDIDPAKRrISLSLR 363
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 10-80 4.93e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 63.14  E-value: 4.93e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504045057  10 EGKVTGITHFGAFVDLsGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLSIKQTIDKP 80
Cdd:PRK07899 213 KGVVSSIVNFGAFVDL-GGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDrERVSLSLKATQEDP 283
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 2.50e-10

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: 53.77  E-value: 2.50e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   6 GTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVD-KDGKIGLSIK 74
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDpEQQRLLLSCK 70
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-66 3.30e-10

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: 53.73  E-value: 3.30e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 504045057   6 GTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIaDNYVKDVNDH--LKINDVVTVKVINVDKD 66
Cdd:cd05689    4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEM-DWTNKNIHPSkvVSLGDEVEVMVLDIDEE 65
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 10-75 6.91e-10

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 55.22  E-value: 6.91e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057  10 EGKVTGITHFGAFVDLsGGVTGLVHISEIADNYV-----------KDVNDHLKINDVVTVKVINV------DKDGKIGLS 72
Cdd:PRK08563  86 EGEVVEVVEFGAFVRI-GPVDGLLHISQIMDDYIsydpkngrligKESKRVLKVGDVVRARIVAVslkerrPRGSKIGLT 164


                 ...
gi 504045057  73 IKQ 75
Cdd:PRK08563 165 MRQ 167
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 3-71 8.45e-10

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: 56.38  E-value: 8.45e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYvkdvndhlKINDVVTVKVINVDKDGKIGL 71
Cdd:COG1107   37 LEPGRYYRGTVDGVADFGVFVDLNDHVTGLLHRSELDQDW--------EVGDEVFVQVKEVRDNGNVDL 97
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 3-72 1.10e-09

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: 52.25  E-value: 1.10e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGK-IGLS 72
Cdd:cd05706    1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKkIALS 71
VacB COG0557
Exoribonuclease R [Transcription];
5-73 2.21e-09

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 55.50  E-value: 2.21e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   5 VGTKLEGKVTGITHFGAFVDLSG-GVTGLVHISEI-ADNYVKDVNDH----------LKINDVVTVKVINVDKD-GKIGL 71
Cdd:COG0557  622 VGEEFEGVISGVTSFGLFVELDElGVEGLVHVSSLgDDYYEYDERRQalvgertgkrYRLGDRVEVRVVRVDLDrRQIDF 701


                 ..
gi 504045057  72 SI 73
Cdd:COG0557  702 EL 703
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 5-69 4.23e-09

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: 50.86  E-value: 4.23e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504045057   5 VGTKLEGKVTGITHFGAFVDLSG-GVTGLVHISEIADNYVKDVNDHL-----------KINDVVTVKVINVDKD-GKI 69
Cdd:cd04471    1 VGEEFDGVISGVTSFGLFVELDNlTVEGLVHVSTLGDDYYEFDEENHalvgertgkvfRLGDKVKVRVVRVDLDrRKI 78
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 3-72 4.75e-09

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: 50.68  E-value: 4.75e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYvkdvndhlKINDVVTVKVINVDKDGKIGLS 72
Cdd:cd04473   14 LEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDY--------EVGDEVIVQVTDIPENGNIDLI 75
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 4-74 4.89e-09

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: 50.56  E-value: 4.89e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504045057   4 EVGTKLEGKVTGITHFGAFVDLSG-GVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGKIGLSIK 74
Cdd:cd05686    2 ALYQIFKGEVASVTEYGAFVKIPGcRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSLS 73
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-66 5.91e-09

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: 50.18  E-value: 5.91e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504045057   6 GTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIA-DNYVKDVNDHLKINDVVTVKVINVDKD 66
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVE 62
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-75 6.48e-09

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: 49.96  E-value: 6.48e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504045057   6 GTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVD-KDGKIGLSIKQ 75
Cdd:cd05691    1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDrKNRKISLSIKA 71
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 10-75 1.09e-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: 50.36  E-value: 1.09e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057  10 EGKVTGITHFGAFVDLsGGVTGLVHISEIADNYV-----------KDVNDHLKINDVVTVKVINV------DKDGKIGLS 72
Cdd:cd04460    4 EGEVVEVVDFGAFVRI-GPVDGLLHISQIMDDYIsydpknkrligEETKRVLKVGDVVRARIVAVslkerrPRESKIGLT 82


                 ...
gi 504045057  73 IKQ 75
Cdd:cd04460   83 MRQ 85
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 13-82 1.38e-08

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 52.97  E-value: 1.38e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057  13 VTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGKIGLSIKQTIDKPAS 82
Cdd:PLN00207 762 IKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQLRLSRRALLPEANS 831
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 6-72 1.89e-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: 48.83  E-value: 1.89e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504045057   6 GTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKD-GKIGLS 72
Cdd:cd05707    1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDnGRIEMT 68
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 5-80 4.07e-08

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 51.64  E-value: 4.07e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   5 VGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIAdnYVKDV---NDHLKINDVVTVKVINVD-KDGKIGLSIKQTIDKP 80
Cdd:PRK12269 578 VNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFS--WVKKTskpSDMVKIGDEVECMILGYDiQAGRVSLGLKQVTANP 655
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 3-75 9.54e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 50.26  E-value: 9.54e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLSG-GVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINV-DKDGKIGLSIKQ 75
Cdd:PRK06676  15 VEVGDVVTGEVLKVEDKQVFVNIEGyKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVeDGEGNLLLSKRR 89
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 3-74 1.87e-07

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: 49.66  E-value: 1.87e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADnyvKDVNDHLKINDVVTVKVINV-DKDGKIGLSIK 74
Cdd:COG0539   16 LKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSD---EPGELEVKVGDEVEVYVEKVeDGEGEIVLSKK 85
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 2.22e-07

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: 45.98  E-value: 2.22e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   6 GTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINV-DKDGKIGLSIK 74
Cdd:cd05687    1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVeDEEGNVVLSKR 70
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 2-74 2.43e-06

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 46.63  E-value: 2.43e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504045057   2 AIEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLK---INDVVTVKVINVD-KDGKIGLSIK 74
Cdd:PRK12269 749 AYGVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPGEALRkyaVGDRVKAVIVDMNvKDRKVAFSVR 825
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 6-61 2.73e-06

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: 42.96  E-value: 2.73e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 504045057   6 GTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYV--KDVNDHLKINDVVTVKVI 61
Cdd:cd05702    1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPdgKNPLSKFKIGQKIKARVI 58
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 2-80 6.00e-06

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 45.47  E-value: 6.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   2 AIEVGTKLEGKVTGITHFGAFVDLsGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDK-DGKIGLSIKQTIDKP 80
Cdd:PRK12269 490 SVHIEDSVSGVVKSFTSFGAFIDL-GGFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQaEKRINLSLKHFQPDP 568
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 6-68 1.02e-05

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: 41.45  E-value: 1.02e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 504045057   6 GTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKDGK 68
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERK 63
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
2-74 1.17e-05

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 44.55  E-value: 1.17e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 504045057   2 AIEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINV-DKDGKIGLSIK 74
Cdd:PRK00087 299 QIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLeDEDGYVVLSKK 372
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 3-66 1.20e-05

S1_Rrp5_repeat_hs14: 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 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240210 [Multi-domain]  Cd Length: 74  Bit Score: 41.61  E-value: 1.20e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504045057   3 IEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKD---VNDHLKINDVVTVKVINVDKD 66
Cdd:cd05705    1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDpslYNKYLPEGKLLTAKVLSVNSE 67
rpsA PRK13806
30S ribosomal protein S1; Provisional
 5-72 1.91e-05

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 43.94  E-value: 1.91e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504045057   5 VGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINVD-KDGKIGLS 72
Cdd:PRK13806 379 PGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDtAKRKISLA 447
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 3-74 2.25e-04

S1_Rrp5_repeat_hs13: 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 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 38.10  E-value: 2.25e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 504045057   3 IEVGTKLEGKVTGIT-HFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKINDVVTVKVINvDKDGKIGLSIK 74
Cdd:cd05704    1 LEEGAVTLGMVTKVIpHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILS-KKDGKYQLSLR 72
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 4-74 2.25e-04

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: 38.30  E-value: 2.25e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 504045057   4 EVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEI----ADNYVKDVNDHLKINDVVTVKVINVDKDGKIGLSIK 74
Cdd:cd05789    5 EVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVnlprTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTR 79
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 5-78 4.04e-04

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: 37.97  E-value: 4.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   5 VGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVK-------------------DVNDHLKINDVVTVKVINVDK 65
Cdd:cd05693    3 EGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTErleeldeeseeeddeeelpDLEDLFSVGQLVRCKVVSLDK 82

                         90
                 ....*....|...
gi 504045057  66 DGKIGLSIKQTID 78
Cdd:cd05693   83 SKSGKKRIELSLE 95
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
2-68 6.93e-04

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 39.16  E-value: 6.93e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504045057   2 AIEVGTKLEGKVTGITHFGAFVDLsGGVTGLVHISEIADNYVKDVNDHLKIndVVTVKVINVDKDGK 68
Cdd:PRK00087 386 AFENGEPVKGKVKEVVKGGLLVDY-GGVRAFLPASHVELGYVEDLSEYKGQ--ELEVKIIEFNRKRR 449
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 5-80 8.63e-04

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 38.92  E-value: 8.63e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   5 VGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIAdnYVKDVN--DH-LKINDVVTVKVINVDKDG-KIGLSIKQTIDKP 80
Cdd:PRK12269 665 VGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLS--WVKRTRpaDHeLEVGKEIECMVIECDPQArRIRLGVKQLSDNP 742
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-74 1.29e-03

S1_RPS1_repeat_ec2_hs2: 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 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 239911 [Multi-domain]  Cd Length: 67  Bit Score: 35.90  E-value: 1.29e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057   6 GTKLEGKVTGITHFGAFVDLsGGVTGLVHISEIADNYVKDVNDHlkINDVVTVKVINVDKDG-KIGLSIK 74
Cdd:cd04465    1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERnNIVLSRR 67
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 30-76 1.71e-03

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 37.26  E-value: 1.71e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 504045057  30 TGLVHISEIADNYVKDVNDHLKINDVVTVKVINVDKdgKIGLSIKQT 76
Cdd:PRK09521  99 LAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYTD--PLQLSTKGK 143
PRK04163 PRK04163
exosome complex protein Rrp4;
11-74 4.34e-03

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 36.41  E-value: 4.34e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504045057  11 GKVTGITHFGAFVDLSGGVTGLVHISE----IADNYVKDVNDHLKINDVVTVKVINVDKDGKIGLSIK 74
Cdd:PRK04163  69 GKVTDVTFSGWEVDINSPYKAYLPVSEvlgrPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLK 136
S1_2 pfam13509
S1 domain; The S1 domain was originally identified as a repeat motif in the ribosomal S1 ...
 5-74 7.08e-03

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: 33.66  E-value: 7.08e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504045057    5 VGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEiadnyvkdVNDHLKINDVVTVkVINVDKDGKIGLSIK 74
Cdd:pfam13509   1 IGKINTLKVIRETDFGYFLDGGEGGEVLLPKRE--------VPEELEIGDEVEV-FLYTDSEDRLVATTK 61
 
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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