NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|302318908|ref|NP_001180543|]
View 

dicer-2 [Bombyx mori]

Protein Classification

DEXHc_dicer and RIBOc domain-containing protein( domain architecture ID 13030105)

protein containing domains DEXHc_dicer, P-loop containing Nucleoside Triphosphate Hydrolases, Dicer_dimer, and RIBOc

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 13-212 2.32e-76

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: 251.80  E-value: 2.32e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   13 KARPYQAILEEIASSKNTIIHLPTGSGKTFIAQRLIKKFRNQLKKPwGEGGKRSFFLVNTVPLVNQQKNVIEMMCPVDgV 92
Cdd:cd18034     2 TPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRKE-KNPKKRAVFLVPTVPLVAQQAEAIRSHTDLK-V 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   93 GAYSSEDGVDYWKKADWDSELARNQVIVMTSQILSDMLTHAYIRIEDINLIIFDECHHAVEDHPMRVIMKHFLNCKAHE- 171
Cdd:cd18034    80 GEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLEGRTs 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 302318908  172 QPRVLGLTATLLNGNVSISKIEETLKQLENTFHATIATVDD 212
Cdd:cd18034   160 RPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
MPH1 super family cl34113
ERCC4-related helicase [Replication, recombination and repair];
14-521 1.84e-45

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


The actual alignment was detected with superfamily member COG1111:

Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 176.84  E-value: 1.84e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   14 ARPYQAILEEIASSKNTIIHLPTGSGKTFIAQRLIKKFrnqLKKPwgegGKRSFFLVNTVPLVNQQKNVIE--MMCPVDG 91
Cdd:COG1111     4 RRLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAER---LHKK----GGKVLFLAPTKPLVEQHAEFFKeaLNIPEDE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   92 VGAYSSEDGVDYwKKADWDSelarNQVIVMTSQILSDMLTHAYIRIEDINLIIFDECHHAVEDHPMRVIMKHFLNCKAHe 171
Cdd:COG1111    77 IVVFTGEVSPEK-RKELWEK----ARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKD- 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  172 qPRVLGLTATLlnGNvSISKIEETLKQLEntfhatIATVddlgEVMTYS-------TNPQEfIQYFRKPqMSEAAKEAIS 244
Cdd:COG1111   151 -PLILGMTASP--GS-DEEKIEEVCENLG------IENV----EVRTEEdpdvapyVHDTE-VEWIRVE-LPEELKEIRD 214

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  245 LLN--------TLQNLVMSVKLPVSLPSKD---FKKTpCQRDISNDPNKIVKAVKNLIVGM----ITNLEEmglyggSLG 309
Cdd:COG1111   215 LLNevlddrlkKLKELGVIVSTSPDLSKKDllaLQKK-LQRRIREDDSEGYRAISILAEALklrhALELLE------TQG 287

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  310 ILAYIVLLERLKRKASTKEEnllystvithSTEARMILLD-----AMENETGYDkiIKHSseKILQLIDLLKEYnplILE 384
Cdd:COG1111   288 VEALLRYLERLEEEARSSGG----------SKASKRLVSDprfrkAMRLAEEAD--IEHP--KLSKLREILKEQ---LGT 350

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  385 KPGEllKVnhsrkplcgIIFTKQRFTSKILYnilmdlkkarpdefEFLKHDfvvGFSINPF--KSTREEHY-LKKSSQKA 461
Cdd:COG1111   351 NPDS--RI---------IVFTQYRDTAEMIV--------------EFLSEP---GIKAGRFvgQASKEGDKgLTQKEQIE 402

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 302318908  462 ILG-FNNGDLNCLISTSVIEEGLDIPQCALVVRYDA-PTEYRSyIQSKGR-ARSSEASFVILV 521
Cdd:COG1111   403 ILErFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPvPSEIRS-IQRKGRtGRKREGRVVVLI 464
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1440-1605 1.34e-38

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


:

Pssm-ID: 238333  Cd Length: 133  Bit Score: 140.83  E-value: 1.34e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908 1440 LLNALSHSSYIRNRLTSSYERLEFLGDAIIDFLVTSHIFENCRELKPGEMTDLRSALVNNVTFAAYTVKLGLHKYLcsel 1519
Cdd:cd00593     3 LLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYL---- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908 1520 npslekaimkFVEHQIERNHEiefdvlllisevdcqvaeyVDVPKVLSDIFEALVGAVYLDSGgnLETVWSVLYKIMHVE 1599
Cdd:cd00593    79 ----------RLGKGEEKSGG-------------------RLRPKILADVFEALIGAIYLDGG--FEAARKFLLRLLGPL 127


                  ....*.
gi 302318908 1600 IDSFSK 1605
Cdd:cd00593   128 IEEISL 133
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 587-673 2.74e-27

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: 106.81  E-value: 2.74e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   587 AISLLSRYCSILPHDQFTTITPVWLQEVVENGaKKQVTVILPIGSPVkEEIKGDPYSNTKTAKRSAALKACIKLHELGEL 666
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGG-KFVCTVTLPINSPL-RSIEGPPWRSKKLAKRSAAFEACKALHKAGLL 78


                   ....*....
gi 302318908   667 --HpltLLP 673
Cdd:pfam03368   79 ddH---LLP 84
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1192-1384 2.94e-17

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


:

Pssm-ID: 238333  Cd Length: 133  Bit Score: 79.96  E-value: 2.94e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908 1192 LAALTT---INSNDTFDLERPETLGDSFLKFAASLYLHHKFPNMNEGQLTNIKGKLISNRNLYYAGAKFNLGGRMKVEQF 1268
Cdd:cd00593     4 LEALTHpsyANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908 1269 SPRSdflvpgffappkleefieQRQIRPtfligiqfteeevmtgelseeswesvmnnfqngiaeaepegcaqnsmqcyvh 1348
Cdd:cd00593    84 EEKS------------------GGRLRP---------------------------------------------------- 93

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 302318908 1349 sqavadKSIADSVEALIGTYLLSGGILAAVKLLEWM 1384
Cdd:cd00593    94 ------KILADVFEALIGAIYLDGGFEAARKFLLRL 123
PAZ super family cl00301
PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two ...
 851-961 4.24e-17

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


The actual alignment was detected with superfamily member cd02843:

Pssm-ID: 469713  Cd Length: 122  Bit Score: 79.03  E-value: 4.24e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  851 IDWATMQTHHTVPPV--AAPSVEERKSLVVTEENYTNCIVTPWYRGTILPERYVVTKVLEYMTPKSQFDADCYESYANYY 928
Cdd:cd02843     7 IDWEFMEKIEANARIgpRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEYETFEEYY 86

                          90       100       110
                  ....*....|....*....|....*....|...
gi 302318908  929 ANNYNLDIlGSESQPLLEVRNISTRMNCLLPRA 961
Cdd:cd02843    87 KKKYKLDI-QNLNQPLLDVDHTSTRLNLLTPRY 118
 
Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 13-212 2.32e-76

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: 251.80  E-value: 2.32e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   13 KARPYQAILEEIASSKNTIIHLPTGSGKTFIAQRLIKKFRNQLKKPwGEGGKRSFFLVNTVPLVNQQKNVIEMMCPVDgV 92
Cdd:cd18034     2 TPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRKE-KNPKKRAVFLVPTVPLVAQQAEAIRSHTDLK-V 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   93 GAYSSEDGVDYWKKADWDSELARNQVIVMTSQILSDMLTHAYIRIEDINLIIFDECHHAVEDHPMRVIMKHFLNCKAHE- 171
Cdd:cd18034    80 GEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLEGRTs 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 302318908  172 QPRVLGLTATLLNGNVSISKIEETLKQLENTFHATIATVDD 212
Cdd:cd18034   160 RPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
14-521 1.84e-45

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 176.84  E-value: 1.84e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   14 ARPYQAILEEIASSKNTIIHLPTGSGKTFIAQRLIKKFrnqLKKPwgegGKRSFFLVNTVPLVNQQKNVIE--MMCPVDG 91
Cdd:COG1111     4 RRLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAER---LHKK----GGKVLFLAPTKPLVEQHAEFFKeaLNIPEDE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   92 VGAYSSEDGVDYwKKADWDSelarNQVIVMTSQILSDMLTHAYIRIEDINLIIFDECHHAVEDHPMRVIMKHFLNCKAHe 171
Cdd:COG1111    77 IVVFTGEVSPEK-RKELWEK----ARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKD- 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  172 qPRVLGLTATLlnGNvSISKIEETLKQLEntfhatIATVddlgEVMTYS-------TNPQEfIQYFRKPqMSEAAKEAIS 244
Cdd:COG1111   151 -PLILGMTASP--GS-DEEKIEEVCENLG------IENV----EVRTEEdpdvapyVHDTE-VEWIRVE-LPEELKEIRD 214

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  245 LLN--------TLQNLVMSVKLPVSLPSKD---FKKTpCQRDISNDPNKIVKAVKNLIVGM----ITNLEEmglyggSLG 309
Cdd:COG1111   215 LLNevlddrlkKLKELGVIVSTSPDLSKKDllaLQKK-LQRRIREDDSEGYRAISILAEALklrhALELLE------TQG 287

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  310 ILAYIVLLERLKRKASTKEEnllystvithSTEARMILLD-----AMENETGYDkiIKHSseKILQLIDLLKEYnplILE 384
Cdd:COG1111   288 VEALLRYLERLEEEARSSGG----------SKASKRLVSDprfrkAMRLAEEAD--IEHP--KLSKLREILKEQ---LGT 350

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  385 KPGEllKVnhsrkplcgIIFTKQRFTSKILYnilmdlkkarpdefEFLKHDfvvGFSINPF--KSTREEHY-LKKSSQKA 461
Cdd:COG1111   351 NPDS--RI---------IVFTQYRDTAEMIV--------------EFLSEP---GIKAGRFvgQASKEGDKgLTQKEQIE 402

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 302318908  462 ILG-FNNGDLNCLISTSVIEEGLDIPQCALVVRYDA-PTEYRSyIQSKGR-ARSSEASFVILV 521
Cdd:COG1111   403 ILErFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPvPSEIRS-IQRKGRtGRKREGRVVVLI 464
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1440-1605 1.34e-38

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


Pssm-ID: 238333  Cd Length: 133  Bit Score: 140.83  E-value: 1.34e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908 1440 LLNALSHSSYIRNRLTSSYERLEFLGDAIIDFLVTSHIFENCRELKPGEMTDLRSALVNNVTFAAYTVKLGLHKYLcsel 1519
Cdd:cd00593     3 LLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYL---- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908 1520 npslekaimkFVEHQIERNHEiefdvlllisevdcqvaeyVDVPKVLSDIFEALVGAVYLDSGgnLETVWSVLYKIMHVE 1599
Cdd:cd00593    79 ----------RLGKGEEKSGG-------------------RLRPKILADVFEALIGAIYLDGG--FEAARKFLLRLLGPL 127


                  ....*.
gi 302318908 1600 IDSFSK 1605
Cdd:cd00593   128 IEEISL 133
PRK13766 PRK13766
Hef nuclease; Provisional
 14-521 1.20e-37

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 153.49  E-value: 1.20e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   14 ARPYQAILEEIASSKNTIIHLPTGSGKTFIA-----QRLIKKfrnqlkkpwgegGKRSFFLVNTVPLVNQQKNVIE--MM 86
Cdd:PRK13766   16 ARLYQQLLAATALKKNTLVVLPTGLGKTAIAllviaERLHKK------------GGKVLILAPTKPLVEQHAEFFRkfLN 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   87 CPVDGV----GAYSSEDGVDYWKKAdwdselarnQVIVMTSQ-ILSDMLThAYIRIEDINLIIFDECHHAVEDHPMRVIM 161
Cdd:PRK13766   84 IPEEKIvvftGEVSPEKRAELWEKA---------KVIVATPQvIENDLIA-GRISLEDVSLLIFDEAHRAVGNYAYVYIA 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  162 KHFLNcKAHEqPRVLGLTATllNGNvSISKIEETLkqlENTF--HATIATVDDLgEVMTYsTNPQEfIQYFRKpQMSEAA 239
Cdd:PRK13766  154 ERYHE-DAKN-PLVLGLTAS--PGS-DEEKIKEVC---ENLGieHVEVRTEDDP-DVKPY-VHKVK-IEWVRV-ELPEEL 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  240 KEAISLLN--------TLQNLVMSVKLPVSLPSKDF----KKTpcQRDISNDPNKIVKAVKnlIVGMITNLE---EMGLY 304
Cdd:PRK13766  222 KEIRDLLNealkdrlkKLKELGVIVSISPDVSKKELlglqKKL--QQEIANDDSEGYEAIS--ILAEAMKLRhavELLET 297

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  305 GGSLGILAYivlLERLKRKASTKeenllystviTHSTEARMILLD-----AMENETGYDkiIKHSseKILQLIDLLKEyn 379
Cdd:PRK13766  298 QGVEALRRY---LERLREEARSS----------GGSKASKRLVEDprfrkAVRKAKELD--IEHP--KLEKLREIVKE-- 358

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  380 plILE-KPGEllKVnhsrkplcgIIFTKQRFTSKILYNILMDlkkarpDEFEFLKhdFVvGfsinpfKSTREEHylKKSS 458
Cdd:PRK13766  359 --QLGkNPDS--RI---------IVFTQYRDTAEKIVDLLEK------EGIKAVR--FV-G------QASKDGD--KGMS 408

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 302318908  459 QK----AILGFNNGDLNCLISTSVIEEGLDIPQCALVVRYDA-PTEYRSyIQSKGRA-RSSEASFVILV 521
Cdd:PRK13766  409 QKeqieILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPvPSEIRS-IQRKGRTgRQEEGRVVVLI 476
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 364-521 8.90e-36

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: 133.10  E-value: 8.90e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  364 SSEKILQLIDLLKEYNPlilekpgellKVNHsrkpLCGIIFTKQRFTSKILYNILMDLKKARPdefeFLKHDFVVGFSIN 443
Cdd:cd18802     5 VIPKLQKLIEILREYFP----------KTPD----FRGIIFVERRATAVVLSRLLKEHPSTLA----FIRCGFLIGRGNS 66

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 302318908  444 PfKSTREEHYLKKssQKAIL-GFNNGDLNCLISTSVIEEGLDIPQCALVVRYDAPTEYRSYIQSKGRARSSEASFVILV 521
Cdd:cd18802    67 S-QRKRSLMTQRK--QKETLdKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1420-1602 7.78e-34

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 130.60  E-value: 7.78e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908 1420 NNSRTDVEKILNYTFKDSTFLLNALSHSSYIR-NRLTSSYERLEFLGDAIIDFLVTSHIFENCRELKPGEMTDLRSALVN 1498
Cdd:COG0571     1 SEDLEELEERLGYRFKDPELLEQALTHRSYANeHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908 1499 NVTFAAYTVKLGLHKYLcsELNPSLEKAimkfvehQIERNheiefdvlllisevdcqvaeyvdvPKVLSDIFEALVGAVY 1578
Cdd:COG0571    81 EETLAEIARELGLGDYL--RLGKGEEKS-------GGRRR------------------------PSILADAFEALIGAIY 127

                         170       180
                  ....*....|....*....|....
gi 302318908 1579 LDSGgnLETVWSVLYKIMHVEIDS 1602
Cdd:COG0571   128 LDGG--LEAARKFVLRLFEPRLEE 149
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1427-1610 1.42e-32

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: 126.93  E-value: 1.42e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  1427 EKILNYTFKDSTFLLNALSHSSYI--RNRLTSSYERLEFLGDAIIDFLVTSHIFENCRELKPGEMTDLRSALVNNVTFAA 1504
Cdd:TIGR02191    2 EKRLGYKFKNPELLEQALTHRSYAneHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAE 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  1505 YTVKLGLHKYLcsELNPSLEKaimkfvehqiernheiefdvlllisevdcqvAEYVDVPKVLSDIFEALVGAVYLDSGgn 1584
Cdd:TIGR02191   82 VARELGLGDFL--LLGKGEEK-------------------------------SGGRRRDSILADAFEALIGAIYLDSG-- 126

                          170       180
                   ....*....|....*....|....*.
gi 302318908  1585 LETVWSVLYKIMHVEIDSFSKRIPKQ 1610
Cdd:TIGR02191  127 LEAARKFILKLLIPRIDAIIKEETLK 152
RIBOc smart00535
Ribonuclease III family;
1440-1603 1.77e-30

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 117.32  E-value: 1.77e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   1440 LLNALSHSSYIRNRLtsSYERLEFLGDAIIDFLVTSHIFENCRELKPGEMTDLRSALVNNVTFAAYTVKLGLHKYLcsel 1519
Cdd:smart00535    3 LLRALTHASYSNEHE--HNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFI---- 76

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   1520 npslekaimkfvehQIERNHEIefdvlllisevdcqvAEYVDVPKVLSDIFEALVGAVYLDSGgnLETVWSVLYKIMHVE 1599
Cdd:smart00535   77 --------------RLGRGEAI---------------SGGRDKPKILADVFEALIGAIYLDSG--LEAAREFIRDLLGPR 125


                    ....
gi 302318908   1600 IDSF 1603
Cdd:smart00535  126 LDEL 129
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 587-673 2.74e-27

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: 106.81  E-value: 2.74e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   587 AISLLSRYCSILPHDQFTTITPVWLQEVVENGaKKQVTVILPIGSPVkEEIKGDPYSNTKTAKRSAALKACIKLHELGEL 666
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGG-KFVCTVTLPINSPL-RSIEGPPWRSKKLAKRSAAFEACKALHKAGLL 78


                   ....*....
gi 302318908   667 --HpltLLP 673
Cdd:pfam03368   79 ddH---LLP 84
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1459-1582 4.47e-25

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 100.81  E-value: 4.47e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  1459 ERLEFLGDAIIDFLVTSHIFENCRELKPGEMTDLRSALVNNVTFAAYTVKLGLHKYLcSELNPSLEKAIMKFVEHQIERN 1538
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFL-TEEELDIRRRNNALGKGPKRAD 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 302318908  1539 HEiefdvlllisevdcqvaeyvdvPKVLSDIFEALVGAVYLDSG 1582
Cdd:pfam00636   80 GK----------------------EKVLADAFEALIGALYLDGG 101
DEXDc smart00487
DEAD-like helicases superfamily;
15-201 1.24e-21

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 94.48  E-value: 1.24e-21
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908     15 RPYQ-AILEEIASS-KNTIIHLPTGSGKTFIAQRLIKKfrnQLKKpwgEGGKRSFFLVNTVPLVNQQKNVIEMMCPVDGV 92
Cdd:smart00487   10 RPYQkEAIEALLSGlRDVILAAPTGSGKTLAALLPALE---ALKR---GKGGRVLVLVPTRELAEQWAEELKKLGPSLGL 83

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908     93 GAYSSEDGVDYWKKADwDSELARNQVIVMTSQILSDMLTHAYIRIEDINLIIFDECHHaVEDHPMRVIMKHFLNcKAHEQ 172
Cdd:smart00487   84 KVVGLYGGDSKREQLR-KLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHR-LLDGGFGDQLEKLLK-LLPKN 160

                           170       180
                    ....*....|....*....|....*....
gi 302318908    173 PRVLGLTATLLNgnvsisKIEETLKQLEN 201
Cdd:smart00487  161 VQLLLLSATPPE------EIENLLELFLN 183
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 15-182 3.46e-18

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: 83.45  E-value: 3.46e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908    15 RPYQA-ILEEIASSKNTIIHLPTGSGKTFIAQR-LIKKFRNQLkkpwgeGGKRSFFLVNTVPLVNQQKNVIEMMCPVDGV 92
Cdd:pfam00270    1 TPIQAeAIPAILEGRDVLVQAPTGSGKTLAFLLpALEALDKLD------NGPQALVLAPTRELAEQIYEELKKLGKGLGL 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908    93 GAYSSEDGVDYWKKADwdsELARNQVIVMTSQILSDMLTHAyIRIEDINLIIFDECHHaVEDHPMRVIMKHFLNcKAHEQ 172
Cdd:pfam00270   75 KVASLLGGDSRKEQLE---KLKGPDILVGTPGRLLDLLQER-KLLKNLKLLVLDEAHR-LLDMGFGPDLEEILR-RLPKK 148

                          170
                   ....*....|
gi 302318908   173 PRVLGLTATL 182
Cdd:pfam00270  149 RQILLLSATL 158
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1192-1384 2.94e-17

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


Pssm-ID: 238333  Cd Length: 133  Bit Score: 79.96  E-value: 2.94e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908 1192 LAALTT---INSNDTFDLERPETLGDSFLKFAASLYLHHKFPNMNEGQLTNIKGKLISNRNLYYAGAKFNLGGRMKVEQF 1268
Cdd:cd00593     4 LEALTHpsyANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908 1269 SPRSdflvpgffappkleefieQRQIRPtfligiqfteeevmtgelseeswesvmnnfqngiaeaepegcaqnsmqcyvh 1348
Cdd:cd00593    84 EEKS------------------GGRLRP---------------------------------------------------- 93

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 302318908 1349 sqavadKSIADSVEALIGTYLLSGGILAAVKLLEWM 1384
Cdd:cd00593    94 ------KILADVFEALIGAIYLDGGFEAARKFLLRL 123
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
 851-961 4.24e-17

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


Pssm-ID: 239209  Cd Length: 122  Bit Score: 79.03  E-value: 4.24e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  851 IDWATMQTHHTVPPV--AAPSVEERKSLVVTEENYTNCIVTPWYRGTILPERYVVTKVLEYMTPKSQFDADCYESYANYY 928
Cdd:cd02843     7 IDWEFMEKIEANARIgpRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEYETFEEYY 86

                          90       100       110
                  ....*....|....*....|....*....|...
gi 302318908  929 ANNYNLDIlGSESQPLLEVRNISTRMNCLLPRA 961
Cdd:cd02843    87 KKKYKLDI-QNLNQPLLDVDHTSTRLNLLTPRY 118
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
15-181 8.07e-16

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 82.77  E-value: 8.07e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   15 RPYQA-ILEEIAS-----SKNTIIHLPTGSGKTFIAQRLIKKFRNqlkkpwgegGKRSFFLVNTVPLVNQQKNVIEMMCP 88
Cdd:COG1061    82 RPYQQeALEALLAalergGGRGLVVAPTGTGKTVLALALAAELLR---------GKRVLVLVPRRELLEQWAEELRRFLG 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   89 VDGVGAYSSEDGVDywkkadwdselarnqVIVMTSQILSDMLTHAYIRiEDINLIIFDECHHAVEDHpMRVIMKHFlnck 168
Cdd:COG1061   153 DPLAGGGKKDSDAP---------------ITVATYQSLARRAHLDELG-DRFGLVIIDEAHHAGAPS-YRRILEAF---- 211

                         170
                  ....*....|...
gi 302318908  169 ahEQPRVLGLTAT 181
Cdd:COG1061   212 --PAAYRLGLTAT 222
RIBOc smart00535
Ribonuclease III family;
1194-1260 1.28e-13

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 69.17  E-value: 1.28e-13
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 302318908   1194 ALTTIN-SNDTFDLERPETLGDSFLKFAASLYLHHKFPNMNEGQLTNIKGKLISNRNLYYAGAKFNLG 1260
Cdd:smart00535    6 ALTHASySNEHEHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLG 73
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 459-510 6.09e-13

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: 66.47  E-value: 6.09e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 302318908   459 QKAILGFNNGDLNCLISTSVIEEGLDIPQCALVVRYDAPTEYRSYIQSKGRA 510
Cdd:pfam00271   54 EEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1207-1271 4.22e-12

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 63.83  E-value: 4.22e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 302318908  1207 ERPETLGDSFLKFAASLYLHHKFPNMNEGQLTNIKGKLISNRNLYYAGAKFNLGGRMKVEQFSPR 1271
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDIR 65
HELICc smart00490
helicase superfamily c-terminal domain;
459-510 1.13e-11

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 62.23  E-value: 1.13e-11
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|..
gi 302318908    459 QKAILGFNNGDLNCLISTSVIEEGLDIPQCALVVRYDAPTEYRSYIQSKGRA 510
Cdd:smart00490   27 EEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1207-1260 3.52e-07

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 53.18  E-value: 3.52e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 302318908 1207 ERPETLGDSFLKFAASLYLHHKFPNMNEGQLTNIKGKLISNRNLYYAGAKFNLG 1260
Cdd:COG0571    41 ERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAEIARELGLG 94
PRK01172 PRK01172
ATP-dependent DNA helicase;
21-186 5.55e-05

ATP-dependent DNA helicase;


Pssm-ID: 100801 [Multi-domain]  Cd Length: 674  Bit Score: 47.96  E-value: 5.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   21 LEEIASSKNTIIHLPTGSGKTFIAQRLI-KKFRNQLKkpwgeggkrSFFLVntvPLVNQQKNVIEMMCPVDGVGAYSSED 99
Cdd:PRK01172   31 IEQLRKGENVIVSVPTAAGKTLIAYSAIyETFLAGLK---------SIYIV---PLRSLAMEKYEELSRLRSLGMRVKIS 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  100 GVDYWKKADWdseLARNQVIVMTSQILSDMLTHAYIRIEDINLIIFDEChHAVEDHPMRVIMKHFLNCKAHEQP--RVLG 177
Cdd:PRK01172   99 IGDYDDPPDF---IKRYDVVILTSEKADSLIHHDPYIINDVGLIVADEI-HIIGDEDRGPTLETVLSSARYVNPdaRILA 174


                  ....*....
gi 302318908  178 LTATLLNGN 186
Cdd:PRK01172  175 LSATVSNAN 183
uvrb TIGR00631
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ...
 468-510 4.05e-03

excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273185 [Multi-domain]  Cd Length: 655  Bit Score: 41.90  E-value: 4.05e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 302318908   468 GDLNCLISTSVIEEGLDIPQCALVVRYDAPTE-----YRSYIQSKGRA 510
Cdd:TIGR00631  491 GEFDVLVGINLLREGLDLPEVSLVAILDADKEgflrsERSLIQTIGRA 538
 
Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 13-212 2.32e-76

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: 251.80  E-value: 2.32e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   13 KARPYQAILEEIASSKNTIIHLPTGSGKTFIAQRLIKKFRNQLKKPwGEGGKRSFFLVNTVPLVNQQKNVIEMMCPVDgV 92
Cdd:cd18034     2 TPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRKE-KNPKKRAVFLVPTVPLVAQQAEAIRSHTDLK-V 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   93 GAYSSEDGVDYWKKADWDSELARNQVIVMTSQILSDMLTHAYIRIEDINLIIFDECHHAVEDHPMRVIMKHFLNCKAHE- 171
Cdd:cd18034    80 GEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLEGRTs 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 302318908  172 QPRVLGLTATLLNGNVSISKIEETLKQLENTFHATIATVDD 212
Cdd:cd18034   160 RPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
14-521 1.84e-45

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 176.84  E-value: 1.84e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   14 ARPYQAILEEIASSKNTIIHLPTGSGKTFIAQRLIKKFrnqLKKPwgegGKRSFFLVNTVPLVNQQKNVIE--MMCPVDG 91
Cdd:COG1111     4 RRLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAER---LHKK----GGKVLFLAPTKPLVEQHAEFFKeaLNIPEDE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   92 VGAYSSEDGVDYwKKADWDSelarNQVIVMTSQILSDMLTHAYIRIEDINLIIFDECHHAVEDHPMRVIMKHFLNCKAHe 171
Cdd:COG1111    77 IVVFTGEVSPEK-RKELWEK----ARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKD- 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  172 qPRVLGLTATLlnGNvSISKIEETLKQLEntfhatIATVddlgEVMTYS-------TNPQEfIQYFRKPqMSEAAKEAIS 244
Cdd:COG1111   151 -PLILGMTASP--GS-DEEKIEEVCENLG------IENV----EVRTEEdpdvapyVHDTE-VEWIRVE-LPEELKEIRD 214

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  245 LLN--------TLQNLVMSVKLPVSLPSKD---FKKTpCQRDISNDPNKIVKAVKNLIVGM----ITNLEEmglyggSLG 309
Cdd:COG1111   215 LLNevlddrlkKLKELGVIVSTSPDLSKKDllaLQKK-LQRRIREDDSEGYRAISILAEALklrhALELLE------TQG 287

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  310 ILAYIVLLERLKRKASTKEEnllystvithSTEARMILLD-----AMENETGYDkiIKHSseKILQLIDLLKEYnplILE 384
Cdd:COG1111   288 VEALLRYLERLEEEARSSGG----------SKASKRLVSDprfrkAMRLAEEAD--IEHP--KLSKLREILKEQ---LGT 350

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  385 KPGEllKVnhsrkplcgIIFTKQRFTSKILYnilmdlkkarpdefEFLKHDfvvGFSINPF--KSTREEHY-LKKSSQKA 461
Cdd:COG1111   351 NPDS--RI---------IVFTQYRDTAEMIV--------------EFLSEP---GIKAGRFvgQASKEGDKgLTQKEQIE 402

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 302318908  462 ILG-FNNGDLNCLISTSVIEEGLDIPQCALVVRYDA-PTEYRSyIQSKGR-ARSSEASFVILV 521
Cdd:COG1111   403 ILErFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPvPSEIRS-IQRKGRtGRKREGRVVVLI 464
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 13-210 2.20e-39

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


Pssm-ID: 350685 [Multi-domain]  Cd Length: 201  Bit Score: 145.65  E-value: 2.20e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   13 KARPYQAILEEIAS-SKNTIIHLPTGSGKTFIAQrLIKKFRNQlKKPWGEGGKrSFFLVNTVPLVNQQKNVIEMMCPVDG 91
Cdd:cd17927     2 KPRNYQLELAQPALkGKNTIICLPTGSGKTFVAV-LICEHHLK-KFPAGRKGK-VVFLANKVPLVEQQKEVFRKHFERPG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   92 --VGAYSSEDGVDYWKKADWdselARNQVIVMTSQILSDMLTHA-YIRIEDINLIIFDECHHAVEDHPMRVIMKHFLNCK 168
Cdd:cd17927    79 ykVTGLSGDTSENVSVEQIV----ESSDVIIVTPQILVNDLKSGtIVSLSDFSLLVFDECHNTTKNHPYNEIMFRYLDQK 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 302318908  169 ---AHEQPRVLGLTATLLNGNV-SISKIEETLKQLENTFHA-TIATV 210
Cdd:cd17927   155 lgsSGPLPQILGLTASPGVGGAkNTEEALEHICKLCANLDIsVIATV 201
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1440-1605 1.34e-38

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


Pssm-ID: 238333  Cd Length: 133  Bit Score: 140.83  E-value: 1.34e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908 1440 LLNALSHSSYIRNRLTSSYERLEFLGDAIIDFLVTSHIFENCRELKPGEMTDLRSALVNNVTFAAYTVKLGLHKYLcsel 1519
Cdd:cd00593     3 LLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYL---- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908 1520 npslekaimkFVEHQIERNHEiefdvlllisevdcqvaeyVDVPKVLSDIFEALVGAVYLDSGgnLETVWSVLYKIMHVE 1599
Cdd:cd00593    79 ----------RLGKGEEKSGG-------------------RLRPKILADVFEALIGAIYLDGG--FEAARKFLLRLLGPL 127


                  ....*.
gi 302318908 1600 IDSFSK 1605
Cdd:cd00593   128 IEEISL 133
PRK13766 PRK13766
Hef nuclease; Provisional
 14-521 1.20e-37

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 153.49  E-value: 1.20e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   14 ARPYQAILEEIASSKNTIIHLPTGSGKTFIA-----QRLIKKfrnqlkkpwgegGKRSFFLVNTVPLVNQQKNVIE--MM 86
Cdd:PRK13766   16 ARLYQQLLAATALKKNTLVVLPTGLGKTAIAllviaERLHKK------------GGKVLILAPTKPLVEQHAEFFRkfLN 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   87 CPVDGV----GAYSSEDGVDYWKKAdwdselarnQVIVMTSQ-ILSDMLThAYIRIEDINLIIFDECHHAVEDHPMRVIM 161
Cdd:PRK13766   84 IPEEKIvvftGEVSPEKRAELWEKA---------KVIVATPQvIENDLIA-GRISLEDVSLLIFDEAHRAVGNYAYVYIA 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  162 KHFLNcKAHEqPRVLGLTATllNGNvSISKIEETLkqlENTF--HATIATVDDLgEVMTYsTNPQEfIQYFRKpQMSEAA 239
Cdd:PRK13766  154 ERYHE-DAKN-PLVLGLTAS--PGS-DEEKIKEVC---ENLGieHVEVRTEDDP-DVKPY-VHKVK-IEWVRV-ELPEEL 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  240 KEAISLLN--------TLQNLVMSVKLPVSLPSKDF----KKTpcQRDISNDPNKIVKAVKnlIVGMITNLE---EMGLY 304
Cdd:PRK13766  222 KEIRDLLNealkdrlkKLKELGVIVSISPDVSKKELlglqKKL--QQEIANDDSEGYEAIS--ILAEAMKLRhavELLET 297

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  305 GGSLGILAYivlLERLKRKASTKeenllystviTHSTEARMILLD-----AMENETGYDkiIKHSseKILQLIDLLKEyn 379
Cdd:PRK13766  298 QGVEALRRY---LERLREEARSS----------GGSKASKRLVEDprfrkAVRKAKELD--IEHP--KLEKLREIVKE-- 358

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  380 plILE-KPGEllKVnhsrkplcgIIFTKQRFTSKILYNILMDlkkarpDEFEFLKhdFVvGfsinpfKSTREEHylKKSS 458
Cdd:PRK13766  359 --QLGkNPDS--RI---------IVFTQYRDTAEKIVDLLEK------EGIKAVR--FV-G------QASKDGD--KGMS 408

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 302318908  459 QK----AILGFNNGDLNCLISTSVIEEGLDIPQCALVVRYDA-PTEYRSyIQSKGRA-RSSEASFVILV 521
Cdd:PRK13766  409 QKeqieILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPvPSEIRS-IQRKGRTgRQEEGRVVVLI 476
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 364-521 8.90e-36

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: 133.10  E-value: 8.90e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  364 SSEKILQLIDLLKEYNPlilekpgellKVNHsrkpLCGIIFTKQRFTSKILYNILMDLKKARPdefeFLKHDFVVGFSIN 443
Cdd:cd18802     5 VIPKLQKLIEILREYFP----------KTPD----FRGIIFVERRATAVVLSRLLKEHPSTLA----FIRCGFLIGRGNS 66

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 302318908  444 PfKSTREEHYLKKssQKAIL-GFNNGDLNCLISTSVIEEGLDIPQCALVVRYDAPTEYRSYIQSKGRARSSEASFVILV 521
Cdd:cd18802    67 S-QRKRSLMTQRK--QKETLdKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1420-1602 7.78e-34

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 130.60  E-value: 7.78e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908 1420 NNSRTDVEKILNYTFKDSTFLLNALSHSSYIR-NRLTSSYERLEFLGDAIIDFLVTSHIFENCRELKPGEMTDLRSALVN 1498
Cdd:COG0571     1 SEDLEELEERLGYRFKDPELLEQALTHRSYANeHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908 1499 NVTFAAYTVKLGLHKYLcsELNPSLEKAimkfvehQIERNheiefdvlllisevdcqvaeyvdvPKVLSDIFEALVGAVY 1578
Cdd:COG0571    81 EETLAEIARELGLGDYL--RLGKGEEKS-------GGRRR------------------------PSILADAFEALIGAIY 127

                         170       180
                  ....*....|....*....|....
gi 302318908 1579 LDSGgnLETVWSVLYKIMHVEIDS 1602
Cdd:COG0571   128 LDGG--LEAARKFVLRLFEPRLEE 149
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1427-1610 1.42e-32

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: 126.93  E-value: 1.42e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  1427 EKILNYTFKDSTFLLNALSHSSYI--RNRLTSSYERLEFLGDAIIDFLVTSHIFENCRELKPGEMTDLRSALVNNVTFAA 1504
Cdd:TIGR02191    2 EKRLGYKFKNPELLEQALTHRSYAneHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAE 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  1505 YTVKLGLHKYLcsELNPSLEKaimkfvehqiernheiefdvlllisevdcqvAEYVDVPKVLSDIFEALVGAVYLDSGgn 1584
Cdd:TIGR02191   82 VARELGLGDFL--LLGKGEEK-------------------------------SGGRRRDSILADAFEALIGAIYLDSG-- 126

                          170       180
                   ....*....|....*....|....*.
gi 302318908  1585 LETVWSVLYKIMHVEIDSFSKRIPKQ 1610
Cdd:TIGR02191  127 LEAARKFILKLLIPRIDAIIKEETLK 152
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 13-210 3.28e-31

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: 122.20  E-value: 3.28e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   13 KARPYQAILEEIA-SSKNTIIHLPTGSGKTF----IAQRLIKKFRNQlkkpwGEGGkRSFFLVNTVPLVNQQK----NVI 83
Cdd:cd18036     2 ELRNYQLELVLPAlRGKNTIICAPTGSGKTRvavyICRHHLEKRRSA-----GEKG-RVVVLVNKVPLVEQQLekffKYF 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   84 EMMCPVDGVGAYSSEdgvdywkKADWDSELARNQVIVMTSQILSDMLTHAYI----RIEDINLIIFDECHHAVEDHPMRV 159
Cdd:cd18036    76 RKGYKVTGLSGDSSH-------KVSFGQIVKASDVIICTPQILINNLLSGREeervYLSDFSLLIFDECHHTQKEHPYNK 148

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 302318908  160 IMKHFLNCKAH---EQPRVLGLTATL-LNGNVSISKIEETLKQLENTFHA-TIATV 210
Cdd:cd18036   149 IMRMYLDKKLSsqgPLPQILGLTASPgVGGARSFEEALEHILKLCANLDAsVIATV 204
RIBOc smart00535
Ribonuclease III family;
1440-1603 1.77e-30

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 117.32  E-value: 1.77e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   1440 LLNALSHSSYIRNRLtsSYERLEFLGDAIIDFLVTSHIFENCRELKPGEMTDLRSALVNNVTFAAYTVKLGLHKYLcsel 1519
Cdd:smart00535    3 LLRALTHASYSNEHE--HNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFI---- 76

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   1520 npslekaimkfvehQIERNHEIefdvlllisevdcqvAEYVDVPKVLSDIFEALVGAVYLDSGgnLETVWSVLYKIMHVE 1599
Cdd:smart00535   77 --------------RLGRGEAI---------------SGGRDKPKILADVFEALIGAIYLDSG--LEAAREFIRDLLGPR 125


                    ....
gi 302318908   1600 IDSF 1603
Cdd:smart00535  126 LDEL 129
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 587-673 2.74e-27

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: 106.81  E-value: 2.74e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   587 AISLLSRYCSILPHDQFTTITPVWLQEVVENGaKKQVTVILPIGSPVkEEIKGDPYSNTKTAKRSAALKACIKLHELGEL 666
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGG-KFVCTVTLPINSPL-RSIEGPPWRSKKLAKRSAAFEACKALHKAGLL 78


                   ....*....
gi 302318908   667 --HpltLLP 673
Cdd:pfam03368   79 ddH---LLP 84
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1459-1582 4.47e-25

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 100.81  E-value: 4.47e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  1459 ERLEFLGDAIIDFLVTSHIFENCRELKPGEMTDLRSALVNNVTFAAYTVKLGLHKYLcSELNPSLEKAIMKFVEHQIERN 1538
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFL-TEEELDIRRRNNALGKGPKRAD 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 302318908  1539 HEiefdvlllisevdcqvaeyvdvPKVLSDIFEALVGAVYLDSG 1582
Cdd:pfam00636   80 GK----------------------EKVLADAFEALIGALYLDGG 101
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
 13-210 3.37e-22

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


Pssm-ID: 350831 [Multi-domain]  Cd Length: 202  Bit Score: 96.43  E-value: 3.37e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   13 KARPYQAILEEIA-SSKNTIIHLPTGSGKTFIAQrLIKKFrnQLKK-PWGEGGKrSFFLVNTVPLVNQQKNVIEMMCPVD 90
Cdd:cd18073     2 KPRNYQLELALPAmKGKNTIICAPTGCGKTFVSL-LICEH--HLKKfPQGQKGK-VVFFATKVPVYEQQKSVFSKYFERH 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   91 GVGAYSSEDGVDYWKKADWDSElaRNQVIVMTSQILSDMLTHAYI-RIEDINLIIFDECHHAVEDHPMRVIMKHFLNCK- 168
Cdd:cd18073    78 GYRVTGISGATAENVPVEQIIE--NNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSGNHPYNMIMFRYLDQKl 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 302318908  169 ---AHEQPRVLGLTATLLNGNV-SISKIEETLKQLENTFHAT-IATV 210
Cdd:cd18073   156 ggsSGPLPQIIGLTASVGVGDAkNTDEALDYICKLCASLDASvIATV 202
DEXDc smart00487
DEAD-like helicases superfamily;
15-201 1.24e-21

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 94.48  E-value: 1.24e-21
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908     15 RPYQ-AILEEIASS-KNTIIHLPTGSGKTFIAQRLIKKfrnQLKKpwgEGGKRSFFLVNTVPLVNQQKNVIEMMCPVDGV 92
Cdd:smart00487   10 RPYQkEAIEALLSGlRDVILAAPTGSGKTLAALLPALE---ALKR---GKGGRVLVLVPTRELAEQWAEELKKLGPSLGL 83

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908     93 GAYSSEDGVDYWKKADwDSELARNQVIVMTSQILSDMLTHAYIRIEDINLIIFDECHHaVEDHPMRVIMKHFLNcKAHEQ 172
Cdd:smart00487   84 KVVGLYGGDSKREQLR-KLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHR-LLDGGFGDQLEKLLK-LLPKN 160

                           170       180
                    ....*....|....*....|....*....
gi 302318908    173 PRVLGLTATLLNgnvsisKIEETLKQLEN 201
Cdd:smart00487  161 VQLLLLSATPPE------EIENLLELFLN 183
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 243-353 1.24e-18

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


Pssm-ID: 277191  Cd Length: 104  Bit Score: 82.72  E-value: 1.24e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  243 ISLLNTLQNLVMSVKLPVSLPSKDfkktpcqRDISNDPNKIVKAVKNLIVGMITNLEEMGLYGGSLGILAYIVLLERLKR 322
Cdd:cd15903     1 LSLLDEIIEFLNDCKLFDPEVYIE-------SLLLDRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKK 73

                          90       100       110
                  ....*....|....*....|....*....|.
gi 302318908  323 KASTKEENLLYSTVITHSTEARMILLDAMEN 353
Cdd:cd15903    74 KSTDEKHRLFLRYVITQLRKIRKLLEDEMKN 104
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 15-182 3.46e-18

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: 83.45  E-value: 3.46e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908    15 RPYQA-ILEEIASSKNTIIHLPTGSGKTFIAQR-LIKKFRNQLkkpwgeGGKRSFFLVNTVPLVNQQKNVIEMMCPVDGV 92
Cdd:pfam00270    1 TPIQAeAIPAILEGRDVLVQAPTGSGKTLAFLLpALEALDKLD------NGPQALVLAPTRELAEQIYEELKKLGKGLGL 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908    93 GAYSSEDGVDYWKKADwdsELARNQVIVMTSQILSDMLTHAyIRIEDINLIIFDECHHaVEDHPMRVIMKHFLNcKAHEQ 172
Cdd:pfam00270   75 KVASLLGGDSRKEQLE---KLKGPDILVGTPGRLLDLLQER-KLLKNLKLLVLDEAHR-LLDMGFGPDLEEILR-RLPKK 148

                          170
                   ....*....|
gi 302318908   173 PRVLGLTATL 182
Cdd:pfam00270  149 RQILLLSATL 158
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
 15-193 1.13e-17

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


Pssm-ID: 350791 [Multi-domain]  Cd Length: 182  Bit Score: 82.76  E-value: 1.13e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   15 RPYQAILEEIASSKNTIIHLPTGSGKTFIAQRLIKKF-RnqlkkpWGEGGKrSFFLVNTVPLVNQQknvIEMMCPVDGVG 93
Cdd:cd18033     4 RDYQFTIVQKALFQNTLVALPTGLGKTFIAAVVMLNYyR------WFPKGK-IVFMAPTKPLVSQQ---IEACYKITGIP 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   94 AYSSEDGVDYWKKADWDSELARNQVIVMTSQILSDMLTHAYIRIEDINLIIFDECHHAVEDHPMRVIMKHFLNCKAHEqp 173
Cdd:cd18033    74 SSQTAELTGSVPPTKRAELWASKRVFFLTPQTLENDLKEGDCDPKSIVCLVIDEAHRATGNYAYCQVVRELMRYNSHF-- 151

                         170       180
                  ....*....|....*....|....*....
gi 302318908  174 RVLGLTATLLNG---------NVSISKIE 193
Cdd:cd18033   152 RILALTATPGSKleavqqvidNLLISHIE 180
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 28-181 1.46e-17

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: 81.30  E-value: 1.46e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   28 KNTIIHLPTGSGKTFIAQRLIkkfRNQLKKPwgegGKRSFFLVNTVPLVNQQ-KNVIEMMCPVDGVGAYSSedgvDYWKK 106
Cdd:cd00046     2 ENVLITAPTGSGKTLAALLAA---LLLLLKK----GKKVLVLVPTKALALQTaERLRELFGPGIRVAVLVG----GSSAE 70

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 302318908  107 ADWDSELARNQVIVMT-SQILSDMLTHAYIRIEDINLIIFDECHHAVEDHPMRVIMKhFLNCKAHE-QPRVLGLTAT 181
Cdd:cd00046    71 EREKNKLGDADIIIATpDMLLNLLLREDRLFLKDLKLIIVDEAHALLIDSRGALILD-LAVRKAGLkNAQVILLSAT 146
ResIII pfam04851
Type III restriction enzyme, res subunit;
15-181 1.96e-17

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 81.18  E-value: 1.96e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908    15 RPYQ-----AILEEIAS-SKNTIIHLPTGSGKTFIAQRLIKKFRNQLKKpwgeggKRSFFLVNTVPLVNQQKNVIE--MM 86
Cdd:pfam04851    5 RPYQieaieNLLESIKNgQKRGLIVMATGSGKTLTAAKLIARLFKKGPI------KKVLFLVPRKDLLEQALEEFKkfLP 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908    87 CPVDGVGAYSSEdgvdywKKadwDSELARNQVIVMTSQILS--DMLTHAYIRIEDINLIIFDECHHAVEDHpMRVIMKHF 164
Cdd:pfam04851   79 NYVEIGEIISGD------KK---DESVDDNKIVVTTIQSLYkaLELASLELLPDFFDVIIIDEAHRSGASS-YRNILEYF 148

                          170
                   ....*....|....*..
gi 302318908   165 lnckahEQPRVLGLTAT 181
Cdd:pfam04851  149 ------KPAFLLGLTAT 159
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1192-1384 2.94e-17

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


Pssm-ID: 238333  Cd Length: 133  Bit Score: 79.96  E-value: 2.94e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908 1192 LAALTT---INSNDTFDLERPETLGDSFLKFAASLYLHHKFPNMNEGQLTNIKGKLISNRNLYYAGAKFNLGGRMKVEQF 1268
Cdd:cd00593     4 LEALTHpsyANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908 1269 SPRSdflvpgffappkleefieQRQIRPtfligiqfteeevmtgelseeswesvmnnfqngiaeaepegcaqnsmqcyvh 1348
Cdd:cd00593    84 EEKS------------------GGRLRP---------------------------------------------------- 93

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 302318908 1349 sqavadKSIADSVEALIGTYLLSGGILAAVKLLEWM 1384
Cdd:cd00593    94 ------KILADVFEALIGAIYLDGGFEAARKFLLRL 123
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 1440-1584 3.04e-17

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: 79.53  E-value: 3.04e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  1440 LLNALSHSSYiRNRLTSSYERLEFLGDAIIDFLVTSHIFENcRELKPGEMTDLRSALVNNVTFAAYTVKLGLHKYLcsel 1519
Cdd:pfam14622    4 LLQALTHKSY-ANGRKPYNERLEFLGDAVLELSVSEYLFKK-PDLDEGGLTKLRASIVSEESLAEIAREIGLGKYL---- 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 302318908  1520 npslekaimkfvehqiernheiefdvLLLISEVDCQVAEYvdvPKVLSDIFEALVGAVYLDSGGN 1584
Cdd:pfam14622   78 --------------------------RLGKGEEETGGSGR---ESILADALEALIGAIYLDGGFE 113
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
 851-961 4.24e-17

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


Pssm-ID: 239209  Cd Length: 122  Bit Score: 79.03  E-value: 4.24e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  851 IDWATMQTHHTVPPV--AAPSVEERKSLVVTEENYTNCIVTPWYRGTILPERYVVTKVLEYMTPKSQFDADCYESYANYY 928
Cdd:cd02843     7 IDWEFMEKIEANARIgpRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEYETFEEYY 86

                          90       100       110
                  ....*....|....*....|....*....|...
gi 302318908  929 ANNYNLDIlGSESQPLLEVRNISTRMNCLLPRA 961
Cdd:cd02843    87 KKKYKLDI-QNLNQPLLDVDHTSTRLNLLTPRY 118
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 13-199 1.53e-16

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: 79.48  E-value: 1.53e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   13 KARPYQAILEEIASSKNTIIHLPTGSGKTFIAQrLIKKFRNQLKkpwgegGKRSFFLVNTVPLVNQQ----KNVIEMMCP 88
Cdd:cd18035     2 ERRLYQVLIAAVALNGNTLIVLPTGLGKTIIAI-LVAADRLTKK------GGKVLILAPSRPLVEQHaenlKRVLNIPDK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   89 VDGV-GAYSSEDGVDYWKKAdwdselarnQVIVMTSQILSDMLTHAYIRIEDINLIIFDECHHAVEDHPMRVIMKHFLnc 167
Cdd:cd18035    75 ITSLtGEVKPEERAERWDAS---------KIIVATPQVIENDLLAGRITLDDVSLLIFDEAHHAVGNYAYVYIAHRYK-- 143

                         170       180       190
                  ....*....|....*....|....*....|..
gi 302318908  168 KAHEQPRVLGLTATllnGNVSISKIEETLKQL 199
Cdd:cd18035   144 REANNPLILGLTAS---PGSDKEKIMEICENL 172
DEXHc_RLR-2 cd18074
DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma ...
 15-210 1.92e-16

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: 79.90  E-value: 1.92e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   15 RPYQAILEEIA-SSKNTIIHLPTGSGKTFIAQRLIKKFRNQLKKPwGEGGKrSFFLVNTVPLVNQ--QKNVIEMMCPVDG 91
Cdd:cd18074     4 RDYQMEVAKPAlEGKNIIICLPTGSGKTRVAVYITKDHLDKKRKA-SEPGK-VIVLVNKVPLVEQhyRKEFNPFLKHWYQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   92 VGAYSSedgvDYWKKADWDSELARNQVIVMTSQILSDMLTHAY------IRIEDINLIIFDECHHAVEDHPMRVIMKHFL 165
Cdd:cd18074    82 VIGLSG----DSQLKISFPEVVKRYDVIICTAQILENSLLNATeeedegVQLSDFSLIIIDECHHTQKEAVYNNIMRRYL 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 302318908  166 NCKAHE------------QPRVLGLTATL-LNGNVSISKIEE-TLKQLENTFHATIATV 210
Cdd:cd18074   158 KQKIKNrkqkkenkplipLPQILGLTASPgVGGAKNNKKAEEhILKICANLDAFRIMTV 216
DEXHc_RLR-3 cd18075
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ...
 15-199 3.87e-16

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


Pssm-ID: 350833 [Multi-domain]  Cd Length: 200  Bit Score: 78.75  E-value: 3.87e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   15 RPYQaiLEEIASS---KNTIIHLPTGSGKTFIAQRLIKKFRNqlkkpwGEGGKRSFFLVNTVPLVNQQ-KNVIEMMCPVD 90
Cdd:cd18075     4 HGYQ--WEVVAPAlrgKNSIIWLPTGAGKTRAAVYVARRHLE------TKRGAKVAVLVNKVHLVDQHlEKEFHVLLDKY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   91 GVGAYSSEDGvdywkKADWDSELAR-NQVIVMTSQILSDMLT----HAYIRIEDINLIIFDECHHAVEDHPMRVIMKHFL 165
Cdd:cd18075    76 TVTAISGDSS-----HKCFFGQLARgSDVVICTAQILQNALLsgeeEAHVELTDFSLLVIDECHHTHKEAVYNKIMLSYL 150

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 302318908  166 N---CKAHEQPRVLGLTATL-LNGNVSISKIEETLKQL 199
Cdd:cd18075   151 EkklSRQGDLPQILGLTASPgTGGATSFDGAVEHILQI 188
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
15-181 8.07e-16

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 82.77  E-value: 8.07e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   15 RPYQA-ILEEIAS-----SKNTIIHLPTGSGKTFIAQRLIKKFRNqlkkpwgegGKRSFFLVNTVPLVNQQKNVIEMMCP 88
Cdd:COG1061    82 RPYQQeALEALLAalergGGRGLVVAPTGTGKTVLALALAAELLR---------GKRVLVLVPRRELLEQWAEELRRFLG 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   89 VDGVGAYSSEDGVDywkkadwdselarnqVIVMTSQILSDMLTHAYIRiEDINLIIFDECHHAVEDHpMRVIMKHFlnck 168
Cdd:COG1061   153 DPLAGGGKKDSDAP---------------ITVATYQSLARRAHLDELG-DRFGLVIIDEAHHAGAPS-YRRILEAF---- 211

                         170
                  ....*....|...
gi 302318908  169 ahEQPRVLGLTAT 181
Cdd:COG1061   212 --PAAYRLGLTAT 222
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 15-182 1.99e-15

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: 75.03  E-value: 1.99e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   15 RPYQ-----AILEEIASSKNTIIhLPTGSGKTFIAQRLIKKFRNqlkkpwgeggKRSFFLVNTVPLVNQQKNVIEMMCPV 89
Cdd:cd17926     2 RPYQeealeAWLAHKNNRRGILV-LPTGSGKTLTALALIAYLKE----------LRTLIVVPTDALLDQWKERFEDFLGD 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   90 DGVGAYSSEdgvdywKKADWDSelarNQVIVMTSQILSDMLTHAYIRIEDINLIIFDECHHAVEDHpMRVIMKHFlncka 169
Cdd:cd17926    71 SSIGLIGGG------KKKDFDD----ANVVVATYQSLSNLAEEEKDLFDQFGLLIVDEAHHLPAKT-FSEILKEL----- 134

                         170
                  ....*....|...
gi 302318908  170 hEQPRVLGLTATL 182
Cdd:cd17926   135 -NAKYRLGLTATP 146
RIBOc smart00535
Ribonuclease III family;
1194-1260 1.28e-13

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 69.17  E-value: 1.28e-13
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 302318908   1194 ALTTIN-SNDTFDLERPETLGDSFLKFAASLYLHHKFPNMNEGQLTNIKGKLISNRNLYYAGAKFNLG 1260
Cdd:smart00535    6 ALTHASySNEHEHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLG 73
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 15-181 1.43e-13

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: 70.28  E-value: 1.43e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   15 RPYQ-----AILEEIASSKNTI-IHLPTGSGKTFIAQRLIKKFrnqLKKPWgegGKRSFFLVNTVPLVNQQKNVIEMMCP 88
Cdd:cd18032     2 RYYQqeaieALEEAREKGQRRAlLVMATGTGKTYTAAFLIKRL---LEANR---KKRILFLAHREELLEQAERSFKEVLP 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   89 VDGVGAYSSEDGVDYWKKadwdselarnqVIVMTSQILSDMLTHAYIRIEDINLIIFDECHHAVEDHpMRVIMKHFlnck 168
Cdd:cd18032    76 DGSFGNLKGGKKKPDDAR-----------VVFATVQTLNKRKRLEKFPPDYFDLIIIDEAHHAIASS-YRKILEYF---- 139

                         170
                  ....*....|...
gi 302318908  169 ahEQPRVLGLTAT 181
Cdd:cd18032   140 --EPAFLLGLTAT 150
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 16-184 4.19e-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: 69.21  E-value: 4.19e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   16 PYQA-ILEEIASS-KNTIIHLPTGSGKTFIAQRLIkkFRNqlkkpWGEGGKRSFFLVNTVPLVNQQKN-VIEMMCPVDG- 91
Cdd:cd17921     4 PIQReALRALYLSgDSVLVSAPTSSGKTLIAELAI--LRA-----LATSGGKAVYIAPTRALVNQKEAdLRERFGPLGKn 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   92 VGAYSSEDGVDywkkadwDSELARNQVIVMTSQILSDMLTHAYIR-IEDINLIIFDECHHaVEDhPMR-----VIMKHFL 165
Cdd:cd17921    77 VGLLTGDPSVN-------KLLLAEADILVATPEKLDLLLRNGGERlIQDVRLVVVDEAHL-IGD-GERgvvleLLLSRLL 147

                         170
                  ....*....|....*....
gi 302318908  166 NckAHEQPRVLGLTATLLN 184
Cdd:cd17921   148 R--INKNARFVGLSATLPN 164
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 459-510 6.09e-13

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: 66.47  E-value: 6.09e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 302318908   459 QKAILGFNNGDLNCLISTSVIEEGLDIPQCALVVRYDAPTEYRSYIQSKGRA 510
Cdd:pfam00271   54 EEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1207-1271 4.22e-12

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 63.83  E-value: 4.22e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 302318908  1207 ERPETLGDSFLKFAASLYLHHKFPNMNEGQLTNIKGKLISNRNLYYAGAKFNLGGRMKVEQFSPR 1271
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDIR 65
HELICc smart00490
helicase superfamily c-terminal domain;
459-510 1.13e-11

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 62.23  E-value: 1.13e-11
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|..
gi 302318908    459 QKAILGFNNGDLNCLISTSVIEEGLDIPQCALVVRYDAPTEYRSYIQSKGRA 510
Cdd:smart00490   27 EEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 383-521 1.22e-08

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: 55.44  E-value: 1.22e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  383 LEKPGELLKVNHSRKPLCG----IIFTKQRFTSKILYNILM-DLKKARPDEFeflkhdfvVGFSinpfkSTREEHYLKKS 457
Cdd:cd18801    11 LEKLEEIVKEHFKKKQEGSdtrvIIFSEFRDSAEEIVNFLSkIRPGIRATRF--------IGQA-----SGKSSKGMSQK 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 302318908  458 SQKAIL-GFNNGDLNCLISTSVIEEGLDIPQCALVVRYDA-PTEYRSyIQSKGRARSSEASFVILV 521
Cdd:cd18801    78 EQKEVIeQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDAsPSPIRM-IQRMGRTGRKRQGRVVVL 142
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
16-187 1.42e-08

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 59.52  E-value: 1.42e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   16 PYQ--AILEEIASSKNTIIHLPTGSGKTFIAQRLIkkfRNQLKKpwgegGKRSFFLVNTVPLVNQQKNVIEMMCPVDGV- 92
Cdd:COG1204    25 PPQaeALEAGLLEGKNLVVSAPTASGKTLIAELAI---LKALLN-----GGKALYIVPLRALASEKYREFKRDFEELGIk 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   93 -----GAYSSEDGvdywkkadwdsELARNQVIVMTSQILSDMLTHAYIRIEDINLIIFDECHHaVEDhPMR-----VIMK 162
Cdd:COG1204    97 vgvstGDYDSDDE-----------WLGRYDILVATPEKLDSLLRNGPSWLRDVDLVVVDEAHL-IDD-ESRgptleVLLA 163

                         170       180
                  ....*....|....*....|....*
gi 302318908  163 HFLncKAHEQPRVLGLTATLlnGNV 187
Cdd:COG1204   164 RLR--RLNPEAQIVALSATI--GNA 184
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
 17-184 2.06e-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: 55.80  E-value: 2.06e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   17 YQAILEEIASSKNTIIHLPTGSGKTFIAQRLIKKFrnqlkkpWGEGGKrSFFLVNTVPLVNQQ------KNVIEMMCPVD 90
Cdd:cd18028     7 AEAVRAGLLKGENLLISIPTASGKTLIAEMAMVNT-------LLEGGK-ALYLVPLRALASEKyeefkkLEEIGLKVGIS 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   91 gVGAYSSEdgvDYWkkadwdseLARNQVIVMTSQILSDMLTHAYIRIEDINLIIFDECHHAVEDH---PMRVIMKHFLnc 167
Cdd:cd18028    79 -TGDYDED---DEW--------LGDYDIIVATYEKFDSLLRHSPSWLRDVGVVVVDEIHLISDEErgpTLESIVARLR-- 144

                         170
                  ....*....|....*..
gi 302318908  168 KAHEQPRVLGLTATLLN 184
Cdd:cd18028   145 RLNPNTQIIGLSATIGN 161
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 440-510 1.36e-07

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: 50.40  E-value: 1.36e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 302318908  440 FSINPFKSTREEHYLKKSSqkailgfnngdLNCLISTSVIEEGLDIPQCALVVRYDAPTEYRSYIQSKGRA 510
Cdd:cd18785     4 VKIIVFTNSIEHAEEIASS-----------LEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRA 63
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1207-1260 3.52e-07

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 53.18  E-value: 3.52e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 302318908 1207 ERPETLGDSFLKFAASLYLHHKFPNMNEGQLTNIKGKLISNRNLYYAGAKFNLG 1260
Cdd:COG0571    41 ERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAEIARELGLG 94
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 459-511 3.53e-07

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: 50.97  E-value: 3.53e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 302318908  459 QKAILGFNNGDLNCLISTSVIEEGLDIPQCALVVRYDAPTEYRSYIQSKGR-AR 511
Cdd:cd18787    67 ERALKKFRSGKVRVLVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRtGR 120
PRK01172 PRK01172
ATP-dependent DNA helicase;
21-186 5.55e-05

ATP-dependent DNA helicase;


Pssm-ID: 100801 [Multi-domain]  Cd Length: 674  Bit Score: 47.96  E-value: 5.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   21 LEEIASSKNTIIHLPTGSGKTFIAQRLI-KKFRNQLKkpwgeggkrSFFLVntvPLVNQQKNVIEMMCPVDGVGAYSSED 99
Cdd:PRK01172   31 IEQLRKGENVIVSVPTAAGKTLIAYSAIyETFLAGLK---------SIYIV---PLRSLAMEKYEELSRLRSLGMRVKIS 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  100 GVDYWKKADWdseLARNQVIVMTSQILSDMLTHAYIRIEDINLIIFDEChHAVEDHPMRVIMKHFLNCKAHEQP--RVLG 177
Cdd:PRK01172   99 IGDYDDPPDF---IKRYDVVILTSEKADSLIHHDPYIINDVGLIVADEI-HIIGDEDRGPTLETVLSSARYVNPdaRILA 174


                  ....*....
gi 302318908  178 LTATLLNGN 186
Cdd:PRK01172  175 LSATVSNAN 183
HsdR COG4096
Type I site-specific restriction endonuclease, part of a restriction-modification system ...
 9-181 9.97e-05

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


Pssm-ID: 443272 [Multi-domain]  Cd Length: 806  Bit Score: 47.14  E-value: 9.97e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908    9 YHEQKARPYQ-----AILEEIASSKNTI-IHLPTGSGKTFIAQRLIKKFrnqLKKPWgegGKRSFFLVNTVPLVNQQKNv 82
Cdd:COG4096   154 NDGIALRYYQieairRVEEAIAKGQRRAlLVMATGTGKTRTAIALIYRL---LKAGR---AKRILFLADRNALVDQAKN- 226

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   83 iemmcpvdgvgAYSS--EDGVDYWKKADWDSELARN-QVIV-----MTSQILSDMLTHAY--IRIEDINLIIFDECHHAV 152
Cdd:COG4096   227 -----------AFKPflPDLDAFTKLYNKSKDIDKSaRVYFstyqtMMNRIDGEEEEPGYrqFPPDFFDLIIIDECHRGI 295

                         170       180
                  ....*....|....*....|....*....
gi 302318908  153 edhpmRVIMKHFlncKAheqpRVLGLTAT 181
Cdd:COG4096   296 ys-kwRAILDYF---DA----LQIGLTAT 316
DEXHc_cas3 cd17930
DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase ...
 28-182 1.28e-04

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


Pssm-ID: 350688 [Multi-domain]  Cd Length: 186  Bit Score: 44.59  E-value: 1.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   28 KNTIIHLPTGSGKTFIAQRLIKKFRNQLKKPwgeggkRSFFLVNTVPLVNQQKNVI-EMMCPVDG-------------VG 93
Cdd:cd17930     2 GLVILEAPTGSGKTEAALLWALKLAARGGKR------RIIYALPTRATINQMYERIrEILGRLDDedkvlllhskaalEL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   94 AYSSEDGVDYWKKADWDSELARN----QVIVMTS-QILSDMLT--HAYIRIEDI--NLIIFDEChHAVEDHPMRVI---- 160
Cdd:cd17930    76 LESDEEPDDDPVEAVDWALLLKRswlaPIVVTTIdQLLESLLKykHFERRLHGLanSVVVLDEV-QAYDPEYMALLlkal 154

                         170       180
                  ....*....|....*....|....
gi 302318908  161 --MKHFLNCKaheqprVLGLTATL 182
Cdd:cd17930   155 leLLGELGGP------VVLMTATL 172
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 468-520 1.32e-04

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


Pssm-ID: 350177 [Multi-domain]  Cd Length: 171  Bit Score: 44.16  E-value: 1.32e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 302318908  468 GDLNCLISTSVIEEGLDIPQCALVVRYDAPTE-----YRSYIQSKGRARSSEASFVIL 520
Cdd:cd18790    76 GEFDVLVGINLLREGLDLPEVSLVAILDADKEgflrsETSLIQTIGRAARNVNGKVIL 133
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 467-532 2.72e-04

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 45.61  E-value: 2.72e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 302318908  467 NGDLNCLISTSVIEEGLDIPQCALVVRYDAPTEYRSYIQSKGR-ARSSEASFVILVdIEDKQSFLIK 532
Cdd:PRK11634  293 DGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRtGRAGRAGRALLF-VENRERRLLR 358
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 389-521 7.07e-04

C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR 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: 350183 [Multi-domain]  Cd Length: 150  Bit Score: 41.87  E-value: 7.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908  389 LLKVNHSRKPLcgiIFTKQRFTSKILYNILMDLKKARPDEFEFLKHdfvvGFSINpfKSTRE--EHYLKKssqkailgfn 466
Cdd:cd18796    32 IFLLERHKSTL---VFTNTRSQAERLAQRLRELCPDRVPPDFIALH----HGSLS--RELREevEAALKR---------- 92

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 302318908  467 nGDLNCLISTSVIEEGLDIPQCALVVRYDAPTEYRSYIQSKGRA--RSSEASFVILV 521
Cdd:cd18796    93 -GDLKVVVATSSLELGIDIGDVDLVIQIGSPKSVARLLQRLGRSghRPGAASKGRLV 148
DEXHc_XPB cd18029
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ...
 11-183 9.87e-04

DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription factor complex helicase XPB subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350787 [Multi-domain]  Cd Length: 169  Bit Score: 41.90  E-value: 9.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   11 EQKARPYQailEEIASS-------KNTIIHLPTGSGKTFI---AQRLIKkfrnqlkkpwgeggKRSFFLVNTVPLVNQQK 80
Cdd:cd18029     6 STQLRPYQ---EKALSKmfgngraRSGVIVLPCGAGKTLVgitAACTIK--------------KSTLVLCTSAVSVEQWR 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   81 NVIEMMC--PVDGVGAYSSEDGVDYWKKAdwdselarnqVIVMTSQILSD--------MLTHAYIRIEDINLIIFDECHh 150
Cdd:cd18029    69 RQFLDWTtiDDEQIGRFTSDKKEIFPEAG----------VTVSTYSMLANtrkrspesEKFMEFITEREWGLIILDEVH- 137

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 302318908  151 aVEDHPM--RVIMKHFLNCKaheqprvLGLTATLL 183
Cdd:cd18029   138 -VVPAPMfrRVLTLQKAHCK-------LGLTATLV 164
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
 464-521 9.91e-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: 41.09  E-value: 9.91e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 302318908  464 GFNNGDLNCLISTSVIEEGLDIPQCALVVRYDAPTEYRSYIQSKGRA-RSSEASFVILV 521
Cdd:cd18797    87 ELFNGELLGVVATNALELGIDIGGLDAVVLAGYPGSLASLWQQAGRAgRRGKDSLVILV 145
DEXHc_priA cd17929
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ...
 17-181 9.96e-04

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: 41.81  E-value: 9.96e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   17 YQAILEEIASSKNTIIHLPTGSGKTFIAQRLIKKFRNQlkkpwgegGKRSFFLVNTVPLVNQQKNVIEMMCPvDGVGAYS 96
Cdd:cd17929     5 YEAIVSSLGGFKTFLLHGVTGSGKTEVYIELIEKVLAK--------GKQVLVLVPEISLTPQLIKRFKKRFG-DKVAVLH 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   97 SE----DGVDYWKKAdwdselARNQVIVMT---SQILSDMlthayiriEDINLIIFDECH------------HAVEdhpM 157
Cdd:cd17929    76 SKlsdkERADEWRKI------KRGEAKVVIgarSALFAPF--------KNLGLIIVDEEHdssykqdsgpryHARD---V 138

                         170       180
                  ....*....|....*....|....
gi 302318908  158 RVIMKHFLNCkaheqPRVLGlTAT 181
Cdd:cd17929   139 AIYRAKLENA-----PVVLG-SAT 156
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 464-521 1.19e-03

ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, recombination and repair];


Pssm-ID: 440818 [Multi-domain]  Cd Length: 758  Bit Score: 43.67  E-value: 1.19e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 302318908  464 GFNNGDLNCLISTSVIEEGLDIPQCALVVRYDAPTEYRSYIQSKGRA-RSSEASFVILV 521
Cdd:COG1205   339 GLRSGELLGVVSTNALELGIDIGGLDAVVLAGYPGTRASFWQQAGRAgRRGQDSLVVLV 397
DEXHc_RE_I_HsdR cd18030
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ...
 14-166 1.29e-03

DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of type I restriction-modification enzymes contains the DNA cleavage and ATP-dependent DNA translocation activities of the heteromeric complex. It 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: 350788 [Multi-domain]  Cd Length: 208  Bit Score: 41.83  E-value: 1.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   14 ARPYQ-----AILEEIASSKNT-------IIHLPTGSGKTFIAQRLIKKFRNQLKKPwgeggkRSFFLVNTVPLVNQQKN 81
Cdd:cd18030    22 ARYYQyyaveAALERIKTATNKdgdkkggYIWHTQGSGKSLTMFKAAKLLIEDPKNP------KVVFVVDRKDLDYQTSS 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302318908   82 VIEMMCPVDGVGAYSSEDGVDYWKKADwdselarNQVIVMTSQILSDM---LTHAYIRIEDINLIIFDECHHAVEDHPMR 158
Cdd:cd18030    96 TFSRFAAEDVVRANSTKELKELLKNLS-------GGIIVTTIQKFNNAvkeESKPVLIYRKNIVVIVDEAHRSQFGELAK 168


                  ....*...
gi 302318908  159 VIMKHFLN 166
Cdd:cd18030   169 ALKKALPN 176
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 463-531 1.65e-03

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


Pssm-ID: 350186 [Multi-domain]  Cd Length: 116  Bit Score: 39.85  E-value: 1.65e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 302318908  463 LGFNNGDLNCLISTSVIEEGLDIPQCALVVrYDAPTEYRS-YIQSKGRA-RSSeasfvilvdiEDKQSFLI 531
Cdd:cd18799    53 LFFGELKPPILVTVDLLTTGVDIPEVDNVV-FLRPTESRTlFLQMLGRGlRLH----------EGKDFFTI 112
uvrb TIGR00631
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ...
 468-510 4.05e-03

excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273185 [Multi-domain]  Cd Length: 655  Bit Score: 41.90  E-value: 4.05e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 302318908   468 GDLNCLISTSVIEEGLDIPQCALVVRYDAPTE-----YRSYIQSKGRA 510
Cdd:TIGR00631  491 GEFDVLVGINLLREGLDLPEVSLVAILDADKEgflrsERSLIQTIGRA 538
PTZ00424 PTZ00424
helicase 45; Provisional
 465-524 7.64e-03

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 40.58  E-value: 7.64e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 302318908  465 FNNGDLNCLISTSVIEEGLDIPQCALVVRYDAPTEYRSYIQSKGRA-----RSSEASFVILVDIE 524
Cdd:PTZ00424  313 FRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSgrfgrKGVAINFVTPDDIE 377
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
459-504 7.67e-03

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 40.52  E-value: 7.67e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 302318908  459 QKAILGFNNGDLNCLISTSVIEEGLDIPQCALVVRYDAPTEYRSYI 504
Cdd:COG0513   281 ERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYV 326
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 459-521 9.33e-03

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: 38.86  E-value: 9.33e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 302318908  459 QKAILGFNNGDLNCLISTSVIEEGLDIPQCALVVRYDAPTEYRSYI-QSKGR-ARSSEASFVILV 521
Cdd:cd18811    77 DAVMAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLhQLRGRvGRGDHQSYCLLV 141
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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