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Conserved domains on  [gi|618468591|ref|NP_001278557|]
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endoribonuclease Dicer isoform 1 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
42-239 1.07e-99

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: 318.83  E-value: 1.07e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   42 YTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELSYQIRGdFSRNGKRTVFLVNSANQVAQQVSAVRTHSDLKV 121
Cdd:cd18034     1 FTPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRK-EKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  122 GEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENC---PS 198
Cdd:cd18034    80 GEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLegrTS 159
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 618468591  199 CPRILGLTASILNGKCDPEELEEKIQKLEKILKSNAETATD 239
Cdd:cd18034   160 RPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
886-1008 2.19e-69

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


:

Pssm-ID: 239209  Cd Length: 122  Bit Score: 228.48  E-value: 2.19e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  886 DSSTLDIDFKFMEDIEkSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 965
Cdd:cd02843     1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 618468591  966 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 1008
Cdd:cd02843    80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
372-564 6.08e-56

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


:

Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 190.88  E-value: 6.08e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  372 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 451
Cdd:cd18802     4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  452 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprNKQMEAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKC 531
Cdd:cd18802    36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109
                         170       180       190
                  ....*....|....*....|....*....|...
gi 618468591  532 NLVVRFDLPTEYRSYVQSKGRARAPISNYIMLA 564
Cdd:cd18802   110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
1682-1846 9.83e-40

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


:

Pssm-ID: 238333  Cd Length: 133  Bit Score: 144.29  E-value: 9.83e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591 1682 YLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1761
Cdd:cd00593     2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKY---- 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591 1762 spelfhviddfvqFQLEKNEMQGMDSElrrseedeekeedieVPKAMGDIFESLAGAIYMDSGMslETVWQVYYPMMRPL 1841
Cdd:cd00593    78 -------------LRLGKGEEKSGGRL---------------RPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPL 127

                  ....*
gi 618468591 1842 IEKFS 1846
Cdd:cd00593   128 IEEIS 132
DSRM_DICER cd10843
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ...
1851-1913 2.67e-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: 2.67e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 618468591 1851 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLK 1913
Cdd:cd10843     1 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGRFKGVGRNYRIAKSAAARRALRSLK 63
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
630-718 2.61e-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: 121.45  E-value: 2.61e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   630 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMSCVRLAERVVALICCEKLHKIGELD 709
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79

                   ....*....
gi 618468591   710 DHLMPVGKE 718
Cdd:pfam03368   80 DHLLPLTKK 88
RIBOc smart00535
Ribonuclease III family;
1296-1387 2.78e-25

Ribonuclease III family;


:

Pssm-ID: 197778  Cd Length: 129  Bit Score: 102.68  E-value: 2.78e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   1296 LILQALTLSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIF 1374
Cdd:smart00535    2 LLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81
                            90
                    ....*....|...
gi 618468591   1375 DPPVNWLPPGYVV 1387
Cdd:smart00535   82 EAISGGRDKPKIL 94
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
271-365 4.38e-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: 4.38e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  271 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 341
Cdd:cd15903     1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80
                          90       100
                  ....*....|....*....|....
gi 618468591  342 RKFLLFTDTFLRKIHALCEEHFSP 365
Cdd:cd15903    81 RLFLRYVITQLRKIRKLLEDEMKN 104
 
Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
42-239 1.07e-99

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: 318.83  E-value: 1.07e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   42 YTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELSYQIRGdFSRNGKRTVFLVNSANQVAQQVSAVRTHSDLKV 121
Cdd:cd18034     1 FTPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRK-EKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  122 GEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENC---PS 198
Cdd:cd18034    80 GEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLegrTS 159
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 618468591  199 CPRILGLTASILNGKCDPEELEEKIQKLEKILKSNAETATD 239
Cdd:cd18034   160 RPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
886-1008 2.19e-69

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


Pssm-ID: 239209  Cd Length: 122  Bit Score: 228.48  E-value: 2.19e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  886 DSSTLDIDFKFMEDIEkSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 965
Cdd:cd02843     1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 618468591  966 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 1008
Cdd:cd02843    80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
372-564 6.08e-56

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


Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 190.88  E-value: 6.08e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  372 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 451
Cdd:cd18802     4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  452 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprNKQMEAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKC 531
Cdd:cd18802    36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109
                         170       180       190
                  ....*....|....*....|....*....|...
gi 618468591  532 NLVVRFDLPTEYRSYVQSKGRARAPISNYIMLA 564
Cdd:cd18802   110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
1682-1846 9.83e-40

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


Pssm-ID: 238333  Cd Length: 133  Bit Score: 144.29  E-value: 9.83e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591 1682 YLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1761
Cdd:cd00593     2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKY---- 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591 1762 spelfhviddfvqFQLEKNEMQGMDSElrrseedeekeedieVPKAMGDIFESLAGAIYMDSGMslETVWQVYYPMMRPL 1841
Cdd:cd00593    78 -------------LRLGKGEEKSGGRL---------------RPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPL 127

                  ....*
gi 618468591 1842 IEKFS 1846
Cdd:cd00593   128 IEEIS 132
DSRM_DICER cd10843
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ...
1851-1913 2.67e-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: 2.67e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 618468591 1851 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLK 1913
Cdd:cd10843     1 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGRFKGVGRNYRIAKSAAARRALRSLK 63
RIBOc smart00535
Ribonuclease III family;
1682-1845 6.61e-37

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 135.81  E-value: 6.61e-37
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   1682 YLLQAFTHASYHYNTitDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1761
Cdd:smart00535    2 LLLRALTHASYSNEH--EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEF---- 75
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   1762 spelfhviddfvqFQLEKNEmqgMDSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSGmsLETVWQVYYPMMRPL 1841
Cdd:smart00535   76 -------------IRLGRGE---AISGGRDK------------PKILADVFEALIGAIYLDSG--LEAAREFIRDLLGPR 125

                    ....
gi 618468591   1842 IEKF 1845
Cdd:smart00535  126 LDEL 129
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1666-1916 1.84e-36

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 138.31  E-value: 1.84e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591 1666 FENFEKKINYRFKNKAYLLQAFTHASY-HYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTI 1744
Cdd:COG0571     4 LEELEERLGYRFKDPELLEQALTHRSYaNEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEET 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591 1745 FASLAVKYDyhkyfkavspelfhvIDDFVqfQLEKNEMQgmdSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSG 1824
Cdd:COG0571    84 LAEIARELG---------------LGDYL--RLGKGEEK---SGGRRR------------PSILADAFEALIGAIYLDGG 131
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591 1825 msLETVWQVYYPMMRPLIEKFSANVPRS-----------------PVRELLEME-PETAK-FspaertydgkvRVTVEVV 1885
Cdd:COG0571   132 --LEAARKFVLRLFEPRLEEIAPGGAGKdyktalqewlqarglplPEYEVVEEEgPDHAKtF-----------TVEVLVG 198
                         250       260       270
                  ....*....|....*....|....*....|.
gi 618468591 1886 GKGKFKGVGRSYRIAKSAAARRALRSLKANQ 1916
Cdd:COG0571   199 GKVLGEGTGRSKKEAEQAAAKAALEKLGKKE 229
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
1669-1912 2.11e-36

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 138.11  E-value: 2.11e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  1669 FEKKINYRFKNKAYLLQAFTHASYHYNT--ITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFA 1746
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYANEHhkDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  1747 SLAVKYDYHKYFKavspelfhviddfvqfqLEKNEMQgmdSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSGMS 1826
Cdd:TIGR02191   81 EVARELGLGDFLL-----------------LGKGEEK---SGGRRR------------DSILADAFEALIGAIYLDSGLE 128
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  1827 LETVW--QVYYPMMRPLIEKFSANVPRSPVRELL----------EMEPETAKfsPAERTYdgkvRVTVEVVGKGKFKGVG 1894
Cdd:TIGR02191  129 AARKFilKLLIPRIDAIIKEETLKDYKTALQEWAqargkplpeyRLIKEEGP--DHDKEF----TVEVSVNGEPYGEGKG 202
                          250
                   ....*....|....*...
gi 618468591  1895 RSYRIAKSAAARRALRSL 1912
Cdd:TIGR02191  203 KSKKEAEQNAAKAALEKL 220
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
44-552 3.12e-34

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 142.56  E-value: 3.12e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   44 PRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELsyqirgdFSRNGKRTVFLVNS---ANQVAQQVSAVRTHSDLK 120
Cdd:COG1111     4 RRLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAER-------LHKKGGKVLFLAPTkplVEQHAEFFKEALNIPEDE 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  121 VGEYSNlEVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCP 200
Cdd:COG1111    77 IVVFTG-EVSPEKRKELWE----KARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKDP 151
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  201 RILGLTASilngkcdPEELEEKIQKLEKILK-SNAETATDlvvldrytSQPceivvDCGPFT-DRSGLYERLLM--ELEE 276
Cdd:COG1111   152 LILGMTAS-------PGSDEEKIEEVCENLGiENVEVRTE--------EDP-----DVAPYVhDTEVEWIRVELpeELKE 211
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  277 ALNFIN-----------DCNISVHSKERDST--------LISKQILSDCRAVLVVLGPwcadkVAGMM------------ 325
Cdd:COG1111   212 IRDLLNevlddrlkklkELGVIVSTSPDLSKkdllalqkKLQRRIREDDSEGYRAISI-----LAEALklrhalelletq 286
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  326 -VRELQKYIKhEQEELHRKFL-------LFTDTFLRKIHALCE----EHfspasldlkfvtPKVIKLLEILRKYKpyerq 393
Cdd:COG1111   287 gVEALLRYLE-RLEEEARSSGgskaskrLVSDPRFRKAMRLAEeadiEH------------PKLSKLREILKEQL----- 348
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  394 qfesvewynNRNQDNYVswsdsedddedeeieekekpetnfpspftnilcgIIFVERRYTAVVLNRLIKEAGkqdpelay 473
Cdd:COG1111   349 ---------GTNPDSRI----------------------------------IVFTQYRDTAEMIVEFLSEPG-------- 377
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  474 ISSNFITGHGIGKNQPRNKQmeaefRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDL-PTEYRSyVQSKGR 552
Cdd:COG1111   378 IKAGRFVGQASKEGDKGLTQ-----KEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPvPSEIRS-IQRKGR 451
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
630-718 2.61e-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: 121.45  E-value: 2.61e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   630 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMSCVRLAERVVALICCEKLHKIGELD 709
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79

                   ....*....
gi 618468591   710 DHLMPVGKE 718
Cdd:pfam03368   80 DHLLPLTKK 88
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
925-1065 7.66e-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: 110.45  E-value: 7.66e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591    925 EDYQDAVIIPRYRNfdqpHRFYVADVYTDLTPLSKFPSPEYE--TFAEYYKTKYNLDLTNLNQPLLdVDHTSsrlnlltp 1002
Cdd:smart00949   25 KDLKGLIVLTRYNN----KTYRIDDIDWNLAPKSTFEKSDGSeiTFVEYYKQKYNITIRDPNQPLL-VSRPK-------- 91
                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 618468591   1003 RHLNQKGKalplssaekrkakweslQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLL 1065
Cdd:smart00949   92 RRRNQNGK-----------------GEPVLLPPELCFITGLTDRMRKDFMLMKSIADRTRLSP 137
RIBOc smart00535
Ribonuclease III family;
1296-1387 2.78e-25

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 102.68  E-value: 2.78e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   1296 LILQALTLSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIF 1374
Cdd:smart00535    2 LLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81
                            90
                    ....*....|...
gi 618468591   1375 DPPVNWLPPGYVV 1387
Cdd:smart00535   82 EAISGGRDKPKIL 94
PRK13766 PRK13766
Hef nuclease; Provisional
37-553 3.18e-25

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 114.20  E-value: 3.18e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   37 IHDNIYTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELsyqirgdFSRNGKRTVFLVNSANQVAQQVSAVRTH 116
Cdd:PRK13766    9 IKPNTIEARLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAER-------LHKKGGKVLILAPTKPLVEQHAEFFRKF 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  117 SDLKVGEYSNL--EVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPY----REIM 190
Cdd:PRK13766   82 LNIPEEKIVVFtgEVSPEKRAELWE----KAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYvyiaERYH 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  191 KLCENcpscPRILGLTASilNGKcDPEELEEKIQKLeKIlkSNAE--TATDLVVlDRYTSqpcEIVVDcgpftdrsglYE 268
Cdd:PRK13766  158 EDAKN----PLVLGLTAS--PGS-DEEKIKEVCENL-GI--EHVEvrTEDDPDV-KPYVH---KVKIE----------WV 213
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  269 RLLM--ELEEALNFINDCnisvhSKERdstlisKQILSDCRaVLVVLGPWCADK-VAGMMvRELQKYIKHEQEEL----- 340
Cdd:PRK13766  214 RVELpeELKEIRDLLNEA-----LKDR------LKKLKELG-VIVSISPDVSKKeLLGLQ-KKLQQEIANDDSEGyeais 280
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  341 ---------HRKFLLFT---DTFLRKIHALCEEHFSPAS--------LDLKF------------VTPKVIKLLEILRKyk 388
Cdd:PRK13766  281 ilaeamklrHAVELLETqgvEALRRYLERLREEARSSGGskaskrlvEDPRFrkavrkakeldiEHPKLEKLREIVKE-- 358
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  389 pyerqQFEsvewynnRNQDNYVswsdsedddedeeieekekpetnfpspftnilcgIIFVERRYTA-VVLNRLIKEagkq 467
Cdd:PRK13766  359 -----QLG-------KNPDSRI----------------------------------IVFTQYRDTAeKIVDLLEKE---- 388
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  468 dpelayissNFITGHGIGKNQPRN-KQMEAefRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFD-LPTEYRS 545
Cdd:PRK13766  389 ---------GIKAVRFVGQASKDGdKGMSQ--KEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEpVPSEIRS 457

                  ....*...
gi 618468591  546 yVQSKGRA 553
Cdd:PRK13766  458 -IQRKGRT 464
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
271-365 4.38e-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: 4.38e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  271 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 341
Cdd:cd15903     1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80
                          90       100
                  ....*....|....*....|....
gi 618468591  342 RKFLLFTDTFLRKIHALCEEHFSP 365
Cdd:cd15903    81 RLFLRYVITQLRKIRKLLEDEMKN 104
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
1296-1376 6.32e-25

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


Pssm-ID: 238333  Cd Length: 133  Bit Score: 101.92  E-value: 6.32e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591 1296 LILQALT---LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVS 1372
Cdd:cd00593     2 LLLEALThpsYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLG 81

                  ....
gi 618468591 1373 IFDP 1376
Cdd:cd00593    82 KGEE 85
DEXDc smart00487
DEAD-like helicases superfamily;
40-242 8.39e-23

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 98.33  E-value: 8.39e-23
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591     40 NIYTPRKYQVELLEAALD--HNTIVCLNTGSGKTFIAVLLTKELSYqirgdfSRNGKRTVFLVNS---ANQVAQQVSAVR 114
Cdd:smart00487    5 GFEPLRPYQKEAIEALLSglRDVILAAPTGSGKTLAALLPALEALK------RGKGGRVLVLVPTrelAEQWAEELKKLG 78
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591    115 THSDLK-VGEYSNLEVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLC 193
Cdd:smart00487   79 PSLGLKvVGLYGGDSKREQLRKLESG----KTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLL 154
                           170       180       190       200
                    ....*....|....*....|....*....|....*....|....*....
gi 618468591    194 ENCPSCPRILGLTASILNgkcDPEELEEKIQKLEKILKSNAETATDLVV 242
Cdd:smart00487  155 KLLPKNVQLLLLSATPPE---EIENLLELFLNDPVFIDVGFTPLEPIEQ 200
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1702-1824 1.17e-21

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 91.57  E-value: 1.17e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  1702 QRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELfhviddfvqfqleKNE 1781
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI-------------RRR 67
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 618468591  1782 MQGMDSELRRSEEDeekeedievPKAMGDIFESLAGAIYMDSG 1824
Cdd:pfam00636   68 NNALGKGPKRADGK---------EKVLADAFEALIGALYLDGG 101
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
914-1064 4.29e-20

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


Pssm-ID: 460472  Cd Length: 123  Bit Score: 87.63  E-value: 4.29e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   914 YTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFP--SPEYETFAEYYKTKYNLDLTNLNQPLLDVd 991
Cdd:pfam02170    8 QQQKDRRDFRKEAKKALKGLKVYTTYNNPRTYRIDGITFDPTPESTFPlkDGKEITVVDYFKKKYNIDLKYPDQPLLLV- 86
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 618468591   992 htssrlnlltprhlnqkgkalplssaeKRKakweslQNKQILVPELCAihpIPASLWRKAVCLPSILYRLHCL 1064
Cdd:pfam02170   87 ---------------------------GKK------RPKVYLPPELCN---LVDGQRYTKKLMPSIAQRTRLL 123
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1313-1376 2.75e-15

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 73.08  E-value: 2.75e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 618468591  1313 ERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIFDP 1376
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI 64
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
501-553 1.52e-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: 1.52e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 618468591   501 QEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 553
Cdd:pfam00271   53 REEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
45-221 5.45e-13

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


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 68.81  E-value: 5.45e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591    45 RKYQVELLEAAL-DHNTIVCLNTGSGKTFIAVL-LTKELsyqirgDFSRNGKRTVFLV---NSANQVAQQVSavrthsdl 119
Cdd:pfam00270    1 TPIQAEAIPAILeGRDVLVQAPTGSGKTLAFLLpALEAL------DKLDNGPQALVLAptrELAEQIYEELK-------- 66
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   120 KVGEYSNLEVNASWT-KERWNQ--EFTKHQVLIMTCYVALNVLKNGYLsLSDINLLVFDECHLaILDHPYREIMKLC-EN 195
Cdd:pfam00270   67 KLGKGLGLKVASLLGgDSRKEQleKLKGPDILVGTPGRLLDLLQERKL-LKNLKLLVLDEAHR-LLDMGFGPDLEEIlRR 144
                          170       180
                   ....*....|....*....|....*.
gi 618468591   196 CPSCPRILGLTASIlngkcdPEELEE 221
Cdd:pfam00270  145 LPKKRQILLLSATL------PRNLED 164
HELICc smart00490
helicase superfamily c-terminal domain;
499-553 1.24e-12

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 64.93  E-value: 1.24e-12
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 618468591    499 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 553
Cdd:smart00490   24 EEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
1292-1367 2.17e-11

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 65.69  E-value: 2.17e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  1292 PNPGLILQALT-----LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLP 1366
Cdd:TIGR02191   10 KNPELLEQALThrsyaNEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVARELGLG 89

                   .
gi 618468591  1367 S 1367
Cdd:TIGR02191   90 D 90
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1283-1365 9.19e-11

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 63.96  E-value: 9.19e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591 1283 IGYSSRtlgpNPGLILQALT---LSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYR 1358
Cdd:COG0571    11 LGYRFK----DPELLEQALThrsYANEHGGLeNNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAE 86

                  ....*..
gi 618468591 1359 LGKKKGL 1365
Cdd:COG0571    87 IARELGL 93
DSRM smart00358
Double-stranded RNA binding motif;
1850-1913 5.40e-08

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 51.49  E-value: 5.40e-08
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 618468591   1850 PRSPVRELLEMEPETAKFSPAERT-YDGKVRVTVEVVGKGK--FKGVGRSYRIAKSAAARRALRSLK 1913
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEEgPDHAPRFTVTVKVGGKrtGEGEGSSKKEAKQRAAEAALRSLK 67
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
444-589 7.14e-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: 7.14e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  444 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFItgHGiGKNQprnkqmeaefRKQEEVLRKFRAHETNLLIATSIVE 523
Cdd:COG0513   244 AIVFCNTKRGADRLAEKLQKRG--------ISAAAL--HG-DLSQ----------GQRERALDAFRNGKIRVLVATDVAA 302
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 618468591  524 EGVDIPKCNLVVRFDLPTEYRSYV---------QSKGRArapisnyIMLADtdkiksfEEDLKTYKAIEKILRNK 589
Cdd:COG0513   303 RGIDIDDVSHVINYDLPEDPEDYVhrigrtgraGAEGTA-------ISLVT-------PDERRLLRAIEKLIGQK 363
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
444-594 4.55e-05

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 48.01  E-value: 4.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  444 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGhgigknqprnkqmEAEFRKQEEVLRKFRAHETNLLIATSIVE 523
Cdd:PRK11192  248 SIVFVRTRERVHELAGWLRKAG--------INCCYLEG-------------EMVQAKRNEAIKRLTDGRVNVLVATDVAA 306
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  524 EGVDIPKCNLVVRFDLPTEYRSYVQSKGR-ARA-----PIS-----NYIMLadtDKIKSF-EEDLK---------TYKAI 582
Cdd:PRK11192  307 RGIDIDDVSHVINFDMPRSADTYLHRIGRtGRAgrkgtAISlveahDHLLL---GKIERYiEEPLKarvidelrpKTKAP 383
                         170
                  ....*....|..
gi 618468591  583 EKILRNKCSKSV 594
Cdd:PRK11192  384 SEKKTGKPSKKV 395
 
Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
42-239 1.07e-99

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: 318.83  E-value: 1.07e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   42 YTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELSYQIRGdFSRNGKRTVFLVNSANQVAQQVSAVRTHSDLKV 121
Cdd:cd18034     1 FTPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRK-EKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  122 GEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENC---PS 198
Cdd:cd18034    80 GEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLegrTS 159
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 618468591  199 CPRILGLTASILNGKCDPEELEEKIQKLEKILKSNAETATD 239
Cdd:cd18034   160 RPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
886-1008 2.19e-69

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


Pssm-ID: 239209  Cd Length: 122  Bit Score: 228.48  E-value: 2.19e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  886 DSSTLDIDFKFMEDIEkSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 965
Cdd:cd02843     1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 618468591  966 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 1008
Cdd:cd02843    80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
42-238 3.52e-66

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: 222.69  E-value: 3.52e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   42 YTPRKYQVELLEAAL-DHNTIVCLNTGSGKTFIAVLLTKELSYQIRgdfSRNGKRTVFLVNSANQVAQQVSAVRTHSD-- 118
Cdd:cd17927     1 FKPRNYQLELAQPALkGKNTIICLPTGSGKTFVAVLICEHHLKKFP---AGRKGKVVFLANKVPLVEQQKEVFRKHFErp 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  119 -LKVGEYSNlevnASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYL-SLSDINLLVFDECHLAILDHPYREIMKLCENC 196
Cdd:cd17927    78 gYKVTGLSG----DTSENVSVEQIVESSDVIIVTPQILVNDLKSGTIvSLSDFSLLVFDECHNTTKNHPYNEIMFRYLDQ 153
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 618468591  197 PS-----CPRILGLTASILNGKC-DPEELEEKIQKLEKILKSNAETAT 238
Cdd:cd17927   154 KLgssgpLPQILGLTASPGVGGAkNTEEALEHICKLCANLDISVIATV 201
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
372-564 6.08e-56

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


Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 190.88  E-value: 6.08e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  372 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 451
Cdd:cd18802     4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  452 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprNKQMEAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKC 531
Cdd:cd18802    36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109
                         170       180       190
                  ....*....|....*....|....*....|...
gi 618468591  532 NLVVRFDLPTEYRSYVQSKGRARAPISNYIMLA 564
Cdd:cd18802   110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
1682-1846 9.83e-40

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


Pssm-ID: 238333  Cd Length: 133  Bit Score: 144.29  E-value: 9.83e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591 1682 YLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1761
Cdd:cd00593     2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKY---- 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591 1762 spelfhviddfvqFQLEKNEMQGMDSElrrseedeekeedieVPKAMGDIFESLAGAIYMDSGMslETVWQVYYPMMRPL 1841
Cdd:cd00593    78 -------------LRLGKGEEKSGGRL---------------RPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPL 127

                  ....*
gi 618468591 1842 IEKFS 1846
Cdd:cd00593   128 IEEIS 132
DSRM_DICER cd10843
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ...
1851-1913 2.67e-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: 2.67e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 618468591 1851 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLK 1913
Cdd:cd10843     1 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGRFKGVGRNYRIAKSAAARRALRSLK 63
RIBOc smart00535
Ribonuclease III family;
1682-1845 6.61e-37

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 135.81  E-value: 6.61e-37
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   1682 YLLQAFTHASYHYNTitDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1761
Cdd:smart00535    2 LLLRALTHASYSNEH--EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEF---- 75
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   1762 spelfhviddfvqFQLEKNEmqgMDSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSGmsLETVWQVYYPMMRPL 1841
Cdd:smart00535   76 -------------IRLGRGE---AISGGRDK------------PKILADVFEALIGAIYLDSG--LEAAREFIRDLLGPR 125

                    ....
gi 618468591   1842 IEKF 1845
Cdd:smart00535  126 LDEL 129
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1666-1916 1.84e-36

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 138.31  E-value: 1.84e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591 1666 FENFEKKINYRFKNKAYLLQAFTHASY-HYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTI 1744
Cdd:COG0571     4 LEELEERLGYRFKDPELLEQALTHRSYaNEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEET 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591 1745 FASLAVKYDyhkyfkavspelfhvIDDFVqfQLEKNEMQgmdSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSG 1824
Cdd:COG0571    84 LAEIARELG---------------LGDYL--RLGKGEEK---SGGRRR------------PSILADAFEALIGAIYLDGG 131
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591 1825 msLETVWQVYYPMMRPLIEKFSANVPRS-----------------PVRELLEME-PETAK-FspaertydgkvRVTVEVV 1885
Cdd:COG0571   132 --LEAARKFVLRLFEPRLEEIAPGGAGKdyktalqewlqarglplPEYEVVEEEgPDHAKtF-----------TVEVLVG 198
                         250       260       270
                  ....*....|....*....|....*....|.
gi 618468591 1886 GKGKFKGVGRSYRIAKSAAARRALRSLKANQ 1916
Cdd:COG0571   199 GKVLGEGTGRSKKEAEQAAAKAALEKLGKKE 229
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
1669-1912 2.11e-36

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 138.11  E-value: 2.11e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  1669 FEKKINYRFKNKAYLLQAFTHASYHYNT--ITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFA 1746
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYANEHhkDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  1747 SLAVKYDYHKYFKavspelfhviddfvqfqLEKNEMQgmdSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSGMS 1826
Cdd:TIGR02191   81 EVARELGLGDFLL-----------------LGKGEEK---SGGRRR------------DSILADAFEALIGAIYLDSGLE 128
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  1827 LETVW--QVYYPMMRPLIEKFSANVPRSPVRELL----------EMEPETAKfsPAERTYdgkvRVTVEVVGKGKFKGVG 1894
Cdd:TIGR02191  129 AARKFilKLLIPRIDAIIKEETLKDYKTALQEWAqargkplpeyRLIKEEGP--DHDKEF----TVEVSVNGEPYGEGKG 202
                          250
                   ....*....|....*...
gi 618468591  1895 RSYRIAKSAAARRALRSL 1912
Cdd:TIGR02191  203 KSKKEAEQNAAKAALEKL 220
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
44-552 3.12e-34

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 142.56  E-value: 3.12e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   44 PRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELsyqirgdFSRNGKRTVFLVNS---ANQVAQQVSAVRTHSDLK 120
Cdd:COG1111     4 RRLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAER-------LHKKGGKVLFLAPTkplVEQHAEFFKEALNIPEDE 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  121 VGEYSNlEVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCP 200
Cdd:COG1111    77 IVVFTG-EVSPEKRKELWE----KARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKDP 151
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  201 RILGLTASilngkcdPEELEEKIQKLEKILK-SNAETATDlvvldrytSQPceivvDCGPFT-DRSGLYERLLM--ELEE 276
Cdd:COG1111   152 LILGMTAS-------PGSDEEKIEEVCENLGiENVEVRTE--------EDP-----DVAPYVhDTEVEWIRVELpeELKE 211
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  277 ALNFIN-----------DCNISVHSKERDST--------LISKQILSDCRAVLVVLGPwcadkVAGMM------------ 325
Cdd:COG1111   212 IRDLLNevlddrlkklkELGVIVSTSPDLSKkdllalqkKLQRRIREDDSEGYRAISI-----LAEALklrhalelletq 286
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  326 -VRELQKYIKhEQEELHRKFL-------LFTDTFLRKIHALCE----EHfspasldlkfvtPKVIKLLEILRKYKpyerq 393
Cdd:COG1111   287 gVEALLRYLE-RLEEEARSSGgskaskrLVSDPRFRKAMRLAEeadiEH------------PKLSKLREILKEQL----- 348
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  394 qfesvewynNRNQDNYVswsdsedddedeeieekekpetnfpspftnilcgIIFVERRYTAVVLNRLIKEAGkqdpelay 473
Cdd:COG1111   349 ---------GTNPDSRI----------------------------------IVFTQYRDTAEMIVEFLSEPG-------- 377
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  474 ISSNFITGHGIGKNQPRNKQmeaefRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDL-PTEYRSyVQSKGR 552
Cdd:COG1111   378 IKAGRFVGQASKEGDKGLTQ-----KEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPvPSEIRS-IQRKGR 451
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
630-718 2.61e-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: 121.45  E-value: 2.61e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   630 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMSCVRLAERVVALICCEKLHKIGELD 709
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79

                   ....*....
gi 618468591   710 DHLMPVGKE 718
Cdd:pfam03368   80 DHLLPLTKK 88
PAZ cd02825
PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two ...
886-1008 1.51e-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: 120.26  E-value: 1.51e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  886 DSSTLDIDFKFMEDIEKSEARIGIPSTKYTKETPfVFKLEDYQDaviipryrnfdQPHRFYVADVYTDLTPLS--KFPSP 963
Cdd:cd02825     1 ADPVIETMCKFPKDREIDTPLLDSPREEFTKELK-GLKVEDTHN-----------PLNRVYRPDGETRLKAPSqlKHSDG 68
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 618468591  964 EYETFAEYYKTKYNLDLTNLNQPLLDVDHTS--SRLNLLTPRHLNQK 1008
Cdd:cd02825    69 KEITFADYFKERYNLTLTDLNQPLLIVKFSSkkSYSILLPPELCVIT 115
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
925-1065 7.66e-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: 110.45  E-value: 7.66e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591    925 EDYQDAVIIPRYRNfdqpHRFYVADVYTDLTPLSKFPSPEYE--TFAEYYKTKYNLDLTNLNQPLLdVDHTSsrlnlltp 1002
Cdd:smart00949   25 KDLKGLIVLTRYNN----KTYRIDDIDWNLAPKSTFEKSDGSeiTFVEYYKQKYNITIRDPNQPLL-VSRPK-------- 91
                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 618468591   1003 RHLNQKGKalplssaekrkakweslQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLL 1065
Cdd:smart00949   92 RRRNQNGK-----------------GEPVLLPPELCFITGLTDRMRKDFMLMKSIADRTRLSP 137
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
43-226 2.33e-26

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


Pssm-ID: 350794 [Multi-domain]  Cd Length: 204  Bit Score: 108.72  E-value: 2.33e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   43 TPRKYQVELLEAALD-HNTIVCLNTGSGKTFIAVLLTKElSYQIRGDFSRNGkRTVFLVNSANQVAQQvSAVRTHSDLKV 121
Cdd:cd18036     2 ELRNYQLELVLPALRgKNTIICAPTGSGKTRVAVYICRH-HLEKRRSAGEKG-RVVVLVNKVPLVEQQ-LEKFFKYFRKG 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  122 GEYSNLEvNASWTKERWNQEFTKHQVLIMTCYVALNVLKNG----YLSLSDINLLVFDECHLAILDHPYREIM------K 191
Cdd:cd18036    79 YKVTGLS-GDSSHKVSFGQIVKASDVIICTPQILINNLLSGreeeRVYLSDFSLLIFDECHHTQKEHPYNKIMrmyldkK 157
                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 618468591  192 LCENCPScPRILGLTASI-LNGKCDPEELEEKIQKL 226
Cdd:cd18036   158 LSSQGPL-PQILGLTASPgVGGARSFEEALEHILKL 192
RIBOc smart00535
Ribonuclease III family;
1296-1387 2.78e-25

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 102.68  E-value: 2.78e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   1296 LILQALTLSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIF 1374
Cdd:smart00535    2 LLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81
                            90
                    ....*....|...
gi 618468591   1375 DPPVNWLPPGYVV 1387
Cdd:smart00535   82 EAISGGRDKPKIL 94
PRK13766 PRK13766
Hef nuclease; Provisional
37-553 3.18e-25

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 114.20  E-value: 3.18e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   37 IHDNIYTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELsyqirgdFSRNGKRTVFLVNSANQVAQQVSAVRTH 116
Cdd:PRK13766    9 IKPNTIEARLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAER-------LHKKGGKVLILAPTKPLVEQHAEFFRKF 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  117 SDLKVGEYSNL--EVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPY----REIM 190
Cdd:PRK13766   82 LNIPEEKIVVFtgEVSPEKRAELWE----KAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYvyiaERYH 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  191 KLCENcpscPRILGLTASilNGKcDPEELEEKIQKLeKIlkSNAE--TATDLVVlDRYTSqpcEIVVDcgpftdrsglYE 268
Cdd:PRK13766  158 EDAKN----PLVLGLTAS--PGS-DEEKIKEVCENL-GI--EHVEvrTEDDPDV-KPYVH---KVKIE----------WV 213
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  269 RLLM--ELEEALNFINDCnisvhSKERdstlisKQILSDCRaVLVVLGPWCADK-VAGMMvRELQKYIKHEQEEL----- 340
Cdd:PRK13766  214 RVELpeELKEIRDLLNEA-----LKDR------LKKLKELG-VIVSISPDVSKKeLLGLQ-KKLQQEIANDDSEGyeais 280
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  341 ---------HRKFLLFT---DTFLRKIHALCEEHFSPAS--------LDLKF------------VTPKVIKLLEILRKyk 388
Cdd:PRK13766  281 ilaeamklrHAVELLETqgvEALRRYLERLREEARSSGGskaskrlvEDPRFrkavrkakeldiEHPKLEKLREIVKE-- 358
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  389 pyerqQFEsvewynnRNQDNYVswsdsedddedeeieekekpetnfpspftnilcgIIFVERRYTA-VVLNRLIKEagkq 467
Cdd:PRK13766  359 -----QLG-------KNPDSRI----------------------------------IVFTQYRDTAeKIVDLLEKE---- 388
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  468 dpelayissNFITGHGIGKNQPRN-KQMEAefRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFD-LPTEYRS 545
Cdd:PRK13766  389 ---------GIKAVRFVGQASKDGdKGMSQ--KEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEpVPSEIRS 457

                  ....*...
gi 618468591  546 yVQSKGRA 553
Cdd:PRK13766  458 -IQRKGRT 464
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
271-365 4.38e-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: 4.38e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  271 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 341
Cdd:cd15903     1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80
                          90       100
                  ....*....|....*....|....
gi 618468591  342 RKFLLFTDTFLRKIHALCEEHFSP 365
Cdd:cd15903    81 RLFLRYVITQLRKIRKLLEDEMKN 104
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
1296-1376 6.32e-25

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


Pssm-ID: 238333  Cd Length: 133  Bit Score: 101.92  E-value: 6.32e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591 1296 LILQALT---LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVS 1372
Cdd:cd00593     2 LLLEALThpsYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLG 81

                  ....
gi 618468591 1373 IFDP 1376
Cdd:cd00593    82 KGEE 85
DEXDc smart00487
DEAD-like helicases superfamily;
40-242 8.39e-23

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 98.33  E-value: 8.39e-23
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591     40 NIYTPRKYQVELLEAALD--HNTIVCLNTGSGKTFIAVLLTKELSYqirgdfSRNGKRTVFLVNS---ANQVAQQVSAVR 114
Cdd:smart00487    5 GFEPLRPYQKEAIEALLSglRDVILAAPTGSGKTLAALLPALEALK------RGKGGRVLVLVPTrelAEQWAEELKKLG 78
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591    115 THSDLK-VGEYSNLEVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLC 193
Cdd:smart00487   79 PSLGLKvVGLYGGDSKREQLRKLESG----KTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLL 154
                           170       180       190       200
                    ....*....|....*....|....*....|....*....|....*....
gi 618468591    194 ENCPSCPRILGLTASILNgkcDPEELEEKIQKLEKILKSNAETATDLVV 242
Cdd:smart00487  155 KLLPKNVQLLLLSATPPE---EIENLLELFLNDPVFIDVGFTPLEPIEQ 200
helicase_insert_domain cd12088
helicase_insert_domain; helicase_insert_domain; This helical domain can be found inserted in a ...
271-362 2.86e-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: 2.86e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  271 LMELEEALNFINDCNIsvhskerDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHeqeELHRKFLLFTDT 350
Cdd:cd12088     1 KMILSQLLRDTESLLK-------LLYTAHLRKLNDALELLEDAGIWDALKYIKMFFTEVREGIFD---ELERKLTLRFDE 70
                          90
                  ....*....|..
gi 618468591  351 FLRKIHALCEEH 362
Cdd:cd12088    71 KLQKLIALSRDP 82
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
44-226 5.52e-22

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


Pssm-ID: 350831 [Multi-domain]  Cd Length: 202  Bit Score: 96.04  E-value: 5.52e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   44 PRKYQVELLEAALD-HNTIVCLNTGSGKTFIAVLLTKelsYQIRgDFSRNGK-RTVFLVNSANQVAQQVSAVRTH---SD 118
Cdd:cd18073     3 PRNYQLELALPAMKgKNTIICAPTGCGKTFVSLLICE---HHLK-KFPQGQKgKVVFFATKVPVYEQQKSVFSKYferHG 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  119 LKV----GEYSNLeVNASWTKErwnqeftKHQVLIMTCYVALNVLKNGYL-SLSDINLLVFDECHLAILDHPYREIM--- 190
Cdd:cd18073    79 YRVtgisGATAEN-VPVEQIIE-------NNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSGNHPYNMIMfry 150
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 618468591  191 ---KLCENCPSCPRILGLTASILNGKC-DPEELEEKIQKL 226
Cdd:cd18073   151 ldqKLGGSSGPLPQIIGLTASVGVGDAkNTDEALDYICKL 190
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
45-226 6.18e-22

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


Pssm-ID: 350791 [Multi-domain]  Cd Length: 182  Bit Score: 95.08  E-value: 6.18e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   45 RKYQVELLEAALDHNTIVCLNTGSGKTFIA--VLLtkelsyqirgDFSR---NGKrTVFLVNSANQVAQQVSAVrtHSDL 119
Cdd:cd18033     4 RDYQFTIVQKALFQNTLVALPTGLGKTFIAavVML----------NYYRwfpKGK-IVFMAPTKPLVSQQIEAC--YKIT 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  120 KVGEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSC 199
Cdd:cd18033    71 GIPSSQTAELTGSVPPTKRAELWASKRVFFLTPQTLENDLKEGDCDPKSIVCLVIDEAHRATGNYAYCQVVRELMRYNSH 150
                         170       180
                  ....*....|....*....|....*..
gi 618468591  200 PRILGLTASILNgkcDPEELEEKIQKL 226
Cdd:cd18033   151 FRILALTATPGS---KLEAVQQVIDNL 174
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1702-1824 1.17e-21

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 91.57  E-value: 1.17e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  1702 QRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELfhviddfvqfqleKNE 1781
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI-------------RRR 67
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 618468591  1782 MQGMDSELRRSEEDeekeedievPKAMGDIFESLAGAIYMDSG 1824
Cdd:pfam00636   68 NNALGKGPKRADGK---------EKVLADAFEALIGALYLDGG 101
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
914-1064 4.29e-20

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


Pssm-ID: 460472  Cd Length: 123  Bit Score: 87.63  E-value: 4.29e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   914 YTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFP--SPEYETFAEYYKTKYNLDLTNLNQPLLDVd 991
Cdd:pfam02170    8 QQQKDRRDFRKEAKKALKGLKVYTTYNNPRTYRIDGITFDPTPESTFPlkDGKEITVVDYFKKKYNIDLKYPDQPLLLV- 86
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 618468591   992 htssrlnlltprhlnqkgkalplssaeKRKakweslQNKQILVPELCAihpIPASLWRKAVCLPSILYRLHCL 1064
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 ...
1683-1825 1.75e-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: 1.75e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  1683 LLQAFTHASYHYNTiTDCYQRLEFLGDAILDYLITKHLYEDPRQhSPGVLTDLRSALVNNTIFASLAvkydyhkyfkavs 1762
Cdd:pfam14622    4 LLQALTHKSYANGR-KPYNERLEFLGDAVLELSVSEYLFKKPDL-DEGGLTKLRASIVSEESLAEIA------------- 68
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 618468591  1763 pelfhviddfVQFQLEKNEMQGMDSELRRSeedeekeedIEVPKAMGDIFESLAGAIYMDSGM 1825
Cdd:pfam14622   69 ----------REIGLGKYLRLGKGEEETGG---------SGRESILADALEALIGAIYLDGGF 112
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1313-1376 2.75e-15

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 73.08  E-value: 2.75e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 618468591  1313 ERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIFDP 1376
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 ...
922-1044 5.96e-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: 73.61  E-value: 5.96e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  922 FKLEDYQDAVIIpryrnfdQPH--RFYVADVYTDLTPLSKFP---SPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSR 996
Cdd:cd02844    26 FCACDLKGSVVT-------APHngRFYVISGILDLNANSSFPgkeGLGYATYAEYFKEKYGIVLNHPNQPLLKGKQIFNL 98
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 618468591  997 LNLLTPRhLNQKGkalplSSAEKRKakwesLQNKQILVPELCAIHPIP 1044
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, ...
501-553 1.52e-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: 1.52e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 618468591   501 QEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 553
Cdd:pfam00271   53 REEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
46-219 4.69e-14

DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350679 [Multi-domain]  Cd Length: 181  Bit Score: 72.29  E-value: 4.69e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   46 KYQVELLEAAL--DHNTIVCLNTGSGKTFIAVLLtkelsyqIRGDFSRNGKRTVFLVNS---ANQVAQQVSAVRTHSDLK 120
Cdd:cd17921     4 PIQREALRALYlsGDSVLVSAPTSSGKTLIAELA-------ILRALATSGGKAVYIAPTralVNQKEADLRERFGPLGKN 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  121 VGE-YSNLEVNASWTKERwnqeftkhQVLIMTcYVALNVL--KNGYLSLSDINLLVFDECHL-------AILDHPYREIM 190
Cdd:cd17921    77 VGLlTGDPSVNKLLLAEA--------DILVAT-PEKLDLLlrNGGERLIQDVRLVVVDEAHLigdgergVVLELLLSRLL 147
                         170       180
                  ....*....|....*....|....*....
gi 618468591  191 KLCENCpscpRILGLTASILNgkcdPEEL 219
Cdd:cd17921   148 RINKNA----RFVGLSATLPN----AEDL 168
DEXHc_RLR-3 cd18075
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ...
45-208 8.14e-14

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


Pssm-ID: 350833 [Multi-domain]  Cd Length: 200  Bit Score: 72.20  E-value: 8.14e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   45 RKYQVELLEAALD-HNTIVCLNTGSGKTFIAVLLTKelsyqiRGDFSRNGKRTVFLVNSANQVAQQVSAVRTHSDlkvGE 123
Cdd:cd18075     4 HGYQWEVVAPALRgKNSIIWLPTGAGKTRAAVYVAR------RHLETKRGAKVAVLVNKVHLVDQHLEKEFHVLL---DK 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  124 YSNLEVNA-SWTKERWNQEFTKHQVLIMTCYVALNVLKNG----YLSLSDINLLVFDECHLAILDHPYREIM------KL 192
Cdd:cd18075    75 YTVTAISGdSSHKCFFGQLARGSDVVICTAQILQNALLSGeeeaHVELTDFSLLVIDECHHTHKEAVYNKIMlsylekKL 154
                         170
                  ....*....|....*.
gi 618468591  193 CENCPsCPRILGLTAS 208
Cdd:cd18075   155 SRQGD-LPQILGLTAS 169
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
44-226 1.13e-13

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


Pssm-ID: 350793 [Multi-domain]  Cd Length: 181  Bit Score: 71.39  E-value: 1.13e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   44 PRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLtkelsyqIRGDFSRNGKRTVFLVNSANQVAQQVSAVRT--HSDLKV 121
Cdd:cd18035     3 RRLYQVLIAAVALNGNTLIVLPTGLGKTIIAILV-------AADRLTKKGGKVLILAPSRPLVEQHAENLKRvlNIPDKI 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  122 GEYSNlEVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCPR 201
Cdd:cd18035    76 TSLTG-EVKPEERAERWD----ASKIIVATPQVIENDLLAGRITLDDVSLLIFDEAHHAVGNYAYVYIAHRYKREANNPL 150
                         170       180
                  ....*....|....*....|....*
gi 618468591  202 ILGLTASilnGKCDPEELEEKIQKL 226
Cdd:cd18035   151 ILGLTAS---PGSDKEKIMEICENL 172
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
45-221 5.45e-13

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


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 68.81  E-value: 5.45e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591    45 RKYQVELLEAAL-DHNTIVCLNTGSGKTFIAVL-LTKELsyqirgDFSRNGKRTVFLV---NSANQVAQQVSavrthsdl 119
Cdd:pfam00270    1 TPIQAEAIPAILeGRDVLVQAPTGSGKTLAFLLpALEAL------DKLDNGPQALVLAptrELAEQIYEELK-------- 66
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   120 KVGEYSNLEVNASWT-KERWNQ--EFTKHQVLIMTCYVALNVLKNGYLsLSDINLLVFDECHLaILDHPYREIMKLC-EN 195
Cdd:pfam00270   67 KLGKGLGLKVASLLGgDSRKEQleKLKGPDILVGTPGRLLDLLQERKL-LKNLKLLVLDEAHR-LLDMGFGPDLEEIlRR 144
                          170       180
                   ....*....|....*....|....*.
gi 618468591   196 CPSCPRILGLTASIlngkcdPEELEE 221
Cdd:pfam00270  145 LPKKRQILLLSATL------PRNLED 164
ResIII pfam04851
Type III restriction enzyme, res subunit;
41-207 1.15e-12

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 67.70  E-value: 1.15e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591    41 IYTPRKYQVE----LLEAALDHNTIVCLN--TGSGKTFIAVLLTKELSYqirgdfSRNGKRTVFLVNSANQVAQQvsavr 114
Cdd:pfam04851    1 KLELRPYQIEaienLLESIKNGQKRGLIVmaTGSGKTLTAAKLIARLFK------KGPIKKVLFLVPRKDLLEQA----- 69
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   115 thsdlkVGEYSNLEVNASWTKERWNQEFTKHQV----LIMTCYVALNV-LKNGYLSLSD--INLLVFDECHLAILDHpYR 187
Cdd:pfam04851   70 ------LEEFKKFLPNYVEIGEIISGDKKDESVddnkIVVTTIQSLYKaLELASLELLPdfFDVIIIDEAHRSGASS-YR 142
                          170       180
                   ....*....|....*....|
gi 618468591   188 EIMKLCencpSCPRILGLTA 207
Cdd:pfam04851  143 NILEYF----KPAFLLGLTA 158
HELICc smart00490
helicase superfamily c-terminal domain;
499-553 1.24e-12

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 64.93  E-value: 1.24e-12
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 618468591    499 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 553
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 ...
445-553 1.24e-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: 1.24e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  445 IIFVERRYTAvvlNRLIKEAGKQDPELAyiSSNFItGHGIGKNQPRNKQMEaefrkQEEVLRKFRAHETNLLIATSIVEE 524
Cdd:cd18801    34 IIFSEFRDSA---EEIVNFLSKIRPGIR--ATRFI-GQASGKSSKGMSQKE-----QKEVIEQFRKGGYNVLVATSIGEE 102
                          90       100       110
                  ....*....|....*....|....*....|
gi 618468591  525 GVDIPKCNLVVRFD-LPTEYRSyVQSKGRA 553
Cdd:cd18801   103 GLDIGEVDLIICYDaSPSPIRM-IQRMGRT 131
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
1292-1367 2.17e-11

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 65.69  E-value: 2.17e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  1292 PNPGLILQALT-----LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLP 1366
Cdd:TIGR02191   10 KNPELLEQALThrsyaNEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVARELGLG 89

                   .
gi 618468591  1367 S 1367
Cdd:TIGR02191   90 D 90
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
445-555 2.83e-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: 2.83e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  445 IIFVERRYTAVVLNRLIKEAGkqdpelayISSNFItgHGiGKNQprnkqmeaefRKQEEVLRKFRAHETNLLIATSIVEE 524
Cdd:cd18787    31 IIFVNTKKRVDRLAELLEELG--------IKVAAL--HG-DLSQ----------EERERALKKFRSGKVRVLVATDVAAR 89
                          90       100       110
                  ....*....|....*....|....*....|..
gi 618468591  525 GVDIPKCNLVVRFDLPTEYRSYVQSKGR-ARA 555
Cdd:cd18787    90 GLDIPGVDHVINYDLPRDAEDYVHRIGRtGRA 121
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
42-207 2.91e-11

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 68.51  E-value: 2.91e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   42 YTPRKYQVELLEAALDHNT------IVCLNTGSGKTFIAVLLTKELsyqirgdfsRNGKRTVFLVNSANQVAQqvsavrT 115
Cdd:COG1061    79 FELRPYQQEALEALLAALErgggrgLVVAPTGTGKTVLALALAAEL---------LRGKRVLVLVPRRELLEQ------W 143
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  116 HSDLKvgEYSNLEVNASWTKERWNQ-EFTKHQVLIMtcYVALNVLKNgylslsDINLLVFDECHLAILDHpYREIMKLCE 194
Cdd:COG1061   144 AEELR--RFLGDPLAGGGKKDSDAPiTVATYQSLAR--RAHLDELGD------RFGLVIIDEAHHAGAPS-YRRILEAFP 212
                         170
                  ....*....|...
gi 618468591  195 ncpsCPRILGLTA 207
Cdd:COG1061   213 ----AAYRLGLTA 221
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
44-208 4.51e-11

DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are 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: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 62.71  E-value: 4.51e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   44 PRKYQVELLEAALDHNT----IVCLNTGSGKTFIAVLLTKELSYqirgdfsrngKRTVFLVNSANQVAQqvsavrthsdl 119
Cdd:cd17926     1 LRPYQEEALEAWLAHKNnrrgILVLPTGSGKTLTALALIAYLKE----------LRTLIVVPTDALLDQ----------- 59
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  120 kvgeysnlevnaswTKERWNQEFTKHQVLIMTC-----------YVAL-----NVLKNGYLSLSDINLLVFDECHLAild 183
Cdd:cd17926    60 --------------WKERFEDFLGDSSIGLIGGgkkkdfddanvVVATyqslsNLAEEEKDLFDQFGLLIVDEAHHL--- 122
                         170       180
                  ....*....|....*....|....*...
gi 618468591  184 hP---YREIMKLCEncpsCPRILGLTAS 208
Cdd:cd17926   123 -PaktFSEILKELN----AKYRLGLTAT 145
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
48-221 4.83e-11

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 67.61  E-value: 4.83e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   48 QVELLEAAL--DHNTIVCLNTGSGKTFIAVL-LTKELsyqirgdfsRNGKRTVFLVNS---ANQVAQQVSAVRTHSDLKV 121
Cdd:COG1204    27 QAEALEAGLleGKNLVVSAPTASGKTLIAELaILKAL---------LNGGKALYIVPLralASEKYREFKRDFEELGIKV 97
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  122 GE-YSNLEVNASWTKERwnqeftkhQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLaiLDHPYR----EIM--KLCE 194
Cdd:COG1204    98 GVsTGDYDSDDEWLGRY--------DILVATPEKLDSLLRNGPSWLRDVDLVVVDEAHL--IDDESRgptlEVLlaRLRR 167
                         170       180
                  ....*....|....*....|....*..
gi 618468591  195 NCPScPRILGLTASILNgkcdPEELEE 221
Cdd:COG1204   168 LNPE-AQIVALSATIGN----AEEIAE 189
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1283-1365 9.19e-11

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 63.96  E-value: 9.19e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591 1283 IGYSSRtlgpNPGLILQALT---LSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYR 1358
Cdd:COG0571    11 LGYRFK----DPELLEQALThrsYANEHGGLeNNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAE 86

                  ....*..
gi 618468591 1359 LGKKKGL 1365
Cdd:COG0571    87 IARELGL 93
DEXHc_RLR-2 cd18074
DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma ...
43-226 1.05e-10

DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma differentiation-associated protein 5 or Mda5 and IFIH1) is a viral double-stranded RNA (dsRNA) receptor that shares sequence similarity and signaling pathways with RIG-I, yet plays essential functions in antiviral immunity through distinct specificity for viral RNA. RLR-2 recognizes the internal duplex structure, whereas RIG-I recognizes the terminus of dsRNA. RLR-2 uses direct protein-protein contacts to stack along dsRNA in a head-to-tail arrangement. The signaling domain (tandem CARD), which decorates the outside of the core RLR-2 filament, also has an intrinsic propensity to oligomerize into an elongated structure that activates the signaling adaptor, MAVS. RLR-2 uses long dsRNA as a signaling platform to cooperatively assemble the core filament, which in turn promotes stochastic assembly of the tandem CARD oligomers for signaling. LGP2 appears to positively and negatively regulate RLR-2 and RIG-I signaling, respectively. RLR-2 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: 350832 [Multi-domain]  Cd Length: 216  Bit Score: 63.34  E-value: 1.05e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   43 TPRKYQVELLEAALD-HNTIVCLNTGSGKTFIAVLLTKELSYQIRGDfSRNGKrTVFLVNSANQVAQQVSA-----VRTH 116
Cdd:cd18074     2 TLRDYQMEVAKPALEgKNIIICLPTGSGKTRVAVYITKDHLDKKRKA-SEPGK-VIVLVNKVPLVEQHYRKefnpfLKHW 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  117 SDLkVGEYSNLEVNASWTKerwnqEFTKHQVLIMTCYVALNVLKNGY------LSLSDINLLVFDECHLAILDHPYREIM 190
Cdd:cd18074    80 YQV-IGLSGDSQLKISFPE-----VVKRYDVIICTAQILENSLLNATeeedegVQLSDFSLIIIDECHHTQKEAVYNNIM 153
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 618468591  191 KLC------------ENCPSC--PRILGLTASI-LNGKCDPEELEEKIQKL 226
Cdd:cd18074   154 RRYlkqkiknrkqkkENKPLIplPQILGLTASPgVGGAKNNKKAEEHILKI 204
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
58-207 8.59e-09

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 56.26  E-value: 8.59e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   58 HNTIVCLNTGSGKTFIAVLltkelsyQIRGDFSRNGKRTVFLV---NSANQVAQQVSAVRTHsDLKVGEYsnleVNASWT 134
Cdd:cd00046     2 ENVLITAPTGSGKTLAALL-------AALLLLLKKGKKVLVLVptkALALQTAERLRELFGP-GIRVAVL----VGGSSA 69
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  135 KERWNQEFTKHQVLIMTC-YVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCE------NCpscpRILGLTA 207
Cdd:cd00046    70 EEREKNKLGDADIIIATPdMLLNLLLREDRLFLKDLKLIIVDEAHALLIDSRGALILDLAVrkaglkNA----QVILLSA 145
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
44-207 9.87e-09

DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350790 [Multi-domain]  Cd Length: 163  Bit Score: 56.42  E-value: 9.87e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   44 PRKYQVELLEA---ALDHNT---IVCLNTGSGKTFIAVLLTKELSyqirgdFSRNGKRTVFLVNSANQVAQQVSAVRTH- 116
Cdd:cd18032     1 PRYYQQEAIEAleeAREKGQrraLLVMATGTGKTYTAAFLIKRLL------EANRKKRILFLAHREELLEQAERSFKEVl 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  117 SDLKVGEYSNLEVNASWTKerwnqeftkhqVLIMTcYVALNvlKNGYLSLSDIN---LLVFDECHLAILDHpYREIMKLC 193
Cdd:cd18032    75 PDGSFGNLKGGKKKPDDAR-----------VVFAT-VQTLN--KRKRLEKFPPDyfdLIIIDEAHHAIASS-YRKILEYF 139
                         170
                  ....*....|....
gi 618468591  194 ENCPscprILGLTA 207
Cdd:cd18032   140 EPAF----LLGLTA 149
PAZ_piwi_like cd02845
PAZ domain, Piwi_like subfamily. In multi-cellular organisms, the Piwi protein appears to be ...
928-1038 1.37e-08

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


Pssm-ID: 239211  Cd Length: 117  Bit Score: 54.57  E-value: 1.37e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  928 QDAVIIPRYRNfdqphRFY-VADVYTDLTPLSKFPSPEYE--TFAEYYKTKYNLDLTNLNQPLLdvdhtssrlnlltprh 1004
Cdd:cd02845    29 IGSIVLTRYNN-----KTYrIDDIDFDKTPLSTFKKSDGTeiTFVEYYKKQYNIEITDLNQPLL---------------- 87
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 618468591 1005 lnqkgkalpLSSAEKRKAKweSLQNKQI-LVPELC 1038
Cdd:cd02845    88 ---------VSRPKRRDPR--GGEKEPIyLIPELC 111
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
1294-1369 4.47e-08

Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3.


Pssm-ID: 434075  Cd Length: 127  Bit Score: 53.33  E-value: 4.47e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 618468591  1294 PGLILQALT---LSNASDGFNlERLEMLGDSFLKHAITTYLFcTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRM 1369
Cdd:pfam14622    1 EELLLQALThksYANGRKPYN-ERLEFLGDAVLELSVSEYLF-KKPDLDEGGLTKLRASIVSEESLAEIAREIGLGKYL 77
DSRM smart00358
Double-stranded RNA binding motif;
1850-1913 5.40e-08

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 51.49  E-value: 5.40e-08
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 618468591   1850 PRSPVRELLEMEPETAKFSPAERT-YDGKVRVTVEVVGKGK--FKGVGRSYRIAKSAAARRALRSLK 1913
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEEgPDHAPRFTVTVKVGGKrtGEGEGSSKKEAKQRAAEAALRSLK 67
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
512-553 6.67e-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: 6.67e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 618468591  512 ETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 553
Cdd:cd18785    22 SLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRA 63
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
444-589 7.14e-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: 7.14e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  444 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFItgHGiGKNQprnkqmeaefRKQEEVLRKFRAHETNLLIATSIVE 523
Cdd:COG0513   244 AIVFCNTKRGADRLAEKLQKRG--------ISAAAL--HG-DLSQ----------GQRERALDAFRNGKIRVLVATDVAA 302
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 618468591  524 EGVDIPKCNLVVRFDLPTEYRSYV---------QSKGRArapisnyIMLADtdkiksfEEDLKTYKAIEKILRNK 589
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 ...
493-584 1.12e-06

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


Pssm-ID: 350179 [Multi-domain]  Cd Length: 160  Bit Score: 50.34  E-value: 1.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  493 QMEAEfrKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVV-----RFDLPTEYrsyvQSKGR-ARAPISNYIMLADT 566
Cdd:cd18792    69 KMTED--EKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIiedadRFGLSQLH----QLRGRvGRGKHQSYCYLLYP 142
                          90
                  ....*....|....*...
gi 618468591  567 DKIKSFEEDLKTYKAIEK 584
Cdd:cd18792   143 DPKKLTETAKKRLRAIAE 160
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
444-553 3.16e-05

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


Pssm-ID: 350186 [Multi-domain]  Cd Length: 116  Bit Score: 44.86  E-value: 3.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  444 GIIFVERRYTAVVLNRLIKEAGkqdPELAYISSNFItghgigknqprnkqmeAEFRKQEEVLR-KFRAHETNLLIATSIV 522
Cdd:cd18799     9 TLIFCVSIEHAEFMAEAFNEAG---IDAVALNSDYS----------------DRERGDEALILlFFGELKPPILVTVDLL 69
                          90       100       110
                  ....*....|....*....|....*....|..
gi 618468591  523 EEGVDIPKCNLVVrFDLPTEYRS-YVQSKGRA 553
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 ...
460-571 3.33e-05

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


Pssm-ID: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 46.18  E-value: 3.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  460 LIKEAGKQDPELA-----YISSNFITGHGIGKNQPRNKQMEaefrkQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLV 534
Cdd:cd18811    35 LIEESEKLDLKAAvamyeYLKERFRPELNVGLLHGRLKSDE-----KDAVMAEFREGEVDILVSTTVIEVGVDVPNATVM 109
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 618468591  535 V-----RFDLPTEYrsyvQSKGR-ARAPISNYIMLADTDKIKS 571
Cdd:cd18811   110 ViedaeRFGLSQLH----QLRGRvGRGDHQSYCLLVYKDPLTE 148
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
444-594 4.55e-05

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 48.01  E-value: 4.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  444 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGhgigknqprnkqmEAEFRKQEEVLRKFRAHETNLLIATSIVE 523
Cdd:PRK11192  248 SIVFVRTRERVHELAGWLRKAG--------INCCYLEG-------------EMVQAKRNEAIKRLTDGRVNVLVATDVAA 306
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  524 EGVDIPKCNLVVRFDLPTEYRSYVQSKGR-ARA-----PIS-----NYIMLadtDKIKSF-EEDLK---------TYKAI 582
Cdd:PRK11192  307 RGIDIDDVSHVINFDMPRSADTYLHRIGRtGRAgrkgtAISlveahDHLLL---GKIERYiEEPLKarvidelrpKTKAP 383
                         170
                  ....*....|..
gi 618468591  583 EKILRNKCSKSV 594
Cdd:PRK11192  384 SEKKTGKPSKKV 395
PTZ00424 PTZ00424
helicase 45; Provisional
499-578 5.40e-05

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 47.90  E-value: 5.40e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  499 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA----RAPIS-NYIMLADTDKIKSFE 573
Cdd:PTZ00424  304 KDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSgrfgRKGVAiNFVTPDDIEQLKEIE 383

                  ....*
gi 618468591  574 EDLKT 578
Cdd:PTZ00424  384 RHYNT 388
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
48-221 6.18e-05

DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350786 [Multi-domain]  Cd Length: 177  Bit Score: 45.79  E-value: 6.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   48 QVELLEAAL--DHNTIVCLNTGSGKTFIAVL-LTKELSyqirgdfsrNGKRTVFLV---NSANQVAQQVSAVRTHS---D 118
Cdd:cd18028     6 QAEAVRAGLlkGENLLISIPTASGKTLIAEMaMVNTLL---------EGGKALYLVplrALASEKYEEFKKLEEIGlkvG 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  119 LKVGEYSnlevnaswTKERWNQEFtkhQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLaiLDHPYRE------IMKL 192
Cdd:cd18028    77 ISTGDYD--------EDDEWLGDY---DIIVATYEKFDSLLRHSPSWLRDVGVVVVDEIHL--ISDEERGptlesiVARL 143
                         170       180
                  ....*....|....*....|....*....
gi 618468591  193 CENCPSCpRILGLTASILNgkcdPEELEE 221
Cdd:cd18028   144 RRLNPNT-QIIGLSATIGN----PDELAE 167
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
502-539 7.30e-05

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 47.84  E-value: 7.30e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 618468591  502 EEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVV-----RFDL 539
Cdd:PRK10917  521 DAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVienaeRFGL 563
DEADc cd00268
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...
34-228 1.74e-04

DEAD-box helicase domain of 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. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350669 [Multi-domain]  Cd Length: 196  Bit Score: 44.74  E-value: 1.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   34 QEAIHD-NIYTPRKYQVELLEAALD-HNTIVCLNTGSGKT--FIAVLLTKeLSYQIRGdfSRNGKRTVFLVNS---ANQV 106
Cdd:cd00268     2 LKALKKlGFEKPTPIQAQAIPLILSgRDVIGQAQTGSGKTlaFLLPILEK-LLPEPKK--KGRGPQALVLAPTrelAMQI 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  107 AQQVSAVRTHSDLKVgeysnlevnASWT----KERWNQEFTKH-QVLIMTCYVALNVLKNGYLSLSDINLLVFDEchlA- 180
Cdd:cd00268    79 AEVARKLGKGTGLKV---------AAIYggapIKKQIEALKKGpDIVVGTPGRLLDLIERGKLDLSNVKYLVLDE---Ad 146
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 618468591  181 -ILDHPYREIM-KLCENCPSCPRILGLTASIlngkcdPEELEEKIQKLEK 228
Cdd:cd00268   147 rMLDMGFEEDVeKILSALPKDRQTLLFSATL------PEEVKELAKKFLK 190
PTZ00110 PTZ00110
helicase; Provisional
499-577 4.40e-04

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 45.15  E-value: 4.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  499 RKQEE---VLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQ---SKGRARAPISNYIMLAdTDKIKSF 572
Cdd:PTZ00110  411 KKQEErtwVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHrigRTGRAGAKGASYTFLT-PDKYRLA 489

                  ....*
gi 618468591  573 EEDLK 577
Cdd:PTZ00110  490 RDLVK 494
RecG COG1200
RecG-like helicase [Replication, recombination and repair];
502-529 4.51e-04

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


Pssm-ID: 440813 [Multi-domain]  Cd Length: 684  Bit Score: 45.04  E-value: 4.51e-04
                          10        20
                  ....*....|....*....|....*...
gi 618468591  502 EEVLRKFRAHETNLLIATSIVEEGVDIP 529
Cdd:COG1200   519 DAVMAAFKAGEIDVLVATTVIEVGVDVP 546
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
503-583 5.23e-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: 5.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  503 EVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTE-----YRSYVQSKGRA-RAPISNYIMLAD--TDKIKsfee 574
Cdd:cd18790    68 EIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEgflrsETSLIQTIGRAaRNVNGKVILYADkiTDSMQ---- 143

                  ....*....
gi 618468591  575 dlktyKAIE 583
Cdd:cd18790   144 -----KAIE 147
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
491-552 5.93e-04

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 44.84  E-value: 5.93e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 618468591  491 NKQMEAEFRkqEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGR 552
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 ...
1880-1912 1.05e-03

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: 1.05e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 618468591 1880 VTVEVVGKgKFKGVGRSYRIAKSAAARRALRSL 1912
Cdd:cd19865    32 MSVEVNGQ-TFEGTGRSKKKAKLEAAEKALRSF 63
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
493-584 1.05e-03

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


Pssm-ID: 350197 [Multi-domain]  Cd Length: 151  Bit Score: 41.56  E-value: 1.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  493 QMEAEfrKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVV-----RFDLPTEYrsyvQSKGR-ARAPISNYIMLADT 566
Cdd:cd18810    60 QMTEN--ELEEVMLEFAKGEYDILVCTTIIESGIDIPNANTIIieradKFGLAQLY----QLRGRvGRSKERAYAYFLYP 133
                          90
                  ....*....|....*...
gi 618468591  567 DKIKSFEEDLKTYKAIEK 584
Cdd:cd18810   134 DQKKLTEDALKRLEAIQE 151
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
1851-1912 1.78e-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: 1.78e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 618468591 1851 RSPVRELLE---MEPETAKFSPAERTYDGKVRVTVEVVGKGK--FKGVGRSYRIAKSAAARRALRSL 1912
Cdd:cd19875     1 KNPVSALNEycqKRGLSLEFVDVSVGPDHCPGFTASATIDGIvfASATGTSKKEAKRAAAKLALKKL 67
DEADc_DDX47 cd17954
DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can ...
43-116 2.53e-03

DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can shuttle between the nucleus and the cytoplasm, and has an RNA-independent ATPase activity. DX47 is a member of the DEAD-box helicases, 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. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350712 [Multi-domain]  Cd Length: 203  Bit Score: 41.15  E-value: 2.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   43 TPRKYQVELLEAALDHNTIVCL-NTGSGKT-----------------FIAVLL--TKELSYQIRGDFSRNGK----RTVF 98
Cdd:cd17954    22 KPTKIQEEAIPVALQGRDIIGLaETGSGKTaafalpilqallenpqrFFALVLapTRELAQQISEQFEALGSsiglKSAV 101
                          90
                  ....*....|....*....
gi 618468591   99 LVNSANQVAQQVS-AVRTH 116
Cdd:cd17954   102 LVGGMDMMAQAIAlAKKPH 120
DEXHc_DDX60 cd18025
DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an ...
44-231 2.59e-03

DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an IFN-inducible cytoplasmic helicase that plays a role in RIG-I-mediated type I interferon (IFN) nuclease-mediated viral RNA degradation. DDX60 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350783 [Multi-domain]  Cd Length: 192  Bit Score: 41.20  E-value: 2.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   44 PRKYQVELLEAaLDHN--TIVCLNTGSGKTFIAVlltkelsYQIRGDFSRNGKRTVFLVNSA----NQVAQQVSAVRTHS 117
Cdd:cd18025     2 PDAWQRELLDI-VDRResALIVAPTSSGKTFISY-------YCMEKVLRESDDGVVVYVAPTkalvNQVVAEVYARFSKK 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  118 DLKVGEYsnleVNASWTKERWNQEFTKHQVLImTCYVALNVLkngYLSLSD------INLLVFDECHL--AILDHPYREI 189
Cdd:cd18025    74 YPPSGKS----LWGVFTRDYRHNNPMNCQVLI-TVPECLEIL---LLSPHNaswvprIKYVIFDEIHSigQSEDGAVWEQ 145
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 618468591  190 MKLCENCPscprILGLTASILNgkcdPEELEEKIQKLEKILK 231
Cdd:cd18025   146 LLLLIPCP----FLALSATIGN----PQKFHEWLQSVQRARK 179
Mfd COG1197
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ...
478-532 3.39e-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: 3.39e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 618468591  478 FITGHGigknqprnkQMEAefRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCN 532
Cdd:COG1197   824 IAVAHG---------QMSE--RELERVMLDFYEGEFDVLVCTTIIETGIDIPNAN 867
DEXHc_RecQ cd17920
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ...
43-226 4.17e-03

DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box helicase superfamily is a family of highly conserved DNA repair helicases. This domain contains the ATP-binding region.


Pssm-ID: 350678 [Multi-domain]  Cd Length: 200  Bit Score: 40.60  E-value: 4.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591   43 TPRKYQVELLEAALDH-NTIVCLNTGSGKTFI----AVLLTKE-------LSY---QIRGdFSRNGKRTVFLvNSANQVA 107
Cdd:cd17920    12 EFRPGQLEAINAVLAGrDVLVVMPTGGGKSLCyqlpALLLDGVtlvvsplISLmqdQVDR-LQQLGIRAAAL-NSTLSPE 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  108 QQVSAVRthsDLKVGEYSNLEVnaswTKER-WNQEFtkhqvlimtcyvaLNVLKNGYlSLSDINLLVFDECHLaILD--H 184
Cdd:cd17920    90 EKREVLL---RIKNGQYKLLYV----TPERlLSPDF-------------LELLQRLP-ERKRLALIVVDEAHC-VSQwgH 147
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 618468591  185 ---P-YREIMKLCENCPSCPrILGLTASilngkCDPEELEEKIQKL 226
Cdd:cd17920   148 dfrPdYLRLGRLRRALPGVP-ILALTAT-----ATPEVREDILKRL 187
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
495-553 4.38e-03

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 41.70  E-value: 4.38e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 618468591  495 EAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 553
Cdd:PLN00206  401 EKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRA 459
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
455-589 6.37e-03

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


Pssm-ID: 440816 [Multi-domain]  Cd Length: 535  Bit Score: 41.22  E-value: 6.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  455 VVLN---------RLIKEAGKqDPELAYISSNFITGHgigknqprnkqmeaefRKQ--EEVLRKFRAHETNLLIATSIVE 523
Cdd:COG1203   371 VIVNtvkdaqelyEALKEKLP-DEEVYLLHSRFCPAD----------------RSEieKEIKERLERGKPCILVSTQVVE 433
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 618468591  524 EGVDI-----------------------------PKCNLVVrFDLPTEYRSYVQSK---GRARAPISNYIMLADTDKIKS 571
Cdd:COG1203   434 AGVDIdfdvvirdlapldsliqragrcnrhgrkeEEGNVYV-FDPEDEGGGYVYDKpllERTRELLREHDEILPEDKREL 512
                         170
                  ....*....|....*...
gi 618468591  572 FEEdlkTYKAIEKILRNK 589
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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