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Conserved domains on  [gi|1384417171|gb|AWE75151|]
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VP8 [Kadipiro virus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
seadorna_dsRNA super family cl25970
seadornavirus double-stranded RNA-binding protein; This protein family occurs in the ...
 3-208 1.96e-77

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.


The actual alignment was detected with superfamily member TIGR04238:

Pssm-ID: 275074 [Multi-domain]  Cd Length: 201  Bit Score: 234.45  E-value: 1.96e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1384417171   3 NVKGMLQELCVKRGLELPVYEKLSKVGPDHAPTITVKLTANGIEVVEAASSRAQAERLAAATLYEKIKH---LEVHDERK 79
Cdd:TIGR04238   1 NVVGMLQELAVKRGLELPVYEKVGKEGPDHAPTFTIKLTANDIEVIEAASSKKQAEKLAAATIYEDMKEnglLEVHDTRK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1384417171  80 SVSIMSILMVS--FANLLITKVVDLFSISKQDIVYCSdiddvtDDVHFDPTLSNLMSSGLTDRSAW-NRLYKLLSDLAFE 156
Cdd:TIGR04238  81 SVSIMSILLVSkfFANALINKVIDLFSTCKQDIILCS------DDVTFDYGLSNLMSSGLLLRSAWyNRLYKLLSDLALE 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1384417171 157 NGFNCIVRKngkgllFRSLQNDNLVASESFKSNSLNVSFNTTEDKEVSMLCY 208
Cdd:TIGR04238 155 NGFNCITRH------FRSLLNDDLVANESFKNSILIVAFDTDEKKEVSMLVY 200
 
Name Accession Description Interval E-value
seadorna_dsRNA TIGR04238
seadornavirus double-stranded RNA-binding protein; This protein family occurs in the ...
 3-208 1.96e-77

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: 234.45  E-value: 1.96e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1384417171   3 NVKGMLQELCVKRGLELPVYEKLSKVGPDHAPTITVKLTANGIEVVEAASSRAQAERLAAATLYEKIKH---LEVHDERK 79
Cdd:TIGR04238   1 NVVGMLQELAVKRGLELPVYEKVGKEGPDHAPTFTIKLTANDIEVIEAASSKKQAEKLAAATIYEDMKEnglLEVHDTRK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1384417171  80 SVSIMSILMVS--FANLLITKVVDLFSISKQDIVYCSdiddvtDDVHFDPTLSNLMSSGLTDRSAW-NRLYKLLSDLAFE 156
Cdd:TIGR04238  81 SVSIMSILLVSkfFANALINKVIDLFSTCKQDIILCS------DDVTFDYGLSNLMSSGLLLRSAWyNRLYKLLSDLALE 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1384417171 157 NGFNCIVRKngkgllFRSLQNDNLVASESFKSNSLNVSFNTTEDKEVSMLCY 208
Cdd:TIGR04238 155 NGFNCITRH------FRSLLNDDLVANESFKNSILIVAFDTDEKKEVSMLVY 200
DSRM smart00358
Double-stranded RNA binding motif;
5-70 1.11e-13

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 64.59  E-value: 1.11e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1384417171    5 KGMLQELCVKRGLElPVYEKLSKVGPDHAPTITVKLTANGIEVVEA-ASSRAQAERLAAATLYEKIK 70
Cdd:smart00358   2 KSLLQELAQKRKLP-PEYELVKEEGPDHAPRFTVTVKVGGKRTGEGeGSSKKEAKQRAAEAALRSLK 67
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 5-69 4.50e-13

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: 63.28  E-value: 4.50e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1384417171   5 KGMLQELCVKRGLELPVYEKLSKVGPDHAPTITVKLTANGIEVVEA-ASSRAQAERLAAATLYEKI 69
Cdd:cd10845     4 KTALQEYLQKRGLPLPEYELVEEEGPDHNKTFTVEVKVNGKVIGEGtGRSKKEAEQAAAKAALEKL 69
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
5-70 6.26e-13

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 66.66  E-value: 6.26e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1384417171   5 KGMLQELCVKRGLELPVYEKLSKVGPDHAPTITVKLTANGIEVVEA-ASSRAQAERLAAATLYEKIK 70
Cdd:COG0571   160 KTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGtGRSKKEAEQAAAKAALEKLG 226
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 5-69 2.58e-10

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: 55.31  E-value: 2.58e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1384417171   5 KGMLQELCVKRGLElPVYEKLSKVGPDHAPTITVKLTANGIEVVEA-ASSRAQAERLAAATLYEKI 69
Cdd:pfam00035   2 KSLLQEYAQKNGKP-PPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGtGSSKKEAEQLAAEKALEKL 66
 
Name Accession Description Interval E-value
seadorna_dsRNA TIGR04238
seadornavirus double-stranded RNA-binding protein; This protein family occurs in the ...
 3-208 1.96e-77

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: 234.45  E-value: 1.96e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1384417171   3 NVKGMLQELCVKRGLELPVYEKLSKVGPDHAPTITVKLTANGIEVVEAASSRAQAERLAAATLYEKIKH---LEVHDERK 79
Cdd:TIGR04238   1 NVVGMLQELAVKRGLELPVYEKVGKEGPDHAPTFTIKLTANDIEVIEAASSKKQAEKLAAATIYEDMKEnglLEVHDTRK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1384417171  80 SVSIMSILMVS--FANLLITKVVDLFSISKQDIVYCSdiddvtDDVHFDPTLSNLMSSGLTDRSAW-NRLYKLLSDLAFE 156
Cdd:TIGR04238  81 SVSIMSILLVSkfFANALINKVIDLFSTCKQDIILCS------DDVTFDYGLSNLMSSGLLLRSAWyNRLYKLLSDLALE 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1384417171 157 NGFNCIVRKngkgllFRSLQNDNLVASESFKSNSLNVSFNTTEDKEVSMLCY 208
Cdd:TIGR04238 155 NGFNCITRH------FRSLLNDDLVANESFKNSILIVAFDTDEKKEVSMLVY 200
DSRM smart00358
Double-stranded RNA binding motif;
5-70 1.11e-13

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 64.59  E-value: 1.11e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1384417171    5 KGMLQELCVKRGLElPVYEKLSKVGPDHAPTITVKLTANGIEVVEA-ASSRAQAERLAAATLYEKIK 70
Cdd:smart00358   2 KSLLQELAQKRKLP-PEYELVKEEGPDHAPRFTVTVKVGGKRTGEGeGSSKKEAKQRAAEAALRSLK 67
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 5-69 4.50e-13

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: 63.28  E-value: 4.50e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1384417171   5 KGMLQELCVKRGLELPVYEKLSKVGPDHAPTITVKLTANGIEVVEA-ASSRAQAERLAAATLYEKI 69
Cdd:cd10845     4 KTALQEYLQKRGLPLPEYELVEEEGPDHNKTFTVEVKVNGKVIGEGtGRSKKEAEQAAAKAALEKL 69
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
5-70 6.26e-13

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 66.66  E-value: 6.26e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1384417171   5 KGMLQELCVKRGLELPVYEKLSKVGPDHAPTITVKLTANGIEVVEA-ASSRAQAERLAAATLYEKIK 70
Cdd:COG0571   160 KTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGtGRSKKEAEQAAAKAALEKLG 226
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 5-69 2.58e-10

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: 55.31  E-value: 2.58e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1384417171   5 KGMLQELCVKRGLElPVYEKLSKVGPDHAPTITVKLTANGIEVVEA-ASSRAQAERLAAATLYEKI 69
Cdd:pfam00035   2 KSLLQEYAQKNGKP-PPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGtGSSKKEAEQLAAEKALEKL 66
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 6-70 3.55e-09

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: 52.26  E-value: 3.55e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1384417171   6 GMLQELCVKRGLElPVYEKLSKVGPDHAPTITVKLTANGIEVVEAASSRAQAERLAAATLYEKIK 70
Cdd:cd19862     5 SVLQELCAKRGIT-PKYELISSEGAVHEPTFTFRVTVGDITATGSGTSKKKAKHAAAENALEQLK 68
DSRM_PRKRA-like_rpt2 cd19863
second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...
 6-69 2.71e-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: 49.68  E-value: 2.71e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1384417171   6 GMLQELCVKRGLELPVYEKLSKVGPDHAPTITVKLTANGIEVVEAASSRAQAERLAAATLYEKI 69
Cdd:cd19863     4 GILQELCVQRRWRLPEYEVEQESGPPHEKEFTIACRVENFSETGSGKSKKLAKRAAAEKMLTRL 67
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 5-69 3.78e-08

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: 52.98  E-value: 3.78e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1384417171   5 KGMLQELCVKRGLELPVYEKLSKVGPDHAPTITVKLTANGIEVVEA-ASSRAQAERLAAATLYEKI 69
Cdd:TIGR02191 155 KTALQEWAQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGkGKSKKEAEQNAAKAALEKL 220
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 9-62 7.21e-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: 48.44  E-value: 7.21e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1384417171   9 QELCVKRGLELPVYEkLSKVGPDHAPTITVKLTANGIEVVEAASSRAQAERLAA 62
Cdd:cd00048     1 NELCQKNKWPPPEYE-TVEEGGPHNPRFTCTVTVNGQTFEGEGKSKKEAKQAAA 53
DSRM_AtDRB-like_rpt1 cd19907
first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 5-63 1.44e-07

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: 47.86  E-value: 1.44e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1384417171   5 KGMLQELCVKRGLELPVYEKLsKVGPDHAPTITVKLTANGI--EVVEAASSRAQAERLAAA 63
Cdd:cd19907     3 KSQLQEYAQKSCLNLPVYACI-REGPDHAPRFRATVTFNGVifESPPGFPTLKAAEHSAAE 62
DSRM_AtDRB-like cd19878
double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins ...
 5-62 1.04e-06

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: 45.20  E-value: 1.04e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1384417171   5 KGMLQELCVKRGLELPVYEkLSKVGPDHAPTITVKLTANGIEVV-EAASSRAQAERLAA 62
Cdd:cd19878     2 KNLLQEYAQKKKIPLPKYE-SAKSGPSHQPTFVSTVIVLGVRFSsEGAKNKKQAEQSAA 59
DSRM_AtDRB-like_rpt2 cd19908
second double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 5-70 1.42e-06

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: 45.16  E-value: 1.42e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1384417171   5 KGMLQELCVKRGLELPVYEKlSKVGPDHAPTITVKLTANGIEVV-EAASSRAQAERLAAATLYEKIK 70
Cdd:cd19908     4 KNLLQEYAQKAGLPLPLYTT-VRSGPGHVPTFTCTVEIAGITFTgEAAKTKKQAEKSAARTAWSSIK 69
DND1_DSRM pfam14709
double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead ...
 5-63 5.47e-06

double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead end protein 1 (DND1_HUMAN) homologous to double strand RNA binding domains (PF00035, PF00333)


Pssm-ID: 405408  Cd Length: 80  Bit Score: 43.87  E-value: 5.47e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1384417171   5 KGMLQELCVKRGLELPVYEKLSKVGPDHAPTITVKLTANGIEV-----------VEAASSRAQAERLAAA 63
Cdd:pfam14709   4 VSHLEELCQKNKWGSPVYELHSTAGPDGKQLFTYKVVIPGIETpfpgviwifmpGKLCSTKEEAKEAAAE 73
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 3-62 5.75e-06

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: 43.41  E-value: 5.75e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1384417171   3 NVKGMLQELCVKRGLELPVyeKLSKVGPDHAPTITVKLTANGIEVVEA-ASSRAQAERLAA 62
Cdd:cd19875     2 NPVSALNEYCQKRGLSLEF--VDVSVGPDHCPGFTASATIDGIVFASAtGTSKKEAKRAAA 60
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 7-46 1.00e-04

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group 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: 380699  Cd Length: 75  Bit Score: 39.96  E-value: 1.00e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1384417171   7 MLQELCVKRGLELPVYEKLSKVGPDHAPTITVKLTANGIE 46
Cdd:cd19870     7 ALMELCNKRKWGPPEFRLVEESGPPHRKHFLFKVVVNGVE 46
DSRM_DCL_plant cd19869
double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ...
 9-71 1.49e-04

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: 39.27  E-value: 1.49e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1384417171   9 QELCVKRGLELPVYEKLSKVGPDHAP----TITVKLTANGIEVV---EAASSRAQAERLAAATLYEKIKH 71
Cdd:cd19869     1 NEICLKRRWPMPVYRCVEEEGPAHAKrftyMVRVKIPERGWTIEcegEPMRSKKRAKDSAALLLLEYLKK 70
DSRM_PRKRA_rpt2 cd19891
second double-stranded RNA binding motif of protein activator of the interferon-induced ...
 6-68 1.85e-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: 1.85e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1384417171   6 GMLQELCVKRGLELPVYEKLSKVGPDHAPTITVKLTANGIEVVEAASSRAQAERLAAATLYEK 68
Cdd:cd19891     4 GSLQELAVQKGWRLPEYTLAQESGPPHKREFTITCRVETFVETGTGTSKKVAKRNAAEKLLAK 66
DSRM_TARBP2_rpt2 cd10844
second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and ...
 3-69 3.81e-04

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: 38.16  E-value: 3.81e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1384417171   3 NVKGMLQELCVKRGLELPVYEKLSKVGPDHAPTITVKLTANGIEVVEAASSRAQAERLAAATLYEKI 69
Cdd:cd10844     1 NPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKMLLRI 67
DSRM_STAU_rpt3 cd19859
third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 6-69 4.44e-03

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: 35.07  E-value: 4.44e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1384417171   6 GMLQELCVKRGLELPvYEKLSKVGPDHAPTITVKLTANGIEVVEAASSRAQAERLAAATLYEKI 69
Cdd:cd19859     3 SLVHEIALKRNLTVN-FEVLRESGPPHMKNFITRCTVGSFVTEGEGNSKKVSKKRAAEKMLEEL 65
DSRM_RNAse_III_meta_like cd19877
double-stranded RNA binding motif of metazoan ribonuclease III (RNase III) and similar ...
 2-62 6.06e-03

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: 34.94  E-value: 6.06e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1384417171   2 NNVKGMLQELCV-KRGLE-----LPVYEKLSKVGPDHAPTITVKLTANGIEVVEA-ASSRAQAERLAA 62
Cdd:cd19877     1 NDPKSQLQQCCLtLRTEGkkepdIPEYKVLQKSGPTNTRVYTVAVYFRGERIATGtGSSIQQAEMNAA 68
 
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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