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Conserved domains on  [gi|392895692|ref|NP_498761|]
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Death-promoting deoxyribonuclease [Caenorhabditis elegans]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 11-213 2.57e-80

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: 262.97  E-value: 2.57e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   11 FNPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGvQLFAPLDQGGKRAFFVVEKVNLVEQQAIHIEVHTSFKV 90
Cdd:cd18034     1 FTPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMG-ELNRKEKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   91 GQVHGQTSSGLWdSKEQCDQFMKRHHVVVITAQCLLDLIRHAYLKIEDMCVLIFDECHHALGSqHPYRSIMVDYKLLKKD 170
Cdd:cd18034    80 GEYSGEMGVDKW-TKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGD-HPYARIMKEFYHLEGR 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 392895692  171 KPVPRVLGLTASLIKAKVAPEKLMEQLKKLESAMDSVIETASD 213
Cdd:cd18034   158 TSRPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
 836-956 5.92e-66

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: 218.85  E-value: 5.92e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  836 DMSYTINMKYVSEVV-ANMENMPRIPKDEVRRQYKFNAEDYKDAIVMPWYRNLEQPVFYYVAEILPEWRPSSKFPDTHFE 914
Cdd:cd02843     1 DSSTLDIDWEFMEKIeANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEYE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 392895692  915 TFNEYFIKKYKLEIYDQNQSLLDVDFTSTRLNLLQPRIQNQP 956
Cdd:cd02843    81 TFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 357-505 1.82e-50

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: 175.09  E-value: 1.82e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  357 RVIRLFEILETFNPEFQKErmklekaEHLSAIIFVDQRYIAYSLLLMMRHIKSwepKFKFVNPDYVVGASGRNLASSdSQ 436
Cdd:cd18802     5 VIPKLQKLIEILREYFPKT-------PDFRGIIFVERRATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQRKR-SL 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 392895692  437 GLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAGSRYVITV 505
Cdd:cd18802    74 MTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1659-1824 3.70e-38

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: 139.67  E-value: 3.70e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692 1659 YLVQAFTHASYINNRVTGCYQRLEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIam 1738
Cdd:cd00593     2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLR-- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692 1739 cpglyhmIEKFVKLCSERnfdtnfnaemymvtteeeidegqeediEVPKAMGDIFESVAGAIYLDSGrnLDTTWQVIFHM 1818
Cdd:cd00593    80 -------LGKGEEKSGGR---------------------------LRPKILADVFEALIGAIYLDGG--FEAARKFLLRL 123


                  ....*.
gi 392895692 1819 MRGTIE 1824
Cdd:cd00593   124 LGPLIE 129
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 571-664 2.12e-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: 118.75  E-value: 2.12e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   571 AIALINRYCSKLPSDIFTRLVPHNQIIPIEENgvtKYCAELLLPINSPIKHAIVLknPMPNKKTAQMAVALEACRQLHLE 650
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGG---KFVCTVTLPINSPLRSIEGP--PWRSKKLAKRSAAFEACKALHKA 75

                           90
                   ....*....|....
gi 392895692   651 GELDDNLLPKGRES 664
Cdd:pfam03368   76 GLLDDHLLPLTKKK 89
DSRM_DICER cd10843
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ...
 1832-1895 8.93e-31

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: 115.98  E-value: 8.93e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 392895692 1832 RSPIRELMEFEQSKVRFSKMERiLESGKVRVTVEVVNNMRFTGMGRNYRIAKATAAKRALKYLH 1895
Cdd:cd10843     1 RSPVRELLEMEPETAKFSPAER-TYDGKVRVTVEVVGKGRFKGVGRNYRIAKSAAARRALRSLK 63
RIBOc smart00535
Ribonuclease III family;
1395-1520 3.63e-30

Ribonuclease III family;


:

Pssm-ID: 197778  Cd Length: 129  Bit Score: 116.55  E-value: 3.63e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   1395 CLLLTALTTSNAADGM-SLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQLIVANK 1473
Cdd:smart00535    1 SLLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGR 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*...
gi 392895692   1474 FDAHDSWLPPCYIPTCDFKAPNTDDAEEKD-NEIERILDGQVIEEKPE 1520
Cdd:smart00535   81 GEAISGGRDKPKILADVFEALIGAIYLDSGlEAAREFIRDLLGPRLDE 128
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 248-343 1.90e-18

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: 82.33  E-value: 1.90e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  248 IEIFDETVAFVNTTTEFHP---------DLDLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQVWEKELGKIIKSQVLpDK 318
Cdd:cd15903     1 LSLLDEIIEFLNDCKLFDPevyieslllDRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTD-EK 79

                          90       100
                  ....*....|....*....|....*
gi 392895692  319 TLRFLNMAKTSMITIKRLLEPEMKK 343
Cdd:cd15903    80 HRLFLRYVITQLRKIRKLLEDEMKN 104
 
Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 11-213 2.57e-80

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: 262.97  E-value: 2.57e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   11 FNPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGvQLFAPLDQGGKRAFFVVEKVNLVEQQAIHIEVHTSFKV 90
Cdd:cd18034     1 FTPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMG-ELNRKEKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   91 GQVHGQTSSGLWdSKEQCDQFMKRHHVVVITAQCLLDLIRHAYLKIEDMCVLIFDECHHALGSqHPYRSIMVDYKLLKKD 170
Cdd:cd18034    80 GEYSGEMGVDKW-TKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGD-HPYARIMKEFYHLEGR 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 392895692  171 KPVPRVLGLTASLIKAKVAPEKLMEQLKKLESAMDSVIETASD 213
Cdd:cd18034   158 TSRPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
 836-956 5.92e-66

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: 218.85  E-value: 5.92e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  836 DMSYTINMKYVSEVV-ANMENMPRIPKDEVRRQYKFNAEDYKDAIVMPWYRNLEQPVFYYVAEILPEWRPSSKFPDTHFE 914
Cdd:cd02843     1 DSSTLDIDWEFMEKIeANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEYE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 392895692  915 TFNEYFIKKYKLEIYDQNQSLLDVDFTSTRLNLLQPRIQNQP 956
Cdd:cd02843    81 TFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 357-505 1.82e-50

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: 175.09  E-value: 1.82e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  357 RVIRLFEILETFNPEFQKErmklekaEHLSAIIFVDQRYIAYSLLLMMRHIKSwepKFKFVNPDYVVGASGRNLASSdSQ 436
Cdd:cd18802     5 VIPKLQKLIEILREYFPKT-------PDFRGIIFVERRATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQRKR-SL 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 392895692  437 GLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAGSRYVITV 505
Cdd:cd18802    74 MTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1659-1824 3.70e-38

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: 139.67  E-value: 3.70e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692 1659 YLVQAFTHASYINNRVTGCYQRLEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIam 1738
Cdd:cd00593     2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLR-- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692 1739 cpglyhmIEKFVKLCSERnfdtnfnaemymvtteeeidegqeediEVPKAMGDIFESVAGAIYLDSGrnLDTTWQVIFHM 1818
Cdd:cd00593    80 -------LGKGEEKSGGR---------------------------LRPKILADVFEALIGAIYLDGG--FEAARKFLLRL 123


                  ....*.
gi 392895692 1819 MRGTIE 1824
Cdd:cd00593   124 LGPLIE 129
RIBOc smart00535
Ribonuclease III family;
1659-1826 1.90e-35

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 131.96  E-value: 1.90e-35
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   1659 YLVQAFTHASYINNRvtGCYQRLEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKhFIAM 1738
Cdd:smart00535    2 LLLRALTHASYSNEH--EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGE-FIRL 78

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   1739 CPGLyhmiekfvKLCSERnfdtnfnaemymvtteeeidegqeediEVPKAMGDIFESVAGAIYLDSGrnLDTTWQVIFHM 1818
Cdd:smart00535   79 GRGE--------AISGGR---------------------------DKPKILADVFEALIGAIYLDSG--LEAAREFIRDL 121


                    ....*...
gi 392895692   1819 MRGTIELC 1826
Cdd:smart00535  122 LGPRLDEL 129
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1642-1898 4.21e-35

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 134.46  E-value: 4.21e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692 1642 QFTQLEEKIGYRFKERAYLVQAFTHASYIN-NRVTGCYQRLEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNT 1720
Cdd:COG0571     3 DLEELEERLGYRFKDPELLEQALTHRSYANeHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692 1721 IFASLAVKFEFQKhFIAMCPGlyhmiekfvklcsERNFDTNFNaemymvtteeeidegqeedievPKAMGDIFESVAGAI 1800
Cdd:COG0571    83 TLAEIARELGLGD-YLRLGKG-------------EEKSGGRRR----------------------PSILADAFEALIGAI 126

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692 1801 YLDSGrnLDTTWQVIFHMMRGTIE-LCCANPPRSPIRELMEFEQSKvrfsKMERIL-----ESG----KV-RVTVEVVNN 1869
Cdd:COG0571   127 YLDGG--LEAARKFVLRLFEPRLEeIAPGGAGKDYKTALQEWLQAR----GLPLPEyevveEEGpdhaKTfTVEVLVGGK 200

                         250       260
                  ....*....|....*....|....*....
gi 392895692 1870 MRFTGMGRNYRIAKATAAKRALKYLHQIE 1898
Cdd:COG0571   201 VLGEGTGRSKKEAEQAAAKAALEKLGKKE 229
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1646-1894 1.22e-31

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: 124.24  E-value: 1.22e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  1646 LEEKIGYRFKERAYLVQAFTHASYIN--NRVTGCYQRLEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFA 1723
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYANehHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  1724 SLAVKFEFqKHFI-----AMCPGLYHMiekfvklcsernfdtnfnaemymvtteeeidegqeedievPKAMGDIFESVAG 1798
Cdd:TIGR02191   81 EVARELGL-GDFLllgkgEEKSGGRRR----------------------------------------DSILADAFEALIG 119

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  1799 AIYLDSGRNLDTTW--QVIFHMMRGTIELccaNPPRSPIRELMEFEQSK----VRFSKMERILESGKVRVTVEVVNNMRF 1872
Cdd:TIGR02191  120 AIYLDSGLEAARKFilKLLIPRIDAIIKE---ETLKDYKTALQEWAQARgkplPEYRLIKEEGPDHDKEFTVEVSVNGEP 196

                          250       260
                   ....*....|....*....|....
gi 392895692  1873 --TGMGRNYRIAKATAAKRALKYL 1894
Cdd:TIGR02191  197 ygEGKGKSKKEAEQNAAKAALEKL 220
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 571-664 2.12e-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: 118.75  E-value: 2.12e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   571 AIALINRYCSKLPSDIFTRLVPHNQIIPIEENgvtKYCAELLLPINSPIKHAIVLknPMPNKKTAQMAVALEACRQLHLE 650
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGG---KFVCTVTLPINSPLRSIEGP--PWRSKKLAKRSAAFEACKALHKA 75

                           90
                   ....*....|....
gi 392895692   651 GELDDNLLPKGRES 664
Cdd:pfam03368   76 GLLDDHLLPLTKKK 89
DSRM_DICER cd10843
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ...
 1832-1895 8.93e-31

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: 115.98  E-value: 8.93e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 392895692 1832 RSPIRELMEFEQSKVRFSKMERiLESGKVRVTVEVVNNMRFTGMGRNYRIAKATAAKRALKYLH 1895
Cdd:cd10843     1 RSPVRELLEMEPETAKFSPAER-TYDGKVRVTVEVVGKGRFKGVGRNYRIAKSAAARRALRSLK 63
RIBOc smart00535
Ribonuclease III family;
1395-1520 3.63e-30

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 116.55  E-value: 3.63e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   1395 CLLLTALTTSNAADGM-SLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQLIVANK 1473
Cdd:smart00535    1 SLLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGR 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*...
gi 392895692   1474 FDAHDSWLPPCYIPTCDFKAPNTDDAEEKD-NEIERILDGQVIEEKPE 1520
Cdd:smart00535   81 GEAISGGRDKPKILADVFEALIGAIYLDSGlEAAREFIRDLLGPRLDE 128
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
13-510 6.90e-29

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 125.61  E-value: 6.90e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   13 PRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYgvqlfapLDQGGKRAFFVVEKVNLVEQQAIHIEVHT---SFK 89
Cdd:COG1111     4 RRLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAER-------LHKKGGKVLFLAPTKPLVEQHAEFFKEALnipEDE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   90 VGQVHGQTS----SGLWDSKEqcdqfmkrhhVVVITAQCLLDLIRHAYLKIEDMCVLIFDECHHALGSqHPYRSIMVDYK 165
Cdd:COG1111    77 IVVFTGEVSpekrKELWEKAR----------IIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGN-YAYVYIAERYH 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  166 LLKKDkpvPRVLGLTASLIKAKvapEKLMEQLKKLesAMDSVI---ETASDLvslskygaKPYevvIICKDFEIGCLGIP 242
Cdd:COG1111   146 EDAKD---PLILGMTASPGSDE---EKIEEVCENL--GIENVEvrtEEDPDV--------APY---VHDTEVEWIRVELP 206

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  243 nfDTVIEIFDETVAFVN----TTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLgpwaawRTAQVWEKELGKIIkSQVLpdK 318
Cdd:COG1111   207 --EELKEIRDLLNEVLDdrlkKLKELGVIVSTSPDLSKKDLLALQKKLQRRI------REDDSEGYRAISIL-AEAL--K 275

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  319 TLRFLNMAKTSMIT-----IKRLLEPEMKKIKSIEALRPYVPQRVIRLFEILETFNPEFQK-ERMKLEKAEHLS------ 386
Cdd:COG1111   276 LRHALELLETQGVEallryLERLEEEARSSGGSKASKRLVSDPRFRKAMRLAEEADIEHPKlSKLREILKEQLGtnpdsr 355

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  387 AIIFVDQRYIAYSLL--LMMRHIKSwePKFkfvnpdyvVGASGRNlassDSQGL-HKRQTEVLRRFHRNEINCLIATSVL 463
Cdd:COG1111   356 IIVFTQYRDTAEMIVefLSEPGIKA--GRF--------VGQASKE----GDKGLtQKEQIEILERFRAGEFNVLVATSVA 421

                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*...
gi 392895692  464 EEGVDVKQCNLVIKFDR-PLDMRSyVQSKGRARRAGSRYVITVEEKDT 510
Cdd:COG1111   422 EEGLDIPEVDLVIFYEPvPSEIRS-IQRKGRTGRKREGRVVVLIAKGT 468
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
 853-1027 1.29e-24

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: 101.21  E-value: 1.29e-24
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692    853 MENMPRIPKDEVRRQYkfNAEDYKDAIVMPWYRNleqpVFYYVAEILPEWRPSSKFPDTHFE--TFNEYFIKKYKLEIYD 930
Cdd:smart00949    7 MRQLPSQGNRSNFQDR--CAKDLKGLIVLTRYNN----KTYRIDDIDWNLAPKSTFEKSDGSeiTFVEYYKQKYNITIRD 80

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692    931 QNQSLLdVDFTSTRlnllqpRIQNQPrrsrtvsnsstsnipqasasdskesntsvphsSQRQILVPELMDIHPISATLWN 1010
Cdd:smart00949   81 PNQPLL-VSRPKRR------RNQNGK--------------------------------GEPVLLPPELCFITGLTDRMRK 121

                           170
                    ....*....|....*..
gi 392895692   1011 VIAALPSIFYRVNQLLL 1027
Cdd:smart00949  122 DFMLMKSIADRTRLSPL 138
PRK13766 PRK13766
Hef nuclease; Provisional
 13-510 1.57e-22

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 105.34  E-value: 1.57e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   13 PRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYgvqlfapLDQGGKRAFFVVEKVNLVEQQA--------IHIEV 84
Cdd:PRK13766   16 ARLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAER-------LHKKGGKVLILAPTKPLVEQHAeffrkflnIPEEK 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   85 HTSFkVGQVHGQTSSGLWDSKEqcdqfmkrhhVVVITAQCLL-DLI--RhayLKIEDMCVLIFDECHHALGSqHPYRSIM 161
Cdd:PRK13766   89 IVVF-TGEVSPEKRAELWEKAK----------VIVATPQVIEnDLIagR---ISLEDVSLLIFDEAHRAVGN-YAYVYIA 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  162 VDYKLLKKDkpvPRVLGLTASlikakvaP----EKLMEQLKKLesAMDSVI---ETASDLvslskygaKPY--EVVIICK 232
Cdd:PRK13766  154 ERYHEDAKN---PLVLGLTAS-------PgsdeEKIKEVCENL--GIEHVEvrtEDDPDV--------KPYvhKVKIEWV 213

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  233 DFEIGclgiPNFDTVIEIFDETvafvntttefhpdldldprrpIKDSLKTtravFRQLGpWAAWRTAQVWEKEL---GKI 309
Cdd:PRK13766  214 RVELP----EELKEIRDLLNEA---------------------LKDRLKK----LKELG-VIVSISPDVSKKELlglQKK 263

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  310 IKSQVLPD---------------KTLRFLNMAKTSMIT-----IKRLLEPEMKKIKSIEALR----PYVpQRVIRLFEIL 365
Cdd:PRK13766  264 LQQEIANDdsegyeaisilaeamKLRHAVELLETQGVEalrryLERLREEARSSGGSKASKRlvedPRF-RKAVRKAKEL 342

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  366 ETFNPEFQKERM----KLEKAEHLSAIIFVDQRYIAYSL--LLMMRHIKSwepkFKFVnpdyvvGASGRnlasSDSQGL- 438
Cdd:PRK13766  343 DIEHPKLEKLREivkeQLGKNPDSRIIVFTQYRDTAEKIvdLLEKEGIKA----VRFV------GQASK----DGDKGMs 408

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 392895692  439 HKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDR-PLDMRSyVQSKGRARRAGSRYVITVEEKDT 510
Cdd:PRK13766  409 QKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPvPSEIRS-IQRKGRTGRQEEGRVVVLIAKGT 480
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1679-1805 5.43e-22

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 92.34  E-value: 5.43e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  1679 QRLEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIAMCPGLYHMIEKFVKlcSERNF 1758
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDIRRRNNALGK--GPKRA 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 392895692  1759 DTNfnaemymvtteeeidegqeedievPKAMGDIFESVAGAIYLDSG 1805
Cdd:pfam00636   79 DGK------------------------EKVLADAFEALIGALYLDGG 101
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1396-1610 1.38e-21

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: 92.29  E-value: 1.38e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692 1396 LLLTALTTSNAAD---GMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQLIVAN 1472
Cdd:cd00593     2 LLLEALTHPSYANehgRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692 1473 KFdahdswlppcyiptcdfkapntddaEEKDNEIERildgqvieekpenktgwdiggdvsksttdgietitfpkqarvgn 1552
Cdd:cd00593    82 KG-------------------------EEKSGGRLR-------------------------------------------- 92

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 392895692 1553 ddisplpynlltqqhisDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKVIQKDQK 1610
Cdd:cd00593    93 -----------------PKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133
DEXDc smart00487
DEAD-like helicases superfamily;
11-186 3.56e-21

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 93.33  E-value: 3.56e-21
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692     11 FNPRDYQVELLDKATK--KNTIVQLGTGSGKTFIAVLLLKEYGvqlfapLDQGGKRAFFVVEKVNLVEQQAIHIEVHTSF 88
Cdd:smart00487    7 EPLRPYQKEAIEALLSglRDVILAAPTGSGKTLAALLPALEAL------KRGKGGRVLVLVPTRELAEQWAEELKKLGPS 80

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692     89 KVGQVHGQTSSGlwDSKEQCDQFMKRH-HVVVITAQCLLDLIRHAYLKIEDMCVLIFDECHHALGSQHpyRSIMvdYKLL 167
Cdd:smart00487   81 LGLKVVGLYGGD--SKREQLRKLESGKtDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGF--GDQL--EKLL 154

                           170
                    ....*....|....*....
gi 392895692    168 KKDKPVPRVLGLTASLIKA 186
Cdd:smart00487  155 KLLPKNVQLLLLSATPPEE 173
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 248-343 1.90e-18

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: 82.33  E-value: 1.90e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  248 IEIFDETVAFVNTTTEFHP---------DLDLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQVWEKELGKIIKSQVLpDK 318
Cdd:cd15903     1 LSLLDEIIEFLNDCKLFDPevyieslllDRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTD-EK 79

                          90       100
                  ....*....|....*....|....*
gi 392895692  319 TLRFLNMAKTSMITIKRLLEPEMKK 343
Cdd:cd15903    80 HRLFLRYVITQLRKIRKLLEDEMKN 104
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
 853-1025 2.89e-16

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: 76.85  E-value: 2.89e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   853 MENMPRIPKDEVRRQYKfnAEDYKDAIVMPWYRNLEQPVFYYVAEILPEWRPSSKFP--DTHFETFNEYFIKKYKLEIYD 930
Cdd:pfam02170    1 LDFLKRLQQQKDRRDFR--KEAKKALKGLKVYTTYNNPRTYRIDGITFDPTPESTFPlkDGKEITVVDYFKKKYNIDLKY 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   931 QNQSLLDVdftstrlnllqpriqnqPRRSRTVsnsstsnipqasasdskesntsvphssqrqILVPELMDihpISATLWN 1010
Cdd:pfam02170   79 PDQPLLLV-----------------GKKRPKV------------------------------YLPPELCN---LVDGQRY 108

                          170
                   ....*....|....*
gi 392895692  1011 VIAALPSIFYRVNQL 1025
Cdd:pfam02170  109 TKKLMPSIAQRTRLL 123
HELICc smart00490
helicase superfamily c-terminal domain;
434-498 8.82e-16

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 73.79  E-value: 8.82e-16
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 392895692    434 DSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAG 498
Cdd:smart00490   18 HGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 415-498 4.07e-15

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: 73.01  E-value: 4.07e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   415 KFVNPDYVVGASGRNLASSDSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRA 494
Cdd:pfam00271   26 KTLEAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105


                   ....
gi 392895692   495 RRAG 498
Cdd:pfam00271  106 GRAG 109
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1413-1475 1.89e-13

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 68.07  E-value: 1.89e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 392895692  1413 ERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQLIVANKFD 1475
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELD 63
ResIII pfam04851
Type III restriction enzyme, res subunit;
11-181 6.13e-12

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 65.77  E-value: 6.13e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692    11 FNPRDYQVELLD------KATKKNTIVQLGTGSGKTFIAVLLLKEYgvqlfapLDQGG-KRAFFVVEKVNLVEQQAIHIE 83
Cdd:pfam04851    2 LELRPYQIEAIEnllesiKNGQKRGLIVMATGSGKTLTAAKLIARL-------FKKGPiKKVLFLVPRKDLLEQALEEFK 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692    84 VHTSFKVGQvhgqtsSGLWdsKEQCDQFMKRH-HVVVITAQCL--------LDLIRHAYLkiedmcVLIFDECHHALGSQ 154
Cdd:pfam04851   75 KFLPNYVEI------GEII--SGDKKDESVDDnKIVVTTIQSLykalelasLELLPDFFD------VIIIDEAHRSGASS 140

                          170       180
                   ....*....|....*....|....*..
gi 392895692   155 hpYRSImvdyklLKKDKPvPRVLGLTA 181
Cdd:pfam04851  141 --YRNI------LEYFKP-AFLLGLTA 158
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1390-1470 1.04e-07

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: 54.52  E-value: 1.04e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  1390 LGVSPC---LLLTALTTSNAA-----DGMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGK 1461
Cdd:TIGR02191    5 LGYKFKnpeLLEQALTHRSYAnehhkDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVAR 84


                   ....*....
gi 392895692  1462 KLGIPQLIV 1470
Cdd:TIGR02191   85 ELGLGDFLL 93
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1396-1469 9.65e-07

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 52.02  E-value: 9.65e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 392895692 1396 LLLTALTTSNAADGMSL----ERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQLI 1469
Cdd:COG0571    20 LLEQALTHRSYANEHGGlennERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAEIARELGLGDYL 97
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 426-509 1.95e-06

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 52.93  E-value: 1.95e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  426 SGRNLASSD---SQGLhKRQTevLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAG--SR 500
Cdd:PRK11634  268 NGYNSAALNgdmNQAL-REQT--LERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGraGR 344


                  ....*....
gi 392895692  501 YVITVEEKD 509
Cdd:PRK11634  345 ALLFVENRE 353
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
435-527 2.25e-05

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 48.99  E-value: 2.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  435 SQGlhKRqTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAGSR-YVITVeekdtaAC 513
Cdd:COG0513   276 SQG--QR-ERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYVHRIGRTGRAGAEgTAISL------VT 346

                          90
                  ....*....|....
gi 392895692  514 DSDLKDFQQIEKIL 527
Cdd:COG0513   347 PDERRLLRAIEKLI 360
DSRM smart00358
Double-stranded RNA binding motif;
1834-1894 6.78e-04

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 39.94  E-value: 6.78e-04
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 392895692   1834 PIRELMEFEQS---KVRFSKMERILESGKVRVTVEVV--NNMRFTGMGRNYRIAKATAAKRALKYL 1894
Cdd:smart00358    1 PKSLLQELAQKrklPPEYELVKEEGPDHAPRFTVTVKvgGKRTGEGEGSSKKEAKQRAAEAALRSL 66
 
Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 11-213 2.57e-80

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: 262.97  E-value: 2.57e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   11 FNPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGvQLFAPLDQGGKRAFFVVEKVNLVEQQAIHIEVHTSFKV 90
Cdd:cd18034     1 FTPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMG-ELNRKEKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   91 GQVHGQTSSGLWdSKEQCDQFMKRHHVVVITAQCLLDLIRHAYLKIEDMCVLIFDECHHALGSqHPYRSIMVDYKLLKKD 170
Cdd:cd18034    80 GEYSGEMGVDKW-TKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGD-HPYARIMKEFYHLEGR 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 392895692  171 KPVPRVLGLTASLIKAKVAPEKLMEQLKKLESAMDSVIETASD 213
Cdd:cd18034   158 TSRPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
 836-956 5.92e-66

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: 218.85  E-value: 5.92e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  836 DMSYTINMKYVSEVV-ANMENMPRIPKDEVRRQYKFNAEDYKDAIVMPWYRNLEQPVFYYVAEILPEWRPSSKFPDTHFE 914
Cdd:cd02843     1 DSSTLDIDWEFMEKIeANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEYE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 392895692  915 TFNEYFIKKYKLEIYDQNQSLLDVDFTSTRLNLLQPRIQNQP 956
Cdd:cd02843    81 TFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 357-505 1.82e-50

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: 175.09  E-value: 1.82e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  357 RVIRLFEILETFNPEFQKErmklekaEHLSAIIFVDQRYIAYSLLLMMRHIKSwepKFKFVNPDYVVGASGRNLASSdSQ 436
Cdd:cd18802     5 VIPKLQKLIEILREYFPKT-------PDFRGIIFVERRATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQRKR-SL 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 392895692  437 GLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAGSRYVITV 505
Cdd:cd18802    74 MTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 11-211 6.10e-39

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: 144.50  E-value: 6.10e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   11 FNPRDYQVELLDKATK-KNTIVQLGTGSGKTFIAVLLLKEYGVQLfaPLDQGGKRAFFvVEKVNLVEQQAIHIEVHT--- 86
Cdd:cd17927     1 FKPRNYQLELAQPALKgKNTIICLPTGSGKTFVAVLICEHHLKKF--PAGRKGKVVFL-ANKVPLVEQQKEVFRKHFerp 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   87 SFKVGQVHGQTSSGLWDSKEqcdqfMKRHHVVVITAQCLLDLIRHAYL-KIEDMCVLIFDECHHALGsQHPYRSIMVDYK 165
Cdd:cd17927    78 GYKVTGLSGDTSENVSVEQI-----VESSDVIIVTPQILVNDLKSGTIvSLSDFSLLVFDECHNTTK-NHPYNEIMFRYL 151

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 392895692  166 L--LKKDKPVPRVLGLTAS-LIKAKVAPEKLMEQLKKLESAMD-SVIETA 211
Cdd:cd17927   152 DqkLGSSGPLPQILGLTASpGVGGAKNTEEALEHICKLCANLDiSVIATV 201
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1659-1824 3.70e-38

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: 139.67  E-value: 3.70e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692 1659 YLVQAFTHASYINNRVTGCYQRLEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIam 1738
Cdd:cd00593     2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLR-- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692 1739 cpglyhmIEKFVKLCSERnfdtnfnaemymvtteeeidegqeediEVPKAMGDIFESVAGAIYLDSGrnLDTTWQVIFHM 1818
Cdd:cd00593    80 -------LGKGEEKSGGR---------------------------LRPKILADVFEALIGAIYLDGG--FEAARKFLLRL 123


                  ....*.
gi 392895692 1819 MRGTIE 1824
Cdd:cd00593   124 LGPLIE 129
RIBOc smart00535
Ribonuclease III family;
1659-1826 1.90e-35

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 131.96  E-value: 1.90e-35
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   1659 YLVQAFTHASYINNRvtGCYQRLEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKhFIAM 1738
Cdd:smart00535    2 LLLRALTHASYSNEH--EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGE-FIRL 78

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   1739 CPGLyhmiekfvKLCSERnfdtnfnaemymvtteeeidegqeediEVPKAMGDIFESVAGAIYLDSGrnLDTTWQVIFHM 1818
Cdd:smart00535   79 GRGE--------AISGGR---------------------------DKPKILADVFEALIGAIYLDSG--LEAAREFIRDL 121


                    ....*...
gi 392895692   1819 MRGTIELC 1826
Cdd:smart00535  122 LGPRLDEL 129
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1642-1898 4.21e-35

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 134.46  E-value: 4.21e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692 1642 QFTQLEEKIGYRFKERAYLVQAFTHASYIN-NRVTGCYQRLEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNT 1720
Cdd:COG0571     3 DLEELEERLGYRFKDPELLEQALTHRSYANeHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692 1721 IFASLAVKFEFQKhFIAMCPGlyhmiekfvklcsERNFDTNFNaemymvtteeeidegqeedievPKAMGDIFESVAGAI 1800
Cdd:COG0571    83 TLAEIARELGLGD-YLRLGKG-------------EEKSGGRRR----------------------PSILADAFEALIGAI 126

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692 1801 YLDSGrnLDTTWQVIFHMMRGTIE-LCCANPPRSPIRELMEFEQSKvrfsKMERIL-----ESG----KV-RVTVEVVNN 1869
Cdd:COG0571   127 YLDGG--LEAARKFVLRLFEPRLEeIAPGGAGKDYKTALQEWLQAR----GLPLPEyevveEEGpdhaKTfTVEVLVGGK 200

                         250       260
                  ....*....|....*....|....*....
gi 392895692 1870 MRFTGMGRNYRIAKATAAKRALKYLHQIE 1898
Cdd:COG0571   201 VLGEGTGRSKKEAEQAAAKAALEKLGKKE 229
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 11-211 3.14e-32

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: 125.28  E-value: 3.14e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   11 FNPRDYQVELLDKATK-KNTIVQLGTGSGKTFIAVLLLKEYgVQLFAPLDQGGKRAFFvVEKVNLVEQQAiHIEVH---T 86
Cdd:cd18036     1 LELRNYQLELVLPALRgKNTIICAPTGSGKTRVAVYICRHH-LEKRRSAGEKGRVVVL-VNKVPLVEQQL-EKFFKyfrK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   87 SFKVGQVHGQTSsglwdSKEQCDQFMKRHHVVVITAQCLLDLIR----HAYLKIEDMCVLIFDECHHALGsQHPYRSIM- 161
Cdd:cd18036    78 GYKVTGLSGDSS-----HKVSFGQIVKASDVIICTPQILINNLLsgreEERVYLSDFSLLIFDECHHTQK-EHPYNKIMr 151

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 392895692  162 --VDYKLLKKDkPVPRVLGLTASL-IKAKVAPEKLMEQLKKLESAMD-SVIETA 211
Cdd:cd18036   152 myLDKKLSSQG-PLPQILGLTASPgVGGARSFEEALEHILKLCANLDaSVIATV 204
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1646-1894 1.22e-31

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: 124.24  E-value: 1.22e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  1646 LEEKIGYRFKERAYLVQAFTHASYIN--NRVTGCYQRLEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFA 1723
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYANehHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  1724 SLAVKFEFqKHFI-----AMCPGLYHMiekfvklcsernfdtnfnaemymvtteeeidegqeedievPKAMGDIFESVAG 1798
Cdd:TIGR02191   81 EVARELGL-GDFLllgkgEEKSGGRRR----------------------------------------DSILADAFEALIG 119

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  1799 AIYLDSGRNLDTTW--QVIFHMMRGTIELccaNPPRSPIRELMEFEQSK----VRFSKMERILESGKVRVTVEVVNNMRF 1872
Cdd:TIGR02191  120 AIYLDSGLEAARKFilKLLIPRIDAIIKE---ETLKDYKTALQEWAQARgkplPEYRLIKEEGPDHDKEFTVEVSVNGEP 196

                          250       260
                   ....*....|....*....|....
gi 392895692  1873 --TGMGRNYRIAKATAAKRALKYL 1894
Cdd:TIGR02191  197 ygEGKGKSKKEAEQNAAKAALEKL 220
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 571-664 2.12e-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: 118.75  E-value: 2.12e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   571 AIALINRYCSKLPSDIFTRLVPHNQIIPIEENgvtKYCAELLLPINSPIKHAIVLknPMPNKKTAQMAVALEACRQLHLE 650
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGG---KFVCTVTLPINSPLRSIEGP--PWRSKKLAKRSAAFEACKALHKA 75

                           90
                   ....*....|....
gi 392895692   651 GELDDNLLPKGRES 664
Cdd:pfam03368   76 GLLDDHLLPLTKKK 89
DSRM_DICER cd10843
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ...
 1832-1895 8.93e-31

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: 115.98  E-value: 8.93e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 392895692 1832 RSPIRELMEFEQSKVRFSKMERiLESGKVRVTVEVVNNMRFTGMGRNYRIAKATAAKRALKYLH 1895
Cdd:cd10843     1 RSPVRELLEMEPETAKFSPAER-TYDGKVRVTVEVVGKGRFKGVGRNYRIAKSAAARRALRSLK 63
RIBOc smart00535
Ribonuclease III family;
1395-1520 3.63e-30

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 116.55  E-value: 3.63e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   1395 CLLLTALTTSNAADGM-SLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQLIVANK 1473
Cdd:smart00535    1 SLLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGR 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*...
gi 392895692   1474 FDAHDSWLPPCYIPTCDFKAPNTDDAEEKD-NEIERILDGQVIEEKPE 1520
Cdd:smart00535   81 GEAISGGRDKPKILADVFEALIGAIYLDSGlEAAREFIRDLLGPRLDE 128
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
13-510 6.90e-29

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 125.61  E-value: 6.90e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   13 PRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYgvqlfapLDQGGKRAFFVVEKVNLVEQQAIHIEVHT---SFK 89
Cdd:COG1111     4 RRLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAER-------LHKKGGKVLFLAPTKPLVEQHAEFFKEALnipEDE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   90 VGQVHGQTS----SGLWDSKEqcdqfmkrhhVVVITAQCLLDLIRHAYLKIEDMCVLIFDECHHALGSqHPYRSIMVDYK 165
Cdd:COG1111    77 IVVFTGEVSpekrKELWEKAR----------IIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGN-YAYVYIAERYH 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  166 LLKKDkpvPRVLGLTASLIKAKvapEKLMEQLKKLesAMDSVI---ETASDLvslskygaKPYevvIICKDFEIGCLGIP 242
Cdd:COG1111   146 EDAKD---PLILGMTASPGSDE---EKIEEVCENL--GIENVEvrtEEDPDV--------APY---VHDTEVEWIRVELP 206

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  243 nfDTVIEIFDETVAFVN----TTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLgpwaawRTAQVWEKELGKIIkSQVLpdK 318
Cdd:COG1111   207 --EELKEIRDLLNEVLDdrlkKLKELGVIVSTSPDLSKKDLLALQKKLQRRI------REDDSEGYRAISIL-AEAL--K 275

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  319 TLRFLNMAKTSMIT-----IKRLLEPEMKKIKSIEALRPYVPQRVIRLFEILETFNPEFQK-ERMKLEKAEHLS------ 386
Cdd:COG1111   276 LRHALELLETQGVEallryLERLEEEARSSGGSKASKRLVSDPRFRKAMRLAEEADIEHPKlSKLREILKEQLGtnpdsr 355

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  387 AIIFVDQRYIAYSLL--LMMRHIKSwePKFkfvnpdyvVGASGRNlassDSQGL-HKRQTEVLRRFHRNEINCLIATSVL 463
Cdd:COG1111   356 IIVFTQYRDTAEMIVefLSEPGIKA--GRF--------VGQASKE----GDKGLtQKEQIEILERFRAGEFNVLVATSVA 421

                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*...
gi 392895692  464 EEGVDVKQCNLVIKFDR-PLDMRSyVQSKGRARRAGSRYVITVEEKDT 510
Cdd:COG1111   422 EEGLDIPEVDLVIFYEPvPSEIRS-IQRKGRTGRKREGRVVVLIAKGT 468
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
 11-210 1.47e-25

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: 106.06  E-value: 1.47e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   11 FNPRDYQVELLDKATK-KNTIVQLGTGSGKTFIAvLLLKEYGVQLFaPLDQGGKRAFFvVEKVNLVEQQAI----HIEVH 85
Cdd:cd18073     1 FKPRNYQLELALPAMKgKNTIICAPTGCGKTFVS-LLICEHHLKKF-PQGQKGKVVFF-ATKVPVYEQQKSvfskYFERH 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   86 tSFKVGQVHGQTSSGLwdskeQCDQFMKRHHVVVITAQCLLDLIRHAYL-KIEDMCVLIFDECHHALGsQHPYRSIMVDY 164
Cdd:cd18073    78 -GYRVTGISGATAENV-----PVEQIIENNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSG-NHPYNMIMFRY 150

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 392895692  165 ---KLLKKDKPVPRVLGLTASL--IKAKVAPEKLmEQLKKLESAMD-SVIET 210
Cdd:cd18073   151 ldqKLGGSSGPLPQIIGLTASVgvGDAKNTDEAL-DYICKLCASLDaSVIAT 201
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
 853-1027 1.29e-24

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: 101.21  E-value: 1.29e-24
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692    853 MENMPRIPKDEVRRQYkfNAEDYKDAIVMPWYRNleqpVFYYVAEILPEWRPSSKFPDTHFE--TFNEYFIKKYKLEIYD 930
Cdd:smart00949    7 MRQLPSQGNRSNFQDR--CAKDLKGLIVLTRYNN----KTYRIDDIDWNLAPKSTFEKSDGSeiTFVEYYKQKYNITIRD 80

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692    931 QNQSLLdVDFTSTRlnllqpRIQNQPrrsrtvsnsstsnipqasasdskesntsvphsSQRQILVPELMDIHPISATLWN 1010
Cdd:smart00949   81 PNQPLL-VSRPKRR------RNQNGK--------------------------------GEPVLLPPELCFITGLTDRMRK 121

                           170
                    ....*....|....*..
gi 392895692   1011 VIAALPSIFYRVNQLLL 1027
Cdd:smart00949  122 DFMLMKSIADRTRLSPL 138
PRK13766 PRK13766
Hef nuclease; Provisional
 13-510 1.57e-22

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 105.34  E-value: 1.57e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   13 PRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYgvqlfapLDQGGKRAFFVVEKVNLVEQQA--------IHIEV 84
Cdd:PRK13766   16 ARLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAER-------LHKKGGKVLILAPTKPLVEQHAeffrkflnIPEEK 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   85 HTSFkVGQVHGQTSSGLWDSKEqcdqfmkrhhVVVITAQCLL-DLI--RhayLKIEDMCVLIFDECHHALGSqHPYRSIM 161
Cdd:PRK13766   89 IVVF-TGEVSPEKRAELWEKAK----------VIVATPQVIEnDLIagR---ISLEDVSLLIFDEAHRAVGN-YAYVYIA 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  162 VDYKLLKKDkpvPRVLGLTASlikakvaP----EKLMEQLKKLesAMDSVI---ETASDLvslskygaKPY--EVVIICK 232
Cdd:PRK13766  154 ERYHEDAKN---PLVLGLTAS-------PgsdeEKIKEVCENL--GIEHVEvrtEDDPDV--------KPYvhKVKIEWV 213

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  233 DFEIGclgiPNFDTVIEIFDETvafvntttefhpdldldprrpIKDSLKTtravFRQLGpWAAWRTAQVWEKEL---GKI 309
Cdd:PRK13766  214 RVELP----EELKEIRDLLNEA---------------------LKDRLKK----LKELG-VIVSISPDVSKKELlglQKK 263

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  310 IKSQVLPD---------------KTLRFLNMAKTSMIT-----IKRLLEPEMKKIKSIEALR----PYVpQRVIRLFEIL 365
Cdd:PRK13766  264 LQQEIANDdsegyeaisilaeamKLRHAVELLETQGVEalrryLERLREEARSSGGSKASKRlvedPRF-RKAVRKAKEL 342

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  366 ETFNPEFQKERM----KLEKAEHLSAIIFVDQRYIAYSL--LLMMRHIKSwepkFKFVnpdyvvGASGRnlasSDSQGL- 438
Cdd:PRK13766  343 DIEHPKLEKLREivkeQLGKNPDSRIIVFTQYRDTAEKIvdLLEKEGIKA----VRFV------GQASK----DGDKGMs 408

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 392895692  439 HKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDR-PLDMRSyVQSKGRARRAGSRYVITVEEKDT 510
Cdd:PRK13766  409 QKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPvPSEIRS-IQRKGRTGRQEEGRVVVLIAKGT 480
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1679-1805 5.43e-22

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 92.34  E-value: 5.43e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  1679 QRLEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIAMCPGLYHMIEKFVKlcSERNF 1758
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDIRRRNNALGK--GPKRA 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 392895692  1759 DTNfnaemymvtteeeidegqeedievPKAMGDIFESVAGAIYLDSG 1805
Cdd:pfam00636   79 DGK------------------------EKVLADAFEALIGALYLDGG 101
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1396-1610 1.38e-21

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: 92.29  E-value: 1.38e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692 1396 LLLTALTTSNAAD---GMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQLIVAN 1472
Cdd:cd00593     2 LLLEALTHPSYANehgRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692 1473 KFdahdswlppcyiptcdfkapntddaEEKDNEIERildgqvieekpenktgwdiggdvsksttdgietitfpkqarvgn 1552
Cdd:cd00593    82 KG-------------------------EEKSGGRLR-------------------------------------------- 92

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 392895692 1553 ddisplpynlltqqhisDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKVIQKDQK 1610
Cdd:cd00593    93 -----------------PKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133
DEXDc smart00487
DEAD-like helicases superfamily;
11-186 3.56e-21

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 93.33  E-value: 3.56e-21
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692     11 FNPRDYQVELLDKATK--KNTIVQLGTGSGKTFIAVLLLKEYGvqlfapLDQGGKRAFFVVEKVNLVEQQAIHIEVHTSF 88
Cdd:smart00487    7 EPLRPYQKEAIEALLSglRDVILAAPTGSGKTLAALLPALEAL------KRGKGGRVLVLVPTRELAEQWAEELKKLGPS 80

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692     89 KVGQVHGQTSSGlwDSKEQCDQFMKRH-HVVVITAQCLLDLIRHAYLKIEDMCVLIFDECHHALGSQHpyRSIMvdYKLL 167
Cdd:smart00487   81 LGLKVVGLYGGD--SKREQLRKLESGKtDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGF--GDQL--EKLL 154

                           170
                    ....*....|....*....
gi 392895692    168 KKDKPVPRVLGLTASLIKA 186
Cdd:smart00487  155 KLLPKNVQLLLLSATPPEE 173
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 248-343 1.90e-18

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: 82.33  E-value: 1.90e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  248 IEIFDETVAFVNTTTEFHP---------DLDLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQVWEKELGKIIKSQVLpDK 318
Cdd:cd15903     1 LSLLDEIIEFLNDCKLFDPevyieslllDRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTD-EK 79

                          90       100
                  ....*....|....*....|....*
gi 392895692  319 TLRFLNMAKTSMITIKRLLEPEMKK 343
Cdd:cd15903    80 HRLFLRYVITQLRKIRKLLEDEMKN 104
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
 853-1025 2.89e-16

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: 76.85  E-value: 2.89e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   853 MENMPRIPKDEVRRQYKfnAEDYKDAIVMPWYRNLEQPVFYYVAEILPEWRPSSKFP--DTHFETFNEYFIKKYKLEIYD 930
Cdd:pfam02170    1 LDFLKRLQQQKDRRDFR--KEAKKALKGLKVYTTYNNPRTYRIDGITFDPTPESTFPlkDGKEITVVDYFKKKYNIDLKY 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   931 QNQSLLDVdftstrlnllqpriqnqPRRSRTVsnsstsnipqasasdskesntsvphssqrqILVPELMDihpISATLWN 1010
Cdd:pfam02170   79 PDQPLLLV-----------------GKKRPKV------------------------------YLPPELCN---LVDGQRY 108

                          170
                   ....*....|....*
gi 392895692  1011 VIAALPSIFYRVNQL 1025
Cdd:pfam02170  109 TKKLMPSIAQRTRLL 123
DEXHc_RLR-3 cd18075
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ...
 14-182 4.63e-16

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: 78.75  E-value: 4.63e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   14 RDYQVELLDKATK-KNTIVQLGTGSGKTFIAVLLLKEYgvqlfAPLDQGGKRAFfVVEKVNLVEQqaiHIEVHTSFKVGQ 92
Cdd:cd18075     4 HGYQWEVVAPALRgKNSIIWLPTGAGKTRAAVYVARRH-----LETKRGAKVAV-LVNKVHLVDQ---HLEKEFHVLLDK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   93 VHGQTSSGlwDSKEQC--DQFMKRHHVVVITAQ----CLLDLIRHAYLKIEDMCVLIFDECHHAlGSQHPYRSIMVDY-- 164
Cdd:cd18075    75 YTVTAISG--DSSHKCffGQLARGSDVVICTAQilqnALLSGEEEAHVELTDFSLLVIDECHHT-HKEAVYNKIMLSYle 151

                         170
                  ....*....|....*...
gi 392895692  165 KLLKKDKPVPRVLGLTAS 182
Cdd:cd18075   152 KKLSRQGDLPQILGLTAS 169
HELICc smart00490
helicase superfamily c-terminal domain;
434-498 8.82e-16

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 73.79  E-value: 8.82e-16
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 392895692    434 DSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAG 498
Cdd:smart00490   18 HGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 415-498 4.07e-15

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: 73.01  E-value: 4.07e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   415 KFVNPDYVVGASGRNLASSDSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRA 494
Cdd:pfam00271   26 KTLEAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105


                   ....
gi 392895692   495 RRAG 498
Cdd:pfam00271  106 GRAG 109
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
 14-182 1.23e-14

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: 73.90  E-value: 1.23e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   14 RDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYgvqlFAPLDQGgkRAFFVVEKVNLVEQQaihieVHTSFKV--- 90
Cdd:cd18033     4 RDYQFTIVQKALFQNTLVALPTGLGKTFIAAVVMLNY----YRWFPKG--KIVFMAPTKPLVSQQ-----IEACYKItgi 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   91 ---------GQVHGQTSSGLWDSKEqcdqfmkrhhVVVITAQCLLDLIRHAYLKIEDMCVLIFDECHHALGsQHPYRSIM 161
Cdd:cd18033    73 pssqtaeltGSVPPTKRAELWASKR----------VFFLTPQTLENDLKEGDCDPKSIVCLVIDEAHRATG-NYAYCQVV 141

                         170       180
                  ....*....|....*....|.
gi 392895692  162 vdyKLLKKDKPVPRVLGLTAS 182
Cdd:cd18033   142 ---RELMRYNSHFRILALTAT 159
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 1660-1807 2.38e-14

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: 71.44  E-value: 2.38e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  1660 LVQAFTHASYINNRvTGCYQRLEFLGDAVLDYMITRYLFEDSRQySPGVLTDLRSALVNNTIFASLAVKFEFQKhFIAMC 1739
Cdd:pfam14622    4 LLQALTHKSYANGR-KPYNERLEFLGDAVLELSVSEYLFKKPDL-DEGGLTKLRASIVSEESLAEIAREIGLGK-YLRLG 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 392895692  1740 PGLYHMIEKfvklcsernfdtnfnaemymvtteeeidegqeediEVPKAMGDIFESVAGAIYLDSGRN 1807
Cdd:pfam14622   81 KGEEETGGS-----------------------------------GRESILADALEALIGAIYLDGGFE 113
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 13-195 7.42e-14

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


Pssm-ID: 350793 [Multi-domain]  Cd Length: 181  Bit Score: 71.78  E-value: 7.42e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   13 PRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKeygvqlfAPLDQGGKRAFFVVEKVNLVEQQAIHIE--VHTSFKV 90
Cdd:cd18035     3 RRLYQVLIAAVALNGNTLIVLPTGLGKTIIAILVAA-------DRLTKKGGKVLILAPSRPLVEQHAENLKrvLNIPDKI 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   91 GQVHGQTSSglwdskEQCDQFMKRHHVVVITAQCLLDLIRHAYLKIEDMCVLIFDECHHALGSqHPYRSIMVDYKLLKKD 170
Cdd:cd18035    76 TSLTGEVKP------EERAERWDASKIIVATPQVIENDLLAGRITLDDVSLLIFDEAHHAVGN-YAYVYIAHRYKREANN 148

                         170       180
                  ....*....|....*....|....*
gi 392895692  171 kpvPRVLGLTASlikAKVAPEKLME 195
Cdd:cd18035   149 ---PLILGLTAS---PGSDKEKIME 167
DEXHc_RLR-2 cd18074
DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma ...
 14-182 1.49e-13

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: 71.82  E-value: 1.49e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   14 RDYQVELLDKATK-KNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQGgkRAFFVVEKVNLVEQ---QAIHIEVHTSFK 89
Cdd:cd18074     4 RDYQMEVAKPALEgKNIIICLPTGSGKTRVAVYITKDHLDKKRKASEPG--KVIVLVNKVPLVEQhyrKEFNPFLKHWYQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   90 VGQVHGQTssglwDSKEQCDQFMKRHHVVVITAQCLLD-LIR-----HAYLKIEDMCVLIFDECHHAlGSQHPYRSIMVD 163
Cdd:cd18074    82 VIGLSGDS-----QLKISFPEVVKRYDVIICTAQILENsLLNateeeDEGVQLSDFSLIIIDECHHT-QKEAVYNNIMRR 155

                         170       180       190
                  ....*....|....*....|....*....|
gi 392895692  164 Y--------KLLKKDK---PVPRVLGLTAS 182
Cdd:cd18074   156 YlkqkiknrKQKKENKpliPLPQILGLTAS 185
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1413-1475 1.89e-13

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 68.07  E-value: 1.89e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 392895692  1413 ERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQLIVANKFD 1475
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELD 63
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
11-181 7.87e-13

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 73.52  E-value: 7.87e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   11 FNPRDYQVELLDK------ATKKNTIVQLGTGSGKTFIAVLLLKEYgvqlfapldQGGKRAFFVVEKVNLVEQQAIHIEV 84
Cdd:COG1061    79 FELRPYQQEALEAllaaleRGGGRGLVVAPTGTGKTVLALALAAEL---------LRGKRVLVLVPRRELLEQWAEELRR 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   85 HTSfkvgqvhgqtssglwDSKEQCDQFMKRHHVVVITAQcllDLIRHAYLK--IEDMCVLIFDECHHALGSQhpYRsimv 162
Cdd:COG1061   150 FLG---------------DPLAGGGKKDSDAPITVATYQ---SLARRAHLDelGDRFGLVIIDEAHHAGAPS--YR---- 205

                         170
                  ....*....|....*....
gi 392895692  163 dyKLLKKDKPvPRVLGLTA 181
Cdd:COG1061   206 --RILEAFPA-AYRLGLTA 221
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 27-181 8.33e-13

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: 67.81  E-value: 8.33e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   27 KNTIVQLGTGSGKTFIAVLLLKEYgvqlfapLDQGGKRAFFVVEKVNLVEQQA----------IHIEVHTSFKvgqvhgq 96
Cdd:cd00046     2 ENVLITAPTGSGKTLAALLAALLL-------LLKKGKKVLVLVPTKALALQTAerlrelfgpgIRVAVLVGGS------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   97 tssglwDSKEQCDQFMKRHHVVVITAQCLLDLI-RHAYLKIEDMCVLIFDECHHALGSQHPYRsiMVDYKLLKKDKPVPR 175
Cdd:cd00046    68 ------SAEEREKNKLGDADIIIATPDMLLNLLlREDRLFLKDLKLIIVDEAHALLIDSRGAL--ILDLAVRKAGLKNAQ 139


                  ....*.
gi 392895692  176 VLGLTA 181
Cdd:cd00046   140 VILLSA 145
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 13-183 1.06e-12

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: 67.33  E-value: 1.06e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   13 PRDYQVELLDKATKKNT----IVQLGTGSGKTFIAVLLLKEYGVqlfapldqggKRAFFVVEKVNLVEQQAIHIEvhTSF 88
Cdd:cd17926     1 LRPYQEEALEAWLAHKNnrrgILVLPTGSGKTLTALALIAYLKE----------LRTLIVVPTDALLDQWKERFE--DFL 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   89 KVGQVhGQTSSGLWDSKEQCDqfmkrhhVVVITAQCLLDLIRHAYLKIEDMCVLIFDECHHALGSQhpYRSIMVDYKllk 168
Cdd:cd17926    69 GDSSI-GLIGGGKKKDFDDAN-------VVVATYQSLSNLAEEEKDLFDQFGLLIVDEAHHLPAKT--FSEILKELN--- 135

                         170
                  ....*....|....*
gi 392895692  169 kdkpVPRVLGLTASL 183
Cdd:cd17926   136 ----AKYRLGLTATP 146
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 13-181 1.23e-12

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: 67.59  E-value: 1.23e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   13 PRDYQVELLDKAT------KKNTIVQLGTGSGKTFIAVLL---LKEYGvqlfapldqGGKRAFFVVEKVNLVEQQAIHIE 83
Cdd:cd18032     1 PRYYQQEAIEALEearekgQRRALLVMATGTGKTYTAAFLikrLLEAN---------RKKRILFLAHREELLEQAERSFK 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   84 VHTSFKvgqvhgqTSSGLWDSKEQCDQFmkrhHVVVITAQCLLDLIRHAYLKIEDMCVLIFDECHHALGSQhpYRsimvd 163
Cdd:cd18032    72 EVLPDG-------SFGNLKGGKKKPDDA----RVVFATVQTLNKRKRLEKFPPDYFDLIIIDEAHHAIASS--YR----- 133

                         170
                  ....*....|....*...
gi 392895692  164 yKLLKKDKPVPrVLGLTA 181
Cdd:cd18032   134 -KILEYFEPAF-LLGLTA 149
ResIII pfam04851
Type III restriction enzyme, res subunit;
11-181 6.13e-12

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 65.77  E-value: 6.13e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692    11 FNPRDYQVELLD------KATKKNTIVQLGTGSGKTFIAVLLLKEYgvqlfapLDQGG-KRAFFVVEKVNLVEQQAIHIE 83
Cdd:pfam04851    2 LELRPYQIEAIEnllesiKNGQKRGLIVMATGSGKTLTAAKLIARL-------FKKGPiKKVLFLVPRKDLLEQALEEFK 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692    84 VHTSFKVGQvhgqtsSGLWdsKEQCDQFMKRH-HVVVITAQCL--------LDLIRHAYLkiedmcVLIFDECHHALGSQ 154
Cdd:pfam04851   75 KFLPNYVEI------GEII--SGDKKDESVDDnKIVVTTIQSLykalelasLELLPDFFD------VIIIDEAHRSGASS 140

                          170       180
                   ....*....|....*....|....*..
gi 392895692   155 hpYRSImvdyklLKKDKPvPRVLGLTA 181
Cdd:pfam04851  141 --YRNI------LEYFKP-AFLLGLTA 158
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 27-185 9.95e-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: 62.26  E-value: 9.95e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692    27 KNTIVQLGTGSGKTFIAVLLLkeygVQLFAPLDqGGKRAFFVVEKVNLVEQQAIHIEV---HTSFKVGQVHGqtssglWD 103
Cdd:pfam00270   15 RDVLVQAPTGSGKTLAFLLPA----LEALDKLD-NGPQALVLAPTRELAEQIYEELKKlgkGLGLKVASLLG------GD 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   104 SKEQCDQFMKRHHVVVITAQCLLDLIRHAyLKIEDMCVLIFDECHHALGSQhpYRSIMvdYKLLKKDKPVPRVLGLTASL 183
Cdd:pfam00270   84 SRKEQLEKLKGPDILVGTPGRLLDLLQER-KLLKNLKLLVLDEAHRLLDMG--FGPDL--EEILRRLPKKRQILLLSATL 158


                   ..
gi 392895692   184 IK 185
Cdd:pfam00270  159 PR 160
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 451-503 1.24e-10

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: 59.25  E-value: 1.24e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 392895692  451 RNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAGSRYVI 503
Cdd:cd18785    20 ASSLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGGKDEGE 72
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 365-503 3.37e-09

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: 57.37  E-value: 3.37e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  365 LETFNP------EFQKERMKLEKAEHLS-AIIFVDQRYIAYSLLLMMRHIKSwepkfkFVNPDYVVG-ASGRNLASSdSQ 436
Cdd:cd18801     4 VEKIHPklekleEIVKEHFKKKQEGSDTrVIIFSEFRDSAEEIVNFLSKIRP------GIRATRFIGqASGKSSKGM-SQ 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 392895692  437 glhKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFD---RPLDMrsyVQSKGRA--RRAGSRYVI 503
Cdd:cd18801    77 ---KEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDaspSPIRM---IQRMGRTgrKRQGRVVVL 142
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 379-504 6.66e-09

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: 55.98  E-value: 6.66e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  379 LEKAEHLSAIIFVDQRYIAYSLLLMMRHIKswepkfkfvnpdYVVGAsgrnLASSDSQglHKRqTEVLRRFHRNEINCLI 458
Cdd:cd18787    22 LEKLKPGKAIIFVNTKKRVDRLAELLEELG------------IKVAA----LHGDLSQ--EER-ERALKKFRSGKVRVLV 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 392895692  459 ATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAGSR-YVIT 504
Cdd:cd18787    83 ATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRKgTAIT 129
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1390-1470 1.04e-07

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: 54.52  E-value: 1.04e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  1390 LGVSPC---LLLTALTTSNAA-----DGMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGK 1461
Cdd:TIGR02191    5 LGYKFKnpeLLEQALTHRSYAnehhkDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVAR 84


                   ....*....
gi 392895692  1462 KLGIPQLIV 1470
Cdd:TIGR02191   85 ELGLGDFLL 93
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 11-148 2.18e-07

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: 53.03  E-value: 2.18e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   11 FNPrdYQVELLDKA--TKKNTIVQLGTGSGKTFIAVLLLkeygVQLFApldQGGKRAFFVV---EKVNLVEQQAIHIEVH 85
Cdd:cd17921     2 LNP--IQREALRALylSGDSVLVSAPTSSGKTLIAELAI----LRALA---TSGGKAVYIAptrALVNQKEADLRERFGP 72

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 392895692   86 TSFKVGQVHGQTSSglwdskeqCDQFMKRHHVVVITAQCLLDLIR-HAYLKIEDMCVLIFDECH 148
Cdd:cd17921    73 LGKNVGLLTGDPSV--------NKLLLAEADILVATPEKLDLLLRnGGERLIQDVRLVVVDEAH 128
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1396-1469 9.65e-07

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 52.02  E-value: 9.65e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 392895692 1396 LLLTALTTSNAADGMSL----ERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQLI 1469
Cdd:COG0571    20 LLEQALTHRSYANEHGGlennERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAEIARELGLGDYL 97
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
 17-183 9.94e-07

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


Pssm-ID: 350786 [Multi-domain]  Cd Length: 177  Bit Score: 50.80  E-value: 9.94e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   17 QVELLDK--ATKKNTIVQLGTGSGKTFIAVL-LLKEygvqlfapLDQGGKrAFFVVEKVNLVEqqaihiEVHTSFK---- 89
Cdd:cd18028     6 QAEAVRAglLKGENLLISIPTASGKTLIAEMaMVNT--------LLEGGK-ALYLVPLRALAS------EKYEEFKklee 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   90 VGQVHGqTSSGLWDSKeqcDQFMKRHHVVVITAQCLLDLIRHAYLKIEDMCVLIFDEChHALGSQHPYRSIMVDYKLLKK 169
Cdd:cd18028    71 IGLKVG-ISTGDYDED---DEWLGDYDIIVATYEKFDSLLRHSPSWLRDVGVVVVDEI-HLISDEERGPTLESIVARLRR 145

                         170
                  ....*....|....
gi 392895692  170 DKPVPRVLGLTASL 183
Cdd:cd18028   146 LNPNTQIIGLSATI 159
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 1396-1469 1.12e-06

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: 49.48  E-value: 1.12e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 392895692  1396 LLLTALTTSNAADGMSL--ERFETIGDSFLKFATTDYLYHTlLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQLI 1469
Cdd:pfam14622    3 LLLQALTHKSYANGRKPynERLEFLGDAVLELSVSEYLFKK-PDLDEGGLTKLRASIVSEESLAEIAREIGLGKYL 77
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
11-181 1.72e-06

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 52.98  E-value: 1.72e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   11 FNPrdYQVELLDKA--TKKNTIVQLGTGSGKTFIAVL-LLKEygvqlfapLDQGGKrAFFVV-------EKVNLVEQQAI 80
Cdd:COG1204    23 LYP--PQAEALEAGllEGKNLVVSAPTASGKTLIAELaILKA--------LLNGGK-ALYIVplralasEKYREFKRDFE 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   81 HIEVhtsfKVGQvhgqtSSGLWDSKeqcDQFMKRHHVVVITAQCLLDLIRHAYLKIEDMCVLIFDECHHaLGSqhPYRSI 160
Cdd:COG1204    92 ELGI----KVGV-----STGDYDSD---DEWLGRYDILVATPEKLDSLLRNGPSWLRDVDLVVVDEAHL-IDD--ESRGP 156

                         170       180
                  ....*....|....*....|....
gi 392895692  161 ---MVDYKLLKKdKPVPRVLGLTA 181
Cdd:COG1204   157 tleVLLARLRRL-NPEAQIVALSA 179
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 426-509 1.95e-06

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 52.93  E-value: 1.95e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  426 SGRNLASSD---SQGLhKRQTevLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAG--SR 500
Cdd:PRK11634  268 NGYNSAALNgdmNQAL-REQT--LERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGraGR 344


                  ....*....
gi 392895692  501 YVITVEEKD 509
Cdd:PRK11634  345 ALLFVENRE 353
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 440-509 9.18e-06

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: 46.40  E-value: 9.18e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 392895692  440 KRQTEVLRRFHRNEINCLIATSV--LEEGVDVKQCNLVIkFDRPLDMRS-YVQSKGRARRagsryviTVEEKD 509
Cdd:cd18799    44 ERGDEALILLFFGELKPPILVTVdlLTTGVDIPEVDNVV-FLRPTESRTlFLQMLGRGLR-------LHEGKD 108
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
435-527 2.25e-05

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 48.99  E-value: 2.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  435 SQGlhKRqTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAGSR-YVITVeekdtaAC 513
Cdd:COG0513   276 SQG--QR-ERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYVHRIGRTGRAGAEgTAISL------VT 346

                          90
                  ....*....|....
gi 392895692  514 DSDLKDFQQIEKIL 527
Cdd:COG0513   347 PDERRLLRAIEKLI 360
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 440-498 4.89e-05

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 48.25  E-value: 4.89e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 392895692  440 KRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAG 498
Cdd:PLN00206  405 KERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMG 463
PAZ cd02825
PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two ...
 894-955 5.06e-05

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: 44.37  E-value: 5.06e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 392895692  894 YVAEILpEWRPSSK---FPDTHFETFNEYFIKKYKLEIYDQNQSLLDVDFTST--RLNLLQPRIQNQ 955
Cdd:cd02825    49 YRPDGE-TRLKAPSqlkHSDGKEITFADYFKERYNLTLTDLNQPLLIVKFSSKksYSILLPPELCVI 114
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
 388-505 5.26e-05

C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases 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: 350184 [Multi-domain]  Cd Length: 146  Bit Score: 45.33  E-value: 5.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  388 IIFVDQRYIAYsllLMMRHIKSwepkfkfvnpDYVVGASGRNLASSDSQGLHK---RQTEvlRRFHRNEINCLIATSVLE 464
Cdd:cd18797    39 IVFCRSRKLAE---LLLRYLKA----------RLVEEGPLASKVASYRAGYLAedrREIE--AELFNGELLGVVATNALE 103

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 392895692  465 EGVDVKQCNLVIKFDRPLDMRSYVQSKGRA-RRAGSRYVITV 505
Cdd:cd18797   104 LGIDIGGLDAVVLAGYPGSLASLWQQAGRAgRRGKDSLVILV 145
PTZ00110 PTZ00110
helicase; Provisional
 440-500 8.05e-05

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 47.46  E-value: 8.05e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 392895692  440 KRQTE---VLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAGSR 500
Cdd:PTZ00110  411 KKQEErtwVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAK 474
PRK00254 PRK00254
ski2-like helicase; Provisional
 27-197 9.82e-05

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 47.50  E-value: 9.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   27 KNTIVQLGTGSGKTFIAVLllkeygVQLFAPLDQGGKraffvveKVNLVEQQAIHIEVHTSFKVGQVHG---QTSSGLWD 103
Cdd:PRK00254   40 KNLVLAIPTASGKTLVAEI------VMVNKLLREGGK-------AVYLVPLKALAEEKYREFKDWEKLGlrvAMTTGDYD 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  104 SKeqcDQFMKRHHVVVITAQCLLDLIRHAYLKIEDMCVLIFDEChHALGSQHPYRSI-MVDYKLLKKdkpvPRVLGLTAS 182
Cdd:PRK00254  107 ST---DEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEI-HLIGSYDRGATLeMILTHMLGR----AQILGLSAT 178

                         170
                  ....*....|....*
gi 392895692  183 LIKakvaPEKLMEQL 197
Cdd:PRK00254  179 VGN----AEELAEWL 189
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 443-498 1.32e-04

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: 43.74  E-value: 1.32e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 392895692  443 TEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAG 498
Cdd:cd18794    70 RDVQRKWLRDKIQVIVATVAFGMGIDKPDVRFVIHYSLPKSMESYYQESGRAGRDG 125
PTZ00424 PTZ00424
helicase 45; Provisional
 445-510 3.07e-04

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 45.20  E-value: 3.07e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  445 VLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAGSRYV----ITVEEKDT 510
Cdd:PTZ00424  309 IMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVainfVTPDDIEQ 378
DSRM smart00358
Double-stranded RNA binding motif;
1834-1894 6.78e-04

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 39.94  E-value: 6.78e-04
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 392895692   1834 PIRELMEFEQS---KVRFSKMERILESGKVRVTVEVV--NNMRFTGMGRNYRIAKATAAKRALKYL 1894
Cdd:smart00358    1 PKSLLQELAQKrklPPEYELVKEEGPDHAPRFTVTVKvgGKRTGEGEGSSKKEAKQRAAEAALRSL 66
PAZ_CAF_like cd02844
PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has ...
 870-1005 1.10e-03

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: 41.25  E-value: 1.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692  870 FNAEDYKDAIVMPWYRNleqpVFYYVAEILpEWRPSSKFP---DTHFETFNEYFIKKYKLEIYDQNQSLLDVDFTSTRLN 946
Cdd:cd02844    26 FCACDLKGSVVTAPHNG----RFYVISGIL-DLNANSSFPgkeGLGYATYAEYFKEKYGIVLNHPNQPLLKGKQIFNLHN 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 392895692  947 LLQPRIQNqprrsrtvsnsstsnipqasasdsKESNTSVPHSSQRQILVPELMDIHPIS 1005
Cdd:cd02844   101 LLHNRFEE------------------------KGESEEKEKDRYFVELPPELCSVIDLP 135
DSRM_STRBP-like_rpt2 cd19897
second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...
 1832-1894 1.78e-03

second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3). 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. Members of this STRBP/ILF3 group contain an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380726  Cd Length: 64  Bit Score: 38.50  E-value: 1.78e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 392895692 1832 RSPIRELMEfeqsKVRFSKMERILESGKV---RVTVEV-VNNMRFTGMGRNYRIAKATAAKRALKYL 1894
Cdd:cd19897     1 KNPVMELNE----KRRGLKYELISETGGShdkRFVMEVeVDGQKFQGAGSNKKVAKANAALAALEKL 63
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
 439-502 2.47e-03

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 42.59  E-value: 2.47e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 392895692  439 HKRqTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAGSRYV 502
Cdd:PRK01297  372 HKR-IKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGV 434
uvsW PHA02558
UvsW helicase; Provisional
 13-190 5.36e-03

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 41.53  E-value: 5.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   13 PRDYQVELLDKATKKNTIV-QLGTGSGKTFIAVLLLKEYgvqlfapLDQGGKRAFFVVEKVNLVEQQAIHIEVHTSFKVG 91
Cdd:PHA02558  115 PHWYQYDAVYEGLKNNRRLlNLPTSAGKSLIQYLLSRYY-------LENYEGKVLIIVPTTSLVTQMIDDFVDYRLFPRE 187

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392895692   92 QVHGQTSSGLWDSKEQcdqfmkrhhVVVITAQCLLDLIRHAYLKIEDMcvlIFDECHHALGsqhpyRSIMvdyKLLKKDK 171
Cdd:PHA02558  188 AMHKIYSGTAKDTDAP---------IVVSTWQSAVKQPKEWFDQFGMV---IVDECHLFTG-----KSLT---SIITKLD 247

                         170
                  ....*....|....*....
gi 392895692  172 PVPRVLGLTASLIKAKVAP 190
Cdd:PHA02558  248 NCKFKFGLTGSLRDGKANI 266
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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