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Conserved domains on  [gi|2074816069|ref|NP_001382620|]
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endoribonuclease Dicer isoform 6 [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 ...
 697-819 3.20e-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: 228.10  E-value: 3.20e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  697 DSSTLDIDFKFMEDIEkSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 776
Cdd:cd02843      1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 2074816069  777 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 819
Cdd:cd02843     80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 183-375 5.56e-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: 5.56e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  183 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 262
Cdd:cd18802      4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  263 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprNKQMEAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKC 342
Cdd:cd18802     36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109

                          170       180       190
                   ....*....|....*....|....*....|...
gi 2074816069  343 NLVVRFDLPTEYRSYVQSKGRARAPISNYIMLA 375
Cdd:cd18802    110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1493-1657 7.63e-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: 7.63e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1493 YLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1572
Cdd:cd00593      2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKY---- 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1573 spelfhviddfvqFQLEKNEMQGMDSElrrseedeekeedieVPKAMGDIFESLAGAIYMDSGMslETVWQVYYPMMRPL 1652
Cdd:cd00593     78 -------------LRLGKGEEKSGGRL---------------RPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPL 127


                   ....*
gi 2074816069 1653 IEKFS 1657
Cdd:cd00593    128 IEEIS 132
DSRM_DICER cd10843
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ...
 1662-1724 2.41e-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: 2.41e-39
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816069 1662 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLK 1724
Cdd:cd10843      1 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGRFKGVGRNYRIAKSAAARRALRSLK 63
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 441-529 2.69e-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: 2.69e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  441 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMSCVRLAERVVALICCEKLHKIGELD 520
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79


                   ....*....
gi 2074816069  521 DHLMPVGKE 529
Cdd:pfam03368   80 DHLLPLTKK 88
RIBOc smart00535
Ribonuclease III family;
1107-1198 2.33e-25

Ribonuclease III family;


:

Pssm-ID: 197778  Cd Length: 129  Bit Score: 102.68  E-value: 2.33e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  1107 LILQALTLSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIF 1185
Cdd:smart00535    2 LLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81

                            90
                    ....*....|...
gi 2074816069  1186 DPPVNWLPPGYVV 1198
Cdd:smart00535   82 EAISGGRDKPKIL 94
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 82-176 4.06e-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: 4.06e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069   82 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 152
Cdd:cd15903      1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                           90       100
                   ....*....|....*....|....
gi 2074816069  153 RKFLLFTDTFLRKIHALCEEHFSP 176
Cdd:cd15903     81 RLFLRYVITQLRKIRKLLEDEMKN 104
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 1-50 5.35e-14

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.


The actual alignment was detected with superfamily member cd18034:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 200  Bit Score: 72.68  E-value: 5.35e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2074816069    1 MKLCENC---PSCPRILGLTASILNGKCDPEELEEKIQKLEKILKSNAETATD 50
Cdd:cd18034    148 MKEFYHLegrTSRPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
 
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 ...
 697-819 3.20e-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: 228.10  E-value: 3.20e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  697 DSSTLDIDFKFMEDIEkSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 776
Cdd:cd02843      1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 2074816069  777 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 819
Cdd:cd02843     80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 183-375 5.56e-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: 5.56e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  183 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 262
Cdd:cd18802      4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  263 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprNKQMEAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKC 342
Cdd:cd18802     36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109

                          170       180       190
                   ....*....|....*....|....*....|...
gi 2074816069  343 NLVVRFDLPTEYRSYVQSKGRARAPISNYIMLA 375
Cdd:cd18802    110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1493-1657 7.63e-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: 7.63e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1493 YLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1572
Cdd:cd00593      2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKY---- 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1573 spelfhviddfvqFQLEKNEMQGMDSElrrseedeekeedieVPKAMGDIFESLAGAIYMDSGMslETVWQVYYPMMRPL 1652
Cdd:cd00593     78 -------------LRLGKGEEKSGGRL---------------RPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPL 127


                   ....*
gi 2074816069 1653 IEKFS 1657
Cdd:cd00593    128 IEEIS 132
DSRM_DICER cd10843
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ...
 1662-1724 2.41e-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: 2.41e-39
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816069 1662 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLK 1724
Cdd:cd10843      1 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGRFKGVGRNYRIAKSAAARRALRSLK 63
RIBOc smart00535
Ribonuclease III family;
1493-1656 5.39e-37

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 136.19  E-value: 5.39e-37
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  1493 YLLQAFTHASYHYNTitDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1572
Cdd:smart00535    2 LLLRALTHASYSNEH--EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEF---- 75

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  1573 spelfhviddfvqFQLEKNEmqgMDSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSGmsLETVWQVYYPMMRPL 1652
Cdd:smart00535   76 -------------IRLGRGE---AISGGRDK------------PKILADVFEALIGAIYLDSG--LEAAREFIRDLLGPR 125


                    ....
gi 2074816069  1653 IEKF 1656
Cdd:smart00535  126 LDEL 129
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1477-1727 1.64e-36

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 138.31  E-value: 1.64e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1477 FENFEKKINYRFKNKAYLLQAFTHASY-HYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTI 1555
Cdd:COG0571      4 LEELEERLGYRFKDPELLEQALTHRSYaNEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEET 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1556 FASLAVKYDyhkyfkavspelfhvIDDFVqfQLEKNEMQgmdSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSG 1635
Cdd:COG0571     84 LAEIARELG---------------LGDYL--RLGKGEEK---SGGRRR------------PSILADAFEALIGAIYLDGG 131

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1636 msLETVWQVYYPMMRPLIEKFSANVPRS-----------------PVRELLEME-PETAK-FspaertydgkvRVTVEVV 1696
Cdd:COG0571    132 --LEAARKFVLRLFEPRLEEIAPGGAGKdyktalqewlqarglplPEYEVVEEEgPDHAKtF-----------TVEVLVG 198

                          250       260       270
                   ....*....|....*....|....*....|.
gi 2074816069 1697 GKGKFKGVGRSYRIAKSAAARRALRSLKANQ 1727
Cdd:COG0571    199 GKVLGEGTGRSKKEAEQAAAKAALEKLGKKE 229
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1480-1723 1.81e-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: 1.81e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1480 FEKKINYRFKNKAYLLQAFTHASYHYNT--ITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFA 1557
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYANEHhkDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1558 SLAVKYDYHKYFKavspelfhviddfvqfqLEKNEMQgmdSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSGMS 1637
Cdd:TIGR02191   81 EVARELGLGDFLL-----------------LGKGEEK---SGGRRR------------DSILADAFEALIGAIYLDSGLE 128

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1638 LETVW--QVYYPMMRPLIEKFSANVPRSPVRELL----------EMEPETAKfsPAERTYdgkvRVTVEVVGKGKFKGVG 1705
Cdd:TIGR02191  129 AARKFilKLLIPRIDAIIKEETLKDYKTALQEWAqargkplpeyRLIKEEGP--DHDKEF----TVEVSVNGEPYGEGKG 202

                          250
                   ....*....|....*...
gi 2074816069 1706 RSYRIAKSAAARRALRSL 1723
Cdd:TIGR02191  203 KSKKEAEQNAAKAALEKL 220
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 441-529 2.69e-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: 2.69e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  441 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMSCVRLAERVVALICCEKLHKIGELD 520
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79


                   ....*....
gi 2074816069  521 DHLMPVGKE 529
Cdd:pfam03368   80 DHLLPLTKK 88
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
 736-876 9.01e-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: 9.01e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069   736 EDYQDAVIIPRYRNfdqpHRFYVADVYTDLTPLSKFPSPEYE--TFAEYYKTKYNLDLTNLNQPLLdVDHTSsrlnlltp 813
Cdd:smart00949   25 KDLKGLIVLTRYNN----KTYRIDDIDWNLAPKSTFEKSDGSeiTFVEYYKQKYNITIRDPNQPLL-VSRPK-------- 91

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816069   814 RHLNQKGKalplssaekrkakweslQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLL 876
Cdd:smart00949   92 RRRNQNGK-----------------GEPVLLPPELCFITGLTDRMRKDFMLMKSIADRTRLSP 137
RIBOc smart00535
Ribonuclease III family;
1107-1198 2.33e-25

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 102.68  E-value: 2.33e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  1107 LILQALTLSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIF 1185
Cdd:smart00535    2 LLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81

                            90
                    ....*....|...
gi 2074816069  1186 DPPVNWLPPGYVV 1198
Cdd:smart00535   82 EAISGGRDKPKIL 94
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 82-176 4.06e-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: 4.06e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069   82 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 152
Cdd:cd15903      1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                           90       100
                   ....*....|....*....|....
gi 2074816069  153 RKFLLFTDTFLRKIHALCEEHFSP 176
Cdd:cd15903     81 RLFLRYVITQLRKIRKLLEDEMKN 104
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1107-1187 5.25e-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: 5.25e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1107 LILQALT---LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVS 1183
Cdd:cd00593      2 LLLEALThpsYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLG 81


                   ....
gi 2074816069 1184 IFDP 1187
Cdd:cd00593     82 KGEE 85
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1513-1635 9.33e-22

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 91.57  E-value: 9.33e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1513 QRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELfhviddfvqfqleKNE 1592
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI-------------RRR 67

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 2074816069 1593 MQGMDSELRRSEEDeekeedievPKAMGDIFESLAGAIYMDSG 1635
Cdd:pfam00636   68 NNALGKGPKRADGK---------EKVLADAFEALIGALYLDGG 101
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
 725-875 5.26e-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: 87.25  E-value: 5.26e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  725 YTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFP--SPEYETFAEYYKTKYNLDLTNLNQPLLDVd 802
Cdd:pfam02170    8 QQQKDRRDFRKEAKKALKGLKVYTTYNNPRTYRIDGITFDPTPESTFPlkDGKEITVVDYFKKKYNIDLKYPDQPLLLV- 86

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816069  803 htssrlnlltprhlnqkgkalplssaeKRKakweslQNKQILVPELCAihpIPASLWRKAVCLPSILYRLHCL 875
Cdd:pfam02170   87 ---------------------------GKK------RPKVYLPPELCN---LVDGQRYTKKLMPSIAQRTRLL 123
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1124-1187 2.41e-15

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 73.08  E-value: 2.41e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2074816069 1124 ERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIFDP 1187
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI 64
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 312-364 1.37e-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: 1.37e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2074816069  312 QEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 364
Cdd:pfam00271   53 REEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 1-50 5.35e-14

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: 72.68  E-value: 5.35e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2074816069    1 MKLCENC---PSCPRILGLTASILNGKCDPEELEEKIQKLEKILKSNAETATD 50
Cdd:cd18034    148 MKEFYHLegrTSRPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
256-363 9.19e-14

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 76.69  E-value: 9.19e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  256 IIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGHGIGKNQPRNKQmeaefRKQEEVLRKFRAHETNLLIATSIVEE 335
Cdd:COG1111    357 IVFTQYRDTAEMIVEFLSEPG--------IKAGRFVGQASKEGDKGLTQ-----KEQIEILERFRAGEFNVLVATSVAEE 423

                           90       100
                   ....*....|....*....|....*....
gi 2074816069  336 GVDIPKCNLVVRFDL-PTEYRSyVQSKGR 363
Cdd:COG1111    424 GLDIPEVDLVIFYEPvPSEIRS-IQRKGR 451
HELICc smart00490
helicase superfamily c-terminal domain;
310-364 1.12e-12

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 64.93  E-value: 1.12e-12
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 2074816069   310 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 364
Cdd:smart00490   24 EEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
PRK13766 PRK13766
Hef nuclease; Provisional
 310-364 1.52e-11

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 69.52  E-value: 1.52e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2074816069  310 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFD-LPTEYRSyVQSKGRA 364
Cdd:PRK13766   410 KEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEpVPSEIRS-IQRKGRT 464
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1103-1178 1.90e-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: 1.90e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1103 PNPGLILQALT-----LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLP 1177
Cdd:TIGR02191   10 KNPELLEQALThrsyaNEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVARELGLG 89


                   .
gi 2074816069 1178 S 1178
Cdd:TIGR02191   90 D 90
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1094-1176 8.21e-11

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 63.96  E-value: 8.21e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1094 IGYSSRtlgpNPGLILQALT---LSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYR 1169
Cdd:COG0571     11 LGYRFK----DPELLEQALThrsYANEHGGLeNNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAE 86


                   ....*..
gi 2074816069 1170 LGKKKGL 1176
Cdd:COG0571     87 IARELGL 93
DSRM smart00358
Double-stranded RNA binding motif;
1661-1724 4.87e-08

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 51.49  E-value: 4.87e-08
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2074816069  1661 PRSPVRELLEMEPETAKFSPAERT-YDGKVRVTVEVVGKGK--FKGVGRSYRIAKSAAARRALRSLK 1724
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEEgPDHAPRFTVTVKVGGKrtGEGEGSSKKEAKQRAAEAALRSLK 67
 
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 ...
 697-819 3.20e-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: 228.10  E-value: 3.20e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  697 DSSTLDIDFKFMEDIEkSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 776
Cdd:cd02843      1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 2074816069  777 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 819
Cdd:cd02843     80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 183-375 5.56e-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: 5.56e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  183 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 262
Cdd:cd18802      4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  263 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprNKQMEAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKC 342
Cdd:cd18802     36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109

                          170       180       190
                   ....*....|....*....|....*....|...
gi 2074816069  343 NLVVRFDLPTEYRSYVQSKGRARAPISNYIMLA 375
Cdd:cd18802    110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1493-1657 7.63e-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: 7.63e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1493 YLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1572
Cdd:cd00593      2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKY---- 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1573 spelfhviddfvqFQLEKNEMQGMDSElrrseedeekeedieVPKAMGDIFESLAGAIYMDSGMslETVWQVYYPMMRPL 1652
Cdd:cd00593     78 -------------LRLGKGEEKSGGRL---------------RPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPL 127


                   ....*
gi 2074816069 1653 IEKFS 1657
Cdd:cd00593    128 IEEIS 132
DSRM_DICER cd10843
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ...
 1662-1724 2.41e-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: 2.41e-39
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816069 1662 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLK 1724
Cdd:cd10843      1 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGRFKGVGRNYRIAKSAAARRALRSLK 63
RIBOc smart00535
Ribonuclease III family;
1493-1656 5.39e-37

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 136.19  E-value: 5.39e-37
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  1493 YLLQAFTHASYHYNTitDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1572
Cdd:smart00535    2 LLLRALTHASYSNEH--EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEF---- 75

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  1573 spelfhviddfvqFQLEKNEmqgMDSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSGmsLETVWQVYYPMMRPL 1652
Cdd:smart00535   76 -------------IRLGRGE---AISGGRDK------------PKILADVFEALIGAIYLDSG--LEAAREFIRDLLGPR 125


                    ....
gi 2074816069  1653 IEKF 1656
Cdd:smart00535  126 LDEL 129
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1477-1727 1.64e-36

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 138.31  E-value: 1.64e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1477 FENFEKKINYRFKNKAYLLQAFTHASY-HYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTI 1555
Cdd:COG0571      4 LEELEERLGYRFKDPELLEQALTHRSYaNEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEET 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1556 FASLAVKYDyhkyfkavspelfhvIDDFVqfQLEKNEMQgmdSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSG 1635
Cdd:COG0571     84 LAEIARELG---------------LGDYL--RLGKGEEK---SGGRRR------------PSILADAFEALIGAIYLDGG 131

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1636 msLETVWQVYYPMMRPLIEKFSANVPRS-----------------PVRELLEME-PETAK-FspaertydgkvRVTVEVV 1696
Cdd:COG0571    132 --LEAARKFVLRLFEPRLEEIAPGGAGKdyktalqewlqarglplPEYEVVEEEgPDHAKtF-----------TVEVLVG 198

                          250       260       270
                   ....*....|....*....|....*....|.
gi 2074816069 1697 GKGKFKGVGRSYRIAKSAAARRALRSLKANQ 1727
Cdd:COG0571    199 GKVLGEGTGRSKKEAEQAAAKAALEKLGKKE 229
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1480-1723 1.81e-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: 1.81e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1480 FEKKINYRFKNKAYLLQAFTHASYHYNT--ITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFA 1557
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYANEHhkDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1558 SLAVKYDYHKYFKavspelfhviddfvqfqLEKNEMQgmdSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSGMS 1637
Cdd:TIGR02191   81 EVARELGLGDFLL-----------------LGKGEEK---SGGRRR------------DSILADAFEALIGAIYLDSGLE 128

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1638 LETVW--QVYYPMMRPLIEKFSANVPRSPVRELL----------EMEPETAKfsPAERTYdgkvRVTVEVVGKGKFKGVG 1705
Cdd:TIGR02191  129 AARKFilKLLIPRIDAIIKEETLKDYKTALQEWAqargkplpeyRLIKEEGP--DHDKEF----TVEVSVNGEPYGEGKG 202

                          250
                   ....*....|....*...
gi 2074816069 1706 RSYRIAKSAAARRALRSL 1723
Cdd:TIGR02191  203 KSKKEAEQNAAKAALEKL 220
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 441-529 2.69e-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: 2.69e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  441 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMSCVRLAERVVALICCEKLHKIGELD 520
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79


                   ....*....
gi 2074816069  521 DHLMPVGKE 529
Cdd:pfam03368   80 DHLLPLTKK 88
PAZ cd02825
PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two ...
 697-819 2.29e-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: 119.49  E-value: 2.29e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  697 DSSTLDIDFKFMEDIEKSEARIGIPSTKYTKETPfVFKLEDYQDaviipryrnfdQPHRFYVADVYTDLTPLS--KFPSP 774
Cdd:cd02825      1 ADPVIETMCKFPKDREIDTPLLDSPREEFTKELK-GLKVEDTHN-----------PLNRVYRPDGETRLKAPSqlKHSDG 68

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2074816069  775 EYETFAEYYKTKYNLDLTNLNQPLLDVDHTS--SRLNLLTPRHLNQK 819
Cdd:cd02825     69 KEITFADYFKERYNLTLTDLNQPLLIVKFSSkkSYSILLPPELCVIT 115
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
 736-876 9.01e-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: 9.01e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069   736 EDYQDAVIIPRYRNfdqpHRFYVADVYTDLTPLSKFPSPEYE--TFAEYYKTKYNLDLTNLNQPLLdVDHTSsrlnlltp 813
Cdd:smart00949   25 KDLKGLIVLTRYNN----KTYRIDDIDWNLAPKSTFEKSDGSeiTFVEYYKQKYNITIRDPNQPLL-VSRPK-------- 91

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816069   814 RHLNQKGKalplssaekrkakweslQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLL 876
Cdd:smart00949   92 RRRNQNGK-----------------GEPVLLPPELCFITGLTDRMRKDFMLMKSIADRTRLSP 137
RIBOc smart00535
Ribonuclease III family;
1107-1198 2.33e-25

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 102.68  E-value: 2.33e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  1107 LILQALTLSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIF 1185
Cdd:smart00535    2 LLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81

                            90
                    ....*....|...
gi 2074816069  1186 DPPVNWLPPGYVV 1198
Cdd:smart00535   82 EAISGGRDKPKIL 94
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 82-176 4.06e-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: 4.06e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069   82 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 152
Cdd:cd15903      1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                           90       100
                   ....*....|....*....|....
gi 2074816069  153 RKFLLFTDTFLRKIHALCEEHFSP 176
Cdd:cd15903     81 RLFLRYVITQLRKIRKLLEDEMKN 104
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1107-1187 5.25e-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: 5.25e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1107 LILQALT---LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVS 1183
Cdd:cd00593      2 LLLEALThpsYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLG 81


                   ....
gi 2074816069 1184 IFDP 1187
Cdd:cd00593     82 KGEE 85
helicase_insert_domain cd12088
helicase_insert_domain; helicase_insert_domain; This helical domain can be found inserted in a ...
 82-173 2.73e-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: 92.53  E-value: 2.73e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069   82 LMELEEALNFINDCNIsvhskerDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHeqeELHRKFLLFTDT 161
Cdd:cd12088      1 KMILSQLLRDTESLLK-------LLYTAHLRKLNDALELLEDAGIWDALKYIKMFFTEVREGIFD---ELERKLTLRFDE 70

                           90
                   ....*....|..
gi 2074816069  162 FLRKIHALCEEH 173
Cdd:cd12088     71 KLQKLIALSRDP 82
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1513-1635 9.33e-22

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 91.57  E-value: 9.33e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1513 QRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELfhviddfvqfqleKNE 1592
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI-------------RRR 67

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 2074816069 1593 MQGMDSELRRSEEDeekeedievPKAMGDIFESLAGAIYMDSG 1635
Cdd:pfam00636   68 NNALGKGPKRADGK---------EKVLADAFEALIGALYLDGG 101
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
 725-875 5.26e-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: 87.25  E-value: 5.26e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  725 YTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFP--SPEYETFAEYYKTKYNLDLTNLNQPLLDVd 802
Cdd:pfam02170    8 QQQKDRRDFRKEAKKALKGLKVYTTYNNPRTYRIDGITFDPTPESTFPlkDGKEITVVDYFKKKYNIDLKYPDQPLLLV- 86

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816069  803 htssrlnlltprhlnqkgkalplssaeKRKakweslQNKQILVPELCAihpIPASLWRKAVCLPSILYRLHCL 875
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 ...
 1494-1636 1.47e-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: 1.47e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1494 LLQAFTHASYHYNTiTDCYQRLEFLGDAILDYLITKHLYEDPRQhSPGVLTDLRSALVNNTIFASLAvkydyhkyfkavs 1573
Cdd:pfam14622    4 LLQALTHKSYANGR-KPYNERLEFLGDAVLELSVSEYLFKKPDL-DEGGLTKLRASIVSEESLAEIA------------- 68

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816069 1574 pelfhviddfVQFQLEKNEMQGMDSELRRSeedeekeedIEVPKAMGDIFESLAGAIYMDSGM 1636
Cdd:pfam14622   69 ----------REIGLGKYLRLGKGEEETGG---------SGRESILADALEALIGAIYLDGGF 112
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1124-1187 2.41e-15

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 73.08  E-value: 2.41e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2074816069 1124 ERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIFDP 1187
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 ...
 733-855 6.37e-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: 6.37e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  733 FKLEDYQDAVIIpryrnfdQPH--RFYVADVYTDLTPLSKFP---SPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSR 807
Cdd:cd02844     26 FCACDLKGSVVT-------APHngRFYVISGILDLNANSSFPgkeGLGYATYAEYFKEKYGIVLNHPNQPLLKGKQIFNL 98

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 2074816069  808 LNLLTPRhLNQKGkalplSSAEKRKakwesLQNKQILVPELCAIHPIP 855
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, ...
 312-364 1.37e-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: 1.37e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2074816069  312 QEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 364
Cdd:pfam00271   53 REEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 1-50 5.35e-14

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: 72.68  E-value: 5.35e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2074816069    1 MKLCENC---PSCPRILGLTASILNGKCDPEELEEKIQKLEKILKSNAETATD 50
Cdd:cd18034    148 MKEFYHLegrTSRPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
256-363 9.19e-14

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 76.69  E-value: 9.19e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  256 IIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGHGIGKNQPRNKQmeaefRKQEEVLRKFRAHETNLLIATSIVEE 335
Cdd:COG1111    357 IVFTQYRDTAEMIVEFLSEPG--------IKAGRFVGQASKEGDKGLTQ-----KEQIEILERFRAGEFNVLVATSVAEE 423

                           90       100
                   ....*....|....*....|....*....
gi 2074816069  336 GVDIPKCNLVVRFDL-PTEYRSyVQSKGR 363
Cdd:COG1111    424 GLDIPEVDLVIFYEPvPSEIRS-IQRKGR 451
HELICc smart00490
helicase superfamily c-terminal domain;
310-364 1.12e-12

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 64.93  E-value: 1.12e-12
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 2074816069   310 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 364
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 ...
 256-364 1.11e-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: 1.11e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  256 IIFVERRYTAvvlNRLIKEAGKQDPELAyiSSNFItGHGIGKNQPRNKQMEaefrkQEEVLRKFRAHETNLLIATSIVEE 335
Cdd:cd18801     34 IIFSEFRDSA---EEIVNFLSKIRPGIR--ATRFI-GQASGKSSKGMSQKE-----QKEVIEQFRKGGYNVLVATSIGEE 102

                           90       100       110
                   ....*....|....*....|....*....|
gi 2074816069  336 GVDIPKCNLVVRFD-LPTEYRSyVQSKGRA 364
Cdd:cd18801    103 GLDIGEVDLIICYDaSPSPIRM-IQRMGRT 131
PRK13766 PRK13766
Hef nuclease; Provisional
 310-364 1.52e-11

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 69.52  E-value: 1.52e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2074816069  310 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFD-LPTEYRSyVQSKGRA 364
Cdd:PRK13766   410 KEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEpVPSEIRS-IQRKGRT 464
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1103-1178 1.90e-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: 1.90e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1103 PNPGLILQALT-----LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLP 1177
Cdd:TIGR02191   10 KNPELLEQALThrsyaNEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVARELGLG 89


                   .
gi 2074816069 1178 S 1178
Cdd:TIGR02191   90 D 90
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 256-366 2.54e-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: 2.54e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  256 IIFVERRYTAVVLNRLIKEAGkqdpelayISSNFItgHGiGKNQprnkqmeaefRKQEEVLRKFRAHETNLLIATSIVEE 335
Cdd:cd18787     31 IIFVNTKKRVDRLAELLEELG--------IKVAAL--HG-DLSQ----------EERERALKKFRSGKVRVLVATDVAAR 89

                           90       100       110
                   ....*....|....*....|....*....|..
gi 2074816069  336 GVDIPKCNLVVRFDLPTEYRSYVQSKGR-ARA 366
Cdd:cd18787     90 GLDIPGVDHVINYDLPRDAEDYVHRIGRtGRA 121
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1094-1176 8.21e-11

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 63.96  E-value: 8.21e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069 1094 IGYSSRtlgpNPGLILQALT---LSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYR 1169
Cdd:COG0571     11 LGYRFK----DPELLEQALThrsYANEHGGLeNNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAE 86


                   ....*..
gi 2074816069 1170 LGKKKGL 1176
Cdd:COG0571     87 IARELGL 93
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 1-49 8.43e-09

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: 57.44  E-value: 8.43e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2074816069    1 MKLCENCPS-----CPRILGLTASILNGKC-DPEELEEKIQKLEKILKSNAETAT 49
Cdd:cd17927    147 MFRYLDQKLgssgpLPQILGLTASPGVGGAkNTEEALEHICKLCANLDISVIATV 201
PAZ_piwi_like cd02845
PAZ domain, Piwi_like subfamily. In multi-cellular organisms, the Piwi protein appears to be ...
 739-849 1.63e-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: 54.19  E-value: 1.63e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  739 QDAVIIPRYRNfdqphRFY-VADVYTDLTPLSKFPSPEYE--TFAEYYKTKYNLDLTNLNQPLLdvdhtssrlnlltprh 815
Cdd:cd02845     29 IGSIVLTRYNN-----KTYrIDDIDFDKTPLSTFKKSDGTeiTFVEYYKKQYNIEITDLNQPLL---------------- 87

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 2074816069  816 lnqkgkalpLSSAEKRKAKweSLQNKQI-LVPELC 849
Cdd:cd02845     88 ---------VSRPKRRDPR--GGEKEPIyLIPELC 111
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 1105-1180 3.98e-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: 3.98e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2074816069 1105 PGLILQALT---LSNASDGFNlERLEMLGDSFLKHAITTYLFcTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRM 1180
Cdd:pfam14622    1 EELLLQALThksYANGRKPYN-ERLEFLGDAVLELSVSEYLF-KKPDLDEGGLTKLRASIVSEESLAEIAREIGLGKYL 77
DSRM smart00358
Double-stranded RNA binding motif;
1661-1724 4.87e-08

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 51.49  E-value: 4.87e-08
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2074816069  1661 PRSPVRELLEMEPETAKFSPAERT-YDGKVRVTVEVVGKGK--FKGVGRSYRIAKSAAARRALRSLK 1724
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEEgPDHAPRFTVTVKVGGKrtGEGEGSSKKEAKQRAAEAALRSLK 67
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 323-364 6.01e-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: 6.01e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 2074816069  323 ETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 364
Cdd:cd18785     22 SLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRA 63
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
255-400 6.35e-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: 6.35e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  255 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFItgHGiGKNQprnkqmeaefRKQEEVLRKFRAHETNLLIATSIVE 334
Cdd:COG0513    244 AIVFCNTKRGADRLAEKLQKRG--------ISAAAL--HG-DLSQ----------GQRERALDAFRNGKIRVLVATDVAA 302

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2074816069  335 EGVDIPKCNLVVRFDLPTEYRSYV---------QSKGRArapisnyIMLADtdkiksfEEDLKTYKAIEKILRNK 400
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 ...
 304-395 9.46e-07

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: 9.46e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  304 QMEAEfrKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVV-----RFDLPTEYrsyvQSKGR-ARAPISNYIMLADT 377
Cdd:cd18792     69 KMTED--EKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIiedadRFGLSQLH----QLRGRvGRGKHQSYCYLLYP 142

                           90
                   ....*....|....*...
gi 2074816069  378 DKIKSFEEDLKTYKAIEK 395
Cdd:cd18792    143 DPKKLTETAKKRLRAIAE 160
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
255-364 1.46e-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: 1.46e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  255 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGhgigknqprnkQMEAEFRkqEEVLRKFRAHETNLLIATSIVE 334
Cdd:COG1061    308 TLVFCSSVDHAEALAELLNEAG--------IRAAVVTG-----------DTPKKER--EEILEAFRDGELRILVTVDVLN 366

                           90       100       110
                   ....*....|....*....|....*....|...
gi 2074816069  335 EGVDIPKCNLVV--RfdlPTEYRS-YVQSKGRA 364
Cdd:COG1061    367 EGVDVPRLDVAIllR---PTGSPReFIQRLGRG 396
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 255-364 2.84e-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: 2.84e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  255 GIIFVERRYTAVVLNRLIKEAGkqdPELAYISSNFItghgigknqprnkqmeAEFRKQEEVLR-KFRAHETNLLIATSIV 333
Cdd:cd18799      9 TLIFCVSIEHAEFMAEAFNEAG---IDAVALNSDYS----------------DRERGDEALILlFFGELKPPILVTVDLL 69

                           90       100       110
                   ....*....|....*....|....*....|..
gi 2074816069  334 EEGVDIPKCNLVVrFDLPTEYRS-YVQSKGRA 364
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 ...
 271-382 2.98e-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: 2.98e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  271 LIKEAGKQDPELA-----YISSNFITGHGIGKNQPRNKQMEaefrkQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLV 345
Cdd:cd18811     35 LIEESEKLDLKAAvamyeYLKERFRPELNVGLLHGRLKSDE-----KDAVMAEFREGEVDILVSTTVIEVGVDVPNATVM 109

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 2074816069  346 V-----RFDLPTEYrsyvQSKGR-ARAPISNYIMLADTDKIKS 382
Cdd:cd18811    110 ViedaeRFGLSQLH----QLRGRvGRGDHQSYCLLVYKDPLTE 148
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 255-405 4.06e-05

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 48.01  E-value: 4.06e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  255 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGhgigknqprnkqmEAEFRKQEEVLRKFRAHETNLLIATSIVE 334
Cdd:PRK11192   248 SIVFVRTRERVHELAGWLRKAG--------INCCYLEG-------------EMVQAKRNEAIKRLTDGRVNVLVATDVAA 306

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  335 EGVDIPKCNLVVRFDLPTEYRSYVQSKGR-ARA-----PIS-----NYIMLadtDKIKSF-EEDLK---------TYKAI 393
Cdd:PRK11192   307 RGIDIDDVSHVINFDMPRSADTYLHRIGRtGRAgrkgtAISlveahDHLLL---GKIERYiEEPLKarvidelrpKTKAP 383

                          170
                   ....*....|..
gi 2074816069  394 EKILRNKCSKSV 405
Cdd:PRK11192   384 SEKKTGKPSKKV 395
PTZ00424 PTZ00424
helicase 45; Provisional
 310-389 4.90e-05

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 47.90  E-value: 4.90e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  310 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA----RAPIS-NYIMLADTDKIKSFE 384
Cdd:PTZ00424   304 KDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSgrfgRKGVAiNFVTPDDIEQLKEIE 383


                   ....*
gi 2074816069  385 EDLKT 389
Cdd:PTZ00424   384 RHYNT 388
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
 313-350 6.51e-05

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 47.84  E-value: 6.51e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 2074816069  313 EEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVV-----RFDL 350
Cdd:PRK10917   521 DAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVienaeRFGL 563
PTZ00110 PTZ00110
helicase; Provisional
 310-388 3.96e-04

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 45.15  E-value: 3.96e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  310 RKQEE---VLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQ---SKGRARAPISNYIMLAdTDKIKSF 383
Cdd:PTZ00110   411 KKQEErtwVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHrigRTGRAGAKGASYTFLT-PDKYRLA 489


                   ....*
gi 2074816069  384 EEDLK 388
Cdd:PTZ00110   490 RDLVK 494
RecG COG1200
RecG-like helicase [Replication, recombination and repair];
313-340 4.03e-04

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


Pssm-ID: 440813 [Multi-domain]  Cd Length: 684  Bit Score: 45.04  E-value: 4.03e-04
                           10        20
                   ....*....|....*....|....*...
gi 2074816069  313 EEVLRKFRAHETNLLIATSIVEEGVDIP 340
Cdd:COG1200    519 DAVMAAFKAGEIDVLVATTVIEVGVDVP 546
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 314-394 4.69e-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: 4.69e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  314 EVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTE-----YRSYVQSKGRA-RAPISNYIMLAD--TDKIKsfee 385
Cdd:cd18790     68 EIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEgflrsETSLIQTIGRAaRNVNGKVILYADkiTDSMQ---- 143


                   ....*....
gi 2074816069  386 dlktyKAIE 394
Cdd:cd18790    144 -----KAIE 147
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 302-363 5.29e-04

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 44.84  E-value: 5.29e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2074816069  302 NKQMEAEFRkqEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGR 363
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 ...
 1691-1723 9.44e-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: 9.44e-04
                           10        20        30
                   ....*....|....*....|....*....|...
gi 2074816069 1691 VTVEVVGKgKFKGVGRSYRIAKSAAARRALRSL 1723
Cdd:cd19865     32 MSVEVNGQ-TFEGTGRSKKKAKLEAAEKALRSF 63
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 304-395 9.46e-04

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: 9.46e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  304 QMEAEfrKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVV-----RFDLPTEYrsyvQSKGR-ARAPISNYIMLADT 377
Cdd:cd18810     60 QMTEN--ELEEVMLEFAKGEYDILVCTTIIESGIDIPNANTIIieradKFGLAQLY----QLRGRvGRSKERAYAYFLYP 133

                           90
                   ....*....|....*...
gi 2074816069  378 DKIKSFEEDLKTYKAIEK 395
Cdd:cd18810    134 DQKKLTEDALKRLEAIQE 151
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 1662-1723 1.61e-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: 1.61e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2074816069 1662 RSPVRELLE---MEPETAKFSPAERTYDGKVRVTVEVVGKGK--FKGVGRSYRIAKSAAARRALRSL 1723
Cdd:cd19875      1 KNPVSALNEycqKRGLSLEFVDVSVGPDHCPGFTASATIDGIvfASATGTSKKEAKRAAAKLALKKL 67
Mfd COG1197
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ...
 289-343 3.03e-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: 3.03e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2074816069  289 FITGHGigknqprnkQMEAefRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCN 343
Cdd:COG1197    824 IAVAHG---------QMSE--RELERVMLDFYEGEFDVLVCTTIIETGIDIPNAN 867
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 306-364 4.05e-03

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 41.70  E-value: 4.05e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2074816069  306 EAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 364
Cdd:PLN00206   401 EKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRA 459
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 266-400 5.36e-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: 41.61  E-value: 5.36e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  266 VVLN---------RLIKEAGKqDPELAYISSNFITGHgigknqprnkqmeaefRKQ--EEVLRKFRAHETNLLIATSIVE 334
Cdd:COG1203    371 VIVNtvkdaqelyEALKEKLP-DEEVYLLHSRFCPAD----------------RSEieKEIKERLERGKPCILVSTQVVE 433

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816069  335 EGVDI-----------------------------PKCNLVVrFDLPTEYRSYVQSK---GRARAPISNYIMLADTDKIKS 382
Cdd:COG1203    434 AGVDIdfdvvirdlapldsliqragrcnrhgrkeEEGNVYV-FDPEDEGGGYVYDKpllERTRELLREHDEILPEDKREL 512

                          170
                   ....*....|....*...
gi 2074816069  383 FEEdlkTYKAIEKILRNK 400
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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