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Conserved domains on  [gi|571476045|ref|XP_006586846|]
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endoribonuclease Dicer homolog 2 isoform X2 [Glycine max]

Protein Classification

Dicer and PAZ domain-containing protein( domain architecture ID 13030049)

Dicer and PAZ (Piwi Argonaut and Zwille) domain-containing protein

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 ...
 61-259 1.55e-89

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: 288.78  E-value: 1.55e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   61 ARSYQLEALYKAIHENTIVYLETGSGKTLIAIMLLRSYAHQLRKPSPY--IAVFLVPQVVLVSQQAEAVKRHTDLKVGMY 138
Cdd:cd18034     3 PRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRKEKNPkkRAVFLVPTVPLVAQQAEAIRSHTDLKVGEY 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  139 WGDMGVDFWDAATWKQEMEKHEVLVMTPAILLSCLRHSFFKLNMINVLIMDECHHARGKHPYACIMTEFYHhqlKSGISD 218
Cdd:cd18034    83 SGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYH---LEGRTS 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 571476045  219 LPRIFGMTASPIKSKvgKSESSWSENIQKLMILMHSKVYTC 259
Cdd:cd18034   160 RPRILGLTASPVNGK--GDPKSVEKKIQQLEELLNSTIKTV 198
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 406-536 5.86e-50

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


:

Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 173.55  E-value: 5.86e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  406 SKVCCLVDSLLEYRGLT-DMRCIIFVERIITAIVLEDLLNTLLPKYNSWKTKFIAGYNFGLQNQ----SRTKQNEIVNEF 480
Cdd:cd18802     7 PKLQKLIEILREYFPKTpDFRGIIFVERRATAVVLSRLLKEHPSTLAFIRCGFLIGRGNSSQRKrslmTQRKQKETLDKF 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 571476045  481 RMGLVNIIVATSILEEGLDVQRCNLVIRFDPCPTVCSFIQSRGRARMRNSDYILMV 536
Cdd:cd18802    87 RDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1192-1347 2.91e-40

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


:

Pssm-ID: 238333  Cd Length: 133  Bit Score: 145.45  E-value: 2.91e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045 1192 SLLVEALTHGSYMLPEVPRCYQRLEFLGDSVLDYLITWHLYNEYPGMSPGQLTDMRAASVNNDCYAWSAIKHGLHKHVLH 1271
Cdd:cd00593     1 SLLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571476045 1272 ASQELHKHiavtlnnfdklsssstfgyesEASPPKVLGDIIESLAGAILVDSGFnkEVVWQSIRPLLEPLVTPETL 1347
Cdd:cd00593    81 GKGEEKSG---------------------GRLRPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPLIEEISL 133
PAZ super family cl00301
PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two ...
 849-962 6.06e-29

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


The actual alignment was detected with superfamily member cd02844:

Pssm-ID: 469713  Cd Length: 135  Bit Score: 112.90  E-value: 6.06e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  849 IETKSGLVCTCKLQDALVCTSHPGgkiYFYITTGIMELHGNSPMELR-GGEVTTYKKYYEQHHGIQLQFENQWLLKARHH 927
Cdd:cd02844    19 LHLADGSFCACDLKGSVVTAPHNG---RFYVISGILDLNANSSFPGKeGLGYATYAEYFKEKYGIVLNHPNQPLLKGKQI 95

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 571476045  928 FKVKNYCHGQKQGKDGASKA-----FVELPPELCSIVMSP 962
Cdd:cd02844    96 FNLHNLLHNRFEEKGESEEKekdryFVELPPELCSVIDLP 135
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1009-1151 1.99e-28

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: 111.55  E-value: 1.99e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045 1009 LEAITTKRCNEA---FHYESLETLGDSFLKYAASQQLFKTYKNHHEGLLSVKREKIISNAALCKLGCSSGLPGFIRNEPF 1085
Cdd:cd00593     4 LEALTHPSYANEhgrFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKG 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571476045 1086 DPHawtipgdkpeslkleelvikgkkiyvhGKRKLNRKIIADVVEALIGAFLSTGGEISALLFMDW 1151
Cdd:cd00593    84 EEK---------------------------SGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLR 122
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 596-670 6.90e-20

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: 85.62  E-value: 6.90e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   596 SISLIYLYCSRLPADGYFKPAPRWD-------KETGTLYLPKSCPLQPI--CVEGNKKHLKNIACLEACKQLHKIGALTD 666
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEvteveggKFVCTVTLPINSPLRSIegPPWRSKKLAKRSAAFEACKALHKAGLLDD 80


                   ....
gi 571476045   667 NLVP 670
Cdd:pfam03368   81 HLLP 84
DSRM smart00358
Double-stranded RNA binding motif;
1351-1417 9.33e-06

Double-stranded RNA binding motif;


:

Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 44.56  E-value: 9.33e-06
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 571476045   1351 PIRELNELCQKRSYKIVLEDVSRK--DGVTNYRMKVEADGVIHeYEYTGPALRDtAKKIACKEILNSLK 1417
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEEgpDHAPRFTVTVKVGGKRT-GEGEGSSKKE-AKQRAAEAALRSLK 67
 
Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 61-259 1.55e-89

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: 288.78  E-value: 1.55e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   61 ARSYQLEALYKAIHENTIVYLETGSGKTLIAIMLLRSYAHQLRKPSPY--IAVFLVPQVVLVSQQAEAVKRHTDLKVGMY 138
Cdd:cd18034     3 PRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRKEKNPkkRAVFLVPTVPLVAQQAEAIRSHTDLKVGEY 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  139 WGDMGVDFWDAATWKQEMEKHEVLVMTPAILLSCLRHSFFKLNMINVLIMDECHHARGKHPYACIMTEFYHhqlKSGISD 218
Cdd:cd18034    83 SGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYH---LEGRTS 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 571476045  219 LPRIFGMTASPIKSKvgKSESSWSENIQKLMILMHSKVYTC 259
Cdd:cd18034   160 RPRILGLTASPVNGK--GDPKSVEKKIQQLEELLNSTIKTV 198
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 406-536 5.86e-50

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


Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 173.55  E-value: 5.86e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  406 SKVCCLVDSLLEYRGLT-DMRCIIFVERIITAIVLEDLLNTLLPKYNSWKTKFIAGYNFGLQNQ----SRTKQNEIVNEF 480
Cdd:cd18802     7 PKLQKLIEILREYFPKTpDFRGIIFVERRATAVVLSRLLKEHPSTLAFIRCGFLIGRGNSSQRKrslmTQRKQKETLDKF 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 571476045  481 RMGLVNIIVATSILEEGLDVQRCNLVIRFDPCPTVCSFIQSRGRARMRNSDYILMV 536
Cdd:cd18802    87 RDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1192-1347 2.91e-40

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


Pssm-ID: 238333  Cd Length: 133  Bit Score: 145.45  E-value: 2.91e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045 1192 SLLVEALTHGSYMLPEVPRCYQRLEFLGDSVLDYLITWHLYNEYPGMSPGQLTDMRAASVNNDCYAWSAIKHGLHKHVLH 1271
Cdd:cd00593     1 SLLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571476045 1272 ASQELHKHiavtlnnfdklsssstfgyesEASPPKVLGDIIESLAGAILVDSGFnkEVVWQSIRPLLEPLVTPETL 1347
Cdd:cd00593    81 GKGEEKSG---------------------GRLRPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPLIEEISL 133
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
61-560 3.07e-40

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 160.67  E-value: 3.07e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   61 ARSYQLEALYKAIHENTIVYLETGSGKTLIAIMLLRSYAHQLRKPspyiAVFLVPQVVLVSQQAEAVKRHT---DLKVGM 137
Cdd:COG1111     4 RRLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAERLHKKGGK----VLFLAPTKPLVEQHAEFFKEALnipEDEIVV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  138 YWGDMGVDFwDAATWkqemEKHEVLVMTPAILLSCLRHSFFKLNMINVLIMDECHHARGKHPYACImTEFYHHQLKSgis 217
Cdd:COG1111    80 FTGEVSPEK-RKELW----EKARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYI-AERYHEDAKD--- 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  218 dlPRIFGMTASPikskvGKSESSWSENIQKLMIlmhSKVytcvseAVITEFIPTSTPKFKFYSNNGIQFVLFEELASKLK 297
Cdd:COG1111   151 --PLILGMTASP-----GSDEEKIEEVCENLGI---ENV------EVRTEEDPDVAPYVHDTEVEWIRVELPEELKEIRD 214

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  298 MLKEQHEL---TLRSSDFTKSIAESAQKRitkifcslmfcldELgvwlaLKAAESLSSNEIESFSWGHSGDRVVKDFI-- 372
Cdd:COG1111   215 LLNEVLDDrlkKLKELGVIVSTSPDLSKK-------------DL-----LALQKKLQRRIREDDSEGYRAISILAEALkl 276

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  373 ------LE--GVHALKSYLQ------CDPQWSIGDN-IKSDVK----MGLL---------TSKVCCLVDSLLEYRGltDM 424
Cdd:COG1111   277 rhalelLEtqGVEALLRYLErleeeaRSSGGSKASKrLVSDPRfrkaMRLAeeadiehpkLSKLREILKEQLGTNP--DS 354

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  425 RCIIFVERIITAivlEDLLNTLlpKYNSWKT-KFIA-GYNFGLQNQSRTKQNEIVNEFRMGLVNIIVATSILEEGLDVQR 502
Cdd:COG1111   355 RIIVFTQYRDTA---EMIVEFL--SEPGIKAgRFVGqASKEGDKGLTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPE 429

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 571476045  503 CNLVIRFDPCPTVCSFIQSRGRArMRNSD---YILMVKSgdsvtcSRLEKYLASAdiMRKE 560
Cdd:COG1111   430 VDLVIFYEPVPSEIRSIQRKGRT-GRKREgrvVVLIAKG------TRDEAYYWSS--RRKE 481
RIBOc smart00535
Ribonuclease III family;
1192-1344 1.48e-33

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 126.18  E-value: 1.48e-33
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   1192 SLLVEALTHGSYMLPEvpRCYQRLEFLGDSVLDYLITWHLYNEYPGMSPGQLTDMRAASVNNDCYAWSAIKHGLHKHVLH 1271
Cdd:smart00535    1 SLLLRALTHASYSNEH--EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRL 78

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 571476045   1272 ASQELHKHiavtlnnfdklsssstfgyesEASPPKVLGDIIESLAGAILVDSGFnkEVVWQSIRPLLEPLVTP 1344
Cdd:smart00535   79 GRGEAISG---------------------GRDKPKILADVFEALIGAIYLDSGL--EAAREFIRDLLGPRLDE 128
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1180-1367 6.40e-32

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 124.83  E-value: 6.40e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045 1180 LESQLKYSFHDHSLLVEALTHGSYmLPEVPRC--YQRLEFLGDSVLDYLITWHLYNEYPGMSPGQLTDMRAASVNND-CY 1256
Cdd:COG0571     7 LEERLGYRFKDPELLEQALTHRSY-ANEHGGLenNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEEtLA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045 1257 AWsAIKHGLHKHVLHASQELhkhiavtlnnfdklsssSTFGYESEAsppkVLGDIIESLAGAILVDSGFnkEVVWQSIRP 1336
Cdd:COG0571    86 EI-ARELGLGDYLRLGKGEE-----------------KSGGRRRPS----ILADAFEALIGAIYLDGGL--EAARKFVLR 141

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 571476045 1337 LLEPLVTpETLKLHPIR----ELNELCQKR-----SYKIV 1367
Cdd:COG0571   142 LFEPRLE-EIAPGGAGKdyktALQEWLQARglplpEYEVV 180
PAZ_CAF_like cd02844
PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has ...
 849-962 6.06e-29

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: 112.90  E-value: 6.06e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  849 IETKSGLVCTCKLQDALVCTSHPGgkiYFYITTGIMELHGNSPMELR-GGEVTTYKKYYEQHHGIQLQFENQWLLKARHH 927
Cdd:cd02844    19 LHLADGSFCACDLKGSVVTAPHNG---RFYVISGILDLNANSSFPGKeGLGYATYAEYFKEKYGIVLNHPNQPLLKGKQI 95

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 571476045  928 FKVKNYCHGQKQGKDGASKA-----FVELPPELCSIVMSP 962
Cdd:cd02844    96 FNLHNLLHNRFEEKGESEEKekdryFVELPPELCSVIDLP 135
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1180-1367 1.46e-28

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: 114.99  E-value: 1.46e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  1180 LESQLKYSFHDHSLLVEALTHGSYM--LPEVPRCYQRLEFLGDSVLDYLITWHLYNEYPGMSPGQLTDMRAASVNNDCYA 1257
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYAneHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  1258 WSAIKHGLHKHVLHASQELhkhiavtlnnfdklsssSTFGYESeaspPKVLGDIIESLAGAILVDSGFnkEVVWQSIRPL 1337
Cdd:TIGR02191   81 EVARELGLGDFLLLGKGEE-----------------KSGGRRR----DSILADAFEALIGAIYLDSGL--EAARKFILKL 137

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 571476045  1338 LEPLVT---PETLKLHPIRELNELCQKR-----SYKIV 1367
Cdd:TIGR02191  138 LIPRIDaiiKEETLKDYKTALQEWAQARgkplpEYRLI 175
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1009-1151 1.99e-28

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: 111.55  E-value: 1.99e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045 1009 LEAITTKRCNEA---FHYESLETLGDSFLKYAASQQLFKTYKNHHEGLLSVKREKIISNAALCKLGCSSGLPGFIRNEPF 1085
Cdd:cd00593     4 LEALTHPSYANEhgrFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKG 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571476045 1086 DPHawtipgdkpeslkleelvikgkkiyvhGKRKLNRKIIADVVEALIGAFLSTGGEISALLFMDW 1151
Cdd:cd00593    84 EEK---------------------------SGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLR 122
PRK13766 PRK13766
Hef nuclease; Provisional
 53-560 3.16e-28

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 123.06  E-value: 3.16e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   53 IAPDVLPfARSYQLEALYKAIHENTIVYLETGSGKTLIAIMLLRSYAHQLRKPspyiAVFLVPQVVLVSQQAEAVKRHT- 131
Cdd:PRK13766    9 IKPNTIE-ARLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAERLHKKGGK----VLILAPTKPLVEQHAEFFRKFLn 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  132 --DLKVGMYWGDMG----VDFWDAATwkqemekheVLVMTPAILLSCLRHSFFKLNMINVLIMDECHHARGKHPYACImT 205
Cdd:PRK13766   84 ipEEKIVVFTGEVSpekrAELWEKAK---------VIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYVYI-A 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  206 EFYHHQLKSgisdlPRIFGMTASPikskvGKSESSWSENIQKLMIlmhSKVytcvseAVITEFIPTSTPKFKFYSNNGIQ 285
Cdd:PRK13766  154 ERYHEDAKN-----PLVLGLTASP-----GSDEEKIKEVCENLGI---EHV------EVRTEDDPDVKPYVHKVKIEWVR 214

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  286 FVLFEELASKLKMLKEQHEL---TLRSSDFTKSIAESAQKRitkifcslmfcldELgvwlaLKAAESLSSNEIESFSWGH 362
Cdd:PRK13766  215 VELPEELKEIRDLLNEALKDrlkKLKELGVIVSISPDVSKK-------------EL-----LGLQKKLQQEIANDDSEGY 276

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  363 SGDRVVKDFI--------LE--GVHALKSYLQ------CDPQWSIGD-NIKSDVKM----------GLL---TSKVCCLV 412
Cdd:PRK13766  277 EAISILAEAMklrhavelLEtqGVEALRRYLErlreeaRSSGGSKASkRLVEDPRFrkavrkakelDIEhpkLEKLREIV 356

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  413 DSLLEYRGltDMRCIIFVERIITAIVLEDLLNTllpkyNSWKT-KFI----AGYNFGLqnqSRTKQNEIVNEFRMGLVNI 487
Cdd:PRK13766  357 KEQLGKNP--DSRIIVFTQYRDTAEKIVDLLEK-----EGIKAvRFVgqasKDGDKGM---SQKEQIEILDKFRAGEFNV 426

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571476045  488 IVATSILEEGLDVQRCNLVIRFDPCPTVCSFIQSRGRArMRNSD---YILMVKSgdsvtcSRLEKYLASAdiMRKE 560
Cdd:PRK13766  427 LVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRT-GRQEEgrvVVLIAKG------TRDEAYYWSS--RRKE 493
RIBOc smart00535
Ribonuclease III family;
1007-1156 1.29e-23

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 97.67  E-value: 1.29e-23
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   1007 KVLEAITTKRC-NEAFHYESLETLGDSFLKYAASQQLFKTYKNHHEGLLSVKREKIISNAALCKLGCSSGLPGFIRNEPF 1085
Cdd:smart00535    2 LLLRALTHASYsNEHEHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 571476045   1086 DPHAwtipgdkpeslkleelvikgkkiyvHGKRKlnRKIIADVVEALIGA-FLSTGGEISALLFMDWVGIKV 1156
Cdd:smart00535   82 EAIS-------------------------GGRDK--PKILADVFEALIGAiYLDSGLEAAREFIRDLLGPRL 126
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1213-1324 2.21e-22

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 93.11  E-value: 2.21e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  1213 QRLEFLGDSVLDYLITWHLYNEYPGMSPGQLTDMRAASVNNDCYAWSAIKHGLHKHVLHASQELHKHIAvTLNNFDKLSS 1292
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDIRRRNN-ALGKGPKRAD 79

                           90       100       110
                   ....*....|....*....|....*....|..
gi 571476045  1293 SSTfgyeseasppKVLGDIIESLAGAILVDSG 1324
Cdd:pfam00636   80 GKE----------KVLADAFEALIGALYLDGG 101
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 596-670 6.90e-20

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: 85.62  E-value: 6.90e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   596 SISLIYLYCSRLPADGYFKPAPRWD-------KETGTLYLPKSCPLQPI--CVEGNKKHLKNIACLEACKQLHKIGALTD 666
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEvteveggKFVCTVTLPINSPLRSIegPPWRSKKLAKRSAAFEACKALHKAGLLDD 80


                   ....
gi 571476045   667 NLVP 670
Cdd:pfam03368   81 HLLP 84
DEXDc smart00487
DEAD-like helicases superfamily;
62-270 1.04e-19

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 88.70  E-value: 1.04e-19
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045     62 RSYQLEALYKAIH--ENTIVYLETGSGKTLIAIMLLrsyAHQLRKPSPYIAVFLVPQVVLVSQQAEAVKR---HTDLKVG 136
Cdd:smart00487   10 RPYQKEAIEALLSglRDVILAAPTGSGKTLAALLPA---LEALKRGKGGRVLVLVPTRELAEQWAEELKKlgpSLGLKVV 86

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045    137 MYWGdmGVDFWDAATwKQEMEKHEVLVMTPAILLSCLRHSFFKLNMINVLIMDECHHARGKHpYACIMTEFYHHQLKSgi 216
Cdd:smart00487   87 GLYG--GDSKREQLR-KLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGG-FGDQLEKLLKLLPKN-- 160

                           170       180       190       200       210
                    ....*....|....*....|....*....|....*....|....*....|....
gi 571476045    217 sdlPRIFGMTASPikskvgksesswSENIQKLMILMHSKVYTCVSEAVITEFIP 270
Cdd:smart00487  161 ---VQLLLLSATP------------PEEIENLLELFLNDPVFIDVGFTPLEPIE 199
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1024-1141 9.37e-19

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 82.71  E-value: 9.37e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  1024 ESLETLGDSFLKYAASQQLFKTYKNHHEGLLSVKREKIISNAALCKLGCSSGLPGFIRNEPFDPHAW-TIPGDKPESLKL 1102
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDIRRRnNALGKGPKRADG 80

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 571476045  1103 EElvikgkkiyvhgkrklnrKIIADVVEALIGAFLSTGG 1141
Cdd:pfam00636   81 KE------------------KVLADAFEALIGALYLDGG 101
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 406-525 1.40e-15

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


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 73.78  E-value: 1.40e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   406 SKVCCLVDSLLEYRGltdMRCIIFVERIitaivlEDLLNTLLPKYNSWKTKFIAGynfglqNQSRTKQNEIVNEFRMGLV 485
Cdd:pfam00271    1 EKLEALLELLKKERG---GKVLIFSQTK------KTLEAELLLEKEGIKVARLHG------DLSQEEREEILEDFRKGKI 65

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 571476045   486 NIIVATSILEEGLDVQRCNLVIRFDPCPTVCSFIQSRGRA 525
Cdd:pfam00271   66 DVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 62-232 3.07e-15

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


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 74.97  E-value: 3.07e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045    62 RSYQLEALYKAIH-ENTIVYLETGSGKTLIAIMLLrsYAHQLRKPSPYIAVFLVPQVVLVSQQAEAVKR---HTDLKVGM 137
Cdd:pfam00270    1 TPIQAEAIPAILEgRDVLVQAPTGSGKTLAFLLPA--LEALDKLDNGPQALVLAPTRELAEQIYEELKKlgkGLGLKVAS 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   138 YWGdmGVDFWDAatwKQEMEKHEVLVMTPAILLSCLRHSfFKLNMINVLIMDECHhargkhpyaCIMTEFYHHQLKSGIS 217
Cdd:pfam00270   79 LLG--GDSRKEQ---LEKLKGPDILVGTPGRLLDLLQER-KLLKNLKLLVLDEAH---------RLLDMGFGPDLEEILR 143

                          170
                   ....*....|....*...
gi 571476045   218 DLP---RIFGMTASPIKS 232
Cdd:pfam00270  144 RLPkkrQILLLSATLPRN 161
HELICc smart00490
helicase superfamily c-terminal domain;
469-525 2.11e-12

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 64.16  E-value: 2.11e-12
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 571476045    469 SRTKQNEIVNEFRMGLVNIIVATSILEEGLDVQRCNLVIRFDPCPTVCSFIQSRGRA 525
Cdd:smart00490   22 SQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1022-1140 2.64e-12

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: 67.61  E-value: 2.64e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  1022 HYESLETLGDSFLKYAASQQLFKTYKNHHEGLLSVKREKIISNAALCKLGcssglpgfirnepfdphawtipgdkpESLK 1101
Cdd:TIGR02191   34 NNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVA--------------------------RELG 87

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 571476045  1102 LEELVIKGKKIYVHGKRKlNRKIIADVVEALIGA-FLSTG 1140
Cdd:TIGR02191   88 LGDFLLLGKGEEKSGGRR-RDSILADAFEALIGAiYLDSG 126
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
 857-980 5.01e-10

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: 58.74  E-value: 5.01e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   857 CTCKLQDALVCTSHPGGKiyFYITTGIMELH-GNSPMELRGGEVTTYKKYYEQHHGIQLQFENQWLLKarhhfkvknycH 935
Cdd:pfam02170   20 AKKALKGLKVYTTYNNPR--TYRIDGITFDPtPESTFPLKDGKEITVVDYFKKKYNIDLKYPDQPLLL-----------V 86

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 571476045   936 GQKQGKdgaskafVELPPELCSIVmspikDSIIYTFSFIPSIMHR 980
Cdd:pfam02170   87 GKKRPK-------VYLPPELCNLV-----DGQRYTKKLMPSIAQR 119
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1022-1140 2.24e-09

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 59.34  E-value: 2.24e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045 1022 HYESLETLGDSFLKYAASQQLFKTYKNHHEGLLSVKREKIISNAALCKLGCSSGLPGFIRnepfdphawtipgdkpeslk 1101
Cdd:COG0571    39 NNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAEIARELGLGDYLR-------------------- 98

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 571476045 1102 L---EELviKGkkiyvhGKRKLNrkIIADVVEALIGA-FLSTG 1140
Cdd:COG0571    99 LgkgEEK--SG------GRRRPS--ILADAFEALIGAiYLDGG 131
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
 889-980 1.53e-08

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: 54.60  E-value: 1.53e-08
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045    889 NSPMELRGGEVTTYKKYYEQHHGIQLQFENQWLLkarhhfKVKNYCHGQKQGKDGAskafVELPPELCSIVmsPIKDSII 968
Cdd:smart00949   53 KSTFEKSDGSEITFVEYYKQKYNITIRDPNQPLL------VSRPKRRRNQNGKGEP----VLLPPELCFIT--GLTDRMR 120

                            90
                    ....*....|..
gi 571476045    969 YTFSFIPSIMHR 980
Cdd:smart00949  121 KDFMLMKSIADR 132
DSRM smart00358
Double-stranded RNA binding motif;
1351-1417 9.33e-06

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 44.56  E-value: 9.33e-06
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 571476045   1351 PIRELNELCQKRSYKIVLEDVSRK--DGVTNYRMKVEADGVIHeYEYTGPALRDtAKKIACKEILNSLK 1417
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEEgpDHAPRFTVTVKVGGKRT-GEGEGSSKKE-AKQRAAEAALRSLK 67
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 427-527 4.94e-04

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 44.39  E-value: 4.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  427 IIFVERIITAivleDLLNTLLPKYNSWKTKFIAGynfglqNQSRTKQNEIVNEFRMGLVNIIVATSILEEGLDVQRCNLV 506
Cdd:PLN00206  371 VVFVSSRLGA----DLLANAITVVTGLKALSIHG------EKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQV 440

                          90       100
                  ....*....|....*....|..
gi 571476045  507 IRFDPCPTVCSFIQSRGRA-RM 527
Cdd:PLN00206  441 IIFDMPNTIKEYIHQIGRAsRM 462
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 1349-1416 6.10e-04

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380704  Cd Length: 67  Bit Score: 39.56  E-value: 6.10e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 571476045 1349 LHPIRELNELCQKRSYKIVLEDVSR-KDGVTNYRMKVEADGVIheyeyTGPALRDT---AKKIACKEILNSL 1416
Cdd:cd19875     1 KNPVSALNEYCQKRGLSLEFVDVSVgPDHCPGFTASATIDGIV-----FASATGTSkkeAKRAAAKLALKKL 67
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 1351-1416 1.14e-03

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


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 38.75  E-value: 1.14e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 571476045  1351 PIRELNELCQKRSYKIVLEDVSRKDGVTN--YRMKVEADGviHEYEYTGPALRDTAKKIACKEILNSL 1416
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSpkFTVTVKVDG--KLYGSGTGSSKKEAEQLAAEKALEKL 66
 
Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 61-259 1.55e-89

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: 288.78  E-value: 1.55e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   61 ARSYQLEALYKAIHENTIVYLETGSGKTLIAIMLLRSYAHQLRKPSPY--IAVFLVPQVVLVSQQAEAVKRHTDLKVGMY 138
Cdd:cd18034     3 PRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRKEKNPkkRAVFLVPTVPLVAQQAEAIRSHTDLKVGEY 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  139 WGDMGVDFWDAATWKQEMEKHEVLVMTPAILLSCLRHSFFKLNMINVLIMDECHHARGKHPYACIMTEFYHhqlKSGISD 218
Cdd:cd18034    83 SGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYH---LEGRTS 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 571476045  219 LPRIFGMTASPIKSKvgKSESSWSENIQKLMILMHSKVYTC 259
Cdd:cd18034   160 RPRILGLTASPVNGK--GDPKSVEKKIQQLEELLNSTIKTV 198
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 406-536 5.86e-50

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


Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 173.55  E-value: 5.86e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  406 SKVCCLVDSLLEYRGLT-DMRCIIFVERIITAIVLEDLLNTLLPKYNSWKTKFIAGYNFGLQNQ----SRTKQNEIVNEF 480
Cdd:cd18802     7 PKLQKLIEILREYFPKTpDFRGIIFVERRATAVVLSRLLKEHPSTLAFIRCGFLIGRGNSSQRKrslmTQRKQKETLDKF 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 571476045  481 RMGLVNIIVATSILEEGLDVQRCNLVIRFDPCPTVCSFIQSRGRARMRNSDYILMV 536
Cdd:cd18802    87 RDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1192-1347 2.91e-40

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


Pssm-ID: 238333  Cd Length: 133  Bit Score: 145.45  E-value: 2.91e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045 1192 SLLVEALTHGSYMLPEVPRCYQRLEFLGDSVLDYLITWHLYNEYPGMSPGQLTDMRAASVNNDCYAWSAIKHGLHKHVLH 1271
Cdd:cd00593     1 SLLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571476045 1272 ASQELHKHiavtlnnfdklsssstfgyesEASPPKVLGDIIESLAGAILVDSGFnkEVVWQSIRPLLEPLVTPETL 1347
Cdd:cd00593    81 GKGEEKSG---------------------GRLRPKILADVFEALIGAIYLDGGF--EAARKFLLRLLGPLIEEISL 133
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
61-560 3.07e-40

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 160.67  E-value: 3.07e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   61 ARSYQLEALYKAIHENTIVYLETGSGKTLIAIMLLRSYAHQLRKPspyiAVFLVPQVVLVSQQAEAVKRHT---DLKVGM 137
Cdd:COG1111     4 RRLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAERLHKKGGK----VLFLAPTKPLVEQHAEFFKEALnipEDEIVV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  138 YWGDMGVDFwDAATWkqemEKHEVLVMTPAILLSCLRHSFFKLNMINVLIMDECHHARGKHPYACImTEFYHHQLKSgis 217
Cdd:COG1111    80 FTGEVSPEK-RKELW----EKARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYI-AERYHEDAKD--- 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  218 dlPRIFGMTASPikskvGKSESSWSENIQKLMIlmhSKVytcvseAVITEFIPTSTPKFKFYSNNGIQFVLFEELASKLK 297
Cdd:COG1111   151 --PLILGMTASP-----GSDEEKIEEVCENLGI---ENV------EVRTEEDPDVAPYVHDTEVEWIRVELPEELKEIRD 214

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  298 MLKEQHEL---TLRSSDFTKSIAESAQKRitkifcslmfcldELgvwlaLKAAESLSSNEIESFSWGHSGDRVVKDFI-- 372
Cdd:COG1111   215 LLNEVLDDrlkKLKELGVIVSTSPDLSKK-------------DL-----LALQKKLQRRIREDDSEGYRAISILAEALkl 276

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  373 ------LE--GVHALKSYLQ------CDPQWSIGDN-IKSDVK----MGLL---------TSKVCCLVDSLLEYRGltDM 424
Cdd:COG1111   277 rhalelLEtqGVEALLRYLErleeeaRSSGGSKASKrLVSDPRfrkaMRLAeeadiehpkLSKLREILKEQLGTNP--DS 354

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  425 RCIIFVERIITAivlEDLLNTLlpKYNSWKT-KFIA-GYNFGLQNQSRTKQNEIVNEFRMGLVNIIVATSILEEGLDVQR 502
Cdd:COG1111   355 RIIVFTQYRDTA---EMIVEFL--SEPGIKAgRFVGqASKEGDKGLTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPE 429

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 571476045  503 CNLVIRFDPCPTVCSFIQSRGRArMRNSD---YILMVKSgdsvtcSRLEKYLASAdiMRKE 560
Cdd:COG1111   430 VDLVIFYEPVPSEIRSIQRKGRT-GRKREgrvVVLIAKG------TRDEAYYWSS--RRKE 481
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 61-260 3.42e-38

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: 142.19  E-value: 3.42e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   61 ARSYQLEALYKAIH-ENTIVYLETGSGKTLIAIMLLRSYAHQLRKPSPYIAVFLVPQVVLVSQQAEAVKRHTD---LKVG 136
Cdd:cd17927     3 PRNYQLELAQPALKgKNTIICLPTGSGKTFVAVLICEHHLKKFPAGRKGKVVFLANKVPLVEQQKEVFRKHFErpgYKVT 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  137 MYWGDMGVDFWdaatWKQEMEKHEVLVMTPAILLSCLRH-SFFKLNMINVLIMDECHHARGKHPYACIMTEFYHHQLKSG 215
Cdd:cd17927    83 GLSGDTSENVS----VEQIVESSDVIIVTPQILVNDLKSgTIVSLSDFSLLVFDECHNTTKNHPYNEIMFRYLDQKLGSS 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 571476045  216 IsDLPRIFGMTASPIKSKVGKSESSwSENIQKLMILMHSKVYTCV 260
Cdd:cd17927   159 G-PLPQILGLTASPGVGGAKNTEEA-LEHICKLCANLDISVIATV 201
RIBOc smart00535
Ribonuclease III family;
1192-1344 1.48e-33

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 126.18  E-value: 1.48e-33
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   1192 SLLVEALTHGSYMLPEvpRCYQRLEFLGDSVLDYLITWHLYNEYPGMSPGQLTDMRAASVNNDCYAWSAIKHGLHKHVLH 1271
Cdd:smart00535    1 SLLLRALTHASYSNEH--EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRL 78

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 571476045   1272 ASQELHKHiavtlnnfdklsssstfgyesEASPPKVLGDIIESLAGAILVDSGFnkEVVWQSIRPLLEPLVTP 1344
Cdd:smart00535   79 GRGEAISG---------------------GRDKPKILADVFEALIGAIYLDSGL--EAAREFIRDLLGPRLDE 128
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1180-1367 6.40e-32

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 124.83  E-value: 6.40e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045 1180 LESQLKYSFHDHSLLVEALTHGSYmLPEVPRC--YQRLEFLGDSVLDYLITWHLYNEYPGMSPGQLTDMRAASVNND-CY 1256
Cdd:COG0571     7 LEERLGYRFKDPELLEQALTHRSY-ANEHGGLenNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEEtLA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045 1257 AWsAIKHGLHKHVLHASQELhkhiavtlnnfdklsssSTFGYESEAsppkVLGDIIESLAGAILVDSGFnkEVVWQSIRP 1336
Cdd:COG0571    86 EI-ARELGLGDYLRLGKGEE-----------------KSGGRRRPS----ILADAFEALIGAIYLDGGL--EAARKFVLR 141

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 571476045 1337 LLEPLVTpETLKLHPIR----ELNELCQKR-----SYKIV 1367
Cdd:COG0571   142 LFEPRLE-EIAPGGAGKdyktALQEWLQARglplpEYEVV 180
PAZ_CAF_like cd02844
PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has ...
 849-962 6.06e-29

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: 112.90  E-value: 6.06e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  849 IETKSGLVCTCKLQDALVCTSHPGgkiYFYITTGIMELHGNSPMELR-GGEVTTYKKYYEQHHGIQLQFENQWLLKARHH 927
Cdd:cd02844    19 LHLADGSFCACDLKGSVVTAPHNG---RFYVISGILDLNANSSFPGKeGLGYATYAEYFKEKYGIVLNHPNQPLLKGKQI 95

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 571476045  928 FKVKNYCHGQKQGKDGASKA-----FVELPPELCSIVMSP 962
Cdd:cd02844    96 FNLHNLLHNRFEEKGESEEKekdryFVELPPELCSVIDLP 135
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1180-1367 1.46e-28

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: 114.99  E-value: 1.46e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  1180 LESQLKYSFHDHSLLVEALTHGSYM--LPEVPRCYQRLEFLGDSVLDYLITWHLYNEYPGMSPGQLTDMRAASVNNDCYA 1257
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYAneHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  1258 WSAIKHGLHKHVLHASQELhkhiavtlnnfdklsssSTFGYESeaspPKVLGDIIESLAGAILVDSGFnkEVVWQSIRPL 1337
Cdd:TIGR02191   81 EVARELGLGDFLLLGKGEE-----------------KSGGRRR----DSILADAFEALIGAIYLDSGL--EAARKFILKL 137

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 571476045  1338 LEPLVT---PETLKLHPIRELNELCQKR-----SYKIV 1367
Cdd:TIGR02191  138 LIPRIDaiiKEETLKDYKTALQEWAQARgkplpEYRLI 175
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1009-1151 1.99e-28

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: 111.55  E-value: 1.99e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045 1009 LEAITTKRCNEA---FHYESLETLGDSFLKYAASQQLFKTYKNHHEGLLSVKREKIISNAALCKLGCSSGLPGFIRNEPF 1085
Cdd:cd00593     4 LEALTHPSYANEhgrFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKG 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571476045 1086 DPHawtipgdkpeslkleelvikgkkiyvhGKRKLNRKIIADVVEALIGAFLSTGGEISALLFMDW 1151
Cdd:cd00593    84 EEK---------------------------SGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLR 122
PRK13766 PRK13766
Hef nuclease; Provisional
 53-560 3.16e-28

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 123.06  E-value: 3.16e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   53 IAPDVLPfARSYQLEALYKAIHENTIVYLETGSGKTLIAIMLLRSYAHQLRKPspyiAVFLVPQVVLVSQQAEAVKRHT- 131
Cdd:PRK13766    9 IKPNTIE-ARLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAERLHKKGGK----VLILAPTKPLVEQHAEFFRKFLn 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  132 --DLKVGMYWGDMG----VDFWDAATwkqemekheVLVMTPAILLSCLRHSFFKLNMINVLIMDECHHARGKHPYACImT 205
Cdd:PRK13766   84 ipEEKIVVFTGEVSpekrAELWEKAK---------VIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYVYI-A 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  206 EFYHHQLKSgisdlPRIFGMTASPikskvGKSESSWSENIQKLMIlmhSKVytcvseAVITEFIPTSTPKFKFYSNNGIQ 285
Cdd:PRK13766  154 ERYHEDAKN-----PLVLGLTASP-----GSDEEKIKEVCENLGI---EHV------EVRTEDDPDVKPYVHKVKIEWVR 214

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  286 FVLFEELASKLKMLKEQHEL---TLRSSDFTKSIAESAQKRitkifcslmfcldELgvwlaLKAAESLSSNEIESFSWGH 362
Cdd:PRK13766  215 VELPEELKEIRDLLNEALKDrlkKLKELGVIVSISPDVSKK-------------EL-----LGLQKKLQQEIANDDSEGY 276

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  363 SGDRVVKDFI--------LE--GVHALKSYLQ------CDPQWSIGD-NIKSDVKM----------GLL---TSKVCCLV 412
Cdd:PRK13766  277 EAISILAEAMklrhavelLEtqGVEALRRYLErlreeaRSSGGSKASkRLVEDPRFrkavrkakelDIEhpkLEKLREIV 356

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  413 DSLLEYRGltDMRCIIFVERIITAIVLEDLLNTllpkyNSWKT-KFI----AGYNFGLqnqSRTKQNEIVNEFRMGLVNI 487
Cdd:PRK13766  357 KEQLGKNP--DSRIIVFTQYRDTAEKIVDLLEK-----EGIKAvRFVgqasKDGDKGM---SQKEQIEILDKFRAGEFNV 426

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571476045  488 IVATSILEEGLDVQRCNLVIRFDPCPTVCSFIQSRGRArMRNSD---YILMVKSgdsvtcSRLEKYLASAdiMRKE 560
Cdd:PRK13766  427 LVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRT-GRQEEgrvVVLIAKG------TRDEAYYWSS--RRKE 493
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 62-248 6.59e-27

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: 109.87  E-value: 6.59e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   62 RSYQLEALYKAIH-ENTIVYLETGSGKTLIAIMLLRSYAHQLRKPS-PYIAVFLVPQVVLVSQQAEAVKRHTDlkvGMYW 139
Cdd:cd18036     4 RNYQLELVLPALRgKNTIICAPTGSGKTRVAVYICRHHLEKRRSAGeKGRVVVLVNKVPLVEQQLEKFFKYFR---KGYK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  140 -----GDMGVDfwdaATWKQEMEKHEVLVMTPAILLSCLR----HSFFKLNMINVLIMDECHHARGKHPYACIMTEFYHH 210
Cdd:cd18036    81 vtglsGDSSHK----VSFGQIVKASDVIICTPQILINNLLsgreEERVYLSDFSLLIFDECHHTQKEHPYNKIMRMYLDK 156

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 571476045  211 QLKSGIsDLPRIFGMTASPiKSKVGKSESSWSENIQKL 248
Cdd:cd18036   157 KLSSQG-PLPQILGLTASP-GVGGARSFEEALEHILKL 192
RIBOc smart00535
Ribonuclease III family;
1007-1156 1.29e-23

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 97.67  E-value: 1.29e-23
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   1007 KVLEAITTKRC-NEAFHYESLETLGDSFLKYAASQQLFKTYKNHHEGLLSVKREKIISNAALCKLGCSSGLPGFIRNEPF 1085
Cdd:smart00535    2 LLLRALTHASYsNEHEHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLGRG 81

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 571476045   1086 DPHAwtipgdkpeslkleelvikgkkiyvHGKRKlnRKIIADVVEALIGA-FLSTGGEISALLFMDWVGIKV 1156
Cdd:smart00535   82 EAIS-------------------------GGRDK--PKILADVFEALIGAiYLDSGLEAAREFIRDLLGPRL 126
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
 61-228 2.29e-23

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: 99.51  E-value: 2.29e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   61 ARSYQLEALYKAIH-ENTIVYLETGSGKTLIAIMLLRSYAHQLRKPSPYIAVFLVPQVVLVSQQAEAVKRH---TDLKVG 136
Cdd:cd18073     3 PRNYQLELALPAMKgKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFATKVPVYEQQKSVFSKYferHGYRVT 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  137 MYWGDMGvdfwDAATWKQEMEKHEVLVMTPAILLSCLRH-SFFKLNMINVLIMDECHHARGKHPYACIMTEFYHHQLKSG 215
Cdd:cd18073    83 GISGATA----ENVPVEQIIENNDIIILTPQILVNNLKKgTIPSLSIFTLMIFDECHNTSGNHPYNMIMFRYLDQKLGGS 158

                         170
                  ....*....|...
gi 571476045  216 ISDLPRIFGMTAS 228
Cdd:cd18073   159 SGPLPQIIGLTAS 171
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1213-1324 2.21e-22

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 93.11  E-value: 2.21e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  1213 QRLEFLGDSVLDYLITWHLYNEYPGMSPGQLTDMRAASVNNDCYAWSAIKHGLHKHVLHASQELHKHIAvTLNNFDKLSS 1292
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDIRRRNN-ALGKGPKRAD 79

                           90       100       110
                   ....*....|....*....|....*....|..
gi 571476045  1293 SSTfgyeseasppKVLGDIIESLAGAILVDSG 1324
Cdd:pfam00636   80 GKE----------KVLADAFEALIGALYLDGG 101
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 596-670 6.90e-20

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: 85.62  E-value: 6.90e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   596 SISLIYLYCSRLPADGYFKPAPRWD-------KETGTLYLPKSCPLQPI--CVEGNKKHLKNIACLEACKQLHKIGALTD 666
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEvteveggKFVCTVTLPINSPLRSIegPPWRSKKLAKRSAAFEACKALHKAGLLDD 80


                   ....
gi 571476045   667 NLVP 670
Cdd:pfam03368   81 HLLP 84
DEXDc smart00487
DEAD-like helicases superfamily;
62-270 1.04e-19

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 88.70  E-value: 1.04e-19
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045     62 RSYQLEALYKAIH--ENTIVYLETGSGKTLIAIMLLrsyAHQLRKPSPYIAVFLVPQVVLVSQQAEAVKR---HTDLKVG 136
Cdd:smart00487   10 RPYQKEAIEALLSglRDVILAAPTGSGKTLAALLPA---LEALKRGKGGRVLVLVPTRELAEQWAEELKKlgpSLGLKVV 86

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045    137 MYWGdmGVDFWDAATwKQEMEKHEVLVMTPAILLSCLRHSFFKLNMINVLIMDECHHARGKHpYACIMTEFYHHQLKSgi 216
Cdd:smart00487   87 GLYG--GDSKREQLR-KLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGG-FGDQLEKLLKLLPKN-- 160

                           170       180       190       200       210
                    ....*....|....*....|....*....|....*....|....*....|....
gi 571476045    217 sdlPRIFGMTASPikskvgksesswSENIQKLMILMHSKVYTCVSEAVITEFIP 270
Cdd:smart00487  161 ---VQLLLLSATP------------PEEIENLLELFLNDPVFIDVGFTPLEPIE 199
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
 62-229 5.97e-19

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: 86.22  E-value: 5.97e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   62 RSYQLEALYKAIHENTIVYLETGSGKTLIAIMLLRSYahqLR-KPSPYIaVFLVPQVVLVSQQAEAVKRHTdlkvGMYWG 140
Cdd:cd18033     4 RDYQFTIVQKALFQNTLVALPTGLGKTFIAAVVMLNY---YRwFPKGKI-VFMAPTKPLVSQQIEACYKIT----GIPSS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  141 DMGV--DFWDAATWKQEMEKHEVLVMTPAILLSCLRHSFFKLNMINVLIMDECHHARGKHPYACIMtefyHHQLKSGISd 218
Cdd:cd18033    76 QTAEltGSVPPTKRAELWASKRVFFLTPQTLENDLKEGDCDPKSIVCLVIDEAHRATGNYAYCQVV----RELMRYNSH- 150

                         170
                  ....*....|.
gi 571476045  219 lPRIFGMTASP 229
Cdd:cd18033   151 -FRILALTATP 160
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1024-1141 9.37e-19

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 82.71  E-value: 9.37e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  1024 ESLETLGDSFLKYAASQQLFKTYKNHHEGLLSVKREKIISNAALCKLGCSSGLPGFIRNEPFDPHAW-TIPGDKPESLKL 1102
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDIRRRnNALGKGPKRADG 80

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 571476045  1103 EElvikgkkiyvhgkrklnrKIIADVVEALIGAFLSTGG 1141
Cdd:pfam00636   81 KE------------------KVLADAFEALIGALYLDGG 101
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 406-525 1.40e-15

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


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 73.78  E-value: 1.40e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   406 SKVCCLVDSLLEYRGltdMRCIIFVERIitaivlEDLLNTLLPKYNSWKTKFIAGynfglqNQSRTKQNEIVNEFRMGLV 485
Cdd:pfam00271    1 EKLEALLELLKKERG---GKVLIFSQTK------KTLEAELLLEKEGIKVARLHG------DLSQEEREEILEDFRKGKI 65

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 571476045   486 NIIVATSILEEGLDVQRCNLVIRFDPCPTVCSFIQSRGRA 525
Cdd:pfam00271   66 DVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 74-227 2.04e-15

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: 74.75  E-value: 2.04e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   74 HENTIVYLETGSGKTLIAIMLLRSYAHQLRKPspyiAVFLVPQVVLVSQQAEAVKR--HTDLKVGMYWGDMgvdfwDAAT 151
Cdd:cd00046     1 GENVLITAPTGSGKTLAALLAALLLLLKKGKK----VLVLVPTKALALQTAERLRElfGPGIRVAVLVGGS-----SAEE 71

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 571476045  152 WKQEMEKHE-VLVMTPA-ILLSCLRHSFFKLNMINVLIMDECHHARGKHPYACIMTEfYHHQLKSGISdlpRIFGMTA 227
Cdd:cd00046    72 REKNKLGDAdIIIATPDmLLNLLLREDRLFLKDLKLIIVDEAHALLIDSRGALILDL-AVRKAGLKNA---QVILLSA 145
DEXHc_RLR-3 cd18075
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ...
 62-229 2.08e-15

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: 76.43  E-value: 2.08e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   62 RSYQLEALYKAIH-ENTIVYLETGSGKTLIAIMLLRSYAHQLRKPSpyiAVFLVPQVVLVSQQAEAVKRHTD--LKVGMY 138
Cdd:cd18075     4 HGYQWEVVAPALRgKNSIIWLPTGAGKTRAAVYVARRHLETKRGAK---VAVLVNKVHLVDQHLEKEFHVLLdkYTVTAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  139 WGDMGvdfwDAATWKQEMEKHEVLVMTPAILLSCL----RHSFFKLNMINVLIMDECHHARGKHPYACIMTEFYHHQLkS 214
Cdd:cd18075    81 SGDSS----HKCFFGQLARGSDVVICTAQILQNALlsgeEEAHVELTDFSLLVIDECHHTHKEAVYNKIMLSYLEKKL-S 155

                         170
                  ....*....|....*
gi 571476045  215 GISDLPRIFGMTASP 229
Cdd:cd18075   156 RQGDLPQILGLTASP 170
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 423-536 3.01e-15

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: 74.31  E-value: 3.01e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  423 DMRCIIFVERIITAivlEDLLNTLLPKYNSWK-TKFIAGYNF-GLQNQSRTKQNEIVNEFRMGLVNIIVATSILEEGLDV 500
Cdd:cd18801    30 DTRVIIFSEFRDSA---EEIVNFLSKIRPGIRaTRFIGQASGkSSKGMSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDI 106

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 571476045  501 QRCNLVIRFDPCPTVCSFIQSRGRARMRNSDYILMV 536
Cdd:cd18801   107 GEVDLIICYDASPSPIRMIQRMGRTGRKRQGRVVVL 142
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 62-232 3.07e-15

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


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 74.97  E-value: 3.07e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045    62 RSYQLEALYKAIH-ENTIVYLETGSGKTLIAIMLLrsYAHQLRKPSPYIAVFLVPQVVLVSQQAEAVKR---HTDLKVGM 137
Cdd:pfam00270    1 TPIQAEAIPAILEgRDVLVQAPTGSGKTLAFLLPA--LEALDKLDNGPQALVLAPTRELAEQIYEELKKlgkGLGLKVAS 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   138 YWGdmGVDFWDAatwKQEMEKHEVLVMTPAILLSCLRHSfFKLNMINVLIMDECHhargkhpyaCIMTEFYHHQLKSGIS 217
Cdd:pfam00270   79 LLG--GDSRKEQ---LEKLKGPDILVGTPGRLLDLLQER-KLLKNLKLLVLDEAH---------RLLDMGFGPDLEEILR 143

                          170
                   ....*....|....*...
gi 571476045   218 DLP---RIFGMTASPIKS 232
Cdd:pfam00270  144 RLPkkrQILLLSATLPRN 161
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 1192-1330 9.37e-15

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: 72.21  E-value: 9.37e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  1192 SLLVEALTHGSYMlPEVPRCYQRLEFLGDSVLDYLITWHLYnEYPGMSPGQLTDMRAASVNNDCYAWSAIKHGLHKHVLH 1271
Cdd:pfam14622    2 ELLLQALTHKSYA-NGRKPYNERLEFLGDAVLELSVSEYLF-KKPDLDEGGLTKLRASIVSEESLAEIAREIGLGKYLRL 79

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 571476045  1272 ASQELHkhiavtlnnfdklssSSTFGYESeasppkVLGDIIESLAGAILVDSGFN--KEVV 1330
Cdd:pfam14622   80 GKGEEE---------------TGGSGRES------ILADALEALIGAIYLDGGFEvaKEFI 119
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 61-229 2.03e-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: 72.93  E-value: 2.03e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   61 ARSYQLEALYKAIHENTIVYLETGSGKTLIAIMLLrsyAHQLRKPSPYIaVFLVPQVVLVSQQAEAVKR--HTDLKVGMY 138
Cdd:cd18035     3 RRLYQVLIAAVALNGNTLIVLPTGLGKTIIAILVA---ADRLTKKGGKV-LILAPSRPLVEQHAENLKRvlNIPDKITSL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  139 WGDMGVDfWDAATWKqemeKHEVLVMTPAILLSCLRHSFFKLNMINVLIMDECHHARGKHPYACIMTEFYHHqlksgiSD 218
Cdd:cd18035    79 TGEVKPE-ERAERWD----ASKIIVATPQVIENDLLAGRITLDDVSLLIFDEAHHAVGNYAYVYIAHRYKRE------AN 147

                         170
                  ....*....|.
gi 571476045  219 LPRIFGMTASP 229
Cdd:cd18035   148 NPLILGLTASP 158
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
3-229 2.06e-13

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 74.68  E-value: 2.06e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045    3 SSLSLSVYGGKKRKRESAQRSNSLVDqkgkETMEEAPSMEMDTDSQEDQNIAPDVLPfaRSYQLEALYKAI------HEN 76
Cdd:COG1061    29 SLLRNLVEARRLAIKEGTREDGRRLP----EEDTERELAEAEALEAGDEASGTSFEL--RPYQQEALEALLaalergGGR 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   77 TIVYLETGSGKTLIAIMLLRSYAHQLRkpspyiAVFLVPQVVLVSQQAEAVKRHTDLKvgmywgdmgvdfwDAATWKQEM 156
Cdd:COG1061   103 GLVVAPTGTGKTVLALALAAELLRGKR------VLVLVPRRELLEQWAEELRRFLGDP-------------LAGGGKKDS 163

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 571476045  157 EKHeVLVMTPAILLSCLRHSFFKlNMINVLIMDECHHARGKHpYACIMTEFyhhqlksgisDLPRIFGMTASP 229
Cdd:COG1061   164 DAP-ITVATYQSLARRAHLDELG-DRFGLVIIDEAHHAGAPS-YRRILEAF----------PAAYRLGLTATP 223
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 64-192 6.46e-13

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


Pssm-ID: 350679 [Multi-domain]  Cd Length: 181  Bit Score: 68.44  E-value: 6.46e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   64 YQLEALYKAIH--ENTIVYLETGSGKTLIA-IMLLRSYAHQLRKpspyiAVFLVPQVVLVSQQAEAVK---RHTDLKVGM 137
Cdd:cd17921     5 IQREALRALYLsgDSVLVSAPTSSGKTLIAeLAILRALATSGGK-----AVYIAPTRALVNQKEADLRerfGPLGKNVGL 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 571476045  138 YWGDMGVDfwdaatwKQEMEKHEVLVMTPAILLS-CLRHSFFKLNMINVLIMDECH 192
Cdd:cd17921    80 LTGDPSVN-------KLLLAEADILVATPEKLDLlLRNGGERLIQDVRLVVVDEAH 128
ResIII pfam04851
Type III restriction enzyme, res subunit;
62-230 7.56e-13

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 67.70  E-value: 7.56e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045    62 RSYQLEALYKAI------HENTIVYLETGSGKTLIAIMLLRSYAHQLRKPSpyiAVFLVPQVVLVSQQAEAVKRHTDLKV 135
Cdd:pfam04851    5 RPYQIEAIENLLesikngQKRGLIVMATGSGKTLTAAKLIARLFKKGPIKK---VLFLVPRKDLLEQALEEFKKFLPNYV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   136 gmywgdMGVDFWDAATWKQEMEKHEVLVMTPAILLSCLRHSF--FKLNMINVLIMDECHHARGKHpYACIMTEFyhhqlk 213
Cdd:pfam04851   82 ------EIGEIISGDKKDESVDDNKIVVTTIQSLYKALELASleLLPDFFDVIIIDEAHRSGASS-YRNILEYF------ 148

                          170
                   ....*....|....*..
gi 571476045   214 sgisDLPRIFGMTASPI 230
Cdd:pfam04851  149 ----KPAFLLGLTATPE 161
HELICc smart00490
helicase superfamily c-terminal domain;
469-525 2.11e-12

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 64.16  E-value: 2.11e-12
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 571476045    469 SRTKQNEIVNEFRMGLVNIIVATSILEEGLDVQRCNLVIRFDPCPTVCSFIQSRGRA 525
Cdd:smart00490   22 SQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1022-1140 2.64e-12

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: 67.61  E-value: 2.64e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  1022 HYESLETLGDSFLKYAASQQLFKTYKNHHEGLLSVKREKIISNAALCKLGcssglpgfirnepfdphawtipgdkpESLK 1101
Cdd:TIGR02191   34 NNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVA--------------------------RELG 87

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 571476045  1102 LEELVIKGKKIYVHGKRKlNRKIIADVVEALIGA-FLSTG 1140
Cdd:TIGR02191   88 LGDFLLLGKGEEKSGGRR-RDSILADAFEALIGAiYLDSG 126
DEXHc_RLR-2 cd18074
DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma ...
 62-248 2.27e-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: 64.88  E-value: 2.27e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   62 RSYQLEALYKAIH-ENTIVYLETGSGKTLIAIMLLRSYAHQLRKPS-PYIAVFLVPQVVLVSQQAEA-----VKRHtdLK 134
Cdd:cd18074     4 RDYQMEVAKPALEgKNIIICLPTGSGKTRVAVYITKDHLDKKRKASePGKVIVLVNKVPLVEQHYRKefnpfLKHW--YQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  135 VGMYWGDMGVDFwdaaTWKQEMEKHEVLVMTPAILLSCLRHSF------FKLNMINVLIMDECHHARGKHPYACIMTEFY 208
Cdd:cd18074    82 VIGLSGDSQLKI----SFPEVVKRYDVIICTAQILENSLLNATeeedegVQLSDFSLIIIDECHHTQKEAVYNNIMRRYL 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 571476045  209 HHQLKS--------GISDLPRIFGMTASPiksKVG--KSESSWSENIQKL 248
Cdd:cd18074   158 KQKIKNrkqkkenkPLIPLPQILGLTASP---GVGgaKNNKKAEEHILKI 204
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
 857-980 5.01e-10

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: 58.74  E-value: 5.01e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   857 CTCKLQDALVCTSHPGGKiyFYITTGIMELH-GNSPMELRGGEVTTYKKYYEQHHGIQLQFENQWLLKarhhfkvknycH 935
Cdd:pfam02170   20 AKKALKGLKVYTTYNNPR--TYRIDGITFDPtPESTFPLKDGKEITVVDYFKKKYNIDLKYPDQPLLL-----------V 86

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 571476045   936 GQKQGKdgaskafVELPPELCSIVmspikDSIIYTFSFIPSIMHR 980
Cdd:pfam02170   87 GKKRPK-------VYLPPELCNLV-----DGQRYTKKLMPSIAQR 119
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 407-527 5.03e-10

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: 58.67  E-value: 5.03e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  407 KVCCLVDSLLEyrGLTDMRCIIFVERIITAIVLEDLLntllpKYNSWKTKFIAGynfGLQNQSRTKqneIVNEFRMGLVN 486
Cdd:cd18787    13 KKLLLLLLLLE--KLKPGKAIIFVNTKKRVDRLAELL-----EELGIKVAALHG---DLSQEERER---ALKKFRSGKVR 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 571476045  487 IIVATSILEEGLDVQRCNLVIRFDPCPTVCSFIQsR-GR-ARM 527
Cdd:cd18787    80 VLVATDVAARGLDIPGVDHVINYDLPRDAEDYVH-RiGRtGRA 121
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 468-531 5.06e-10

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


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 56.94  E-value: 5.06e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 571476045  468 QSRTKQNEIVNEFrmglvNIIVATSILEEGLDVQRCNLVIRFDPCPTVCSFIQSRGRArMRNSD 531
Cdd:cd18785    11 NSIEHAEEIASSL-----EILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRA-GRGGK 68
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1022-1140 2.24e-09

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 59.34  E-value: 2.24e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045 1022 HYESLETLGDSFLKYAASQQLFKTYKNHHEGLLSVKREKIISNAALCKLGCSSGLPGFIRnepfdphawtipgdkpeslk 1101
Cdd:COG0571    39 NNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAEIARELGLGDYLR-------------------- 98

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 571476045 1102 L---EELviKGkkiyvhGKRKLNrkIIADVVEALIGA-FLSTG 1140
Cdd:COG0571    99 LgkgEEK--SG------GRRRPS--ILADAFEALIGAiYLDGG 131
PAZ cd02825
PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two ...
 851-959 2.85e-09

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: 56.31  E-value: 2.85e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  851 TKSGLVCTCKLQDALVCTSHPGGKIyFYITTGIMELHGNSPMELRGGEVTTYKKYYEQHHGIQLQFENQWLLKARHHFKv 930
Cdd:cd02825    23 DSPREEFTKELKGLKVEDTHNPLNR-VYRPDGETRLKAPSQLKHSDGKEITFADYFKERYNLTLTDLNQPLLIVKFSSK- 100

                          90       100
                  ....*....|....*....|....*....
gi 571476045  931 knychgqKQGKDgaskafvELPPELCSIV 959
Cdd:cd02825   101 -------KSYSI-------LLPPELCVIT 115
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 62-194 3.17e-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: 57.57  E-value: 3.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   62 RSYQLEALYK---AIHENT---IVYLETGSGKTLIAIMLLRSYAHQLRKPSpyiAVFLVPQVVLVSQQAEAVKRHT-DLK 134
Cdd:cd18032     2 RYYQQEAIEAleeAREKGQrraLLVMATGTGKTYTAAFLIKRLLEANRKKR---ILFLAHREELLEQAERSFKEVLpDGS 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 571476045  135 VGMYWGDmgvdfwdaatwKQEMEKHEVLV-----MTPAILLSCLRHSFFKLnminvLIMDECHHA 194
Cdd:cd18032    79 FGNLKGG-----------KKKPDDARVVFatvqtLNKRKRLEKFPPDYFDL-----IIIDEAHHA 127
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 62-229 5.78e-09

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: 56.16  E-value: 5.78e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   62 RSYQLEALYKAI-HENT---IVYLETGSGKTLIAIMLLRsYAHQLRkpspyiAVFLVPQVVLVSQQAEAVKRHTDLKVGM 137
Cdd:cd17926     2 RPYQEEALEAWLaHKNNrrgILVLPTGSGKTLTALALIA-YLKELR------TLIVVPTDALLDQWKERFEDFLGDSSIG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  138 YWGDMGVDFWDAAtwkqemekhEVLVMTPAILLSCLRHSFFKLNMINVLIMDECHHARGKHpYACIMTEFYHhqlksgis 217
Cdd:cd17926    75 LIGGGKKKDFDDA---------NVVVATYQSLSNLAEEEKDLFDQFGLLIVDEAHHLPAKT-FSEILKELNA-------- 136

                         170
                  ....*....|..
gi 571476045  218 dlPRIFGMTASP 229
Cdd:cd17926   137 --KYRLGLTATP 146
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
 65-192 1.13e-08

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: 56.19  E-value: 1.13e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   65 QLEALYKAIH--ENTIVYLETGSGKTLIAIMLLRSYAHQLRKpspyiAVFLVPQVVLVSQQAEAVKRHTD--LKVGMYWG 140
Cdd:cd18028     6 QAEAVRAGLLkgENLLISIPTASGKTLIAEMAMVNTLLEGGK-----ALYLVPLRALASEKYEEFKKLEEigLKVGISTG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 571476045  141 dmgvDFWDAATWkqeMEKHEVLVMTPAILLSCLRHSFFKLNMINVLIMDECH 192
Cdd:cd18028    81 ----DYDEDDEW---LGDYDIIVATYEKFDSLLRHSPSWLRDVGVVVVDEIH 125
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
 889-980 1.53e-08

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: 54.60  E-value: 1.53e-08
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045    889 NSPMELRGGEVTTYKKYYEQHHGIQLQFENQWLLkarhhfKVKNYCHGQKQGKDGAskafVELPPELCSIVmsPIKDSII 968
Cdd:smart00949   53 KSTFEKSDGSEITFVEYYKQKYNITIRDPNQPLL------VSRPKRRRNQNGKGEP----VLLPPELCFIT--GLTDRMR 120

                            90
                    ....*....|..
gi 571476045    969 YTFSFIPSIMHR 980
Cdd:smart00949  121 KDFMLMKSIADR 132
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
65-192 2.69e-07

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 54.90  E-value: 2.69e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   65 QLEALYKAI--HENTIVYLETGSGKTLIAIMLLRSYAhqlrkPSPYIAVFLVPQVVLVSQQAEAVKR---HTDLKVGMyw 139
Cdd:COG1204    27 QAEALEAGLleGKNLVVSAPTASGKTLIAELAILKAL-----LNGGKALYIVPLRALASEKYREFKRdfeELGIKVGV-- 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 571476045  140 gDMGVDFWDAAtwkqEMEKHEVLVMTPAILLSCLRHSFFKLNMINVLIMDECH 192
Cdd:COG1204   100 -STGDYDSDDE----WLGRYDILVATPEKLDSLLRNGPSWLRDVDLVVVDEAH 147
DEADc_DDX47 cd17954
DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can ...
 65-190 6.11e-06

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: 48.47  E-value: 6.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   65 QLEALYKAIHENTIVYL-ETGSGKTL-IAIMLLRsyaHQLRKPSPYIAVFLVPQVVL---VSQQAEAVKRHTDLKVGMYW 139
Cdd:cd17954    27 QEEAIPVALQGRDIIGLaETGSGKTAaFALPILQ---ALLENPQRFFALVLAPTRELaqqISEQFEALGSSIGLKSAVLV 103

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 571476045  140 GdmGVDFWDAAtwKQEMEKHEVLVMTPAILLSCLRHSF-FKLNMINVLIMDE 190
Cdd:cd17954   104 G--GMDMMAQA--IALAKKPHVIVATPGRLVDHLENTKgFSLKSLKFLVMDE 151
DSRM smart00358
Double-stranded RNA binding motif;
1351-1417 9.33e-06

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 44.56  E-value: 9.33e-06
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 571476045   1351 PIRELNELCQKRSYKIVLEDVSRK--DGVTNYRMKVEADGVIHeYEYTGPALRDtAKKIACKEILNSLK 1417
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEEgpDHAPRFTVTVKVGGKRT-GEGEGSSKKE-AKQRAAEAALRSLK 67
DEADc cd00268
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...
 82-191 1.11e-05

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: 47.82  E-value: 1.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   82 ETGSGKTL-----IAIMLLRSYAHQLRKPspyIAVFLVP------QVvlvSQQAEAVKRHTDLKVGMYWGdmGVDFWDaa 150
Cdd:cd00268    35 QTGSGKTLafllpILEKLLPEPKKKGRGP---QALVLAPtrelamQI---AEVARKLGKGTGLKVAAIYG--GAPIKK-- 104

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 571476045  151 twKQEMEKH--EVLVMTPAILLSCLRHSFFKLNMINVLIMDEC 191
Cdd:cd00268   105 --QIEALKKgpDIVVGTPGRLLDLIERGKLDLSNVKYLVLDEA 145
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 450-511 2.81e-05

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


Pssm-ID: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 45.80  E-value: 2.81e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 571476045  450 YNSWKTKFIAGYNFGLQNqSRTKQNE---IVNEFRMGLVNIIVATSILEEGLDVQRCNLVIRFDP 511
Cdd:cd18811    51 YEYLKERFRPELNVGLLH-GRLKSDEkdaVMAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDA 114
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 1022-1142 3.20e-05

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: 44.86  E-value: 3.20e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  1022 HYESLETLGDSFLKYAASQQLFKtYKNHHEGLLSVKREKIISNAALCKLGCSSGLPGFIRnepfdphaWtipGDKPESLK 1101
Cdd:pfam14622   20 YNERLEFLGDAVLELSVSEYLFK-KPDLDEGGLTKLRASIVSEESLAEIAREIGLGKYLR--------L---GKGEEETG 87

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 571476045  1102 leelvikgkkiyvhGKRklNRKIIADVVEALIGA-FLSTGGE 1142
Cdd:pfam14622   88 --------------GSG--RESILADALEALIGAiYLDGGFE 113
PRK00254 PRK00254
ski2-like helicase; Provisional
 65-192 1.69e-04

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 45.96  E-value: 1.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   65 QLEALYKAIHE--NTIVYLETGSGKTLIA-IMLLRSYAHQLRKpspyiAVFLVPQVVLVSQQAEAVK--RHTDLKVGMYW 139
Cdd:PRK00254   28 QAEALKSGVLEgkNLVLAIPTASGKTLVAeIVMVNKLLREGGK-----AVYLVPLKALAEEKYREFKdwEKLGLRVAMTT 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 571476045  140 GDM-GVDFWdaatwkqeMEKHEVLVMTPAILLSCLRHSFFKLNMINVLIMDECH 192
Cdd:PRK00254  103 GDYdSTDEW--------LGKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIH 148
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
 49-190 2.14e-04

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 45.67  E-value: 2.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   49 EDQNIAPDVL--------PFARSYQLEAL-YKAIHENTIVYLETGSGKTliAIMLLRSYAHQLRKPSP---YI----AVF 112
Cdd:PRK01297   90 HDFNLAPELMhaihdlgfPYCTPIQAQVLgYTLAGHDAIGRAQTGTGKT--AAFLISIINQLLQTPPPkerYMgeprALI 167

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  113 LVPQ---VVLVSQQAEAVKRHTDLKVGMYWGdmGVDFwdAATWKQEMEKH-EVLVMTPAILLSCLRHSFFKLNMINVLIM 188
Cdd:PRK01297  168 IAPTrelVVQIAKDAAALTKYTGLNVMTFVG--GMDF--DKQLKQLEARFcDILVATPGRLLDFNQRGEVHLDMVEVMVL 243


                  ..
gi 571476045  189 DE 190
Cdd:PRK01297  244 DE 245
DEADc_DDX51 cd17956
DEAD-box helicase domain of DEAD box protein 51; DDX51 aids cell cancer proliferation by ...
 83-190 2.92e-04

DEAD-box helicase domain of DEAD box protein 51; DDX51 aids cell cancer proliferation by regulating multiple signalling pathways. Mammalian DEAD box protein Ddx51 acts in 3' end maturation of 28S rRNA by promoting the release of U8 snoRNA.It 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: 350714 [Multi-domain]  Cd Length: 231  Bit Score: 44.16  E-value: 2.92e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   83 TGSGKTL---IAI--MLLRSYAHQLRkpspyiAVFLVPQVVLVSQ---QAEAVKRHTDLKVGMYWGDMgvDFWDAATWKQ 154
Cdd:cd17956    45 TGSGKTLayvLPIvqALSKRVVPRLR------ALIVVPTKELVQQvykVFESLCKGTGLKVVSLSGQK--SFKKEQKLLL 116

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 571476045  155 EMEKHE------VLVMTPAILLSCLRH-SFFKLNMINVLIMDE 190
Cdd:cd17956   117 VDTSGRylsrvdILVATPGRLVDHLNStPGFTLKHLRFLVIDE 159
DEADc_DDX27 cd17947
DEAD-box helicase domain of DEAD box protein 27; DDX27 (also called RHLP, deficiency of ...
 82-191 3.15e-04

DEAD-box helicase domain of DEAD box protein 27; DDX27 (also called RHLP, deficiency of ribosomal subunits protein 1 homolog, and probable ATP-dependent RNA helicase DDX27) is involved in the processing of 5.8S and 28S ribosomal RNAs. More specifically, the encoded protein localizes to the nucleolus, where it interacts with the PeBoW complex to ensure proper 3' end formation of 47S rRNA. DDX27 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: 350705 [Multi-domain]  Cd Length: 196  Bit Score: 43.40  E-value: 3.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   82 ETGSGKTliAIMLLRSYAHQLRKPS--PYI-AVFLVP------QVVLVSQQaeaVKRHTDLKVGMYWGDMGVDfwdaatw 152
Cdd:cd17947    35 VTGSGKT--AAFLLPILERLLYRPKkkAATrVLVLVPtrelamQCFSVLQQ---LAQFTDITFALAVGGLSLK------- 102

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 571476045  153 KQEME---KHEVLVMTPAILLSCLRHSF-FKLNMINVLIMDEC 191
Cdd:cd17947   103 AQEAAlraRPDIVIATPGRLIDHLRNSPsFDLDSIEILVLDEA 145
PAZ_piwi_like cd02845
PAZ domain, Piwi_like subfamily. In multi-cellular organisms, the Piwi protein appears to be ...
 889-956 3.90e-04

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


Pssm-ID: 239211  Cd Length: 117  Bit Score: 41.48  E-value: 3.90e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 571476045  889 NSPMELRGGEVTTYKKYYEQHHGIQLQFENQWLLKARhhfkvknychGQKQGKDGASKAFVELPPELC 956
Cdd:cd02845    54 LSTFKKSDGTEITFVEYYKKQYNIEITDLNQPLLVSR----------PKRRDPRGGEKEPIYLIPELC 111
DEADc_DDX28 cd17948
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ...
 64-190 4.12e-04

DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box polypeptide 28) plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function. DDX28 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: 350706 [Multi-domain]  Cd Length: 231  Bit Score: 43.51  E-value: 4.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   64 YQLEALYKAIH-ENTIVYLETGSGKTL------IAIMLLRSYAHQLRKPSPyIAVFLVPQVVLVSQ---QAEAVKRHTDL 133
Cdd:cd17948    16 VQKQGIPSILRgRNTLCAAETGSGKTLtyllpiIQRLLRYKLLAEGPFNAP-RGLVITPSRELAEQigsVAQSLTEGLGL 94

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 571476045  134 KVGMYWGDMGVdfwdAATWKQEMEKHEVLVMTPAILLSCLRHSFFKLNMINVLIMDE 190
Cdd:cd17948    95 KVKVITGGRTK----RQIRNPHFEEVDILVATPGALSKLLTSRIYSLEQLRHLVLDE 147
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
 425-536 4.88e-04

C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350184 [Multi-domain]  Cd Length: 146  Bit Score: 41.86  E-value: 4.88e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  425 RCIIFVE-RIITAIVLEDLLNtLLPKYNSWKTKfIAGYNFGLQNQSRtkqNEIVNEFRMGLVNIIVATSILEEGLDVQRC 503
Cdd:cd18797    37 KTIVFCRsRKLAELLLRYLKA-RLVEEGPLASK-VASYRAGYLAEDR---REIEAELFNGELLGVVATNALELGIDIGGL 111

                          90       100       110
                  ....*....|....*....|....*....|....
gi 571476045  504 NLVIRFDPCPTVCSFIQSRGRA-RMRNSDYILMV 536
Cdd:cd18797   112 DAVVLAGYPGSLASLWQQAGRAgRRGKDSLVILV 145
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 427-527 4.94e-04

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 44.39  E-value: 4.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  427 IIFVERIITAivleDLLNTLLPKYNSWKTKFIAGynfglqNQSRTKQNEIVNEFRMGLVNIIVATSILEEGLDVQRCNLV 506
Cdd:PLN00206  371 VVFVSSRLGA----DLLANAITVVTGLKALSIHG------EKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQV 440

                          90       100
                  ....*....|....*....|..
gi 571476045  507 IRFDPCPTVCSFIQSRGRA-RM 527
Cdd:PLN00206  441 IIFDMPNTIKEYIHQIGRAsRM 462
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 1349-1416 6.10e-04

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380704  Cd Length: 67  Bit Score: 39.56  E-value: 6.10e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 571476045 1349 LHPIRELNELCQKRSYKIVLEDVSR-KDGVTNYRMKVEADGVIheyeyTGPALRDT---AKKIACKEILNSL 1416
Cdd:cd19875     1 KNPVSALNEYCQKRGLSLEFVDVSVgPDHCPGFTASATIDGIV-----FASATGTSkkeAKRAAAKLALKKL 67
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 1351-1416 1.14e-03

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


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 38.75  E-value: 1.14e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 571476045  1351 PIRELNELCQKRSYKIVLEDVSRKDGVTN--YRMKVEADGviHEYEYTGPALRDTAKKIACKEILNSL 1416
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSpkFTVTVKVDG--KLYGSGTGSSKKEAEQLAAEKALEKL 66
DEXHc_Hrq1-like cd17923
DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a ...
 63-196 1.93e-03

DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. Hrq1 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: 350681 [Multi-domain]  Cd Length: 182  Bit Score: 41.03  E-value: 1.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   63 SYQLEAlYKAIH--ENTIVYLETGSGKTL---IAIMllrsyAHQLRKPSPYiAVFLVPQVVLVSQQAEAVKR-----HTD 132
Cdd:cd17923     3 SHQAEA-IEAARagRSVVVTTGTASGKSLcyqLPIL-----EALLRDPGSR-ALYLYPTKALAQDQLRSLRElleqlGLG 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 571476045  133 LKVGMYWGDMGVdfwDAATWKQEMEKHeVLVMTPAIL-LSCLRHSFFK---LNMINVLIMDECHHARG 196
Cdd:cd17923    76 IRVATYDGDTPR---EERRAIIRNPPR-ILLTNPDMLhYALLPHHDRWarfLRNLRYVVLDEAHTYRG 139
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
45-192 2.69e-03

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


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 42.23  E-value: 2.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   45 TDSQEDQNIAPDvlPFarsyQLEALyKAIHE--NTIVYLETGSGKTLIAImllrsYAHQL-----RKpspyiAVFLVPQV 117
Cdd:COG4581    16 ADFAEERGFELD--PF----QEEAI-LALEAgrSVLVAAPTGSGKTLVAE-----FAIFLalargRR-----SFYTAPIK 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571476045  118 VLVSQQ-AEAVKRHTDLKVGMYWGDMGVDFwDAAtwkqemekheVLVMTPAILLSCLRHSFFKLNMINVLIMDECH 192
Cdd:COG4581    79 ALSNQKfFDLVERFGAENVGLLTGDASVNP-DAP----------IVVMTTEILRNMLYREGADLEDVGVVVMDEFH 143
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
83-190 3.10e-03

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 41.67  E-value: 3.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   83 TGSGKT---LIAIM--LLRSYAHQLRkpspyiAVFLVP------QvvlVSQQAEAVKRHTDLKVGMYWGdmGVDFwdaat 151
Cdd:COG0513    48 TGTGKTaafLLPLLqrLDPSRPRAPQ------ALILAPtrelalQ---VAEELRKLAKYLGLRVATVYG--GVSI----- 111

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 571476045  152 wKQEME--KH--EVLVMTPAILLSCLRHSFFKLNMINVLIMDE 190
Cdd:COG0513   112 -GRQIRalKRgvDIVVATPGRLLDLIERGALDLSGVETLVLDE 153
DEADc_DDX52 cd17957
DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ...
 83-190 3.33e-03

DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ubiquitously expressed in testis, endometrium, and other tissues in humans. DDX52 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350715 [Multi-domain]  Cd Length: 198  Bit Score: 40.27  E-value: 3.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   83 TGSGKTL-IAI-MLLRSYAHqlRKPSPYIAVFLVPQVVLVSQ-QAEAVK--RHTDLKVGMYWGDMGVDFWDAATWKQeme 157
Cdd:cd17957    36 TGSGKTLaFLIpILQKLGKP--RKKKGLRALILAPTRELASQiYRELLKlsKGTGLRIVLLSKSLEAKAKDGPKSIT--- 110

                          90       100       110
                  ....*....|....*....|....*....|...
gi 571476045  158 KHEVLVMTPAILLSCLRHSFFKLNMINVLIMDE 190
Cdd:cd17957   111 KYDILVSTPLRLVFLLKQGPIDLSSVEYLVLDE 143
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 471-510 4.03e-03

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 41.47  E-value: 4.03e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 571476045  471 TKQNEIVNEFRMGLVNIIVATSILEEGLDVQRCNLVIRFD 510
Cdd:PRK11192  282 AKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFD 321
DEXHc_cas3 cd17930
DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase ...
 75-192 4.22e-03

DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase responsible for degradation of dsDNA. The two enzymatic units of Cas3, a histidine-aspartate (HD) nuclease and a Superfamily 2 (SF2) helicase, may be expressed from separate genes as Cas3' (SF2 helicase) and Cas3'' (HD nuclease) or may be fused as a single HD-SF2 polypeptide. The nucleolytic activity of most Cas3 enzymes is transition metal ion-dependent. Cas3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350688 [Multi-domain]  Cd Length: 186  Bit Score: 39.97  E-value: 4.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   75 ENTIVYLETGSGKTLIAIM--LLRSYAHQLRKpspyiAVFLVPQVVLVSQQAEAVK-----RHTDLKVG----------M 137
Cdd:cd17930     2 GLVILEAPTGSGKTEAALLwaLKLAARGGKRR-----IIYALPTRATINQMYERIReilgrLDDEDKVLllhskaalelL 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 571476045  138 YWGDMGVDFWDAATWKQEMEKH----EVLVMTP-AILLSCL--RHSFFKL-NMIN-VLIMDECH 192
Cdd:cd17930    77 ESDEEPDDDPVEAVDWALLLKRswlaPIVVTTIdQLLESLLkyKHFERRLhGLANsVVVLDEVQ 140
DEXHc_CHD1_2 cd17993
DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and ...
 62-141 4.43e-03

DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and similar proteins; Chromodomain-helicase-DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin-remodeling factor which functions as the substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. It is not only involved in transcription-related chromatin-remodeling, but is also required to maintain a specific chromatin configuration across the genome. CHD1 is also associated with histone deacetylase (HDAC) activity. Chromodomain-helicase-DNA-binding protein 2 (CHD2) is a DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. It is involved in myogenesis via interaction with MYOD1; it binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression. Both 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: 350751 [Multi-domain]  Cd Length: 218  Bit Score: 40.42  E-value: 4.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   62 RSYQLEALYKAIH-----ENTIVYLETGSGKTLIAIMLLRSYAHQLRKPSPYIAVflVPQVVLVSQQAEAVKRHTDLKVG 136
Cdd:cd17993     3 RDYQLTGLNWLAHswckgNNGILADEMGLGKTVQTISFLSYLFHSQQQYGPFLVV--VPLSTMPAWQREFAKWAPDMNVI 80


                  ....*
gi 571476045  137 MYWGD 141
Cdd:cd17993    81 VYLGD 85
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 411-525 4.64e-03

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. 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: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 39.00  E-value: 4.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045  411 LVDSLLEYRGLTDMRCIIFVERIITAIVLEDLLntllpKYNSWKTKFIAGynfglqNQSRTKQNEIVNEFR---MGLVnI 487
Cdd:cd18793    15 ALLELLEELREPGEKVLIFSQFTDTLDILEEAL-----RERGIKYLRLDG------STSSKERQKLVDRFNedpDIRV-F 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 571476045  488 IVATSILEEGLDVQRCNLVIRFDPC--PTVcsFIQSRGRA 525
Cdd:cd18793    83 LLSTKAGGVGLNLTAANRVILYDPWwnPAV--EEQAIDRA 120
DEXHc_priA cd17929
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ...
 66-192 7.33e-03

DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA 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: 350687 [Multi-domain]  Cd Length: 178  Bit Score: 39.11  E-value: 7.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571476045   66 LEALYKAIHENTIVYLE--TGSGKTLIAIMLLRSYAHQLRKpspyiAVFLVPQVVLVSQQAEAVKRHTDLKVGMYWGDMG 143
Cdd:cd17929     5 YEAIVSSLGGFKTFLLHgvTGSGKTEVYIELIEKVLAKGKQ-----VLVLVPEISLTPQLIKRFKKRFGDKVAVLHSKLS 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 571476045  144 vDFWDAATWKQemekheVLVMTPAILL---SCLRHSFFKLNMInvlIMDECH 192
Cdd:cd17929    80 -DKERADEWRK------IKRGEAKVVIgarSALFAPFKNLGLI---IVDEEH 121
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 472-531 7.62e-03

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: 38.77  E-value: 7.62e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 571476045  472 KQNEIVNEFRMGLVNIIVATSILEEGLDVQRCNLVIRFDP-----CPTVCSFIQSRGRArMRNSD 531
Cdd:cd18790    65 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDAdkegfLRSETSLIQTIGRA-ARNVN 128
PTZ00424 PTZ00424
helicase 45; Provisional
 476-550 7.76e-03

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 40.58  E-value: 7.76e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571476045  476 IVNEFRMGLVNIIVATSILEEGLDVQRCNLVIRFDPCPTVCSFIQSRGRA-RM-RNSDYILMVKSGDSVTCSRLEKY 550
Cdd:PTZ00424  309 IMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSgRFgRKGVAINFVTPDDIEQLKEIERH 385
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 475-511 9.46e-03

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: 38.40  E-value: 9.46e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 571476045  475 EIVNEFRMGLVNIIVATSILEEGLDVQRCNLVIRFDP 511
Cdd:cd18792    77 AVMLEFREGEYDILVSTTVIEVGIDVPNANTMIIEDA 113
uvsW PHA02558
UvsW helicase; Provisional
 62-122 9.50e-03

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 40.38  E-value: 9.50e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 571476045   62 RSYQLEALYKAIHENTIVY-LETGSGKTLIAIMLLRSYAhQLRKPSPYIavfLVPQVVLVSQ 122
Cdd:PHA02558  116 HWYQYDAVYEGLKNNRRLLnLPTSAGKSLIQYLLSRYYL-ENYEGKVLI---IVPTTSLVTQ 173
 
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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