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Conserved domains on  [gi|15595967|ref|NP_249461|]
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ribonuclease III [Pseudomonas aeruginosa PAO1]

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];
2-212 3.57e-113

dsRNA-specific ribonuclease [Transcription];


:

Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 323.20  E-value: 3.57e-113
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967   2 SNSLDRLERKLGYTFKDRDLMVLALTHRSYA-----GRNNERLEFLGDAILNFVIGEALFHHFPQAREGQLSRLRARLVK 76
Cdd:COG0571   1 SEDLEELEERLGYRFKDPELLEQALTHRSYAnehggLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVS 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967  77 GETLALLARGFEVGDYLRLGSGELKSGGFRRESILADAMEALIGAIYLDTGMDSARERIIAWLGPQLRELTPVDTNKDPK 156
Cdd:COG0571  81 EETLAEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAGKDYK 160

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15595967 157 TRLQEFLQSRGCDLPRYEVVDIQGEPHCRTFFVDCEVAlLSDKTHGHGGSRRIAEQ 212
Cdd:COG0571 161 TALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVG-GKVLGEGTGRSKKEAEQ 215
 
Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
2-212 3.57e-113

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 323.20  E-value: 3.57e-113
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967   2 SNSLDRLERKLGYTFKDRDLMVLALTHRSYA-----GRNNERLEFLGDAILNFVIGEALFHHFPQAREGQLSRLRARLVK 76
Cdd:COG0571   1 SEDLEELEERLGYRFKDPELLEQALTHRSYAnehggLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVS 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967  77 GETLALLARGFEVGDYLRLGSGELKSGGFRRESILADAMEALIGAIYLDTGMDSARERIIAWLGPQLRELTPVDTNKDPK 156
Cdd:COG0571  81 EETLAEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAGKDYK 160

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15595967 157 TRLQEFLQSRGCDLPRYEVVDIQGEPHCRTFFVDCEVAlLSDKTHGHGGSRRIAEQ 212
Cdd:COG0571 161 TALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVG-GKVLGEGTGRSKKEAEQ 215
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 8-212 3.93e-90

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: 264.45  E-value: 3.93e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967     8 LERKLGYTFKDRDLMVLALTHRSYA------GRNNERLEFLGDAILNFVIGEALFHHFPQAREGQLSRLRARLVKGETLA 81
Cdd:TIGR02191   1 LEKRLGYKFKNPELLEQALTHRSYAnehhkdVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967    82 LLARGFEVGDYLRLGSGELKSGGFRRESILADAMEALIGAIYLDTGMDSARERIIAWLGPQLRELTPVDTNKDPKTRLQE 161
Cdd:TIGR02191  81 EVARELGLGDFLLLGKGEEKSGGRRRDSILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIIKEETLKDYKTALQE 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 15595967   162 FLQSRGCDLPRYEVVDIQGEPHCRTFFVDCEVALLSdKTHGHGGSRRIAEQ 212
Cdd:TIGR02191 161 WAQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEP-YGEGKGKSKKEAEQ 210
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 20-148 2.59e-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: 170.49  E-value: 2.59e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967  20 DLMVLALTHRSYA----GRNNERLEFLGDAILNFVIGEALFHHFPQAREGQLSRLRARLVKGETLALLARGFEVGDYLRL 95
Cdd:cd00593   1 SLLLEALTHPSYAnehgRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRL 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 15595967  96 GSGELKSGGFRRESILADAMEALIGAIYLDTGMDSARERIIAWLGPQLRELTP 148
Cdd:cd00593  81 GKGEEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133
RIBOc smart00535
Ribonuclease III family;
20-146 2.50e-53

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 167.78  E-value: 2.50e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967     20 DLMVLALTHRSYA--GRNNERLEFLGDAILNFVIGEALFHHFPQAREGQLSRLRARLVKGETLALLARGFEVGDYLRLGS 97
Cdd:smart00535   1 SLLLRALTHASYSneHEHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGR 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 15595967     98 GELKSGGFRRESILADAMEALIGAIYLDTGMDSARERIIAWLGPQLREL 146
Cdd:smart00535  81 GEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLDEL 129
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 20-143 5.59e-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: 151.56  E-value: 5.59e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967    20 DLMVLALTHRSYA---GRNNERLEFLGDAILNFVIGEALFHHFPQArEGQLSRLRARLVKGETLALLARGFEVGDYLRLG 96
Cdd:pfam14622   2 ELLLQALTHKSYAngrKPYNERLEFLGDAVLELSVSEYLFKKPDLD-EGGLTKLRASIVSEESLAEIAREIGLGKYLRLG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 15595967    97 SGELKSGGFRRESILADAMEALIGAIYLDTGMDSARERIIAWLGPQL 143
Cdd:pfam14622  81 KGEEETGGSGRESILADALEALIGAIYLDGGFEVAKEFILKKILPDL 127
 
Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
2-212 3.57e-113

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 323.20  E-value: 3.57e-113
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967   2 SNSLDRLERKLGYTFKDRDLMVLALTHRSYA-----GRNNERLEFLGDAILNFVIGEALFHHFPQAREGQLSRLRARLVK 76
Cdd:COG0571   1 SEDLEELEERLGYRFKDPELLEQALTHRSYAnehggLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVS 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967  77 GETLALLARGFEVGDYLRLGSGELKSGGFRRESILADAMEALIGAIYLDTGMDSARERIIAWLGPQLRELTPVDTNKDPK 156
Cdd:COG0571  81 EETLAEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAGKDYK 160

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15595967 157 TRLQEFLQSRGCDLPRYEVVDIQGEPHCRTFFVDCEVAlLSDKTHGHGGSRRIAEQ 212
Cdd:COG0571 161 TALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVG-GKVLGEGTGRSKKEAEQ 215
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 8-212 3.93e-90

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: 264.45  E-value: 3.93e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967     8 LERKLGYTFKDRDLMVLALTHRSYA------GRNNERLEFLGDAILNFVIGEALFHHFPQAREGQLSRLRARLVKGETLA 81
Cdd:TIGR02191   1 LEKRLGYKFKNPELLEQALTHRSYAnehhkdVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967    82 LLARGFEVGDYLRLGSGELKSGGFRRESILADAMEALIGAIYLDTGMDSARERIIAWLGPQLRELTPVDTNKDPKTRLQE 161
Cdd:TIGR02191  81 EVARELGLGDFLLLGKGEEKSGGRRRDSILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIIKEETLKDYKTALQE 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 15595967   162 FLQSRGCDLPRYEVVDIQGEPHCRTFFVDCEVALLSdKTHGHGGSRRIAEQ 212
Cdd:TIGR02191 161 WAQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEP-YGEGKGKSKKEAEQ 210
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 20-148 2.59e-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: 170.49  E-value: 2.59e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967  20 DLMVLALTHRSYA----GRNNERLEFLGDAILNFVIGEALFHHFPQAREGQLSRLRARLVKGETLALLARGFEVGDYLRL 95
Cdd:cd00593   1 SLLLEALTHPSYAnehgRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRL 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 15595967  96 GSGELKSGGFRRESILADAMEALIGAIYLDTGMDSARERIIAWLGPQLRELTP 148
Cdd:cd00593  81 GKGEEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133
RIBOc smart00535
Ribonuclease III family;
20-146 2.50e-53

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 167.78  E-value: 2.50e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967     20 DLMVLALTHRSYA--GRNNERLEFLGDAILNFVIGEALFHHFPQAREGQLSRLRARLVKGETLALLARGFEVGDYLRLGS 97
Cdd:smart00535   1 SLLLRALTHASYSneHEHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGR 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 15595967     98 GELKSGGFRRESILADAMEALIGAIYLDTGMDSARERIIAWLGPQLREL 146
Cdd:smart00535  81 GEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLDEL 129
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 20-143 5.59e-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: 151.56  E-value: 5.59e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967    20 DLMVLALTHRSYA---GRNNERLEFLGDAILNFVIGEALFHHFPQArEGQLSRLRARLVKGETLALLARGFEVGDYLRLG 96
Cdd:pfam14622   2 ELLLQALTHKSYAngrKPYNERLEFLGDAVLELSVSEYLFKKPDLD-EGGLTKLRASIVSEESLAEIAREIGLGKYLRLG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 15595967    97 SGELKSGGFRRESILADAMEALIGAIYLDTGMDSARERIIAWLGPQL 143
Cdd:pfam14622  81 KGEEETGGSGRESILADALEALIGAIYLDGGFEVAKEFILKKILPDL 127
Ribonuclease_3 pfam00636
Ribonuclease III domain;
37-127 5.73e-29

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 104.66  E-value: 5.73e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967    37 ERLEFLGDAILNFVIGEALFHHFPQAREGQLSRLRARLVKGETLALLARGFEVGDYLR------------LGSGELKSGG 104
Cdd:pfam00636   1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTeeeldirrrnnaLGKGPKRADG 80

                          90       100
                  ....*....|....*....|...
gi 15595967   105 frRESILADAMEALIGAIYLDTG 127
Cdd:pfam00636  81 --KEKVLADAFEALIGALYLDGG 101
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 153-212 2.39e-18

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: 75.99  E-value: 2.39e-18
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967 153 KDPKTRLQEFLQSRGCDLPRYEVVDIQGEPHCRTFFVDCEVAlLSDKTHGHGGSRRIAEQ 212
Cdd:cd10845   1 KDYKTALQEYLQKRGLPLPEYELVEEEGPDHNKTFTVEVKVN-GKVIGEGTGRSKKEAEQ 59
DSRM smart00358
Double-stranded RNA binding motif;
155-214 3.72e-09

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 51.49  E-value: 3.72e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967    155 PKTRLQEFLQSRGCdLPRYEVVDIQGEPHCRTFFVDCEVALlSDKTHGHGGSRRIAEQVA 214
Cdd:smart00358   1 PKSLLQELAQKRKL-PPEYELVKEEGPDHAPRFTVTVKVGG-KRTGEGEGSSKKEAKQRA 58
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 155-214 9.29e-06

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 42.22  E-value: 9.29e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15595967   155 PKTRLQEFLQSRGcDLPRYEVVDIQGEPHCRTFFVDCEVallSDKTH--GHGGSRRIAEQVA 214
Cdd:pfam00035   1 PKSLLQEYAQKNG-KPPPYEYVSEEGPPHSPKFTVTVKV---DGKLYgsGTGSSKKEAEQLA 58
seadorna_dsRNA TIGR04238
seadornavirus double-stranded RNA-binding protein; This protein family occurs in the ...
 154-212 1.34e-05

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


Pssm-ID: 275074 [Multi-domain]  Cd Length: 201  Bit Score: 44.55  E-value: 1.34e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595967   154 DPKTRLQEFLQSRGCDLPRYEVVDIQGEPHCRTFFVDCEvalLSDKTH-GHGGSRRIAEQ 212
Cdd:TIGR04238   1 NVVGMLQELAVKRGLELPVYEKVGKEGPDHAPTFTIKLT---ANDIEViEAASSKKQAEK 57
DSRM_PRKRA-like_rpt2 cd19863
second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...
 159-210 4.45e-05

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: 40.44  E-value: 4.45e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15595967 159 LQEFLQSRGCDLPRYEVVDIQGEPHCRTFFVDCEVALLSDKthGHGGSRRIA 210
Cdd:cd19863   6 LQELCVQRRWRLPEYEVEQESGPPHEKEFTIACRVENFSET--GSGKSKKLA 55
DSRM_PRKRA_rpt2 cd19891
second double-stranded RNA binding motif of protein activator of the interferon-induced ...
 154-212 1.20e-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: 36.46  E-value: 1.20e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15595967 154 DPKTRLQEFLQSRGCDLPRYEVVDIQGEPHCRTFFVDCEVALLSDKthGHGGSRRIAEQ 212
Cdd:cd19891   1 NPIGSLQELAVQKGWRLPEYTLAQESGPPHKREFTITCRVETFVET--GTGTSKKVAKR 57
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 160-214 3.49e-03

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: 34.95  E-value: 3.49e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 15595967 160 QEFLQSRGCDLPRYEVVDIQGePHCRTFFvdCEVALLSDKTHGHGGSRRIAEQVA 214
Cdd:cd00048   1 NELCQKNKWPPPEYETVEEGG-PHNPRFT--CTVTVNGQTFEGEGKSKKEAKQAA 52
 
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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