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Conserved domains on  [gi|6323895|ref|NP_013966|]
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ribonuclease III [Saccharomyces cerevisiae S288C]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_3_N pfam18497
Ribonuclease III N-terminal domain; This is the N-terminal domain of eukaryotic ribonuclease 3 ...
 44-147 1.48e-36

Ribonuclease III N-terminal domain; This is the N-terminal domain of eukaryotic ribonuclease 3 (RNase III, EC:3.1.26.3). Structure analysis of Saccharomyces cerevisiaeRNase III (Rnt1p) :RNA revealed specific contacts between the N-terminal domain (NTD) dimer and the 5' end region of the tetraloop. Deletion of the NTD led to cleavage at alternative site(s), suggesting that this region increases the precision of the cleavage site selectivity.


:

Pssm-ID: 436545  Cd Length: 95  Bit Score: 129.64  E-value: 1.48e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895     44 YKYLEVIQLEHAVTKLVESYNKIIELSPNLVAYNEAVNNQDRVPVQILPSLSRYQLKLAAELKTLHDLKKDAILTEITDY 123
Cdd:pfam18497   1 YGYSDVLQLEHAVTKLQESLKKIIELSPNLKELKELLNSLEKIPVELLPSLSRYKLKLAAELKSLYELGKLPIFDEIINY 80

                          90       100
                  ....*....|....*....|....
gi 6323895    124 ENEFDteqkqpilqEISKADMEKL 147
Cdd:pfam18497  81 EEKFD---------PLEEEDLEKL 95
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 207-354 5.35e-35

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


:

Pssm-ID: 238333  Cd Length: 133  Bit Score: 126.96  E-value: 5.35e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895  207 DLAIRArvFIHKStikdkvylSGSEMINAHNERLEFLGDSILNSVMTLIIYNKFPDYSEGQLSTLRMNLVSNEQIKQWSI 286
Cdd:cd00593   1 SLLLEA--LTHPS--------YANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLAR 70

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6323895  287 MYNFHEKLKTNfdlKDENSNFQNGKLKLYADVFEAYIGGLMEDdprNNLPKIRKWLRKLAKPVIEEAT 354
Cdd:cd00593  71 ELGLGKYLRLG---KGEEKSGGRLRPKILADVFEALIGAIYLD---GGFEAARKFLLRLLGPLIEEIS 132
DSRM_RNT1p-like cd19876
double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and ...
 367-436 3.74e-22

double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and similar proteins; RNT1p (EC 3.1.26.3; also known as ribonuclease III (RNase III)) is a dsRNA-specific nuclease that cleaves eukaryotic pre-ribosomal RNA at the U3 snoRNP-dependent A0 site in the 5'-external transcribed spacer (ETS) and in the 3'-ETS. RNT1p contains a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


:

Pssm-ID: 380705  Cd Length: 69  Bit Score: 89.70  E-value: 3.74e-22
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895  367 DMNAKRQLYSLIGYASLRLHYVTVKKPTAVDPNSIVECRVgDGTVLGTGVGRNIKIAGIRAAENALRDKK 436
Cdd:cd19876   1 DKFAKQKLYSLIGPASLKPEYVVVKKEGGNDPNYTVACRI-NGEVLGTGVGRSIKKAGQRAAMSALSNKK 69
 
Name Accession Description Interval E-value
RNase_3_N pfam18497
Ribonuclease III N-terminal domain; This is the N-terminal domain of eukaryotic ribonuclease 3 ...
 44-147 1.48e-36

Ribonuclease III N-terminal domain; This is the N-terminal domain of eukaryotic ribonuclease 3 (RNase III, EC:3.1.26.3). Structure analysis of Saccharomyces cerevisiaeRNase III (Rnt1p) :RNA revealed specific contacts between the N-terminal domain (NTD) dimer and the 5' end region of the tetraloop. Deletion of the NTD led to cleavage at alternative site(s), suggesting that this region increases the precision of the cleavage site selectivity.


Pssm-ID: 436545  Cd Length: 95  Bit Score: 129.64  E-value: 1.48e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895     44 YKYLEVIQLEHAVTKLVESYNKIIELSPNLVAYNEAVNNQDRVPVQILPSLSRYQLKLAAELKTLHDLKKDAILTEITDY 123
Cdd:pfam18497   1 YGYSDVLQLEHAVTKLQESLKKIIELSPNLKELKELLNSLEKIPVELLPSLSRYKLKLAAELKSLYELGKLPIFDEIINY 80

                          90       100
                  ....*....|....*....|....
gi 6323895    124 ENEFDteqkqpilqEISKADMEKL 147
Cdd:pfam18497  81 EEKFD---------PLEEEDLEKL 95
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 207-354 5.35e-35

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


Pssm-ID: 238333  Cd Length: 133  Bit Score: 126.96  E-value: 5.35e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895  207 DLAIRArvFIHKStikdkvylSGSEMINAHNERLEFLGDSILNSVMTLIIYNKFPDYSEGQLSTLRMNLVSNEQIKQWSI 286
Cdd:cd00593   1 SLLLEA--LTHPS--------YANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLAR 70

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6323895  287 MYNFHEKLKTNfdlKDENSNFQNGKLKLYADVFEAYIGGLMEDdprNNLPKIRKWLRKLAKPVIEEAT 354
Cdd:cd00593  71 ELGLGKYLRLG---KGEEKSGGRLRPKILADVFEALIGAIYLD---GGFEAARKFLLRLLGPLIEEIS 132
RIBOc smart00535
Ribonuclease III family;
213-353 3.25e-34

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 124.64  E-value: 3.25e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895     213 RVFIHKStikdkvYLSGSEminaHNERLEFLGDSILNSVMTLIIYNKFPDYSEGQLSTLRMNLVSNEQIKQWSIMYNFHE 292
Cdd:smart00535   5 RALTHAS------YSNEHE----HNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGE 74

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6323895     293 KLKTNFDLKDENSnfqNGKLKLYADVFEAYIGGLMEDDprnNLPKIRKWLRKLAKPVIEEA 353
Cdd:smart00535  75 FIRLGRGEAISGG---RDKPKILADVFEALIGAIYLDS---GLEAAREFIRDLLGPRLDEL 129
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 204-432 8.51e-29

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 113.07  E-value: 8.51e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895    204 EIQDLAIRARVFIHKStikdkvYLSGSEMINAHNERLEFLGDSILNSVMTLIIYNKFPDYSEGQLSTLRMNLVSNEQIKQ 283
Cdd:TIGR02191   8 KFKNPELLEQALTHRS------YANEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895    284 WSIMYNFHEKLKTNfdlKDENSNFQNGKLKLYADVFEAYIGGLMEDdprNNLPKIRKWLRKLAKPVIEEatrnqvalEKT 363
Cdd:TIGR02191  82 VARELGLGDFLLLG---KGEEKSGGRRRDSILADAFEALIGAIYLD---SGLEAARKFILKLLIPRIDA--------IIK 147

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6323895    364 DKLDMNAKRQL--YSLIGYASLrLHYVTVK--KPtAVDPNSIVECRVGdGTVLGTGVGRNIKIAGIRAAENAL 432
Cdd:TIGR02191 148 EETLKDYKTALqeWAQARGKPL-PEYRLIKeeGP-DHDKEFTVEVSVN-GEPYGEGKGKSKKEAEQNAAKAAL 217
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
206-433 3.26e-28

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 111.73  E-value: 3.26e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895  206 QDLAIRArvFIHKSTIKDKVYLsgseminAHNERLEFLGDSILNSVMTLIIYNKFPDYSEGQLSTLRMNLVSNEQIKQWS 285
Cdd:COG0571  18 PELLEQA--LTHRSYANEHGGL-------ENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAEIA 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895  286 IMYNFHEKLKtnfdL-KDENSNFQNGKLKLYADVFEAYIGGLMEDdprNNLPKIRKWLRKLAKPVIEEATrnqvalekTD 364
Cdd:COG0571  89 RELGLGDYLR----LgKGEEKSGGRRRPSILADAFEALIGAIYLD---GGLEAARKFVLRLFEPRLEEIA--------PG 153

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6323895  365 KLDMNAK--------RQLYSLIGYaslRLhyVTVKKPtAVDPNSIVECRVgDGTVLGTGVGRNIKIAGIRAAENALR 433
Cdd:COG0571 154 GAGKDYKtalqewlqARGLPLPEY---EV--VEEEGP-DHAKTFTVEVLV-GGKVLGEGTGRSKKEAEQAAAKAALE 223
DSRM_RNT1p-like cd19876
double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and ...
 367-436 3.74e-22

double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and similar proteins; RNT1p (EC 3.1.26.3; also known as ribonuclease III (RNase III)) is a dsRNA-specific nuclease that cleaves eukaryotic pre-ribosomal RNA at the U3 snoRNP-dependent A0 site in the 5'-external transcribed spacer (ETS) and in the 3'-ETS. RNT1p contains a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380705  Cd Length: 69  Bit Score: 89.70  E-value: 3.74e-22
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895  367 DMNAKRQLYSLIGYASLRLHYVTVKKPTAVDPNSIVECRVgDGTVLGTGVGRNIKIAGIRAAENALRDKK 436
Cdd:cd19876   1 DKFAKQKLYSLIGPASLKPEYVVVKKEGGNDPNYTVACRI-NGEVLGTGVGRSIKKAGQRAAMSALSNKK 69
Ribonuclease_3 pfam00636
Ribonuclease III domain;
238-326 1.84e-20

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 86.17  E-value: 1.84e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895    238 ERLEFLGDSILNSVMTLIIYNKFPDYSEGQLSTLRMNLVSNEQIKQWSIMYNFHEKLKT-NFDLKDENSNF------QNG 310
Cdd:pfam00636   1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEeELDIRRRNNALgkgpkrADG 80

                          90
                  ....*....|....*.
gi 6323895    311 KLKLYADVFEAYIGGL 326
Cdd:pfam00636  81 KEKVLADAFEALIGAL 96
DSRM smart00358
Double-stranded RNA binding motif;
370-434 9.94e-09

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 51.49  E-value: 9.94e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6323895     370 AKRQLYSLIGYASLRLHYVTVK-KPTAVDPNSIVECRVGdGTVLGTGVGRNIKIAGIRAAENALRD 434
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKeEGPDHAPRFTVTVKVG-GKRTGEGEGSSKKEAKQRAAEAALRS 65
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 370-433 4.48e-07

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 46.84  E-value: 4.48e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6323895    370 AKRQLYSLIGYASLRLHYVTVKKPT-AVDPNSIVECRVgDGTVLGTGVGRNIKIAGIRAAENALR 433
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGpPHSPKFTVTVKV-DGKLYGSGTGSSKKEAEQLAAEKALE 64
 
Name Accession Description Interval E-value
RNase_3_N pfam18497
Ribonuclease III N-terminal domain; This is the N-terminal domain of eukaryotic ribonuclease 3 ...
 44-147 1.48e-36

Ribonuclease III N-terminal domain; This is the N-terminal domain of eukaryotic ribonuclease 3 (RNase III, EC:3.1.26.3). Structure analysis of Saccharomyces cerevisiaeRNase III (Rnt1p) :RNA revealed specific contacts between the N-terminal domain (NTD) dimer and the 5' end region of the tetraloop. Deletion of the NTD led to cleavage at alternative site(s), suggesting that this region increases the precision of the cleavage site selectivity.


Pssm-ID: 436545  Cd Length: 95  Bit Score: 129.64  E-value: 1.48e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895     44 YKYLEVIQLEHAVTKLVESYNKIIELSPNLVAYNEAVNNQDRVPVQILPSLSRYQLKLAAELKTLHDLKKDAILTEITDY 123
Cdd:pfam18497   1 YGYSDVLQLEHAVTKLQESLKKIIELSPNLKELKELLNSLEKIPVELLPSLSRYKLKLAAELKSLYELGKLPIFDEIINY 80

                          90       100
                  ....*....|....*....|....
gi 6323895    124 ENEFDteqkqpilqEISKADMEKL 147
Cdd:pfam18497  81 EEKFD---------PLEEEDLEKL 95
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 207-354 5.35e-35

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


Pssm-ID: 238333  Cd Length: 133  Bit Score: 126.96  E-value: 5.35e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895  207 DLAIRArvFIHKStikdkvylSGSEMINAHNERLEFLGDSILNSVMTLIIYNKFPDYSEGQLSTLRMNLVSNEQIKQWSI 286
Cdd:cd00593   1 SLLLEA--LTHPS--------YANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLAR 70

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6323895  287 MYNFHEKLKTNfdlKDENSNFQNGKLKLYADVFEAYIGGLMEDdprNNLPKIRKWLRKLAKPVIEEAT 354
Cdd:cd00593  71 ELGLGKYLRLG---KGEEKSGGRLRPKILADVFEALIGAIYLD---GGFEAARKFLLRLLGPLIEEIS 132
RIBOc smart00535
Ribonuclease III family;
213-353 3.25e-34

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 124.64  E-value: 3.25e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895     213 RVFIHKStikdkvYLSGSEminaHNERLEFLGDSILNSVMTLIIYNKFPDYSEGQLSTLRMNLVSNEQIKQWSIMYNFHE 292
Cdd:smart00535   5 RALTHAS------YSNEHE----HNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGE 74

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6323895     293 KLKTNFDLKDENSnfqNGKLKLYADVFEAYIGGLMEDDprnNLPKIRKWLRKLAKPVIEEA 353
Cdd:smart00535  75 FIRLGRGEAISGG---RDKPKILADVFEALIGAIYLDS---GLEAAREFIRDLLGPRLDEL 129
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 204-432 8.51e-29

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 113.07  E-value: 8.51e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895    204 EIQDLAIRARVFIHKStikdkvYLSGSEMINAHNERLEFLGDSILNSVMTLIIYNKFPDYSEGQLSTLRMNLVSNEQIKQ 283
Cdd:TIGR02191   8 KFKNPELLEQALTHRS------YANEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895    284 WSIMYNFHEKLKTNfdlKDENSNFQNGKLKLYADVFEAYIGGLMEDdprNNLPKIRKWLRKLAKPVIEEatrnqvalEKT 363
Cdd:TIGR02191  82 VARELGLGDFLLLG---KGEEKSGGRRRDSILADAFEALIGAIYLD---SGLEAARKFILKLLIPRIDA--------IIK 147

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6323895    364 DKLDMNAKRQL--YSLIGYASLrLHYVTVK--KPtAVDPNSIVECRVGdGTVLGTGVGRNIKIAGIRAAENAL 432
Cdd:TIGR02191 148 EETLKDYKTALqeWAQARGKPL-PEYRLIKeeGP-DHDKEFTVEVSVN-GEPYGEGKGKSKKEAEQNAAKAAL 217
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
206-433 3.26e-28

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 111.73  E-value: 3.26e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895  206 QDLAIRArvFIHKSTIKDKVYLsgseminAHNERLEFLGDSILNSVMTLIIYNKFPDYSEGQLSTLRMNLVSNEQIKQWS 285
Cdd:COG0571  18 PELLEQA--LTHRSYANEHGGL-------ENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAEIA 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895  286 IMYNFHEKLKtnfdL-KDENSNFQNGKLKLYADVFEAYIGGLMEDdprNNLPKIRKWLRKLAKPVIEEATrnqvalekTD 364
Cdd:COG0571  89 RELGLGDYLR----LgKGEEKSGGRRRPSILADAFEALIGAIYLD---GGLEAARKFVLRLFEPRLEEIA--------PG 153

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6323895  365 KLDMNAK--------RQLYSLIGYaslRLhyVTVKKPtAVDPNSIVECRVgDGTVLGTGVGRNIKIAGIRAAENALR 433
Cdd:COG0571 154 GAGKDYKtalqewlqARGLPLPEY---EV--VEEEGP-DHAKTFTVEVLV-GGKVLGEGTGRSKKEAEQAAAKAALE 223
DSRM_RNT1p-like cd19876
double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and ...
 367-436 3.74e-22

double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and similar proteins; RNT1p (EC 3.1.26.3; also known as ribonuclease III (RNase III)) is a dsRNA-specific nuclease that cleaves eukaryotic pre-ribosomal RNA at the U3 snoRNP-dependent A0 site in the 5'-external transcribed spacer (ETS) and in the 3'-ETS. RNT1p contains a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380705  Cd Length: 69  Bit Score: 89.70  E-value: 3.74e-22
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895  367 DMNAKRQLYSLIGYASLRLHYVTVKKPTAVDPNSIVECRVgDGTVLGTGVGRNIKIAGIRAAENALRDKK 436
Cdd:cd19876   1 DKFAKQKLYSLIGPASLKPEYVVVKKEGGNDPNYTVACRI-NGEVLGTGVGRSIKKAGQRAAMSALSNKK 69
Ribonuclease_3 pfam00636
Ribonuclease III domain;
238-326 1.84e-20

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 86.17  E-value: 1.84e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895    238 ERLEFLGDSILNSVMTLIIYNKFPDYSEGQLSTLRMNLVSNEQIKQWSIMYNFHEKLKT-NFDLKDENSNF------QNG 310
Cdd:pfam00636   1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEeELDIRRRNNALgkgpkrADG 80

                          90
                  ....*....|....*.
gi 6323895    311 KLKLYADVFEAYIGGL 326
Cdd:pfam00636  81 KEKVLADAFEALIGAL 96
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 236-324 1.88e-11

Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3.


Pssm-ID: 434075  Cd Length: 127  Bit Score: 61.42  E-value: 1.88e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323895    236 HNERLEFLGDSILNSVMTLIIYnKFPDYSEGQLSTLRMNLVSNEQIKQWSIMYNFHEKLktnFDLKDENSNFQNGKLKLY 315
Cdd:pfam14622  20 YNERLEFLGDAVLELSVSEYLF-KKPDLDEGGLTKLRASIVSEESLAEIAREIGLGKYL---RLGKGEEETGGSGRESIL 95


                  ....*....
gi 6323895    316 ADVFEAYIG 324
Cdd:pfam14622  96 ADALEALIG 104
DSRM smart00358
Double-stranded RNA binding motif;
370-434 9.94e-09

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 51.49  E-value: 9.94e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6323895     370 AKRQLYSLIGYASLRLHYVTVK-KPTAVDPNSIVECRVGdGTVLGTGVGRNIKIAGIRAAENALRD 434
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKeEGPDHAPRFTVTVKVG-GKRTGEGEGSSKKEAKQRAAEAALRS 65
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 370-433 4.48e-07

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 46.84  E-value: 4.48e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6323895    370 AKRQLYSLIGYASLRLHYVTVKKPT-AVDPNSIVECRVgDGTVLGTGVGRNIKIAGIRAAENALR 433
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGpPHSPKFTVTVKV-DGKLYGSGTGSSKKEAEQLAAEKALE 64
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 384-432 2.91e-03

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


Pssm-ID: 380679 [Multi-domain]  Cd Length: 57  Bit Score: 36.11  E-value: 2.91e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 6323895  384 RLHYVTVKKPTAVDPNSIVECRVGDGTvlGTGVGRNIKIAGIRAAENAL 432
Cdd:cd00048  11 PPEYETVEEGGPHNPRFTCTVTVNGQT--FEGEGKSKKEAKQAAAEKAL 57
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 401-433 7.70e-03

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 35.16  E-value: 7.70e-03
                        10        20        30
                ....*....|....*....|....*....|...
gi 6323895  401 IVECRVgDGTVLGTGVGRNIKIAGIRAAENALR 433
Cdd:cd10845  36 TVEVKV-NGKVIGEGTGRSKKEAEQAAAKAALE 67
 
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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