NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1958786380|ref|XP_038969292|]
View 

endoribonuclease Dicer isoform X2 [Rattus norvegicus]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 19-209 4.81e-91

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: 293.79  E-value: 4.81e-91
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   19 VELLEAALDHNTIVCLNTGSGKTFIAVLLTKELAHQIRGDLSPHaKRTVFLVNSANQVAQQVSAVRTHSDLKVGEYSNLE 98
Cdd:cd18034      8 LELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRKEKNPK-KRAVFLVPTVPLVAQQAEAIRSHTDLKVGEYSGEM 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   99 VNASWTKERWSQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCDSC---PSCPRILGL 175
Cdd:cd18034     87 GVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLegrTSRPRILGL 166

                          170       180       190
                   ....*....|....*....|....*....|....
gi 1958786380  176 TASILNGKCDPDELEEKIQKLEKILKSGAETATD 209
Cdd:cd18034    167 TASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
 856-978 1.42e-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: 229.25  E-value: 1.42e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  856 DSSTLDIDFKFMEDIEkSEARIGIPSTKYSKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 935
Cdd:cd02843      1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1958786380  936 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 978
Cdd:cd02843     80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 342-534 4.08e-57

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: 194.35  E-value: 4.08e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  342 YVTPKVMKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddddeeieekekpetnfpspfTNILCGIIFVERR 421
Cdd:cd18802      4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  422 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprSKQMEAEFRKQEEVLRKFRAHETNLLIATSVVEEGVDIPKC 501
Cdd:cd18802     36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109

                          170       180       190
                   ....*....|....*....|....*....|...
gi 1958786380  502 NLVVRFDLPTEYRSYVQSKGRARAPISNYVMLA 534
Cdd:cd18802    110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1648-1812 6.42e-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: 144.68  E-value: 6.42e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1648 YLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1727
Cdd:cd00593      2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKY---- 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1728 spelfhviddfvqFQLEKNEMQGMDSElrrseedeekeedieVPKAMGDIFESLAGAIYMDSGMslEVVWQVYYPMMRPL 1807
Cdd:cd00593     78 -------------LRLGKGEEKSGGRL---------------RPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPL 127


                   ....*
gi 1958786380 1808 IEKFS 1812
Cdd:cd00593    128 IEEIS 132
DSRM_DICER cd10843
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ...
 1817-1879 2.62e-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: 2.62e-39
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958786380 1817 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLK 1879
Cdd:cd10843      1 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGRFKGVGRNYRIAKSAAARRALRSLK 63
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 600-688 2.49e-31

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: 118.37  E-value: 2.49e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  600 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMGCVRLAERVVALICCEKLHKIGELD 679
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79


                   ....*....
gi 1958786380  680 EHLMPVGKE 688
Cdd:pfam03368   80 DHLLPLTKK 88
RIBOc smart00535
Ribonuclease III family;
1266-1357 3.41e-25

Ribonuclease III family;


:

Pssm-ID: 197778  Cd Length: 129  Bit Score: 102.30  E-value: 3.41e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  1266 LILQALTLSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKQGLPSRMVVSIF 1344
Cdd:smart00535    2 LLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81

                            90
                    ....*....|...
gi 1958786380  1345 DPPVNWLPPGYVV 1357
Cdd:smart00535   82 EAISGGRDKPKIL 94
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 241-335 1.19e-24

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: 100.05  E-value: 1.19e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  241 LMELEEALDFINDCNVSVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 311
Cdd:cd15903      1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                           90       100
                   ....*....|....*....|....
gi 1958786380  312 RKFLLFTDTLLRKIHALCEEYFSP 335
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 ...
 19-209 4.81e-91

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: 293.79  E-value: 4.81e-91
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   19 VELLEAALDHNTIVCLNTGSGKTFIAVLLTKELAHQIRGDLSPHaKRTVFLVNSANQVAQQVSAVRTHSDLKVGEYSNLE 98
Cdd:cd18034      8 LELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRKEKNPK-KRAVFLVPTVPLVAQQAEAIRSHTDLKVGEYSGEM 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   99 VNASWTKERWSQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCDSC---PSCPRILGL 175
Cdd:cd18034     87 GVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLegrTSRPRILGL 166

                          170       180       190
                   ....*....|....*....|....*....|....
gi 1958786380  176 TASILNGKCDPDELEEKIQKLEKILKSGAETATD 209
Cdd:cd18034    167 TASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
 856-978 1.42e-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: 229.25  E-value: 1.42e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  856 DSSTLDIDFKFMEDIEkSEARIGIPSTKYSKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 935
Cdd:cd02843      1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1958786380  936 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 978
Cdd:cd02843     80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 342-534 4.08e-57

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: 194.35  E-value: 4.08e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  342 YVTPKVMKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddddeeieekekpetnfpspfTNILCGIIFVERR 421
Cdd:cd18802      4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  422 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprSKQMEAEFRKQEEVLRKFRAHETNLLIATSVVEEGVDIPKC 501
Cdd:cd18802     36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109

                          170       180       190
                   ....*....|....*....|....*....|...
gi 1958786380  502 NLVVRFDLPTEYRSYVQSKGRARAPISNYVMLA 534
Cdd:cd18802    110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1648-1812 6.42e-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: 144.68  E-value: 6.42e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1648 YLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1727
Cdd:cd00593      2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKY---- 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1728 spelfhviddfvqFQLEKNEMQGMDSElrrseedeekeedieVPKAMGDIFESLAGAIYMDSGMslEVVWQVYYPMMRPL 1807
Cdd:cd00593     78 -------------LRLGKGEEKSGGRL---------------RPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPL 127


                   ....*
gi 1958786380 1808 IEKFS 1812
Cdd:cd00593    128 IEEIS 132
DSRM_DICER cd10843
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ...
 1817-1879 2.62e-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: 2.62e-39
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958786380 1817 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLK 1879
Cdd:cd10843      1 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGRFKGVGRNYRIAKSAAARRALRSLK 63
RIBOc smart00535
Ribonuclease III family;
1648-1811 4.28e-37

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 136.58  E-value: 4.28e-37
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  1648 YLLQAFTHASYHYNTitDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1727
Cdd:smart00535    2 LLLRALTHASYSNEH--EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEF---- 75

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  1728 spelfhviddfvqFQLEKNEmqgMDSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSGmsLEVVWQVYYPMMRPL 1807
Cdd:smart00535   76 -------------IRLGRGE---AISGGRDK------------PKILADVFEALIGAIYLDSG--LEAAREFIRDLLGPR 125


                    ....
gi 1958786380  1808 IEKF 1811
Cdd:smart00535  126 LDEL 129
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1635-1878 8.12e-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: 136.18  E-value: 8.12e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1635 FEKKINYIFKNKAYLLQAFTHASYHYNT--ITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFA 1712
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYANEHhkDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1713 SLAVKYDYHKYFKavspelfhviddfvqfqLEKNEMQgmdSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSGMS 1792
Cdd:TIGR02191   81 EVARELGLGDFLL-----------------LGKGEEK---SGGRRR------------DSILADAFEALIGAIYLDSGLE 128

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1793 L--EVVWQVYYPMMRPLIEKFSANVPRSPVRELL----------EMEPETAKfsPAERTYdgkvRVTVEVVGKGKFKGVG 1860
Cdd:TIGR02191  129 AarKFILKLLIPRIDAIIKEETLKDYKTALQEWAqargkplpeyRLIKEEGP--DHDKEF----TVEVSVNGEPYGEGKG 202

                          250
                   ....*....|....*...
gi 1958786380 1861 RSYRIAKSAAARRALRSL 1878
Cdd:TIGR02191  203 KSKKEAEQNAAKAALEKL 220
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1632-1882 2.27e-35

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 135.23  E-value: 2.27e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1632 FENFEKKINYIFKNKAYLLQAFTHASY-HYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTI 1710
Cdd:COG0571      4 LEELEERLGYRFKDPELLEQALTHRSYaNEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEET 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1711 FASLAVKYDyhkyfkavspelfhvIDDFVqfQLEKNEMQgmdSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSG 1790
Cdd:COG0571     84 LAEIARELG---------------LGDYL--RLGKGEEK---SGGRRR------------PSILADAFEALIGAIYLDGG 131

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1791 msLEVVWQVYYPMMRPLIEKFSANVPRS-----------------PVRELLEME-PETAK-FspaertydgkvRVTVEVV 1851
Cdd:COG0571    132 --LEAARKFVLRLFEPRLEEIAPGGAGKdyktalqewlqarglplPEYEVVEEEgPDHAKtF-----------TVEVLVG 198

                          250       260       270
                   ....*....|....*....|....*....|.
gi 1958786380 1852 GKGKFKGVGRSYRIAKSAAARRALRSLKANQ 1882
Cdd:COG0571    199 GKVLGEGTGRSKKEAEQAAAKAALEKLGKKE 229
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 600-688 2.49e-31

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: 118.37  E-value: 2.49e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  600 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMGCVRLAERVVALICCEKLHKIGELD 679
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79


                   ....*....
gi 1958786380  680 EHLMPVGKE 688
Cdd:pfam03368   80 DHLLPLTKK 88
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
19-522 2.50e-31

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 133.32  E-value: 2.50e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   19 VELLEAALDHNTIVCLNTGSGKTFIAVLLTKELAHQIRGD---LSPhakrTVFLVNsanQVAQQVSAVRTHSDLKVGEYS 95
Cdd:COG1111      9 LNLAASALRKNTLVVLPTGLGKTAVALLVIAERLHKKGGKvlfLAP----TKPLVE---QHAEFFKEALNIPEDEIVVFT 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   96 NlEVNASWTKERWSqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCDSCPSCPRILGL 175
Cdd:COG1111     82 G-EVSPEKRKELWE----KARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKDPLILGM 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  176 TASilngkcdPDELEEKIQklekilksgaETATDLVVldrytsqpcEIVV-------DCGPFT-DRSGLYERLLM--ELE 245
Cdd:COG1111    157 TAS-------PGSDEEKIE----------EVCENLGI---------ENVEvrteedpDVAPYVhDTEVEWIRVELpeELK 210

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  246 EALDFIN-----------DCNVSVHSKERDST--------LISKQILSDCRAVLVVLGPwcadkVAGMM----------- 295
Cdd:COG1111    211 EIRDLLNevlddrlkklkELGVIVSTSPDLSKkdllalqkKLQRRIREDDSEGYRAISI-----LAEALklrhalellet 285

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  296 --VRELQKYIKhEQEELHRKFL-------LFTDTLLRKIHALCEEYfspasldlKYVTPKVMKLLEILRKYKpyerqqfe 366
Cdd:COG1111    286 qgVEALLRYLE-RLEEEARSSGgskaskrLVSDPRFRKAMRLAEEA--------DIEHPKLSKLREILKEQL-------- 348

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  367 svewynNRNQDNYVswsdsedddddeeieekekpetnfpspftnilcgIIFVERRYTAVVLNRLIKEAGkqdpelayISS 446
Cdd:COG1111    349 ------GTNPDSRI----------------------------------IVFTQYRDTAEMIVEFLSEPG--------IKA 380

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958786380  447 NFITGHGIGKNQPRSKQmeaefRKQEEVLRKFRAHETNLLIATSVVEEGVDIPKCNLVVRFDL-PTEYRSyVQSKGR 522
Cdd:COG1111    381 GRFVGQASKEGDKGLTQ-----KEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPvPSEIRS-IQRKGR 451
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
 861-1035 1.77e-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: 112.38  E-value: 1.77e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   861 DIDFKFMEDIEksEARIGIPSTKYSKEtpfvfkleDYQDAVIIPRYRNfdqpHRFYVADVYTDLTPLSKFPSPEYE--TF 938
Cdd:smart00949    1 ETVLDFMRQLP--SQGNRSNFQDRCAK--------DLKGLIVLTRYNN----KTYRIDDIDWNLAPKSTFEKSDGSeiTF 66

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   939 AEYYKTKYNLDLTNLNQPLLdVDHTSsrlnlltpRHLNQKGKalplssaekrkakweslQNKQILVPELCAIHPIPASLW 1018
Cdd:smart00949   67 VEYYKQKYNITIRDPNQPLL-VSRPK--------RRRNQNGK-----------------GEPVLLPPELCFITGLTDRMR 120

                           170
                    ....*....|....*..
gi 1958786380  1019 RKAVCLPSILYRLHCLL 1035
Cdd:smart00949  121 KDFMLMKSIADRTRLSP 137
RIBOc smart00535
Ribonuclease III family;
1266-1357 3.41e-25

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 102.30  E-value: 3.41e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  1266 LILQALTLSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKQGLPSRMVVSIF 1344
Cdd:smart00535    2 LLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81

                            90
                    ....*....|...
gi 1958786380  1345 DPPVNWLPPGYVV 1357
Cdd:smart00535   82 EAISGGRDKPKIL 94
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 241-335 1.19e-24

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: 100.05  E-value: 1.19e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  241 LMELEEALDFINDCNVSVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 311
Cdd:cd15903      1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                           90       100
                   ....*....|....*....|....
gi 1958786380  312 RKFLLFTDTLLRKIHALCEEYFSP 335
Cdd:cd15903     81 RLFLRYVITQLRKIRKLLEDEMKN 104
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1266-1346 1.44e-24

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: 100.77  E-value: 1.44e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1266 LILQALT---LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKQGLPSRMVVS 1342
Cdd:cd00593      2 LLLEALThpsYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLG 81


                   ....
gi 1958786380 1343 IFDP 1346
Cdd:cd00593     82 KGEE 85
PRK13766 PRK13766
Hef nuclease; Provisional
 25-523 1.03e-21

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 102.64  E-value: 1.03e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   25 ALDHNTIVCLNTGSGKTFIAVLLTKELAHQIRGD---LSPhakrTVFLVNsanqvaQQVSAVRTHSDLKVGEYSNL--EV 99
Cdd:PRK13766    27 ALKKNTLVVLPTGLGKTAIALLVIAERLHKKGGKvliLAP----TKPLVE------QHAEFFRKFLNIPEEKIVVFtgEV 96

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  100 NASWTKERWsqefTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPY----REIMKLCDScpscPRILGL 175
Cdd:PRK13766    97 SPEKRAELW----EKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYvyiaERYHEDAKN----PLVLGL 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  176 TASilngkcdPDELEEKIQKLEKILksGAEtatdlvvldrytsqpcEIVV------DCGPFT-DRSGLYERLLM--ELEE 246
Cdd:PRK13766   169 TAS-------PGSDEEKIKEVCENL--GIE----------------HVEVrteddpDVKPYVhKVKIEWVRVELpeELKE 223

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  247 ALDFINDCnvsvhSKERdstlisKQILSDCRaVLVVLGPWCADK-VAGMMvRELQKYIKHEQEEL--------------H 311
Cdd:PRK13766   224 IRDLLNEA-----LKDR------LKKLKELG-VIVSISPDVSKKeLLGLQ-KKLQQEIANDDSEGyeaisilaeamklrH 290

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  312 RKFLLFT---DTLLRKIHALCEE-----------------YFSPASLDLKYVT---PKVMKLLEILRKykpyerqQFEsv 368
Cdd:PRK13766   291 AVELLETqgvEALRRYLERLREEarssggskaskrlvedpRFRKAVRKAKELDiehPKLEKLREIVKE-------QLG-- 361

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  369 ewynnRNQDNYVswsdsedddddeeieekekpetnfpspftnilcgIIFVERRYTA-VVLNRLIKEagkqdpelayissN 447
Cdd:PRK13766   362 -----KNPDSRI----------------------------------IVFTQYRDTAeKIVDLLEKE-------------G 389

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958786380  448 FITGHGIGK-NQPRSKQMEAefRKQEEVLRKFRAHETNLLIATSVVEEGVDIPKCNLVVRFD-LPTEYRSyVQSKGRA 523
Cdd:PRK13766   390 IKAVRFVGQaSKDGDKGMSQ--KEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEpVPSEIRS-IQRKGRT 464
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1668-1790 1.13e-21

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 91.57  E-value: 1.13e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1668 QRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELfhviddfvqfqleKNE 1747
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI-------------RRR 67

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1958786380 1748 MQGMDSELRRSEEDeekeedievPKAMGDIFESLAGAIYMDSG 1790
Cdd:pfam00636   68 NNALGKGPKRADGK---------EKVLADAFEALIGALYLDGG 101
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
 884-1034 2.27e-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: 88.40  E-value: 2.27e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  884 YSKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFP--SPEYETFAEYYKTKYNLDLTNLNQPLLDVd 961
Cdd:pfam02170    8 QQQKDRRDFRKEAKKALKGLKVYTTYNNPRTYRIDGITFDPTPESTFPlkDGKEITVVDYFKKKYNIDLKYPDQPLLLV- 86

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958786380  962 htssrlnlltprhlnqkgkalplssaeKRKakweslQNKQILVPELCAihpIPASLWRKAVCLPSILYRLHCL 1034
Cdd:pfam02170   87 ---------------------------GKK------RPKVYLPPELCN---LVDGQRYTKKLMPSIAQRTRLL 123
DEXDc smart00487
DEAD-like helicases superfamily;
20-212 2.51e-19

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 88.32  E-value: 2.51e-19
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380    20 ELLEAALD--HNTIVCLNTGSGKTFIAVLLTKELAHQIRGdlsphaKRTVFLVNSANQVAQQVSAVRTHSDLKVGEYSNL 97
Cdd:smart00487   15 EAIEALLSglRDVILAAPTGSGKTLAALLPALEALKRGKG------GRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGL 88

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380    98 EVNASWTKERWSQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCDSCPSCPRILGLTA 177
Cdd:smart00487   89 YGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSA 168

                           170       180       190
                    ....*....|....*....|....*....|....*
gi 1958786380   178 SILNgkcDPDELEEKIQKLEKILKSGAETATDLVV 212
Cdd:smart00487  169 TPPE---EIENLLELFLNDPVFIDVGFTPLEPIEQ 200
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1283-1346 6.62e-15

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 72.31  E-value: 6.62e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958786380 1283 ERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKQGLPSRMVVSIFDP 1346
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI 64
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 471-523 1.08e-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: 71.86  E-value: 1.08e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958786380  471 QEEVLRKFRAHETNLLIATSVVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 523
Cdd:pfam00271   53 REEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
HELICc smart00490
helicase superfamily c-terminal domain;
469-523 8.75e-13

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 65.31  E-value: 8.75e-13
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 1958786380   469 RKQEEVLRKFRAHETNLLIATSVVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 523
Cdd:smart00490   24 EEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
ResIII pfam04851
Type III restriction enzyme, res subunit;
20-177 2.61e-11

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 63.85  E-value: 2.61e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   20 ELLEAALDHNTIVCLN--TGSGKTFIAVLLTKELAHqirgdlSPHAKRTVFLVNSANQVAQQvsavrthsdlkVGEYSNL 97
Cdd:pfam04851   14 NLLESIKNGQKRGLIVmaTGSGKTLTAAKLIARLFK------KGPIKKVLFLVPRKDLLEQA-----------LEEFKKF 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   98 EVNASWTKERWSQEFTKHQV----LIMTCYVALNV-LKNGYLSLSD--INLLVFDECHLAILDHpYREIMKLCdscpSCP 170
Cdd:pfam04851   77 LPNYVEIGEIISGDKKDESVddnkIVVTTIQSLYKaLELASLELLPdfFDVIIIDEAHRSGASS-YRNILEYF----KPA 151


                   ....*..
gi 1958786380  171 RILGLTA 177
Cdd:pfam04851  152 FLLGLTA 158
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1263-1335 4.72e-11

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 64.73  E-value: 4.72e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958786380 1263 NPGLILQALT---LSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKQGL 1335
Cdd:COG0571     17 DPELLEQALThrsYANEHGGLeNNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAEIARELGL 93
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1262-1337 5.06e-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: 64.53  E-value: 5.06e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1262 PNPGLILQALT-----LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKQGLP 1336
Cdd:TIGR02191   10 KNPELLEQALThrsyaNEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVARELGLG 89


                   .
gi 1958786380 1337 S 1337
Cdd:TIGR02191   90 D 90
DSRM smart00358
Double-stranded RNA binding motif;
1816-1879 5.31e-08

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 51.49  E-value: 5.31e-08
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958786380  1816 PRSPVRELLEMEPETAKFSPAERT-YDGKVRVTVEVVGKGK--FKGVGRSYRIAKSAAARRALRSLK 1879
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEEgPDHAPRFTVTVKVGGKrtGEGEGSSKKEAKQRAAEAALRSLK 67
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
414-559 7.63e-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: 7.63e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  414 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFItgHGiGKNQprskqmeaefRKQEEVLRKFRAHETNLLIATSVVE 493
Cdd:COG0513    244 AIVFCNTKRGADRLAEKLQKRG--------ISAAAL--HG-DLSQ----------GQRERALDAFRNGKIRVLVATDVAA 302

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958786380  494 EGVDIPKCNLVVRFDLPTEYRSYV---------QSKGRArapisnyVMLADtdkiksfEEDLKTYKAIEKILRNK 559
Cdd:COG0513    303 RGIDIDDVSHVINYDLPEDPEDYVhrigrtgraGAEGTA-------ISLVT-------PDERRLLRAIEKLIGQK 363
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
 472-509 5.01e-06

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 51.69  E-value: 5.01e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1958786380  472 EEVLRKFRAHETNLLIATSVVEEGVDIPKCNLVV-----RFDL 509
Cdd:PRK10917   521 DAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVienaeRFGL 563
 
Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 19-209 4.81e-91

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: 293.79  E-value: 4.81e-91
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   19 VELLEAALDHNTIVCLNTGSGKTFIAVLLTKELAHQIRGDLSPHaKRTVFLVNSANQVAQQVSAVRTHSDLKVGEYSNLE 98
Cdd:cd18034      8 LELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRKEKNPK-KRAVFLVPTVPLVAQQAEAIRSHTDLKVGEYSGEM 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   99 VNASWTKERWSQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCDSC---PSCPRILGL 175
Cdd:cd18034     87 GVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLegrTSRPRILGL 166

                          170       180       190
                   ....*....|....*....|....*....|....
gi 1958786380  176 TASILNGKCDPDELEEKIQKLEKILKSGAETATD 209
Cdd:cd18034    167 TASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
 856-978 1.42e-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: 229.25  E-value: 1.42e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  856 DSSTLDIDFKFMEDIEkSEARIGIPSTKYSKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 935
Cdd:cd02843      1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1958786380  936 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 978
Cdd:cd02843     80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 342-534 4.08e-57

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: 194.35  E-value: 4.08e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  342 YVTPKVMKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddddeeieekekpetnfpspfTNILCGIIFVERR 421
Cdd:cd18802      4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  422 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprSKQMEAEFRKQEEVLRKFRAHETNLLIATSVVEEGVDIPKC 501
Cdd:cd18802     36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109

                          170       180       190
                   ....*....|....*....|....*....|...
gi 1958786380  502 NLVVRFDLPTEYRSYVQSKGRARAPISNYVMLA 534
Cdd:cd18802    110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 19-208 6.05e-57

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: 196.11  E-value: 6.05e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   19 VELLEAAL-DHNTIVCLNTGSGKTFIAVLLTKELAHQIRgdlSPHAKRTVFLVNSANQVAQQVSAVRTHSD---LKVGEY 94
Cdd:cd17927      8 LELAQPALkGKNTIICLPTGSGKTFVAVLICEHHLKKFP---AGRKGKVVFLANKVPLVEQQKEVFRKHFErpgYKVTGL 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   95 SNlevnASWTKERWSQEFTKHQVLIMTCYVALNVLKNGYL-SLSDINLLVFDECHLAILDHPYREIMKLCDSCPS----- 168
Cdd:cd17927     85 SG----DTSENVSVEQIVESSDVIIVTPQILVNDLKSGTIvSLSDFSLLVFDECHNTTKNHPYNEIMFRYLDQKLgssgp 160

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 1958786380  169 CPRILGLTASILNGKC-DPDELEEKIQKLEKILKSGAETAT 208
Cdd:cd17927    161 LPQILGLTASPGVGGAkNTEEALEHICKLCANLDISVIATV 201
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1648-1812 6.42e-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: 144.68  E-value: 6.42e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1648 YLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1727
Cdd:cd00593      2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKY---- 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1728 spelfhviddfvqFQLEKNEMQGMDSElrrseedeekeedieVPKAMGDIFESLAGAIYMDSGMslEVVWQVYYPMMRPL 1807
Cdd:cd00593     78 -------------LRLGKGEEKSGGRL---------------RPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPL 127


                   ....*
gi 1958786380 1808 IEKFS 1812
Cdd:cd00593    128 IEEIS 132
DSRM_DICER cd10843
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ...
 1817-1879 2.62e-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: 2.62e-39
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958786380 1817 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLK 1879
Cdd:cd10843      1 RSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGRFKGVGRNYRIAKSAAARRALRSLK 63
RIBOc smart00535
Ribonuclease III family;
1648-1811 4.28e-37

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 136.58  E-value: 4.28e-37
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  1648 YLLQAFTHASYHYNTitDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYfkav 1727
Cdd:smart00535    2 LLLRALTHASYSNEH--EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEF---- 75

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  1728 spelfhviddfvqFQLEKNEmqgMDSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSGmsLEVVWQVYYPMMRPL 1807
Cdd:smart00535   76 -------------IRLGRGE---AISGGRDK------------PKILADVFEALIGAIYLDSG--LEAAREFIRDLLGPR 125


                    ....
gi 1958786380  1808 IEKF 1811
Cdd:smart00535  126 LDEL 129
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1635-1878 8.12e-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: 136.18  E-value: 8.12e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1635 FEKKINYIFKNKAYLLQAFTHASYHYNT--ITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFA 1712
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYANEHhkDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1713 SLAVKYDYHKYFKavspelfhviddfvqfqLEKNEMQgmdSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSGMS 1792
Cdd:TIGR02191   81 EVARELGLGDFLL-----------------LGKGEEK---SGGRRR------------DSILADAFEALIGAIYLDSGLE 128

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1793 L--EVVWQVYYPMMRPLIEKFSANVPRSPVRELL----------EMEPETAKfsPAERTYdgkvRVTVEVVGKGKFKGVG 1860
Cdd:TIGR02191  129 AarKFILKLLIPRIDAIIKEETLKDYKTALQEWAqargkplpeyRLIKEEGP--DHDKEF----TVEVSVNGEPYGEGKG 202

                          250
                   ....*....|....*...
gi 1958786380 1861 RSYRIAKSAAARRALRSL 1878
Cdd:TIGR02191  203 KSKKEAEQNAAKAALEKL 220
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1632-1882 2.27e-35

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 135.23  E-value: 2.27e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1632 FENFEKKINYIFKNKAYLLQAFTHASY-HYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTI 1710
Cdd:COG0571      4 LEELEERLGYRFKDPELLEQALTHRSYaNEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEET 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1711 FASLAVKYDyhkyfkavspelfhvIDDFVqfQLEKNEMQgmdSELRRSeedeekeedievPKAMGDIFESLAGAIYMDSG 1790
Cdd:COG0571     84 LAEIARELG---------------LGDYL--RLGKGEEK---SGGRRR------------PSILADAFEALIGAIYLDGG 131

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1791 msLEVVWQVYYPMMRPLIEKFSANVPRS-----------------PVRELLEME-PETAK-FspaertydgkvRVTVEVV 1851
Cdd:COG0571    132 --LEAARKFVLRLFEPRLEEIAPGGAGKdyktalqewlqarglplPEYEVVEEEgPDHAKtF-----------TVEVLVG 198

                          250       260       270
                   ....*....|....*....|....*....|.
gi 1958786380 1852 GKGKFKGVGRSYRIAKSAAARRALRSLKANQ 1882
Cdd:COG0571    199 GKVLGEGTGRSKKEAEQAAAKAALEKLGKKE 229
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 600-688 2.49e-31

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: 118.37  E-value: 2.49e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  600 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMGCVRLAERVVALICCEKLHKIGELD 679
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79


                   ....*....
gi 1958786380  680 EHLMPVGKE 688
Cdd:pfam03368   80 DHLLPLTKK 88
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
19-522 2.50e-31

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 133.32  E-value: 2.50e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   19 VELLEAALDHNTIVCLNTGSGKTFIAVLLTKELAHQIRGD---LSPhakrTVFLVNsanQVAQQVSAVRTHSDLKVGEYS 95
Cdd:COG1111      9 LNLAASALRKNTLVVLPTGLGKTAVALLVIAERLHKKGGKvlfLAP----TKPLVE---QHAEFFKEALNIPEDEIVVFT 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   96 NlEVNASWTKERWSqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCDSCPSCPRILGL 175
Cdd:COG1111     82 G-EVSPEKRKELWE----KARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKDPLILGM 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  176 TASilngkcdPDELEEKIQklekilksgaETATDLVVldrytsqpcEIVV-------DCGPFT-DRSGLYERLLM--ELE 245
Cdd:COG1111    157 TAS-------PGSDEEKIE----------EVCENLGI---------ENVEvrteedpDVAPYVhDTEVEWIRVELpeELK 210

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  246 EALDFIN-----------DCNVSVHSKERDST--------LISKQILSDCRAVLVVLGPwcadkVAGMM----------- 295
Cdd:COG1111    211 EIRDLLNevlddrlkklkELGVIVSTSPDLSKkdllalqkKLQRRIREDDSEGYRAISI-----LAEALklrhalellet 285

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  296 --VRELQKYIKhEQEELHRKFL-------LFTDTLLRKIHALCEEYfspasldlKYVTPKVMKLLEILRKYKpyerqqfe 366
Cdd:COG1111    286 qgVEALLRYLE-RLEEEARSSGgskaskrLVSDPRFRKAMRLAEEA--------DIEHPKLSKLREILKEQL-------- 348

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  367 svewynNRNQDNYVswsdsedddddeeieekekpetnfpspftnilcgIIFVERRYTAVVLNRLIKEAGkqdpelayISS 446
Cdd:COG1111    349 ------GTNPDSRI----------------------------------IVFTQYRDTAEMIVEFLSEPG--------IKA 380

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958786380  447 NFITGHGIGKNQPRSKQmeaefRKQEEVLRKFRAHETNLLIATSVVEEGVDIPKCNLVVRFDL-PTEYRSyVQSKGR 522
Cdd:COG1111    381 GRFVGQASKEGDKGLTQ-----KEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPvPSEIRS-IQRKGR 451
PAZ cd02825
PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two ...
 856-978 3.65e-31

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


Pssm-ID: 239207  Cd Length: 115  Bit Score: 119.10  E-value: 3.65e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  856 DSSTLDIDFKFMEDIEKSEARIGIPSTKYSKETPfVFKLEDYQDaviipryrnfdQPHRFYVADVYTDLTPLS--KFPSP 933
Cdd:cd02825      1 ADPVIETMCKFPKDREIDTPLLDSPREEFTKELK-GLKVEDTHN-----------PLNRVYRPDGETRLKAPSqlKHSDG 68

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1958786380  934 EYETFAEYYKTKYNLDLTNLNQPLLDVDHTS--SRLNLLTPRHLNQK 978
Cdd:cd02825     69 KEITFADYFKERYNLTLTDLNQPLLIVKFSSkkSYSILLPPELCVIT 115
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
 861-1035 1.77e-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: 112.38  E-value: 1.77e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   861 DIDFKFMEDIEksEARIGIPSTKYSKEtpfvfkleDYQDAVIIPRYRNfdqpHRFYVADVYTDLTPLSKFPSPEYE--TF 938
Cdd:smart00949    1 ETVLDFMRQLP--SQGNRSNFQDRCAK--------DLKGLIVLTRYNN----KTYRIDDIDWNLAPKSTFEKSDGSeiTF 66

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   939 AEYYKTKYNLDLTNLNQPLLdVDHTSsrlnlltpRHLNQKGKalplssaekrkakweslQNKQILVPELCAIHPIPASLW 1018
Cdd:smart00949   67 VEYYKQKYNITIRDPNQPLL-VSRPK--------RRRNQNGK-----------------GEPVLLPPELCFITGLTDRMR 120

                           170
                    ....*....|....*..
gi 1958786380  1019 RKAVCLPSILYRLHCLL 1035
Cdd:smart00949  121 KDFMLMKSIADRTRLSP 137
RIBOc smart00535
Ribonuclease III family;
1266-1357 3.41e-25

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 102.30  E-value: 3.41e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  1266 LILQALTLSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKQGLPSRMVVSIF 1344
Cdd:smart00535    2 LLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81

                            90
                    ....*....|...
gi 1958786380  1345 DPPVNWLPPGYVV 1357
Cdd:smart00535   82 EAISGGRDKPKIL 94
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 241-335 1.19e-24

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: 100.05  E-value: 1.19e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  241 LMELEEALDFINDCNVSVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 311
Cdd:cd15903      1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                           90       100
                   ....*....|....*....|....
gi 1958786380  312 RKFLLFTDTLLRKIHALCEEYFSP 335
Cdd:cd15903     81 RLFLRYVITQLRKIRKLLEDEMKN 104
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1266-1346 1.44e-24

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: 100.77  E-value: 1.44e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1266 LILQALT---LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKQGLPSRMVVS 1342
Cdd:cd00593      2 LLLEALThpsYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLG 81


                   ....
gi 1958786380 1343 IFDP 1346
Cdd:cd00593     82 KGEE 85
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 20-196 1.94e-22

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: 97.16  E-value: 1.94e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   20 ELLEAALD-HNTIVCLNTGSGKTFIAVLLTKelaHQIRGDLSPHAK-RTVFLVNSANQVAQQvSAVRTHSDLKVGEYSNL 97
Cdd:cd18036      9 ELVLPALRgKNTIICAPTGSGKTRVAVYICR---HHLEKRRSAGEKgRVVVLVNKVPLVEQQ-LEKFFKYFRKGYKVTGL 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   98 EvNASWTKERWSQEFTKHQVLIMTCYVALNVLKNG----YLSLSDINLLVFDECHLAILDHPYREIM------KLCDSCP 167
Cdd:cd18036     85 S-GDSSHKVSFGQIVKASDVIICTPQILINNLLSGreeeRVYLSDFSLLIFDECHHTQKEHPYNKIMrmyldkKLSSQGP 163

                          170       180       190
                   ....*....|....*....|....*....|
gi 1958786380  168 ScPRILGLTASI-LNGKCDPDELEEKIQKL 196
Cdd:cd18036    164 L-PQILGLTASPgVGGARSFEEALEHILKL 192
PRK13766 PRK13766
Hef nuclease; Provisional
 25-523 1.03e-21

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 102.64  E-value: 1.03e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   25 ALDHNTIVCLNTGSGKTFIAVLLTKELAHQIRGD---LSPhakrTVFLVNsanqvaQQVSAVRTHSDLKVGEYSNL--EV 99
Cdd:PRK13766    27 ALKKNTLVVLPTGLGKTAIALLVIAERLHKKGGKvliLAP----TKPLVE------QHAEFFRKFLNIPEEKIVVFtgEV 96

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  100 NASWTKERWsqefTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPY----REIMKLCDScpscPRILGL 175
Cdd:PRK13766    97 SPEKRAELW----EKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYvyiaERYHEDAKN----PLVLGL 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  176 TASilngkcdPDELEEKIQKLEKILksGAEtatdlvvldrytsqpcEIVV------DCGPFT-DRSGLYERLLM--ELEE 246
Cdd:PRK13766   169 TAS-------PGSDEEKIKEVCENL--GIE----------------HVEVrteddpDVKPYVhKVKIEWVRVELpeELKE 223

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  247 ALDFINDCnvsvhSKERdstlisKQILSDCRaVLVVLGPWCADK-VAGMMvRELQKYIKHEQEEL--------------H 311
Cdd:PRK13766   224 IRDLLNEA-----LKDR------LKKLKELG-VIVSISPDVSKKeLLGLQ-KKLQQEIANDDSEGyeaisilaeamklrH 290

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  312 RKFLLFT---DTLLRKIHALCEE-----------------YFSPASLDLKYVT---PKVMKLLEILRKykpyerqQFEsv 368
Cdd:PRK13766   291 AVELLETqgvEALRRYLERLREEarssggskaskrlvedpRFRKAVRKAKELDiehPKLEKLREIVKE-------QLG-- 361

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  369 ewynnRNQDNYVswsdsedddddeeieekekpetnfpspftnilcgIIFVERRYTA-VVLNRLIKEagkqdpelayissN 447
Cdd:PRK13766   362 -----KNPDSRI----------------------------------IVFTQYRDTAeKIVDLLEKE-------------G 389

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958786380  448 FITGHGIGK-NQPRSKQMEAefRKQEEVLRKFRAHETNLLIATSVVEEGVDIPKCNLVVRFD-LPTEYRSyVQSKGRA 523
Cdd:PRK13766   390 IKAVRFVGQaSKDGDKGMSQ--KEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEpVPSEIRS-IQRKGRT 464
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1668-1790 1.13e-21

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 91.57  E-value: 1.13e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1668 QRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELfhviddfvqfqleKNE 1747
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI-------------RRR 67

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1958786380 1748 MQGMDSELRRSEEDeekeedievPKAMGDIFESLAGAIYMDSG 1790
Cdd:pfam00636   68 NNALGKGPKRADGK---------EKVLADAFEALIGALYLDGG 101
helicase_insert_domain cd12088
helicase_insert_domain; helicase_insert_domain; This helical domain can be found inserted in a ...
 241-332 6.70e-21

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: 88.68  E-value: 6.70e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  241 LMELEEALDFINDCNvsvhskeRDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHeqeELHRKFLLFTDT 320
Cdd:cd12088      1 KMILSQLLRDTESLL-------KLLYTAHLRKLNDALELLEDAGIWDALKYIKMFFTEVREGIFD---ELERKLTLRFDE 70

                           90
                   ....*....|..
gi 1958786380  321 LLRKIHALCEEY 332
Cdd:cd12088     71 KLQKLIALSRDP 82
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
 884-1034 2.27e-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: 88.40  E-value: 2.27e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  884 YSKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFP--SPEYETFAEYYKTKYNLDLTNLNQPLLDVd 961
Cdd:pfam02170    8 QQQKDRRDFRKEAKKALKGLKVYTTYNNPRTYRIDGITFDPTPESTFPlkDGKEITVVDYFKKKYNIDLKYPDQPLLLV- 86

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958786380  962 htssrlnlltprhlnqkgkalplssaeKRKakweslQNKQILVPELCAihpIPASLWRKAVCLPSILYRLHCL 1034
Cdd:pfam02170   87 ---------------------------GKK------RPKVYLPPELCN---LVDGQRYTKKLMPSIAQRTRLL 123
DEXDc smart00487
DEAD-like helicases superfamily;
20-212 2.51e-19

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 88.32  E-value: 2.51e-19
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380    20 ELLEAALD--HNTIVCLNTGSGKTFIAVLLTKELAHQIRGdlsphaKRTVFLVNSANQVAQQVSAVRTHSDLKVGEYSNL 97
Cdd:smart00487   15 EAIEALLSglRDVILAAPTGSGKTLAALLPALEALKRGKG------GRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGL 88

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380    98 EVNASWTKERWSQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCDSCPSCPRILGLTA 177
Cdd:smart00487   89 YGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSA 168

                           170       180       190
                    ....*....|....*....|....*....|....*
gi 1958786380   178 SILNgkcDPDELEEKIQKLEKILKSGAETATDLVV 212
Cdd:smart00487  169 TPPE---EIENLLELFLNDPVFIDVGFTPLEPIEQ 200
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
 20-196 8.07e-19

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: 86.80  E-value: 8.07e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   20 ELLEAALD-HNTIVCLNTGSGKTFIAVLLTKelaHQIRGDLSPHAKRTVFLVNSANQVAQQVSAVRTH---SDLKV---- 91
Cdd:cd18073      9 ELALPAMKgKNTIICAPTGCGKTFVSLLICE---HHLKKFPQGQKGKVVFFATKVPVYEQQKSVFSKYferHGYRVtgis 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   92 GEYSNLeVNASWTKErwsqeftKHQVLIMTCYVALNVLKNGYL-SLSDINLLVFDECHLAILDHPYREIM------KLCD 164
Cdd:cd18073     86 GATAEN-VPVEQIIE-------NNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSGNHPYNMIMfryldqKLGG 157

                          170       180       190
                   ....*....|....*....|....*....|...
gi 1958786380  165 SCPSCPRILGLTASILNGKC-DPDELEEKIQKL 196
Cdd:cd18073    158 SSGPLPQIIGLTASVGVGDAkNTDEALDYICKL 190
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
 19-178 1.66e-17

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: 82.37  E-value: 1.66e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   19 VELLEAALDHNTIVCLNTGSGKTFIAVLLtkeLAHQIRgdLSPHAKrTVFLVNSANQVAQQVSAVrtHSDLKVGEYSNLE 98
Cdd:cd18033      8 FTIVQKALFQNTLVALPTGLGKTFIAAVV---MLNYYR--WFPKGK-IVFMAPTKPLVSQQIEAC--YKITGIPSSQTAE 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   99 VNASWTKERWSQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCDSCPSCPRILGLTAS 178
Cdd:cd18033     80 LTGSVPPTKRAELWASKRVFFLTPQTLENDLKEGDCDPKSIVCLVIDEAHRATGNYAYCQVVRELMRYNSHFRILALTAT 159
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 1649-1791 1.72e-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: 1.72e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1649 LLQAFTHASYHYNTiTDCYQRLEFLGDAILDYLITKHLYEDPRQhSPGVLTDLRSALVNNTIFASLAvkydyhkyfkavs 1728
Cdd:pfam14622    4 LLQALTHKSYANGR-KPYNERLEFLGDAVLELSVSEYLFKKPDL-DEGGLTKLRASIVSEESLAEIA------------- 68

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958786380 1729 pelfhviddfVQFQLEKNEMQGMDSELRRSeedeekeedIEVPKAMGDIFESLAGAIYMDSGM 1791
Cdd:pfam14622   69 ----------REIGLGKYLRLGKGEEETGG---------SGRESILADALEALIGAIYLDGGF 112
PAZ_CAF_like cd02844
PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has ...
 892-1014 6.38e-15

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


Pssm-ID: 239210  Cd Length: 135  Bit Score: 73.22  E-value: 6.38e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  892 FKLEDYQDAVIIpryrnfdQPH--RFYVADVYTDLTPLSKFP---SPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSR 966
Cdd:cd02844     26 FCACDLKGSVVT-------APHngRFYVISGILDLNANSSFPgkeGLGYATYAEYFKEKYGIVLNHPNQPLLKGKQIFNL 98

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1958786380  967 LNLLTPRhLNQKGkalplSSAEKRKakwesLQNKQILVPELCAIHPIP 1014
Cdd:cd02844     99 HNLLHNR-FEEKG-----ESEEKEK-----DRYFVELPPELCSVIDLP 135
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1283-1346 6.62e-15

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 72.31  E-value: 6.62e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958786380 1283 ERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKQGLPSRMVVSIFDP 1346
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI 64
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 471-523 1.08e-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: 71.86  E-value: 1.08e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958786380  471 QEEVLRKFRAHETNLLIATSVVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 523
Cdd:pfam00271   53 REEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
HELICc smart00490
helicase superfamily c-terminal domain;
469-523 8.75e-13

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 65.31  E-value: 8.75e-13
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 1958786380   469 RKQEEVLRKFRAHETNLLIATSVVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 523
Cdd:smart00490   24 EEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 20-181 1.15e-12

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: 68.06  E-value: 1.15e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   20 ELLEAAL--DHNTIVCLNTGSGKTFIAvlltkELAhqIRGDLSPHAKRTVFLVNS---ANQVAQQVSAVRTHSDLKVGE- 93
Cdd:cd17921      8 EALRALYlsGDSVLVSAPTSSGKTLIA-----ELA--ILRALATSGGKAVYIAPTralVNQKEADLRERFGPLGKNVGLl 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   94 YSNLEVNASWTKERwsqeftkhQVLIMTcYVALNVL--KNGYLSLSDINLLVFDECHLaiLDHPYRE------IMKLCDS 165
Cdd:cd17921     81 TGDPSVNKLLLAEA--------DILVAT-PEKLDLLlrNGGERLIQDVRLVVVDEAHL--IGDGERGvvlellLSRLLRI 149

                          170
                   ....*....|....*.
gi 1958786380  166 CPSCpRILGLTASILN 181
Cdd:cd17921    150 NKNA-RFVGLSATLPN 164
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 415-525 8.71e-12

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: 64.07  E-value: 8.71e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  415 IIFVERRYTAVVLNRLIKEAGkqdpelayISSNFItgHGiGKNQprskqmeaefRKQEEVLRKFRAHETNLLIATSVVEE 494
Cdd:cd18787     31 IIFVNTKKRVDRLAELLEELG--------IKVAAL--HG-DLSQ----------EERERALKKFRSGKVRVLVATDVAAR 89

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1958786380  495 GVDIPKCNLVVRFDLPTEYRSYVQSKGR-ARA 525
Cdd:cd18787     90 GLDIPGVDHVINYDLPRDAEDYVHRIGRtGRA 121
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 415-523 1.35e-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: 63.91  E-value: 1.35e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  415 IIFVERRYTAvvlNRLIKEAGKQDPELAyiSSNFItGHGIGKNQPRSKQMEaefrkQEEVLRKFRAHETNLLIATSVVEE 494
Cdd:cd18801     34 IIFSEFRDSA---EEIVNFLSKIRPGIR--ATRFI-GQASGKSSKGMSQKE-----QKEVIEQFRKGGYNVLVATSIGEE 102

                           90       100       110
                   ....*....|....*....|....*....|
gi 1958786380  495 GVDIPKCNLVVRFD-LPTEYRSyVQSKGRA 523
Cdd:cd18801    103 GLDIGEVDLIICYDaSPSPIRM-IQRMGRT 131
DEXHc_RLR-3 cd18075
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ...
 20-178 2.04e-11

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: 65.26  E-value: 2.04e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   20 ELLEAALD-HNTIVCLNTGSGKTFIAVLLTKELAHQIRGdlsphaKRTVFLVNSANQVAQQVSAVRTHSDlkvGEYSNLE 98
Cdd:cd18075      9 EVVAPALRgKNSIIWLPTGAGKTRAAVYVARRHLETKRG------AKVAVLVNKVHLVDQHLEKEFHVLL---DKYTVTA 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   99 VNA-SWTKERWSQEFTKHQVLIMTCYVALNVLKNG----YLSLSDINLLVFDECHLAILDHPYREIM------KLCDSCP 167
Cdd:cd18075     80 ISGdSSHKCFFGQLARGSDVVICTAQILQNALLSGeeeaHVELTDFSLLVIDECHHTHKEAVYNKIMlsylekKLSRQGD 159

                          170
                   ....*....|.
gi 1958786380  168 sCPRILGLTAS 178
Cdd:cd18075    160 -LPQILGLTAS 169
ResIII pfam04851
Type III restriction enzyme, res subunit;
20-177 2.61e-11

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 63.85  E-value: 2.61e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   20 ELLEAALDHNTIVCLN--TGSGKTFIAVLLTKELAHqirgdlSPHAKRTVFLVNSANQVAQQvsavrthsdlkVGEYSNL 97
Cdd:pfam04851   14 NLLESIKNGQKRGLIVmaTGSGKTLTAAKLIARLFK------KGPIKKVLFLVPRKDLLEQA-----------LEEFKKF 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   98 EVNASWTKERWSQEFTKHQV----LIMTCYVALNV-LKNGYLSLSD--INLLVFDECHLAILDHpYREIMKLCdscpSCP 170
Cdd:pfam04851   77 LPNYVEIGEIISGDKKDESVddnkIVVTTIQSLYKaLELASLELLPdfFDVIIIDEAHRSGASS-YRNILEYF----KPA 151


                   ....*..
gi 1958786380  171 RILGLTA 177
Cdd:pfam04851  152 FLLGLTA 158
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 27-191 4.65e-11

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: 63.03  E-value: 4.65e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   27 DHNTIVCLNTGSGKTFIAVLLtkeLAHQIrgDLSPHAKRTVFLV---NSANQVAQQVSavrthsdlKVGEYSNLEVNASW 103
Cdd:pfam00270   14 GRDVLVQAPTGSGKTLAFLLP---ALEAL--DKLDNGPQALVLAptrELAEQIYEELK--------KLGKGLGLKVASLL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  104 T-KERWSQ--EFTKHQVLIMTCYVALNVLKNGYLsLSDINLLVFDECHLaILDHPYREIMKLC-DSCPSCPRILGLTASI 179
Cdd:pfam00270   81 GgDSRKEQleKLKGPDILVGTPGRLLDLLQERKL-LKNLKLLVLDEAHR-LLDMGFGPDLEEIlRRLPKKRQILLLSATL 158

                          170
                   ....*....|..
gi 1958786380  180 lngkcdPDELEE 191
Cdd:pfam00270  159 ------PRNLED 164
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1263-1335 4.72e-11

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 64.73  E-value: 4.72e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958786380 1263 NPGLILQALT---LSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKQGL 1335
Cdd:COG0571     17 DPELLEQALThrsYANEHGGLeNNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAEIARELGL 93
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1262-1337 5.06e-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: 64.53  E-value: 5.06e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380 1262 PNPGLILQALT-----LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKQGLP 1336
Cdd:TIGR02191   10 KNPELLEQALThrsyaNEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVARELGLG 89


                   .
gi 1958786380 1337 S 1337
Cdd:TIGR02191   90 D 90
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 25-196 1.28e-10

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: 62.15  E-value: 1.28e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   25 ALDHNTIVCLNTGSGKTFIAVLLtkelahqIRGDLSPHAKRTVFLVNSANQVAQQVSAVRT--HSDLKVGEYSNlEVNAS 102
Cdd:cd18035     14 ALNGNTLIVLPTGLGKTIIAILV-------AADRLTKKGGKVLILAPSRPLVEQHAENLKRvlNIPDKITSLTG-EVKPE 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  103 WTKERWSqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCDSCPSCPRILGLTASilnG 182
Cdd:cd18035     86 ERAERWD----ASKIIVATPQVIENDLLAGRITLDDVSLLIFDEAHHAVGNYAYVYIAHRYKREANNPLILGLTAS---P 158

                          170
                   ....*....|....
gi 1958786380  183 KCDPDELEEKIQKL 196
Cdd:cd18035    159 GSDKEKIMEICENL 172
PAZ_piwi_like cd02845
PAZ domain, Piwi_like subfamily. In multi-cellular organisms, the Piwi protein appears to be ...
 898-1008 5.73e-09

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: 55.73  E-value: 5.73e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  898 QDAVIIPRYRNfdqphRFY-VADVYTDLTPLSKFPSPEYE--TFAEYYKTKYNLDLTNLNQPLLdvdhtssrlnlltprh 974
Cdd:cd02845     29 IGSIVLTRYNN-----KTYrIDDIDFDKTPLSTFKKSDGTeiTFVEYYKKQYNIEITDLNQPLL---------------- 87

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1958786380  975 lnqkgkalpLSSAEKRKAKweSLQNKQI-LVPELC 1008
Cdd:cd02845     88 ---------VSRPKRRDPR--GGEKEPIyLIPELC 111
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
20-191 7.71e-09

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 60.29  E-value: 7.71e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   20 ELLEAAL--DHNTIVCLNTGSGKTFIAVL-LTKELAHQirgdlsphaKRTVFLVNS---ANQVAQQVSAVRTHSDLKVGE 93
Cdd:COG1204     29 EALEAGLleGKNLVVSAPTASGKTLIAELaILKALLNG---------GKALYIVPLralASEKYREFKRDFEELGIKVGV 99

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   94 -YSNLEVNASWTKERwsqeftkhQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLaiLDHPYR---------EIMKLC 163
Cdd:COG1204    100 sTGDYDSDDEWLGRY--------DILVATPEKLDSLLRNGPSWLRDVDLVVVDEAHL--IDDESRgptlevllaRLRRLN 169

                          170       180
                   ....*....|....*....|....*...
gi 1958786380  164 DScpscPRILGLTASILNgkcdPDELEE 191
Cdd:COG1204    170 PE----AQIVALSATIGN----AEEIAE 189
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 28-177 1.55e-08

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: 55.49  E-value: 1.55e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   28 HNTIVCLNTGSGKTFIAvlltkelAHQIRGDLSPHAKRTVFLV---NSANQVAQQVSAVRTHsDLKVGEYsnleVNASWT 104
Cdd:cd00046      2 ENVLITAPTGSGKTLAA-------LLAALLLLLKKGKKVLVLVptkALALQTAERLRELFGP-GIRVAVL----VGGSSA 69

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958786380  105 KERWSQEFTKHQVLIMTC-YVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCD--SCPSCPRILGLTA 177
Cdd:cd00046     70 EEREKNKLGDADIIIATPdMLLNLLLREDRLFLKDLKLIIVDEAHALLIDSRGALILDLAVrkAGLKNAQVILLSA 145
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 482-523 3.72e-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: 51.94  E-value: 3.72e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1958786380  482 ETNLLIATSVVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 523
Cdd:cd18785     22 SLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRA 63
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 20-178 5.19e-08

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: 53.85  E-value: 5.19e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   20 ELLEAALDHNT----IVCLNTGSGKTFIAVLLTKELahqirgdlspHAKRTVFLVNSANQVAQqvsavrthsdlkvgeys 95
Cdd:cd17926      7 EALEAWLAHKNnrrgILVLPTGSGKTLTALALIAYL----------KELRTLIVVPTDALLDQ----------------- 59

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   96 nlevnaswTKERWSQEFTKHQVLIMTC-----------YVAL-----NVLKNGYLSLSDINLLVFDECHLAildhP---Y 156
Cdd:cd17926     60 --------WKERFEDFLGDSSIGLIGGgkkkdfddanvVVATyqslsNLAEEEKDLFDQFGLLIVDEAHHL----PaktF 127

                          170       180
                   ....*....|....*....|..
gi 1958786380  157 REIMKLCdscpSCPRILGLTAS 178
Cdd:cd17926    128 SEILKEL----NAKYRLGLTAT 145
DSRM smart00358
Double-stranded RNA binding motif;
1816-1879 5.31e-08

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 51.49  E-value: 5.31e-08
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958786380  1816 PRSPVRELLEMEPETAKFSPAERT-YDGKVRVTVEVVGKGK--FKGVGRSYRIAKSAAARRALRSLK 1879
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEEgPDHAPRFTVTVKVGGKrtGEGEGSSKKEAKQRAAEAALRSLK 67
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
19-177 5.67e-08

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 57.73  E-value: 5.67e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   19 VELLEAALDHNT---IVCLNTGSGKTFIAVLLTKELAHQirgdlsphaKRTVFLVNSANQVAQqvsavrTHSDLKvgEYS 95
Cdd:COG1061     89 LEALLAALERGGgrgLVVAPTGTGKTVLALALAAELLRG---------KRVLVLVPRRELLEQ------WAEELR--RFL 151

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   96 NLEVNASWTKERWSQ-EFTKHQVLIMtcYVALNVLKNgylslsDINLLVFDECHLAILDHpYREIMKLCDScpscPRILG 174
Cdd:COG1061    152 GDPLAGGGKKDSDAPiTVATYQSLAR--RAHLDELGD------RFGLVIIDEAHHAGAPS-YRRILEAFPA----AYRLG 218


                   ...
gi 1958786380  175 LTA 177
Cdd:COG1061    219 LTA 221
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
414-559 7.63e-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: 7.63e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  414 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFItgHGiGKNQprskqmeaefRKQEEVLRKFRAHETNLLIATSVVE 493
Cdd:COG0513    244 AIVFCNTKRGADRLAEKLQKRG--------ISAAAL--HG-DLSQ----------GQRERALDAFRNGKIRVLVATDVAA 302

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958786380  494 EGVDIPKCNLVVRFDLPTEYRSYV---------QSKGRArapisnyVMLADtdkiksfEEDLKTYKAIEKILRNK 559
Cdd:COG0513    303 RGIDIDDVSHVINYDLPEDPEDYVhrigrtgraGAEGTA-------ISLVT-------PDERRLLRAIEKLIGQK 363
DEXHc_RLR-2 cd18074
DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma ...
 19-178 9.62e-08

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: 54.48  E-value: 9.62e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   19 VELLEAALD-HNTIVCLNTGSGKTFIAVLLTKElaHQIRGDLSPHAKRTVFLVNSANQVAQQVSAvRTHSDLKvGEYSNL 97
Cdd:cd18074      8 MEVAKPALEgKNIIICLPTGSGKTRVAVYITKD--HLDKKRKASEPGKVIVLVNKVPLVEQHYRK-EFNPFLK-HWYQVI 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   98 EVNA-SWTKERWSQEFTKHQVLIMTCYVALNVLKNGY------LSLSDINLLVFDECHLAILDHPYREIM---------- 160
Cdd:cd18074     84 GLSGdSQLKISFPEVVKRYDVIICTAQILENSLLNATeeedegVQLSDFSLIIIDECHHTQKEAVYNNIMrrylkqkikn 163

                          170       180
                   ....*....|....*....|..
gi 1958786380  161 ----KLCDSCPSCPRILGLTAS 178
Cdd:cd18074    164 rkqkKENKPLIPLPQILGLTAS 185
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 1264-1339 1.30e-07

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: 52.18  E-value: 1.30e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958786380 1264 PGLILQALT---LSNASDGFNlERLEMLGDSFLKHAITTYLFcTYPDAHEGRLSYMRSKKVSNCNLYRLGKKQGLPSRM 1339
Cdd:pfam14622    1 EELLLQALThksYANGRKPYN-ERLEFLGDAVLELSVSEYLF-KKPDLDEGGLTKLRASIVSEESLAEIAREIGLGKYL 77
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 463-554 8.48e-07

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


Pssm-ID: 350179 [Multi-domain]  Cd Length: 160  Bit Score: 50.73  E-value: 8.48e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  463 QMEAEfrKQEEVLRKFRAHETNLLIATSVVEEGVDIPKCNLVV-----RFDLPTEYrsyvQSKGR-ARAPISNYVMLADT 536
Cdd:cd18792     69 KMTED--EKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIiedadRFGLSQLH----QLRGRvGRGKHQSYCYLLYP 142

                           90
                   ....*....|....*...
gi 1958786380  537 DKIKSFEEDLKTYKAIEK 554
Cdd:cd18792    143 DPKKLTETAKKRLRAIAE 160
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 22-177 1.66e-06

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: 49.87  E-value: 1.66e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   22 LEAALDHNT---IVCLNTGSGKTFIAVLLTKELAHQIRgdlsphAKRTVFLVNSANQVAQQVSAVRTHsdLKVGEYSNLE 98
Cdd:cd18032     12 LEEAREKGQrraLLVMATGTGKTYTAAFLIKRLLEANR------KKRILFLAHREELLEQAERSFKEV--LPDGSFGNLK 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   99 VNaswtkerwSQEFTKHQVLIMTcYVALNvlKNGYLSLSDIN---LLVFDECHLAILDHpYREIMKLCDSCPscprILGL 175
Cdd:cd18032     84 GG--------KKKPDDARVVFAT-VQTLN--KRKRLEKFPPDyfdLIIIDEAHHAIASS-YRKILEYFEPAF----LLGL 147


                   ..
gi 1958786380  176 TA 177
Cdd:cd18032    148 TA 149
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 430-541 4.82e-06

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: 48.49  E-value: 4.82e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  430 LIKEAGKQDPELA-----YISSNFITGHGIGKNQPRSKQMEaefrkQEEVLRKFRAHETNLLIATSVVEEGVDIPKCNLV 504
Cdd:cd18811     35 LIEESEKLDLKAAvamyeYLKERFRPELNVGLLHGRLKSDE-----KDAVMAEFREGEVDILVSTTVIEVGVDVPNATVM 109

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1958786380  505 V-----RFDLPTEYrsyvQSKGR-ARAPISNYVMLADTDKIKS 541
Cdd:cd18811    110 ViedaeRFGLSQLH----QLRGRvGRGDHQSYCLLVYKDPLTE 148
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
 472-509 5.01e-06

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 51.69  E-value: 5.01e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1958786380  472 EEVLRKFRAHETNLLIATSVVEEGVDIPKCNLVV-----RFDL 509
Cdd:PRK10917   521 DAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVienaeRFGL 563
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 414-564 1.18e-05

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 49.94  E-value: 1.18e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  414 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGhgigkNQPRSKQMEAefrkqeevLRKFRAHETNLLIATSVVE 493
Cdd:PRK11192   248 SIVFVRTRERVHELAGWLRKAG--------INCCYLEG-----EMVQAKRNEA--------IKRLTDGRVNVLVATDVAA 306

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  494 EGVDIPKCNLVVRFDLPTEYRSYVQSKGR-ARA-----PIS-----NYVMLadtDKIKSF-EEDLK---------TYKAI 552
Cdd:PRK11192   307 RGIDIDDVSHVINFDMPRSADTYLHRIGRtGRAgrkgtAISlveahDHLLL---GKIERYiEEPLKarvidelrpKTKAP 383

                          170
                   ....*....|..
gi 1958786380  553 EKILRNKCSKSV 564
Cdd:PRK11192   384 SEKKTGKPSKKV 395
PTZ00424 PTZ00424
helicase 45; Provisional
 469-548 2.49e-05

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 48.67  E-value: 2.49e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  469 RKQEEVLRKFRAHETNLLIATSVVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA----RAPIS-NYVMLADTDKIKSFE 543
Cdd:PTZ00424   304 KDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSgrfgRKGVAiNFVTPDDIEQLKEIE 383


                   ....*
gi 1958786380  544 EDLKT 548
Cdd:PTZ00424   384 RHYNT 388
RecG COG1200
RecG-like helicase [Replication, recombination and repair];
472-499 3.43e-05

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


Pssm-ID: 440813 [Multi-domain]  Cd Length: 684  Bit Score: 48.89  E-value: 3.43e-05
                           10        20
                   ....*....|....*....|....*...
gi 1958786380  472 EEVLRKFRAHETNLLIATSVVEEGVDIP 499
Cdd:COG1200    519 DAVMAAFKAGEIDVLVATTVIEVGVDVP 546
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 414-523 4.40e-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: 44.47  E-value: 4.40e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  414 GIIFVERRYTAVVLNRLIKEAGkqdPELAYISSNFItghgigknqprskqmeAEFRKQEEVLRKFRAhETNLLIATSV-- 491
Cdd:cd18799      9 TLIFCVSIEHAEFMAEAFNEAG---IDAVALNSDYS----------------DRERGDEALILLFFG-ELKPPILVTVdl 68

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1958786380  492 VEEGVDIPKCNLVVrFDLPTEYRS-YVQSKGRA 523
Cdd:cd18799     69 LTTGVDIPEVDNVV-FLRPTESRTlFLQMLGRG 100
PTZ00110 PTZ00110
helicase; Provisional
 469-547 1.06e-04

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 47.08  E-value: 1.06e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  469 RKQEE---VLRKFRAHETNLLIATSVVEEGVDIPKCNLVVRFDLPTEYRSYVQ---SKGRARAPISNYVMLAdTDKIKSF 542
Cdd:PTZ00110   411 KKQEErtwVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHrigRTGRAGAKGASYTFLT-PDKYRLA 489


                   ....*
gi 1958786380  543 EEDLK 547
Cdd:PTZ00110   490 RDLVK 494
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 471-522 3.73e-04

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 45.22  E-value: 3.73e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1958786380  471 QEEVLRKFRAHETNLLIATSVVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGR 522
Cdd:PRK11634   284 REQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGR 335
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 448-553 6.03e-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: 6.03e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  448 FITGHGIgknqpRSKQMEAEFRKQE--EVLRKFRAHETNLLIATSVVEEGVDIPKCNLVVRFDLPTE-----YRSYVQSK 520
Cdd:cd18790     46 YLQELGV-----KVRYLHSEIDTLErvEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEgflrsETSLIQTI 120

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1958786380  521 GRA-RAPISNYVMLAD--TDKIKsfeedlktyKAIE 553
Cdd:cd18790    121 GRAaRNVNGKVILYADkiTDSMQ---------KAIE 147
DEADc cd00268
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...
 24-198 8.32e-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: 42.43  E-value: 8.32e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   24 AALD-HNTIVCLNTGSGKTfIAVLLTkeLAHQIRGDLSPHAKRTVFLVNS-----ANQVAQQVSAVRTHSDLKVgeysnl 97
Cdd:cd00268     23 LILSgRDVIGQAQTGSGKT-LAFLLP--ILEKLLPEPKKKGRGPQALVLAptrelAMQIAEVARKLGKGTGLKV------ 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   98 evnASWT----KERWSQEFTKH-QVLIMTCYVALNVLKNGYLSLSDINLLVFDEchlA--ILDHPYREIM-KLCDSCPSC 169
Cdd:cd00268     94 ---AAIYggapIKKQIEALKKGpDIVVGTPGRLLDLIERGKLDLSNVKYLVLDE---AdrMLDMGFEEDVeKILSALPKD 167

                          170       180
                   ....*....|....*....|....*....
gi 1958786380  170 PRILGLTASIlngkcdPDELEEKIQKLEK 198
Cdd:cd00268    168 RQTLLFSATL------PEEVKELAKKFLK 190
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 425-559 9.16e-04

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: 43.92  E-value: 9.16e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  425 VVLN---------RLIKEAGKqDPELAYISSNFITGHgigknqpRSkqmeaefRKQEEVLRKFRAHETNLLIATSVVEEG 495
Cdd:COG1203    371 VIVNtvkdaqelyEALKEKLP-DEEVYLLHSRFCPAD-------RS-------EIEKEIKERLERGKPCILVSTQVVEAG 435

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  496 VDI-----------------------------PKCNLVVrFDLPTEYRSYVQSK---GRARAPISNYVMLADTDKIKSFE 543
Cdd:COG1203    436 VDIdfdvvirdlapldsliqragrcnrhgrkeEEGNVYV-FDPEDEGGGYVYDKpllERTRELLREHDEILPEDKRELIE 514

                          170
                   ....*....|....*.
gi 1958786380  544 EdlkTYKAIEKILRNK 559
Cdd:COG1203    515 E---YYRELYELLPDE 527
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 1846-1878 1.03e-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: 1.03e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1958786380 1846 VTVEVVGKgKFKGVGRSYRIAKSAAARRALRSL 1878
Cdd:cd19865     32 MSVEVNGQ-TFEGTGRSKKKAKLEAAEKALRSF 63
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 458-523 1.40e-03

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 43.24  E-value: 1.40e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958786380  458 QPRSKQMEAEFRKQEEVLRKFRAHETNLLIATSVVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 523
Cdd:PLN00206   394 KALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRA 459
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 1817-1878 1.75e-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: 1.75e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958786380 1817 RSPVRELLE---MEPETAKFSPAERTYDGKVRVTVEVVGKGK--FKGVGRSYRIAKSAAARRALRSL 1878
Cdd:cd19875      1 KNPVSALNEycqKRGLSLEFVDVSVGPDHCPGFTASATIDGIvfASATGTSKKEAKRAAAKLALKKL 67
DEADc_DDX52 cd17957
DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ...
 28-146 2.57e-03

DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ubiquitously expressed in testis, endometrium, and other tissues in humans. DDX52 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: 350715 [Multi-domain]  Cd Length: 198  Bit Score: 41.04  E-value: 2.57e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   28 HNTIVCLNTGSGKT-------------------FIAVLL--TKELAHQIrgdlsphakrtvflVNSANQVAQqVSAVRTH 86
Cdd:cd17957     28 RDLLACAPTGSGKTlaflipilqklgkprkkkgLRALILapTRELASQI--------------YRELLKLSK-GTGLRIV 92

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380   87 SDLKVgeysnLEVNASWTKERWsqefTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDE 146
Cdd:cd17957     93 LLSKS-----LEAKAKDGPKSI----TKYDILVSTPLRLVFLLKQGPIDLSSVEYLVLDE 143
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 463-554 3.58e-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: 40.02  E-value: 3.58e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  463 QMEAEfrKQEEVLRKFRAHETNLLIATSVVEEGVDIPKCNLVV-----RFDLPTEYrsyvQSKGR-ARAPISNYVMLADT 536
Cdd:cd18810     60 QMTEN--ELEEVMLEFAKGEYDILVCTTIIESGIDIPNANTIIieradKFGLAQLY----QLRGRvGRSKERAYAYFLYP 133

                           90
                   ....*....|....*...
gi 1958786380  537 DKIKSFEEDLKTYKAIEK 554
Cdd:cd18810    134 DQKKLTEDALKRLEAIQE 151
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 413-523 6.66e-03

C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. 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: 350181 [Multi-domain]  Cd Length: 134  Bit Score: 38.73  E-value: 6.66e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786380  413 CGIIFVERRYTAVVLNRLIKEAGkqDPELAYissnfitgHGigknqprskQMEAEFRkqEEVLRKFRAHETNLLIATSVV 492
Cdd:cd18794     32 SGIIYCLSRKECEQVAARLQSKG--ISAAAY--------HA---------GLEPSDR--RDVQRKWLRDKIQVIVATVAF 90

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1958786380  493 EEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 523
Cdd:cd18794     91 GMGIDKPDVRFVIHYSLPKSMESYYQESGRA 121
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH