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Conserved domains on  [gi|581977256|ref|WP_024130107|]
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MULTISPECIES: ribonuclease III [Citrobacter]

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
EC:  3.1.26.3
Gene Ontology:  GO:0004525|GO:0006396
PubMed:  18047582|24124076|17194582
SCOP:  4002876

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
6-210 1.04e-113

dsRNA-specific ribonuclease [Transcription];


:

Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 324.36  E-value: 1.04e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256   6 INRLQRKLGYTFTHQELLQQALTHRSAS-----SKHNERLEFLGDSILSFVIANALYHRFPRVDEGDMSRMRATLVRGNT 80
Cdd:COG0571    4 LEELEERLGYRFKDPELLEQALTHRSYAnehggLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEET 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256  81 LAELAREFDLGECLRLGPGELKSGGYRRESILADTVEALIGGVFLDSDIQTVEKLILNWYQTRLNEISPGDKQKDPKTRL 160
Cdd:COG0571   84 LAEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAGKDYKTAL 163

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 581977256 161 QEYLQGRHLPLPSYLVVQVRGEAHDQEFTIHCQVSGlSEPVVGTGSSRRK 210
Cdd:COG0571  164 QEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGG-KVLGEGTGRSKKE 212
 
Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
6-210 1.04e-113

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 324.36  E-value: 1.04e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256   6 INRLQRKLGYTFTHQELLQQALTHRSAS-----SKHNERLEFLGDSILSFVIANALYHRFPRVDEGDMSRMRATLVRGNT 80
Cdd:COG0571    4 LEELEERLGYRFKDPELLEQALTHRSYAnehggLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEET 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256  81 LAELAREFDLGECLRLGPGELKSGGYRRESILADTVEALIGGVFLDSDIQTVEKLILNWYQTRLNEISPGDKQKDPKTRL 160
Cdd:COG0571   84 LAEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAGKDYKTAL 163

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 581977256 161 QEYLQGRHLPLPSYLVVQVRGEAHDQEFTIHCQVSGlSEPVVGTGSSRRK 210
Cdd:COG0571  164 QEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGG-KVLGEGTGRSKKE 212
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 9-210 6.17e-91

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: 266.38  E-value: 6.17e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256    9 LQRKLGYTFTHQELLQQALTHRSASS------KHNERLEFLGDSILSFVIANALYHRFPRVDEGDMSRMRATLVRGNTLA 82
Cdd:TIGR02191   1 LEKRLGYKFKNPELLEQALTHRSYANehhkdvKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256   83 ELAREFDLGECLRLGPGELKSGGYRRESILADTVEALIGGVFLDSDIQTVEKLILNWYQTRLNEISPGDKQKDPKTRLQE 162
Cdd:TIGR02191  81 EVARELGLGDFLLLGKGEEKSGGRRRDSILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIIKEETLKDYKTALQE 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 581977256  163 YLQGRHLPLPSYLVVQVRGEAHDQEFTIHCQVSGLSEpVVGTGSSRRK 210
Cdd:TIGR02191 161 WAQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPY-GEGKGKSKKE 207
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 21-149 8.59e-55

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: 171.64  E-value: 8.59e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256  21 ELLQQALTHRSASS----KHNERLEFLGDSILSFVIANALYHRFPRVDEGDMSRMRATLVRGNTLAELAREFDLGECLRL 96
Cdd:cd00593    1 SLLLEALTHPSYANehgrFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRL 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 581977256  97 GPGELKSGGYRRESILADTVEALIGGVFLDSDIQTVEKLILNWYQTRLNEISP 149
Cdd:cd00593   81 GKGEEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133
RIBOc smart00535
Ribonuclease III family;
21-147 9.24e-54

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 168.94  E-value: 9.24e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256    21 ELLQQALTHRSASSK--HNERLEFLGDSILSFVIANALYHRFPRVDEGDMSRMRATLVRGNTLAELAREFDLGECLRLGP 98
Cdd:smart00535   1 SLLLRALTHASYSNEheHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGR 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 581977256    99 GELKSGGYRRESILADTVEALIGGVFLDSDIQTVEKLILNWYQTRLNEI 147
Cdd:smart00535  81 GEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLDEL 129
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 20-144 4.99e-44

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: 143.85  E-value: 4.99e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256   20 QELLQQALTHRS---ASSKHNERLEFLGDSILSFVIANALYHRFPRvDEGDMSRMRATLVRGNTLAELAREFDLGECLRL 96
Cdd:pfam14622   1 EELLLQALTHKSyanGRKPYNERLEFLGDAVLELSVSEYLFKKPDL-DEGGLTKLRASIVSEESLAEIAREIGLGKYLRL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 581977256   97 GPGELKSGGYRRESILADTVEALIGGVFLDSDIQTVEKLILNWYQTRL 144
Cdd:pfam14622  80 GKGEEETGGSGRESILADALEALIGAIYLDGGFEVAKEFILKKILPDL 127
 
Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
6-210 1.04e-113

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 324.36  E-value: 1.04e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256   6 INRLQRKLGYTFTHQELLQQALTHRSAS-----SKHNERLEFLGDSILSFVIANALYHRFPRVDEGDMSRMRATLVRGNT 80
Cdd:COG0571    4 LEELEERLGYRFKDPELLEQALTHRSYAnehggLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEET 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256  81 LAELAREFDLGECLRLGPGELKSGGYRRESILADTVEALIGGVFLDSDIQTVEKLILNWYQTRLNEISPGDKQKDPKTRL 160
Cdd:COG0571   84 LAEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAGKDYKTAL 163

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 581977256 161 QEYLQGRHLPLPSYLVVQVRGEAHDQEFTIHCQVSGlSEPVVGTGSSRRK 210
Cdd:COG0571  164 QEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGG-KVLGEGTGRSKKE 212
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 9-210 6.17e-91

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: 266.38  E-value: 6.17e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256    9 LQRKLGYTFTHQELLQQALTHRSASS------KHNERLEFLGDSILSFVIANALYHRFPRVDEGDMSRMRATLVRGNTLA 82
Cdd:TIGR02191   1 LEKRLGYKFKNPELLEQALTHRSYANehhkdvKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256   83 ELAREFDLGECLRLGPGELKSGGYRRESILADTVEALIGGVFLDSDIQTVEKLILNWYQTRLNEISPGDKQKDPKTRLQE 162
Cdd:TIGR02191  81 EVARELGLGDFLLLGKGEEKSGGRRRDSILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIIKEETLKDYKTALQE 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 581977256  163 YLQGRHLPLPSYLVVQVRGEAHDQEFTIHCQVSGLSEpVVGTGSSRRK 210
Cdd:TIGR02191 161 WAQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPY-GEGKGKSKKE 207
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 21-149 8.59e-55

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: 171.64  E-value: 8.59e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256  21 ELLQQALTHRSASS----KHNERLEFLGDSILSFVIANALYHRFPRVDEGDMSRMRATLVRGNTLAELAREFDLGECLRL 96
Cdd:cd00593    1 SLLLEALTHPSYANehgrFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRL 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 581977256  97 GPGELKSGGYRRESILADTVEALIGGVFLDSDIQTVEKLILNWYQTRLNEISP 149
Cdd:cd00593   81 GKGEEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133
RIBOc smart00535
Ribonuclease III family;
21-147 9.24e-54

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 168.94  E-value: 9.24e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256    21 ELLQQALTHRSASSK--HNERLEFLGDSILSFVIANALYHRFPRVDEGDMSRMRATLVRGNTLAELAREFDLGECLRLGP 98
Cdd:smart00535   1 SLLLRALTHASYSNEheHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGR 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 581977256    99 GELKSGGYRRESILADTVEALIGGVFLDSDIQTVEKLILNWYQTRLNEI 147
Cdd:smart00535  81 GEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLDEL 129
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 20-144 4.99e-44

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: 143.85  E-value: 4.99e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256   20 QELLQQALTHRS---ASSKHNERLEFLGDSILSFVIANALYHRFPRvDEGDMSRMRATLVRGNTLAELAREFDLGECLRL 96
Cdd:pfam14622   1 EELLLQALTHKSyanGRKPYNERLEFLGDAVLELSVSEYLFKKPDL-DEGGLTKLRASIVSEESLAEIAREIGLGKYLRL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 581977256   97 GPGELKSGGYRRESILADTVEALIGGVFLDSDIQTVEKLILNWYQTRL 144
Cdd:pfam14622  80 GKGEEETGGSGRESILADALEALIGAIYLDGGFEVAKEFILKKILPDL 127
Ribonuclease_3 pfam00636
Ribonuclease III domain;
38-128 3.20e-26

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 97.35  E-value: 3.20e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256   38 ERLEFLGDSILSFVIANALYHRFPRVDEGDMSRMRATLVRGNTLAELAREFDLGECLR------------LGPGELKSGG 105
Cdd:pfam00636   1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTeeeldirrrnnaLGKGPKRADG 80

                          90       100
                  ....*....|....*....|...
gi 581977256  106 yrRESILADTVEALIGGVFLDSD 128
Cdd:pfam00636  81 --KEKVLADAFEALIGALYLDGG 101
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 154-210 7.15e-17

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: 72.14  E-value: 7.15e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 581977256 154 KDPKTRLQEYLQGRHLPLPSYLVVQVRGEAHDQEFTIHCQVSGlSEPVVGTGSSRRK 210
Cdd:cd10845    1 KDYKTALQEYLQKRGLPLPEYELVEEEGPDHNKTFTVEVKVNG-KVIGEGTGRSKKE 56
DSRM smart00358
Double-stranded RNA binding motif;
156-224 1.84e-10

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 54.96  E-value: 1.84e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 581977256   156 PKTRLQEYLQGRHLPlPSYLVVQVRGEAHDQEFTIHCQVSGLSEPVvGTGSSRRKAEQAAAEQALKKLE 224
Cdd:smart00358   1 PKSLLQELAQKRKLP-PEYELVKEEGPDHAPRFTVTVKVGGKRTGE-GEGSSKKEAKQRAAEAALRSLK 67
DSRM_PRKRA-like_rpt2 cd19863
second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...
 160-209 1.46e-08

second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The 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. The 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 second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380692  Cd Length: 67  Bit Score: 50.07  E-value: 1.46e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 581977256 160 LQEYLQGRHLPLPSYLVVQVRGEAHDQEFTIHCQVSGLSEpvVGTGSSRR 209
Cdd:cd19863    6 LQELCVQRRWRLPEYEVEQESGPPHEKEFTIACRVENFSE--TGSGKSKK 53
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 156-223 8.73e-06

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: 42.22  E-value: 8.73e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 581977256  156 PKTRLQEYLQgRHLPLPSYLVVQVRGEAHDQEFTIHCQVSGLsEPVVGTGSSRRKAEQAAAEQALKKL 223
Cdd:pfam00035   1 PKSLLQEYAQ-KNGKPPPYEYVSEEGPPHSPKFTVTVKVDGK-LYGSGTGSSKKEAEQLAAEKALEKL 66
DSRM_TARBP2_rpt2 cd10844
second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and ...
 155-209 2.34e-05

second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar proteins; TARBP2 (also known as 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. TARBP2 contains 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: 380681  Cd Length: 67  Bit Score: 41.25  E-value: 2.34e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 581977256 155 DPKTRLQEYLQGRHLPLPSYLVVQVRGEAHDQEFTIHCQVSGLSEpvVGTGSSRR 209
Cdd:cd10844    1 NPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIE--IGSGTSKK 53
seadorna_dsRNA TIGR04238
seadornavirus double-stranded RNA-binding protein; This protein family occurs in the ...
 155-210 9.85e-05

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: 41.85  E-value: 9.85e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 581977256  155 DPKTRLQEYLQGRHLPLPSYLVVQVRGEAHDQEFTIHCQVSGLSepVVGTGSSRRK 210
Cdd:TIGR04238   1 NVVGMLQELAVKRGLELPVYEKVGKEGPDHAPTFTIKLTANDIE--VIEAASSKKQ 54
DSRM_PRKRA_rpt2 cd19891
second double-stranded RNA binding motif of protein activator of the interferon-induced ...
 155-223 1.07e-04

second 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 second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380720  Cd Length: 67  Bit Score: 39.15  E-value: 1.07e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 581977256 155 DPKTRLQEYLQGRHLPLPSYLVVQVRGEAHDQEFTIHCQVSGLSEpvVGTGSSRRKAEQAAAEQALKKL 223
Cdd:cd19891    1 NPIGSLQELAVQKGWRLPEYTLAQESGPPHKREFTITCRVETFVE--TGTGTSKKVAKRNAAEKLLAKF 67
DSRM_STAU_rpt4 cd19860
fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 155-209 5.20e-04

fourth 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 fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380689  Cd Length: 68  Bit Score: 37.31  E-value: 5.20e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 581977256 155 DPKTRLQEYLQGRHLPLPSYLVVQVRGEAHDQEFTIHCQVSGLSEPvvGTGSSRR 209
Cdd:cd19860    1 NPISRLIQIQQARKEKEPVYSLVAERGTPRRREFVMQVTVGDKTAT--GTGPNKK 53
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 154-223 5.35e-03

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: 34.54  E-value: 5.35e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581977256 154 KDPKTRLQEYLQGRHLPlPSYLVVQVRGEAHDQEFTIHCQVSGLSepVVGTGSSRRKAEQAAAEQALKKL 223
Cdd:cd19862    1 KTPISVLQELCAKRGIT-PKYELISSEGAVHEPTFTFRVTVGDIT--ATGSGTSKKKAKHAAAENALEQL 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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