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Conserved domains on  [gi|2074816265|ref|NP_001382622|]
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endoribonuclease Dicer isoform 7 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 42-239 9.43e-100

DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


:

Pssm-ID: 350792 [Multi-domain]  Cd Length: 200  Bit Score: 318.44  E-value: 9.43e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   42 YTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELSYQIRGdFSRNGKRTVFLVNSANQVAQQVSAVRTHSDLKV 121
Cdd:cd18034      1 FTPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRK-EKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKV 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  122 GEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENC---PS 198
Cdd:cd18034     80 GEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLegrTS 159

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 2074816265  199 CPRILGLTASILNGKCDPEELEEKIQKLEKILKSNAETATD 239
Cdd:cd18034    160 RPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
 886-1008 1.40e-69

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


:

Pssm-ID: 239209  Cd Length: 122  Bit Score: 228.87  E-value: 1.40e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  886 DSSTLDIDFKFMEDIEkSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 965
Cdd:cd02843      1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 2074816265  966 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 1008
Cdd:cd02843     80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 372-564 5.09e-56

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


:

Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 190.88  E-value: 5.09e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  372 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 451
Cdd:cd18802      4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  452 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprNKQMEAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKC 531
Cdd:cd18802     36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109

                          170       180       190
                   ....*....|....*....|....*....|...
gi 2074816265  532 NLVVRFDLPTEYRSYVQSKGRARAPISNYIMLA 564
Cdd:cd18802    110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 630-718 2.59e-32

Dicer dimerization domain; This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerization of Dicer proteins with their respective protein partners.


:

Pssm-ID: 460900  Cd Length: 89  Bit Score: 121.06  E-value: 2.59e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  630 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMSCVRLAERVVALICCEKLHKIGELD 709
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79


                   ....*....
gi 2074816265  710 DHLMPVGKE 718
Cdd:pfam03368   80 DHLLPLTKK 88
RIBOc smart00535
Ribonuclease III family;
1296-1387 2.29e-25

Ribonuclease III family;


:

Pssm-ID: 197778  Cd Length: 129  Bit Score: 102.68  E-value: 2.29e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  1296 LILQALTLSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIF 1374
Cdd:smart00535    2 LLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81

                            90
                    ....*....|...
gi 2074816265  1375 DPPVNWLPPGYVV 1387
Cdd:smart00535   82 EAISGGRDKPKIL 94
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 271-365 5.59e-25

Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a central role in RNA interference by breaking down RNA molecules into fragments of about 22 nucleotides (miRNAs and siRNAs). Loading of RNA onto Dicer and the enzymatic cleavage are supported by dsRNA-binding proteins, including trans-activation response (TAR) RNA-binding protein (TRBP) or protein activator of PKR (PACT). Together with Argonaute, this constitutes the RNA-induced silencing complex (RISC) which functions to load the small RNA fragments onto Argonaute. The Partner-binding domain of Dicer is responsible for interactions with the dsRNA-binding proteins. This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases.


:

Pssm-ID: 277191  Cd Length: 104  Bit Score: 100.82  E-value: 5.59e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  271 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 341
Cdd:cd15903      1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                           90       100
                   ....*....|....*....|....
gi 2074816265  342 RKFLLFTDTFLRKIHALCEEHFSP 365
Cdd:cd15903     81 RLFLRYVITQLRKIRKLLEDEMKN 104
RIBOc super family cl00258
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1669-1708 1.33e-05

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.


The actual alignment was detected with superfamily member TIGR02191:

Pssm-ID: 469693 [Multi-domain]  Cd Length: 220  Bit Score: 48.35  E-value: 1.33e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 2074816265 1669 FEKKINYRFKNKAYLLQAFTHASYHYNTITGKEPTTRLHF 1708
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYANEHHKDVKNNERLEF 40
 
Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 42-239 9.43e-100

DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350792 [Multi-domain]  Cd Length: 200  Bit Score: 318.44  E-value: 9.43e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   42 YTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELSYQIRGdFSRNGKRTVFLVNSANQVAQQVSAVRTHSDLKV 121
Cdd:cd18034      1 FTPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRK-EKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKV 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  122 GEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENC---PS 198
Cdd:cd18034     80 GEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLegrTS 159

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 2074816265  199 CPRILGLTASILNGKCDPEELEEKIQKLEKILKSNAETATD 239
Cdd:cd18034    160 RPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
 886-1008 1.40e-69

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


Pssm-ID: 239209  Cd Length: 122  Bit Score: 228.87  E-value: 1.40e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  886 DSSTLDIDFKFMEDIEkSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 965
Cdd:cd02843      1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 2074816265  966 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 1008
Cdd:cd02843     80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 372-564 5.09e-56

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


Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 190.88  E-value: 5.09e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  372 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 451
Cdd:cd18802      4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  452 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprNKQMEAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKC 531
Cdd:cd18802     36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109

                          170       180       190
                   ....*....|....*....|....*....|...
gi 2074816265  532 NLVVRFDLPTEYRSYVQSKGRARAPISNYIMLA 564
Cdd:cd18802    110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
44-552 2.66e-34

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 142.56  E-value: 2.66e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   44 PRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELsyqirgdFSRNGKRTVFLVNS---ANQVAQQVSAVRTHSDLK 120
Cdd:COG1111      4 RRLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAER-------LHKKGGKVLFLAPTkplVEQHAEFFKEALNIPEDE 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  121 VGEYSNlEVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCP 200
Cdd:COG1111     77 IVVFTG-EVSPEKRKELWE----KARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKDP 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  201 RILGLTASilngkcdPEELEEKIQKLEKILK-SNAETATDlvvldrytSQPceivvDCGPFT-DRSGLYERLLM--ELEE 276
Cdd:COG1111    152 LILGMTAS-------PGSDEEKIEEVCENLGiENVEVRTE--------EDP-----DVAPYVhDTEVEWIRVELpeELKE 211

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  277 ALNFIN-----------DCNISVHSKERDST--------LISKQILSDCRAVLVVLGPwcadkVAGMM------------ 325
Cdd:COG1111    212 IRDLLNevlddrlkklkELGVIVSTSPDLSKkdllalqkKLQRRIREDDSEGYRAISI-----LAEALklrhalelletq 286

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  326 -VRELQKYIKhEQEELHRKFL-------LFTDTFLRKIHALCE----EHfspasldlkfvtPKVIKLLEILRKYKpyerq 393
Cdd:COG1111    287 gVEALLRYLE-RLEEEARSSGgskaskrLVSDPRFRKAMRLAEeadiEH------------PKLSKLREILKEQL----- 348

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  394 qfesvewynNRNQDNYVswsdsedddedeeieekekpetnfpspftnilcgIIFVERRYTAVVLNRLIKEAGkqdpelay 473
Cdd:COG1111    349 ---------GTNPDSRI----------------------------------IVFTQYRDTAEMIVEFLSEPG-------- 377

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  474 ISSNFITGHGIGKNQPRNKQmeaefRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDL-PTEYRSyVQSKGR 552
Cdd:COG1111    378 IKAGRFVGQASKEGDKGLTQ-----KEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPvPSEIRS-IQRKGR 451
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 630-718 2.59e-32

Dicer dimerization domain; This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerization of Dicer proteins with their respective protein partners.


Pssm-ID: 460900  Cd Length: 89  Bit Score: 121.06  E-value: 2.59e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  630 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMSCVRLAERVVALICCEKLHKIGELD 709
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79


                   ....*....
gi 2074816265  710 DHLMPVGKE 718
Cdd:pfam03368   80 DHLLPLTKK 88
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
 925-1065 6.73e-28

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


Pssm-ID: 198017  Cd Length: 138  Bit Score: 110.45  E-value: 6.73e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   925 EDYQDAVIIPRYRNfdqpHRFYVADVYTDLTPLSKFPSPEYE--TFAEYYKTKYNLDLTNLNQPLLdVDHTSsrlnlltp 1002
Cdd:smart00949   25 KDLKGLIVLTRYNN----KTYRIDDIDWNLAPKSTFEKSDGSeiTFVEYYKQKYNITIRDPNQPLL-VSRPK-------- 91

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816265  1003 RHLNQKGKalplssaekrkakweslQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLL 1065
Cdd:smart00949   92 RRRNQNGK-----------------GEPVLLPPELCFITGLTDRMRKDFMLMKSIADRTRLSP 137
RIBOc smart00535
Ribonuclease III family;
1296-1387 2.29e-25

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 102.68  E-value: 2.29e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  1296 LILQALTLSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIF 1374
Cdd:smart00535    2 LLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81

                            90
                    ....*....|...
gi 2074816265  1375 DPPVNWLPPGYVV 1387
Cdd:smart00535   82 EAISGGRDKPKIL 94
PRK13766 PRK13766
Hef nuclease; Provisional
 37-553 2.73e-25

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 114.20  E-value: 2.73e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   37 IHDNIYTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELsyqirgdFSRNGKRTVFLVNSANQVAQQVSAVRTH 116
Cdd:PRK13766     9 IKPNTIEARLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAER-------LHKKGGKVLILAPTKPLVEQHAEFFRKF 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  117 SDLKVGEYSNL--EVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPY----REIM 190
Cdd:PRK13766    82 LNIPEEKIVVFtgEVSPEKRAELWE----KAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYvyiaERYH 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  191 KLCENcpscPRILGLTASilNGKcDPEELEEKIQKLeKIlkSNAE--TATDLVVlDRYTSqpcEIVVDcgpftdrsglYE 268
Cdd:PRK13766   158 EDAKN----PLVLGLTAS--PGS-DEEKIKEVCENL-GI--EHVEvrTEDDPDV-KPYVH---KVKIE----------WV 213

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  269 RLLM--ELEEALNFINDCnisvhSKERdstlisKQILSDCRaVLVVLGPWCADK-VAGMMvRELQKYIKHEQEEL----- 340
Cdd:PRK13766   214 RVELpeELKEIRDLLNEA-----LKDR------LKKLKELG-VIVSISPDVSKKeLLGLQ-KKLQQEIANDDSEGyeais 280

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  341 ---------HRKFLLFT---DTFLRKIHALCEEHFSPAS--------LDLKF------------VTPKVIKLLEILRKyk 388
Cdd:PRK13766   281 ilaeamklrHAVELLETqgvEALRRYLERLREEARSSGGskaskrlvEDPRFrkavrkakeldiEHPKLEKLREIVKE-- 358

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  389 pyerqQFEsvewynnRNQDNYVswsdsedddedeeieekekpetnfpspftnilcgIIFVERRYTA-VVLNRLIKEagkq 467
Cdd:PRK13766   359 -----QLG-------KNPDSRI----------------------------------IVFTQYRDTAeKIVDLLEKE---- 388

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  468 dpelayissNFITGHGIGKNQPRN-KQMEAefRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFD-LPTEYRS 545
Cdd:PRK13766   389 ---------GIKAVRFVGQASKDGdKGMSQ--KEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEpVPSEIRS 457


                   ....*...
gi 2074816265  546 yVQSKGRA 553
Cdd:PRK13766   458 -IQRKGRT 464
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1296-1376 4.95e-25

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


Pssm-ID: 238333  Cd Length: 133  Bit Score: 101.92  E-value: 4.95e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265 1296 LILQALT---LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVS 1372
Cdd:cd00593      2 LLLEALThpsYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLG 81


                   ....
gi 2074816265 1373 IFDP 1376
Cdd:cd00593     82 KGEE 85
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 271-365 5.59e-25

Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a central role in RNA interference by breaking down RNA molecules into fragments of about 22 nucleotides (miRNAs and siRNAs). Loading of RNA onto Dicer and the enzymatic cleavage are supported by dsRNA-binding proteins, including trans-activation response (TAR) RNA-binding protein (TRBP) or protein activator of PKR (PACT). Together with Argonaute, this constitutes the RNA-induced silencing complex (RISC) which functions to load the small RNA fragments onto Argonaute. The Partner-binding domain of Dicer is responsible for interactions with the dsRNA-binding proteins. This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases.


Pssm-ID: 277191  Cd Length: 104  Bit Score: 100.82  E-value: 5.59e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  271 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 341
Cdd:cd15903      1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                           90       100
                   ....*....|....*....|....
gi 2074816265  342 RKFLLFTDTFLRKIHALCEEHFSP 365
Cdd:cd15903     81 RLFLRYVITQLRKIRKLLEDEMKN 104
DEXDc smart00487
DEAD-like helicases superfamily;
40-242 6.74e-23

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 98.33  E-value: 6.74e-23
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265    40 NIYTPRKYQVELLEAALD--HNTIVCLNTGSGKTFIAVLLTKELSYqirgdfSRNGKRTVFLVNS---ANQVAQQVSAVR 114
Cdd:smart00487    5 GFEPLRPYQKEAIEALLSglRDVILAAPTGSGKTLAALLPALEALK------RGKGGRVLVLVPTrelAEQWAEELKKLG 78

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   115 THSDLK-VGEYSNLEVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLC 193
Cdd:smart00487   79 PSLGLKvVGLYGGDSKREQLRKLESG----KTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLL 154

                           170       180       190       200
                    ....*....|....*....|....*....|....*....|....*....
gi 2074816265   194 ENCPSCPRILGLTASILNgkcDPEELEEKIQKLEKILKSNAETATDLVV 242
Cdd:smart00487  155 KLLPKNVQLLLLSATPPE---EIENLLELFLNDPVFIDVGFTPLEPIEQ 200
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
 914-1064 4.16e-20

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


Pssm-ID: 460472  Cd Length: 123  Bit Score: 87.63  E-value: 4.16e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  914 YTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFP--SPEYETFAEYYKTKYNLDLTNLNQPLLDVd 991
Cdd:pfam02170    8 QQQKDRRDFRKEAKKALKGLKVYTTYNNPRTYRIDGITFDPTPESTFPlkDGKEITVVDYFKKKYNIDLKYPDQPLLLV- 86

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816265  992 htssrlnlltprhlnqkgkalplssaeKRKakweslQNKQILVPELCAihpIPASLWRKAVCLPSILYRLHCL 1064
Cdd:pfam02170   87 ---------------------------GKK------RPKVYLPPELCN---LVDGQRYTKKLMPSIAQRTRLL 123
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1313-1376 1.98e-15

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 73.46  E-value: 1.98e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2074816265 1313 ERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIFDP 1376
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI 64
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 501-553 1.35e-14

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 71.47  E-value: 1.35e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2074816265  501 QEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 553
Cdd:pfam00271   53 REEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 45-221 4.83e-13

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


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 68.81  E-value: 4.83e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   45 RKYQVELLEAAL-DHNTIVCLNTGSGKTFIAVL-LTKELsyqirgDFSRNGKRTVFLV---NSANQVAQQVSavrthsdl 119
Cdd:pfam00270    1 TPIQAEAIPAILeGRDVLVQAPTGSGKTLAFLLpALEAL------DKLDNGPQALVLAptrELAEQIYEELK-------- 66

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  120 KVGEYSNLEVNASWT-KERWNQ--EFTKHQVLIMTCYVALNVLKNGYLsLSDINLLVFDECHLaILDHPYREIMKLC-EN 195
Cdd:pfam00270   67 KLGKGLGLKVASLLGgDSRKEQleKLKGPDILVGTPGRLLDLLQERKL-LKNLKLLVLDEAHR-LLDMGFGPDLEEIlRR 144

                          170       180
                   ....*....|....*....|....*.
gi 2074816265  196 CPSCPRILGLTASIlngkcdPEELEE 221
Cdd:pfam00270  145 LPKKRQILLLSATL------PRNLED 164
HELICc smart00490
helicase superfamily c-terminal domain;
499-553 1.11e-12

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 64.93  E-value: 1.11e-12
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 2074816265   499 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 553
Cdd:smart00490   24 EEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1292-1367 1.86e-11

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


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 65.69  E-value: 1.86e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265 1292 PNPGLILQALT-----LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLP 1366
Cdd:TIGR02191   10 KNPELLEQALThrsyaNEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVARELGLG 89


                   .
gi 2074816265 1367 S 1367
Cdd:TIGR02191   90 D 90
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1283-1365 8.12e-11

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 63.96  E-value: 8.12e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265 1283 IGYSSRtlgpNPGLILQALT---LSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYR 1358
Cdd:COG0571     11 LGYRFK----DPELLEQALThrsYANEHGGLeNNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAE 86


                   ....*..
gi 2074816265 1359 LGKKKGL 1365
Cdd:COG0571     87 IARELGL 93
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
444-589 6.28e-08

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 57.08  E-value: 6.28e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  444 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFItgHGiGKNQprnkqmeaefRKQEEVLRKFRAHETNLLIATSIVE 523
Cdd:COG0513    244 AIVFCNTKRGADRLAEKLQKRG--------ISAAAL--HG-DLSQ----------GQRERALDAFRNGKIRVLVATDVAA 302

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2074816265  524 EGVDIPKCNLVVRFDLPTEYRSYV---------QSKGRArapisnyIMLADtdkiksfEEDLKTYKAIEKILRNK 589
Cdd:COG0513    303 RGIDIDDVSHVINYDLPEDPEDYVhrigrtgraGAEGTA-------ISLVT-------PDERRLLRAIEKLIGQK 363
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1669-1708 1.33e-05

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: 48.35  E-value: 1.33e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 2074816265 1669 FEKKINYRFKNKAYLLQAFTHASYHYNTITGKEPTTRLHF 1708
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYANEHHKDVKNNERLEF 40
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1666-1692 2.10e-05

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 47.79  E-value: 2.10e-05
                           10        20
                   ....*....|....*....|....*..
gi 2074816265 1666 FENFEKKINYRFKNKAYLLQAFTHASY 1692
Cdd:COG0571      4 LEELEERLGYRFKDPELLEQALTHRSY 30
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 444-594 4.01e-05

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 48.01  E-value: 4.01e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  444 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGhgigknqprnkqmEAEFRKQEEVLRKFRAHETNLLIATSIVE 523
Cdd:PRK11192   248 SIVFVRTRERVHELAGWLRKAG--------INCCYLEG-------------EMVQAKRNEAIKRLTDGRVNVLVATDVAA 306

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  524 EGVDIPKCNLVVRFDLPTEYRSYVQSKGR-ARA-----PIS-----NYIMLadtDKIKSF-EEDLK---------TYKAI 582
Cdd:PRK11192   307 RGIDIDDVSHVINFDMPRSADTYLHRIGRtGRAgrkgtAISlveahDHLLL---GKIERYiEEPLKarvidelrpKTKAP 383

                          170
                   ....*....|..
gi 2074816265  583 EKILRNKCSKSV 594
Cdd:PRK11192   384 SEKKTGKPSKKV 395
 
Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 42-239 9.43e-100

DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350792 [Multi-domain]  Cd Length: 200  Bit Score: 318.44  E-value: 9.43e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   42 YTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELSYQIRGdFSRNGKRTVFLVNSANQVAQQVSAVRTHSDLKV 121
Cdd:cd18034      1 FTPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRK-EKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKV 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  122 GEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENC---PS 198
Cdd:cd18034     80 GEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLegrTS 159

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 2074816265  199 CPRILGLTASILNGKCDPEELEEKIQKLEKILKSNAETATD 239
Cdd:cd18034    160 RPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
 886-1008 1.40e-69

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


Pssm-ID: 239209  Cd Length: 122  Bit Score: 228.87  E-value: 1.40e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  886 DSSTLDIDFKFMEDIEkSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 965
Cdd:cd02843      1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 2074816265  966 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 1008
Cdd:cd02843     80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 42-238 4.77e-66

DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350685 [Multi-domain]  Cd Length: 201  Bit Score: 222.31  E-value: 4.77e-66
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   42 YTPRKYQVELLEAAL-DHNTIVCLNTGSGKTFIAVLLTKELSYQIRgdfSRNGKRTVFLVNSANQVAQQVSAVRTHSD-- 118
Cdd:cd17927      1 FKPRNYQLELAQPALkGKNTIICLPTGSGKTFVAVLICEHHLKKFP---AGRKGKVVFLANKVPLVEQQKEVFRKHFErp 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  119 -LKVGEYSNlevnASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYL-SLSDINLLVFDECHLAILDHPYREIMKLCENC 196
Cdd:cd17927     78 gYKVTGLSG----DTSENVSVEQIVESSDVIIVTPQILVNDLKSGTIvSLSDFSLLVFDECHNTTKNHPYNEIMFRYLDQ 153

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 2074816265  197 PS-----CPRILGLTASILNGKC-DPEELEEKIQKLEKILKSNAETAT 238
Cdd:cd17927    154 KLgssgpLPQILGLTASPGVGGAkNTEEALEHICKLCANLDISVIATV 201
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 372-564 5.09e-56

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


Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 190.88  E-value: 5.09e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  372 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 451
Cdd:cd18802      4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  452 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprNKQMEAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKC 531
Cdd:cd18802     36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109

                          170       180       190
                   ....*....|....*....|....*....|...
gi 2074816265  532 NLVVRFDLPTEYRSYVQSKGRARAPISNYIMLA 564
Cdd:cd18802    110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
44-552 2.66e-34

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 142.56  E-value: 2.66e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   44 PRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELsyqirgdFSRNGKRTVFLVNS---ANQVAQQVSAVRTHSDLK 120
Cdd:COG1111      4 RRLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAER-------LHKKGGKVLFLAPTkplVEQHAEFFKEALNIPEDE 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  121 VGEYSNlEVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCP 200
Cdd:COG1111     77 IVVFTG-EVSPEKRKELWE----KARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKDP 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  201 RILGLTASilngkcdPEELEEKIQKLEKILK-SNAETATDlvvldrytSQPceivvDCGPFT-DRSGLYERLLM--ELEE 276
Cdd:COG1111    152 LILGMTAS-------PGSDEEKIEEVCENLGiENVEVRTE--------EDP-----DVAPYVhDTEVEWIRVELpeELKE 211

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  277 ALNFIN-----------DCNISVHSKERDST--------LISKQILSDCRAVLVVLGPwcadkVAGMM------------ 325
Cdd:COG1111    212 IRDLLNevlddrlkklkELGVIVSTSPDLSKkdllalqkKLQRRIREDDSEGYRAISI-----LAEALklrhalelletq 286

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  326 -VRELQKYIKhEQEELHRKFL-------LFTDTFLRKIHALCE----EHfspasldlkfvtPKVIKLLEILRKYKpyerq 393
Cdd:COG1111    287 gVEALLRYLE-RLEEEARSSGgskaskrLVSDPRFRKAMRLAEeadiEH------------PKLSKLREILKEQL----- 348

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  394 qfesvewynNRNQDNYVswsdsedddedeeieekekpetnfpspftnilcgIIFVERRYTAVVLNRLIKEAGkqdpelay 473
Cdd:COG1111    349 ---------GTNPDSRI----------------------------------IVFTQYRDTAEMIVEFLSEPG-------- 377

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  474 ISSNFITGHGIGKNQPRNKQmeaefRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDL-PTEYRSyVQSKGR 552
Cdd:COG1111    378 IKAGRFVGQASKEGDKGLTQ-----KEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPvPSEIRS-IQRKGR 451
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 630-718 2.59e-32

Dicer dimerization domain; This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerization of Dicer proteins with their respective protein partners.


Pssm-ID: 460900  Cd Length: 89  Bit Score: 121.06  E-value: 2.59e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  630 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMSCVRLAERVVALICCEKLHKIGELD 709
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79


                   ....*....
gi 2074816265  710 DHLMPVGKE 718
Cdd:pfam03368   80 DHLLPLTKK 88
PAZ cd02825
PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two ...
 886-1008 2.54e-31

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


Pssm-ID: 239207  Cd Length: 115  Bit Score: 119.49  E-value: 2.54e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  886 DSSTLDIDFKFMEDIEKSEARIGIPSTKYTKETPfVFKLEDYQDaviipryrnfdQPHRFYVADVYTDLTPLS--KFPSP 963
Cdd:cd02825      1 ADPVIETMCKFPKDREIDTPLLDSPREEFTKELK-GLKVEDTHN-----------PLNRVYRPDGETRLKAPSqlKHSDG 68

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2074816265  964 EYETFAEYYKTKYNLDLTNLNQPLLDVDHTS--SRLNLLTPRHLNQK 1008
Cdd:cd02825     69 KEITFADYFKERYNLTLTDLNQPLLIVKFSSkkSYSILLPPELCVIT 115
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
 925-1065 6.73e-28

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


Pssm-ID: 198017  Cd Length: 138  Bit Score: 110.45  E-value: 6.73e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   925 EDYQDAVIIPRYRNfdqpHRFYVADVYTDLTPLSKFPSPEYE--TFAEYYKTKYNLDLTNLNQPLLdVDHTSsrlnlltp 1002
Cdd:smart00949   25 KDLKGLIVLTRYNN----KTYRIDDIDWNLAPKSTFEKSDGSeiTFVEYYKQKYNITIRDPNQPLL-VSRPK-------- 91

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816265  1003 RHLNQKGKalplssaekrkakweslQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLL 1065
Cdd:smart00949   92 RRRNQNGK-----------------GEPVLLPPELCFITGLTDRMRKDFMLMKSIADRTRLSP 137
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 43-226 2.06e-26

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


Pssm-ID: 350794 [Multi-domain]  Cd Length: 204  Bit Score: 108.72  E-value: 2.06e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   43 TPRKYQVELLEAALD-HNTIVCLNTGSGKTFIAVLLTKElSYQIRGDFSRNGkRTVFLVNSANQVAQQvSAVRTHSDLKV 121
Cdd:cd18036      2 ELRNYQLELVLPALRgKNTIICAPTGSGKTRVAVYICRH-HLEKRRSAGEKG-RVVVLVNKVPLVEQQ-LEKFFKYFRKG 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  122 GEYSNLEvNASWTKERWNQEFTKHQVLIMTCYVALNVLKNG----YLSLSDINLLVFDECHLAILDHPYREIM------K 191
Cdd:cd18036     79 YKVTGLS-GDSSHKVSFGQIVKASDVIICTPQILINNLLSGreeeRVYLSDFSLLIFDECHHTQKEHPYNKIMrmyldkK 157

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 2074816265  192 LCENCPScPRILGLTASI-LNGKCDPEELEEKIQKL 226
Cdd:cd18036    158 LSSQGPL-PQILGLTASPgVGGARSFEEALEHILKL 192
RIBOc smart00535
Ribonuclease III family;
1296-1387 2.29e-25

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 102.68  E-value: 2.29e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  1296 LILQALTLSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIF 1374
Cdd:smart00535    2 LLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81

                            90
                    ....*....|...
gi 2074816265  1375 DPPVNWLPPGYVV 1387
Cdd:smart00535   82 EAISGGRDKPKIL 94
PRK13766 PRK13766
Hef nuclease; Provisional
 37-553 2.73e-25

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 114.20  E-value: 2.73e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   37 IHDNIYTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELsyqirgdFSRNGKRTVFLVNSANQVAQQVSAVRTH 116
Cdd:PRK13766     9 IKPNTIEARLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAER-------LHKKGGKVLILAPTKPLVEQHAEFFRKF 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  117 SDLKVGEYSNL--EVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPY----REIM 190
Cdd:PRK13766    82 LNIPEEKIVVFtgEVSPEKRAELWE----KAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYvyiaERYH 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  191 KLCENcpscPRILGLTASilNGKcDPEELEEKIQKLeKIlkSNAE--TATDLVVlDRYTSqpcEIVVDcgpftdrsglYE 268
Cdd:PRK13766   158 EDAKN----PLVLGLTAS--PGS-DEEKIKEVCENL-GI--EHVEvrTEDDPDV-KPYVH---KVKIE----------WV 213

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  269 RLLM--ELEEALNFINDCnisvhSKERdstlisKQILSDCRaVLVVLGPWCADK-VAGMMvRELQKYIKHEQEEL----- 340
Cdd:PRK13766   214 RVELpeELKEIRDLLNEA-----LKDR------LKKLKELG-VIVSISPDVSKKeLLGLQ-KKLQQEIANDDSEGyeais 280

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  341 ---------HRKFLLFT---DTFLRKIHALCEEHFSPAS--------LDLKF------------VTPKVIKLLEILRKyk 388
Cdd:PRK13766   281 ilaeamklrHAVELLETqgvEALRRYLERLREEARSSGGskaskrlvEDPRFrkavrkakeldiEHPKLEKLREIVKE-- 358

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  389 pyerqQFEsvewynnRNQDNYVswsdsedddedeeieekekpetnfpspftnilcgIIFVERRYTA-VVLNRLIKEagkq 467
Cdd:PRK13766   359 -----QLG-------KNPDSRI----------------------------------IVFTQYRDTAeKIVDLLEKE---- 388

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  468 dpelayissNFITGHGIGKNQPRN-KQMEAefRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFD-LPTEYRS 545
Cdd:PRK13766   389 ---------GIKAVRFVGQASKDGdKGMSQ--KEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEpVPSEIRS 457


                   ....*...
gi 2074816265  546 yVQSKGRA 553
Cdd:PRK13766   458 -IQRKGRT 464
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1296-1376 4.95e-25

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


Pssm-ID: 238333  Cd Length: 133  Bit Score: 101.92  E-value: 4.95e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265 1296 LILQALT---LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVS 1372
Cdd:cd00593      2 LLLEALThpsYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLG 81


                   ....
gi 2074816265 1373 IFDP 1376
Cdd:cd00593     82 KGEE 85
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 271-365 5.59e-25

Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a central role in RNA interference by breaking down RNA molecules into fragments of about 22 nucleotides (miRNAs and siRNAs). Loading of RNA onto Dicer and the enzymatic cleavage are supported by dsRNA-binding proteins, including trans-activation response (TAR) RNA-binding protein (TRBP) or protein activator of PKR (PACT). Together with Argonaute, this constitutes the RNA-induced silencing complex (RISC) which functions to load the small RNA fragments onto Argonaute. The Partner-binding domain of Dicer is responsible for interactions with the dsRNA-binding proteins. This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases.


Pssm-ID: 277191  Cd Length: 104  Bit Score: 100.82  E-value: 5.59e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  271 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 341
Cdd:cd15903      1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                           90       100
                   ....*....|....*....|....
gi 2074816265  342 RKFLLFTDTFLRKIHALCEEHFSP 365
Cdd:cd15903     81 RLFLRYVITQLRKIRKLLEDEMKN 104
DEXDc smart00487
DEAD-like helicases superfamily;
40-242 6.74e-23

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 98.33  E-value: 6.74e-23
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265    40 NIYTPRKYQVELLEAALD--HNTIVCLNTGSGKTFIAVLLTKELSYqirgdfSRNGKRTVFLVNS---ANQVAQQVSAVR 114
Cdd:smart00487    5 GFEPLRPYQKEAIEALLSglRDVILAAPTGSGKTLAALLPALEALK------RGKGGRVLVLVPTrelAEQWAEELKKLG 78

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   115 THSDLK-VGEYSNLEVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLC 193
Cdd:smart00487   79 PSLGLKvVGLYGGDSKREQLRKLESG----KTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLL 154

                           170       180       190       200
                    ....*....|....*....|....*....|....*....|....*....
gi 2074816265   194 ENCPSCPRILGLTASILNgkcDPEELEEKIQKLEKILKSNAETATDLVV 242
Cdd:smart00487  155 KLLPKNVQLLLLSATPPE---EIENLLELFLNDPVFIDVGFTPLEPIEQ 200
helicase_insert_domain cd12088
helicase_insert_domain; helicase_insert_domain; This helical domain can be found inserted in a ...
 271-362 2.26e-22

helicase_insert_domain; helicase_insert_domain; This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases, like archaeal Hef helicase, MDA5-like helicases and FancM-like helicases. The exact function of this domain is unknown, but seems to play a role in interaction with nucleotides and/or the stabilization of the nucleotide complex.


Pssm-ID: 277187  Cd Length: 82  Bit Score: 92.53  E-value: 2.26e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  271 LMELEEALNFINDCNIsvhskerDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHeqeELHRKFLLFTDT 350
Cdd:cd12088      1 KMILSQLLRDTESLLK-------LLYTAHLRKLNDALELLEDAGIWDALKYIKMFFTEVREGIFD---ELERKLTLRFDE 70

                           90
                   ....*....|..
gi 2074816265  351 FLRKIHALCEEH 362
Cdd:cd12088     71 KLQKLIALSRDP 82
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
 45-226 5.47e-22

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


Pssm-ID: 350791 [Multi-domain]  Cd Length: 182  Bit Score: 95.08  E-value: 5.47e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   45 RKYQVELLEAALDHNTIVCLNTGSGKTFIA--VLLtkelsyqirgDFSR---NGKrTVFLVNSANQVAQQVSAVrtHSDL 119
Cdd:cd18033      4 RDYQFTIVQKALFQNTLVALPTGLGKTFIAavVML----------NYYRwfpKGK-IVFMAPTKPLVSQQIEAC--YKIT 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  120 KVGEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSC 199
Cdd:cd18033     71 GIPSSQTAELTGSVPPTKRAELWASKRVFFLTPQTLENDLKEGDCDPKSIVCLVIDEAHRATGNYAYCQVVRELMRYNSH 150

                          170       180
                   ....*....|....*....|....*..
gi 2074816265  200 PRILGLTASILNgkcDPEELEEKIQKL 226
Cdd:cd18033    151 FRILALTATPGS---KLEAVQQVIDNL 174
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
 44-226 7.58e-22

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


Pssm-ID: 350831 [Multi-domain]  Cd Length: 202  Bit Score: 95.27  E-value: 7.58e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   44 PRKYQVELLEAALD-HNTIVCLNTGSGKTFIAVLLTKelsYQIRgDFSRNGK-RTVFLVNSANQVAQQVSAVRTH---SD 118
Cdd:cd18073      3 PRNYQLELALPAMKgKNTIICAPTGCGKTFVSLLICE---HHLK-KFPQGQKgKVVFFATKVPVYEQQKSVFSKYferHG 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  119 LKV----GEYSNLeVNASWTKErwnqeftKHQVLIMTCYVALNVLKNGYL-SLSDINLLVFDECHLAILDHPYREIM--- 190
Cdd:cd18073     79 YRVtgisGATAEN-VPVEQIIE-------NNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSGNHPYNMIMfry 150

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 2074816265  191 ---KLCENCPSCPRILGLTASILNGKC-DPEELEEKIQKL 226
Cdd:cd18073    151 ldqKLGGSSGPLPQIIGLTASVGVGDAkNTDEALDYICKL 190
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
 914-1064 4.16e-20

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


Pssm-ID: 460472  Cd Length: 123  Bit Score: 87.63  E-value: 4.16e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  914 YTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFP--SPEYETFAEYYKTKYNLDLTNLNQPLLDVd 991
Cdd:pfam02170    8 QQQKDRRDFRKEAKKALKGLKVYTTYNNPRTYRIDGITFDPTPESTFPlkDGKEITVVDYFKKKYNIDLKYPDQPLLLV- 86

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2074816265  992 htssrlnlltprhlnqkgkalplssaeKRKakweslQNKQILVPELCAihpIPASLWRKAVCLPSILYRLHCL 1064
Cdd:pfam02170   87 ---------------------------GKK------RPKVYLPPELCN---LVDGQRYTKKLMPSIAQRTRLL 123
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1313-1376 1.98e-15

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 73.46  E-value: 1.98e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2074816265 1313 ERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIFDP 1376
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDI 64
PAZ_CAF_like cd02844
PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has ...
 922-1044 6.18e-15

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


Pssm-ID: 239210  Cd Length: 135  Bit Score: 73.22  E-value: 6.18e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  922 FKLEDYQDAVIIpryrnfdQPH--RFYVADVYTDLTPLSKFP---SPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSR 996
Cdd:cd02844     26 FCACDLKGSVVT-------APHngRFYVISGILDLNANSSFPgkeGLGYATYAEYFKEKYGIVLNHPNQPLLKGKQIFNL 98

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 2074816265  997 LNLLTPRhLNQKGkalplSSAEKRKakwesLQNKQILVPELCAIHPIP 1044
Cdd:cd02844     99 HNLLHNR-FEEKG-----ESEEKEK-----DRYFVELPPELCSVIDLP 135
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 501-553 1.35e-14

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 71.47  E-value: 1.35e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2074816265  501 QEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 553
Cdd:pfam00271   53 REEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 46-219 4.15e-14

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


Pssm-ID: 350679 [Multi-domain]  Cd Length: 181  Bit Score: 72.29  E-value: 4.15e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   46 KYQVELLEAAL--DHNTIVCLNTGSGKTFIAVLLtkelsyqIRGDFSRNGKRTVFLVNS---ANQVAQQVSAVRTHSDLK 120
Cdd:cd17921      4 PIQREALRALYlsGDSVLVSAPTSSGKTLIAELA-------ILRALATSGGKAVYIAPTralVNQKEADLRERFGPLGKN 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  121 VGE-YSNLEVNASWTKERwnqeftkhQVLIMTcYVALNVL--KNGYLSLSDINLLVFDECHL-------AILDHPYREIM 190
Cdd:cd17921     77 VGLlTGDPSVNKLLLAEA--------DILVAT-PEKLDLLlrNGGERLIQDVRLVVVDEAHLigdgergVVLELLLSRLL 147

                          170       180
                   ....*....|....*....|....*....
gi 2074816265  191 KLCENCpscpRILGLTASILNgkcdPEEL 219
Cdd:cd17921    148 RINKNA----RFVGLSATLPN----AEDL 168
DEXHc_RLR-3 cd18075
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ...
 45-208 7.20e-14

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


Pssm-ID: 350833 [Multi-domain]  Cd Length: 200  Bit Score: 72.20  E-value: 7.20e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   45 RKYQVELLEAALD-HNTIVCLNTGSGKTFIAVLLTKelsyqiRGDFSRNGKRTVFLVNSANQVAQQVSAVRTHSDlkvGE 123
Cdd:cd18075      4 HGYQWEVVAPALRgKNSIIWLPTGAGKTRAAVYVAR------RHLETKRGAKVAVLVNKVHLVDQHLEKEFHVLL---DK 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  124 YSNLEVNA-SWTKERWNQEFTKHQVLIMTCYVALNVLKNG----YLSLSDINLLVFDECHLAILDHPYREIM------KL 192
Cdd:cd18075     75 YTVTAISGdSSHKCFFGQLARGSDVVICTAQILQNALLSGeeeaHVELTDFSLLVIDECHHTHKEAVYNKIMlsylekKL 154

                          170
                   ....*....|....*.
gi 2074816265  193 CENCPsCPRILGLTAS 208
Cdd:cd18075    155 SRQGD-LPQILGLTAS 169
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 44-226 9.25e-14

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


Pssm-ID: 350793 [Multi-domain]  Cd Length: 181  Bit Score: 71.39  E-value: 9.25e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   44 PRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLtkelsyqIRGDFSRNGKRTVFLVNSANQVAQQVSAVRT--HSDLKV 121
Cdd:cd18035      3 RRLYQVLIAAVALNGNTLIVLPTGLGKTIIAILV-------AADRLTKKGGKVLILAPSRPLVEQHAENLKRvlNIPDKI 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  122 GEYSNlEVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCPR 201
Cdd:cd18035     76 TSLTG-EVKPEERAERWD----ASKIIVATPQVIENDLLAGRITLDDVSLLIFDEAHHAVGNYAYVYIAHRYKREANNPL 150

                          170       180
                   ....*....|....*....|....*
gi 2074816265  202 ILGLTASilnGKCDPEELEEKIQKL 226
Cdd:cd18035    151 ILGLTAS---PGSDKEKIMEICENL 172
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 45-221 4.83e-13

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


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 68.81  E-value: 4.83e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   45 RKYQVELLEAAL-DHNTIVCLNTGSGKTFIAVL-LTKELsyqirgDFSRNGKRTVFLV---NSANQVAQQVSavrthsdl 119
Cdd:pfam00270    1 TPIQAEAIPAILeGRDVLVQAPTGSGKTLAFLLpALEAL------DKLDNGPQALVLAptrELAEQIYEELK-------- 66

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  120 KVGEYSNLEVNASWT-KERWNQ--EFTKHQVLIMTCYVALNVLKNGYLsLSDINLLVFDECHLaILDHPYREIMKLC-EN 195
Cdd:pfam00270   67 KLGKGLGLKVASLLGgDSRKEQleKLKGPDILVGTPGRLLDLLQERKL-LKNLKLLVLDEAHR-LLDMGFGPDLEEIlRR 144

                          170       180
                   ....*....|....*....|....*.
gi 2074816265  196 CPSCPRILGLTASIlngkcdPEELEE 221
Cdd:pfam00270  145 LPKKRQILLLSATL------PRNLED 164
ResIII pfam04851
Type III restriction enzyme, res subunit;
41-207 9.98e-13

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 67.70  E-value: 9.98e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   41 IYTPRKYQVE----LLEAALDHNTIVCLN--TGSGKTFIAVLLTKELSYqirgdfSRNGKRTVFLVNSANQVAQQvsavr 114
Cdd:pfam04851    1 KLELRPYQIEaienLLESIKNGQKRGLIVmaTGSGKTLTAAKLIARLFK------KGPIKKVLFLVPRKDLLEQA----- 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  115 thsdlkVGEYSNLEVNASWTKERWNQEFTKHQV----LIMTCYVALNV-LKNGYLSLSD--INLLVFDECHLAILDHpYR 187
Cdd:pfam04851   70 ------LEEFKKFLPNYVEIGEIISGDKKDESVddnkIVVTTIQSLYKaLELASLELLPdfFDVIIIDEAHRSGASS-YR 142

                          170       180
                   ....*....|....*....|
gi 2074816265  188 EIMKLCencpSCPRILGLTA 207
Cdd:pfam04851  143 NILEYF----KPAFLLGLTA 158
HELICc smart00490
helicase superfamily c-terminal domain;
499-553 1.11e-12

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 64.93  E-value: 1.11e-12
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 2074816265   499 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 553
Cdd:smart00490   24 EEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 445-553 1.10e-11

C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350188 [Multi-domain]  Cd Length: 143  Bit Score: 64.30  E-value: 1.10e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  445 IIFVERRYTAvvlNRLIKEAGKQDPELAyiSSNFItGHGIGKNQPRNKQMEaefrkQEEVLRKFRAHETNLLIATSIVEE 524
Cdd:cd18801     34 IIFSEFRDSA---EEIVNFLSKIRPGIR--ATRFI-GQASGKSSKGMSQKE-----QKEVIEQFRKGGYNVLVATSIGEE 102

                           90       100       110
                   ....*....|....*....|....*....|
gi 2074816265  525 GVDIPKCNLVVRFD-LPTEYRSyVQSKGRA 553
Cdd:cd18801    103 GLDIGEVDLIICYDaSPSPIRM-IQRMGRT 131
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1292-1367 1.86e-11

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


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 65.69  E-value: 1.86e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265 1292 PNPGLILQALT-----LSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLP 1366
Cdd:TIGR02191   10 KNPELLEQALThrsyaNEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVARELGLG 89


                   .
gi 2074816265 1367 S 1367
Cdd:TIGR02191   90 D 90
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 445-555 2.52e-11

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


Pssm-ID: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 62.91  E-value: 2.52e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  445 IIFVERRYTAVVLNRLIKEAGkqdpelayISSNFItgHGiGKNQprnkqmeaefRKQEEVLRKFRAHETNLLIATSIVEE 524
Cdd:cd18787     31 IIFVNTKKRVDRLAELLEELG--------IKVAAL--HG-DLSQ----------EERERALKKFRSGKVRVLVATDVAAR 89

                           90       100       110
                   ....*....|....*....|....*....|..
gi 2074816265  525 GVDIPKCNLVVRFDLPTEYRSYVQSKGR-ARA 555
Cdd:cd18787     90 GLDIPGVDHVINYDLPRDAEDYVHRIGRtGRA 121
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
42-207 2.55e-11

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 68.51  E-value: 2.55e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   42 YTPRKYQVELLEAALDHNT------IVCLNTGSGKTFIAVLLTKELsyqirgdfsRNGKRTVFLVNSANQVAQqvsavrT 115
Cdd:COG1061     79 FELRPYQQEALEALLAALErgggrgLVVAPTGTGKTVLALALAAEL---------LRGKRVLVLVPRRELLEQ------W 143

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  116 HSDLKvgEYSNLEVNASWTKERWNQ-EFTKHQVLIMtcYVALNVLKNgylslsDINLLVFDECHLAILDHpYREIMKLCE 194
Cdd:COG1061    144 AEELR--RFLGDPLAGGGKKDSDAPiTVATYQSLAR--RAHLDELGD------RFGLVIIDEAHHAGAPS-YRRILEAFP 212

                          170
                   ....*....|...
gi 2074816265  195 ncpsCPRILGLTA 207
Cdd:COG1061    213 ----AAYRLGLTA 221
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 44-208 4.00e-11

DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 62.71  E-value: 4.00e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   44 PRKYQVELLEAALDHNT----IVCLNTGSGKTFIAVLLTKELSYqirgdfsrngKRTVFLVNSANQVAQqvsavrthsdl 119
Cdd:cd17926      1 LRPYQEEALEAWLAHKNnrrgILVLPTGSGKTLTALALIAYLKE----------LRTLIVVPTDALLDQ----------- 59

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  120 kvgeysnlevnaswTKERWNQEFTKHQVLIMTC-----------YVAL-----NVLKNGYLSLSDINLLVFDECHLAild 183
Cdd:cd17926     60 --------------WKERFEDFLGDSSIGLIGGgkkkdfddanvVVATyqslsNLAEEEKDLFDQFGLLIVDEAHHL--- 122

                          170       180
                   ....*....|....*....|....*...
gi 2074816265  184 hP---YREIMKLCEncpsCPRILGLTAS 208
Cdd:cd17926    123 -PaktFSEILKELN----AKYRLGLTAT 145
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
48-221 4.23e-11

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 67.61  E-value: 4.23e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   48 QVELLEAAL--DHNTIVCLNTGSGKTFIAVL-LTKELsyqirgdfsRNGKRTVFLVNS---ANQVAQQVSAVRTHSDLKV 121
Cdd:COG1204     27 QAEALEAGLleGKNLVVSAPTASGKTLIAELaILKAL---------LNGGKALYIVPLralASEKYREFKRDFEELGIKV 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  122 GE-YSNLEVNASWTKERwnqeftkhQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLaiLDHPYR----EIM--KLCE 194
Cdd:COG1204     98 GVsTGDYDSDDEWLGRY--------DILVATPEKLDSLLRNGPSWLRDVDLVVVDEAHL--IDDESRgptlEVLlaRLRR 167

                          170       180
                   ....*....|....*....|....*..
gi 2074816265  195 NCPScPRILGLTASILNgkcdPEELEE 221
Cdd:COG1204    168 LNPE-AQIVALSATIGN----AEEIAE 189
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1283-1365 8.12e-11

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 63.96  E-value: 8.12e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265 1283 IGYSSRtlgpNPGLILQALT---LSNASDGF-NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYR 1358
Cdd:COG0571     11 LGYRFK----DPELLEQALThrsYANEHGGLeNNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAE 86


                   ....*..
gi 2074816265 1359 LGKKKGL 1365
Cdd:COG0571     87 IARELGL 93
DEXHc_RLR-2 cd18074
DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma ...
 43-226 9.68e-11

DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma differentiation-associated protein 5 or Mda5 and IFIH1) is a viral double-stranded RNA (dsRNA) receptor that shares sequence similarity and signaling pathways with RIG-I, yet plays essential functions in antiviral immunity through distinct specificity for viral RNA. RLR-2 recognizes the internal duplex structure, whereas RIG-I recognizes the terminus of dsRNA. RLR-2 uses direct protein-protein contacts to stack along dsRNA in a head-to-tail arrangement. The signaling domain (tandem CARD), which decorates the outside of the core RLR-2 filament, also has an intrinsic propensity to oligomerize into an elongated structure that activates the signaling adaptor, MAVS. RLR-2 uses long dsRNA as a signaling platform to cooperatively assemble the core filament, which in turn promotes stochastic assembly of the tandem CARD oligomers for signaling. LGP2 appears to positively and negatively regulate RLR-2 and RIG-I signaling, respectively. RLR-2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350832 [Multi-domain]  Cd Length: 216  Bit Score: 63.34  E-value: 9.68e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   43 TPRKYQVELLEAALD-HNTIVCLNTGSGKTFIAVLLTKELSYQIRGDfSRNGKrTVFLVNSANQVAQQVSA-----VRTH 116
Cdd:cd18074      2 TLRDYQMEVAKPALEgKNIIICLPTGSGKTRVAVYITKDHLDKKRKA-SEPGK-VIVLVNKVPLVEQHYRKefnpfLKHW 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  117 SDLkVGEYSNLEVNASWTKerwnqEFTKHQVLIMTCYVALNVLKNGY------LSLSDINLLVFDECHLAILDHPYREIM 190
Cdd:cd18074     80 YQV-IGLSGDSQLKISFPE-----VVKRYDVIICTAQILENSLLNATeeedegVQLSDFSLIIIDECHHTQKEAVYNNIM 153

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2074816265  191 KLC------------ENCPSC--PRILGLTASI-LNGKCDPEELEEKIQKL 226
Cdd:cd18074    154 RRYlkqkiknrkqkkENKPLIplPQILGLTASPgVGGAKNNKKAEEHILKI 204
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 58-207 7.62e-09

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


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 56.26  E-value: 7.62e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   58 HNTIVCLNTGSGKTFIAVLltkelsyQIRGDFSRNGKRTVFLV---NSANQVAQQVSAVRTHsDLKVGEYsnleVNASWT 134
Cdd:cd00046      2 ENVLITAPTGSGKTLAALL-------AALLLLLKKGKKVLVLVptkALALQTAERLRELFGP-GIRVAVL----VGGSSA 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  135 KERWNQEFTKHQVLIMTC-YVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCE------NCpscpRILGLTA 207
Cdd:cd00046     70 EEREKNKLGDADIIIATPdMLLNLLLREDRLFLKDLKLIIVDEAHALLIDSRGALILDLAVrkaglkNA----QVILLSA 145
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 44-207 8.75e-09

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


Pssm-ID: 350790 [Multi-domain]  Cd Length: 163  Bit Score: 56.42  E-value: 8.75e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   44 PRKYQVELLEA---ALDHNT---IVCLNTGSGKTFIAVLLTKELSyqirgdFSRNGKRTVFLVNSANQVAQQVSAVRTH- 116
Cdd:cd18032      1 PRYYQQEAIEAleeAREKGQrraLLVMATGTGKTYTAAFLIKRLL------EANRKKRILFLAHREELLEQAERSFKEVl 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  117 SDLKVGEYSNLEVNASWTKerwnqeftkhqVLIMTcYVALNvlKNGYLSLSDIN---LLVFDECHLAILDHpYREIMKLC 193
Cdd:cd18032     75 PDGSFGNLKGGKKKPDDAR-----------VVFAT-VQTLN--KRKRLEKFPPDyfdLIIIDEAHHAIASS-YRKILEYF 139

                          170
                   ....*....|....
gi 2074816265  194 ENCPscprILGLTA 207
Cdd:cd18032    140 EPAF----LLGLTA 149
PAZ_piwi_like cd02845
PAZ domain, Piwi_like subfamily. In multi-cellular organisms, the Piwi protein appears to be ...
 928-1038 1.61e-08

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


Pssm-ID: 239211  Cd Length: 117  Bit Score: 54.19  E-value: 1.61e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  928 QDAVIIPRYRNfdqphRFY-VADVYTDLTPLSKFPSPEYE--TFAEYYKTKYNLDLTNLNQPLLdvdhtssrlnlltprh 1004
Cdd:cd02845     29 IGSIVLTRYNN-----KTYrIDDIDFDKTPLSTFKKSDGTeiTFVEYYKKQYNIEITDLNQPLL---------------- 87

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 2074816265 1005 lnqkgkalpLSSAEKRKAKweSLQNKQI-LVPELC 1038
Cdd:cd02845     88 ---------VSRPKRRDPR--GGEKEPIyLIPELC 111
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 1294-1369 3.57e-08

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


Pssm-ID: 434075  Cd Length: 127  Bit Score: 53.72  E-value: 3.57e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2074816265 1294 PGLILQALT---LSNASDGFNlERLEMLGDSFLKHAITTYLFcTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRM 1369
Cdd:pfam14622    1 EELLLQALThksYANGRKPYN-ERLEFLGDAVLELSVSEYLF-KKPDLDEGGLTKLRASIVSEESLAEIAREIGLGKYL 77
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 512-553 5.95e-08

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 51.55  E-value: 5.95e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 2074816265  512 ETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 553
Cdd:cd18785     22 SLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRA 63
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
444-589 6.28e-08

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 57.08  E-value: 6.28e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  444 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFItgHGiGKNQprnkqmeaefRKQEEVLRKFRAHETNLLIATSIVE 523
Cdd:COG0513    244 AIVFCNTKRGADRLAEKLQKRG--------ISAAAL--HG-DLSQ----------GQRERALDAFRNGKIRVLVATDVAA 302

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2074816265  524 EGVDIPKCNLVVRFDLPTEYRSYV---------QSKGRArapisnyIMLADtdkiksfEEDLKTYKAIEKILRNK 589
Cdd:COG0513    303 RGIDIDDVSHVINYDLPEDPEDYVhrigrtgraGAEGTA-------ISLVT-------PDERRLLRAIEKLIGQK 363
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 493-584 8.27e-07

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


Pssm-ID: 350179 [Multi-domain]  Cd Length: 160  Bit Score: 50.73  E-value: 8.27e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  493 QMEAEfrKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVV-----RFDLPTEYrsyvQSKGR-ARAPISNYIMLADT 566
Cdd:cd18792     69 KMTED--EKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIiedadRFGLSQLH----QLRGRvGRGKHQSYCYLLYP 142

                           90
                   ....*....|....*...
gi 2074816265  567 DKIKSFEEDLKTYKAIEK 584
Cdd:cd18792    143 DPKKLTETAKKRLRAIAE 160
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1669-1708 1.33e-05

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: 48.35  E-value: 1.33e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 2074816265 1669 FEKKINYRFKNKAYLLQAFTHASYHYNTITGKEPTTRLHF 1708
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYANEHHKDVKNNERLEF 40
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1666-1692 2.10e-05

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 47.79  E-value: 2.10e-05
                           10        20
                   ....*....|....*....|....*..
gi 2074816265 1666 FENFEKKINYRFKNKAYLLQAFTHASY 1692
Cdd:COG0571      4 LEELEERLGYRFKDPELLEQALTHRSY 30
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 444-553 2.81e-05

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


Pssm-ID: 350186 [Multi-domain]  Cd Length: 116  Bit Score: 44.86  E-value: 2.81e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  444 GIIFVERRYTAVVLNRLIKEAGkqdPELAYISSNFItghgigknqprnkqmeAEFRKQEEVLR-KFRAHETNLLIATSIV 522
Cdd:cd18799      9 TLIFCVSIEHAEFMAEAFNEAG---IDAVALNSDYS----------------DRERGDEALILlFFGELKPPILVTVDLL 69

                           90       100       110
                   ....*....|....*....|....*....|..
gi 2074816265  523 EEGVDIPKCNLVVrFDLPTEYRS-YVQSKGRA 553
Cdd:cd18799     70 TTGVDIPEVDNVV-FLRPTESRTlFLQMLGRG 100
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 460-571 2.95e-05

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


Pssm-ID: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 46.18  E-value: 2.95e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  460 LIKEAGKQDPELA-----YISSNFITGHGIGKNQPRNKQMEaefrkQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLV 534
Cdd:cd18811     35 LIEESEKLDLKAAvamyeYLKERFRPELNVGLLHGRLKSDE-----KDAVMAEFREGEVDILVSTTVIEVGVDVPNATVM 109

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 2074816265  535 V-----RFDLPTEYrsyvQSKGR-ARAPISNYIMLADTDKIKS 571
Cdd:cd18811    110 ViedaeRFGLSQLH----QLRGRvGRGDHQSYCLLVYKDPLTE 148
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 444-594 4.01e-05

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 48.01  E-value: 4.01e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  444 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGhgigknqprnkqmEAEFRKQEEVLRKFRAHETNLLIATSIVE 523
Cdd:PRK11192   248 SIVFVRTRERVHELAGWLRKAG--------INCCYLEG-------------EMVQAKRNEAIKRLTDGRVNVLVATDVAA 306

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  524 EGVDIPKCNLVVRFDLPTEYRSYVQSKGR-ARA-----PIS-----NYIMLadtDKIKSF-EEDLK---------TYKAI 582
Cdd:PRK11192   307 RGIDIDDVSHVINFDMPRSADTYLHRIGRtGRAgrkgtAISlveahDHLLL---GKIERYiEEPLKarvidelrpKTKAP 383

                          170
                   ....*....|..
gi 2074816265  583 EKILRNKCSKSV 594
Cdd:PRK11192   384 SEKKTGKPSKKV 395
PTZ00424 PTZ00424
helicase 45; Provisional
 499-578 4.04e-05

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 47.90  E-value: 4.04e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  499 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA----RAPIS-NYIMLADTDKIKSFE 573
Cdd:PTZ00424   304 KDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSgrfgRKGVAiNFVTPDDIEQLKEIE 383


                   ....*
gi 2074816265  574 EDLKT 578
Cdd:PTZ00424   384 RHYNT 388
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
 48-221 5.48e-05

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


Pssm-ID: 350786 [Multi-domain]  Cd Length: 177  Bit Score: 45.79  E-value: 5.48e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   48 QVELLEAAL--DHNTIVCLNTGSGKTFIAVL-LTKELSyqirgdfsrNGKRTVFLV---NSANQVAQQVSAVRTHS---D 118
Cdd:cd18028      6 QAEAVRAGLlkGENLLISIPTASGKTLIAEMaMVNTLL---------EGGKALYLVplrALASEKYEEFKKLEEIGlkvG 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  119 LKVGEYSnlevnaswTKERWNQEFtkhQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLaiLDHPYRE------IMKL 192
Cdd:cd18028     77 ISTGDYD--------EDDEWLGDY---DIIVATYEKFDSLLRHSPSWLRDVGVVVVDEIHL--ISDEERGptlesiVARL 143

                          170       180
                   ....*....|....*....|....*....
gi 2074816265  193 CENCPSCpRILGLTASILNgkcdPEELEE 221
Cdd:cd18028    144 RRLNPNT-QIIGLSATIGN----PDELAE 167
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
 502-539 6.43e-05

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 47.84  E-value: 6.43e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 2074816265  502 EEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVV-----RFDL 539
Cdd:PRK10917   521 DAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVienaeRFGL 563
DEADc cd00268
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...
 34-228 1.54e-04

DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350669 [Multi-domain]  Cd Length: 196  Bit Score: 44.74  E-value: 1.54e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   34 QEAIHD-NIYTPRKYQVELLEAALD-HNTIVCLNTGSGKT--FIAVLLTKeLSYQIRGdfSRNGKRTVFLVNS---ANQV 106
Cdd:cd00268      2 LKALKKlGFEKPTPIQAQAIPLILSgRDVIGQAQTGSGKTlaFLLPILEK-LLPEPKK--KGRGPQALVLAPTrelAMQI 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  107 AQQVSAVRTHSDLKVgeysnlevnASWT----KERWNQEFTKH-QVLIMTCYVALNVLKNGYLSLSDINLLVFDEchlA- 180
Cdd:cd00268     79 AEVARKLGKGTGLKV---------AAIYggapIKKQIEALKKGpDIVVGTPGRLLDLIERGKLDLSNVKYLVLDE---Ad 146

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 2074816265  181 -ILDHPYREIM-KLCENCPSCPRILGLTASIlngkcdPEELEEKIQKLEK 228
Cdd:cd00268    147 rMLDMGFEEDVeKILSALPKDRQTLLFSATL------PEEVKELAKKFLK 190
PTZ00110 PTZ00110
helicase; Provisional
 499-577 3.59e-04

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 45.15  E-value: 3.59e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  499 RKQEE---VLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQ---SKGRARAPISNYIMLAdTDKIKSF 572
Cdd:PTZ00110   411 KKQEErtwVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHrigRTGRAGAKGASYTFLT-PDKYRLA 489


                   ....*
gi 2074816265  573 EEDLK 577
Cdd:PTZ00110   490 RDLVK 494
RecG COG1200
RecG-like helicase [Replication, recombination and repair];
502-529 3.98e-04

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


Pssm-ID: 440813 [Multi-domain]  Cd Length: 684  Bit Score: 45.04  E-value: 3.98e-04
                           10        20
                   ....*....|....*....|....*...
gi 2074816265  502 EEVLRKFRAHETNLLIATSIVEEGVDIP 529
Cdd:COG1200    519 DAVMAAFKAGEIDVLVATTVIEVGVDVP 546
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 503-583 4.64e-04

C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II), and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA. Its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350177 [Multi-domain]  Cd Length: 171  Bit Score: 42.62  E-value: 4.64e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  503 EVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTE-----YRSYVQSKGRA-RAPISNYIMLAD--TDKIKsfee 574
Cdd:cd18790     68 EIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEgflrsETSLIQTIGRAaRNVNGKVILYADkiTDSMQ---- 143


                   ....*....
gi 2074816265  575 dlktyKAIE 583
Cdd:cd18790    144 -----KAIE 147
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 491-552 5.23e-04

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 44.84  E-value: 5.23e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2074816265  491 NKQMEAEFRkqEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGR 552
Cdd:PRK11634   276 NGDMNQALR--EQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGR 335
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 493-584 9.35e-04

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


Pssm-ID: 350197 [Multi-domain]  Cd Length: 151  Bit Score: 41.56  E-value: 9.35e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  493 QMEAEfrKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVV-----RFDLPTEYrsyvQSKGR-ARAPISNYIMLADT 566
Cdd:cd18810     60 QMTEN--ELEEVMLEFAKGEYDILVCTTIIESGIDIPNANTIIieradKFGLAQLY----QLRGRvGRSKERAYAYFLYP 133

                           90
                   ....*....|....*...
gi 2074816265  567 DKIKSFEEDLKTYKAIEK 584
Cdd:cd18810    134 DQKKLTEDALKRLEAIQE 151
DEADc_DDX47 cd17954
DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can ...
 43-116 2.24e-03

DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can shuttle between the nucleus and the cytoplasm, and has an RNA-independent ATPase activity. DX47 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350712 [Multi-domain]  Cd Length: 203  Bit Score: 41.15  E-value: 2.24e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   43 TPRKYQVELLEAALDHNTIVCL-NTGSGKT-----------------FIAVLL--TKELSYQIRGDFSRNGK----RTVF 98
Cdd:cd17954     22 KPTKIQEEAIPVALQGRDIIGLaETGSGKTaafalpilqallenpqrFFALVLapTRELAQQISEQFEALGSsiglKSAV 101

                           90
                   ....*....|....*....
gi 2074816265   99 LVNSANQVAQQVS-AVRTH 116
Cdd:cd17954    102 LVGGMDMMAQAIAlAKKPH 120
DEXHc_DDX60 cd18025
DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an ...
 44-231 2.30e-03

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


Pssm-ID: 350783 [Multi-domain]  Cd Length: 192  Bit Score: 41.20  E-value: 2.30e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   44 PRKYQVELLEAaLDHN--TIVCLNTGSGKTFIAVlltkelsYQIRGDFSRNGKRTVFLVNSA----NQVAQQVSAVRTHS 117
Cdd:cd18025      2 PDAWQRELLDI-VDRResALIVAPTSSGKTFISY-------YCMEKVLRESDDGVVVYVAPTkalvNQVVAEVYARFSKK 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  118 DLKVGEYsnleVNASWTKERWNQEFTKHQVLImTCYVALNVLkngYLSLSD------INLLVFDECHL--AILDHPYREI 189
Cdd:cd18025     74 YPPSGKS----LWGVFTRDYRHNNPMNCQVLI-TVPECLEIL---LLSPHNaswvprIKYVIFDEIHSigQSEDGAVWEQ 145

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 2074816265  190 MKLCENCPscprILGLTASILNgkcdPEELEEKIQKLEKILK 231
Cdd:cd18025    146 LLLLIPCP----FLALSATIGN----PQKFHEWLQSVQRARK 179
Mfd COG1197
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ...
 478-532 2.99e-03

Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];


Pssm-ID: 440810 [Multi-domain]  Cd Length: 1130  Bit Score: 42.36  E-value: 2.99e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2074816265  478 FITGHGigknqprnkQMEAefRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCN 532
Cdd:COG1197    824 IAVAHG---------QMSE--RELERVMLDFYEGEFDVLVCTTIIETGIDIPNAN 867
DEXHc_RecQ cd17920
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ...
 43-226 3.69e-03

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


Pssm-ID: 350678 [Multi-domain]  Cd Length: 200  Bit Score: 40.60  E-value: 3.69e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265   43 TPRKYQVELLEAALDH-NTIVCLNTGSGKTFI----AVLLTKE-------LSY---QIRGdFSRNGKRTVFLvNSANQVA 107
Cdd:cd17920     12 EFRPGQLEAINAVLAGrDVLVVMPTGGGKSLCyqlpALLLDGVtlvvsplISLmqdQVDR-LQQLGIRAAAL-NSTLSPE 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  108 QQVSAVRthsDLKVGEYSNLEVnaswTKER-WNQEFtkhqvlimtcyvaLNVLKNGYlSLSDINLLVFDECHLaILD--H 184
Cdd:cd17920     90 EKREVLL---RIKNGQYKLLYV----TPERlLSPDF-------------LELLQRLP-ERKRLALIVVDEAHC-VSQwgH 147

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 2074816265  185 ---P-YREIMKLCENCPSCPrILGLTASilngkCDPEELEEKIQKL 226
Cdd:cd17920    148 dfrPdYLRLGRLRRALPGVP-ILALTAT-----ATPEVREDILKRL 187
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 495-553 3.80e-03

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 41.70  E-value: 3.80e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2074816265  495 EAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 553
Cdd:PLN00206   401 EKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRA 459
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 455-589 5.17e-03

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


Pssm-ID: 440816 [Multi-domain]  Cd Length: 535  Bit Score: 41.61  E-value: 5.17e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  455 VVLN---------RLIKEAGKqDPELAYISSNFITGHgigknqprnkqmeaefRKQ--EEVLRKFRAHETNLLIATSIVE 523
Cdd:COG1203    371 VIVNtvkdaqelyEALKEKLP-DEEVYLLHSRFCPAD----------------RSEieKEIKERLERGKPCILVSTQVVE 433

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  524 EGVDI-----------------------------PKCNLVVrFDLPTEYRSYVQSK---GRARAPISNYIMLADTDKIKS 571
Cdd:COG1203    434 AGVDIdfdvvirdlapldsliqragrcnrhgrkeEEGNVYV-FDPEDEGGGYVYDKpllERTRELLREHDEILPEDKREL 512

                          170
                   ....*....|....*...
gi 2074816265  572 FEEdlkTYKAIEKILRNK 589
Cdd:COG1203    513 IEE---YYRELYELLPDE 527
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 443-553 8.67e-03

C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350181 [Multi-domain]  Cd Length: 134  Bit Score: 38.34  E-value: 8.67e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816265  443 CGIIFVERRYTAVVLNRLIKEAGkqDPELAYissnfitgHGigknqprnkQMEAEFRkqEEVLRKFRAHETNLLIATSIV 522
Cdd:cd18794     32 SGIIYCLSRKECEQVAARLQSKG--ISAAAY--------HA---------GLEPSDR--RDVQRKWLRDKIQVIVATVAF 90

                           90       100       110
                   ....*....|....*....|....*....|.
gi 2074816265  523 EEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 553
Cdd:cd18794     91 GMGIDKPDVRFVIHYSLPKSMESYYQESGRA 121
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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