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Conserved domains on  [gi|2074816191|ref|NP_001382615|]
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endoribonuclease Dicer isoform 4 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
 792-914 2.19e-69

PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA interference pathway. It generates dsRNAs which are approximately 20 bp long (siRNAs), which in turn target hydrolysis of homologous RNAs. PAZ domains are named after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes.


:

Pssm-ID: 239209  Cd Length: 122  Bit Score: 228.48  E-value: 2.19e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  792 DSSTLDIDFKFMEDIEkSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 871
Cdd:cd02843      1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 2074816191  872 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 914
Cdd:cd02843     80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 11-145 1.12e-63

DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


:

Pssm-ID: 350792 [Multi-domain]  Cd Length: 200  Bit Score: 215.59  E-value: 1.12e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   11 LVAQQVSAVRTHSDLKVGEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDH 90
Cdd:cd18034     63 LVAQQAEAIRSHTDLKVGEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDH 142

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2074816191   91 PYREIMKLCENC---PSCPRILGLTASILNGKCDPEELEEKIQKLEKILKSNAETATD 145
Cdd:cd18034    143 PYARIMKEFYHLegrTSRPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 278-470 6.36e-56

C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


:

Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 190.88  E-value: 6.36e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  278 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 357
Cdd:cd18802      4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  358 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprNKQMEAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKC 437
Cdd:cd18802     36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109

                          170       180       190
                   ....*....|....*....|....*....|...
gi 2074816191  438 NLVVRFDLPTEYRSYVQSKGRARAPISNYIMLA 470
Cdd:cd18802    110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1588-1752 9.70e-40

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: 144.29  E-value: 9.70e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1588 YLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1667
Cdd:cd00593      2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKY---- 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1668 spelfhviddfvqFQLEKNEMQGMDSElrrseedeekeedieVPKAMGDIFESLAGAIYMDSGMslETVWQVYYPMMRPL 1747
Cdd:cd00593     78 -------------LRLGKGEEKSGGRL---------------RPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPL 127


                   ....*
gi 2074816191 1748 IEKFS 1752
Cdd:cd00593    128 IEEIS 132
DSRM_DICER cd10843
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ...
 1757-1819 2.54e-39

double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also known as helicase with RNase motif (HERNA), or helicase MOI) is a double-stranded RNA (dsRNA) endoribonuclease playing a central role in short dsRNA-mediated post-transcriptional gene silencing. It cleaves naturally occurring long dsRNAs and short hairpin pre-microRNAs (miRNA) into fragments of twenty-one to twenty-three nucleotides with 3' overhang of two nucleotides, producing respectively short interfering RNAs (siRNA) and mature microRNAs. Dicer contains 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: 380680  Cd Length: 63  Bit Score: 140.25  E-value: 2.54e-39
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816191 1757 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLK 1819
Cdd:cd10843      1 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGRFKGVGRNYRIAKSAAARRALRSLK 63
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 536-624 2.71e-32

Dicer dimerization domain; This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerization of Dicer proteins with their respective protein partners.


:

Pssm-ID: 460900  Cd Length: 89  Bit Score: 121.06  E-value: 2.71e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  536 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMSCVRLAERVVALICCEKLHKIGELD 615
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79


                   ....*....
gi 2074816191  616 DHLMPVGKE 624
Cdd:pfam03368   80 DHLLPLTKK 88
RIBOc smart00535
Ribonuclease III family;
1202-1293 2.64e-25

Ribonuclease III family;


:

Pssm-ID: 197778  Cd Length: 129  Bit Score: 102.68  E-value: 2.64e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  1202 LILQALTLSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIF 1280
Cdd:smart00535    2 LLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81

                            90
                    ....*....|...
gi 2074816191  1281 DPPVNWLPPGYVV 1293
Cdd:smart00535   82 EAISGGRDKPKIL 94
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 177-271 5.01e-25

Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a central role in RNA interference by breaking down RNA molecules into fragments of about 22 nucleotides (miRNAs and siRNAs). Loading of RNA onto Dicer and the enzymatic cleavage are supported by dsRNA-binding proteins, including trans-activation response (TAR) RNA-binding protein (TRBP) or protein activator of PKR (PACT). Together with Argonaute, this constitutes the RNA-induced silencing complex (RISC) which functions to load the small RNA fragments onto Argonaute. The Partner-binding domain of Dicer is responsible for interactions with the dsRNA-binding proteins. This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases.


:

Pssm-ID: 277191  Cd Length: 104  Bit Score: 101.21  E-value: 5.01e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  177 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 247
Cdd:cd15903      1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                           90       100
                   ....*....|....*....|....
gi 2074816191  248 RKFLLFTDTFLRKIHALCEEHFSP 271
Cdd:cd15903     81 RLFLRYVITQLRKIRKLLEDEMKN 104
 
Name Accession Description Interval E-value
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
 792-914 2.19e-69

PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA interference pathway. It generates dsRNAs which are approximately 20 bp long (siRNAs), which in turn target hydrolysis of homologous RNAs. PAZ domains are named after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes.


Pssm-ID: 239209  Cd Length: 122  Bit Score: 228.48  E-value: 2.19e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  792 DSSTLDIDFKFMEDIEkSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 871
Cdd:cd02843      1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 2074816191  872 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 914
Cdd:cd02843     80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 11-145 1.12e-63

DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350792 [Multi-domain]  Cd Length: 200  Bit Score: 215.59  E-value: 1.12e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   11 LVAQQVSAVRTHSDLKVGEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDH 90
Cdd:cd18034     63 LVAQQAEAIRSHTDLKVGEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDH 142

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2074816191   91 PYREIMKLCENC---PSCPRILGLTASILNGKCDPEELEEKIQKLEKILKSNAETATD 145
Cdd:cd18034    143 PYARIMKEFYHLegrTSRPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 278-470 6.36e-56

C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 190.88  E-value: 6.36e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  278 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 357
Cdd:cd18802      4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  358 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprNKQMEAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKC 437
Cdd:cd18802     36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109

                          170       180       190
                   ....*....|....*....|....*....|...
gi 2074816191  438 NLVVRFDLPTEYRSYVQSKGRARAPISNYIMLA 470
Cdd:cd18802    110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1588-1752 9.70e-40

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: 144.29  E-value: 9.70e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1588 YLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1667
Cdd:cd00593      2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKY---- 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1668 spelfhviddfvqFQLEKNEMQGMDSElrrseedeekeedieVPKAMGDIFESLAGAIYMDSGMslETVWQVYYPMMRPL 1747
Cdd:cd00593     78 -------------LRLGKGEEKSGGRL---------------RPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPL 127


                   ....*
gi 2074816191 1748 IEKFS 1752
Cdd:cd00593    128 IEEIS 132
DSRM_DICER cd10843
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ...
 1757-1819 2.54e-39

double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also known as helicase with RNase motif (HERNA), or helicase MOI) is a double-stranded RNA (dsRNA) endoribonuclease playing a central role in short dsRNA-mediated post-transcriptional gene silencing. It cleaves naturally occurring long dsRNAs and short hairpin pre-microRNAs (miRNA) into fragments of twenty-one to twenty-three nucleotides with 3' overhang of two nucleotides, producing respectively short interfering RNAs (siRNA) and mature microRNAs. Dicer contains 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: 380680  Cd Length: 63  Bit Score: 140.25  E-value: 2.54e-39
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816191 1757 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLK 1819
Cdd:cd10843      1 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGRFKGVGRNYRIAKSAAARRALRSLK 63
RIBOc smart00535
Ribonuclease III family;
1588-1751 6.28e-37

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 135.81  E-value: 6.28e-37
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  1588 YLLQAFTHASYHYNTitDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1667
Cdd:smart00535    2 LLLRALTHASYSNEH--EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEF---- 75

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  1668 spelfhviddfvqFQLEKNEmqgMDSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSGmsLETVWQVYYPMMRPL 1747
Cdd:smart00535   76 -------------IRLGRGE---AISGGRDK------------PKILADVFEALIGAIYLDSG--LEAAREFIRDLLGPR 125


                    ....
gi 2074816191  1748 IEKF 1751
Cdd:smart00535  126 LDEL 129
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1572-1822 1.74e-36

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 138.31  E-value: 1.74e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1572 FENFEKKINYRFKNKAYLLQAFTHASY-HYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTI 1650
Cdd:COG0571      4 LEELEERLGYRFKDPELLEQALTHRSYaNEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEET 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1651 FASLAVKYDyhkyfkavspelfhvIDDFVqfQLEKNEMQgmdSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSG 1730
Cdd:COG0571     84 LAEIARELG---------------LGDYL--RLGKGEEK---SGGRRR------------PSILADAFEALIGAIYLDGG 131

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1731 msLETVWQVYYPMMRPLIEKFSANVPRS-----------------PVRELLEME-PETAK-FspaertydgkvRVTVEVV 1791
Cdd:COG0571    132 --LEAARKFVLRLFEPRLEEIAPGGAGKdyktalqewlqarglplPEYEVVEEEgPDHAKtF-----------TVEVLVG 198

                          250       260       270
                   ....*....|....*....|....*....|.
gi 2074816191 1792 GKGKFKGVGRSYRIAKSAAARRALRSLKANQ 1822
Cdd:COG0571    199 GKVLGEGTGRSKKEAEQAAAKAALEKLGKKE 229
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1575-1818 2.00e-36

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: 138.11  E-value: 2.00e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1575 FEKKINYRFKNKAYLLQAFTHASYHYNT--ITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFA 1652
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYANEHhkDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1653 SLAVKYDYHKYFKavspelfhviddfvqfqLEKNEMQgmdSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSGMS 1732
Cdd:TIGR02191   81 EVARELGLGDFLL-----------------LGKGEEK---SGGRRR------------DSILADAFEALIGAIYLDSGLE 128

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1733 LETVW--QVYYPMMRPLIEKFSANVPRSPVRELL----------EMEPETAKfsPAERTYdgkvRVTVEVVGKGKFKGVG 1800
Cdd:TIGR02191  129 AARKFilKLLIPRIDAIIKEETLKDYKTALQEWAqargkplpeyRLIKEEGP--DHDKEF----TVEVSVNGEPYGEGKG 202

                          250
                   ....*....|....*...
gi 2074816191 1801 RSYRIAKSAAARRALRSL 1818
Cdd:TIGR02191  203 KSKKEAEQNAAKAALEKL 220
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 536-624 2.71e-32

Dicer dimerization domain; This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerization of Dicer proteins with their respective protein partners.


Pssm-ID: 460900  Cd Length: 89  Bit Score: 121.06  E-value: 2.71e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  536 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMSCVRLAERVVALICCEKLHKIGELD 615
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79


                   ....*....
gi 2074816191  616 DHLMPVGKE 624
Cdd:pfam03368   80 DHLLPLTKK 88
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
 831-971 8.40e-28

This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.


Pssm-ID: 198017  Cd Length: 138  Bit Score: 110.07  E-value: 8.40e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   831 EDYQDAVIIPRYRNfdqpHRFYVADVYTDLTPLSKFPSPEYE--TFAEYYKTKYNLDLTNLNQPLLdVDHTSsrlnlltp 908
Cdd:smart00949   25 KDLKGLIVLTRYNN----KTYRIDDIDWNLAPKSTFEKSDGSeiTFVEYYKQKYNITIRDPNQPLL-VSRPK-------- 91

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816191   909 RHLNQKGKalplssaekrkakweslQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLL 971
Cdd:smart00949   92 RRRNQNGK-----------------GEPVLLPPELCFITGLTDRMRKDFMLMKSIADRTRLSP 137
RIBOc smart00535
Ribonuclease III family;
1202-1293 2.64e-25

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 102.68  E-value: 2.64e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  1202 LILQALTLSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIF 1280
Cdd:smart00535    2 LLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81

                            90
                    ....*....|...
gi 2074816191  1281 DPPVNWLPPGYVV 1293
Cdd:smart00535   82 EAISGGRDKPKIL 94
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 177-271 5.01e-25

Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a central role in RNA interference by breaking down RNA molecules into fragments of about 22 nucleotides (miRNAs and siRNAs). Loading of RNA onto Dicer and the enzymatic cleavage are supported by dsRNA-binding proteins, including trans-activation response (TAR) RNA-binding protein (TRBP) or protein activator of PKR (PACT). Together with Argonaute, this constitutes the RNA-induced silencing complex (RISC) which functions to load the small RNA fragments onto Argonaute. The Partner-binding domain of Dicer is responsible for interactions with the dsRNA-binding proteins. This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases.


Pssm-ID: 277191  Cd Length: 104  Bit Score: 101.21  E-value: 5.01e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  177 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 247
Cdd:cd15903      1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                           90       100
                   ....*....|....*....|....
gi 2074816191  248 RKFLLFTDTFLRKIHALCEEHFSP 271
Cdd:cd15903     81 RLFLRYVITQLRKIRKLLEDEMKN 104
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1202-1282 6.11e-25

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: 101.92  E-value: 6.11e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1202 LILQALT---LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVS 1278
Cdd:cd00593      2 LLLEALThpsYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLG 81


                   ....
gi 2074816191 1279 IFDP 1282
Cdd:cd00593     82 KGEE 85
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
41-458 9.24e-23

ERCC4-related helicase [Replication, recombination and repair];


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 105.97  E-value: 9.24e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   41 KERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCPRILGLTASilngkc 120
Cdd:COG1111     90 KELWE----KARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKDPLILGMTAS------ 159

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  121 dPEELEEKIQKLEKILK-SNAETATDlvvldrytSQPceivvDCGPFT-DRSGLYERLLM--ELEEALNFIN-------- 188
Cdd:COG1111    160 -PGSDEEKIEEVCENLGiENVEVRTE--------EDP-----DVAPYVhDTEVEWIRVELpeELKEIRDLLNevlddrlk 225

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  189 ---DCNISVHSKERDST--------LISKQILSDCRAVLVVLGPwcadkVAGMM-------------VRELQKYIKhEQE 244
Cdd:COG1111    226 klkELGVIVSTSPDLSKkdllalqkKLQRRIREDDSEGYRAISI-----LAEALklrhalelletqgVEALLRYLE-RLE 299

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  245 ELHRKFL-------LFTDTFLRKIHALCE----EHfspasldlkfvtPKVIKLLEILRKYKpyerqqfesvewynNRNQD 313
Cdd:COG1111    300 EEARSSGgskaskrLVSDPRFRKAMRLAEeadiEH------------PKLSKLREILKEQL--------------GTNPD 353

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  314 NYVswsdsedddedeeieekekpetnfpspftnilcgIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGHGIGKN 393
Cdd:COG1111    354 SRI----------------------------------IVFTQYRDTAEMIVEFLSEPG--------IKAGRFVGQASKEG 391

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2074816191  394 QPRNKQmeaefRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDL-PTEYRSyVQSKGR 458
Cdd:COG1111    392 DKGLTQ-----KEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPvPSEIRS-IQRKGR 451
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1608-1730 1.11e-21

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 91.57  E-value: 1.11e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1608 QRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELfhviddfvqfqleKNE 1687
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI-------------RRR 67

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 2074816191 1688 MQGMDSELRRSEEDeekeedievPKAMGDIFESLAGAIYMDSG 1730
Cdd:pfam00636   68 NNALGKGPKRADGK---------EKVLADAFEALIGALYLDGG 101
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
 820-970 5.00e-20

PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerization. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteriztic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.


Pssm-ID: 460472  Cd Length: 123  Bit Score: 87.63  E-value: 5.00e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  820 YTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFP--SPEYETFAEYYKTKYNLDLTNLNQPLLDVd 897
Cdd:pfam02170    8 QQQKDRRDFRKEAKKALKGLKVYTTYNNPRTYRIDGITFDPTPESTFPlkDGKEITVVDYFKKKYNIDLKYPDQPLLLV- 86

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816191  898 htssrlnlltprhlnqkgkalplssaeKRKakweslQNKQILVPELCAihpIPASLWRKAVCLPSILYRLHCL 970
Cdd:pfam02170   87 ---------------------------GKK------RPKVYLPPELCN---LVDGQRYTKKLMPSIAQRTRLL 123
PRK13766 PRK13766
Hef nuclease; Provisional
 41-459 4.55e-16

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 84.15  E-value: 4.55e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   41 KERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPY----REIMKLCENcpscPRILGLTASil 116
Cdd:PRK13766   102 AELWE----KAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYvyiaERYHEDAKN----PLVLGLTAS-- 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  117 NGKcDPEELEEKIQKLeKIlkSNAE--TATDLVVlDRYTSqpcEIVVDcgpftdrsglYERLLM--ELEEALNFINDCni 192
Cdd:PRK13766   172 PGS-DEEKIKEVCENL-GI--EHVEvrTEDDPDV-KPYVH---KVKIE----------WVRVELpeELKEIRDLLNEA-- 231

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  193 svhSKERdstlisKQILSDCRaVLVVLGPWCADK-VAGMMvRELQKYIKHEQEEL--------------HRKFLLFT--- 254
Cdd:PRK13766   232 ---LKDR------LKKLKELG-VIVSISPDVSKKeLLGLQ-KKLQQEIANDDSEGyeaisilaeamklrHAVELLETqgv 300

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  255 DTFLRKIHALCEEHFSPAS--------LDLKF------------VTPKVIKLLEILRKykpyerqQFEsvewynnRNQDN 314
Cdd:PRK13766   301 EALRRYLERLREEARSSGGskaskrlvEDPRFrkavrkakeldiEHPKLEKLREIVKE-------QLG-------KNPDS 366

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  315 YVswsdsedddedeeieekekpetnfpspftnilcgIIFVERRYTA-VVLNRLIKEagkqdpelayissNFITGHGIGKN 393
Cdd:PRK13766   367 RI----------------------------------IVFTQYRDTAeKIVDLLEKE-------------GIKAVRFVGQA 399

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2074816191  394 QPRN-KQMEAefRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFD-LPTEYRSyVQSKGRA 459
Cdd:PRK13766   400 SKDGdKGMSQ--KEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEpVPSEIRS-IQRKGRT 464
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1219-1282 2.59e-15

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 73.08  E-value: 2.59e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2074816191 1219 ERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIFDP 1282
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI 64
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 407-459 1.45e-14

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 71.47  E-value: 1.45e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2074816191  407 QEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 459
Cdd:pfam00271   53 REEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
HELICc smart00490
helicase superfamily c-terminal domain;
405-459 1.18e-12

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 64.93  E-value: 1.18e-12
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 2074816191   405 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 459
Cdd:smart00490   24 EEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1198-1273 2.05e-11

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: 65.69  E-value: 2.05e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1198 PNPGLILQALT-----LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLP 1272
Cdd:TIGR02191   10 KNPELLEQALThrsyaNEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVARELGLG 89


                   .
gi 2074816191 1273 S 1273
Cdd:TIGR02191   90 D 90
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1189-1271 8.71e-11

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 63.96  E-value: 8.71e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1189 IGYSSRtlgpNPGLILQALT---LSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYR 1264
Cdd:COG0571     11 LGYRFK----DPELLEQALThrsYANEHGGLeNNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAE 86


                   ....*..
gi 2074816191 1265 LGKKKGL 1271
Cdd:COG0571     87 IARELGL 93
DEXDc smart00487
DEAD-like helicases superfamily;
9-148 1.15e-10

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 62.89  E-value: 1.15e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191     9 STLVAQQVSAVRTHSDLKVGEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAIL 88
Cdd:smart00487   64 RELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLD 143

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191    89 DHPYREIMKLCENCPSCPRILGLTASILNgkcDPEELEEKIQKLEKILKSNAETATDLVV 148
Cdd:smart00487  144 GGFGDQLEKLLKLLPKNVQLLLLSATPPE---EIENLLELFLNDPVFIDVGFTPLEPIEQ 200
DSRM smart00358
Double-stranded RNA binding motif;
1756-1819 5.14e-08

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 51.49  E-value: 5.14e-08
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2074816191  1756 PRSPVRELLEMEPETAKFSPAERT-YDGKVRVTVEVVGKGK--FKGVGRSYRIAKSAAARRALRSLK 1819
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEEgPDHAPRFTVTVKVGGKrtGEGEGSSKKEAKQRAAEAALRSLK 67
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
350-495 6.75e-08

Superfamily II DNA and RNA helicase [Replication, recombination and repair];


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 57.08  E-value: 6.75e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  350 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFItgHGiGKNQprnkqmeaefRKQEEVLRKFRAHETNLLIATSIVE 429
Cdd:COG0513    244 AIVFCNTKRGADRLAEKLQKRG--------ISAAAL--HG-DLSQ----------GQRERALDAFRNGKIRVLVATDVAA 302

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2074816191  430 EGVDIPKCNLVVRFDLPTEYRSYV---------QSKGRArapisnyIMLADtdkiksfEEDLKTYKAIEKILRNK 495
Cdd:COG0513    303 RGIDIDDVSHVINYDLPEDPEDYVhrigrtgraGAEGTA-------ISLVT-------PDERRLLRAIEKLIGQK 363
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 11-127 1.55e-05

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 47.24  E-value: 1.55e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   11 LVAQQVSAVRthsdlKVGEYSNLEVNASWT-KERWNQ--EFTKHQVLIMTCYVALNVLKNGYLsLSDINLLVFDECHLaI 87
Cdd:pfam00270   57 LAEQIYEELK-----KLGKGLGLKVASLLGgDSRKEQleKLKGPDILVGTPGRLLDLLQERKL-LKNLKLLVLDEAHR-L 129

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2074816191   88 LDHPYREIMKLC-ENCPSCPRILGLTASIlngkcdPEELEE 127
Cdd:pfam00270  130 LDMGFGPDLEEIlRRLPKKRQILLLSATL------PRNLED 164
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 350-500 4.30e-05

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 48.01  E-value: 4.30e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  350 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGhgigknqprnkqmEAEFRKQEEVLRKFRAHETNLLIATSIVE 429
Cdd:PRK11192   248 SIVFVRTRERVHELAGWLRKAG--------INCCYLEG-------------EMVQAKRNEAIKRLTDGRVNVLVATDVAA 306

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  430 EGVDIPKCNLVVRFDLPTEYRSYVQSKGR-ARA-----PIS-----NYIMLadtDKIKSF-EEDLK---------TYKAI 488
Cdd:PRK11192   307 RGIDIDDVSHVINFDMPRSADTYLHRIGRtGRAgrkgtAISlveahDHLLL---GKIERYiEEPLKarvidelrpKTKAP 383

                          170
                   ....*....|..
gi 2074816191  489 EKILRNKCSKSV 500
Cdd:PRK11192   384 SEKKTGKPSKKV 395
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
47-127 4.42e-03

Replicative superfamily II helicase [Replication, recombination and repair];


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 41.80  E-value: 4.42e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   47 EFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLaiLDHPYR----EIM--KLCENCPScPRILGLTASILNgkc 120
Cdd:COG1204    110 WLGRYDILVATPEKLDSLLRNGPSWLRDVDLVVVDEAHL--IDDESRgptlEVLlaRLRRLNPE-AQIVALSATIGN--- 183


                   ....*..
gi 2074816191  121 dPEELEE 127
Cdd:COG1204    184 -AEEIAE 189
 
Name Accession Description Interval E-value
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
 792-914 2.19e-69

PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA interference pathway. It generates dsRNAs which are approximately 20 bp long (siRNAs), which in turn target hydrolysis of homologous RNAs. PAZ domains are named after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes.


Pssm-ID: 239209  Cd Length: 122  Bit Score: 228.48  E-value: 2.19e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  792 DSSTLDIDFKFMEDIEkSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 871
Cdd:cd02843      1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 2074816191  872 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 914
Cdd:cd02843     80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 11-145 1.12e-63

DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350792 [Multi-domain]  Cd Length: 200  Bit Score: 215.59  E-value: 1.12e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   11 LVAQQVSAVRTHSDLKVGEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDH 90
Cdd:cd18034     63 LVAQQAEAIRSHTDLKVGEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDH 142

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2074816191   91 PYREIMKLCENC---PSCPRILGLTASILNGKCDPEELEEKIQKLEKILKSNAETATD 145
Cdd:cd18034    143 PYARIMKEFYHLegrTSRPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 278-470 6.36e-56

C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 190.88  E-value: 6.36e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  278 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 357
Cdd:cd18802      4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  358 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprNKQMEAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKC 437
Cdd:cd18802     36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109

                          170       180       190
                   ....*....|....*....|....*....|...
gi 2074816191  438 NLVVRFDLPTEYRSYVQSKGRARAPISNYIMLA 470
Cdd:cd18802    110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1588-1752 9.70e-40

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: 144.29  E-value: 9.70e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1588 YLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1667
Cdd:cd00593      2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKY---- 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1668 spelfhviddfvqFQLEKNEMQGMDSElrrseedeekeedieVPKAMGDIFESLAGAIYMDSGMslETVWQVYYPMMRPL 1747
Cdd:cd00593     78 -------------LRLGKGEEKSGGRL---------------RPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPL 127


                   ....*
gi 2074816191 1748 IEKFS 1752
Cdd:cd00593    128 IEEIS 132
DSRM_DICER cd10843
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ...
 1757-1819 2.54e-39

double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also known as helicase with RNase motif (HERNA), or helicase MOI) is a double-stranded RNA (dsRNA) endoribonuclease playing a central role in short dsRNA-mediated post-transcriptional gene silencing. It cleaves naturally occurring long dsRNAs and short hairpin pre-microRNAs (miRNA) into fragments of twenty-one to twenty-three nucleotides with 3' overhang of two nucleotides, producing respectively short interfering RNAs (siRNA) and mature microRNAs. Dicer contains 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: 380680  Cd Length: 63  Bit Score: 140.25  E-value: 2.54e-39
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816191 1757 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLK 1819
Cdd:cd10843      1 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGRFKGVGRNYRIAKSAAARRALRSLK 63
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 11-144 3.24e-38

DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350685 [Multi-domain]  Cd Length: 201  Bit Score: 142.57  E-value: 3.24e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   11 LVAQQVSAVRTHSD---LKVGEYSNlevnASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYL-SLSDINLLVFDECHLA 86
Cdd:cd17927     62 LVEQQKEVFRKHFErpgYKVTGLSG----DTSENVSVEQIVESSDVIIVTPQILVNDLKSGTIvSLSDFSLLVFDECHNT 137

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2074816191   87 ILDHPYREIMKLCENCPS-----CPRILGLTASILNGKC-DPEELEEKIQKLEKILKSNAETAT 144
Cdd:cd17927    138 TKNHPYNEIMFRYLDQKLgssgpLPQILGLTASPGVGGAkNTEEALEHICKLCANLDISVIATV 201
RIBOc smart00535
Ribonuclease III family;
1588-1751 6.28e-37

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 135.81  E-value: 6.28e-37
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  1588 YLLQAFTHASYHYNTitDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1667
Cdd:smart00535    2 LLLRALTHASYSNEH--EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEF---- 75

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  1668 spelfhviddfvqFQLEKNEmqgMDSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSGmsLETVWQVYYPMMRPL 1747
Cdd:smart00535   76 -------------IRLGRGE---AISGGRDK------------PKILADVFEALIGAIYLDSG--LEAAREFIRDLLGPR 125


                    ....
gi 2074816191  1748 IEKF 1751
Cdd:smart00535  126 LDEL 129
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1572-1822 1.74e-36

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 138.31  E-value: 1.74e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1572 FENFEKKINYRFKNKAYLLQAFTHASY-HYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTI 1650
Cdd:COG0571      4 LEELEERLGYRFKDPELLEQALTHRSYaNEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEET 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1651 FASLAVKYDyhkyfkavspelfhvIDDFVqfQLEKNEMQgmdSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSG 1730
Cdd:COG0571     84 LAEIARELG---------------LGDYL--RLGKGEEK---SGGRRR------------PSILADAFEALIGAIYLDGG 131

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1731 msLETVWQVYYPMMRPLIEKFSANVPRS-----------------PVRELLEME-PETAK-FspaertydgkvRVTVEVV 1791
Cdd:COG0571    132 --LEAARKFVLRLFEPRLEEIAPGGAGKdyktalqewlqarglplPEYEVVEEEgPDHAKtF-----------TVEVLVG 198

                          250       260       270
                   ....*....|....*....|....*....|.
gi 2074816191 1792 GKGKFKGVGRSYRIAKSAAARRALRSLKANQ 1822
Cdd:COG0571    199 GKVLGEGTGRSKKEAEQAAAKAALEKLGKKE 229
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1575-1818 2.00e-36

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: 138.11  E-value: 2.00e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1575 FEKKINYRFKNKAYLLQAFTHASYHYNT--ITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFA 1652
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYANEHhkDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1653 SLAVKYDYHKYFKavspelfhviddfvqfqLEKNEMQgmdSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSGMS 1732
Cdd:TIGR02191   81 EVARELGLGDFLL-----------------LGKGEEK---SGGRRR------------DSILADAFEALIGAIYLDSGLE 128

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1733 LETVW--QVYYPMMRPLIEKFSANVPRSPVRELL----------EMEPETAKfsPAERTYdgkvRVTVEVVGKGKFKGVG 1800
Cdd:TIGR02191  129 AARKFilKLLIPRIDAIIKEETLKDYKTALQEWAqargkplpeyRLIKEEGP--DHDKEF----TVEVSVNGEPYGEGKG 202

                          250
                   ....*....|....*...
gi 2074816191 1801 RSYRIAKSAAARRALRSL 1818
Cdd:TIGR02191  203 KSKKEAEQNAAKAALEKL 220
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 536-624 2.71e-32

Dicer dimerization domain; This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerization of Dicer proteins with their respective protein partners.


Pssm-ID: 460900  Cd Length: 89  Bit Score: 121.06  E-value: 2.71e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  536 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMSCVRLAERVVALICCEKLHKIGELD 615
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79


                   ....*....
gi 2074816191  616 DHLMPVGKE 624
Cdd:pfam03368   80 DHLLPLTKK 88
PAZ cd02825
PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two ...
 792-914 2.03e-31

PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. This parent model also contains structures of an archaeal PAZ domain.


Pssm-ID: 239207  Cd Length: 115  Bit Score: 119.87  E-value: 2.03e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  792 DSSTLDIDFKFMEDIEKSEARIGIPSTKYTKETPfVFKLEDYQDaviipryrnfdQPHRFYVADVYTDLTPLS--KFPSP 869
Cdd:cd02825      1 ADPVIETMCKFPKDREIDTPLLDSPREEFTKELK-GLKVEDTHN-----------PLNRVYRPDGETRLKAPSqlKHSDG 68

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2074816191  870 EYETFAEYYKTKYNLDLTNLNQPLLDVDHTS--SRLNLLTPRHLNQK 914
Cdd:cd02825     69 KEITFADYFKERYNLTLTDLNQPLLIVKFSSkkSYSILLPPELCVIT 115
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
 831-971 8.40e-28

This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.


Pssm-ID: 198017  Cd Length: 138  Bit Score: 110.07  E-value: 8.40e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   831 EDYQDAVIIPRYRNfdqpHRFYVADVYTDLTPLSKFPSPEYE--TFAEYYKTKYNLDLTNLNQPLLdVDHTSsrlnlltp 908
Cdd:smart00949   25 KDLKGLIVLTRYNN----KTYRIDDIDWNLAPKSTFEKSDGSeiTFVEYYKQKYNITIRDPNQPLL-VSRPK-------- 91

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816191   909 RHLNQKGKalplssaekrkakweslQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLL 971
Cdd:smart00949   92 RRRNQNGK-----------------GEPVLLPPELCFITGLTDRMRKDFMLMKSIADRTRLSP 137
RIBOc smart00535
Ribonuclease III family;
1202-1293 2.64e-25

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 102.68  E-value: 2.64e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  1202 LILQALTLSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIF 1280
Cdd:smart00535    2 LLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81

                            90
                    ....*....|...
gi 2074816191  1281 DPPVNWLPPGYVV 1293
Cdd:smart00535   82 EAISGGRDKPKIL 94
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 177-271 5.01e-25

Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a central role in RNA interference by breaking down RNA molecules into fragments of about 22 nucleotides (miRNAs and siRNAs). Loading of RNA onto Dicer and the enzymatic cleavage are supported by dsRNA-binding proteins, including trans-activation response (TAR) RNA-binding protein (TRBP) or protein activator of PKR (PACT). Together with Argonaute, this constitutes the RNA-induced silencing complex (RISC) which functions to load the small RNA fragments onto Argonaute. The Partner-binding domain of Dicer is responsible for interactions with the dsRNA-binding proteins. This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases.


Pssm-ID: 277191  Cd Length: 104  Bit Score: 101.21  E-value: 5.01e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  177 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 247
Cdd:cd15903      1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                           90       100
                   ....*....|....*....|....
gi 2074816191  248 RKFLLFTDTFLRKIHALCEEHFSP 271
Cdd:cd15903     81 RLFLRYVITQLRKIRKLLEDEMKN 104
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1202-1282 6.11e-25

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: 101.92  E-value: 6.11e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1202 LILQALT---LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVS 1278
Cdd:cd00593      2 LLLEALThpsYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLG 81


                   ....
gi 2074816191 1279 IFDP 1282
Cdd:cd00593     82 KGEE 85
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
41-458 9.24e-23

ERCC4-related helicase [Replication, recombination and repair];


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 105.97  E-value: 9.24e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   41 KERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCPRILGLTASilngkc 120
Cdd:COG1111     90 KELWE----KARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKDPLILGMTAS------ 159

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  121 dPEELEEKIQKLEKILK-SNAETATDlvvldrytSQPceivvDCGPFT-DRSGLYERLLM--ELEEALNFIN-------- 188
Cdd:COG1111    160 -PGSDEEKIEEVCENLGiENVEVRTE--------EDP-----DVAPYVhDTEVEWIRVELpeELKEIRDLLNevlddrlk 225

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  189 ---DCNISVHSKERDST--------LISKQILSDCRAVLVVLGPwcadkVAGMM-------------VRELQKYIKhEQE 244
Cdd:COG1111    226 klkELGVIVSTSPDLSKkdllalqkKLQRRIREDDSEGYRAISI-----LAEALklrhalelletqgVEALLRYLE-RLE 299

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  245 ELHRKFL-------LFTDTFLRKIHALCE----EHfspasldlkfvtPKVIKLLEILRKYKpyerqqfesvewynNRNQD 313
Cdd:COG1111    300 EEARSSGgskaskrLVSDPRFRKAMRLAEeadiEH------------PKLSKLREILKEQL--------------GTNPD 353

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  314 NYVswsdsedddedeeieekekpetnfpspftnilcgIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGHGIGKN 393
Cdd:COG1111    354 SRI----------------------------------IVFTQYRDTAEMIVEFLSEPG--------IKAGRFVGQASKEG 391

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2074816191  394 QPRNKQmeaefRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDL-PTEYRSyVQSKGR 458
Cdd:COG1111    392 DKGLTQ-----KEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPvPSEIRS-IQRKGR 451
helicase_insert_domain cd12088
helicase_insert_domain; helicase_insert_domain; This helical domain can be found inserted in a ...
 177-268 3.08e-22

helicase_insert_domain; helicase_insert_domain; This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases, like archaeal Hef helicase, MDA5-like helicases and FancM-like helicases. The exact function of this domain is unknown, but seems to play a role in interaction with nucleotides and/or the stabilization of the nucleotide complex.


Pssm-ID: 277187  Cd Length: 82  Bit Score: 92.15  E-value: 3.08e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  177 LMELEEALNFINDCNIsvhskerDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHeqeELHRKFLLFTDT 256
Cdd:cd12088      1 KMILSQLLRDTESLLK-------LLYTAHLRKLNDALELLEDAGIWDALKYIKMFFTEVREGIFD---ELERKLTLRFDE 70

                           90
                   ....*....|..
gi 2074816191  257 FLRKIHALCEEH 268
Cdd:cd12088     71 KLQKLIALSRDP 82
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1608-1730 1.11e-21

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 91.57  E-value: 1.11e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1608 QRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELfhviddfvqfqleKNE 1687
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI-------------RRR 67

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 2074816191 1688 MQGMDSELRRSEEDeekeedievPKAMGDIFESLAGAIYMDSG 1730
Cdd:pfam00636   68 NNALGKGPKRADGK---------EKVLADAFEALIGALYLDGG 101
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
 820-970 5.00e-20

PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerization. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteriztic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.


Pssm-ID: 460472  Cd Length: 123  Bit Score: 87.63  E-value: 5.00e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  820 YTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFP--SPEYETFAEYYKTKYNLDLTNLNQPLLDVd 897
Cdd:pfam02170    8 QQQKDRRDFRKEAKKALKGLKVYTTYNNPRTYRIDGITFDPTPESTFPlkDGKEITVVDYFKKKYNIDLKYPDQPLLLV- 86

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816191  898 htssrlnlltprhlnqkgkalplssaeKRKakweslQNKQILVPELCAihpIPASLWRKAVCLPSILYRLHCL 970
Cdd:pfam02170   87 ---------------------------GKK------RPKVYLPPELCN---LVDGQRYTKKLMPSIAQRTRLL 123
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 1589-1731 1.66e-16

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: 77.60  E-value: 1.66e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1589 LLQAFTHASYHYNTiTDCYQRLEFLGDAILDYLITKHLYEDPRQhSPGVLTDLRSALVNNTIFASLAvkydyhkyfkavs 1668
Cdd:pfam14622    4 LLQALTHKSYANGR-KPYNERLEFLGDAVLELSVSEYLFKKPDL-DEGGLTKLRASIVSEESLAEIA------------- 68

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816191 1669 pelfhviddfVQFQLEKNEMQGMDSELRRSeedeekeedIEVPKAMGDIFESLAGAIYMDSGM 1731
Cdd:pfam14622   69 ----------REIGLGKYLRLGKGEEETGG---------SGRESILADALEALIGAIYLDGGF 112
PRK13766 PRK13766
Hef nuclease; Provisional
 41-459 4.55e-16

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 84.15  E-value: 4.55e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   41 KERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPY----REIMKLCENcpscPRILGLTASil 116
Cdd:PRK13766   102 AELWE----KAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYvyiaERYHEDAKN----PLVLGLTAS-- 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  117 NGKcDPEELEEKIQKLeKIlkSNAE--TATDLVVlDRYTSqpcEIVVDcgpftdrsglYERLLM--ELEEALNFINDCni 192
Cdd:PRK13766   172 PGS-DEEKIKEVCENL-GI--EHVEvrTEDDPDV-KPYVH---KVKIE----------WVRVELpeELKEIRDLLNEA-- 231

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  193 svhSKERdstlisKQILSDCRaVLVVLGPWCADK-VAGMMvRELQKYIKHEQEEL--------------HRKFLLFT--- 254
Cdd:PRK13766   232 ---LKDR------LKKLKELG-VIVSISPDVSKKeLLGLQ-KKLQQEIANDDSEGyeaisilaeamklrHAVELLETqgv 300

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  255 DTFLRKIHALCEEHFSPAS--------LDLKF------------VTPKVIKLLEILRKykpyerqQFEsvewynnRNQDN 314
Cdd:PRK13766   301 EALRRYLERLREEARSSGGskaskrlvEDPRFrkavrkakeldiEHPKLEKLREIVKE-------QLG-------KNPDS 366

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  315 YVswsdsedddedeeieekekpetnfpspftnilcgIIFVERRYTA-VVLNRLIKEagkqdpelayissNFITGHGIGKN 393
Cdd:PRK13766   367 RI----------------------------------IVFTQYRDTAeKIVDLLEKE-------------GIKAVRFVGQA 399

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2074816191  394 QPRN-KQMEAefRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFD-LPTEYRSyVQSKGRA 459
Cdd:PRK13766   400 SKDGdKGMSQ--KEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEpVPSEIRS-IQRKGRT 464
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1219-1282 2.59e-15

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 73.08  E-value: 2.59e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2074816191 1219 ERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIFDP 1282
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI 64
PAZ_CAF_like cd02844
PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has ...
 828-950 6.54e-15

PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has been implicated in flower morphogenesis and in early Arabidopsis development and might function through posttranscriptional regulation of specific mRNA molecules. PAZ domains are named after the proteins Piwi, Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes.


Pssm-ID: 239210  Cd Length: 135  Bit Score: 73.22  E-value: 6.54e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  828 FKLEDYQDAVIIpryrnfdQPH--RFYVADVYTDLTPLSKFP---SPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSR 902
Cdd:cd02844     26 FCACDLKGSVVT-------APHngRFYVISGILDLNANSSFPgkeGLGYATYAEYFKEKYGIVLNHPNQPLLKGKQIFNL 98

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 2074816191  903 LNLLTPRhLNQKGkalplSSAEKRKakwesLQNKQILVPELCAIHPIP 950
Cdd:cd02844     99 HNLLHNR-FEEKG-----ESEEKEK-----DRYFVELPPELCSVIDLP 135
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 407-459 1.45e-14

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 71.47  E-value: 1.45e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2074816191  407 QEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 459
Cdd:pfam00271   53 REEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
HELICc smart00490
helicase superfamily c-terminal domain;
405-459 1.18e-12

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 64.93  E-value: 1.18e-12
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 2074816191   405 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 459
Cdd:smart00490   24 EEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 351-459 1.17e-11

C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350188 [Multi-domain]  Cd Length: 143  Bit Score: 64.30  E-value: 1.17e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  351 IIFVERRYTAvvlNRLIKEAGKQDPELAyiSSNFItGHGIGKNQPRNKQMEaefrkQEEVLRKFRAHETNLLIATSIVEE 430
Cdd:cd18801     34 IIFSEFRDSA---EEIVNFLSKIRPGIR--ATRFI-GQASGKSSKGMSQKE-----QKEVIEQFRKGGYNVLVATSIGEE 102

                           90       100       110
                   ....*....|....*....|....*....|
gi 2074816191  431 GVDIPKCNLVVRFD-LPTEYRSyVQSKGRA 459
Cdd:cd18801    103 GLDIGEVDLIICYDaSPSPIRM-IQRMGRT 131
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
 51-132 2.00e-11

DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called DEAD box protein 58 (DDX58), is a pathogen-recognition receptor that recognizes viral 5'-triphosphates carrying double-stranded RNA. Upon binding to these microbe-associated molecular patterns (MAMPs), RIG-I forms oligomers and promotes downstream processes that result in type I interferon production and induction of an antiviral state. The optimal ligand for RIG-I has been found to be base-paired or double-stranded RNA (dsRNA) molecules containing a 5' triphosphate (5'-ppp-dsRNA). RIG-I contains two N-terminal caspase activation and recruitment domains (CARDs), which are required for interaction with IPS-1, a superfamily 2 helicase/translocase/ATPase (SF2) domain and a C-terminal regulatory/repressor domain (RD). RIG-I is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350831 [Multi-domain]  Cd Length: 202  Bit Score: 65.23  E-value: 2.00e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   51 HQVLIMTCYVALNVLKNGYL-SLSDINLLVFDECHLAILDHPYREIM------KLCENCPSCPRILGLTASILNGKC-DP 122
Cdd:cd18073    101 NDIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSGNHPYNMIMfryldqKLGGSSGPLPQIIGLTASVGVGDAkNT 180

                           90
                   ....*....|
gi 2074816191  123 EELEEKIQKL 132
Cdd:cd18073    181 DEALDYICKL 190
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1198-1273 2.05e-11

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: 65.69  E-value: 2.05e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1198 PNPGLILQALT-----LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLP 1272
Cdd:TIGR02191   10 KNPELLEQALThrsyaNEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVARELGLG 89


                   .
gi 2074816191 1273 S 1273
Cdd:TIGR02191   90 D 90
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 53-132 2.49e-11

DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350794 [Multi-domain]  Cd Length: 204  Bit Score: 64.80  E-value: 2.49e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   53 VLIMTCYVALNVLKNG----YLSLSDINLLVFDECHLAILDHPYREIM------KLCENCPScPRILGLTASI-LNGKCD 121
Cdd:cd18036    103 VIICTPQILINNLLSGreeeRVYLSDFSLLIFDECHHTQKEHPYNKIMrmyldkKLSSQGPL-PQILGLTASPgVGGARS 181

                           90
                   ....*....|.
gi 2074816191  122 PEELEEKIQKL 132
Cdd:cd18036    182 FEEALEHILKL 192
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 351-461 2.69e-11

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 62.91  E-value: 2.69e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  351 IIFVERRYTAVVLNRLIKEAGkqdpelayISSNFItgHGiGKNQprnkqmeaefRKQEEVLRKFRAHETNLLIATSIVEE 430
Cdd:cd18787     31 IIFVNTKKRVDRLAELLEELG--------IKVAAL--HG-DLSQ----------EERERALKKFRSGKVRVLVATDVAAR 89

                           90       100       110
                   ....*....|....*....|....*....|..
gi 2074816191  431 GVDIPKCNLVVRFDLPTEYRSYVQSKGR-ARA 461
Cdd:cd18787     90 GLDIPGVDHVINYDLPRDAEDYVHRIGRtGRA 121
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1189-1271 8.71e-11

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 63.96  E-value: 8.71e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191 1189 IGYSSRtlgpNPGLILQALT---LSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYR 1264
Cdd:COG0571     11 LGYRFK----DPELLEQALThrsYANEHGGLeNNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAE 86


                   ....*..
gi 2074816191 1265 LGKKKGL 1271
Cdd:COG0571     87 IARELGL 93
DEXDc smart00487
DEAD-like helicases superfamily;
9-148 1.15e-10

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 62.89  E-value: 1.15e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191     9 STLVAQQVSAVRTHSDLKVGEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAIL 88
Cdd:smart00487   64 RELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLD 143

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191    89 DHPYREIMKLCENCPSCPRILGLTASILNgkcDPEELEEKIQKLEKILKSNAETATDLVV 148
Cdd:smart00487  144 GGFGDQLEKLLKLLPKNVQLLLLSATPPE---EIENLLELFLNDPVFIDVGFTPLEPIEQ 200
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
 11-132 5.96e-09

DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA), and Holliday junction substrates. Its ATP-dependent DNA branch migration activity can process branched DNA structures such as a movable replication fork. This activity is strongly stimulated in the presence of CENPS and CENPX. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, it strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA. FANCM is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350791 [Multi-domain]  Cd Length: 182  Bit Score: 57.33  E-value: 5.96e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   11 LVAQQVSAVrtHSDLKVGEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDH 90
Cdd:cd18033     58 LVSQQIEAC--YKITGIPSSQTAELTGSVPPTKRAELWASKRVFFLTPQTLENDLKEGDCDPKSIVCLVIDEAHRATGNY 135

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 2074816191   91 PYREIMKLCENCPSCPRILGLTASILNgkcDPEELEEKIQKL 132
Cdd:cd18033    136 AYCQVVRELMRYNSHFRILALTATPGS---KLEAVQQVIDNL 174
PAZ_piwi_like cd02845
PAZ domain, Piwi_like subfamily. In multi-cellular organisms, the Piwi protein appears to be ...
 834-944 1.46e-08

PAZ domain, Piwi_like subfamily. In multi-cellular organisms, the Piwi protein appears to be essential for the maintenance of germline stem cells. In the Drosophila male germline, Piwi was shown to be involved in the silencing of retrotransposons in the male gametes. The Piwi proteins share their domain architecture with other members of the argonaute family. The PAZ domain has been named after the proteins Piwi, Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes.


Pssm-ID: 239211  Cd Length: 117  Bit Score: 54.57  E-value: 1.46e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  834 QDAVIIPRYRNfdqphRFY-VADVYTDLTPLSKFPSPEYE--TFAEYYKTKYNLDLTNLNQPLLdvdhtssrlnlltprh 910
Cdd:cd02845     29 IGSIVLTRYNN-----KTYrIDDIDFDKTPLSTFKKSDGTeiTFVEYYKKQYNIEITDLNQPLL---------------- 87

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 2074816191  911 lnqkgkalpLSSAEKRKAKweSLQNKQI-LVPELC 944
Cdd:cd02845     88 ---------VSRPKRRDPR--GGEKEPIyLIPELC 111
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 1200-1275 4.25e-08

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: 53.33  E-value: 4.25e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2074816191 1200 PGLILQALT---LSNASDGFNlERLEMLGDSFLKHAITTYLFcTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRM 1275
Cdd:pfam14622    1 EELLLQALThksYANGRKPYN-ERLEFLGDAVLELSVSEYLF-KKPDLDEGGLTKLRASIVSEESLAEIAREIGLGKYL 77
DSRM smart00358
Double-stranded RNA binding motif;
1756-1819 5.14e-08

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 51.49  E-value: 5.14e-08
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2074816191  1756 PRSPVRELLEMEPETAKFSPAERT-YDGKVRVTVEVVGKGK--FKGVGRSYRIAKSAAARRALRSLK 1819
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEEgPDHAPRFTVTVKVGGKrtGEGEGSSKKEAKQRAAEAALRSLK 67
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 418-459 6.34e-08

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 51.55  E-value: 6.34e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 2074816191  418 ETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 459
Cdd:cd18785     22 SLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRA 63
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
350-495 6.75e-08

Superfamily II DNA and RNA helicase [Replication, recombination and repair];


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 57.08  E-value: 6.75e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  350 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFItgHGiGKNQprnkqmeaefRKQEEVLRKFRAHETNLLIATSIVE 429
Cdd:COG0513    244 AIVFCNTKRGADRLAEKLQKRG--------ISAAAL--HG-DLSQ----------GQRERALDAFRNGKIRVLVATDVAA 302

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2074816191  430 EGVDIPKCNLVVRFDLPTEYRSYV---------QSKGRArapisnyIMLADtdkiksfEEDLKTYKAIEKILRNK 495
Cdd:COG0513    303 RGIDIDDVSHVINYDLPEDPEDYVhrigrtgraGAEGTA-------ISLVT-------PDERRLLRAIEKLIGQK 363
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 399-490 1.10e-06

C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350179 [Multi-domain]  Cd Length: 160  Bit Score: 50.34  E-value: 1.10e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  399 QMEAEfrKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVV-----RFDLPTEYrsyvQSKGR-ARAPISNYIMLADT 472
Cdd:cd18792     69 KMTED--EKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIiedadRFGLSQLH----QLRGRvGRGKHQSYCYLLYP 142

                           90
                   ....*....|....*...
gi 2074816191  473 DKIKSFEEDLKTYKAIEK 490
Cdd:cd18792    143 DPKKLTETAKKRLRAIAE 160
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 42-132 3.20e-06

DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350793 [Multi-domain]  Cd Length: 181  Bit Score: 49.44  E-value: 3.20e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   42 ERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCPRILGLTASilnGKCD 121
Cdd:cd18035     89 ERWD----ASKIIVATPQVIENDLLAGRITLDDVSLLIFDEAHHAVGNYAYVYIAHRYKREANNPLILGLTAS---PGSD 161

                           90
                   ....*....|.
gi 2074816191  122 PEELEEKIQKL 132
Cdd:cd18035    162 KEKIMEICENL 172
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
350-459 1.55e-05

Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 49.64  E-value: 1.55e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  350 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGhgigknqprnkQMEAEFRkqEEVLRKFRAHETNLLIATSIVE 429
Cdd:COG1061    308 TLVFCSSVDHAEALAELLNEAG--------IRAAVVTG-----------DTPKKER--EEILEAFRDGELRILVTVDVLN 366

                           90       100       110
                   ....*....|....*....|....*....|...
gi 2074816191  430 EGVDIPKCNLVV--RfdlPTEYRS-YVQSKGRA 459
Cdd:COG1061    367 EGVDVPRLDVAIllR---PTGSPReFIQRLGRG 396
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 11-127 1.55e-05

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 47.24  E-value: 1.55e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   11 LVAQQVSAVRthsdlKVGEYSNLEVNASWT-KERWNQ--EFTKHQVLIMTCYVALNVLKNGYLsLSDINLLVFDECHLaI 87
Cdd:pfam00270   57 LAEQIYEELK-----KLGKGLGLKVASLLGgDSRKEQleKLKGPDILVGTPGRLLDLLQERKL-LKNLKLLVLDEAHR-L 129

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2074816191   88 LDHPYREIMKLC-ENCPSCPRILGLTASIlngkcdPEELEE 127
Cdd:pfam00270  130 LDMGFGPDLEEIlRRLPKKRQILLLSATL------PRNLED 164
DEXHc_RLR-3 cd18075
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ...
 51-114 2.58e-05

DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of genetics and physiology 2 or LGP2 and DHX58) appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. RLR-3 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. RNA binding is required for RLR-3-mediated enhancement of MDA5 activation. RLR-3 end-binding may promote nucleation of MDA5 oligomerization on dsRNA. RLR-3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350833 [Multi-domain]  Cd Length: 200  Bit Score: 47.16  E-value: 2.58e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2074816191   51 HQVLIMTCYVALNVLKNG----YLSLSDINLLVFDECHLAILDHPYREIM------KLCENCPsCPRILGLTAS 114
Cdd:cd18075     97 SDVVICTAQILQNALLSGeeeaHVELTDFSLLVIDECHHTHKEAVYNKIMlsylekKLSRQGD-LPQILGLTAS 169
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 350-459 3.00e-05

C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350186 [Multi-domain]  Cd Length: 116  Bit Score: 44.86  E-value: 3.00e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  350 GIIFVERRYTAVVLNRLIKEAGkqdPELAYISSNFItghgigknqprnkqmeAEFRKQEEVLR-KFRAHETNLLIATSIV 428
Cdd:cd18799      9 TLIFCVSIEHAEFMAEAFNEAG---IDAVALNSDYS----------------DRERGDEALILlFFGELKPPILVTVDLL 69

                           90       100       110
                   ....*....|....*....|....*....|..
gi 2074816191  429 EEGVDIPKCNLVVrFDLPTEYRS-YVQSKGRA 459
Cdd:cd18799     70 TTGVDIPEVDNVV-FLRPTESRTlFLQMLGRG 100
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 366-477 3.16e-05

C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 46.18  E-value: 3.16e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  366 LIKEAGKQDPELA-----YISSNFITGHGIGKNQPRNKQMEaefrkQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLV 440
Cdd:cd18811     35 LIEESEKLDLKAAvamyeYLKERFRPELNVGLLHGRLKSDE-----KDAVMAEFREGEVDILVSTTVIEVGVDVPNATVM 109

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 2074816191  441 V-----RFDLPTEYrsyvQSKGR-ARAPISNYIMLADTDKIKS 477
Cdd:cd18811    110 ViedaeRFGLSQLH----QLRGRvGRGDHQSYCLLVYKDPLTE 148
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 350-500 4.30e-05

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 48.01  E-value: 4.30e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  350 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGhgigknqprnkqmEAEFRKQEEVLRKFRAHETNLLIATSIVE 429
Cdd:PRK11192   248 SIVFVRTRERVHELAGWLRKAG--------INCCYLEG-------------EMVQAKRNEAIKRLTDGRVNVLVATDVAA 306

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  430 EGVDIPKCNLVVRFDLPTEYRSYVQSKGR-ARA-----PIS-----NYIMLadtDKIKSF-EEDLK---------TYKAI 488
Cdd:PRK11192   307 RGIDIDDVSHVINFDMPRSADTYLHRIGRtGRAgrkgtAISlveahDHLLL---GKIERYiEEPLKarvidelrpKTKAP 383

                          170
                   ....*....|..
gi 2074816191  489 EKILRNKCSKSV 500
Cdd:PRK11192   384 SEKKTGKPSKKV 395
PTZ00424 PTZ00424
helicase 45; Provisional
 405-484 5.11e-05

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 47.90  E-value: 5.11e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  405 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA----RAPIS-NYIMLADTDKIKSFE 479
Cdd:PTZ00424   304 KDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSgrfgRKGVAiNFVTPDDIEQLKEIE 383


                   ....*
gi 2074816191  480 EDLKT 484
Cdd:PTZ00424   384 RHYNT 388
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
 408-445 6.91e-05

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 47.84  E-value: 6.91e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 2074816191  408 EEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVV-----RFDL 445
Cdd:PRK10917   521 DAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVienaeRFGL 563
PTZ00110 PTZ00110
helicase; Provisional
 405-483 4.20e-04

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 45.15  E-value: 4.20e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  405 RKQEE---VLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQ---SKGRARAPISNYIMLAdTDKIKSF 478
Cdd:PTZ00110   411 KKQEErtwVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHrigRTGRAGAKGASYTFLT-PDKYRLA 489


                   ....*
gi 2074816191  479 EEDLK 483
Cdd:PTZ00110   490 RDLVK 494
RecG COG1200
RecG-like helicase [Replication, recombination and repair];
408-435 4.27e-04

RecG-like helicase [Replication, recombination and repair];


Pssm-ID: 440813 [Multi-domain]  Cd Length: 684  Bit Score: 45.04  E-value: 4.27e-04
                           10        20
                   ....*....|....*....|....*...
gi 2074816191  408 EEVLRKFRAHETNLLIATSIVEEGVDIP 435
Cdd:COG1200    519 DAVMAAFKAGEIDVLVATTVIEVGVDVP 546
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 409-489 4.96e-04

C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II), and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA. Its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350177 [Multi-domain]  Cd Length: 171  Bit Score: 42.62  E-value: 4.96e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  409 EVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTE-----YRSYVQSKGRA-RAPISNYIMLAD--TDKIKsfee 480
Cdd:cd18790     68 EIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEgflrsETSLIQTIGRAaRNVNGKVILYADkiTDSMQ---- 143


                   ....*....
gi 2074816191  481 dlktyKAIE 489
Cdd:cd18790    144 -----KAIE 147
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 397-458 5.61e-04

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 44.84  E-value: 5.61e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2074816191  397 NKQMEAEFRkqEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGR 458
Cdd:PRK11634   276 NGDMNQALR--EQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGR 335
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 1786-1818 9.96e-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: 39.25  E-value: 9.96e-04
                           10        20        30
                   ....*....|....*....|....*....|...
gi 2074816191 1786 VTVEVVGKgKFKGVGRSYRIAKSAAARRALRSL 1818
Cdd:cd19865     32 MSVEVNGQ-TFEGTGRSKKKAKLEAAEKALRSF 63
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 399-490 1.00e-03

C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350197 [Multi-domain]  Cd Length: 151  Bit Score: 41.56  E-value: 1.00e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  399 QMEAEfrKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVV-----RFDLPTEYrsyvQSKGR-ARAPISNYIMLADT 472
Cdd:cd18810     60 QMTEN--ELEEVMLEFAKGEYDILVCTTIIESGIDIPNANTIIieradKFGLAQLY----QLRGRvGRSKERAYAYFLYP 133

                           90
                   ....*....|....*...
gi 2074816191  473 DKIKSFEEDLKTYKAIEK 490
Cdd:cd18810    134 DQKKLTEDALKRLEAIQE 151
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 1757-1818 1.70e-03

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: 1.70e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2074816191 1757 RSPVRELLE---MEPETAKFSPAERTYDGKVRVTVEVVGKGK--FKGVGRSYRIAKSAAARRALRSL 1818
Cdd:cd19875      1 KNPVSALNEycqKRGLSLEFVDVSVGPDHCPGFTASATIDGIvfASATGTSKKEAKRAAAKLALKKL 67
Mfd COG1197
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ...
 384-438 3.21e-03

Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];


Pssm-ID: 440810 [Multi-domain]  Cd Length: 1130  Bit Score: 42.36  E-value: 3.21e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2074816191  384 FITGHGigknqprnkQMEAefRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCN 438
Cdd:COG1197    824 IAVAHG---------QMSE--RELERVMLDFYEGEFDVLVCTTIIETGIDIPNAN 867
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 401-459 4.11e-03

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 41.70  E-value: 4.11e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2074816191  401 EAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 459
Cdd:PLN00206   401 EKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRA 459
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
47-127 4.42e-03

Replicative superfamily II helicase [Replication, recombination and repair];


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 41.80  E-value: 4.42e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191   47 EFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLaiLDHPYR----EIM--KLCENCPScPRILGLTASILNgkc 120
Cdd:COG1204    110 WLGRYDILVATPEKLDSLLRNGPSWLRDVDLVVVDEAHL--IDDESRgptlEVLlaRLRRLNPE-AQIVALSATIGN--- 183


                   ....*..
gi 2074816191  121 dPEELEE 127
Cdd:COG1204    184 -AEEIAE 189
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 361-495 6.19e-03

CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 440816 [Multi-domain]  Cd Length: 535  Bit Score: 41.22  E-value: 6.19e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  361 VVLN---------RLIKEAGKqDPELAYISSNFITGHgigknqprnkqmeaefRKQ--EEVLRKFRAHETNLLIATSIVE 429
Cdd:COG1203    371 VIVNtvkdaqelyEALKEKLP-DEEVYLLHSRFCPAD----------------RSEieKEIKERLERGKPCILVSTQVVE 433

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816191  430 EGVDI-----------------------------PKCNLVVrFDLPTEYRSYVQSK---GRARAPISNYIMLADTDKIKS 477
Cdd:COG1203    434 AGVDIdfdvvirdlapldsliqragrcnrhgrkeEEGNVYV-FDPEDEGGGYVYDKpllERTRELLREHDEILPEDKREL 512

                          170
                   ....*....|....*...
gi 2074816191  478 FEEdlkTYKAIEKILRNK 495
Cdd:COG1203    513 IEE---YYRELYELLPDE 527
 
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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