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Conserved domains on  [gi|392886816|ref|NP_001122460|]
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Ribonuclease 3 [Caenorhabditis elegans]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
833-1056 8.21e-58

dsRNA-specific ribonuclease [Transcription];


:

Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 198.78  E-value: 8.21e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816  833 ALEERLGIQFNNIRLLAKAFTRRNIPNNDLTKGHNQRLEWLGDSVLQLIVSDFLYRRFPYHHEGHMSLLRTSLVSNQTQA 912
Cdd:COG0571     6 ELEERLGYRFKDPELLEQALTHRSYANEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816  913 VVCDDLGFTEFVI--KApyktpELKL--KDK----ADLVEAFIGALYVDRGIEHCRAFIRIVFCPRLKHFIESEKWNDAK 984
Cdd:COG0571    86 EIARELGLGDYLRlgKG-----EEKSggRRRpsilADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAGKDYK 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 392886816  985 SHLQQWCLAMRDPsssepdMPEYRVLGIEGPTNNRIFKIAVYYKGKRLASAAESNVHKAELRVAELALANLE 1056
Cdd:COG0571   161 TALQEWLQARGLP------LPEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKLG 226
RIBOc smart00535
Ribonuclease III family;
670-791 2.01e-36

Ribonuclease III family;


:

Pssm-ID: 197778  Cd Length: 129  Bit Score: 133.88  E-value: 2.01e-36
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816    670 MSLFNIMKGTSGGEPILHNERLEYLGDAVVELIVSHHLYFMLTHHFEGGLATYRTALVQNRNLATLAKNCRIDEMLQYSH 749
Cdd:smart00535    1 SLLLRALTHASYSNEHEHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGR 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|..
gi 392886816    750 GADLINVAEFKHALANAFEAVMAAIYLDGGLAPCDVIFSKAM 791
Cdd:smart00535   81 GEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLL 122
 
Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
833-1056 8.21e-58

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 198.78  E-value: 8.21e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816  833 ALEERLGIQFNNIRLLAKAFTRRNIPNNDLTKGHNQRLEWLGDSVLQLIVSDFLYRRFPYHHEGHMSLLRTSLVSNQTQA 912
Cdd:COG0571     6 ELEERLGYRFKDPELLEQALTHRSYANEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816  913 VVCDDLGFTEFVI--KApyktpELKL--KDK----ADLVEAFIGALYVDRGIEHCRAFIRIVFCPRLKHFIESEKWNDAK 984
Cdd:COG0571    86 EIARELGLGDYLRlgKG-----EEKSggRRRpsilADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAGKDYK 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 392886816  985 SHLQQWCLAMRDPsssepdMPEYRVLGIEGPTNNRIFKIAVYYKGKRLASAAESNVHKAELRVAELALANLE 1056
Cdd:COG0571   161 TALQEWLQARGLP------LPEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKLG 226
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 834-1055 1.10e-48

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: 172.39  E-value: 1.10e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816   834 LEERLGIQFNNIRLLAKAFTRRNIPNNDLTKG-HNQRLEWLGDSVLQLIVSDFLYRRFPYHHEGHMSLLRTSLVSNQTQA 912
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYANEHHKDVkNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816   913 VVCDDLGFTEFVI--KAPYKTpELKLKDK--ADLVEAFIGALYVDRGIEHCRAFIRIVFCPRLKHFIESEKWNDAKSHLQ 988
Cdd:TIGR02191   81 EVARELGLGDFLLlgKGEEKS-GGRRRDSilADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIIKEETLKDYKTALQ 159

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 392886816   989 QWCLAMRDPSssepdmPEYRVLGIEGPTNNRIFKIAVYYKGKRLASAAESNVHKAELRVAELALANL 1055
Cdd:TIGR02191  160 EWAQARGKPL------PEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAALEKL 220
RIBOc smart00535
Ribonuclease III family;
846-974 1.65e-41

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 148.52  E-value: 1.65e-41
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816    846 RLLAKAFTRRNIPNNdltKGHNQRLEWLGDSVLQLIVSDFLYRRFPYHHEGHMSLLRTSLVSNQTQAVVCDDLGFTEFVI 925
Cdd:smart00535    1 SLLLRALTHASYSNE---HEHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIR 77

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|..
gi 392886816    926 ---KAPYKTPELKLKDKADLVEAFIGALYVDRGIEHCRAFIRIVFCPRLKHF 974
Cdd:smart00535   78 lgrGEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLDEL 129
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 846-976 3.71e-40

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: 144.68  E-value: 3.71e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816  846 RLLAKAFTRRNIPNNDLTKgHNQRLEWLGDSVLQLIVSDFLYRRFPYHHEGHMSLLRTSLVSNQTQAVVCDDLGFTEFVI 925
Cdd:cd00593     1 SLLLEALTHPSYANEHGRF-NNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLR 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 392886816  926 KAP-YKTPELKLKDK--ADLVEAFIGALYVDRGIEHCRAFIRIVFCPRLKHFIE 976
Cdd:cd00593    80 LGKgEEKSGGRLRPKilADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133
RIBOc smart00535
Ribonuclease III family;
670-791 2.01e-36

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 133.88  E-value: 2.01e-36
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816    670 MSLFNIMKGTSGGEPILHNERLEYLGDAVVELIVSHHLYFMLTHHFEGGLATYRTALVQNRNLATLAKNCRIDEMLQYSH 749
Cdd:smart00535    1 SLLLRALTHASYSNEHEHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGR 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|..
gi 392886816    750 GADLINVAEFKHALANAFEAVMAAIYLDGGLAPCDVIFSKAM 791
Cdd:smart00535   81 GEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLL 122
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 680-783 1.61e-32

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: 122.72  E-value: 1.61e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816  680 SGGEPILHNERLEYLGDAVVELIVSHHLYFMLTHHFEGGLATYRTALVQNRNLATLAKNCRIDEMLQYSHGADLINVAEF 759
Cdd:cd00593    13 ANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKGEEKSGGRLR 92

                          90       100
                  ....*....|....*....|....
gi 392886816  760 KHALANAFEAVMAAIYLDGGLAPC 783
Cdd:cd00593    93 PKILADVFEALIGAIYLDGGFEAA 116
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 610-789 1.70e-24

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: 102.67  E-value: 1.70e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816   610 FEEVIEYKFNDRRVIELALMHSSfkshygtpidhvknmitncgyrrkYGAEDKREKKrgimslfnimkgtsggepilHNE 689
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRS------------------------YANEHHKDVK--------------------NNE 36

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816   690 RLEYLGDAVVELIVSHHLYfmltHHF----EGGLATYRTALVQNRNLATLAKNCRIDEMLQYSHGADLINVAEFKHALAN 765
Cdd:TIGR02191   37 RLEFLGDAVLGLVVAEYLF----KNFpdasEGELSRLRAALVSEESLAEVARELGLGDFLLLGKGEEKSGGRRRDSILAD 112

                          170       180
                   ....*....|....*....|....
gi 392886816   766 AFEAVMAAIYLDGGLAPCDVIFSK 789
Cdd:TIGR02191  113 AFEALIGAIYLDSGLEAARKFILK 136
Ribonuclease_3 pfam00636
Ribonuclease III domain;
868-955 5.89e-24

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 97.35  E-value: 5.89e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816   868 QRLEWLGDSVLQLIVSDFLYRRFPYHHEGHMSLLRTSLVSNQTQAVVCDDLGFTEFVI--------------KAPYKTPE 933
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTeeeldirrrnnalgKGPKRADG 80

                           90       100
                   ....*....|....*....|..
gi 392886816   934 lKLKDKADLVEAFIGALYVDRG 955
Cdd:pfam00636   81 -KEKVLADAFEALIGALYLDGG 101
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 687-791 9.88e-20

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: 86.07  E-value: 9.88e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816   687 HNERLEYLGDAVVELIVSHHLYfmltHHF---EGGLATYRTALVQNRNLATLAKNCRIDEMLQYSHGADLINVAEFKHAL 763
Cdd:pfam14622   20 YNERLEFLGDAVLELSVSEYLF----KKPdldEGGLTKLRASIVSEESLAEIAREIGLGKYLRLGKGEEETGGSGRESIL 95

                           90       100
                   ....*....|....*....|....*....
gi 392886816   764 ANAFEAVMAAIYLDGGLAPC-DVIFSKAM 791
Cdd:pfam14622   96 ADALEALIGAIYLDGGFEVAkEFILKKIL 124
 
Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
833-1056 8.21e-58

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 198.78  E-value: 8.21e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816  833 ALEERLGIQFNNIRLLAKAFTRRNIPNNDLTKGHNQRLEWLGDSVLQLIVSDFLYRRFPYHHEGHMSLLRTSLVSNQTQA 912
Cdd:COG0571     6 ELEERLGYRFKDPELLEQALTHRSYANEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816  913 VVCDDLGFTEFVI--KApyktpELKL--KDK----ADLVEAFIGALYVDRGIEHCRAFIRIVFCPRLKHFIESEKWNDAK 984
Cdd:COG0571    86 EIARELGLGDYLRlgKG-----EEKSggRRRpsilADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAGKDYK 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 392886816  985 SHLQQWCLAMRDPsssepdMPEYRVLGIEGPTNNRIFKIAVYYKGKRLASAAESNVHKAELRVAELALANLE 1056
Cdd:COG0571   161 TALQEWLQARGLP------LPEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKLG 226
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 834-1055 1.10e-48

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: 172.39  E-value: 1.10e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816   834 LEERLGIQFNNIRLLAKAFTRRNIPNNDLTKG-HNQRLEWLGDSVLQLIVSDFLYRRFPYHHEGHMSLLRTSLVSNQTQA 912
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYANEHHKDVkNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816   913 VVCDDLGFTEFVI--KAPYKTpELKLKDK--ADLVEAFIGALYVDRGIEHCRAFIRIVFCPRLKHFIESEKWNDAKSHLQ 988
Cdd:TIGR02191   81 EVARELGLGDFLLlgKGEEKS-GGRRRDSilADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIIKEETLKDYKTALQ 159

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 392886816   989 QWCLAMRDPSssepdmPEYRVLGIEGPTNNRIFKIAVYYKGKRLASAAESNVHKAELRVAELALANL 1055
Cdd:TIGR02191  160 EWAQARGKPL------PEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAALEKL 220
RIBOc smart00535
Ribonuclease III family;
846-974 1.65e-41

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 148.52  E-value: 1.65e-41
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816    846 RLLAKAFTRRNIPNNdltKGHNQRLEWLGDSVLQLIVSDFLYRRFPYHHEGHMSLLRTSLVSNQTQAVVCDDLGFTEFVI 925
Cdd:smart00535    1 SLLLRALTHASYSNE---HEHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIR 77

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|..
gi 392886816    926 ---KAPYKTPELKLKDKADLVEAFIGALYVDRGIEHCRAFIRIVFCPRLKHF 974
Cdd:smart00535   78 lgrGEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLDEL 129
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 846-976 3.71e-40

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: 144.68  E-value: 3.71e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816  846 RLLAKAFTRRNIPNNDLTKgHNQRLEWLGDSVLQLIVSDFLYRRFPYHHEGHMSLLRTSLVSNQTQAVVCDDLGFTEFVI 925
Cdd:cd00593     1 SLLLEALTHPSYANEHGRF-NNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLR 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 392886816  926 KAP-YKTPELKLKDK--ADLVEAFIGALYVDRGIEHCRAFIRIVFCPRLKHFIE 976
Cdd:cd00593    80 LGKgEEKSGGRLRPKilADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133
RIBOc smart00535
Ribonuclease III family;
670-791 2.01e-36

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 133.88  E-value: 2.01e-36
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816    670 MSLFNIMKGTSGGEPILHNERLEYLGDAVVELIVSHHLYFMLTHHFEGGLATYRTALVQNRNLATLAKNCRIDEMLQYSH 749
Cdd:smart00535    1 SLLLRALTHASYSNEHEHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGR 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|..
gi 392886816    750 GADLINVAEFKHALANAFEAVMAAIYLDGGLAPCDVIFSKAM 791
Cdd:smart00535   81 GEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLL 122
DSRM_RNAse_III_meta_like cd19877
double-stranded RNA binding motif of metazoan ribonuclease III (RNase III) and similar ...
 981-1055 2.57e-35

double-stranded RNA binding motif of metazoan ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as Drosha, or ribonuclease 3) is a double-stranded RNA (dsRNA)-specific endoribonuclease that is involved in the initial step of microRNA (miRNA) biogenesis. It is a component of the microprocessor complex that is required to process primary miRNA transcripts (pri-miRNAs) to release precursor miRNA (pre-miRNA) in the nucleus. Within the microprocessor complex, RNase III cleaves the 3' and 5' strands of a stem-loop in pri-miRNAs (processing center 11 bp from the dsRNA-ssRNA junction) to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. It is also involved in pre-rRNA processing. Metazoan RNase III is a larger protein than bacterial RNase III. It contains two RNase III domains in the C-terminal half of the protein followed by a double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380706  Cd Length: 75  Bit Score: 128.55  E-value: 2.57e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 392886816  981 NDAKSHLQQWCLAMRDPSSSEPDMPEYRVLGIEGPTNNRIFKIAVYYKGKRLASAAESNVHKAELRVAELALANL 1055
Cdd:cd19877     1 NDPKSQLQQCCLTLRTEGKKEPDIPEYKVLQKSGPTNTRVYTVAVYFRGERIATGTGSSIQQAEMNAAEKALEKL 75
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 680-783 1.61e-32

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: 122.72  E-value: 1.61e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816  680 SGGEPILHNERLEYLGDAVVELIVSHHLYFMLTHHFEGGLATYRTALVQNRNLATLAKNCRIDEMLQYSHGADLINVAEF 759
Cdd:cd00593    13 ANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKGEEKSGGRLR 92

                          90       100
                  ....*....|....*....|....
gi 392886816  760 KHALANAFEAVMAAIYLDGGLAPC 783
Cdd:cd00593    93 PKILADVFEALIGAIYLDGGFEAA 116
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 610-789 1.70e-24

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: 102.67  E-value: 1.70e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816   610 FEEVIEYKFNDRRVIELALMHSSfkshygtpidhvknmitncgyrrkYGAEDKREKKrgimslfnimkgtsggepilHNE 689
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRS------------------------YANEHHKDVK--------------------NNE 36

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816   690 RLEYLGDAVVELIVSHHLYfmltHHF----EGGLATYRTALVQNRNLATLAKNCRIDEMLQYSHGADLINVAEFKHALAN 765
Cdd:TIGR02191   37 RLEFLGDAVLGLVVAEYLF----KNFpdasEGELSRLRAALVSEESLAEVARELGLGDFLLLGKGEEKSGGRRRDSILAD 112

                          170       180
                   ....*....|....*....|....
gi 392886816   766 AFEAVMAAIYLDGGLAPCDVIFSK 789
Cdd:TIGR02191  113 AFEALIGAIYLDSGLEAARKFILK 136
Ribonuclease_3 pfam00636
Ribonuclease III domain;
868-955 5.89e-24

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 97.35  E-value: 5.89e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816   868 QRLEWLGDSVLQLIVSDFLYRRFPYHHEGHMSLLRTSLVSNQTQAVVCDDLGFTEFVI--------------KAPYKTPE 933
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTeeeldirrrnnalgKGPKRADG 80

                           90       100
                   ....*....|....*....|..
gi 392886816   934 lKLKDKADLVEAFIGALYVDRG 955
Cdd:pfam00636   81 -KEKVLADAFEALIGALYLDGG 101
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 847-971 6.32e-20

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: 86.46  E-value: 6.32e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816   847 LLAKAFTRRNIPNNdlTKGHNQRLEWLGDSVLQLIVSDFLYRRFPYhHEGHMSLLRTSLVSNQTQAVVCDDLGFTEFVI- 925
Cdd:pfam14622    3 LLLQALTHKSYANG--RKPYNERLEFLGDAVLELSVSEYLFKKPDL-DEGGLTKLRASIVSEESLAEIAREIGLGKYLRl 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 392886816   926 -KAPYKTPEL-KLKDKADLVEAFIGALYVDRGIEHCRAFIRIVFCPRL 971
Cdd:pfam14622   80 gKGEEETGGSgRESILADALEALIGAIYLDGGFEVAKEFILKKILPDL 127
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 687-791 9.88e-20

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: 86.07  E-value: 9.88e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816   687 HNERLEYLGDAVVELIVSHHLYfmltHHF---EGGLATYRTALVQNRNLATLAKNCRIDEMLQYSHGADLINVAEFKHAL 763
Cdd:pfam14622   20 YNERLEFLGDAVLELSVSEYLF----KKPdldEGGLTKLRASIVSEESLAEIAREIGLGKYLRLGKGEEETGGSGRESIL 95

                           90       100
                   ....*....|....*....|....*....
gi 392886816   764 ANAFEAVMAAIYLDGGLAPC-DVIFSKAM 791
Cdd:pfam14622   96 ADALEALIGAIYLDGGFEVAkEFILKKIL 124
Ribonuclease_3 pfam00636
Ribonuclease III domain;
689-779 1.12e-19

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 85.02  E-value: 1.12e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816   689 ERLEYLGDAVVELIVSHHLYFMLTHHFEGGLATYRTALVQNRNLATLAKNCRIDEMLQYSH----------GADLINVAE 758
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEEldirrrnnalGKGPKRADG 80

                           90       100
                   ....*....|....*....|.
gi 392886816   759 FKHALANAFEAVMAAIYLDGG 779
Cdd:pfam00636   81 KEKVLADAFEALIGALYLDGG 101
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 982-1055 2.38e-12

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: 62.90  E-value: 2.38e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 392886816  982 DAKSHLQQWCLAMRDPSssepdmPEYRVLGIEGPTNNRIFKIAVYYKGKRLASAAESNVHKAELRVAELALANL 1055
Cdd:cd10845     2 DYKTALQEYLQKRGLPL------PEYELVEEEGPDHNKTFTVEVKVNGKVIGEGTGRSKKEAEQAAAKAALEKL 69
DSRM smart00358
Double-stranded RNA binding motif;
983-1056 3.17e-12

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 62.67  E-value: 3.17e-12
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 392886816    983 AKSHLQQWCLAMRDPsssepdmPEYRVLGIEGPTNNRIFKIAVYYKGKRLASAAESNVHKAELRVAELALANLE 1056
Cdd:smart00358    1 PKSLLQELAQKRKLP-------PEYELVKEEGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSLK 67
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 983-1055 5.50e-12

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: 61.86  E-value: 5.50e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 392886816   983 AKSHLQQWCLAMRDPsssepdmPEYRVLGIEGPTNNRIFKIAVYYKGKRLASAAESNVHKAELRVAELALANL 1055
Cdd:pfam00035    1 PKSLLQEYAQKNGKP-------PPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66
ZF_RNaseIII_KREN1-3 cd23747
C2H2 zinc finger and Ribonuclease III domain of Kinetoplastid RNA Editing endonuclease 1 ...
 854-952 3.33e-03

C2H2 zinc finger and Ribonuclease III domain of Kinetoplastid RNA Editing endonuclease 1 (KREN1), KREN2, KREN3, and similar proteins; KREN1-3 (KREPB1-3) are RNase III family endonucleases of the RNA-editing catalytic complex (RECC) involved in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The RECC core complex comprises a U-insertion subcomplex (KRET2 TUTase, KREPA1 zinc-finger protein, and KREL2 RNA ligase), a U-deletion subcomplex (KREX2 exonuclease, KREPA2 zinc-finger protein, and KREL1 RNA ligase), and six structural and/or RNA-binding proteins (KREPA3, KREPA4, KREPA5, KREPA6, KREPB4, and KREPB5). This core complex interacts with one of three RNase III family endonucleases (KREN1, KREN2, and KREN3) that may partner with one or more partner protein(s) with divergent RNase III domains, such as KREN1/KREPB8, KREN2/KREPB7, KREN3/KREPB6. KREPB4-KREPB10 have divergent RNase III domains. RECC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and the RNA-editing substrate-binding complex (RESC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing.


Pssm-ID: 469573  Cd Length: 215  Bit Score: 40.09  E-value: 3.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392886816  854 RRNIPNNDLTKGHN---QRLEWLGDSVLQLIVSDFLYRRFPYHHEG----HMSLLRTSLVSNQTQAVVCDDLGFTEFVik 926
Cdd:cd23747    56 LADVTSSQNAKGRTvefDRLEWIGDNSVKPVLSDRFMRLFPDRSGGsntyRLNCFQGFLDSNVHLEFMFDYLELNELI-- 133

                          90       100
                  ....*....|....*....|....*.
gi 392886816  927 aPYKTPELKLKDKADLVEAFIGALYV 952
Cdd:cd23747   134 -PDREKLVTGKTKADVVEALFGELQL 158
DSRM_DRADA cd19902
double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) ...
 1006-1057 7.75e-03

double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. DRADA family members contain at least one double-stranded RNA binding motifs (DSRM); vertebrate proteins contain three. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380731  Cd Length: 71  Bit Score: 36.11  E-value: 7.75e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 392886816 1006 EYRVLGIEGPTNNRIFKIAVYYKGKRLASAAESNVHKAELRVAELALANLES 1057
Cdd:cd19902    19 EIEVLSQSGPPHNPRFKAAVFVGGRRFPSVEASSKKDAKQEAADLALRALIA 70
 
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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