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Conserved domains on  [gi|2462557479|ref|XP_054173141|]
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ATP-dependent RNA helicase DHX58 isoform X2 [Homo sapiens]

Protein Classification

DEAD/DEAH box helicase; DEAD/DEAH box helicase family protein( domain architecture ID 13208932)

DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA| DEAD/DEAH box containing ATP-dependent helicase family protein may catalyze the unwinding of DNA or RNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 1-200 1.26e-133

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


The actual alignment was detected with superfamily member cd18075:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 200  Bit Score: 385.75  E-value: 1.26e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   1 MELRSYQWEVIMPALEGKNIIIWLPTGAGKTRAAAYVAKRHLETVDGAKVVVLVNRVHLVTQHGEEFRRMLDGRWTVTTL 80
Cdd:cd18075     1 MELHGYQWEVVAPALRGKNSIIWLPTGAGKTRAAVYVARRHLETKRGAKVAVLVNKVHLVDQHLEKEFHVLLDKYTVTAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  81 SGDMGPRAGFGHLARCHDLLICTAELLQMALTSPEEEEHVELTVFSLIVVDECHHTHKDTVYNVIMSQYLELKLQRAQPL 160
Cdd:cd18075    81 SGDSSHKCFFGQLARGSDVVICTAQILQNALLSGEEEAHVELTDFSLLVIDECHHTHKEAVYNKIMLSYLEKKLSRQGDL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2462557479 161 PQVLGLTASPGTGGASKLDGAINHVLQLCANLDTWCIMSP 200
Cdd:cd18075   161 PQILGLTASPGTGGATSFDGAVEHILQICANLDTWVIMSA 200
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 349-483 2.29e-54

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: 179.71  E-value: 2.29e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 349 PKLEMLEKILQRQFSSSNSPRGIIFTRTRQSAHSLLLWLQQQQGLqTVDIRAQLLIGAGNSSQST--HMTQRDQQEVIQK 426
Cdd:cd18802     7 PKLQKLIEILREYFPKTPDFRGIIFVERRATAVVLSRLLKEHPST-LAFIRCGFLIGRGNSSQRKrsLMTQRKQKETLDK 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462557479 427 FQDGTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEISMVQARGRARADQSVYAFVA 483
Cdd:cd18802    86 FRDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
MDA5_ID cd12090
Insert domain of MDA5; MDA5 (melanoma-differentiation-associated gene 5, also known as IFIH1), ...
 227-345 3.55e-49

Insert domain of MDA5; MDA5 (melanoma-differentiation-associated gene 5, also known as IFIH1), as well as RIG-I (Retinoic acid Inducible Gene I, also known as DDX58) and LPG2 (also known as DHX58), contain two N-terminal CARD domains and a C-terminal SF2 helicase domain. They are cytoplasmic DEAD box RNA helicases acting as key innate immune pattern-recognition receptor (PRRs) that play an important role in host antiviral response by sensing incoming viral RNA. Their SF2 helicase domain is comprised of 3 structural domains, the 2 generally conserved helicase domains and a helical domain inserted between the two domains. The inserted domain is involved in conformational changes upon ligand binding.


:

Pssm-ID: 277189  Cd Length: 120  Bit Score: 165.18  E-value: 3.55e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 227 DPFGDLLKKLMDQIHDHLEMPEL---SRKFGTQMYEQQVVKLSEAAALAGLQEQRVYALHLRRYNDALLIHDTVRAVDAL 303
Cdd:cd12090     1 DPFGDIIKKLMTDIEELLKMTPPdiqPREFGTQKYEQWVVTLEKKAAKLGNRALRTCAEHLRKYNDALLINDTARMKDAL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2462557479 304 AALQDFYHREHVTKTQilCAERRLLALFDDRKNELAHLATHG 345
Cdd:cd12090    81 QYLKEFYTNLKEAKFD--ETERFLTDLFEENLEELKKLARDP 120
 
Name Accession Description Interval E-value
DEXHc_RLR-3 cd18075
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ...
 1-200 1.26e-133

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: 385.75  E-value: 1.26e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   1 MELRSYQWEVIMPALEGKNIIIWLPTGAGKTRAAAYVAKRHLETVDGAKVVVLVNRVHLVTQHGEEFRRMLDGRWTVTTL 80
Cdd:cd18075     1 MELHGYQWEVVAPALRGKNSIIWLPTGAGKTRAAVYVARRHLETKRGAKVAVLVNKVHLVDQHLEKEFHVLLDKYTVTAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  81 SGDMGPRAGFGHLARCHDLLICTAELLQMALTSPEEEEHVELTVFSLIVVDECHHTHKDTVYNVIMSQYLELKLQRAQPL 160
Cdd:cd18075    81 SGDSSHKCFFGQLARGSDVVICTAQILQNALLSGEEEAHVELTDFSLLVIDECHHTHKEAVYNKIMLSYLEKKLSRQGDL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2462557479 161 PQVLGLTASPGTGGASKLDGAINHVLQLCANLDTWCIMSP 200
Cdd:cd18075   161 PQILGLTASPGTGGATSFDGAVEHILQICANLDTWVIMSA 200
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 349-483 2.29e-54

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: 179.71  E-value: 2.29e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 349 PKLEMLEKILQRQFSSSNSPRGIIFTRTRQSAHSLLLWLQQQQGLqTVDIRAQLLIGAGNSSQST--HMTQRDQQEVIQK 426
Cdd:cd18802     7 PKLQKLIEILREYFPKTPDFRGIIFVERRATAVVLSRLLKEHPST-LAFIRCGFLIGRGNSSQRKrsLMTQRKQKETLDK 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462557479 427 FQDGTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEISMVQARGRARADQSVYAFVA 483
Cdd:cd18802    86 FRDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
1-522 3.58e-50

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 183.39  E-value: 3.58e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   1 MELRSYQWEVIMPALEgKNIIIWLPTGAGKTRAAAYVAKRHLETVDGaKVVVLVNRVHLVTQHGEEFRRMLDGRWT-VTT 79
Cdd:COG1111     2 IERRLYQLNLAASALR-KNTLVVLPTGLGKTAVALLVIAERLHKKGG-KVLFLAPTKPLVEQHAEFFKEALNIPEDeIVV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  80 LSGDMGP--RAGFGHLARchdLLICTAELLQMALtspeEEEHVELTVFSLIVVDECHHTHKDTVYNVIMSQYLElklQRA 157
Cdd:COG1111    80 FTGEVSPekRKELWEKAR---IIVATPQVIENDL----IAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHE---DAK 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 158 QPLpqVLGLTASPGtggaskldGAINHVLQLCANLDTWCIMSPQNCCPQLQEHSQQpcKQYNLCHRRSQDPFGDLLKKLM 237
Cdd:COG1111   150 DPL--ILGMTASPG--------SDEEKIEEVCENLGIENVEVRTEEDPDVAPYVHD--TEVEWIRVELPEELKEIRDLLN 217

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 238 DQIHDHLEmpELsRKFGTQMYEQQVVKLSEaaaLAGLQE--QRVYALHLRRYNDALLIHDTV----RAVDAL-----AAL 306
Cdd:COG1111   218 EVLDDRLK--KL-KELGVIVSTSPDLSKKD---LLALQKklQRRIREDDSEGYRAISILAEAlklrHALELLetqgvEAL 291

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 307 QDFYHR--EHVTKTQILCAERRLLAlfDDRKNELAHLA-THGPENPKLEMLEKILQRQFSSSNSPRGIIFTRTRQSAHSL 383
Cdd:COG1111   292 LRYLERleEEARSSGGSKASKRLVS--DPRFRKAMRLAeEADIEHPKLSKLREILKEQLGTNPDSRIIVFTQYRDTAEMI 369

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 384 LLWLQQQqglqtvDIRAQLLIGAGNSSQSTHMTQRDQQEVIQKFQDGTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEI 463
Cdd:COG1111   370 VEFLSEP------GIKAGRFVGQASKEGDKGLTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPVPSEI 443

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462557479 464 SMVQARGR-ARADQ-SVYAFVAtEGSRE-------LKREliNEALETLMEQAvAAVQKMDQAEYQAKE 522
Cdd:COG1111   444 RSIQRKGRtGRKREgRVVVLIA-KGTRDeayywssRRKE--KKMKSILKKLK-KLLDKQEKEKLKESA 507
MDA5_ID cd12090
Insert domain of MDA5; MDA5 (melanoma-differentiation-associated gene 5, also known as IFIH1), ...
 227-345 3.55e-49

Insert domain of MDA5; MDA5 (melanoma-differentiation-associated gene 5, also known as IFIH1), as well as RIG-I (Retinoic acid Inducible Gene I, also known as DDX58) and LPG2 (also known as DHX58), contain two N-terminal CARD domains and a C-terminal SF2 helicase domain. They are cytoplasmic DEAD box RNA helicases acting as key innate immune pattern-recognition receptor (PRRs) that play an important role in host antiviral response by sensing incoming viral RNA. Their SF2 helicase domain is comprised of 3 structural domains, the 2 generally conserved helicase domains and a helical domain inserted between the two domains. The inserted domain is involved in conformational changes upon ligand binding.


Pssm-ID: 277189  Cd Length: 120  Bit Score: 165.18  E-value: 3.55e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 227 DPFGDLLKKLMDQIHDHLEMPEL---SRKFGTQMYEQQVVKLSEAAALAGLQEQRVYALHLRRYNDALLIHDTVRAVDAL 303
Cdd:cd12090     1 DPFGDIIKKLMTDIEELLKMTPPdiqPREFGTQKYEQWVVTLEKKAAKLGNRALRTCAEHLRKYNDALLINDTARMKDAL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2462557479 304 AALQDFYHREHVTKTQilCAERRLLALFDDRKNELAHLATHG 345
Cdd:cd12090    81 QYLKEFYTNLKEAKFD--ETERFLTDLFEENLEELKKLARDP 120
PRK13766 PRK13766
Hef nuclease; Provisional
 1-472 3.25e-41

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 158.11  E-value: 3.25e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   1 MELRSYQWEVIMPALEgKNIIIWLPTGAGKTRAAAYVAKRHLETVDGaKVVVLVNRVHLVTQHGEEFRRMLDGRWT-VTT 79
Cdd:PRK13766   14 IEARLYQQLLAATALK-KNTLVVLPTGLGKTAIALLVIAERLHKKGG-KVLILAPTKPLVEQHAEFFRKFLNIPEEkIVV 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  80 LSGDMGP--RAgfghlARCHDLLICTAellqmaltSPEEEEH------VELTVFSLIVVDECHHTHKDTVYNVIMSQYLE 151
Cdd:PRK13766   92 FTGEVSPekRA-----ELWEKAKVIVA--------TPQVIENdliagrISLEDVSLLIFDEAHRAVGNYAYVYIAERYHE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 152 lklQRAQPLpqVLGLTASPGtggaskldGAINHVLQLCANLDTWCImspqnccpQLQEHSQQPCKQYnlCHRRSQDPFGD 231
Cdd:PRK13766  159 ---DAKNPL--VLGLTASPG--------SDEEKIKEVCENLGIEHV--------EVRTEDDPDVKPY--VHKVKIEWVRV 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 232 LLKKLMDQIHDHLEmpelsrkfgtQMYEQQVVKLSEAA------------ALAGLQEQrvyaLHLRRYND------ALLI 293
Cdd:PRK13766  216 ELPEELKEIRDLLN----------EALKDRLKKLKELGvivsispdvskkELLGLQKK----LQQEIANDdsegyeAISI 281

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 294 HDTV----RAVDAL-----AALQDFYHR-------EHVTKtqilcAERRLLAlfDDRKNELAHLAT-HGPENPKLEMLEK 356
Cdd:PRK13766  282 LAEAmklrHAVELLetqgvEALRRYLERlreearsSGGSK-----ASKRLVE--DPRFRKAVRKAKeLDIEHPKLEKLRE 354

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 357 ILQRQFSSSNSPRGIIFTRTRQSAHSLLLWLQQQqglqtvDIRAQLLIGAGNSSQSTHMTQRDQQEVIQKFQDGTLNLLV 436
Cdd:PRK13766  355 IVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKE------GIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLV 428

                         490       500       510
                  ....*....|....*....|....*....|....*.
gi 2462557479 437 ATSVAEEGLDIPHCNVVVRYGLLTNEISMVQARGRA 472
Cdd:PRK13766  429 STSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRT 464
RIG-I_C pfam18119
RIG-I receptor C-terminal domain; This is the C-terminal domain of Innate Immune ...
 216-343 8.80e-34

RIG-I receptor C-terminal domain; This is the C-terminal domain of Innate Immune Pattern-Recognition Receptor RIG-I present in homo sapiens. RIG-I is a key cytosolic pattern-recognition receptors of the vertebrate innate immune system that form the first line of defense against RNA viral infection. RNA binding to RIG-I is mediated both by the C-terminal domain and by the helicase domain. The C-terminal domain specifically binds the 5'triphosphate end with a 10-fold higher affinity compared to 5'OH-dsRNA.


Pssm-ID: 465656  Cd Length: 139  Bit Score: 124.76  E-value: 8.80e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 216 KQYNLCHRRSQDPFGDLLKKLMDQIHDHL-------EMPEL-SRKFGTQMYEQQVVKLSEAAALAGLQEQRV----YALH 283
Cdd:pfam18119   2 KFVVKVTSRKEDPFGDIIKDIMSKIEDHLnksynldDLSKLkPSDKGTQKYEQWIVTLQKKGAEDPEEERRVcralCTEH 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 284 LRRYNDALLIHDTVRAVDALAALQDFYHREhvTKTQILCAERRLLALFDDRKNELAHLAT 343
Cdd:pfam18119  82 LRKYNDALIINDDARTKDALEYLLKFLKEL--KETKFDETERKLYRLFEEKREELQRLAT 139
DEXDc smart00487
DEAD-like helicases superfamily;
2-170 1.82e-22

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 95.25  E-value: 1.82e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479    2 ELRSYQWEVIMPALEG-KNIIIWLPTGAGKTRAAAYVAKRHLETVDGAKVVVLVNRVHLVTQHGEEFRRMLDGRW-TVTT 79
Cdd:smart00487   8 PLRPYQKEAIEALLSGlRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGlKVVG 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   80 LSGDMGPRAGFGHLAR-CHDLLICTAE-LLQMAltspeEEEHVELTVFSLIVVDECHHTHKDTVYNVIMSqylelKLQRA 157
Cdd:smart00487  88 LYGGDSKREQLRKLESgKTDILVTTPGrLLDLL-----ENDKLSLSNVDLVILDEAHRLLDGGFGDQLEK-----LLKLL 157

                          170
                   ....*....|...
gi 2462557479  158 QPLPQVLGLTASP 170
Cdd:smart00487 158 PKNVQLLLLSATP 170
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 350-472 5.63e-20

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: 84.95  E-value: 5.63e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 350 KLEMLEKILQRqfssSNSPRGIIFTRTRQSAHSLLLWLQQqqglqtvDIRAQLLIGagnssqstHMTQRDQQEVIQKFQD 429
Cdd:pfam00271   2 KLEALLELLKK----ERGGKVLIFSQTKKTLEAELLLEKE-------GIKVARLHG--------DLSQEEREEILEDFRK 62

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2462557479 430 GTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEISMVQARGRA 472
Cdd:pfam00271  63 GKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
ResIII pfam04851
Type III restriction enzyme, res subunit;
1-170 1.44e-18

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 82.72  E-value: 1.44e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   1 MELRSYQWEVIMPALEG-----KNIIIWLPTGAGKTRAAAYVAKRHLETVDGAKVVVLVNRVHLVTQHGEEFRRMLDGRW 75
Cdd:pfam04851   2 LELRPYQIEAIENLLESikngqKRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPNYV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  76 TVTT-LSGDMGPRAGFGhlarcHDLLICTAEllqmALTSPEEEEHVELTV--FSLIVVDECHHTHKDTVYNVImsQYLel 152
Cdd:pfam04851  82 EIGEiISGDKKDESVDD-----NKIVVTTIQ----SLYKALELASLELLPdfFDVIIIDEAHRSGASSYRNIL--EYF-- 148

                         170
                  ....*....|....*...
gi 2462557479 153 klqraqPLPQVLGLTASP 170
Cdd:pfam04851 149 ------KPAFLLGLTATP 160
HELICc smart00490
helicase superfamily c-terminal domain;
415-472 2.83e-15

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 70.70  E-value: 2.83e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462557479  415 MTQRDQQEVIQKFQDGTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEISMVQARGRA 472
Cdd:smart00490  21 LSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
350-505 2.72e-11

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 65.55  E-value: 2.72e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 350 KLEMLEKILQRQfsssNSPRGIIFTRTRQsahslllwlqqqqglqTVDIRAQLLIGAGNSSQSTH--MTQRDQQEVIQKF 427
Cdd:COG0513   228 KLELLRRLLRDE----DPERAIVFCNTKR----------------GADRLAEKLQKRGISAAALHgdLSQGQRERALDAF 287

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 428 QDGTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEISMVQaR-GR-ARADQS--VYAFVATEGSRELKRelINEALETLM 503
Cdd:COG0513   288 RNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYVH-RiGRtGRAGAEgtAISLVTPDERRLLRA--IEKLIGQKI 364


                  ..
gi 2462557479 504 EQ 505
Cdd:COG0513   365 EE 366
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 350-448 4.49e-07

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 52.25  E-value: 4.49e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 350 KLEMLEKILQRQfsssNSPRGIIFTRTRQSAHSLLLWLQQQqglqtvDIRAQLLIGagnssqstHMTQRDQQEVIQKFQD 429
Cdd:PRK11192  232 KTALLCHLLKQP----EVTRSIVFVRTRERVHELAGWLRKA------GINCCYLEG--------EMVQAKRNEAIKRLTD 293

                          90
                  ....*....|....*....
gi 2462557479 430 GTLNLLVATSVAEEGLDIP 448
Cdd:PRK11192  294 GRVNVLVATDVAARGIDID 312
 
Name Accession Description Interval E-value
DEXHc_RLR-3 cd18075
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ...
 1-200 1.26e-133

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: 385.75  E-value: 1.26e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   1 MELRSYQWEVIMPALEGKNIIIWLPTGAGKTRAAAYVAKRHLETVDGAKVVVLVNRVHLVTQHGEEFRRMLDGRWTVTTL 80
Cdd:cd18075     1 MELHGYQWEVVAPALRGKNSIIWLPTGAGKTRAAVYVARRHLETKRGAKVAVLVNKVHLVDQHLEKEFHVLLDKYTVTAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  81 SGDMGPRAGFGHLARCHDLLICTAELLQMALTSPEEEEHVELTVFSLIVVDECHHTHKDTVYNVIMSQYLELKLQRAQPL 160
Cdd:cd18075    81 SGDSSHKCFFGQLARGSDVVICTAQILQNALLSGEEEAHVELTDFSLLVIDECHHTHKEAVYNKIMLSYLEKKLSRQGDL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2462557479 161 PQVLGLTASPGTGGASKLDGAINHVLQLCANLDTWCIMSP 200
Cdd:cd18075   161 PQILGLTASPGTGGATSFDGAVEHILQICANLDTWVIMSA 200
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 1-199 2.58e-76

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: 239.30  E-value: 2.58e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   1 MELRSYQWEVIMPALEGKNIIIWLPTGAGKTRAAAYVAKRHLE----TVDGAKVVVLVNRVHLVTQHGEEFRRMLDGRWT 76
Cdd:cd18036     1 LELRNYQLELVLPALRGKNTIICAPTGSGKTRVAVYICRHHLEkrrsAGEKGRVVVLVNKVPLVEQQLEKFFKYFRKGYK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  77 VTTLSGDMGPRAGFGHLARCHDLLICTAELLQMALTSPEEEEHVELTVFSLIVVDECHHTHKDTVYNVIMSQYLELKLQR 156
Cdd:cd18036    81 VTGLSGDSSHKVSFGQIVKASDVIICTPQILINNLLSGREEERVYLSDFSLLIFDECHHTQKEHPYNKIMRMYLDKKLSS 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2462557479 157 AQPLPQVLGLTASPGTGGASKLDGAINHVLQLCANLDTWCIMS 199
Cdd:cd18036   161 QGPLPQILGLTASPGVGGARSFEEALEHILKLCANLDASVIAT 203
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 2-199 1.44e-70

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: 224.23  E-value: 1.44e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   2 ELRSYQWEVIMPALEGKNIIIWLPTGAGKTRAAAYVAKRHLETVD---GAKVVVLVNRVHLVTQHGEEFRRMLDGRW-TV 77
Cdd:cd17927     2 KPRNYQLELAQPALKGKNTIICLPTGSGKTFVAVLICEHHLKKFPagrKGKVVFLANKVPLVEQQKEVFRKHFERPGyKV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  78 TTLSGDMGPRAGFGHLARCHDLLICTAELLQMALTSPEEeehVELTVFSLIVVDECHHTHKDTVYNVIMSQYLELKLQRA 157
Cdd:cd17927    82 TGLSGDTSENVSVEQIVESSDVIIVTPQILVNDLKSGTI---VSLSDFSLLVFDECHNTTKNHPYNEIMFRYLDQKLGSS 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2462557479 158 QPLPQVLGLTASPGTGGASKLDGAINHVLQLCANLDTWCIMS 199
Cdd:cd17927   159 GPLPQILGLTASPGVGGAKNTEEALEHICKLCANLDISVIAT 200
DEXHc_RLR-2 cd18074
DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma ...
 1-199 1.47e-64

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: 208.95  E-value: 1.47e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   1 MELRSYQWEVIMPALEGKNIIIWLPTGAGKTRAAAYVAKRHL----ETVDGAKVVVLVNRVHLVTQH-GEEFRRMLDGRW 75
Cdd:cd18074     1 LTLRDYQMEVAKPALEGKNIIICLPTGSGKTRVAVYITKDHLdkkrKASEPGKVIVLVNKVPLVEQHyRKEFNPFLKHWY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  76 TVTTLSGDMGPRAGFGHLARCHDLLICTAELLQMAL--TSPEEEEHVELTVFSLIVVDECHHTHKDTVYNVIMSQYLELK 153
Cdd:cd18074    81 QVIGLSGDSQLKISFPEVVKRYDVIICTAQILENSLlnATEEEDEGVQLSDFSLIIIDECHHTQKEAVYNNIMRRYLKQK 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2462557479 154 LQRAQ---------PLPQVLGLTASPGTGGASKLDGAINHVLQLCANLDTWCIMS 199
Cdd:cd18074   161 IKNRKqkkenkpliPLPQILGLTASPGVGGAKNNKKAEEHILKICANLDAFRIMT 215
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 349-483 2.29e-54

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: 179.71  E-value: 2.29e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 349 PKLEMLEKILQRQFSSSNSPRGIIFTRTRQSAHSLLLWLQQQQGLqTVDIRAQLLIGAGNSSQST--HMTQRDQQEVIQK 426
Cdd:cd18802     7 PKLQKLIEILREYFPKTPDFRGIIFVERRATAVVLSRLLKEHPST-LAFIRCGFLIGRGNSSQRKrsLMTQRKQKETLDK 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462557479 427 FQDGTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEISMVQARGRARADQSVYAFVA 483
Cdd:cd18802    86 FRDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
1-522 3.58e-50

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 183.39  E-value: 3.58e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   1 MELRSYQWEVIMPALEgKNIIIWLPTGAGKTRAAAYVAKRHLETVDGaKVVVLVNRVHLVTQHGEEFRRMLDGRWT-VTT 79
Cdd:COG1111     2 IERRLYQLNLAASALR-KNTLVVLPTGLGKTAVALLVIAERLHKKGG-KVLFLAPTKPLVEQHAEFFKEALNIPEDeIVV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  80 LSGDMGP--RAGFGHLARchdLLICTAELLQMALtspeEEEHVELTVFSLIVVDECHHTHKDTVYNVIMSQYLElklQRA 157
Cdd:COG1111    80 FTGEVSPekRKELWEKAR---IIVATPQVIENDL----IAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHE---DAK 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 158 QPLpqVLGLTASPGtggaskldGAINHVLQLCANLDTWCIMSPQNCCPQLQEHSQQpcKQYNLCHRRSQDPFGDLLKKLM 237
Cdd:COG1111   150 DPL--ILGMTASPG--------SDEEKIEEVCENLGIENVEVRTEEDPDVAPYVHD--TEVEWIRVELPEELKEIRDLLN 217

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 238 DQIHDHLEmpELsRKFGTQMYEQQVVKLSEaaaLAGLQE--QRVYALHLRRYNDALLIHDTV----RAVDAL-----AAL 306
Cdd:COG1111   218 EVLDDRLK--KL-KELGVIVSTSPDLSKKD---LLALQKklQRRIREDDSEGYRAISILAEAlklrHALELLetqgvEAL 291

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 307 QDFYHR--EHVTKTQILCAERRLLAlfDDRKNELAHLA-THGPENPKLEMLEKILQRQFSSSNSPRGIIFTRTRQSAHSL 383
Cdd:COG1111   292 LRYLERleEEARSSGGSKASKRLVS--DPRFRKAMRLAeEADIEHPKLSKLREILKEQLGTNPDSRIIVFTQYRDTAEMI 369

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 384 LLWLQQQqglqtvDIRAQLLIGAGNSSQSTHMTQRDQQEVIQKFQDGTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEI 463
Cdd:COG1111   370 VEFLSEP------GIKAGRFVGQASKEGDKGLTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPVPSEI 443

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462557479 464 SMVQARGR-ARADQ-SVYAFVAtEGSRE-------LKREliNEALETLMEQAvAAVQKMDQAEYQAKE 522
Cdd:COG1111   444 RSIQRKGRtGRKREgRVVVLIA-KGTRDeayywssRRKE--KKMKSILKKLK-KLLDKQEKEKLKESA 507
MDA5_ID cd12090
Insert domain of MDA5; MDA5 (melanoma-differentiation-associated gene 5, also known as IFIH1), ...
 227-345 3.55e-49

Insert domain of MDA5; MDA5 (melanoma-differentiation-associated gene 5, also known as IFIH1), as well as RIG-I (Retinoic acid Inducible Gene I, also known as DDX58) and LPG2 (also known as DHX58), contain two N-terminal CARD domains and a C-terminal SF2 helicase domain. They are cytoplasmic DEAD box RNA helicases acting as key innate immune pattern-recognition receptor (PRRs) that play an important role in host antiviral response by sensing incoming viral RNA. Their SF2 helicase domain is comprised of 3 structural domains, the 2 generally conserved helicase domains and a helical domain inserted between the two domains. The inserted domain is involved in conformational changes upon ligand binding.


Pssm-ID: 277189  Cd Length: 120  Bit Score: 165.18  E-value: 3.55e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 227 DPFGDLLKKLMDQIHDHLEMPEL---SRKFGTQMYEQQVVKLSEAAALAGLQEQRVYALHLRRYNDALLIHDTVRAVDAL 303
Cdd:cd12090     1 DPFGDIIKKLMTDIEELLKMTPPdiqPREFGTQKYEQWVVTLEKKAAKLGNRALRTCAEHLRKYNDALLINDTARMKDAL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2462557479 304 AALQDFYHREHVTKTQilCAERRLLALFDDRKNELAHLATHG 345
Cdd:cd12090    81 QYLKEFYTNLKEAKFD--ETERFLTDLFEENLEELKKLARDP 120
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
 2-197 6.82e-47

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: 162.30  E-value: 6.82e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   2 ELRSYQWEVIMPALEGKNIIIWLPTGAGKTRAAAYVAKRHLETV---DGAKVVVLVNRVHLVTQHGEEFRRMLDG-RWTV 77
Cdd:cd18073     2 KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFpqgQKGKVVFFATKVPVYEQQKSVFSKYFERhGYRV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  78 TTLSGDMGPRAGFGHLARCHDLLICTAELLQMALTSPEEEEhveLTVFSLIVVDECHHTHKDTVYNVIMSQYLELKL-QR 156
Cdd:cd18073    82 TGISGATAENVPVEQIIENNDIIILTPQILVNNLKKGTIPS---LSIFTLMIFDECHNTSGNHPYNMIMFRYLDQKLgGS 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2462557479 157 AQPLPQVLGLTASPGTGGASKLDGAINHVLQLCANLDTWCI 197
Cdd:cd18073   159 SGPLPQIIGLTASVGVGDAKNTDEALDYICKLCASLDASVI 199
PRK13766 PRK13766
Hef nuclease; Provisional
 1-472 3.25e-41

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 158.11  E-value: 3.25e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   1 MELRSYQWEVIMPALEgKNIIIWLPTGAGKTRAAAYVAKRHLETVDGaKVVVLVNRVHLVTQHGEEFRRMLDGRWT-VTT 79
Cdd:PRK13766   14 IEARLYQQLLAATALK-KNTLVVLPTGLGKTAIALLVIAERLHKKGG-KVLILAPTKPLVEQHAEFFRKFLNIPEEkIVV 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  80 LSGDMGP--RAgfghlARCHDLLICTAellqmaltSPEEEEH------VELTVFSLIVVDECHHTHKDTVYNVIMSQYLE 151
Cdd:PRK13766   92 FTGEVSPekRA-----ELWEKAKVIVA--------TPQVIENdliagrISLEDVSLLIFDEAHRAVGNYAYVYIAERYHE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 152 lklQRAQPLpqVLGLTASPGtggaskldGAINHVLQLCANLDTWCImspqnccpQLQEHSQQPCKQYnlCHRRSQDPFGD 231
Cdd:PRK13766  159 ---DAKNPL--VLGLTASPG--------SDEEKIKEVCENLGIEHV--------EVRTEDDPDVKPY--VHKVKIEWVRV 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 232 LLKKLMDQIHDHLEmpelsrkfgtQMYEQQVVKLSEAA------------ALAGLQEQrvyaLHLRRYND------ALLI 293
Cdd:PRK13766  216 ELPEELKEIRDLLN----------EALKDRLKKLKELGvivsispdvskkELLGLQKK----LQQEIANDdsegyeAISI 281

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 294 HDTV----RAVDAL-----AALQDFYHR-------EHVTKtqilcAERRLLAlfDDRKNELAHLAT-HGPENPKLEMLEK 356
Cdd:PRK13766  282 LAEAmklrHAVELLetqgvEALRRYLERlreearsSGGSK-----ASKRLVE--DPRFRKAVRKAKeLDIEHPKLEKLRE 354

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 357 ILQRQFSSSNSPRGIIFTRTRQSAHSLLLWLQQQqglqtvDIRAQLLIGAGNSSQSTHMTQRDQQEVIQKFQDGTLNLLV 436
Cdd:PRK13766  355 IVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKE------GIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLV 428

                         490       500       510
                  ....*....|....*....|....*....|....*.
gi 2462557479 437 ATSVAEEGLDIPHCNVVVRYGLLTNEISMVQARGRA 472
Cdd:PRK13766  429 STSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRT 464
RIG-I_C pfam18119
RIG-I receptor C-terminal domain; This is the C-terminal domain of Innate Immune ...
 216-343 8.80e-34

RIG-I receptor C-terminal domain; This is the C-terminal domain of Innate Immune Pattern-Recognition Receptor RIG-I present in homo sapiens. RIG-I is a key cytosolic pattern-recognition receptors of the vertebrate innate immune system that form the first line of defense against RNA viral infection. RNA binding to RIG-I is mediated both by the C-terminal domain and by the helicase domain. The C-terminal domain specifically binds the 5'triphosphate end with a 10-fold higher affinity compared to 5'OH-dsRNA.


Pssm-ID: 465656  Cd Length: 139  Bit Score: 124.76  E-value: 8.80e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 216 KQYNLCHRRSQDPFGDLLKKLMDQIHDHL-------EMPEL-SRKFGTQMYEQQVVKLSEAAALAGLQEQRV----YALH 283
Cdd:pfam18119   2 KFVVKVTSRKEDPFGDIIKDIMSKIEDHLnksynldDLSKLkPSDKGTQKYEQWIVTLQKKGAEDPEEERRVcralCTEH 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 284 LRRYNDALLIHDTVRAVDALAALQDFYHREhvTKTQILCAERRLLALFDDRKNELAHLAT 343
Cdd:pfam18119  82 LRKYNDALIINDDARTKDALEYLLKFLKEL--KETKFDETERKLYRLFEEKREELQRLAT 139
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 1-179 9.14e-33

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: 123.92  E-value: 9.14e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   1 MELRSYQWEVIMPALEgKNIIIWLPTGAGKTRAAAYVAKRHLETVDGAK-----VVVLVNRVHLVTQHGEEFRRMLDGRw 75
Cdd:cd18034     1 FTPRSYQLELFEAALK-RNTIVVLPTGSGKTLIAVMLIKEMGELNRKEKnpkkrAVFLVPTVPLVAQQAEAIRSHTDLK- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  76 tVTTLSGDMGPRAG-FGHLARC---HDLLICTAELLQMALTspeeeeHVELTV--FSLIVVDECHHTHKDTVYNVIMSQY 149
Cdd:cd18034    79 -VGEYSGEMGVDKWtKERWKEElekYDVLVMTAQILLDALR------HGFLSLsdINLLIFDECHHATGDHPYARIMKEF 151

                         170       180       190
                  ....*....|....*....|....*....|
gi 2462557479 150 leLKLQRAQPLPQVLGLTASPGTGGASKLD 179
Cdd:cd18034   152 --YHLEGRTSRPRILGLTASPVNGKGDPKS 179
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 333-472 1.72e-25

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: 102.05  E-value: 1.72e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 333 DRKNELAHlathgpenPKLEMLEKILQRQFSSSNSP---RGIIFTRTRQSAHSLLLWLQQQQGLqtvdIRAQLLIGAGNS 409
Cdd:cd18801     1 KRKVEKIH--------PKLEKLEEIVKEHFKKKQEGsdtRVIIFSEFRDSAEEIVNFLSKIRPG----IRATRFIGQASG 68

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462557479 410 SQSTHMTQRDQQEVIQKFQDGTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEISMVQARGRA 472
Cdd:cd18801    69 KSSKGMSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMIQRMGRT 131
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 17-168 4.62e-23

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: 95.16  E-value: 4.62e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  17 GKNIIIWLPTGAGKTRAAAYVAKRHLETvDGAKVVVLVNRVHLVTQHGEEFRRMLDGRWTVTTLSGDMGPRAGFGHLARC 96
Cdd:cd00046     1 GENVLITAPTGSGKTLAALLAALLLLLK-KGKKVLVLVPTKALALQTAERLRELFGPGIRVAVLVGGSSAEEREKNKLGD 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462557479  97 HDLLICTAELLQMALtspEEEEHVELTVFSLIVVDECHHTHKDTVYNVIMSQYLelkLQRAQPLPQVLGLTA 168
Cdd:cd00046    80 ADIIIATPDMLLNLL---LREDRLFLKDLKLIIVDEAHALLIDSRGALILDLAV---RKAGLKNAQVILLSA 145
DEXDc smart00487
DEAD-like helicases superfamily;
2-170 1.82e-22

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 95.25  E-value: 1.82e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479    2 ELRSYQWEVIMPALEG-KNIIIWLPTGAGKTRAAAYVAKRHLETVDGAKVVVLVNRVHLVTQHGEEFRRMLDGRW-TVTT 79
Cdd:smart00487   8 PLRPYQKEAIEALLSGlRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGlKVVG 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   80 LSGDMGPRAGFGHLAR-CHDLLICTAE-LLQMAltspeEEEHVELTVFSLIVVDECHHTHKDTVYNVIMSqylelKLQRA 157
Cdd:smart00487  88 LYGGDSKREQLRKLESgKTDILVTTPGrLLDLL-----ENDKLSLSNVDLVILDEAHRLLDGGFGDQLEK-----LLKLL 157

                          170
                   ....*....|...
gi 2462557479  158 QPLPQVLGLTASP 170
Cdd:smart00487 158 PKNVQLLLLSATP 170
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 350-472 5.63e-20

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: 84.95  E-value: 5.63e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 350 KLEMLEKILQRqfssSNSPRGIIFTRTRQSAHSLLLWLQQqqglqtvDIRAQLLIGagnssqstHMTQRDQQEVIQKFQD 429
Cdd:pfam00271   2 KLEALLELLKK----ERGGKVLIFSQTKKTLEAELLLEKE-------GIKVARLHG--------DLSQEEREEILEDFRK 62

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2462557479 430 GTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEISMVQARGRA 472
Cdd:pfam00271  63 GKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
1-501 7.33e-20

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 92.78  E-value: 7.33e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   1 MELRSYQ------WEVIMPALEGKNIIIwLPTGAGKTRAAAYVAKRHLEtvdGAKVVVLVNRVHLVTQHGEEFRRMLDgr 74
Cdd:COG1061    79 FELRPYQqealeaLLAALERGGGRGLVV-APTGTGKTVLALALAAELLR---GKRVLVLVPRRELLEQWAEELRRFLG-- 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  75 wtvttlsgdmGPRAGFGHLARCHDLLICTaelLQMALTSPEEEEHVELtvFSLIVVDECHHthkdtvynvIMSQYLELKL 154
Cdd:COG1061   153 ----------DPLAGGGKKDSDAPITVAT---YQSLARRAHLDELGDR--FGLVIIDEAHH---------AGAPSYRRIL 208

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 155 QRAQPlPQVLGLTASPGtggasKLDGainhvlqlcanldtwcimspqnccpqlqehsqQPCKQYNLCHRRSQDPFGDLLK 234
Cdd:COG1061   209 EAFPA-AYRLGLTATPF-----RSDG--------------------------------REILLFLFDGIVYEYSLKEAIE 250

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 235 KlmdqihDHLEMPElsrkfgtqmYEQQVVKLSEaaalaglqEQRVYALHLRRYNDAlLIHDTVRAVDALAALQDFYHREH 314
Cdd:COG1061   251 D------GYLAPPE---------YYGIRVDLTD--------ERAEYDALSERLREA-LAADAERKDKILRELLREHPDDR 306

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 315 vtktqilcaerrllalfddrknelahlathgpenpklemlekilqrqfsssnspRGIIFTRTRQSAHslllwlqqqqglq 394
Cdd:COG1061   307 ------------------------------------------------------KTLVFCSSVDHAE------------- 319

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 395 tvDIrAQLLIGAGNSSQ--STHMTQRDQQEVIQKFQDGTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEISMVQARGRA 472
Cdd:COG1061   320 --AL-AELLNEAGIRAAvvTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGRG 396

                         490       500       510
                  ....*....|....*....|....*....|....*..
gi 2462557479 473 -RADQ-----SVYAFVA--TEGSRELKRELINEALET 501
Cdd:COG1061   397 lRPAPgkedaLVYDFVGndVPVLEELAKDLRDLAGYR 433
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 1-192 8.82e-19

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: 84.10  E-value: 8.82e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   1 MELRSYQWEVIMPALEGKNIIIwLPTGAGKTRAAAYVAKRHLETVDGaKVVVLVNRVHLVTQHGEEFRRMLDGRWTVTTL 80
Cdd:cd18035     1 EERRLYQVLIAAVALNGNTLIV-LPTGLGKTIIAILVAADRLTKKGG-KVLILAPSRPLVEQHAENLKRVLNIPDKITSL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  81 SGDMGPRAGFGHLARCHdLLICTAELLQMALTSpeeeEHVELTVFSLIVVDECHHTHKDTVYNVIMSQYlelKLQRAQPL 160
Cdd:cd18035    79 TGEVKPEERAERWDASK-IIVATPQVIENDLLA----GRITLDDVSLLIFDEAHHAVGNYAYVYIAHRY---KREANNPL 150

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2462557479 161 pqVLGLTASPGTggaskldgAINHVLQLCANL 192
Cdd:cd18035   151 --ILGLTASPGS--------DKEKIMEICENL 172
ResIII pfam04851
Type III restriction enzyme, res subunit;
1-170 1.44e-18

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 82.72  E-value: 1.44e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   1 MELRSYQWEVIMPALEG-----KNIIIWLPTGAGKTRAAAYVAKRHLETVDGAKVVVLVNRVHLVTQHGEEFRRMLDGRW 75
Cdd:pfam04851   2 LELRPYQIEAIENLLESikngqKRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPNYV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  76 TVTT-LSGDMGPRAGFGhlarcHDLLICTAEllqmALTSPEEEEHVELTV--FSLIVVDECHHTHKDTVYNVImsQYLel 152
Cdd:pfam04851  82 EIGEiISGDKKDESVDD-----NKIVVTTIQ----SLYKALELASLELLPdfFDVIIIDEAHRSGASSYRNIL--EYF-- 148

                         170
                  ....*....|....*...
gi 2462557479 153 klqraqPLPQVLGLTASP 170
Cdd:pfam04851 149 ------KPAFLLGLTATP 160
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 3-170 3.02e-16

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: 76.06  E-value: 3.02e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   3 LRSYQWEVImPALEG------KNIIIWLPTGAGKTRAAAYVAKRHLETVDGAKVVVLVNRVHLVTQHGEEFRRMLDGRWT 76
Cdd:cd18032     1 PRYYQQEAI-EALEEarekgqRRALLVMATGTGKTYTAAFLIKRLLEANRKKRILFLAHREELLEQAERSFKEVLPDGSF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  77 VTTLSGDMGPRAGfghlarchDLLICTaelLQmALTSPEEEEHVELTVFSLIVVDECHHthkdtvynVIMSQYLELkLQR 156
Cdd:cd18032    80 GNLKGGKKKPDDA--------RVVFAT---VQ-TLNKRKRLEKFPPDYFDLIIIDEAHH--------AIASSYRKI-LEY 138

                         170
                  ....*....|....
gi 2462557479 157 AQPLPQvLGLTASP 170
Cdd:cd18032   139 FEPAFL-LGLTATP 151
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 4-170 9.89e-16

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


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 74.97  E-value: 9.89e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   4 RSYQWEVIMPALEGKNIIIWLPTGAGKTRAAAYVAKRHL-ETVDGAKVVVLVNRVHLVTQHGEEFRRMLDG-RWTVTTLS 81
Cdd:pfam00270   1 TPIQAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALEALdKLDNGPQALVLAPTRELAEQIYEELKKLGKGlGLKVASLL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  82 GDMGPRAGFGHLARCHdLLICTAELLQMALTSPEEEEHVeltvfSLIVVDECHHTHKDTvynviMSQYLELKLQRAQPLP 161
Cdd:pfam00270  81 GGDSRKEQLEKLKGPD-ILVGTPGRLLDLLQERKLLKNL-----KLLVLDEAHRLLDMG-----FGPDLEEILRRLPKKR 149


                  ....*....
gi 2462557479 162 QVLGLTASP 170
Cdd:pfam00270 150 QILLLSATL 158
HELICc smart00490
helicase superfamily c-terminal domain;
415-472 2.83e-15

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 70.70  E-value: 2.83e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462557479  415 MTQRDQQEVIQKFQDGTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEISMVQARGRA 472
Cdd:smart00490  21 LSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 3-170 2.62e-13

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


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 67.33  E-value: 2.62e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   3 LRSYQWEVIMPALEGKNI---IIWLPTGAGKTRAAAYVAKRHLETvdgaKVVVLVNRVHLVTQHGEEFrrmldgrwtVTT 79
Cdd:cd17926     1 LRPYQEEALEAWLAHKNNrrgILVLPTGSGKTLTALALIAYLKEL----RTLIVVPTDALLDQWKERF---------EDF 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  80 LSGDMGPRAGFG--HLARCHDLLICTaellqMALTSPEEEEHVELT-VFSLIVVDECHHTHKDTvYNVIMSQYLELKlqr 156
Cdd:cd17926    68 LGDSSIGLIGGGkkKDFDDANVVVAT-----YQSLSNLAEEEKDLFdQFGLLIVDEAHHLPAKT-FSEILKELNAKY--- 138

                         170
                  ....*....|....
gi 2462557479 157 aqplpqVLGLTASP 170
Cdd:cd17926   139 ------RLGLTATP 146
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 349-482 8.46e-13

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


Pssm-ID: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 65.22  E-value: 8.46e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 349 PKLEMLEKILQRQFSSSNSPRGIIFTRTRQsahslllwlqqqqglqTVDIRAQLLIGAGNSSQSTH--MTQRDQQEVIQK 426
Cdd:cd18787     9 EEEEKKLLLLLLLLEKLKPGKAIIFVNTKK----------------RVDRLAELLEELGIKVAALHgdLSQEERERALKK 72

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 427 FQDGTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEISMVQaR-GR-ARADQS--VYAFV 482
Cdd:cd18787    73 FRSGKVRVLVATDVAARGLDIPGVDHVINYDLPRDAEDYVH-RiGRtGRAGRKgtAITFV 131
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 15-168 4.86e-12

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: 64.59  E-value: 4.86e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  15 LEGKNIIIWLPTGAGKTRAAAYVAKRHLETVDGaKVVVLVNRVHLVTQHGEEFRRML-DGRWTVTTLSGDmgPRAGFGHL 93
Cdd:cd17921    15 LSGDSVLVSAPTSSGKTLIAELAILRALATSGG-KAVYIAPTRALVNQKEADLRERFgPLGKNVGLLTGD--PSVNKLLL 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462557479  94 ARChDLLICTAELLQMALTSPEEEEHVELTvfsLIVVDECHHTHkDTVYNVIMsQYLELKLQRAQPLPQVLGLTA 168
Cdd:cd17921    92 AEA-DILVATPEKLDLLLRNGGERLIQDVR---LVVVDEAHLIG-DGERGVVL-ELLLSRLLRINKNARFVGLSA 160
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
350-505 2.72e-11

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 65.55  E-value: 2.72e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 350 KLEMLEKILQRQfsssNSPRGIIFTRTRQsahslllwlqqqqglqTVDIRAQLLIGAGNSSQSTH--MTQRDQQEVIQKF 427
Cdd:COG0513   228 KLELLRRLLRDE----DPERAIVFCNTKR----------------GADRLAEKLQKRGISAAALHgdLSQGQRERALDAF 287

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 428 QDGTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEISMVQaR-GR-ARADQS--VYAFVATEGSRELKRelINEALETLM 503
Cdd:COG0513   288 RNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYVH-RiGRtGRAGAEgtAISLVTPDERRLLRA--IEKLIGQKI 364


                  ..
gi 2462557479 504 EQ 505
Cdd:COG0513   365 EE 366
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
2-168 5.41e-10

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 61.83  E-value: 5.41e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   2 ELRSYQWEVIMPAL-EGKNIIIWLPTGAGKTRAAAYVAKRHLETvdGAKVVVLVNRVHLVTQHGEEFRRML-DGRWTVTT 79
Cdd:COG1204    22 ELYPPQAEALEAGLlEGKNLVVSAPTASGKTLIAELAILKALLN--GGKALYIVPLRALASEKYREFKRDFeELGIKVGV 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  80 LSGDMGPRAGFghLARChDLLICTAELLQMALTSPEEeehvELTVFSLIVVDECHHTHKDT---VYNVIMSqylelKLQR 156
Cdd:COG1204   100 STGDYDSDDEW--LGRY-DILVATPEKLDSLLRNGPS----WLRDVDLVVVDEAHLIDDESrgpTLEVLLA-----RLRR 167

                         170
                  ....*....|..
gi 2462557479 157 AQPLPQVLGLTA 168
Cdd:COG1204   168 LNPEAQIVALSA 179
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 432-472 3.18e-08

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


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 50.78  E-value: 3.18e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2462557479 432 LNLLVATSVAEEGLDIPHCNVVVRYGLLTNEISMVQARGRA 472
Cdd:cd18785    23 LEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRA 63
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 415-502 4.98e-08

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: 52.35  E-value: 4.98e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 415 MTQRDQQEVIQKFQDGTLNLLVATSVAEEGLDIPHCNVVV-----RYGLLTneisMVQARGR-ARADQSVYAFVATegsr 488
Cdd:cd18811    71 LKSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPNATVMViedaeRFGLSQ----LHQLRGRvGRGDHQSYCLLVY---- 142

                          90
                  ....*....|....
gi 2462557479 489 elKRELINEALETL 502
Cdd:cd18811   143 --KDPLTETAKQRL 154
DEXHc_RecQ cd17920
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ...
 2-168 8.28e-08

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


Pssm-ID: 350678 [Multi-domain]  Cd Length: 200  Bit Score: 52.54  E-value: 8.28e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   2 ELRSYQWEVIMPALEGKNIIIWLPTGAGKTR---AAAYVAkrhletvDGAKVVV--LV----NRVHLVTQHGEEfrrmld 72
Cdd:cd17920    12 EFRPGQLEAINAVLAGRDVLVVMPTGGGKSLcyqLPALLL-------DGVTLVVspLIslmqDQVDRLQQLGIR------ 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  73 grwtVTTLSGDMGPRAGFGHLARCH----DLLICTAELLQ-----MALTSPEEEEHVeltvfSLIVVDECHhthkdtvyn 143
Cdd:cd17920    79 ----AAALNSTLSPEEKREVLLRIKngqyKLLYVTPERLLspdflELLQRLPERKRL-----ALIVVDEAH--------- 140

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2462557479 144 vIMSQ--------YLELKLQRAQ-PLPQVLGLTA 168
Cdd:cd17920   141 -CVSQwghdfrpdYLRLGRLRRAlPGVPILALTA 173
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
 2-193 8.57e-08

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: 52.32  E-value: 8.57e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   2 ELRSYQWEVIMPALEgKNIIIWLPTGAGKTRAAAYVAKRHLETVDGAKVVVLVNRVHLVTQHGEEFRRM--LDGRWTVTt 79
Cdd:cd18033     2 PLRDYQFTIVQKALF-QNTLVALPTGLGKTFIAAVVMLNYYRWFPKGKIVFMAPTKPLVSQQIEACYKItgIPSSQTAE- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  80 LSGDMGP--RAGFGHLARchdLLICTAELLQMALtspeEEEHVELTVFSLIVVDECHHTHKDTVYNVIMSQylelkLQRA 157
Cdd:cd18033    80 LTGSVPPtkRAELWASKR---VFFLTPQTLENDL----KEGDCDPKSIVCLVIDEAHRATGNYAYCQVVRE-----LMRY 147

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2462557479 158 QPLPQVLGLTASPGtggaSKLDGainhVLQLCANLD 193
Cdd:cd18033   148 NSHFRILALTATPG----SKLEA----VQQVIDNLL 175
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 415-502 2.69e-07

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


Pssm-ID: 350179 [Multi-domain]  Cd Length: 160  Bit Score: 50.34  E-value: 2.69e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 415 MTQRDQQEVIQKFQDGTLNLLVATSVAEEGLDIPHCNVVV-----RYGLLTneisMVQARGR-ARADQSVYAFVATEGSR 488
Cdd:cd18792    70 MTEDEKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIiedadRFGLSQ----LHQLRGRvGRGKHQSYCYLLYPDPK 145

                          90
                  ....*....|....
gi 2462557479 489 ELKreliNEALETL 502
Cdd:cd18792   146 KLT----ETAKKRL 155
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 350-448 4.49e-07

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 52.25  E-value: 4.49e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 350 KLEMLEKILQRQfsssNSPRGIIFTRTRQSAHSLLLWLQQQqglqtvDIRAQLLIGagnssqstHMTQRDQQEVIQKFQD 429
Cdd:PRK11192  232 KTALLCHLLKQP----EVTRSIVFVRTRERVHELAGWLRKA------GINCCYLEG--------EMVQAKRNEAIKRLTD 293

                          90
                  ....*....|....*....
gi 2462557479 430 GTLNLLVATSVAEEGLDIP 448
Cdd:PRK11192  294 GRVNVLVATDVAARGIDID 312
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 27-507 2.76e-06

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 50.22  E-value: 2.76e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  27 GAGKTRAAAYVAKRHLETVDGAKVVVLVNrVHLVTQHGEEFRRMLDGrWTVTTLSGDMGPRAGFGHLARcHDLLICTAEL 106
Cdd:COG0553   270 GLGKTIQALALLLELKERGLARPVLIVAP-TSLVGNWQRELAKFAPG-LRVLVLDGTRERAKGANPFED-ADLVITSYGL 346

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 107 LQMaltspeEEEHVELTVFSLIVVDECHH-THKDTvynvimSQYLELKLQRAqplPQVLGLTASPgtggaskldgAINHV 185
Cdd:COG0553   347 LRR------DIELLAAVDWDLVILDEAQHiKNPAT------KRAKAVRALKA---RHRLALTGTP----------VENRL 401

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 186 LQLcanldtWCIMSpqNCCPQL-------QEHSQQPCKQYNlchRRSQDPFGDLLKKLM-----DQIhdhleMPELSRKf 253
Cdd:COG0553   402 EEL------WSLLD--FLNPGLlgslkafRERFARPIEKGD---EEALERLRRLLRPFLlrrtkEDV-----LKDLPEK- 464

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 254 gtqMYEQQVVKLSEAaalaglqEQRVYALHLRRYNDALLIHD-TVRAVDALAALQdfYHRehvtktQILCaerrLLALFD 332
Cdd:COG0553   465 ---TEETLYVELTPE-------QRALYEAVLEYLRRELEGAEgIRRRGLILAALT--RLR------QICS----HPALLL 522

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 333 DRKNELAHlathgpENPKLEMLEKILQRQFSSSNspRGIIFTRTRQsahslllwlqqqqglqTVDIRAQLLIGAGNSSQS 412
Cdd:COG0553   523 EEGAELSG------RSAKLEALLELLEELLAEGE--KVLVFSQFTD----------------TLDLLEERLEERGIEYAY 578

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 413 TH--MTQRDQQEVIQKFQDG--TLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEisMV--QARGRA-----RADQSVYAF 481
Cdd:COG0553   579 LHggTSAEERDELVDRFQEGpeAPVFLISLKAGGEGLNLTAADHVIHYDLWWNP--AVeeQAIDRAhrigqTRDVQVYKL 656

                         490       500
                  ....*....|....*....|....*....
gi 2462557479 482 VaTEGSRElkrELINEALET---LMEQAV 507
Cdd:COG0553   657 V-AEGTIE---EKILELLEEkraLAESVL 681
DEXHc_POLQ-like cd18026
DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in ...
 6-169 8.74e-06

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


Pssm-ID: 350784 [Multi-domain]  Cd Length: 202  Bit Score: 46.83  E-value: 8.74e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   6 YQWEVIM----PALEGKNIIIWLPTGAGKTRAAAYVA-KRHLETvdGAKVVVLVNRVHLVTQHGEEFRRMLDGR-WTVTT 79
Cdd:cd18026    18 YDWQKEClslpGLLEGRNLVYSLPTSGGKTLVAEILMlKRLLER--RKKALFVLPYVSIVQEKVDALSPLFEELgFRVEG 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  80 LSGDMG--PRAGFGHLarchDLLICTAELLQMALTSPEEEEHVELtvFSLIVVDECHHThKDTVYNVIMSQYLELKLQRA 157
Cdd:cd18026    96 YAGNKGrsPPKRRKSL----SVAVCTIEKANSLVNSLIEEGRLDE--LGLVVVDELHML-GDGHRGALLELLLTKLLYAA 168

                         170
                  ....*....|..
gi 2462557479 158 QPLPQVLGLTAS 169
Cdd:cd18026   169 QKNIQIVGMSAT 180
DEXHc_UvsW cd18031
DEXH-box helicase domain of bacteriophage UvsW; Bacteriophage UvsW is part of the WXY system ...
 6-145 1.13e-05

DEXH-box helicase domain of bacteriophage UvsW; Bacteriophage UvsW is part of the WXY system that repairs DNA damage by a process that involves homologous recombination. UvsW 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: 350789 [Multi-domain]  Cd Length: 161  Bit Score: 45.50  E-value: 1.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   6 YQWEVIMPALEGKNIIIWLPTGAGKTRAAAYVAKRHLETVDGaKVVVLVNRVHLVTQHGEEF--RRMLDGRWTVTTLSGD 83
Cdd:cd18031     4 YQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEG-KILIIVPTTALTTQMADDFvdYRLFSHAMIKKIGGGA 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462557479  84 MgpragfGHLARCHDLLIcTAELLQMALTSPEEeehvELTVFSLIVVDECHHTHKDTVYNVI 145
Cdd:cd18031    83 S------KDDKYKNDAPV-VVGTWQTVVKQPKE----WFSQFGMMMNDECHLATGKSISSII 133
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
 15-171 3.39e-05

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


Pssm-ID: 350786 [Multi-domain]  Cd Length: 177  Bit Score: 44.63  E-value: 3.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  15 LEGKNIIIWLPTGAGKTRAAAYVAKRHLetVDGAKVVVLVNRVHLVTQHGEEFRRMLDGRWTVTTLSGDMgpRAGFGHLA 94
Cdd:cd18028    15 LKGENLLISIPTASGKTLIAEMAMVNTL--LEGGKALYLVPLRALASEKYEEFKKLEEIGLKVGISTGDY--DEDDEWLG 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  95 RChDLLICTAELLQMAL-TSPEEEEHVeltvfSLIVVDECHHTHKDT---VYNVIMSqylelKLQRAQPLPQVLGLTASP 170
Cdd:cd18028    91 DY-DIIVATYEKFDSLLrHSPSWLRDV-----GVVVVDEIHLISDEErgpTLESIVA-----RLRRLNPNTQIIGLSATI 159


                  .
gi 2462557479 171 G 171
Cdd:cd18028   160 G 160
uvsW PHA02558
UvsW helicase; Provisional
 2-188 3.74e-05

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 46.16  E-value: 3.74e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   2 ELRSYQWEVIMPALEGKNIIIWLPTGAGKTRAAAYVAKRHLETVDGaKVVVLVNRVHLVTQHGEEFrrmLDGRWTVttlS 81
Cdd:PHA02558  114 EPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLENYEG-KVLIIVPTTSLVTQMIDDF---VDYRLFP---R 186

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  82 GDM-GPRAGfghLARCHDLLICTAElLQMALTSPEEEEHveltVFSLIVVDEChHTHKDTVYNVIMSqylelKLQRAqpl 160
Cdd:PHA02558  187 EAMhKIYSG---TAKDTDAPIVVST-WQSAVKQPKEWFD----QFGMVIVDEC-HLFTGKSLTSIIT-----KLDNC--- 249

                         170       180
                  ....*....|....*....|....*...
gi 2462557479 161 PQVLGLTASpgtggaskLDGAINHVLQL 188
Cdd:PHA02558  250 KFKFGLTGS--------LRDGKANILQY 269
HsdR COG4096
Type I site-specific restriction endonuclease, part of a restriction-modification system ...
 3-134 8.88e-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: 45.22  E-value: 8.88e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   3 LRSYQWEVIMPALE----GKN-IIIWLPTGAGKTRAA---AYV------AKRhletvdgakVVVLVNRVHLVTQHGEEFR 68
Cdd:COG4096   159 LRYYQIEAIRRVEEaiakGQRrALLVMATGTGKTRTAialIYRllkagrAKR---------ILFLADRNALVDQAKNAFK 229

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  69 RMLDGRWTVTTL-SGDMGPRAGfghlARCHdllICT-AELLQMALTSPEEEEHVELTV--FSLIVVDECH 134
Cdd:COG4096   230 PFLPDLDAFTKLyNKSKDIDKS----ARVY---FSTyQTMMNRIDGEEEEPGYRQFPPdfFDLIIIDECH 292
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
 413-454 1.05e-04

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


Pssm-ID: 350176 [Multi-domain]  Cd Length: 153  Bit Score: 42.62  E-value: 1.05e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2462557479 413 THMT-QRDQQEVIQKFQDGTLNLLVATSVAEEGLDIPHCNVVV 454
Cdd:cd18789    75 TGETpQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANVAI 117
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 371-511 1.08e-04

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 44.84  E-value: 1.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 371 IIFTRTRQSahslllwlqqqqglqTVDIrAQLLIGAGNSSQSTH--MTQRDQQEVIQKFQDGTLNLLVATSVAEEGLDIP 448
Cdd:PRK11634  249 IIFVRTKNA---------------TLEV-AEALERNGYNSAALNgdMNQALREQTLERLKDGRLDILIATDVAARGLDVE 312

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462557479 449 HCNVVVRYGLLTNEISMVQARGR-ARADQSVYAFVATEgSRElKRELINeaLETLMEQAVAAVQ 511
Cdd:PRK11634  313 RISLVVNYDIPMDSESYVHRIGRtGRAGRAGRALLFVE-NRE-RRLLRN--IERTMKLTIPEVE 372
DEXHc_Hrq1-like cd17923
DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a ...
 3-134 1.61e-04

DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. Hrq1 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350681 [Multi-domain]  Cd Length: 182  Bit Score: 42.57  E-value: 1.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   3 LRSYQWEVIMPALEGKNIIIWLPTGAGKTRAAAYVAKRHLETVDGAKVVVLVNRVHLVTQHGEEFRRMLDG---RWTVTT 79
Cdd:cd17923     1 LYSHQAEAIEAARAGRSVVVTTGTASGKSLCYQLPILEALLRDPGSRALYLYPTKALAQDQLRSLRELLEQlglGIRVAT 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2462557479  80 LSGDMGPRAGFGHLARCHDLLICTAELLQMALTSPEEEEHVELTVFSLIVVDECH 134
Cdd:cd17923    81 YDGDTPREERRAIIRNPPRILLTNPDMLHYALLPHHDRWARFLRNLRYVVLDEAH 135
PTZ00110 PTZ00110
helicase; Provisional
 347-495 2.55e-04

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 43.61  E-value: 2.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 347 ENPKLEMLEKILQRQFSSSnsPRGIIFTRTRQSAHSLllwlqqqqglqTVDIRAQlligaGNSSQSTH--MTQRDQQEVI 424
Cdd:PTZ00110  359 EHEKRGKLKMLLQRIMRDG--DKILIFVETKKGADFL-----------TKELRLD-----GWPALCIHgdKKQEERTWVL 420

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462557479 425 QKFQDGTLNLLVATSVAEEGLDIPHCNVVVRY---GLLTNEISMVQARGRARADQSVYAFVATEGSReLKRELI 495
Cdd:PTZ00110  421 NEFKTGKSPIMIATDVASRGLDVKDVKYVINFdfpNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYR-LARDLV 493
DEADc cd00268
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...
 7-133 2.72e-04

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


Pssm-ID: 350669 [Multi-domain]  Cd Length: 196  Bit Score: 42.04  E-value: 2.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   7 QWEVIMPALEGKNIIIWLPTGAGKTraAAY-------VAKRHLETVDGAKVVVLVNRVHLVTQHGEEFRRMLDG-RWTVT 78
Cdd:cd00268    17 QAQAIPLILSGRDVIGQAQTGSGKT--LAFllpilekLLPEPKKKGRGPQALVLAPTRELAMQIAEVARKLGKGtGLKVA 94

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462557479  79 TLSGDMGPRAGFGHLARCHDLLICT-AELLQMAltspeEEEHVELTVFSLIVVDEC 133
Cdd:cd00268    95 AIYGGAPIKKQIEALKKGPDIVVGTpGRLLDLI-----ERGKLDLSNVKYLVLDEA 145
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
 413-458 2.90e-04

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 43.60  E-value: 2.90e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2462557479 413 TH--MTQRDQQEVIQKFQDGTLNLLVATSVAEEGLDIPHCNVVV-----RYGL 458
Cdd:PRK10917  511 LHgrMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVienaeRFGL 563
PRK11776 PRK11776
ATP-dependent RNA helicase DbpA; Provisional
 400-502 3.63e-04

ATP-dependent RNA helicase DbpA; Provisional


Pssm-ID: 236977 [Multi-domain]  Cd Length: 460  Bit Score: 42.87  E-value: 3.63e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 400 AQLLIGAGNSSQSTH--MTQRDQQEVIQKFQDGTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEISMVQARGR-ARADQ 476
Cdd:PRK11776  259 ADALNAQGFSALALHgdLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRtGRAGS 338

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2462557479 477 SVYA--FVATEGSR-------ELKRELINEALETL 502
Cdd:PRK11776  339 KGLAlsLVAPEEMQranaiedYLGRKLNWEPLPSL 373
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
 27-170 4.20e-04

DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA 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: 350769 [Multi-domain]  Cd Length: 207  Bit Score: 41.89  E-value: 4.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  27 GAGKTRAAAYVAKRHLETVDGAKVVVLVNRvHLVTQ-HGEEFRRMLDGRWTVTTLSGDMGPRAGFGHLARcHDLLICTAE 105
Cdd:cd18011    27 GLGKTIEAGLIIKELLLRGDAKRVLILCPA-SLVEQwQDELQDKFGLPFLILDRETAAQLRRLIGNPFEE-FPIVIVSLD 104

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462557479 106 LLQmalTSPEEEEHVELTVFSLIVVDECHHTHKDtvYNVIMSQYLELKLQRAQPLPQVLGLTASP 170
Cdd:cd18011   105 LLK---RSEERRGLLLSEEWDLVVVDEAHKLRNS--GGGKETKRYKLGRLLAKRARHVLLLTATP 164
SWI2_SNF2 pfam18766
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins.
 17-137 7.90e-04

SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins.


Pssm-ID: 465860 [Multi-domain]  Cd Length: 222  Bit Score: 40.88  E-value: 7.90e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  17 GKNIIIWLPTGAGKTRAAAYVAKRHLETVDGAKVVVLVNRVHLVTQHGEEFRRMLDGRWTVTTlSGDmgpragfgHLArc 96
Cdd:pfam18766  19 RRGGVIWHTQGSGKSLTMVFLARKLRRELKNPTVVVVTDRNDLDDQLTKTFAACGREVPVQAE-SRK--------DLR-- 87

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2462557479  97 hDLL------ICTaeLLQMALTSPEEEEHVELTVFSLIV-VDECHHTH 137
Cdd:pfam18766  88 -ELLrgsggiIFT--TIQKFGETPDEGFPVLSDRRNIIVlVDEAHRSQ 132
PRK10689 PRK10689
transcription-repair coupling factor; Provisional
 400-484 9.48e-04

transcription-repair coupling factor; Provisional


Pssm-ID: 182649 [Multi-domain]  Cd Length: 1147  Bit Score: 42.04  E-value: 9.48e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  400 AQLLIGAGnssqstHMTQRDQQEVIQKFQDGTLNLLVATSVAEEGLDIPHCNVVV-----RYGLltneISMVQARGR-AR 473
Cdd:PRK10689   836 ARIAIGHG------QMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIieradHFGL----AQLHQLRGRvGR 905

                           90
                   ....*....|.
gi 2462557479  474 ADQSVYAFVAT 484
Cdd:PRK10689   906 SHHQAYAWLLT 916
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 349-472 1.28e-03

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 39.00  E-value: 1.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 349 PKLEMLEKILQRQFSSSNspRGIIFTRTRQsahslllwlqqqqglqTVDIRAQLLIGAGNSSQSTH--MTQRDQQEVIQK 426
Cdd:cd18793    11 GKLEALLELLEELREPGE--KVLIFSQFTD----------------TLDILEEALRERGIKYLRLDgsTSSKERQKLVDR 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2462557479 427 FQ--DGTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEISMVQARGRA 472
Cdd:cd18793    73 FNedPDIRVFLLSTKAGGVGLNLTAANRVILYDPWWNPAVEEQAIDRA 120
DEXHc_RecQ4-like cd18018
DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) ...
 2-168 1.55e-03

DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) is part of the RecQ family of highly conserved DNA repair helicases that is part of 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. Mutations cause Rothmund-Thomson/RAPADILINO/Baller-Gerold syndrome.


Pssm-ID: 350776 [Multi-domain]  Cd Length: 201  Bit Score: 39.93  E-value: 1.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   2 ELRSYQWEVIMPALEGKNIIIWLPTGAGKTRAAAYVAKRHLETVDGAKVVV--LVNrvhLVTQHGEEFRRMLDGrwtvTT 79
Cdd:cd18018    12 SFRPGQEEAIARLLSGRSTLVVLPTGAGKSLCYQLPALLLRRRGPGLTLVVspLIA---LMKDQVDALPRAIKA----AA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  80 LSGDMGPRAGFGHLARCH----DLLICTAEllqmALTSPE--EEEHVELTVfSLIVVDECHhthkdtvynvIMSQ----- 148
Cdd:cd18018    85 LNSSLTREERRRILEKLRagevKILYVSPE----RLVNESfrELLRQTPPI-SLLVVDEAH----------CISEwshnf 149

                         170       180
                  ....*....|....*....|....*
gi 2462557479 149 ---YLELK--LQRAQPLPQVLGLTA 168
Cdd:cd18018   150 rpdYLRLCrvLRELLGAPPVLALTA 174
DEXHc_ASCC3_2 cd18022
C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ...
 18-168 2.01e-03

C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; Activating signal cointegrator 1 complex subunit 3 (ASCC3) is a type II DEAD box helicase that plays a role in the repair of N-alkylated nucleotides. ASCC3 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350780 [Multi-domain]  Cd Length: 189  Bit Score: 39.28  E-value: 2.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  18 KNIIIWLPTGAGKTRAAAYVAKRHLETVDGAKVVVLVNRVHLVTQhgeefrRMLDgrWT----------VTTLSGDMGPR 87
Cdd:cd18022    18 NNVLLGAPTGSGKTIAAELAMFRAFNKYPGSKVVYIAPLKALVRE------RVDD--WKkrfeeklgkkVVELTGDVTPD 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  88 AGFGHLArchDLLICTAELLQMALTSPEEEEHVELTvfSLIVVDECHHTHKD--TVYNVIMSQYLELKLQRAQPLpQVLG 165
Cdd:cd18022    90 MKALADA---DIIITTPEKWDGISRSWQTREYVQQV--SLIIIDEIHLLGSDrgPVLEVIVSRMNYISSQTEKPV-RLVG 163


                  ....
gi 2462557479 166 L-TA 168
Cdd:cd18022   164 LsTA 167
RecG COG1200
RecG-like helicase [Replication, recombination and repair];
415-458 2.97e-03

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


Pssm-ID: 440813 [Multi-domain]  Cd Length: 684  Bit Score: 40.42  E-value: 2.97e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2462557479 415 MTQRDQQEVIQKFQDGTLNLLVATSVAEEGLDIPHCNVVV-----RYGL 458
Cdd:COG1200   513 MKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDVPNATVMVienaeRFGL 561
DEXHc_Brr2_2 cd18021
C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type ...
 19-169 2.98e-03

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


Pssm-ID: 350779 [Multi-domain]  Cd Length: 191  Bit Score: 38.78  E-value: 2.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  19 NIIIWLPTGAGKTRAAAYVAKRHLETVDGAKVVVLVNRVHLVTQHGEEFRRMLDGRW--TVTTLSGDMGprAGFGHLARC 96
Cdd:cd18021    21 NVFVGAPTGSGKTVCAELALLRHWRQNPKGRAVYIAPMQELVDARYKDWRAKFGPLLgkKVVKLTGETS--TDLKLLAKS 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462557479  97 HdLLICTAEllQMALTSPEEEEHVELTVFSLIVVDECHHTHKDT--VYNVIMSQYLELKLQRAQPLpQVLGLTAS 169
Cdd:cd18021    99 D-VILATPE--QWDVLSRRWKQRKNVQSVELFIADELHLIGGENgpVYEVVVSRMRYISSQLEKPI-RIVGLSSS 169
DEXHc_RecG cd17918
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ...
 27-166 3.29e-03

DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350676 [Multi-domain]  Cd Length: 180  Bit Score: 38.55  E-value: 3.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  27 GAGKT----RAAAYVAKRhletvdGAKVVVLVNRVHLVTQHGEEFRRMLdGRWTVTTLSGDMGPRAGFGhlarcHDLLIC 102
Cdd:cd17918    46 GSGKTlvalGAALLAYKN------GKQVAILVPTEILAHQHYEEARKFL-PFINVELVTGGTKAQILSG-----ISLLVG 113

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462557479 103 TAELLQmaltspeEEEHVEltVFSLIVVDECHH---THKDTVYNVIMSQYLELKlqrAQPLPQVLGL 166
Cdd:cd17918   114 THALLH-------LDVKFK--NLDLVIVDEQHRfgvAQREALYNLGATHFLEAT---ATPIPRTLAL 168
PRK04537 PRK04537
ATP-dependent RNA helicase RhlB; Provisional
 412-471 3.71e-03

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235307 [Multi-domain]  Cd Length: 572  Bit Score: 39.93  E-value: 3.71e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 412 STHMTQRDQQEVIQKFQDGTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEISMVQARGR 471
Cdd:PRK04537  288 SGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGR 347
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
2-134 4.44e-03

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


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 39.92  E-value: 4.44e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   2 ELRSYQWEVIMPALEGKNIIIWLPTGAGKTRAAAYVAKRHLETvdGAKVV------VLVNrvhlvtQHGEEFRRMLdGRW 75
Cdd:COG4581    25 ELDPFQEEAILALEAGRSVLVAAPTGSGKTLVAEFAIFLALAR--GRRSFytapikALSN------QKFFDLVERF-GAE 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462557479  76 TVTTLSGDM--GPRAgfghlarchDLLICTAELL-QMALTSPEEEEHVELTVFslivvDECH 134
Cdd:COG4581    96 NVGLLTGDAsvNPDA---------PIVVMTTEILrNMLYREGADLEDVGVVVM-----DEFH 143
DEXHc_LHR-like cd17922
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ...
 17-134 5.08e-03

DEXH-box helicase domain of LHR; 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 from 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: 350680 [Multi-domain]  Cd Length: 166  Bit Score: 37.95  E-value: 5.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479  17 GKNIIIWLPTGAGKTRAAAYVAKRHLETVDGAKVVVL-------VNRvhlvtqhgEEFRRM---LDGR---WTVTTLSGD 83
Cdd:cd17922     1 GRNVLIAAPTGSGKTEAAFLPALSSLADEPEKGVQVLyisplkaLIN--------DQERRLeepLDEIdleIPVAVRHGD 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2462557479  84 MGPRAGFGHLARCHDLLICTAELLQMALTSPEEEEhvELTVFSLIVVDECH 134
Cdd:cd17922    73 TSQSEKAKQLKNPPGILITTPESLELLLVNKKLRE--LFAGLRYVVVDEIH 121
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 349-472 6.24e-03

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


Pssm-ID: 350181 [Multi-domain]  Cd Length: 134  Bit Score: 37.19  E-value: 6.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479 349 PKLEMLEKILQRQFSSSNSP--RGIIFTRTRQsahslllwlqqqqglqTVDIRAQLLIGAGNSSQSTH--MTQRDQQEVI 424
Cdd:cd18794    10 PKDKKDEKLDLLKRIKVEHLggSGIIYCLSRK----------------ECEQVAARLQSKGISAAAYHagLEPSDRRDVQ 73

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2462557479 425 QKFQDGTLNLLVATSVAEEGLDIPHCNVVVRYGLLTNEISMVQARGRA 472
Cdd:cd18794    74 RKWLRDKIQVIVATVAFGMGIDKPDVRFVIHYSLPKSMESYYQESGRA 121
COG0610 COG0610
Type I site-specific restriction-modification system, R (restriction) subunit and related ...
 3-134 6.59e-03

Type I site-specific restriction-modification system, R (restriction) subunit and related helicases ... [Defense mechanisms];


Pssm-ID: 440375 [Multi-domain]  Cd Length: 936  Bit Score: 39.47  E-value: 6.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462557479   3 LRSYQWEVIMPALE--------GKNIIIWLPTGAGKTRAAAYVAK--RHLETVDGAKVVVLVNRVHLVTQHGEEFRRMLD 72
Cdd:COG0610   256 ARYHQYFAVRKAVErvkeaegdGKGGVIWHTQGSGKSLTMVFLAQklARLPDLDNPTVVVVTDRKDLDDQLFDTFKAFGR 335

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462557479  73 GRWTVTTlSGDmgpragfgHLARchdLL-------ICTaeLLQ-MALTSPEEEEHVELTVFSLIV-VDECH 134
Cdd:COG0610   336 ESVVQAE-SRA--------DLRE---LLesdsggiIVT--TIQkFPEALDEIKYPELSDRKNIIViVDEAH 392
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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