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Conserved domains on  [gi|2012627889|ref|WP_207754609|]
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MULTISPECIES: ribonuclease III [Staphylococcus]

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];
3-235 6.12e-104

dsRNA-specific ribonuclease [Transcription];


:

Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 300.09  E-value: 6.12e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889   3 KDFRQRFEQKmneLGIHFDNIKLYQQAFSHSSFINDFNmnRLEHNERLEFLGDAVLEVTVSRYLFDKHPNLPEGNLTKMR 82
Cdd:COG0571     1 SEDLEELEER---LGYRFKDPELLEQALTHRSYANEHG--GLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889  83 ATIVCEPSLVIFANKIQLNQLILLGKGEEKTGGRTRPSLISDAFEAFVGALYLDQGLGAVWHFAEKVIFPYVEDDELIG- 161
Cdd:COG0571    76 AALVSEETLAEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGa 155

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2012627889 162 VVDFKTQFQEFVHSQNKGDVMYRLVKEEGPAHHRLFTSEVILEQQAIAHGQGKTKKESEQKAAERAYHIMRQHK 235
Cdd:COG0571   156 GKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKLGKKE 229
 
Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
3-235 6.12e-104

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 300.09  E-value: 6.12e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889   3 KDFRQRFEQKmneLGIHFDNIKLYQQAFSHSSFINDFNmnRLEHNERLEFLGDAVLEVTVSRYLFDKHPNLPEGNLTKMR 82
Cdd:COG0571     1 SEDLEELEER---LGYRFKDPELLEQALTHRSYANEHG--GLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889  83 ATIVCEPSLVIFANKIQLNQLILLGKGEEKTGGRTRPSLISDAFEAFVGALYLDQGLGAVWHFAEKVIFPYVEDDELIG- 161
Cdd:COG0571    76 AALVSEETLAEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGa 155

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2012627889 162 VVDFKTQFQEFVHSQNKGDVMYRLVKEEGPAHHRLFTSEVILEQQAIAHGQGKTKKESEQKAAERAYHIMRQHK 235
Cdd:COG0571   156 GKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKLGKKE 229
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 16-229 2.90e-98

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: 285.25  E-value: 2.90e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889  16 LGIHFDNIKLYQQAFSHSSFINDfNMNRLEHNERLEFLGDAVLEVTVSRYLFDKHPNLPEGNLTKMRATIVCEPSLVIFA 95
Cdd:TIGR02191   5 LGYKFKNPELLEQALTHRSYANE-HHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVA 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889  96 NKIQLNQLILLGKGEEKTGGRTRPSLISDAFEAFVGALYLDQGLGAVWHFAEKVIFPYVED-DELIGVVDFKTQFQEFVH 174
Cdd:TIGR02191  84 RELGLGDFLLLGKGEEKSGGRRRDSILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAiIKEETLKDYKTALQEWAQ 163

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2012627889 175 SQNKGDVMYRLVKEEGPAHHRLFTSEVILEQQAIAHGQGKTKKESEQKAAERAYH 229
Cdd:TIGR02191 164 ARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAALE 218
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 24-159 6.52e-54

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: 169.72  E-value: 6.52e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889  24 KLYQQAFSHSSFINDfnmNRLEHNERLEFLGDAVLEVTVSRYLFDKHPNLPEGNLTKMRATIVCEPSLVIFANKIQLNQL 103
Cdd:cd00593     1 SLLLEALTHPSYANE---HGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKY 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2012627889 104 ILLGKGEEKTGGRTRPSLISDAFEAFVGALYLDQGLGAVWHFAEKVIFPYVEDDEL 159
Cdd:cd00593    78 LRLGKGEEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 23-152 8.00e-47

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: 151.17  E-value: 8.00e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889  23 IKLYQQAFSHSSFINDfnmnRLEHNERLEFLGDAVLEVTVSRYLFdKHPNLPEGNLTKMRATIVCEPSLVIFANKIQLNQ 102
Cdd:pfam14622   1 EELLLQALTHKSYANG----RKPYNERLEFLGDAVLELSVSEYLF-KKPDLDEGGLTKLRASIVSEESLAEIAREIGLGK 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2012627889 103 LILLGKGEEKTGGRTRPSLISDAFEAFVGALYLDQGLGAVWHFAEKVIFP 152
Cdd:pfam14622  76 YLRLGKGEEETGGSGRESILADALEALIGAIYLDGGFEVAKEFILKKILP 125
RIBOc smart00535
Ribonuclease III family;
24-155 3.78e-45

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 146.98  E-value: 3.78e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889   24 KLYQQAFSHSSFINDFnmnrlEHNERLEFLGDAVLEVTVSRYLFDKHPNLPEGNLTKMRATIVCEPSLVIFANKIQLNQL 103
Cdd:smart00535   1 SLLLRALTHASYSNEH-----EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEF 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2012627889  104 ILLGKGEEKTGGRTRPSLISDAFEAFVGALYLDQGLGAVWHFAEKVIFPYVE 155
Cdd:smart00535  76 IRLGRGEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLD 127
 
Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
3-235 6.12e-104

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 300.09  E-value: 6.12e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889   3 KDFRQRFEQKmneLGIHFDNIKLYQQAFSHSSFINDFNmnRLEHNERLEFLGDAVLEVTVSRYLFDKHPNLPEGNLTKMR 82
Cdd:COG0571     1 SEDLEELEER---LGYRFKDPELLEQALTHRSYANEHG--GLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889  83 ATIVCEPSLVIFANKIQLNQLILLGKGEEKTGGRTRPSLISDAFEAFVGALYLDQGLGAVWHFAEKVIFPYVEDDELIG- 161
Cdd:COG0571    76 AALVSEETLAEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGa 155

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2012627889 162 VVDFKTQFQEFVHSQNKGDVMYRLVKEEGPAHHRLFTSEVILEQQAIAHGQGKTKKESEQKAAERAYHIMRQHK 235
Cdd:COG0571   156 GKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKLGKKE 229
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 16-229 2.90e-98

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: 285.25  E-value: 2.90e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889  16 LGIHFDNIKLYQQAFSHSSFINDfNMNRLEHNERLEFLGDAVLEVTVSRYLFDKHPNLPEGNLTKMRATIVCEPSLVIFA 95
Cdd:TIGR02191   5 LGYKFKNPELLEQALTHRSYANE-HHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVA 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889  96 NKIQLNQLILLGKGEEKTGGRTRPSLISDAFEAFVGALYLDQGLGAVWHFAEKVIFPYVED-DELIGVVDFKTQFQEFVH 174
Cdd:TIGR02191  84 RELGLGDFLLLGKGEEKSGGRRRDSILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAiIKEETLKDYKTALQEWAQ 163

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2012627889 175 SQNKGDVMYRLVKEEGPAHHRLFTSEVILEQQAIAHGQGKTKKESEQKAAERAYH 229
Cdd:TIGR02191 164 ARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAALE 218
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 24-159 6.52e-54

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: 169.72  E-value: 6.52e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889  24 KLYQQAFSHSSFINDfnmNRLEHNERLEFLGDAVLEVTVSRYLFDKHPNLPEGNLTKMRATIVCEPSLVIFANKIQLNQL 103
Cdd:cd00593     1 SLLLEALTHPSYANE---HGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKY 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2012627889 104 ILLGKGEEKTGGRTRPSLISDAFEAFVGALYLDQGLGAVWHFAEKVIFPYVEDDEL 159
Cdd:cd00593    78 LRLGKGEEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 23-152 8.00e-47

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: 151.17  E-value: 8.00e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889  23 IKLYQQAFSHSSFINDfnmnRLEHNERLEFLGDAVLEVTVSRYLFdKHPNLPEGNLTKMRATIVCEPSLVIFANKIQLNQ 102
Cdd:pfam14622   1 EELLLQALTHKSYANG----RKPYNERLEFLGDAVLELSVSEYLF-KKPDLDEGGLTKLRASIVSEESLAEIAREIGLGK 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2012627889 103 LILLGKGEEKTGGRTRPSLISDAFEAFVGALYLDQGLGAVWHFAEKVIFP 152
Cdd:pfam14622  76 YLRLGKGEEETGGSGRESILADALEALIGAIYLDGGFEVAKEFILKKILP 125
RIBOc smart00535
Ribonuclease III family;
24-155 3.78e-45

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 146.98  E-value: 3.78e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889   24 KLYQQAFSHSSFINDFnmnrlEHNERLEFLGDAVLEVTVSRYLFDKHPNLPEGNLTKMRATIVCEPSLVIFANKIQLNQL 103
Cdd:smart00535   1 SLLLRALTHASYSNEH-----EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEF 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2012627889  104 ILLGKGEEKTGGRTRPSLISDAFEAFVGALYLDQGLGAVWHFAEKVIFPYVE 155
Cdd:smart00535  76 IRLGRGEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLD 127
Ribonuclease_3 pfam00636
Ribonuclease III domain;
48-138 4.34e-27

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 100.04  E-value: 4.34e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889  48 ERLEFLGDAVLEVTVSRYLFDKHPNLPEGNLTKMRATIVCEPSLVIFANKIQLNQLIL------------LGKGEEKTGG 115
Cdd:pfam00636   1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTeeeldirrrnnaLGKGPKRADG 80

                          90       100
                  ....*....|....*....|...
gi 2012627889 116 RTrpSLISDAFEAFVGALYLDQG 138
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 ...
 164-228 7.22e-23

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: 87.93  E-value: 7.22e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2012627889 164 DFKTQFQEFVHSQNKGDVMYRLVKEEGPAHHRLFTSEVILEQQAIAHGQGKTKKESEQKAAERAY 228
Cdd:cd10845     2 DYKTALQEYLQKRGLPLPEYELVEEEGPDHNKTFTVEVKVNGKVIGEGTGRSKKEAEQAAAKAAL 66
DSRM smart00358
Double-stranded RNA binding motif;
166-231 4.52e-16

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 69.98  E-value: 4.52e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2012627889  166 KTQFQEFVHSQNKGdVMYRLVKEEGPAHHRLFTSEVILEQQAIAHGQGKTKKESEQKAAERAYHIM 231
Cdd:smart00358   2 KSLLQELAQKRKLP-PEYELVKEEGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSL 66
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 166-231 7.34e-14

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: 64.17  E-value: 7.34e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2012627889 166 KTQFQEFVHsQNKGDVMYRLVKEEGPAHHRLFTSEVILEQQAIAHGQGKTKKESEQKAAERAYHIM 231
Cdd:pfam00035   2 KSLLQEYAQ-KNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 170-228 2.93e-08

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: 48.82  E-value: 2.93e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2012627889 170 QEFVHSQNKGDVMYRLVKEEGPaHHRLFTSEVILEQQaIAHGQGKTKKESEQKAAERAY 228
Cdd:cd00048     1 NELCQKNKWPPPEYETVEEGGP-HNPRFTCTVTVNGQ-TFEGEGKSKKEAKQAAAEKAL 57
DSRM_STAU_rpt1 cd19857
first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 177-227 3.23e-08

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: 48.80  E-value: 3.23e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2012627889 177 NKGDVMYRLVKEEGPAHHRLFTSEVILEQQAIAHGQGKTKKESEQKAAERA 227
Cdd:cd19857    13 NKIRPQYTLVDEEGPAHKKTFTVKLTLGDEEEYEASGSSIKKAQHAAAEKA 63
DSRM_EIF2AK2_rpt1 cd19903
first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...
 176-231 8.51e-08

first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; 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. EIF2AK2 proteins 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: 380732  Cd Length: 68  Bit Score: 47.77  E-value: 8.51e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2012627889 176 QNKGDVMYRLVKEEGPAHHRLFTSEVILEQQAIAHGQGKTKKESEQKAAERAYHIM 231
Cdd:cd19903    13 KQKVVLDYVEVPTSGPSHDPRFTFQVVIDGKEYPEGEGKSKKEAKQAAAKLALEIL 68
DSRM_STAU_rpt3 cd19859
third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 167-225 2.74e-07

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: 46.62  E-value: 2.74e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2012627889 167 TQFQEFVHSQNKgDVMYRLVKEEGPAHHRLFTSEVILeQQAIAHGQGKTKKESEQKAAE 225
Cdd:cd19859     3 SLVHEIALKRNL-TVNFEVLRESGPPHMKNFITRCTV-GSFVTEGEGNSKKVSKKRAAE 59
DSRM_RNAse_III_meta_like cd19877
double-stranded RNA binding motif of metazoan ribonuclease III (RNase III) and similar ...
 164-227 1.20e-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: 42.26  E-value: 1.20e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2012627889 164 DFKTQFQEFV---HSQNKGDV---MYRLVKEEGPAHHRLFTSEVILEQQAIAHGQGKTKKESEQKAAERA 227
Cdd:cd19877     2 DPKSQLQQCCltlRTEGKKEPdipEYKVLQKSGPTNTRVYTVAVYFRGERIATGTGSSIQQAEMNAAEKA 71
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 183-231 1.47e-05

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: 41.86  E-value: 1.47e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2012627889 183 YRLVKEEGPAHHRLFTSEVILEQQAiAHGQGKTKKESEQKAAERAYHIM 231
Cdd:cd19862    20 YELISSEGAVHEPTFTFRVTVGDIT-ATGSGTSKKKAKHAAAENALEQL 67
DSRM_DRADA cd19902
double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) ...
 169-231 4.87e-05

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: 40.35  E-value: 4.87e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2012627889 169 FQEFVHSQNKGdVMYRLVKEEGPAHHRLFTSEVILEQQAIAHGQGKTKKESEQKAAERAYHIM 231
Cdd:cd19902     7 LMEYAQSRGVT-AEIEVLSQSGPPHNPRFKAAVFVGGRRFPSVEASSKKDAKQEAADLALRAL 68
DSRM_STAU2_rpt1 cd19880
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 177-227 1.03e-04

first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins; Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains 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: 380709  Cd Length: 68  Bit Score: 39.31  E-value: 1.03e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2012627889 177 NKGDVMYRLVKEEGPAHHRLFTSEVILEQQaIAHGQGKTKKESEQKAAERA 227
Cdd:cd19880    18 NRIQPQYKLLNERGPAHAKIFTVQLTLGEQ-TWEAEGSSIKKAQHAAASKA 67
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 183-227 1.34e-04

first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA, but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain 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: 380694  Cd Length: 63  Bit Score: 38.87  E-value: 1.34e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2012627889 183 YRLVKEEGPAHHRLFTSEVILEQQAIaHGQGKTKKESEQKAAERA 227
Cdd:cd19865    16 YKLTSQTGPVHAPVFTMSVEVNGQTF-EGTGRSKKKAKLEAAEKA 59
DSRM_DRADA_rpt2 cd19914
second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 174-231 1.35e-04

second 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. Vertebrate DRADA 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: 380743  Cd Length: 71  Bit Score: 39.06  E-value: 1.35e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2012627889 174 HSQNKGD-VMYRLVKEEGPAHHRLFTSEVILEQQAIAHGQGKTKKESEQKAAERAYHIM 231
Cdd:cd19914    10 HSQKSGNmCEFQLLSQEGPPHDPKFTYCVKVGEQTFPSVVANSKKVAKQMAAEEAVKEL 68
DSRM_STAU1_rpt1 cd19879
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 177-227 2.11e-04

first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; 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 1 contains 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: 380708  Cd Length: 66  Bit Score: 38.52  E-value: 2.11e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2012627889 177 NKGDVMYRLVKEEGPAHHRLFTSEVILEQQAiAHGQGKTKKESEQKAAERA 227
Cdd:cd19879    16 NKIQPEYKLLSEQGPAHSKVFTVQLTLGDQH-WEAEGTSIKKAQHAAAAKA 65
DSRM_AtDRB-like cd19878
double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins ...
 165-227 6.09e-04

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: 37.11  E-value: 6.09e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2012627889 165 FKTQFQEFVHsQNKGDVMYRLVKEEGPAHHRLFTSEVILEQQAIAHGQGKTKKESEQKAAERA 227
Cdd:cd19878     1 YKNLLQEYAQ-KKKIPLPKYESAKSGPSHQPTFVSTVIVLGVRFSSEGAKNKKQAEQSAAKVA 62
DSRM_PRKRA_rpt1 cd19889
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 183-232 8.68e-04

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: 36.81  E-value: 8.68e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2012627889 183 YRLVKEEGPAHHRLFTSEVILEQQAIAhGQGKTKKESEQKAAERAYHIMR 232
Cdd:cd19889    21 YELEKSEGQAHLPSFTFRVTVGDITCT-GEGTSKKLAKHRAAEAALNILK 69
DSRM_EIF2AK2 cd20314
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 174-228 1.12e-03

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; 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. EIF2AK2 proteins 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: 380746  Cd Length: 68  Bit Score: 36.60  E-value: 1.12e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2012627889 174 HSQNKG-DVMYRLVKEEGPAHHRLFTSEVILEQQAIAHGQGKTKKESEQKAAERAY 228
Cdd:cd20314    10 YCQKERlTVKYEEEKRSGPTHKPRFFCKYIIDGKEYPEGEGKSKKEAKQAAARLAY 65
DSRM_DCL_plant cd19869
double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ...
 183-227 1.37e-03

double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant Dicer-like (DCL) proteins and other ribonuclease (RNase) III-like (RTL) proteins. DCLs are endoribonucleases involved in RNA-mediated post-transcriptional gene silencing (PTGS). They function in the microRNA (miRNA) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Family members contain 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: 380698  Cd Length: 70  Bit Score: 36.19  E-value: 1.37e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2012627889 183 YRLVKEEGPAHHRLFTSEVIL---EQQAIAHGQG---KTKKESEQKAAERA 227
Cdd:cd19869    14 YRCVEEEGPAHAKRFTYMVRVkipERGWTIECEGepmRSKKRAKDSAALLL 64
DSRM_STAU1_rpt3 cd19883
third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 181-224 6.20e-03

third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; 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 1 contains 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: 380712  Cd Length: 67  Bit Score: 34.60  E-value: 6.20e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2012627889 181 VMYRLVKEEGPAHHRLFTSEVILEQQAiAHGQGKTKKESEQKAA 224
Cdd:cd19883    18 VNFEVTKETGPPHMKSFVTKVSVGEFA-GEGEGKSKKISKKNAA 60
DSRM_STAU_rpt4 cd19860
fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 183-231 7.43e-03

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: 34.23  E-value: 7.43e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2012627889 183 YRLVKEEGPAHHRLFTSEVILEQQaIAHGQGKTKKESEQKAAERAYHIM 231
Cdd:cd19860    20 YSLVAERGTPRRREFVMQVTVGDK-TATGTGPNKKLAKRNAAEAMLELL 67
DSRM_PRKRA_rpt2 cd19891
second double-stranded RNA binding motif of protein activator of the interferon-induced ...
 183-226 8.02e-03

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: 34.15  E-value: 8.02e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2012627889 183 YRLVKEEGPAHHRLFTSEVILEqQAIAHGQGKTKKESEQKAAER 226
Cdd:cd19891    20 YTLAQESGPPHKREFTITCRVE-TFVETGTGTSKKVAKRNAAEK 62
 
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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