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Conserved domains on  [gi|167041438|gb|ABZ06190|]
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putative RNase3 domain protein [uncultured marine microorganism HF4000_006O13]

Protein Classification

ribonuclease III family protein( domain architecture ID 11426290)

ribonuclease III family protein similar to ribonuclease III, which digests double-stranded RNA in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S)

CATH:  1.10.1520.10
Gene Ontology:  GO:0006396|GO:0004525

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
6-224 3.38e-103

dsRNA-specific ribonuclease [Transcription];


:

Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 297.78  E-value: 3.38e-103
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438   6 SWCEQRFHYRFKDDILLQTALTHRSHS-----VDNNERLEFLGDAALDLVISELLYQSYSEQTEGYLSRMRSSLVKGNTL 80
Cdd:COG0571    5 EELEERLGYRFKDPELLEQALTHRSYAnehggLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETL 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438  81 AELAKELDVGGYLILGKGENTSGGRERLSLLSDTLEAMIGAIFLDGGYVAVKNVIIKIFDSRIQALDPKSEHKDHKSVLQ 160
Cdd:COG0571   85 AEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAGKDYKTALQ 164

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 167041438 161 EKLQGVKQGLPVYSLVRSVG-DHNKTFVVECSIKsGEIVTQASGKTLRVAEQKAASKALQAMQND 224
Cdd:COG0571  165 EWLQARGLPLPEYEVVEEEGpDHAKTFTVEVLVG-GKVLGEGTGRSKKEAEQAAAKAALEKLGKK 228
 
Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
6-224 3.38e-103

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 297.78  E-value: 3.38e-103
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438   6 SWCEQRFHYRFKDDILLQTALTHRSHS-----VDNNERLEFLGDAALDLVISELLYQSYSEQTEGYLSRMRSSLVKGNTL 80
Cdd:COG0571    5 EELEERLGYRFKDPELLEQALTHRSYAnehggLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETL 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438  81 AELAKELDVGGYLILGKGENTSGGRERLSLLSDTLEAMIGAIFLDGGYVAVKNVIIKIFDSRIQALDPKSEHKDHKSVLQ 160
Cdd:COG0571   85 AEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAGKDYKTALQ 164

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 167041438 161 EKLQGVKQGLPVYSLVRSVG-DHNKTFVVECSIKsGEIVTQASGKTLRVAEQKAASKALQAMQND 224
Cdd:COG0571  165 EWLQARGLPLPEYEVVEEEGpDHAKTFTVEVLVG-GKVLGEGTGRSKKEAEQAAAKAALEKLGKK 228
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 9-221 2.40e-84

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: 249.43  E-value: 2.40e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438    9 EQRFHYRFKDDILLQTALTHRSHS------VDNNERLEFLGDAALDLVISELLYQSYSEQTEGYLSRMRSSLVKGNTLAE 82
Cdd:TIGR02191   2 EKRLGYKFKNPELLEQALTHRSYAnehhkdVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438   83 LAKELDVGGYLILGKGENTSGGRERLSLLSDTLEAMIGAIFLDGGYVAVKNVIIKIFDSRIQALDPKSEHKDHKSVLQEK 162
Cdd:TIGR02191  82 VARELGLGDFLLLGKGEEKSGGRRRDSILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIIKEETLKDYKTALQEW 161

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438  163 LQGVKQGLPVYSLVRSVG-DHNKTFVVECSIKsGEIVTQASGKTLRVAEQKAASKALQAM 221
Cdd:TIGR02191 162 AQARGKPLPEYRLIKEEGpDHDKEFTVEVSVN-GEPYGEGKGKSKKEAEQNAAKAALEKL 220
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 21-148 4.67e-50

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: 159.32  E-value: 4.67e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438  21 LLQTALTHRS----HSVDNNERLEFLGDAALDLVISELLYQSYSEQTEGYLSRMRSSLVKGNTLAELAKELDVGGYLILG 96
Cdd:cd00593    2 LLLEALTHPSyaneHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLG 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 167041438  97 KGENTSGGRERLSLLSDTLEAMIGAIFLDGGYVAVKNVIIKIFDSRIQALDP 148
Cdd:cd00593   82 KGEEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133
RIBOc smart00535
Ribonuclease III family;
21-146 6.27e-44

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 143.51  E-value: 6.27e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438    21 LLQTALTHRS--HSVDNNERLEFLGDAALDLVISELLYQSYSEQTEGYLSRMRSSLVKGNTLAELAKELDVGGYLILGKG 98
Cdd:smart00535   2 LLLRALTHASysNEHEHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 167041438    99 ENTSGGRERLSLLSDTLEAMIGAIFLDGGYVAVKNVIIKIFDSRIQAL 146
Cdd:smart00535  82 EAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLDEL 129
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 21-137 4.15e-42

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: 138.85  E-value: 4.15e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438   21 LLQTALTHRSHS---VDNNERLEFLGDAALDLVISELLYQSYsEQTEGYLSRMRSSLVKGNTLAELAKELDVGGYLILGK 97
Cdd:pfam14622   3 LLLQALTHKSYAngrKPYNERLEFLGDAVLELSVSEYLFKKP-DLDEGGLTKLRASIVSEESLAEIAREIGLGKYLRLGK 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 167041438   98 GENTSGGRERLSLLSDTLEAMIGAIFLDGGYVAVKNVIIK 137
Cdd:pfam14622  82 GEEETGGSGRESILADALEALIGAIYLDGGFEVAKEFILK 121
 
Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
6-224 3.38e-103

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 297.78  E-value: 3.38e-103
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438   6 SWCEQRFHYRFKDDILLQTALTHRSHS-----VDNNERLEFLGDAALDLVISELLYQSYSEQTEGYLSRMRSSLVKGNTL 80
Cdd:COG0571    5 EELEERLGYRFKDPELLEQALTHRSYAnehggLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETL 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438  81 AELAKELDVGGYLILGKGENTSGGRERLSLLSDTLEAMIGAIFLDGGYVAVKNVIIKIFDSRIQALDPKSEHKDHKSVLQ 160
Cdd:COG0571   85 AEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAGKDYKTALQ 164

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 167041438 161 EKLQGVKQGLPVYSLVRSVG-DHNKTFVVECSIKsGEIVTQASGKTLRVAEQKAASKALQAMQND 224
Cdd:COG0571  165 EWLQARGLPLPEYEVVEEEGpDHAKTFTVEVLVG-GKVLGEGTGRSKKEAEQAAAKAALEKLGKK 228
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 9-221 2.40e-84

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: 249.43  E-value: 2.40e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438    9 EQRFHYRFKDDILLQTALTHRSHS------VDNNERLEFLGDAALDLVISELLYQSYSEQTEGYLSRMRSSLVKGNTLAE 82
Cdd:TIGR02191   2 EKRLGYKFKNPELLEQALTHRSYAnehhkdVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438   83 LAKELDVGGYLILGKGENTSGGRERLSLLSDTLEAMIGAIFLDGGYVAVKNVIIKIFDSRIQALDPKSEHKDHKSVLQEK 162
Cdd:TIGR02191  82 VARELGLGDFLLLGKGEEKSGGRRRDSILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIIKEETLKDYKTALQEW 161

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438  163 LQGVKQGLPVYSLVRSVG-DHNKTFVVECSIKsGEIVTQASGKTLRVAEQKAASKALQAM 221
Cdd:TIGR02191 162 AQARGKPLPEYRLIKEEGpDHDKEFTVEVSVN-GEPYGEGKGKSKKEAEQNAAKAALEKL 220
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 21-148 4.67e-50

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: 159.32  E-value: 4.67e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438  21 LLQTALTHRS----HSVDNNERLEFLGDAALDLVISELLYQSYSEQTEGYLSRMRSSLVKGNTLAELAKELDVGGYLILG 96
Cdd:cd00593    2 LLLEALTHPSyaneHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLG 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 167041438  97 KGENTSGGRERLSLLSDTLEAMIGAIFLDGGYVAVKNVIIKIFDSRIQALDP 148
Cdd:cd00593   82 KGEEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133
RIBOc smart00535
Ribonuclease III family;
21-146 6.27e-44

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 143.51  E-value: 6.27e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438    21 LLQTALTHRS--HSVDNNERLEFLGDAALDLVISELLYQSYSEQTEGYLSRMRSSLVKGNTLAELAKELDVGGYLILGKG 98
Cdd:smart00535   2 LLLRALTHASysNEHEHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 167041438    99 ENTSGGRERLSLLSDTLEAMIGAIFLDGGYVAVKNVIIKIFDSRIQAL 146
Cdd:smart00535  82 EAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLDEL 129
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 21-137 4.15e-42

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: 138.85  E-value: 4.15e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438   21 LLQTALTHRSHS---VDNNERLEFLGDAALDLVISELLYQSYsEQTEGYLSRMRSSLVKGNTLAELAKELDVGGYLILGK 97
Cdd:pfam14622   3 LLLQALTHKSYAngrKPYNERLEFLGDAVLELSVSEYLFKKP-DLDEGGLTKLRASIVSEESLAEIAREIGLGKYLRLGK 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 167041438   98 GENTSGGRERLSLLSDTLEAMIGAIFLDGGYVAVKNVIIK 137
Cdd:pfam14622  82 GEEETGGSGRESILADALEALIGAIYLDGGFEVAKEFILK 121
Ribonuclease_3 pfam00636
Ribonuclease III domain;
37-127 1.77e-25

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 95.42  E-value: 1.77e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438   37 ERLEFLGDAALDLVISELLYQSYSEQTEGYLSRMRSSLVKGNTLAELAKELDVGGYLI------------LGKGENTSGG 104
Cdd:pfam00636   1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTeeeldirrrnnaLGKGPKRADG 80

                          90       100
                  ....*....|....*....|...
gi 167041438  105 RErlSLLSDTLEAMIGAIFLDGG 127
Cdd:pfam00636  81 KE--KVLADAFEALIGALYLDGG 101
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 153-221 3.13e-20

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: 81.00  E-value: 3.13e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438 153 KDHKSVLQEKLQGVKQGLPVYSLVRSVG-DHNKTFVVECSIKsGEIVTQASGKTLRVAEQKAASKALQAM 221
Cdd:cd10845    1 KDYKTALQEYLQKRGLPLPEYELVEEEGpDHNKTFTVEVKVN-GKVIGEGTGRSKKEAEQAAAKAALEKL 69
DSRM smart00358
Double-stranded RNA binding motif;
156-222 1.56e-14

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 65.75  E-value: 1.56e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 167041438   156 KSVLQEKLQgvKQGL-PVYSLVRSVG-DHNKTFVVECSIKsGEIVTQASGKTLRVAEQKAASKALQAMQ 222
Cdd:smart00358   2 KSLLQELAQ--KRKLpPEYELVKEEGpDHAPRFTVTVKVG-GKRTGEGEGSSKKEAKQRAAEAALRSLK 67
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 156-219 2.15e-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: 60.32  E-value: 2.15e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 167041438  156 KSVLQEKLQGVKQGLPVYSLVRSVGDHNKTFVVECSIKsGEIVTQASGKTLRVAEQKAASKALQ 219
Cdd:pfam00035   2 KSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVD-GKLYGSGTGSSKKEAEQLAAEKALE 64
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 160-218 3.86e-12

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: 59.22  E-value: 3.86e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 167041438 160 QEKLQGVKQGLPVYSLVRSVGDHNKTFVVECSIksGEIVTQASGKTLRVAEQKAASKAL 218
Cdd:cd00048    1 NELCQKNKWPPPEYETVEEGGPHNPRFTCTVTV--NGQTFEGEGKSKKEAKQAAAEKAL 57
DSRM_RNT1p-like cd19876
double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and ...
 153-218 2.15e-07

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: 46.56  E-value: 2.15e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 167041438 153 KDHKSVLQEKLqGVKQGLPVYSLVRSVGDHNKTFVVECSIkSGEIVTQASGKTLRVAEQKAASKAL 218
Cdd:cd19876    2 KFAKQKLYSLI-GPASLKPEYVVVKKEGGNDPNYTVACRI-NGEVLGTGVGRSIKKAGQRAAMSAL 65
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 157-224 3.41e-07

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; This family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. This family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380691 [Multi-domain]  Cd Length: 70  Bit Score: 46.10  E-value: 3.41e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438 157 SVLQEKlqGVKQGL-PVYSLVRSVGD-HNKTFVVECSIksGEIVTQASGKTLRVAEQKAASKALQAMQND 224
Cdd:cd19862    5 SVLQEL--CAKRGItPKYELISSEGAvHEPTFTFRVTV--GDITATGSGTSKKKAKHAAAENALEQLKGS 70
DSRM_STAU_rpt3 cd19859
third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 167-221 8.96e-06

third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380688  Cd Length: 65  Bit Score: 42.00  E-value: 8.96e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 167041438 167 KQGLPV-YSLVRSVGD-HNKTFVVECSIksGEIVTQASGKTLRVAEQKAASKALQAM 221
Cdd:cd19859   11 KRNLTVnFEVLRESGPpHMKNFITRCTV--GSFVTEGEGNSKKVSKKRAAEKMLEEL 65
DSRM_AtDRB-like_rpt2 cd19908
second double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 156-222 1.99e-05

second double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins; This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380737 [Multi-domain]  Cd Length: 69  Bit Score: 41.31  E-value: 1.99e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 167041438 156 KSVLQEKLQGVKQGLPVYSLVRSVGDHNKTFVveCSIKSGEIV-TQASGKTLRVAEQKAASKALQAMQ 222
Cdd:cd19908    4 KNLLQEYAQKAGLPLPLYTTVRSGPGHVPTFT--CTVEIAGITfTGEAAKTKKQAEKSAARTAWSSIK 69
DSRM_RNAse_III_meta_like cd19877
double-stranded RNA binding motif of metazoan ribonuclease III (RNase III) and similar ...
 153-219 2.89e-05

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: 41.11  E-value: 2.89e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 167041438 153 KDHKSVLQE-----KLQGVKQG-LPVYSLVRSVG-DHNKTFVVECSIKsGEIVTQASGKTLRVAEQKAASKALQ 219
Cdd:cd19877    1 NDPKSQLQQccltlRTEGKKEPdIPEYKVLQKSGpTNTRVYTVAVYFR-GERIATGTGSSIQQAEMNAAEKALE 73
DSRM_AtDRB-like cd19878
double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins ...
 156-222 4.32e-05

double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins; This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380707 [Multi-domain]  Cd Length: 67  Bit Score: 40.19  E-value: 4.32e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 167041438 156 KSVLQEKLQGVKQGLPVYSLVRSVGDHNKTFVVECSIkSGEIVTQASGKTLRVAEQKAASKALQAMQ 222
Cdd:cd19878    2 KNLLQEYAQKKKIPLPKYESAKSGPSHQPTFVSTVIV-LGVRFSSEGAKNKKQAEQSAAKVALKELG 67
DSRM_AtDRB-like_rpt1 cd19907
first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 155-221 7.06e-05

first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins; This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380736 [Multi-domain]  Cd Length: 69  Bit Score: 39.77  E-value: 7.06e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 167041438 155 HKSVLQEKLQGVKQGLPVYSLVRSVGDHNKTFvvECSIK-SGEIVTQASG-KTLRVAEQKAASKALQAM 221
Cdd:cd19907    2 YKSQLQEYAQKSCLNLPVYACIREGPDHAPRF--RATVTfNGVIFESPPGfPTLKAAEHSAAEVALNSL 68
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 153-219 8.47e-04

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380704  Cd Length: 67  Bit Score: 36.86  E-value: 8.47e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 167041438 153 KDHKSVLQEKLQgvKQGLPV-YSLVRSVGDHNKTFVVECSIkSGEIVTQASGKTLRVAEQKAASKALQ 219
Cdd:cd19875    1 KNPVSALNEYCQ--KRGLSLeFVDVSVGPDHCPGFTASATI-DGIVFASATGTSKKEAKRAAAKLALK 65
DSRM_STAU_rpt1 cd19857
first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 171-218 9.66e-04

first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380686  Cd Length: 64  Bit Score: 36.48  E-value: 9.66e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 167041438 171 PVYSLVRSVGD-HNKTFVVECSIkSGEIVTQASGKTLRVAEQKAASKAL 218
Cdd:cd19857   17 PQYTLVDEEGPaHKKTFTVKLTL-GDEEEYEASGSSIKKAQHAAAEKAL 64
DSRM_DGCR8_rpt1 cd19867
first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and ...
 151-218 1.22e-03

first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and similar proteins; DGCR8 is a component of the microprocessor complex that acts as an RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Within the microprocessor complex, DGCR8 functions as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11bp away from the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. DGCR8 contains two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380696  Cd Length: 74  Bit Score: 36.54  E-value: 1.22e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 167041438 151 EHKDHKSVLQEKLQGVKQGLPVYSlVRSVGDHNKTFVVECSIkSGEIVTQASGKTLRVAEQKAASKAL 218
Cdd:cd19867    4 DGKSPVCILHEYCQRVLKVQPEYN-FTETENAATPFSAEVFI-NGVEYGSGEASSKKLAKQKAARATL 69
seadorna_dsRNA TIGR04238
seadornavirus double-stranded RNA-binding protein; This protein family occurs in the ...
 154-224 2.04e-03

seadornavirus double-stranded RNA-binding protein; This protein family occurs in the seadornavirus virus group, with an N-terminal domain for binding double-stranded RNA, is designated VP12 in Banna virus, VP8 in Kadipiro virus, and VP11 in Liao ning virus.


Pssm-ID: 275074 [Multi-domain]  Cd Length: 201  Bit Score: 38.00  E-value: 2.04e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 167041438  154 DHKSVLQEklQGVKQG--LPVYSLVRSVG-DHNKTFVVECSIKSGEIVTQASGKtlRVAEQKAASKALQAMQND 224
Cdd:TIGR04238   1 NVVGMLQE--LAVKRGleLPVYEKVGKEGpDHAPTFTIKLTANDIEVIEAASSK--KQAEKLAAATIYEDMKEN 70
DSRM_MRPL3_like cd19873
double-stranded RNA binding motif of Saccharomyces cerevisiae mitochondrial 54S ribosomal ...
 167-221 4.69e-03

double-stranded RNA binding motif of Saccharomyces cerevisiae mitochondrial 54S ribosomal protein L3 (MRPL3) and similar proteins; MRPL3 (also called mitochondrial large ribosomal subunit protein mL44) is a component of the mitochondrial ribosome (mitoribosome), a dedicated translation machinery responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. MRPL3 contains a RNase III-like domain and a double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380702  Cd Length: 84  Bit Score: 34.89  E-value: 4.69e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041438 167 KQGL--PVYSLVRSVG--DHNKTFVVecSIKSGE-IVTQASGKTLRVAEQKAASKALQAM 221
Cdd:cd19873   24 REGLepPVSRLLKESGraSHTPTFVV--GVYSGSqKLGEGAGSSIKMAEIRAARDALRKH 81
DSRM_PRKRA_rpt1 cd19889
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 165-224 4.84e-03

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. PRKRA contains three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380718 [Multi-domain]  Cd Length: 71  Bit Score: 34.89  E-value: 4.84e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 167041438 165 GVKQG-LPVYSLVRSVGD-HNKTFVVECSIksGEIVTQASGKTLRVAEQKAASKALQAMQND 224
Cdd:cd19889   12 GTKTGnIPVYELEKSEGQaHLPSFTFRVTV--GDITCTGEGTSKKLAKHRAAEAALNILKGN 71
 
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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