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Conserved domains on  [gi|822477143|gb|AKH66854|]
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putative polyprotein, partial [Thika virus]

Protein Classification

double-stranded RNA binding motif domain-containing protein( domain architecture ID 10040092)

double-stranded RNA binding motif (DSRM) domain-containing protein similar to Adult diarrheal rotavirus strain J19 non-structural protein 1

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 71-117 5.57e-11

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: 56.14  E-value: 5.57e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 822477143  71 EPLYKYERTGAQESPIWRCTLTYNGNVYHASARTKKEAQQKAAEQCV 117
Cdd:cd00048   11 PPEYETVEEGGPHNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57
 
Name Accession Description Interval E-value
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 71-117 5.57e-11

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: 56.14  E-value: 5.57e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 822477143  71 EPLYKYERTGAQESPIWRCTLTYNGNVYHASARTKKEAQQKAAEQCV 117
Cdd:cd00048   11 PPEYETVEEGGPHNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57
DSRM smart00358
Double-stranded RNA binding motif;
57-115 9.77e-10

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 53.04  E-value: 9.77e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 822477143    57 YVSHINHKAQTSSLEPLYKY-ERTGAQESPIWRCTLTYNGNVY-HASARTKKEAQQKAAEQ 115
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELvKEEGPDHAPRFTVTVKVGGKRTgEGEGSSKKEAKQRAAEA 61
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 57-117 5.93e-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: 42.60  E-value: 5.93e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 822477143   57 YVSHINHKAQTSSLEPLYKY-ERTGAQESPIWRCTLTYNGNVYH-ASARTKKEAQQKAAEQCV 117
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYvSEEGPPHSPKFTVTVKVDGKLYGsGTGSSKKEAEQLAAEKAL 63
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
54-115 8.30e-04

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 39.31  E-value: 8.30e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 822477143  54 IMDYVSHINHKAQTSSLE-PLYK-YERTGAQESPIWRCTLTYNGNVY-HASARTKKEAQQKAAEQ 115
Cdd:COG0571  156 GKDYKTALQEWLQARGLPlPEYEvVEEEGPDHAKTFTVEVLVGGKVLgEGTGRSKKEAEQAAAKA 220
 
Name Accession Description Interval E-value
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 71-117 5.57e-11

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: 56.14  E-value: 5.57e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 822477143  71 EPLYKYERTGAQESPIWRCTLTYNGNVYHASARTKKEAQQKAAEQCV 117
Cdd:cd00048   11 PPEYETVEEGGPHNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57
DSRM smart00358
Double-stranded RNA binding motif;
57-115 9.77e-10

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 53.04  E-value: 9.77e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 822477143    57 YVSHINHKAQTSSLEPLYKY-ERTGAQESPIWRCTLTYNGNVY-HASARTKKEAQQKAAEQ 115
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELvKEEGPDHAPRFTVTVKVGGKRTgEGEGSSKKEAKQRAAEA 61
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 57-117 5.93e-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: 42.60  E-value: 5.93e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 822477143   57 YVSHINHKAQTSSLEPLYKY-ERTGAQESPIWRCTLTYNGNVYH-ASARTKKEAQQKAAEQCV 117
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYvSEEGPPHSPKFTVTVKVDGKLYGsGTGSSKKEAEQLAAEKAL 63
DSRM_AtDRB-like_rpt1 cd19907
first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 57-119 7.01e-05

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


Pssm-ID: 380736 [Multi-domain]  Cd Length: 69  Bit Score: 39.77  E-value: 7.01e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 822477143  57 YVSHINHKAQTSSLE-PLYKYERTGAQESPIWRCTLTYNGNVYHASA--RTKKEAQQKAAEQCVTA 119
Cdd:cd19907    2 YKSQLQEYAQKSCLNlPVYACIREGPDHAPRFRATVTFNGVIFESPPgfPTLKAAEHSAAEVALNS 67
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 55-116 8.44e-05

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: 39.40  E-value: 8.44e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 822477143  55 MDYVSHINHKAQTSSLE-PLYKY-ERTGAQESPIWRCTLTYNGNVY-HASARTKKEAQQKAAEQC 116
Cdd:cd10845    1 KDYKTALQEYLQKRGLPlPEYELvEEEGPDHNKTFTVEVKVNGKVIgEGTGRSKKEAEQAAAKAA 65
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 56-114 1.90e-04

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


Pssm-ID: 380704  Cd Length: 67  Bit Score: 38.40  E-value: 1.90e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 822477143  56 DYVSHINHKAQTSSLEPLYKYERTGAQESPIWRCTLTYNGNVY-HASARTKKEAQQKAAE 114
Cdd:cd19875    2 NPVSALNEYCQKRGLSLEFVDVSVGPDHCPGFTASATIDGIVFaSATGTSKKEAKRAAAK 61
DSRM_AtDRB-like_rpt2 cd19908
second double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 65-113 4.82e-04

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: 37.46  E-value: 4.82e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 822477143  65 AQTSSLE-PLYKYERTGAQESPIWRCTLTYNGNVYH-ASARTKKEAQQKAA 113
Cdd:cd19908   11 AQKAGLPlPLYTTVRSGPGHVPTFTCTVEIAGITFTgEAAKTKKQAEKSAA 61
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
54-115 8.30e-04

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 39.31  E-value: 8.30e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 822477143  54 IMDYVSHINHKAQTSSLE-PLYK-YERTGAQESPIWRCTLTYNGNVY-HASARTKKEAQQKAAEQ 115
Cdd:COG0571  156 GKDYKTALQEWLQARGLPlPEYEvVEEEGPDHAKTFTVEVLVGGKVLgEGTGRSKKEAEQAAAKA 220
 
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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