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Conserved domains on  [gi|1376138976|ref|XP_024503581|]
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Endoribonuclease Dicer [Strongyloides ratti]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
13-213 1.81e-61

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


The actual alignment was detected with superfamily member cd18034:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 200  Bit Score: 209.04  E-value: 1.81e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   13 FTPRPYQLEILEKAKKRNVIVQLPTGSGKTYIGILMIKEVQYTVRKsISEGGKRIFFVVNNVCLVEQQARHIKNECELVV 92
Cdd:cd18034      1 FTPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRK-EKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKV 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   93 GELHGESSITVHDTDKIKTFLEQHQVIVLTAQILLDLICFSRISMEDISLLIFDECHHSMGKaHPYSNILSRYDKVPN-E 171
Cdd:cd18034     80 GEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGD-HPYARIMKEFYHLEGrT 158
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1376138976  172 KKPVILGLTASLFNQRLKKNQIENLLLKLEYKMHAEVVTADD 213
Cdd:cd18034    159 SRPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
374-524 9.87e-39

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd18802:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 142  Bit Score: 141.57  E-value: 9.87e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  374 EPYLSNKLKKVIEIL-ETFNKKciedpsvfQSMSCIIFVERRSAAYAIFEVLKELKKLDKarfgFIKADYIVGYNNNKSV 452
Cdd:cd18802      2 EIVVIPKLQKLIEILrEYFPKT--------PDFRGIIFVERRATAVVLSRLLKEHPSTLA----FIRCGFLIGRGNSSQR 69
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1376138976  453 EETTISSKIQDKKLQSFRQGSLNVLVSTDVLEEGFDVRQCNLVIRYKFPKNFRSYVQGRGRVRHKQGLYILL 524
Cdd:cd18802     70 KRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILM 141
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
1571-1740 1.36e-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: 140.83  E-value: 1.36e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1571 YLIQAFSHASYYINRVTSCYQRLEFLGDAVLDFVITRYLFSHEASFNPGTLTDLRSALVNNTMLASVAVDHDFHKYLMEf 1650
Cdd:cd00593      2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRL- 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1651 spklhevvrkfvtfikshenelinldsdlfmvNEDEEDCDGtedVEVPKALGDIFESFVGAVYLDSGrnLNVVWALIYKM 1730
Cdd:cd00593     81 --------------------------------GKGEEKSGG---RLRPKILADVFEALIGAIYLDGG--FEAARKFLLRL 123
                          170
                   ....*....|
gi 1376138976 1731 MKPHLERYTK 1740
Cdd:cd00593    124 LGPLIEEISL 133
PAZ super family cl00301
PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two ...
859-970 6.48e-36

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.


The actual alignment was detected with superfamily member cd02843:

Pssm-ID: 469713  Cd Length: 122  Bit Score: 132.95  E-value: 6.48e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  859 IDFNYMDYILETLEGMFKPPLEEDRKKYVFNESLYENAIVYPWYRSEENRNYYIIGEIMHDVKPSSDFPDNNFKTFEEYF 938
Cdd:cd02843      7 IDWEFMEKIEANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEYETFEEYY 86
                           90       100       110
                   ....*....|....*....|....*....|..
gi 1376138976  939 LEKYKITIYNKDQPLLDVDYTSNRLNLLVPKY 970
Cdd:cd02843     87 KKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRY 118
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
592-682 1.68e-26

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: 104.50  E-value: 1.68e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  592 AITIINRYCQKLPCDNFTVLSPSPDIIENEDGTYECSLLLPANCPYRNIIrsKKPLPSAKLSKMAAAVEACKILHQIKEL 671
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLRSIE--GPPWRSKKLAKRSAAFEACKALHKAGLL 78
                           90
                   ....*....|.
gi 1376138976  672 NDNLLPNGREK 682
Cdd:pfam03368   79 DDHLLPLTKKK 89
RIBOc smart00535
Ribonuclease III family;
1312-1406 2.20e-20

Ribonuclease III family;


:

Pssm-ID: 197778  Cd Length: 129  Bit Score: 88.81  E-value: 2.20e-20
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  1312 LLCALTSRGANDGI-DLERLETIGDSFLKFATTDYLYHKHVNAHEGCLSLLRSKEVSNMKLYFLGKKRNIHNIIINDKFE 1390
Cdd:smart00535    3 LLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRGE 82
                            90
                    ....*....|....*.
gi 1376138976  1391 PHTNWIPPGYVVSSEF 1406
Cdd:smart00535   83 AISGGRDKPKILADVF 98
DSRM_SF super family cl00054
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
1744-1806 3.60e-16

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


The actual alignment was detected with superfamily member cd10843:

Pssm-ID: 444671  Cd Length: 63  Bit Score: 74.38  E-value: 3.60e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1376138976 1744 ISPIRELTESYPDKVQFSKVERDPNTqRVKVYVEVSGT-KITGGGRNFKIAKCNAAKRALKYIK 1806
Cdd:cd10843      1 RSPVRELLEMEPETAKFSPAERTYDG-KVRVTVEVVGKgRFKGVGRNYRIAKSAAARRALRSLK 63
 
Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
13-213 1.81e-61

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: 209.04  E-value: 1.81e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   13 FTPRPYQLEILEKAKKRNVIVQLPTGSGKTYIGILMIKEVQYTVRKsISEGGKRIFFVVNNVCLVEQQARHIKNECELVV 92
Cdd:cd18034      1 FTPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRK-EKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKV 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   93 GELHGESSITVHDTDKIKTFLEQHQVIVLTAQILLDLICFSRISMEDISLLIFDECHHSMGKaHPYSNILSRYDKVPN-E 171
Cdd:cd18034     80 GEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGD-HPYARIMKEFYHLEGrT 158
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1376138976  172 KKPVILGLTASLFNQRLKKNQIENLLLKLEYKMHAEVVTADD 213
Cdd:cd18034    159 SRPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
374-524 9.87e-39

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: 141.57  E-value: 9.87e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  374 EPYLSNKLKKVIEIL-ETFNKKciedpsvfQSMSCIIFVERRSAAYAIFEVLKELKKLDKarfgFIKADYIVGYNNNKSV 452
Cdd:cd18802      2 EIVVIPKLQKLIEILrEYFPKT--------PDFRGIIFVERRATAVVLSRLLKEHPSTLA----FIRCGFLIGRGNSSQR 69
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1376138976  453 EETTISSKIQDKKLQSFRQGSLNVLVSTDVLEEGFDVRQCNLVIRYKFPKNFRSYVQGRGRVRHKQGLYILL 524
Cdd:cd18802     70 KRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILM 141
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
1571-1740 1.36e-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: 140.83  E-value: 1.36e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1571 YLIQAFSHASYYINRVTSCYQRLEFLGDAVLDFVITRYLFSHEASFNPGTLTDLRSALVNNTMLASVAVDHDFHKYLMEf 1650
Cdd:cd00593      2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRL- 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1651 spklhevvrkfvtfikshenelinldsdlfmvNEDEEDCDGtedVEVPKALGDIFESFVGAVYLDSGrnLNVVWALIYKM 1730
Cdd:cd00593     81 --------------------------------GKGEEKSGG---RLRPKILADVFEALIGAIYLDGG--FEAARKFLLRL 123
                          170
                   ....*....|
gi 1376138976 1731 MKPHLERYTK 1740
Cdd:cd00593    124 LGPLIEEISL 133
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
15-524 1.44e-37

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 152.58  E-value: 1.44e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   15 PRPYQLEILEKAKKRNVIVQLPTGSGKTYIGILMIKEVqytvrksISEGGKRIFFVVNNVCLVEQQARHIK---NECELV 91
Cdd:COG1111      4 RRLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAER-------LHKKGGKVLFLAPTKPLVEQHAEFFKealNIPEDE 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   92 VGELHGESSItvhdtDKIKTFLEQHQVIVLTAQILL-DLICfSRISMEDISLLIFDECHHSMGKaHPYSNILSRYdkVPN 170
Cdd:COG1111     77 IVVFTGEVSP-----EKRKELWEKARIIVATPQVIEnDLIA-GRIDLDDVSLLIFDEAHRAVGN-YAYVYIAERY--HED 147
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  171 EKKPVILGLTASLFNQRLKKNQI-ENLLLKleykmHAEVVTADDfSQVLKYSAIPNIKLIecsdfnaeKFDIAQKTLSFV 249
Cdd:COG1111    148 AKDPLILGMTASPGSDEEKIEEVcENLGIE-----NVEVRTEED-PDVAPYVHDTEVEWI--------RVELPEELKEIR 213
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  250 DKLNELVREMEKLLKD-----SRDFDPSqfiKTDINStiANSIYEKFIDTSSKDIRKKISEFVYI-----------TNNL 313
Cdd:COG1111    214 DLLNEVLDDRLKKLKElgvivSTSPDLS---KKDLLA--LQKKLQRRIREDDSEGYRAISILAEAlklrhalelleTQGV 288
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  314 GPFTVYkiCDfwtgDLKNYKNDQTISVKANYVVEaafdvfDSikkeytkKFSTMVTFEEIEPYLSNKLKKVIEIL-ETFN 392
Cdd:COG1111    289 EALLRY--LE----RLEEEARSSGGSKASKRLVS------DP-------RFRKAMRLAEEADIEHPKLSKLREILkEQLG 349
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  393 KKCIEdpsvfqsmSCIIFVERRSAAYAIFEVLKELKkldkarfgfIKADYIVGYNNNKSveETTISSKIQDKKLQSFRQG 472
Cdd:COG1111    350 TNPDS--------RIIVFTQYRDTAEMIVEFLSEPG---------IKAGRFVGQASKEG--DKGLTQKEQIEILERFRAG 410
                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1376138976  473 SLNVLVSTDVLEEGFDVRQCNLVIRYK-FPKNFRSyVQGRGRV-RHKQG-LYILL 524
Cdd:COG1111    411 EFNVLVATSVAEEGLDIPEVDLVIFYEpVPSEIRS-IQRKGRTgRKREGrVVVLI 464
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1552-1806 2.52e-36

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 137.92  E-value: 2.52e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1552 KNLFDIFEQKIGYIFKNKAYLIQAFSHASY-YINRVTSCYQRLEFLGDAVLDFVITRYLFSHEASFNPGTLTDLRSALVN 1630
Cdd:COG0571      1 SEDLEELEERLGYRFKDPELLEQALTHRSYaNEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1631 NTMLASVAVDHDFHKYLmefspklhevvrkfvtfikshenelinldsdlfMVNEDEEDCDGTedvEVPKALGDIFESFVG 1710
Cdd:COG0571     81 EETLAEIARELGLGDYL---------------------------------RLGKGEEKSGGR---RRPSILADAFEALIG 124
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1711 AVYLDSGrnLNVVWALIYKMMKPHLERYTKEPPIS-----------------PI-RELTESYPDkvqfskverdpNTQRV 1772
Cdd:COG0571    125 AIYLDGG--LEAARKFVLRLFEPRLEEIAPGGAGKdyktalqewlqarglplPEyEVVEEEGPD-----------HAKTF 191
                          250       260       270
                   ....*....|....*....|....*....|....*
gi 1376138976 1773 KVYVEVSGTKI-TGGGRNFKIAKCNAAKRALKYIK 1806
Cdd:COG0571    192 TVEVLVGGKVLgEGTGRSKKEAEQAAAKAALEKLG 226
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
859-970 6.48e-36

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: 132.95  E-value: 6.48e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  859 IDFNYMDYILETLEGMFKPPLEEDRKKYVFNESLYENAIVYPWYRSEENRNYYIIGEIMHDVKPSSDFPDNNFKTFEEYF 938
Cdd:cd02843      7 IDWEFMEKIEANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEYETFEEYY 86
                           90       100       110
                   ....*....|....*....|....*....|..
gi 1376138976  939 LEKYKITIYNKDQPLLDVDYTSNRLNLLVPKY 970
Cdd:cd02843     87 KKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRY 118
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
1558-1803 3.03e-35

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: 134.64  E-value: 3.03e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1558 FEQKIGYIFKNKAYLIQAFSHASY--YINRVTSCYQRLEFLGDAVLDFVITRYLFSHEASFNPGTLTDLRSALVNNTMLA 1635
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYanEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1636 SVAVDHDFHKYLmefspklhevvrkfvtfikshenelinldsdlfMVNEDEEDCDGtedVEVPKALGDIFESFVGAVYLD 1715
Cdd:TIGR02191   81 EVARELGLGDFL---------------------------------LLGKGEEKSGG---RRRDSILADAFEALIGAIYLD 124
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1716 SGrnLNVVWALIYKMMKPhleRYTKEPPISPIR-------ELTES-YPDKVQFSKVERD--PNTQRVKVYVEVSGTKI-T 1784
Cdd:TIGR02191  125 SG--LEAARKFILKLLIP---RIDAIIKEETLKdyktalqEWAQArGKPLPEYRLIKEEgpDHDKEFTVEVSVNGEPYgE 199
                          250
                   ....*....|....*....
gi 1376138976 1785 GGGRNFKIAKCNAAKRALK 1803
Cdd:TIGR02191  200 GKGKSKKEAEQNAAKAALE 218
PRK13766 PRK13766
Hef nuclease; Provisional
15-525 5.11e-32

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 135.77  E-value: 5.11e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   15 PRPYQLEILEKAKKRNVIVQLPTGSGKTYIGILMIKEVqytvrksISEGGKRIFFVVNNVCLVEQQARHIK-----NECE 89
Cdd:PRK13766    16 ARLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAER-------LHKKGGKVLILAPTKPLVEQHAEFFRkflniPEEK 88
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   90 LVVgeLHGESSitvhdTDKIKTFLEQHQVIVLTAQ-ILLDLICfSRISMEDISLLIFDECHHSMGKaHPYSNILSRYDKv 168
Cdd:PRK13766    89 IVV--FTGEVS-----PEKRAELWEKAKVIVATPQvIENDLIA-GRISLEDVSLLIFDEAHRAVGN-YAYVYIAERYHE- 158
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  169 pNEKKPVILGLTASLFNQRLKKNQI-ENLLLKleykmHAEVVTADDfSQVLKYsaipniklIECSDFNAEKFDIAQKTLS 247
Cdd:PRK13766   159 -DAKNPLVLGLTASPGSDEEKIKEVcENLGIE-----HVEVRTEDD-PDVKPY--------VHKVKIEWVRVELPEELKE 223
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  248 FVDKLNELVREMEKLLKDSRDFDPSQFI--KTDINStiANSIYEKFIDTSSKDIRKKIS---EFVYI--------TNNLG 314
Cdd:PRK13766   224 IRDLLNEALKDRLKKLKELGVIVSISPDvsKKELLG--LQKKLQQEIANDDSEGYEAISilaEAMKLrhavelleTQGVE 301
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  315 PFTVY--KicdfwtgdLKNYKNDQTISVKANYVVEAafdvfdsikkEYTKKfsTMVTFEEIEPyLSNKLKKVIEIL-ETF 391
Cdd:PRK13766   302 ALRRYleR--------LREEARSSGGSKASKRLVED----------PRFRK--AVRKAKELDI-EHPKLEKLREIVkEQL 360
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  392 NKKciEDPSVfqsmscIIFVERRSAAYAIFEVLKELKkldkarfgfIKADYIVGyNNNKSVEEtTISSKIQDKKLQSFRQ 471
Cdd:PRK13766   361 GKN--PDSRI------IVFTQYRDTAEKIVDLLEKEG---------IKAVRFVG-QASKDGDK-GMSQKEQIEILDKFRA 421
                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1376138976  472 GSLNVLVSTDVLEEGFDVRQCNLVIRYK-FPKNFRSyVQGRGRV-RHKQG-LYILLS 525
Cdd:PRK13766   422 GEFNVLVSTSVAEEGLDIPSVDLVIFYEpVPSEIRS-IQRKGRTgRQEEGrVVVLIA 477
RIBOc smart00535
Ribonuclease III family;
1571-1736 1.99e-30

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 117.32  E-value: 1.99e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  1571 YLIQAFSHASYYINRvtSCYQRLEFLGDAVLDFVITRYLFSHEASFNPGTLTDLRSALVNNTMLASVAVDHDFHKYLmef 1650
Cdd:smart00535    2 LLLRALTHASYSNEH--EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFI--- 76
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  1651 spklhevvrkfvtfikshenelinldsdlfMVNEDEEDCDGTedvEVPKALGDIFESFVGAVYLDSGrnLNVVWALIYKM 1730
Cdd:smart00535   77 ------------------------------RLGRGEAISGGR---DKPKILADVFEALIGAIYLDSG--LEAAREFIRDL 121

                    ....*.
gi 1376138976  1731 MKPHLE 1736
Cdd:smart00535  122 LGPRLD 127
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
592-682 1.68e-26

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: 104.50  E-value: 1.68e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  592 AITIINRYCQKLPCDNFTVLSPSPDIIENEDGTYECSLLLPANCPYRNIIrsKKPLPSAKLSKMAAAVEACKILHQIKEL 671
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLRSIE--GPPWRSKKLAKRSAAFEACKALHKAGLL 78
                           90
                   ....*....|.
gi 1376138976  672 NDNLLPNGREK 682
Cdd:pfam03368   79 DDHLLPLTKKK 89
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1591-1717 2.03e-23

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 96.19  E-value: 2.03e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1591 QRLEFLGDAVLDFVITRYLFSHEASFNPGTLTDLRSALVNNTMLASVAVDHDFHKYLmefspklhevvrkfvtfiKSHEN 1670
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFL------------------TEEEL 62
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1376138976 1671 ELINLDSDLfmvNEDEEDCDGTEdvevpKALGDIFESFVGAVYLDSG 1717
Cdd:pfam00636   63 DIRRRNNAL---GKGPKRADGKE-----KVLADAFEALIGALYLDGG 101
DEXDc smart00487
DEAD-like helicases superfamily;
13-217 1.99e-21

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 94.10  E-value: 1.99e-21
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976    13 FTPRPYQLEILEKAKK--RNVIVQLPTGSGKTYIGILMIKEVQYtvrksiSEGGKRIFFVVNNVCLVEQQARHIKNECEL 90
Cdd:smart00487    7 EPLRPYQKEAIEALLSglRDVILAAPTGSGKTLAALLPALEALK------RGKGGRVLVLVPTRELAEQWAEELKKLGPS 80
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976    91 VVGELHGESSITVHDTDKIKTFLEQHQVIVLTAQILLDLICFSRISMEDISLLIFDECHH--SMGKAHPYSNILSRydkv 168
Cdd:smart00487   81 LGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRllDGGFGDQLEKLLKL---- 156
                           170       180       190       200
                    ....*....|....*....|....*....|....*....|....*....
gi 1376138976   169 pNEKKPVILGLTASLFNQRLKknqIENLLLKLEYKMHAEVVTADDFSQV 217
Cdd:smart00487  157 -LPKNVQLLLLSATPPEEIEN---LLELFLNDPVFIDVGFTPLEPIEQF 201
RIBOc smart00535
Ribonuclease III family;
1312-1406 2.20e-20

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 88.81  E-value: 2.20e-20
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  1312 LLCALTSRGANDGI-DLERLETIGDSFLKFATTDYLYHKHVNAHEGCLSLLRSKEVSNMKLYFLGKKRNIHNIIINDKFE 1390
Cdd:smart00535    3 LLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRGE 82
                            90
                    ....*....|....*.
gi 1376138976  1391 PHTNWIPPGYVVSSEF 1406
Cdd:smart00535   83 AISGGRDKPKILADVF 98
ResIII pfam04851
Type III restriction enzyme, res subunit;
13-181 1.52e-18

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 84.65  E-value: 1.52e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   13 FTPRPYQLEILE------KAKKRNVIVQLPTGSGKTYIGILMIKevqytvRKSISEGGKRIFFVVNNVCLVEQQARHIKN 86
Cdd:pfam04851    2 LELRPYQIEAIEnllesiKNGQKRGLIVMATGSGKTLTAAKLIA------RLFKKGPIKKVLFLVPRKDLLEQALEEFKK 75
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   87 ---ECELVVGELHGESSITVHDTDKIKTFLEQHqvivLTAQILLDLICFSRismEDISLLIFDECHHSMGKAhpYSNILS 163
Cdd:pfam04851   76 flpNYVEIGEIISGDKKDESVDDNKIVVTTIQS----LYKALELASLELLP---DFFDVIIIDEAHRSGASS--YRNILE 146
                          170
                   ....*....|....*...
gi 1376138976  164 rydkvpNEKKPVILGLTA 181
Cdd:pfam04851  147 ------YFKPAFLLGLTA 158
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
893-1021 1.98e-18

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: 83.49  E-value: 1.98e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   893 YENAIVYPWYRseeNRNYYIIGeIMHDVKPSSDFPDNNFK--TFEEYFLEKYKITIYNKDQPLLdvdytsnrlnllvpky 970
Cdd:smart00949   27 LKGLIVLTRYN---NKTYRIDD-IDWNLAPKSTFEKSDGSeiTFVEYYKQKYNITIRDPNQPLL---------------- 86
                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|.
gi 1376138976   971 PSKSSRPLKNSRSSQRQILVPELVSIHPIKSTHWSIIGALPSIFYRYNCLL 1021
Cdd:smart00949   87 VSRPKRRRNQNGKGEPVLLPPELCFITGLTDRMRKDFMLMKSIADRTRLSP 137
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
1311-1394 1.10e-17

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: 81.12  E-value: 1.10e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1311 ILLCALTSRGANDGI---DLERLETIGDSFLKFATTDYLYHKHVNAHEGCLSLLRSKEVSNMKLYFLGKKRNIHNIIIND 1387
Cdd:cd00593      2 LLLEALTHPSYANEHgrfNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLG 81

                   ....*..
gi 1376138976 1388 KFEPHTN 1394
Cdd:cd00593     82 KGEEKSG 88
DSRM_DICER cd10843
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ...
1744-1806 3.60e-16

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: 74.38  E-value: 3.60e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1376138976 1744 ISPIRELTESYPDKVQFSKVERDPNTqRVKVYVEVSGT-KITGGGRNFKIAKCNAAKRALKYIK 1806
Cdd:cd10843      1 RSPVRELLEMEPETAKFSPAERTYDG-KVRVTVEVVGKgRFKGVGRNYRIAKSAAARRALRSLK 63
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
379-514 1.98e-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: 73.78  E-value: 1.98e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  379 NKLKKVIEILETFNKKCIedpsvfqsmscIIFVERRSAAYAifEVLKELKKldkarfgfIKADYIVGynnnksveetTIS 458
Cdd:pfam00271    1 EKLEALLELLKKERGGKV-----------LIFSQTKKTLEA--ELLLEKEG--------IKVARLHG----------DLS 49
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1376138976  459 SKIQDKKLQSFRQGSLNVLVSTDVLEEGFDVRQCNLVIRYKFPKNFRSYVQGRGRV 514
Cdd:pfam00271   50 QEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1328-1391 2.82e-12

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 64.60  E-value: 2.82e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1376138976 1328 ERLETIGDSFLKFATTDYLYHKHVNAHEGCLSLLRSKEVSNMKLYFLGKKRNIHNIIINDKFEP 1391
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI 64
HELICc smart00490
helicase superfamily c-terminal domain;
456-514 7.57e-12

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 62.61  E-value: 7.57e-12
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 1376138976   456 TISSKIQDKKLQSFRQGSLNVLVSTDVLEEGFDVRQCNLVIRYKFPKNFRSYVQGRGRV 514
Cdd:smart00490   20 GLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
895-1016 8.26e-12

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: 64.14  E-value: 8.26e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  895 NAIVYPWYrseENRNYYIIGEIMHDVKPSSDFPDNNFK--TFEEYFLEKYKITIYNKDQPLLDVdytsnrlnllvpkyps 972
Cdd:pfam02170   26 GLKVYTTY---NNPRTYRIDGITFDPTPESTFPLKDGKeiTVVDYFKKKYNIDLKYPDQPLLLV---------------- 86
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1376138976  973 KSSRPlknsrssqRQILVPELVSIHPiksTHWSIIGALPSIFYR 1016
Cdd:pfam02170   87 GKKRP--------KVYLPPELCNLVD---GQRYTKKLMPSIAQR 119
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
1308-1385 8.24e-09

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: 57.98  E-value: 8.24e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1308 NPAILLCALT-----SRGANDGIDLERLETIGDSFLKFATTDYLYHKHVNAHEGCLSLLRSKEVSNMKLYFLGKKRNIHN 1382
Cdd:TIGR02191   11 NPELLEQALThrsyaNEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVARELGLGD 90

                   ...
gi 1376138976 1383 III 1385
Cdd:TIGR02191   91 FLL 93
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1308-1367 7.34e-07

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 52.02  E-value: 7.34e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1376138976 1308 NPAILLCALT----SRGANDGIDLERLETIGDSFLKFATTDYLYHKHVNAHEGCLSLLRSKEVS 1367
Cdd:COG0571     17 DPELLEQALThrsyANEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVS 80
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
408-555 1.16e-05

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 50.23  E-value: 1.16e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  408 IIFVERRSAAYAIFEVLKelkkldkaRFGFIKAdyIVGYNNNKSVEETTisskiqdkkLQSFRQGSLNVLVSTDVLEEGF 487
Cdd:PRK11634   249 IIFVRTKNATLEVAEALE--------RNGYNSA--ALNGDMNQALREQT---------LERLKDGRLDILIATDVAARGL 309
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  488 DVRQCNLVIRYKFPKNFRSYVQGRGRVRH--KQGLYILLSDSKsledDKAELKNFEECETLLIQRFRTPN 555
Cdd:PRK11634   310 DVERISLVVNYDIPMDSESYVHRIGRTGRagRAGRALLFVENR----ERRLLRNIERTMKLTIPEVELPN 375
DSRM smart00358
Double-stranded RNA binding motif;
1743-1806 1.59e-05

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 44.18  E-value: 1.59e-05
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1376138976  1743 PISPIRELTESYPDKVQFSKVERD--PNTQRVKVYVEVSGTKI-TGGGRNFKIAKCNAAKRALKYIK 1806
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEEgpDHAPRFTVTVKVGGKRTgEGEGSSKKEAKQRAAEAALRSLK 67
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
379-542 4.19e-05

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 48.22  E-value: 4.19e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  379 NKLKKVIEILETfnkkciEDPSvfqsmSCIIFVERRSAAYAIFEVLKELKkldkarfgfIKADYIVGynnNKSVEEttis 458
Cdd:COG0513    227 DKLELLRRLLRD------EDPE-----RAIVFCNTKRGADRLAEKLQKRG---------ISAAALHG---DLSQGQ---- 279
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  459 skiQDKKLQSFRQGSLNVLVSTDVLEEGFDVRQCNLVIRYKFPKNFRSYVQ--GR-GRVrHKQGLYILLSDskslEDDKA 535
Cdd:COG0513    280 ---RERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYVHriGRtGRA-GAEGTAISLVT----PDERR 351

                   ....*..
gi 1376138976  536 ELKNFEE 542
Cdd:COG0513    352 LLRAIEK 358
DEXH_lig_assoc TIGR04121
DEXH box helicase, DNA ligase-associated; Members of this protein family are DEAD/DEAH box ...
13-47 2.58e-03

DEXH box helicase, DNA ligase-associated; Members of this protein family are DEAD/DEAH box helicases found associated with a bacterial ATP-dependent DNA ligase, part of a four-gene system that occurs in about 12 % of prokaryotic reference genomes. The actual motif in this family is DE[VILW]H.


Pssm-ID: 274994 [Multi-domain]  Cd Length: 804  Bit Score: 42.54  E-value: 2.58e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1376138976   13 FTPRPYQLEILEKAKK-RNVIVQLPTGSGKTYIGIL 47
Cdd:TIGR04121   12 WTPRPFQLEMWAAALEgRSGLLIAPTGSGKTLAGFL 47
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
1743-1805 8.90e-03

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 36.44  E-value: 8.90e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1376138976 1743 PISPIRELTESYPDKVQFSKVERD--PNTQRVKVYVEVSGTKITGG-GRNFKIAKCNAAKRALKYI 1805
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVSEEgpPHSPKFTVTVKVDGKLYGSGtGSSKKEAEQLAAEKALEKL 66
 
Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
13-213 1.81e-61

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: 209.04  E-value: 1.81e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   13 FTPRPYQLEILEKAKKRNVIVQLPTGSGKTYIGILMIKEVQYTVRKsISEGGKRIFFVVNNVCLVEQQARHIKNECELVV 92
Cdd:cd18034      1 FTPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRK-EKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKV 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   93 GELHGESSITVHDTDKIKTFLEQHQVIVLTAQILLDLICFSRISMEDISLLIFDECHHSMGKaHPYSNILSRYDKVPN-E 171
Cdd:cd18034     80 GEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGD-HPYARIMKEFYHLEGrT 158
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1376138976  172 KKPVILGLTASLFNQRLKKNQIENLLLKLEYKMHAEVVTADD 213
Cdd:cd18034    159 SRPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
13-211 1.87e-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: 146.04  E-value: 1.87e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   13 FTPRPYQLEILEKAKK-RNVIVQLPTGSGKTYIGILMIKEvqYTVRKSISEGGKRIFFVvNNVCLVEQQA---RHIKNEC 88
Cdd:cd17927      1 FKPRNYQLELAQPALKgKNTIICLPTGSGKTFVAVLICEH--HLKKFPAGRKGKVVFLA-NKVPLVEQQKevfRKHFERP 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   89 ELVVGELHGESSITVHDTDKIKTfleqHQVIVLTAQILL-DLICFSRISMEDISLLIFDECHHSMGKaHPYSNILSRYDK 167
Cdd:cd17927     78 GYKVTGLSGDTSENVSVEQIVES----SDVIIVTPQILVnDLKSGTIVSLSDFSLLVFDECHNTTKN-HPYNEIMFRYLD 152
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 1376138976  168 ---VPNEKKPVILGLTASLFNQRLKKNQ-IENLLLKLEYKMHAEVVTA 211
Cdd:cd17927    153 qklGSSGPLPQILGLTASPGVGGAKNTEeALEHICKLCANLDISVIAT 200
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
374-524 9.87e-39

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: 141.57  E-value: 9.87e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  374 EPYLSNKLKKVIEIL-ETFNKKciedpsvfQSMSCIIFVERRSAAYAIFEVLKELKKLDKarfgFIKADYIVGYNNNKSV 452
Cdd:cd18802      2 EIVVIPKLQKLIEILrEYFPKT--------PDFRGIIFVERRATAVVLSRLLKEHPSTLA----FIRCGFLIGRGNSSQR 69
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1376138976  453 EETTISSKIQDKKLQSFRQGSLNVLVSTDVLEEGFDVRQCNLVIRYKFPKNFRSYVQGRGRVRHKQGLYILL 524
Cdd:cd18802     70 KRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILM 141
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
1571-1740 1.36e-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: 140.83  E-value: 1.36e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1571 YLIQAFSHASYYINRVTSCYQRLEFLGDAVLDFVITRYLFSHEASFNPGTLTDLRSALVNNTMLASVAVDHDFHKYLMEf 1650
Cdd:cd00593      2 LLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRL- 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1651 spklhevvrkfvtfikshenelinldsdlfmvNEDEEDCDGtedVEVPKALGDIFESFVGAVYLDSGrnLNVVWALIYKM 1730
Cdd:cd00593     81 --------------------------------GKGEEKSGG---RLRPKILADVFEALIGAIYLDGG--FEAARKFLLRL 123
                          170
                   ....*....|
gi 1376138976 1731 MKPHLERYTK 1740
Cdd:cd00593    124 LGPLIEEISL 133
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
15-524 1.44e-37

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 152.58  E-value: 1.44e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   15 PRPYQLEILEKAKKRNVIVQLPTGSGKTYIGILMIKEVqytvrksISEGGKRIFFVVNNVCLVEQQARHIK---NECELV 91
Cdd:COG1111      4 RRLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAER-------LHKKGGKVLFLAPTKPLVEQHAEFFKealNIPEDE 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   92 VGELHGESSItvhdtDKIKTFLEQHQVIVLTAQILL-DLICfSRISMEDISLLIFDECHHSMGKaHPYSNILSRYdkVPN 170
Cdd:COG1111     77 IVVFTGEVSP-----EKRKELWEKARIIVATPQVIEnDLIA-GRIDLDDVSLLIFDEAHRAVGN-YAYVYIAERY--HED 147
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  171 EKKPVILGLTASLFNQRLKKNQI-ENLLLKleykmHAEVVTADDfSQVLKYSAIPNIKLIecsdfnaeKFDIAQKTLSFV 249
Cdd:COG1111    148 AKDPLILGMTASPGSDEEKIEEVcENLGIE-----NVEVRTEED-PDVAPYVHDTEVEWI--------RVELPEELKEIR 213
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  250 DKLNELVREMEKLLKD-----SRDFDPSqfiKTDINStiANSIYEKFIDTSSKDIRKKISEFVYI-----------TNNL 313
Cdd:COG1111    214 DLLNEVLDDRLKKLKElgvivSTSPDLS---KKDLLA--LQKKLQRRIREDDSEGYRAISILAEAlklrhalelleTQGV 288
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  314 GPFTVYkiCDfwtgDLKNYKNDQTISVKANYVVEaafdvfDSikkeytkKFSTMVTFEEIEPYLSNKLKKVIEIL-ETFN 392
Cdd:COG1111    289 EALLRY--LE----RLEEEARSSGGSKASKRLVS------DP-------RFRKAMRLAEEADIEHPKLSKLREILkEQLG 349
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  393 KKCIEdpsvfqsmSCIIFVERRSAAYAIFEVLKELKkldkarfgfIKADYIVGYNNNKSveETTISSKIQDKKLQSFRQG 472
Cdd:COG1111    350 TNPDS--------RIIVFTQYRDTAEMIVEFLSEPG---------IKAGRFVGQASKEG--DKGLTQKEQIEILERFRAG 410
                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1376138976  473 SLNVLVSTDVLEEGFDVRQCNLVIRYK-FPKNFRSyVQGRGRV-RHKQG-LYILL 524
Cdd:COG1111    411 EFNVLVATSVAEEGLDIPEVDLVIFYEpVPSEIRS-IQRKGRTgRKREGrVVVLI 464
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1552-1806 2.52e-36

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 137.92  E-value: 2.52e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1552 KNLFDIFEQKIGYIFKNKAYLIQAFSHASY-YINRVTSCYQRLEFLGDAVLDFVITRYLFSHEASFNPGTLTDLRSALVN 1630
Cdd:COG0571      1 SEDLEELEERLGYRFKDPELLEQALTHRSYaNEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1631 NTMLASVAVDHDFHKYLmefspklhevvrkfvtfikshenelinldsdlfMVNEDEEDCDGTedvEVPKALGDIFESFVG 1710
Cdd:COG0571     81 EETLAEIARELGLGDYL---------------------------------RLGKGEEKSGGR---RRPSILADAFEALIG 124
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1711 AVYLDSGrnLNVVWALIYKMMKPHLERYTKEPPIS-----------------PI-RELTESYPDkvqfskverdpNTQRV 1772
Cdd:COG0571    125 AIYLDGG--LEAARKFVLRLFEPRLEEIAPGGAGKdyktalqewlqarglplPEyEVVEEEGPD-----------HAKTF 191
                          250       260       270
                   ....*....|....*....|....*....|....*
gi 1376138976 1773 KVYVEVSGTKI-TGGGRNFKIAKCNAAKRALKYIK 1806
Cdd:COG0571    192 TVEVLVGGKVLgEGTGRSKKEAEQAAAKAALEKLG 226
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
859-970 6.48e-36

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: 132.95  E-value: 6.48e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  859 IDFNYMDYILETLEGMFKPPLEEDRKKYVFNESLYENAIVYPWYRSEENRNYYIIGEIMHDVKPSSDFPDNNFKTFEEYF 938
Cdd:cd02843      7 IDWEFMEKIEANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEYETFEEYY 86
                           90       100       110
                   ....*....|....*....|....*....|..
gi 1376138976  939 LEKYKITIYNKDQPLLDVDYTSNRLNLLVPKY 970
Cdd:cd02843     87 KKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRY 118
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
1558-1803 3.03e-35

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: 134.64  E-value: 3.03e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1558 FEQKIGYIFKNKAYLIQAFSHASY--YINRVTSCYQRLEFLGDAVLDFVITRYLFSHEASFNPGTLTDLRSALVNNTMLA 1635
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYanEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1636 SVAVDHDFHKYLmefspklhevvrkfvtfikshenelinldsdlfMVNEDEEDCDGtedVEVPKALGDIFESFVGAVYLD 1715
Cdd:TIGR02191   81 EVARELGLGDFL---------------------------------LLGKGEEKSGG---RRRDSILADAFEALIGAIYLD 124
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1716 SGrnLNVVWALIYKMMKPhleRYTKEPPISPIR-------ELTES-YPDKVQFSKVERD--PNTQRVKVYVEVSGTKI-T 1784
Cdd:TIGR02191  125 SG--LEAARKFILKLLIP---RIDAIIKEETLKdyktalqEWAQArGKPLPEYRLIKEEgpDHDKEFTVEVSVNGEPYgE 199
                          250
                   ....*....|....*....
gi 1376138976 1785 GGGRNFKIAKCNAAKRALK 1803
Cdd:TIGR02191  200 GKGKSKKEAEQNAAKAALE 218
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
13-183 6.49e-34

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: 130.29  E-value: 6.49e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   13 FTPRPYQLEILEKAKK-RNVIVQLPTGSGKTYIGILMIKEvQYTVRKSISEGGKRIFFVvNNVCLVEQQARHIKNECELV 91
Cdd:cd18036      1 LELRNYQLELVLPALRgKNTIICAPTGSGKTRVAVYICRH-HLEKRRSAGEKGRVVVLV-NKVPLVEQQLEKFFKYFRKG 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   92 --VGELHGESSITVHDTDkiktFLEQHQVIVLTAQILLDLIC----FSRISMEDISLLIFDECHHSmGKAHPYSNILSRY 165
Cdd:cd18036     79 ykVTGLSGDSSHKVSFGQ----IVKASDVIICTPQILINNLLsgreEERVYLSDFSLLIFDECHHT-QKEHPYNKIMRMY 153
                          170       180
                   ....*....|....*....|.
gi 1376138976  166 DK---VPNEKKPVILGLTASL 183
Cdd:cd18036    154 LDkklSSQGPLPQILGLTASP 174
PRK13766 PRK13766
Hef nuclease; Provisional
15-525 5.11e-32

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 135.77  E-value: 5.11e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   15 PRPYQLEILEKAKKRNVIVQLPTGSGKTYIGILMIKEVqytvrksISEGGKRIFFVVNNVCLVEQQARHIK-----NECE 89
Cdd:PRK13766    16 ARLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAER-------LHKKGGKVLILAPTKPLVEQHAEFFRkflniPEEK 88
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   90 LVVgeLHGESSitvhdTDKIKTFLEQHQVIVLTAQ-ILLDLICfSRISMEDISLLIFDECHHSMGKaHPYSNILSRYDKv 168
Cdd:PRK13766    89 IVV--FTGEVS-----PEKRAELWEKAKVIVATPQvIENDLIA-GRISLEDVSLLIFDEAHRAVGN-YAYVYIAERYHE- 158
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  169 pNEKKPVILGLTASLFNQRLKKNQI-ENLLLKleykmHAEVVTADDfSQVLKYsaipniklIECSDFNAEKFDIAQKTLS 247
Cdd:PRK13766   159 -DAKNPLVLGLTASPGSDEEKIKEVcENLGIE-----HVEVRTEDD-PDVKPY--------VHKVKIEWVRVELPEELKE 223
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  248 FVDKLNELVREMEKLLKDSRDFDPSQFI--KTDINStiANSIYEKFIDTSSKDIRKKIS---EFVYI--------TNNLG 314
Cdd:PRK13766   224 IRDLLNEALKDRLKKLKELGVIVSISPDvsKKELLG--LQKKLQQEIANDDSEGYEAISilaEAMKLrhavelleTQGVE 301
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  315 PFTVY--KicdfwtgdLKNYKNDQTISVKANYVVEAafdvfdsikkEYTKKfsTMVTFEEIEPyLSNKLKKVIEIL-ETF 391
Cdd:PRK13766   302 ALRRYleR--------LREEARSSGGSKASKRLVED----------PRFRK--AVRKAKELDI-EHPKLEKLREIVkEQL 360
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  392 NKKciEDPSVfqsmscIIFVERRSAAYAIFEVLKELKkldkarfgfIKADYIVGyNNNKSVEEtTISSKIQDKKLQSFRQ 471
Cdd:PRK13766   361 GKN--PDSRI------IVFTQYRDTAEKIVDLLEKEG---------IKAVRFVG-QASKDGDK-GMSQKEQIEILDKFRA 421
                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1376138976  472 GSLNVLVSTDVLEEGFDVRQCNLVIRYK-FPKNFRSyVQGRGRV-RHKQG-LYILLS 525
Cdd:PRK13766   422 GEFNVLVSTSVAEEGLDIPSVDLVIFYEpVPSEIRS-IQRKGRTgRQEEGrVVVLIA 477
RIBOc smart00535
Ribonuclease III family;
1571-1736 1.99e-30

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 117.32  E-value: 1.99e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  1571 YLIQAFSHASYYINRvtSCYQRLEFLGDAVLDFVITRYLFSHEASFNPGTLTDLRSALVNNTMLASVAVDHDFHKYLmef 1650
Cdd:smart00535    2 LLLRALTHASYSNEH--EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFI--- 76
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  1651 spklhevvrkfvtfikshenelinldsdlfMVNEDEEDCDGTedvEVPKALGDIFESFVGAVYLDSGrnLNVVWALIYKM 1730
Cdd:smart00535   77 ------------------------------RLGRGEAISGGR---DKPKILADVFEALIGAIYLDSG--LEAAREFIRDL 121

                    ....*.
gi 1376138976  1731 MKPHLE 1736
Cdd:smart00535  122 LGPRLD 127
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
592-682 1.68e-26

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: 104.50  E-value: 1.68e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  592 AITIINRYCQKLPCDNFTVLSPSPDIIENEDGTYECSLLLPANCPYRNIIrsKKPLPSAKLSKMAAAVEACKILHQIKEL 671
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLRSIE--GPPWRSKKLAKRSAAFEACKALHKAGLL 78
                           90
                   ....*....|.
gi 1376138976  672 NDNLLPNGREK 682
Cdd:pfam03368   79 DDHLLPLTKKK 89
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1591-1717 2.03e-23

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 96.19  E-value: 2.03e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1591 QRLEFLGDAVLDFVITRYLFSHEASFNPGTLTDLRSALVNNTMLASVAVDHDFHKYLmefspklhevvrkfvtfiKSHEN 1670
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFL------------------TEEEL 62
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1376138976 1671 ELINLDSDLfmvNEDEEDCDGTEdvevpKALGDIFESFVGAVYLDSG 1717
Cdd:pfam00636   63 DIRRRNNAL---GKGPKRADGKE-----KVLADAFEALIGALYLDGG 101
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
7-544 4.12e-22

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 102.80  E-value: 4.12e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976    7 EVSDEVFTPRPYQLEILEK------AKKRNVIVQLPTGSGKTYIGILMIKEVQytvrksiseGGKRIFFVVNNVCLVEQQ 80
Cdd:COG1061     73 EASGTSFELRPYQQEALEAllaaleRGGGRGLVVAPTGTGKTVLALALAAELL---------RGKRVLVLVPRRELLEQW 143
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   81 ARHIKnecelvvgELHGESSITVHDTDkiktflEQHQVIVLTAQILLDLICFSRISmEDISLLIFDECHHSMGKAhpYSN 160
Cdd:COG1061    144 AEELR--------RFLGDPLAGGGKKD------SDAPITVATYQSLARRAHLDELG-DRFGLVIIDEAHHAGAPS--YRR 206
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  161 ILSRYdkvpneKKPVILGLTASLFnqrlkknqienlllkleykmhaevvtaddfsqvlkysaipnikliecsdfnaekfd 240
Cdd:COG1061    207 ILEAF------PAAYRLGLTATPF-------------------------------------------------------- 224
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  241 iaqktlsfvdklnelvREmekllkDSRDFDPSQFIKTdinstiansIYEkfidtssKDIRKKISEFVyitnnLGPFTVYK 320
Cdd:COG1061    225 ----------------RS------DGREILLFLFDGI---------VYE-------YSLKEAIEDGY-----LAPPEYYG 261
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  321 ICDFWTGDLKNYkndqtisvkanyvveaafdvfDSIKKEYTKKfstmvtfeeIEPYLSNKLKKVIEILETFNKKciedps 400
Cdd:COG1061    262 IRVDLTDERAEY---------------------DALSERLREA---------LAADAERKDKILRELLREHPDD------ 305
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  401 vfqsMSCIIFVERRSAAYAIFEVLKELKkldkarfgfIKADYIVGynnnksveETtiSSKIQDKKLQSFRQGSLNVLVST 480
Cdd:COG1061    306 ----RKTLVFCSSVDHAEALAELLNEAG---------IRAAVVTG--------DT--PKKEREEILEAFRDGELRILVTV 362
                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1376138976  481 DVLEEGFDVRQCNLVI--RYKfpKNFRSYVQGRGRV----RHKQGLYILL---SDSKSLEDDKAELKNFEECE 544
Cdd:COG1061    363 DVLNEGVDVPRLDVAIllRPT--GSPREFIQRLGRGlrpaPGKEDALVYDfvgNDVPVLEELAKDLRDLAGYR 433
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
13-210 1.25e-21

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: 94.89  E-value: 1.25e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   13 FTPRPYQLEILEKAKK-RNVIVQLPTGSGKTYIGILmIKEVQYtvrKSISEGGK-RIFFVVNNVCLVEQQARHIKNECE- 89
Cdd:cd18073      1 FKPRNYQLELALPAMKgKNTIICAPTGCGKTFVSLL-ICEHHL---KKFPQGQKgKVVFFATKVPVYEQQKSVFSKYFEr 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   90 --LVVGELHGESSITVhdtdKIKTFLEQHQVIVLTAQILLDLICFSRI-SMEDISLLIFDECHHSMGKaHPYSNILSRY- 165
Cdd:cd18073     77 hgYRVTGISGATAENV----PVEQIIENNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSGN-HPYNMIMFRYl 151
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1376138976  166 -DKVPNEKKPV--ILGLTASLFNQRLKK-NQIENLLLKLEYKMHAEVVT 210
Cdd:cd18073    152 dQKLGGSSGPLpqIIGLTASVGVGDAKNtDEALDYICKLCASLDASVIA 200
DEXDc smart00487
DEAD-like helicases superfamily;
13-217 1.99e-21

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 94.10  E-value: 1.99e-21
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976    13 FTPRPYQLEILEKAKK--RNVIVQLPTGSGKTYIGILMIKEVQYtvrksiSEGGKRIFFVVNNVCLVEQQARHIKNECEL 90
Cdd:smart00487    7 EPLRPYQKEAIEALLSglRDVILAAPTGSGKTLAALLPALEALK------RGKGGRVLVLVPTRELAEQWAEELKKLGPS 80
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976    91 VVGELHGESSITVHDTDKIKTFLEQHQVIVLTAQILLDLICFSRISMEDISLLIFDECHH--SMGKAHPYSNILSRydkv 168
Cdd:smart00487   81 LGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRllDGGFGDQLEKLLKL---- 156
                           170       180       190       200
                    ....*....|....*....|....*....|....*....|....*....
gi 1376138976   169 pNEKKPVILGLTASLFNQRLKknqIENLLLKLEYKMHAEVVTADDFSQV 217
Cdd:smart00487  157 -LPKNVQLLLLSATPPEEIEN---LLELFLNDPVFIDVGFTPLEPIEQF 201
RIBOc smart00535
Ribonuclease III family;
1312-1406 2.20e-20

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 88.81  E-value: 2.20e-20
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  1312 LLCALTSRGANDGI-DLERLETIGDSFLKFATTDYLYHKHVNAHEGCLSLLRSKEVSNMKLYFLGKKRNIHNIIINDKFE 1390
Cdd:smart00535    3 LLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRGE 82
                            90
                    ....*....|....*.
gi 1376138976  1391 PHTNWIPPGYVVSSEF 1406
Cdd:smart00535   83 AISGGRDKPKILADVF 98
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
15-182 4.50e-20

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: 89.50  E-value: 4.50e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   15 PRPYQLEILEKAKKRNVIVQLPTGSGKTYIGILMIKEVqytvrksISEGGKRIFFVVNNVCLVEQQA---RHIKNECELV 91
Cdd:cd18035      3 RRLYQVLIAAVALNGNTLIVLPTGLGKTIIAILVAADR-------LTKKGGKVLILAPSRPLVEQHAenlKRVLNIPDKI 75
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   92 VGeLHGESsitvhDTDKIKTFLEQHQVIVLTAQILLDLICFSRISMEDISLLIFDECHHSMGKaHPYSNILSRYDKvpNE 171
Cdd:cd18035     76 TS-LTGEV-----KPEERAERWDASKIIVATPQVIENDLLAGRITLDDVSLLIFDEAHHAVGN-YAYVYIAHRYKR--EA 146
                          170
                   ....*....|.
gi 1376138976  172 KKPVILGLTAS 182
Cdd:cd18035    147 NNPLILGLTAS 157
ResIII pfam04851
Type III restriction enzyme, res subunit;
13-181 1.52e-18

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 84.65  E-value: 1.52e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   13 FTPRPYQLEILE------KAKKRNVIVQLPTGSGKTYIGILMIKevqytvRKSISEGGKRIFFVVNNVCLVEQQARHIKN 86
Cdd:pfam04851    2 LELRPYQIEAIEnllesiKNGQKRGLIVMATGSGKTLTAAKLIA------RLFKKGPIKKVLFLVPRKDLLEQALEEFKK 75
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   87 ---ECELVVGELHGESSITVHDTDKIKTFLEQHqvivLTAQILLDLICFSRismEDISLLIFDECHHSMGKAhpYSNILS 163
Cdd:pfam04851   76 flpNYVEIGEIISGDKKDESVDDNKIVVTTIQS----LYKALELASLELLP---DFFDVIIIDEAHRSGASS--YRNILE 146
                          170
                   ....*....|....*...
gi 1376138976  164 rydkvpNEKKPVILGLTA 181
Cdd:pfam04851  147 ------YFKPAFLLGLTA 158
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
893-1021 1.98e-18

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: 83.49  E-value: 1.98e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   893 YENAIVYPWYRseeNRNYYIIGeIMHDVKPSSDFPDNNFK--TFEEYFLEKYKITIYNKDQPLLdvdytsnrlnllvpky 970
Cdd:smart00949   27 LKGLIVLTRYN---NKTYRIDD-IDWNLAPKSTFEKSDGSeiTFVEYYKQKYNITIRDPNQPLL---------------- 86
                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|.
gi 1376138976   971 PSKSSRPLKNSRSSQRQILVPELVSIHPIKSTHWSIIGALPSIFYRYNCLL 1021
Cdd:smart00949   87 VSRPKRRRNQNGKGEPVLLPPELCFITGLTDRMRKDFMLMKSIADRTRLSP 137
DEXHc_RLR-3 cd18075
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ...
16-182 6.85e-18

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: 83.75  E-value: 6.85e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   16 RPYQLEILEKA-KKRNVIVQLPTGSGKTYIGILMIKEVQYTVRksisegGKRIFFVVNNVCLVEQqarHIKNEcelvVGE 94
Cdd:cd18075      4 HGYQWEVVAPAlRGKNSIIWLPTGAGKTRAAVYVARRHLETKR------GAKVAVLVNKVHLVDQ---HLEKE----FHV 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   95 LHGESSITVHDTD-KIKTFLEQ----HQVIVLTAQILLDLICF----SRISMEDISLLIFDECHHSMgKAHPYSNILSRY 165
Cdd:cd18075     71 LLDKYTVTAISGDsSHKCFFGQlargSDVVICTAQILQNALLSgeeeAHVELTDFSLLVIDECHHTH-KEAVYNKIMLSY 149
                          170       180
                   ....*....|....*....|
gi 1376138976  166 --DKVPNEKK-PVILGLTAS 182
Cdd:cd18075    150 leKKLSRQGDlPQILGLTAS 169
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
1311-1394 1.10e-17

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: 81.12  E-value: 1.10e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1311 ILLCALTSRGANDGI---DLERLETIGDSFLKFATTDYLYHKHVNAHEGCLSLLRSKEVSNMKLYFLGKKRNIHNIIIND 1387
Cdd:cd00593      2 LLLEALTHPSYANEHgrfNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLG 81

                   ....*..
gi 1376138976 1388 KFEPHTN 1394
Cdd:cd00593     82 KGEEKSG 88
DEXHc_RLR-2 cd18074
DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma ...
14-182 1.30e-17

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: 83.37  E-value: 1.30e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   14 TPRPYQLEILEKA-KKRNVIVQLPTGSGKTYIGILMIKEvQYTVRKSISEGGKRIfFVVNNVCLVEQQARH-----IKNE 87
Cdd:cd18074      2 TLRDYQMEVAKPAlEGKNIIICLPTGSGKTRVAVYITKD-HLDKKRKASEPGKVI-VLVNKVPLVEQHYRKefnpfLKHW 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   88 CElvVGELHGESSITVHDTDKIKtfleQHQVIVLTAQILLDLICFSR------ISMEDISLLIFDECHHSMgKAHPYSNI 161
Cdd:cd18074     80 YQ--VIGLSGDSQLKISFPEVVK----RYDVIICTAQILENSLLNATeeedegVQLSDFSLIIIDECHHTQ-KEAVYNNI 152
                          170       180       190
                   ....*....|....*....|....*....|...
gi 1376138976  162 LSRY--DKVPNEKK----------PVILGLTAS 182
Cdd:cd18074    153 MRRYlkQKIKNRKQkkenkpliplPQILGLTAS 185
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
15-181 6.83e-17

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: 79.91  E-value: 6.83e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   15 PRPYQLEILEK------AKKRNVIVQLPTGSGKTYIGILMIKEVQYTVRKsiseggKRIFFVVNNVCLVEQQARHIKNec 88
Cdd:cd18032      1 PRYYQQEAIEAleeareKGQRRALLVMATGTGKTYTAAFLIKRLLEANRK------KRILFLAHREELLEQAERSFKE-- 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   89 elvvgeLHGESSITVHDTDKIKTflEQHQVIVLTAQILLDLICFSRISMEDISLLIFDECHHSMGKAhpYSNILSRYDKV 168
Cdd:cd18032     73 ------VLPDGSFGNLKGGKKKP--DDARVVFATVQTLNKRKRLEKFPPDYFDLIIIDEAHHAIASS--YRKILEYFEPA 142
                          170
                   ....*....|...
gi 1376138976  169 pnekkpVILGLTA 181
Cdd:cd18032    143 ------FLLGLTA 149
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
15-183 2.17e-16

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: 77.73  E-value: 2.17e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   15 PRPYQLEILEKAKKRNV----IVQLPTGSGKTYIGILMIKEvqytvRKSiseggKRIFFVVNNVCLVEQQARHIKNecel 90
Cdd:cd17926      1 LRPYQEEALEAWLAHKNnrrgILVLPTGSGKTLTALALIAY-----LKE-----LRTLIVVPTDALLDQWKERFED---- 66
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   91 vvgeLHGESSITVHDTDKIKTFLEQhQVIVLTAQILLDLICFSRISMEDISLLIFDECHHSMGKAhpYSNILSRYdkvpn 170
Cdd:cd17926     67 ----FLGDSSIGLIGGGKKKDFDDA-NVVVATYQSLSNLAEEEKDLFDQFGLLIVDEAHHLPAKT--FSEILKEL----- 134
                          170
                   ....*....|...
gi 1376138976  171 eKKPVILGLTASL 183
Cdd:cd17926    135 -NAKYRLGLTATP 146
DSRM_DICER cd10843
double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Dicer (also ...
1744-1806 3.60e-16

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: 74.38  E-value: 3.60e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1376138976 1744 ISPIRELTESYPDKVQFSKVERDPNTqRVKVYVEVSGT-KITGGGRNFKIAKCNAAKRALKYIK 1806
Cdd:cd10843      1 RSPVRELLEMEPETAKFSPAERTYDG-KVRVTVEVVGKgRFKGVGRNYRIAKSAAARRALRSLK 63
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
1572-1719 4.95e-16

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


Pssm-ID: 434075  Cd Length: 127  Bit Score: 76.06  E-value: 4.95e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1572 LIQAFSHASYyINRVTSCYQRLEFLGDAVLDFVITRYLFSHeASFNPGTLTDLRSALVNNTMLASVAVDHDFHKYLMefs 1651
Cdd:pfam14622    4 LLQALTHKSY-ANGRKPYNERLEFLGDAVLELSVSEYLFKK-PDLDEGGLTKLRASIVSEESLAEIAREIGLGKYLR--- 78
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1376138976 1652 pklhevvrkfvtfikshenelinldsdlfmVNEDEEDcdgTEDVEVPKALGDIFESFVGAVYLDSGRN 1719
Cdd:pfam14622   79 ------------------------------LGKGEEE---TGGSGRESILADALEALIGAIYLDGGFE 113
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
379-514 1.98e-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: 73.78  E-value: 1.98e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  379 NKLKKVIEILETFNKKCIedpsvfqsmscIIFVERRSAAYAifEVLKELKKldkarfgfIKADYIVGynnnksveetTIS 458
Cdd:pfam00271    1 EKLEALLELLKKERGGKV-----------LIFSQTKKTLEA--ELLLEKEG--------IKVARLHG----------DLS 49
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1376138976  459 SKIQDKKLQSFRQGSLNVLVSTDVLEEGFDVRQCNLVIRYKFPKNFRSYVQGRGRV 514
Cdd:pfam00271   50 QEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
16-183 4.44e-15

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: 74.59  E-value: 4.44e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   16 RPYQLEILEKA-KKRNVIVQLPTGSGKTYIGIL-MIKEVqytvrkSISEGGKRIFFVVNNVCLVEQQARHIKNECELVVG 93
Cdd:pfam00270    1 TPIQAEAIPAIlEGRDVLVQAPTGSGKTLAFLLpALEAL------DKLDNGPQALVLAPTRELAEQIYEELKKLGKGLGL 74
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   94 ELHgeSSITVHDTDKIKTFLEQHQVIVLTAQILLDLICFSRiSMEDISLLIFDECHHSMGKAHP--YSNILSRydkVPNE 171
Cdd:pfam00270   75 KVA--SLLGGDSRKEQLEKLKGPDILVGTPGRLLDLLQERK-LLKNLKLLVLDEAHRLLDMGFGpdLEEILRR---LPKK 148
                          170
                   ....*....|..
gi 1376138976  172 KKpvILGLTASL 183
Cdd:pfam00270  149 RQ--ILLLSATL 158
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
17-149 7.95e-15

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: 74.61  E-value: 7.95e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   17 PYQLEILEKA--KKRNVIVQLPTGSGKTYIGILMIkevqytvRKSISEGGKRIFFVVNNVCLVEQQARHIKN---ECELV 91
Cdd:cd17921      4 PIQREALRALylSGDSVLVSAPTSSGKTLIAELAI-------LRALATSGGKAVYIAPTRALVNQKEADLRErfgPLGKN 76
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1376138976   92 VGELHGESSITvhdtdkiKTFLEQHQVIVLTAQILLDLICFSRI-SMEDISLLIFDECH 149
Cdd:cd17921     77 VGLLTGDPSVN-------KLLLAEADILVATPEKLDLLLRNGGErLIQDVRLVVVDEAH 128
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
16-203 1.20e-13

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: 71.20  E-value: 1.20e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   16 RPYQLEILEKAKKRNVIVQLPTGSGKTYIG-ILMIKEVQYTVRksisegGKrIFFVVNNVCLVEQQARhiknECELVVG- 93
Cdd:cd18033      4 RDYQFTIVQKALFQNTLVALPTGLGKTFIAaVVMLNYYRWFPK------GK-IVFMAPTKPLVSQQIE----ACYKITGi 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   94 ------ELHGESSitvhdTDKIKTFLEQHQVIVLTAQILLDLICFSRISMEDISLLIFDECHHSMGkAHPYSNILSRYDK 167
Cdd:cd18033     73 pssqtaELTGSVP-----PTKRAELWASKRVFFLTPQTLENDLKEGDCDPKSIVCLVIDEAHRATG-NYAYCQVVRELMR 146
                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 1376138976  168 VPNEKKpvILGLTASLfNQRLKKNQ--IENLLL-KLEYK 203
Cdd:cd18033    147 YNSHFR--ILALTATP-GSKLEAVQqvIDNLLIsHIEIR 182
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
370-524 2.43e-13

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: 68.92  E-value: 2.43e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  370 FEEIEPylsnKLKKVIEILetfnKKCIEDPSVFQSMSCIIFVERRSAAYAIfevlkeLKKLDKARFGfIKADYIVGYNNN 449
Cdd:cd18801      4 VEKIHP----KLEKLEEIV----KEHFKKKQEGSDTRVIIFSEFRDSAEEI------VNFLSKIRPG-IRATRFIGQASG 68
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1376138976  450 KSVEetTISSKIQDKKLQSFRQGSLNVLVSTDVLEEGFDVRQCNLVIRYKFPKNFRSYVQGRGRV-RHKQG-LYILL 524
Cdd:cd18801     69 KSSK--GMSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMIQRMGRTgRKRQGrVVVLL 143
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1328-1391 2.82e-12

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 64.60  E-value: 2.82e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1376138976 1328 ERLETIGDSFLKFATTDYLYHKHVNAHEGCLSLLRSKEVSNMKLYFLGKKRNIHNIIINDKFEP 1391
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI 64
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
406-513 3.00e-12

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


Pssm-ID: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 65.61  E-value: 3.00e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  406 SCIIFVERRSAAYAIFEVLKELKkldkarfgfIKADYIVGynnNKSVEEttisskiQDKKLQSFRQGSLNVLVSTDVLEE 485
Cdd:cd18787     29 KAIIFVNTKKRVDRLAELLEELG---------IKVAALHG---DLSQEE-------RERALKKFRSGKVRVLVATDVAAR 89
                           90       100       110
                   ....*....|....*....|....*....|.
gi 1376138976  486 GFDVRQCNLVIRYKFPKNFRSYVQ--GR-GR 513
Cdd:cd18787     90 GLDIPGVDHVINYDLPRDAEDYVHriGRtGR 120
HELICc smart00490
helicase superfamily c-terminal domain;
456-514 7.57e-12

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 62.61  E-value: 7.57e-12
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 1376138976   456 TISSKIQDKKLQSFRQGSLNVLVSTDVLEEGFDVRQCNLVIRYKFPKNFRSYVQGRGRV 514
Cdd:smart00490   20 GLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
895-1016 8.26e-12

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: 64.14  E-value: 8.26e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  895 NAIVYPWYrseENRNYYIIGEIMHDVKPSSDFPDNNFK--TFEEYFLEKYKITIYNKDQPLLDVdytsnrlnllvpkyps 972
Cdd:pfam02170   26 GLKVYTTY---NNPRTYRIDGITFDPTPESTFPLKDGKeiTVVDYFKKKYNIDLKYPDQPLLLV---------------- 86
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1376138976  973 KSSRPlknsrssqRQILVPELVSIHPiksTHWSIIGALPSIFYR 1016
Cdd:pfam02170   87 GKKRP--------KVYLPPELCNLVD---GQRYTKKLMPSIAQR 119
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
30-181 1.12e-11

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: 64.35  E-value: 1.12e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   30 NVIVQLPTGSGKTYIGILMIKEVqytvrksISEGGKRIFFVVNNVCLVEQQARHIKNE--CELVVGELHGESSitvhDTD 107
Cdd:cd00046      3 NVLITAPTGSGKTLAALLAALLL-------LLKKGKKVLVLVPTKALALQTAERLRELfgPGIRVAVLVGGSS----AEE 71
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1376138976  108 KIKTFLEQHQVIVLTAQILLDLICFS-RISMEDISLLIFDECHHsMGKAHPYSNILSRYDKVPNEKKPVILGLTA 181
Cdd:cd00046     72 REKNKLGDADIIIATPDMLLNLLLREdRLFLKDLKLIIVDEAHA-LLIDSRGALILDLAVRKAGLKNAQVILLSA 145
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
473-524 7.04e-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: 56.94  E-value: 7.04e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1376138976  473 SLNVLVSTDVLEEGFDVRQCNLVIRYKFPKNFRSYVQGRGRVRH---KQGLYILL 524
Cdd:cd18785     22 SLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRggkDEGEVILF 76
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
1308-1385 8.24e-09

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: 57.98  E-value: 8.24e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1308 NPAILLCALT-----SRGANDGIDLERLETIGDSFLKFATTDYLYHKHVNAHEGCLSLLRSKEVSNMKLYFLGKKRNIHN 1382
Cdd:TIGR02191   11 NPELLEQALThrsyaNEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVARELGLGD 90

                   ...
gi 1376138976 1383 III 1385
Cdd:TIGR02191   91 FLL 93
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
17-149 6.60e-08

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 57.21  E-value: 6.60e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   17 PYQLEILEKA--KKRNVIVQLPTGSGKTYIGILMIkevqytvRKSISEGGKrIFFVVNNVCLVEQQARHIKNECE---LV 91
Cdd:COG1204     25 PPQAEALEAGllEGKNLVVSAPTASGKTLIAELAI-------LKALLNGGK-ALYIVPLRALASEKYREFKRDFEelgIK 96
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1376138976   92 VGelhgessITVHDTDKIKTFLEQHQVIVLTAQILLDLICFSRISMEDISLLIFDECH 149
Cdd:COG1204     97 VG-------VSTGDYDSDDEWLGRYDILVATPEKLDSLLRNGPSWLRDVDLVVVDEAH 147
PAZ_CAF_like cd02844
PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has ...
888-999 1.01e-07

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: 52.81  E-value: 1.01e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  888 FNESLYENAIVYpwyrSEENRNYYIIGEIMhDVKPSSDFP---DNNFKTFEEYFLEKYKITIYNKDQPLLDVDYTSNRLN 964
Cdd:cd02844     26 FCACDLKGSVVT----APHNGRFYVISGIL-DLNANSSFPgkeGLGYATYAEYFKEKYGIVLNHPNQPLLKGKQIFNLHN 100
                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1376138976  965 LLVPKYPSKSSRPLKNsRSSQRQILVPELVSIHPI 999
Cdd:cd02844    101 LLHNRFEEKGESEEKE-KDRYFVELPPELCSVIDL 134
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
17-149 1.35e-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: 53.49  E-value: 1.35e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   17 PYQLEILEK--AKKRNVIVQLPTGSGKTYIGILMIKevqytvrKSISEGGKRIfFVVNNVCLVEQQARHIK--NECELVV 92
Cdd:cd18028      4 PPQAEAVRAglLKGENLLISIPTASGKTLIAEMAMV-------NTLLEGGKAL-YLVPLRALASEKYEEFKklEEIGLKV 75
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1376138976   93 GelhgessITVHDTDKIKTFLEQHQVIVLTAQILLDLICFSRISMEDISLLIFDECH 149
Cdd:cd18028     76 G-------ISTGDYDEDDEWLGDYDIIVATYEKFDSLLRHSPSWLRDVGVVVVDEIH 125
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1308-1367 7.34e-07

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 52.02  E-value: 7.34e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1376138976 1308 NPAILLCALT----SRGANDGIDLERLETIGDSFLKFATTDYLYHKHVNAHEGCLSLLRSKEVS 1367
Cdd:COG0571     17 DPELLEQALThrsyANEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVS 80
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
13-149 4.74e-06

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


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 51.48  E-value: 4.74e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   13 FTPRPYQLE-ILEKAKKRNVIVQLPTGSGKTYIGIlmikevqYTVRKSISEgGKRIFFvvnnVC----LVEQQARhikne 87
Cdd:COG4581     24 FELDPFQEEaILALEAGRSVLVAAPTGSGKTLVAE-------FAIFLALAR-GRRSFY----TApikaLSNQKFF----- 86
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1376138976   88 cELV-------VGELHGESSItvhdtdkiktfLEQHQVIVLTAQILLDLICFSRISMEDISLLIFDECH 149
Cdd:COG4581     87 -DLVerfgaenVGLLTGDASV-----------NPDAPIVVMTTEILRNMLYREGADLEDVGVVVMDEFH 143
DEXHc_XPB cd18029
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ...
15-183 5.34e-06

DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription factor complex helicase XPB subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB 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: 350787 [Multi-domain]  Cd Length: 169  Bit Score: 48.45  E-value: 5.34e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   15 PRPYQLEILEK----AKKRNVIVQLPTGSGKTYIGILMIKevqyTVRKSiseggkrIFFVVNNVCLVEQQARHIKNECEL 90
Cdd:cd18029      9 LRPYQEKALSKmfgnGRARSGVIVLPCGAGKTLVGITAAC----TIKKS-------TLVLCTSAVSVEQWRRQFLDWTTI 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   91 vvgelhGESSITVHDTDKiKTFLEQHQVIVLTAQIL-------LDLICFSR-ISMEDISLLIFDECHhsMGKAHPYSNIL 162
Cdd:cd18029     78 ------DDEQIGRFTSDK-KEIFPEAGVTVSTYSMLantrkrsPESEKFMEfITEREWGLIILDEVH--VVPAPMFRRVL 148
                          170       180
                   ....*....|....*....|.
gi 1376138976  163 sryDKVPNEKKpviLGLTASL 183
Cdd:cd18029    149 ---TLQKAHCK---LGLTATL 163
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
406-523 6.65e-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: 46.78  E-value: 6.65e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  406 SCIIFVERRSAAYAIFEVLKELkkldkarfgFIKADYIvgynNNKSVEETTISSKIQDKKlqsFRQGSLNVLVSTDVLEE 485
Cdd:cd18799      8 KTLIFCVSIEHAEFMAEAFNEA---------GIDAVAL----NSDYSDRERGDEALILLF---FGELKPPILVTVDLLTT 71
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1376138976  486 GFDVRQCNLVIrykFPKNFRS---YVQ--GRG-RVRH-KQGLYIL 523
Cdd:cd18799     72 GVDIPEVDNVV---FLRPTESrtlFLQmlGRGlRLHEgKDFFTIL 113
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
408-555 1.16e-05

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 50.23  E-value: 1.16e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  408 IIFVERRSAAYAIFEVLKelkkldkaRFGFIKAdyIVGYNNNKSVEETTisskiqdkkLQSFRQGSLNVLVSTDVLEEGF 487
Cdd:PRK11634   249 IIFVRTKNATLEVAEALE--------RNGYNSA--ALNGDMNQALREQT---------LERLKDGRLDILIATDVAARGL 309
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  488 DVRQCNLVIRYKFPKNFRSYVQGRGRVRH--KQGLYILLSDSKsledDKAELKNFEECETLLIQRFRTPN 555
Cdd:PRK11634   310 DVERISLVVNYDIPMDSESYVHRIGRTGRagRAGRALLFVENR----ERRLLRNIERTMKLTIPEVELPN 375
PTZ00424 PTZ00424
helicase 45; Provisional
457-541 1.19e-05

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 49.82  E-value: 1.19e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  457 ISSKIQDKKLQSFRQGSLNVLVSTDVLEEGFDVRQCNLVIRYKFPKNFRSYVQ--GRGRVRHKQGLYILLSDSksleDDK 534
Cdd:PTZ00424   301 MDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHriGRSGRFGRKGVAINFVTP----DDI 376

                   ....*..
gi 1376138976  535 AELKNFE 541
Cdd:PTZ00424   377 EQLKEIE 383
DSRM smart00358
Double-stranded RNA binding motif;
1743-1806 1.59e-05

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 44.18  E-value: 1.59e-05
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1376138976  1743 PISPIRELTESYPDKVQFSKVERD--PNTQRVKVYVEVSGTKI-TGGGRNFKIAKCNAAKRALKYIK 1806
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEEgpDHAPRFTVTVKVGGKRTgEGEGSSKKEAKQRAAEAALRSLK 67
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
379-542 4.19e-05

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 48.22  E-value: 4.19e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  379 NKLKKVIEILETfnkkciEDPSvfqsmSCIIFVERRSAAYAIFEVLKELKkldkarfgfIKADYIVGynnNKSVEEttis 458
Cdd:COG0513    227 DKLELLRRLLRD------EDPE-----RAIVFCNTKRGADRLAEKLQKRG---------ISAAALHG---DLSQGQ---- 279
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  459 skiQDKKLQSFRQGSLNVLVSTDVLEEGFDVRQCNLVIRYKFPKNFRSYVQ--GR-GRVrHKQGLYILLSDskslEDDKA 535
Cdd:COG0513    280 ---RERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYVHriGRtGRA-GAEGTAISLVT----PDERR 351

                   ....*..
gi 1376138976  536 ELKNFEE 542
Cdd:COG0513    352 LLRAIEK 358
uvsW PHA02558
UvsW helicase; Provisional
14-265 4.96e-05

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 48.08  E-value: 4.96e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   14 TPRPYQLE-ILEKAKKRNVIVQLPTGSGKTYIGILMikevqytVRKSISEGGKRIFFVVNNVCLVEQQARHIKNECELVV 92
Cdd:PHA02558   114 EPHWYQYDaVYEGLKNNRRLLNLPTSAGKSLIQYLL-------SRYYLENYEGKVLIIVPTTSLVTQMIDDFVDYRLFPR 186
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   93 GELHGESSITVHDTDKiktfleqhQVIVLTAQILLDLI--CFSRISMedislLIFDECHHSMGKAhpYSNILSRYDKVPN 170
Cdd:PHA02558   187 EAMHKIYSGTAKDTDA--------PIVVSTWQSAVKQPkeWFDQFGM-----VIVDECHLFTGKS--LTSIITKLDNCKF 251
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  171 EkkpviLGLTASLFNQRLKKNQIENLLLKLEykmhaEVVTADDF---SQVLKYsaipNIKLIEC----SDFNAEKFDIAQ 243
Cdd:PHA02558   252 K-----FGLTGSLRDGKANILQYVGLFGDIF-----KPVTTSQLmeeGQVTDL----KINSIFLrypdEDRVKLKGEDYQ 317
                          250       260
                   ....*....|....*....|....*
gi 1376138976  244 KTLSFV---DKLNELVREMEKLLKD 265
Cdd:PHA02558   318 EEIKYItshTKRNKWIANLALKLAK 342
PRK01172 PRK01172
ATP-dependent DNA helicase;
6-149 5.00e-05

ATP-dependent DNA helicase;


Pssm-ID: 100801 [Multi-domain]  Cd Length: 674  Bit Score: 48.34  E-value: 5.00e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976    6 FEVSDevFTPRPYQLEILEKAKK-RNVIVQLPTGSGKTYIGIlmikevqYTVRKSISEGGKRIFFVVNNVCLVEqqarhi 84
Cdd:PRK01172    16 FTGND--FELYDHQRMAIEQLRKgENVIVSVPTAAGKTLIAY-------SAIYETFLAGLKSIYIVPLRSLAME------ 80
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1376138976   85 KNECELVVGELHGESSITVHDTDKIKTFLEQHQVIVLTAQILLDLICFSRISMEDISLLIFDECH 149
Cdd:PRK01172    81 KYEELSRLRSLGMRVKISIGDYDDPPDFIKRYDVVILTSEKADSLIHHDPYIINDVGLIVADEIH 145
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
411-542 9.81e-05

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


Pssm-ID: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 44.64  E-value: 9.81e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  411 VERRSAAYAIFEVLKELKKLDKAR--------FGFIKADYIVGYNNNKsveettISSKIQDKKLQSFRQGSLNVLVSTDV 482
Cdd:cd18811     23 IAKGRQAYVIYPLIEESEKLDLKAavamyeylKERFRPELNVGLLHGR------LKSDEKDAVMAEFREGEVDILVSTTV 96
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1376138976  483 LEEGFDVRQCNLVIRYKfPKNF--RSYVQGRGRVRH--KQGLYILLSDSKSLEDDKAELKNFEE 542
Cdd:cd18811     97 IEVGVDVPNATVMVIED-AERFglSQLHQLRGRVGRgdHQSYCLLVYKDPLTETAKQRLRVMTE 159
PRK00254 PRK00254
ski2-like helicase; Provisional
17-185 1.56e-04

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 46.73  E-value: 1.56e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   17 PYQLEILEKA--KKRNVIVQLPTGSGKTYIGILMIkevqytVRKSISEGGKRIFFVVNNVcLVEQQARHIKNECELVVge 94
Cdd:PRK00254    26 PPQAEALKSGvlEGKNLVLAIPTASGKTLVAEIVM------VNKLLREGGKAVYLVPLKA-LAEEKYREFKDWEKLGL-- 96
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   95 lhgESSITVHDTDKIKTFLEQHQVIVLTAQILLDLICFSRISMEDISLLIFDECH--HSMGKAHPYSNILSRYDkvpneK 172
Cdd:PRK00254    97 ---RVAMTTGDYDSTDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHliGSYDRGATLEMILTHML-----G 168
                          170
                   ....*....|...
gi 1376138976  173 KPVILGLTASLFN 185
Cdd:PRK00254   169 RAQILGLSATVGN 181
HsdR COG4096
Type I site-specific restriction endonuclease, part of a restriction-modification system ...
13-181 1.63e-04

Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms];


Pssm-ID: 443272 [Multi-domain]  Cd Length: 806  Bit Score: 46.76  E-value: 1.63e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   13 FTPRPYQLE-I--LEKA---KKRNVIVQLPTGSGKTYIGILMIKEVQYTVRKsiseggKRIFFVVNNVCLVEQQARHIKN 86
Cdd:COG4096    157 IALRYYQIEaIrrVEEAiakGQRRALLVMATGTGKTRTAIALIYRLLKAGRA------KRILFLADRNALVDQAKNAFKP 230
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   87 ecelvvgelHGESSITVHDTDKIKTFLEQH-QVIVLTAQILLDLIC-------FSRISMEDISLLIFDECHHSmgkahpy 158
Cdd:COG4096    231 ---------FLPDLDAFTKLYNKSKDIDKSaRVYFSTYQTMMNRIDgeeeepgYRQFPPDFFDLIIIDECHRG------- 294
                          170       180
                   ....*....|....*....|...
gi 1376138976  159 snILSRYDKVPNEKKPVILGLTA 181
Cdd:COG4096    295 --IYSKWRAILDYFDALQIGLTA 315
DEXHc_Brr2_2 cd18021
C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type ...
30-187 1.89e-04

C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350779 [Multi-domain]  Cd Length: 191  Bit Score: 44.17  E-value: 1.89e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   30 NVIVQLPTGSGKTYIGILMIkevqytVRKSISEGGKRIFFVVNNVCLVEQQAR----HIKNECELVVGELHGESSitvhd 105
Cdd:cd18021     21 NVFVGAPTGSGKTVCAELAL------LRHWRQNPKGRAVYIAPMQELVDARYKdwraKFGPLLGKKVVKLTGETS----- 89
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  106 TD-KIktfLEQHQVIVLTAQiLLDLICF---SRISMEDISLLIFDECHHSMGKAHP-YSNILSR--YDKVPNEKKPVILG 178
Cdd:cd18021     90 TDlKL---LAKSDVILATPE-QWDVLSRrwkQRKNVQSVELFIADELHLIGGENGPvYEVVVSRmrYISSQLEKPIRIVG 165

                   ....*....
gi 1376138976  179 LTASLFNQR 187
Cdd:cd18021    166 LSSSLANAR 174
DEXHc_cas3 cd17930
DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase ...
29-149 2.51e-04

DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase responsible for degradation of dsDNA. The two enzymatic units of Cas3, a histidine-aspartate (HD) nuclease and a Superfamily 2 (SF2) helicase, may be expressed from separate genes as Cas3' (SF2 helicase) and Cas3'' (HD nuclease) or may be fused as a single HD-SF2 polypeptide. The nucleolytic activity of most Cas3 enzymes is transition metal ion-dependent. Cas3 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: 350688 [Multi-domain]  Cd Length: 186  Bit Score: 43.82  E-value: 2.51e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   29 RNVIVQLPTGSGKTYIGILmikevqYTVRKSISEGGKRIFFVVNNVCLVEQQARHIKN-----ECELVVGELHGESSITV 103
Cdd:cd17930      2 GLVILEAPTGSGKTEAALL------WALKLAARGGKRRIIYALPTRATINQMYERIREilgrlDDEDKVLLLHSKAALEL 75
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1376138976  104 HDTDKIKTFLE--------------QHQVIVLTA-QILLDL-------ICFSRISMediSLLIFDECH 149
Cdd:cd17930     76 LESDEEPDDDPveavdwalllkrswLAPIVVTTIdQLLESLlkykhfeRRLHGLAN---SVVVLDEVQ 140
PAZ_piwi_like cd02845
PAZ domain, Piwi_like subfamily. In multi-cellular organisms, the Piwi protein appears to be ...
907-993 3.46e-04

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


Pssm-ID: 239211  Cd Length: 117  Bit Score: 41.86  E-value: 3.46e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  907 NRNYYIIGEIMHDVKPSSDFPDNNFK--TFEEYFLEKYKITIYNKDQPLLdvdytsnrlnllvpkypsKSSRPLKNSRSS 984
Cdd:cd02845     38 NNKTYRIDDIDFDKTPLSTFKKSDGTeiTFVEYYKKQYNIEITDLNQPLL------------------VSRPKRRDPRGG 99
                           90
                   ....*....|.
gi 1376138976  985 QRQI--LVPEL 993
Cdd:cd02845    100 EKEPiyLIPEL 110
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
462-542 4.34e-04

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 44.90  E-value: 4.34e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  462 QDKK---LQSFRQGSLNVLVSTDVLEEGFDVRQCNLVIRYKFPKNFRSYVQGRGRVRH--KQGLYIllsdSKSLEDDKAE 536
Cdd:PRK01297   371 QHKRiktLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRagASGVSI----SFAGEDDAFQ 446

                   ....*.
gi 1376138976  537 LKNFEE 542
Cdd:PRK01297   447 LPEIEE 452
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
1328-1377 4.39e-04

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: 41.78  E-value: 4.39e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1328 ERLETIGDSFLKFATTDYLYHKHvNAHEGCLSLLRSKEVSNMKLYFLGKK 1377
Cdd:pfam14622   22 ERLEFLGDAVLELSVSEYLFKKP-DLDEGGLTKLRASIVSEESLAEIARE 70
PTZ00110 PTZ00110
helicase; Provisional
463-513 6.51e-04

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 44.38  E-value: 6.51e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1376138976  463 DKK-------LQSFRQGSLNVLVSTDVLEEGFDVRQCNLVIRYKFPKNFRSYVQGRGR 513
Cdd:PTZ00110   410 DKKqeertwvLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGR 467
PAZ cd02825
PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two ...
902-968 8.13e-04

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: 40.91  E-value: 8.13e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1376138976  902 YRSEENRNYYIIGEImhDVKPSSDF--PDNNFKTFEEYFLEKYKITIYNKDQPLLDVDYTS--NRLNLLVP 968
Cdd:cd02825     41 THNPLNRVYRPDGET--RLKAPSQLkhSDGKEITFADYFKERYNLTLTDLNQPLLIVKFSSkkSYSILLPP 109
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
407-519 1.20e-03

C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350176 [Multi-domain]  Cd Length: 153  Bit Score: 41.47  E-value: 1.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  407 CIIFVERRSAAYAIFEVLKelkkldkarfgfikADYIVGYNNNKSVEETtisskiqdkkLQSFRQGSLNVLVSTDVLEEG 486
Cdd:cd18789     52 IIVFTDNVEALYRYAKRLL--------------KPFITGETPQSEREEI----------LQNFREGEYNTLVVSKVGDEG 107
                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1376138976  487 FDVRQCN--LVIRYKFpKNFRSYVQGRGRV-RHKQG 519
Cdd:cd18789    108 IDLPEANvaIQISGHG-GSRRQEAQRLGRIlRPKKG 142
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
17-149 1.44e-03

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


Pssm-ID: 440816 [Multi-domain]  Cd Length: 535  Bit Score: 43.53  E-value: 1.44e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   17 PYQLEILEKAK------KRNVIVQLPTGSGKTYIGILmikevqYTVRKSISEGGKRIFFVVNNVCLVEQQARHIKNECEL 90
Cdd:COG1203    130 PLQNEALELALeaaeeePGLFILTAPTGGGKTEAALL------FALRLAAKHGGRRIIYALPFTSIINQTYDRLRDLFGE 203
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1376138976   91 VVGELHGESSITVHDTDKIKTFLEQH----------QVIVLTA-QILLDLIC--------FSRISmedISLLIFDECH 149
Cdd:COG1203    204 DVLLHHSLADLDLLEEEEEYESEARWlkllkelwdaPVVVTTIdQLFESLFSnrkgqerrLHNLA---NSVIILDEVQ 278
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
408-513 1.70e-03

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 43.01  E-value: 1.70e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  408 IIFVERRsaayaifEVLKELK-KLDKARfgfIKADYIVGynnnksveettisSKIQDKKLQS---FRQGSLNVLVSTDVL 483
Cdd:PRK11192   249 IVFVRTR-------ERVHELAgWLRKAG---INCCYLEG-------------EMVQAKRNEAikrLTDGRVNVLVATDVA 305
                           90       100       110
                   ....*....|....*....|....*....|
gi 1376138976  484 EEGFDVRQCNLVIRYKFPKNFRSYVQGRGR 513
Cdd:PRK11192   306 ARGIDIDDVSHVINFDMPRSADTYLHRIGR 335
DEXH_lig_assoc TIGR04121
DEXH box helicase, DNA ligase-associated; Members of this protein family are DEAD/DEAH box ...
13-47 2.58e-03

DEXH box helicase, DNA ligase-associated; Members of this protein family are DEAD/DEAH box helicases found associated with a bacterial ATP-dependent DNA ligase, part of a four-gene system that occurs in about 12 % of prokaryotic reference genomes. The actual motif in this family is DE[VILW]H.


Pssm-ID: 274994 [Multi-domain]  Cd Length: 804  Bit Score: 42.54  E-value: 2.58e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1376138976   13 FTPRPYQLEILEKAKK-RNVIVQLPTGSGKTYIGIL 47
Cdd:TIGR04121   12 WTPRPFQLEMWAAALEgRSGLLIAPTGSGKTLAGFL 47
DSRM_STRBP-like_rpt2 cd19897
second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...
1745-1803 4.03e-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: 37.34  E-value: 4.03e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976 1745 SPIRELTESYPD-KVQFSKVERDPNTQRVKVYVEVSGTKITGGGRNFKIAKCNAAKRALK 1803
Cdd:cd19897      2 NPVMELNEKRRGlKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKANAALAALE 61
DEXHc_POLQ-like cd18026
DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in ...
17-149 5.00e-03

DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in the repair of genomic double-strand breaks (DSBs). POLQ contains an N-terminal type II DEAD box helicase domain which contains the ATP-binding region.


Pssm-ID: 350784 [Multi-domain]  Cd Length: 202  Bit Score: 40.28  E-value: 5.00e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   17 PYQLEILEKAK---KRNVIVQLPTGSGKTYIG-ILMIKEVQYTVRKSIseggkrifFVVNNVCLVEQQARHIKN---ECE 89
Cdd:cd18026     19 DWQKECLSLPGlleGRNLVYSLPTSGGKTLVAeILMLKRLLERRKKAL--------FVLPYVSIVQEKVDALSPlfeELG 90
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1376138976   90 LVVGELHGESSITVHDTDKIKTfleqhqVIVLT---AQILLD-LICFSRIsmEDISLLIFDECH 149
Cdd:cd18026     91 FRVEGYAGNKGRSPPKRRKSLS------VAVCTiekANSLVNsLIEEGRL--DELGLVVVDELH 146
DEXHc_Brr2_1 cd18019
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD ...
30-149 5.24e-03

N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350777 [Multi-domain]  Cd Length: 214  Bit Score: 40.43  E-value: 5.24e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   30 NVIVQLPTGSGKTYIGIL-MIKEVQYTVRK--SISEGGKRIFFVVNNVCLVEQQARHIKNECE---LVVGELHGESSITv 103
Cdd:cd18019     35 NLLLCAPTGAGKTNVALLtILREIGKHRNPdgTINLDAFKIVYIAPMKALVQEMVGNFSKRLApygITVAELTGDQQLT- 113
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1376138976  104 hdtdkiKTFLEQHQVIVLTAQiLLDLIcfSRISMED-----ISLLIFDECH 149
Cdd:cd18019    114 ------KEQISETQIIVTTPE-KWDII--TRKSGDRtytqlVRLIIIDEIH 155
DEXHc_RecQ cd17920
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ...
11-199 5.89e-03

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


Pssm-ID: 350678 [Multi-domain]  Cd Length: 200  Bit Score: 39.83  E-value: 5.89e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   11 EVF---TPRPYQLEILEKA-KKRNVIVQLPTGSGKTyigilMIKEVQYTVRKSISeggkrifFVVNN-VCLVEQQARHIK 85
Cdd:cd17920      6 EVFgydEFRPGQLEAINAVlAGRDVLVVMPTGGGKS-----LCYQLPALLLDGVT-------LVVSPlISLMQDQVDRLQ 73
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976   86 NECeLVVGELHGESSITVHDTDKIKTFLEQHQVIVLTAQILLDLICFSRI----SMEDISLLIFDECH------H----S 151
Cdd:cd17920     74 QLG-IRAAALNSTLSPEEKREVLLRIKNGQYKLLYVTPERLLSPDFLELLqrlpERKRLALIVVDEAHcvsqwgHdfrpD 152
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 1376138976  152 MGKAHpysNILSRYDKVPnekkpvILGLTASLfNQRLKKNQIENLLLK 199
Cdd:cd17920    153 YLRLG---RLRRALPGVP------ILALTATA-TPEVREDILKRLGLR 190
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
407-524 6.21e-03

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: 39.16  E-value: 6.21e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376138976  407 CIIFVERRSAAYAIFEVLKELKKLDKARFGFIKAdYIVGYNnnksVEEttiSSKIQDKklqsFRQGSLNVLVSTDVLEEG 486
Cdd:cd18797     38 TIVFCRSRKLAELLLRYLKARLVEEGPLASKVAS-YRAGYL----AED---RREIEAE----LFNGELLGVVATNALELG 105
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1376138976  487 FDVRQCNLVIRYKFPKNFRSYVQ--GR-GRvRHKQGLYILL 524
Cdd:cd18797    106 IDIGGLDAVVLAGYPGSLASLWQqaGRaGR-RGKDSLVILV 145
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
1743-1805 8.90e-03

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 36.44  E-value: 8.90e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1376138976 1743 PISPIRELTESYPDKVQFSKVERD--PNTQRVKVYVEVSGTKITGG-GRNFKIAKCNAAKRALKYI 1805
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVSEEgpPHSPKFTVTVKVDGKLYGSGtGSSKKEAEQLAAEKALEKL 66
 
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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