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Conserved domains on  [gi|1899282647|gb|QNO54086|]
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RecBCD enzyme subunit RecD [Methanosarcinales archaeon ANME-1 ERB6]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 1007248)

DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA; similar to Saccharomyces cerevisiae DNA polymerase alpha-associated DNA helicase A that acts as DNA polymerase alpha-associated DNA helicase which may be involved in DNA replication

EC:  3.6.4.12
Gene Ontology:  GO:0003678|GO:0003677|GO:0016887|GO:0005524
PubMed:  16935882|1552844

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
TIGR00376 super family cl36628
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 16-660 0e+00

DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair]


The actual alignment was detected with superfamily member TIGR00376:

Pssm-ID: 273041 [Multi-domain]  Cd Length: 636  Bit Score: 634.93  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647  16 LEREEQMRLHEEEMRRLSGREREEKGRAFLRMKGKSQGlGLGGKHLVKFRKQNAgftlPDSEIEVGDLVLVSKTNPWDED 95
Cdd:TIGR00376   1 LERDAEISAMMNEIRRLSLKQRERRGRAILNLQGKIRG-GLLGFLLVRFGRRKA----IATEISVGDIVLVSRGNPLQSD 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647  96 nPTGTVAEKTSYFLTVAFDEAPPGFAFrKDLRIDLFVNDITFQRMIEALKKFKRLPRRRKDKLLGNAAP-DFEKVGEIEF 174
Cdd:TIGR00376  76 -LTGVVTRVGKRFITVALEESVPQWSL-KRVRIDLYANDVTFKRMKEALRALTENHSRLLEFLLGREAPsKASEIHDFQF 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 175 FNQELNKSQREAVLRSLAARDFFLIHGPPGTGKTITCIEIIAQLVEHGREhersynILAAADSNVAVDNLVERLDKIGVN 254
Cdd:TIGR00376 154 FDPNLNESQKEAVLFALSSKDLFLIHGPPGTGKTRTVVELIRQLVKRGLR------VLVTAPSNIAVDNLLERLALCDQK 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 255 VVRIGHPARVIPSLRKRSLDYLIQEEPEYIKAQELRENAYEIKERMKSFIVPEMRWRRGLSDEAIMQLAREGRTIRGIPK 334
Cdd:TIGR00376 228 IVRLGHPARLLKSNKQHSLDYLIENHPKYQIVADIREKIDELIEERNKKTKPSPQKRRGLSDIKILRKALKKREARGIES 307

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 335 HKIEGMRKWLDLKHGIDKLFGDARELEEKAVKRIILEAEvicATNSTVGSEILKGAKFDLAVIDEATQSTEPSSLISVLK 414
Cdd:TIGR00376 308 LKIASMAEWIETNKSIDRLLKLLPESEERIMNEILAESD---ATNSMAGSEILNGQYFDVAVIDEASQAMEPSCLIPLLK 384

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 415 TKRFIMAGDHKQLPPTILNENAArgNLSRSLFERLLEMYGDKIRvMLDVQYRMNDAIAEFPGKEFYDGKLRADESVKKHN 494
Cdd:TIGR00376 385 ARKLILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEYPERSR-TLNVQYRMNQKIMEFPSREFYNGKLTAHESVANIL 461

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 495 LFDLLP----ESKLIDEDAKPFLFIDTGGSERFkERTRRGSTSKENAGEAKLVEEIAERLLSLGVKPEDIAVISPYDDQV 570
Cdd:TIGR00376 462 LRDLPKveatESEDDLETGIPLLFIDTSGCELF-ELKEADSTSKYNPGEAELVSEIIQALVKMGVPANDIGVITPYDAQV 540

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 571 ALIRK--ELRVEGLEIKTVDGFQGREKEVVIVSFVRSNKSREIGFLRDLRRLNVSITRAKRKLVLIGDSHTLEREGCYKR 648
Cdd:TIGR00376 541 DLLRQllEHRHIDIEVSSVDGFQGREKEVIIISFVRSNRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKR 620

                         650
                  ....*....|..
gi 1899282647 649 LVALAKERGGYK 660
Cdd:TIGR00376 621 LIEWCKQHGEVR 632
 
Name Accession Description Interval E-value
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 16-660 0e+00

DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273041 [Multi-domain]  Cd Length: 636  Bit Score: 634.93  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647  16 LEREEQMRLHEEEMRRLSGREREEKGRAFLRMKGKSQGlGLGGKHLVKFRKQNAgftlPDSEIEVGDLVLVSKTNPWDED 95
Cdd:TIGR00376   1 LERDAEISAMMNEIRRLSLKQRERRGRAILNLQGKIRG-GLLGFLLVRFGRRKA----IATEISVGDIVLVSRGNPLQSD 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647  96 nPTGTVAEKTSYFLTVAFDEAPPGFAFrKDLRIDLFVNDITFQRMIEALKKFKRLPRRRKDKLLGNAAP-DFEKVGEIEF 174
Cdd:TIGR00376  76 -LTGVVTRVGKRFITVALEESVPQWSL-KRVRIDLYANDVTFKRMKEALRALTENHSRLLEFLLGREAPsKASEIHDFQF 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 175 FNQELNKSQREAVLRSLAARDFFLIHGPPGTGKTITCIEIIAQLVEHGREhersynILAAADSNVAVDNLVERLDKIGVN 254
Cdd:TIGR00376 154 FDPNLNESQKEAVLFALSSKDLFLIHGPPGTGKTRTVVELIRQLVKRGLR------VLVTAPSNIAVDNLLERLALCDQK 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 255 VVRIGHPARVIPSLRKRSLDYLIQEEPEYIKAQELRENAYEIKERMKSFIVPEMRWRRGLSDEAIMQLAREGRTIRGIPK 334
Cdd:TIGR00376 228 IVRLGHPARLLKSNKQHSLDYLIENHPKYQIVADIREKIDELIEERNKKTKPSPQKRRGLSDIKILRKALKKREARGIES 307

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 335 HKIEGMRKWLDLKHGIDKLFGDARELEEKAVKRIILEAEvicATNSTVGSEILKGAKFDLAVIDEATQSTEPSSLISVLK 414
Cdd:TIGR00376 308 LKIASMAEWIETNKSIDRLLKLLPESEERIMNEILAESD---ATNSMAGSEILNGQYFDVAVIDEASQAMEPSCLIPLLK 384

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 415 TKRFIMAGDHKQLPPTILNENAArgNLSRSLFERLLEMYGDKIRvMLDVQYRMNDAIAEFPGKEFYDGKLRADESVKKHN 494
Cdd:TIGR00376 385 ARKLILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEYPERSR-TLNVQYRMNQKIMEFPSREFYNGKLTAHESVANIL 461

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 495 LFDLLP----ESKLIDEDAKPFLFIDTGGSERFkERTRRGSTSKENAGEAKLVEEIAERLLSLGVKPEDIAVISPYDDQV 570
Cdd:TIGR00376 462 LRDLPKveatESEDDLETGIPLLFIDTSGCELF-ELKEADSTSKYNPGEAELVSEIIQALVKMGVPANDIGVITPYDAQV 540

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 571 ALIRK--ELRVEGLEIKTVDGFQGREKEVVIVSFVRSNKSREIGFLRDLRRLNVSITRAKRKLVLIGDSHTLEREGCYKR 648
Cdd:TIGR00376 541 DLLRQllEHRHIDIEVSSVDGFQGREKEVIIISFVRSNRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKR 620

                         650
                  ....*....|..
gi 1899282647 649 LVALAKERGGYK 660
Cdd:TIGR00376 621 LIEWCKQHGEVR 632
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
114-656 2.57e-84

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 282.79  E-value: 2.57e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 114 DEAPPGFAFRKDLRIDLFVNDITFQRMIEALKKFKRLPRRRKDKLLGNAAPDFEKVGEIEFFNQELNKSQREAVLRSLAA 193
Cdd:COG1112   275 ELLAALSLALLALLAALALALLLLAALALLLALALAALLALLALLALLAARLAAALAALLLLLLLEELALLAALLLLLEL 354

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 194 RDFFLIHGPPGTGKTITCIEIIAQLVEHGREHERSYNILAAADSNVAVDNLVERLDKIGVNVVRIGHPARVIPSLRKRSL 273
Cdd:COG1112   355 ALLRLLAALLLALALLLLLALEELLLLALLRLLAEGLALLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALL 434

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 274 DYLIQEEPEYIKAQELRENAYEIKERMKSFIVPEMRWRRGLSDEAIMQ--LAREGRTIRGIPKHKIEGMRKWLDLKHGID 351
Cdd:COG1112   435 AALLALLLLLAAALAALLALLLLLLLALAALLLLLAAAAALLALALLEslLEELIEEHPEELEKLIAELREAARLRRALR 514

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 352 KLFGDARELEEKAVKRIILEAEVICATNSTVGSEI-LKGAKFDLAVIDEATQSTEPSSLISVLKTKRFIMAGDHKQLPPT 430
Cdd:COG1112   515 RELKKRRELRKLLWDALLELAPVVGMTPASVARLLpLGEGSFDLVIIDEASQATLAEALGALARAKRVVLVGDPKQLPPV 594

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 431 ILNENAAR---GNLSRSLFERLLEMYGDkIRVMLDVQYRMNDAIAEFPGKEFYDGKLRADESVKKHNLfdllpeskliDE 507
Cdd:COG1112   595 VFGEEAEEvaeEGLDESLLDRLLARLPE-RGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSPKARRL----------AD 663

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 508 DAKPFLFIDTGGserfkeRTRRGSTSKENAGEAKLVEEIAERLLSLGVKPEDIAVISPYDDQVALIRKELR------VEG 581
Cdd:COG1112   664 PDSPLVFIDVDG------VYERRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELLRealgdgLEP 737

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 582 LEIKTVDGFQGREKEVVIVSFVRSNK---SREIGFL-RDLRRLNVSITRAKRKLVLIGDSHTLEREG---CYKRLVALAK 654
Cdd:COG1112   738 VFVGTVDRFQGDERDVIIFSLVYSNDedvPRNFGFLnGGPRRLNVAVSRARRKLIVVGSRELLDSDPstpALKRLLEYLE 817


                  ..
gi 1899282647 655 ER 656
Cdd:COG1112   818 RA 819
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 441-637 5.15e-81

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.


Pssm-ID: 463780 [Multi-domain]  Cd Length: 196  Bit Score: 254.78  E-value: 5.15e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 441 LSRSLFERLLEMYGDKIrVMLDVQYRMNDAIAEFPGKEFYDGKLRADESVKKHNLFDLLpeskLIDEDAKPFLFIDTGGS 520
Cdd:pfam13087   1 LDRSLFERLQELGPSAV-VMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPDDF----HLPDPLGPLVFIDVDGS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 521 ErfkERTRRGSTSKENAGEAKLVEEIAERLLSLGV-KPEDIAVISPYDDQVALIRKELRVE-----GLEIKTVDGFQGRE 594
Cdd:pfam13087  76 E---EEESDGGTSYSNEAEAELVVQLVEKLIKSGPeEPSDIGVITPYRAQVRLIRKLLKRKlggklEIEVNTVDGFQGRE 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1899282647 595 KEVVIVSFVRSNKSREIGFLRDLRRLNVSITRAKRKLVLIGDS 637
Cdd:pfam13087 153 KDVIIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNA 195
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 178-466 1.31e-80

DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, or IGHMBP2) is a 5' to 3' helicase that unwinds RNA and DNA duplexes in an ATP-dependent reaction. It is a DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence (5'-GGGCT-3') related to the immunoglobulin mu chain switch region. The IGHMBP2 gene is responsible for Charcot-Marie-Tooth disease (CMT) type 2S and spinal muscular atrophy with respiratory distress type 1 (SMARD1). It is also thought to play a role in frontotemporal dementia (FTD) with amyotrophic lateral sclerosis (ALS) and major depressive disorder (MDD). SMUBP2 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: 350802 [Multi-domain]  Cd Length: 191  Bit Score: 253.69  E-value: 1.31e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 178 ELNKSQREAVLRSLAARDFFLIHGPPGTGKTITCIEIIAQLVEhgreheRSYNILAAADSNVAVDNLVERLDKIGVNVVR 257
Cdd:cd18044     1 NLNDSQKEAVKFALSQKDVALIHGPPGTGKTTTVVEIILQAVK------RGEKVLACAPSNIAVDNLVERLVALKVKVVR 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 258 IGHPARVIPSLRKRSLDYLiqeepeyikaqelrenayeikermksfivpemrwrrglsdeaimqlaregrtirgipkhki 337
Cdd:cd18044    75 IGHPARLLESVLDHSLDAL------------------------------------------------------------- 93

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 338 egmrkwldlkhgidklfgdareleekavkriiLEAEVICATNSTVGSE-ILKGAKFDLAVIDEATQSTEPSSLISVLKTK 416
Cdd:cd18044    94 --------------------------------VAAQVVLATNTGAGSRqLLPNELFDVVVIDEAAQALEASCWIPLLKAR 141

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1899282647 417 RFIMAGDHKQLPPTILNENAARGNLSRSLFERLLEMYGDKIRVMLDVQYR 466
Cdd:cd18044   142 RCILAGDHKQLPPTILSDKAARGGLGVTLFERLVNLYGESVVRMLTVQYR 191
 
Name Accession Description Interval E-value
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 16-660 0e+00

DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273041 [Multi-domain]  Cd Length: 636  Bit Score: 634.93  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647  16 LEREEQMRLHEEEMRRLSGREREEKGRAFLRMKGKSQGlGLGGKHLVKFRKQNAgftlPDSEIEVGDLVLVSKTNPWDED 95
Cdd:TIGR00376   1 LERDAEISAMMNEIRRLSLKQRERRGRAILNLQGKIRG-GLLGFLLVRFGRRKA----IATEISVGDIVLVSRGNPLQSD 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647  96 nPTGTVAEKTSYFLTVAFDEAPPGFAFrKDLRIDLFVNDITFQRMIEALKKFKRLPRRRKDKLLGNAAP-DFEKVGEIEF 174
Cdd:TIGR00376  76 -LTGVVTRVGKRFITVALEESVPQWSL-KRVRIDLYANDVTFKRMKEALRALTENHSRLLEFLLGREAPsKASEIHDFQF 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 175 FNQELNKSQREAVLRSLAARDFFLIHGPPGTGKTITCIEIIAQLVEHGREhersynILAAADSNVAVDNLVERLDKIGVN 254
Cdd:TIGR00376 154 FDPNLNESQKEAVLFALSSKDLFLIHGPPGTGKTRTVVELIRQLVKRGLR------VLVTAPSNIAVDNLLERLALCDQK 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 255 VVRIGHPARVIPSLRKRSLDYLIQEEPEYIKAQELRENAYEIKERMKSFIVPEMRWRRGLSDEAIMQLAREGRTIRGIPK 334
Cdd:TIGR00376 228 IVRLGHPARLLKSNKQHSLDYLIENHPKYQIVADIREKIDELIEERNKKTKPSPQKRRGLSDIKILRKALKKREARGIES 307

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 335 HKIEGMRKWLDLKHGIDKLFGDARELEEKAVKRIILEAEvicATNSTVGSEILKGAKFDLAVIDEATQSTEPSSLISVLK 414
Cdd:TIGR00376 308 LKIASMAEWIETNKSIDRLLKLLPESEERIMNEILAESD---ATNSMAGSEILNGQYFDVAVIDEASQAMEPSCLIPLLK 384

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 415 TKRFIMAGDHKQLPPTILNENAArgNLSRSLFERLLEMYGDKIRvMLDVQYRMNDAIAEFPGKEFYDGKLRADESVKKHN 494
Cdd:TIGR00376 385 ARKLILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEYPERSR-TLNVQYRMNQKIMEFPSREFYNGKLTAHESVANIL 461

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 495 LFDLLP----ESKLIDEDAKPFLFIDTGGSERFkERTRRGSTSKENAGEAKLVEEIAERLLSLGVKPEDIAVISPYDDQV 570
Cdd:TIGR00376 462 LRDLPKveatESEDDLETGIPLLFIDTSGCELF-ELKEADSTSKYNPGEAELVSEIIQALVKMGVPANDIGVITPYDAQV 540

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 571 ALIRK--ELRVEGLEIKTVDGFQGREKEVVIVSFVRSNKSREIGFLRDLRRLNVSITRAKRKLVLIGDSHTLEREGCYKR 648
Cdd:TIGR00376 541 DLLRQllEHRHIDIEVSSVDGFQGREKEVIIISFVRSNRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKR 620

                         650
                  ....*....|..
gi 1899282647 649 LVALAKERGGYK 660
Cdd:TIGR00376 621 LIEWCKQHGEVR 632
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
114-656 2.57e-84

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 282.79  E-value: 2.57e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 114 DEAPPGFAFRKDLRIDLFVNDITFQRMIEALKKFKRLPRRRKDKLLGNAAPDFEKVGEIEFFNQELNKSQREAVLRSLAA 193
Cdd:COG1112   275 ELLAALSLALLALLAALALALLLLAALALLLALALAALLALLALLALLAARLAAALAALLLLLLLEELALLAALLLLLEL 354

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 194 RDFFLIHGPPGTGKTITCIEIIAQLVEHGREHERSYNILAAADSNVAVDNLVERLDKIGVNVVRIGHPARVIPSLRKRSL 273
Cdd:COG1112   355 ALLRLLAALLLALALLLLLALEELLLLALLRLLAEGLALLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALL 434

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 274 DYLIQEEPEYIKAQELRENAYEIKERMKSFIVPEMRWRRGLSDEAIMQ--LAREGRTIRGIPKHKIEGMRKWLDLKHGID 351
Cdd:COG1112   435 AALLALLLLLAAALAALLALLLLLLLALAALLLLLAAAAALLALALLEslLEELIEEHPEELEKLIAELREAARLRRALR 514

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 352 KLFGDARELEEKAVKRIILEAEVICATNSTVGSEI-LKGAKFDLAVIDEATQSTEPSSLISVLKTKRFIMAGDHKQLPPT 430
Cdd:COG1112   515 RELKKRRELRKLLWDALLELAPVVGMTPASVARLLpLGEGSFDLVIIDEASQATLAEALGALARAKRVVLVGDPKQLPPV 594

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 431 ILNENAAR---GNLSRSLFERLLEMYGDkIRVMLDVQYRMNDAIAEFPGKEFYDGKLRADESVKKHNLfdllpeskliDE 507
Cdd:COG1112   595 VFGEEAEEvaeEGLDESLLDRLLARLPE-RGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSPKARRL----------AD 663

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 508 DAKPFLFIDTGGserfkeRTRRGSTSKENAGEAKLVEEIAERLLSLGVKPEDIAVISPYDDQVALIRKELR------VEG 581
Cdd:COG1112   664 PDSPLVFIDVDG------VYERRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELLRealgdgLEP 737

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 582 LEIKTVDGFQGREKEVVIVSFVRSNK---SREIGFL-RDLRRLNVSITRAKRKLVLIGDSHTLEREG---CYKRLVALAK 654
Cdd:COG1112   738 VFVGTVDRFQGDERDVIIFSLVYSNDedvPRNFGFLnGGPRRLNVAVSRARRKLIVVGSRELLDSDPstpALKRLLEYLE 817


                  ..
gi 1899282647 655 ER 656
Cdd:COG1112   818 RA 819
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 441-637 5.15e-81

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.


Pssm-ID: 463780 [Multi-domain]  Cd Length: 196  Bit Score: 254.78  E-value: 5.15e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 441 LSRSLFERLLEMYGDKIrVMLDVQYRMNDAIAEFPGKEFYDGKLRADESVKKHNLFDLLpeskLIDEDAKPFLFIDTGGS 520
Cdd:pfam13087   1 LDRSLFERLQELGPSAV-VMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPDDF----HLPDPLGPLVFIDVDGS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 521 ErfkERTRRGSTSKENAGEAKLVEEIAERLLSLGV-KPEDIAVISPYDDQVALIRKELRVE-----GLEIKTVDGFQGRE 594
Cdd:pfam13087  76 E---EEESDGGTSYSNEAEAELVVQLVEKLIKSGPeEPSDIGVITPYRAQVRLIRKLLKRKlggklEIEVNTVDGFQGRE 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1899282647 595 KEVVIVSFVRSNKSREIGFLRDLRRLNVSITRAKRKLVLIGDS 637
Cdd:pfam13087 153 KDVIIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNA 195
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 178-466 1.31e-80

DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, or IGHMBP2) is a 5' to 3' helicase that unwinds RNA and DNA duplexes in an ATP-dependent reaction. It is a DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence (5'-GGGCT-3') related to the immunoglobulin mu chain switch region. The IGHMBP2 gene is responsible for Charcot-Marie-Tooth disease (CMT) type 2S and spinal muscular atrophy with respiratory distress type 1 (SMARD1). It is also thought to play a role in frontotemporal dementia (FTD) with amyotrophic lateral sclerosis (ALS) and major depressive disorder (MDD). SMUBP2 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: 350802 [Multi-domain]  Cd Length: 191  Bit Score: 253.69  E-value: 1.31e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 178 ELNKSQREAVLRSLAARDFFLIHGPPGTGKTITCIEIIAQLVEhgreheRSYNILAAADSNVAVDNLVERLDKIGVNVVR 257
Cdd:cd18044     1 NLNDSQKEAVKFALSQKDVALIHGPPGTGKTTTVVEIILQAVK------RGEKVLACAPSNIAVDNLVERLVALKVKVVR 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 258 IGHPARVIPSLRKRSLDYLiqeepeyikaqelrenayeikermksfivpemrwrrglsdeaimqlaregrtirgipkhki 337
Cdd:cd18044    75 IGHPARLLESVLDHSLDAL------------------------------------------------------------- 93

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 338 egmrkwldlkhgidklfgdareleekavkriiLEAEVICATNSTVGSE-ILKGAKFDLAVIDEATQSTEPSSLISVLKTK 416
Cdd:cd18044    94 --------------------------------VAAQVVLATNTGAGSRqLLPNELFDVVVIDEAAQALEASCWIPLLKAR 141

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1899282647 417 RFIMAGDHKQLPPTILNENAARGNLSRSLFERLLEMYGDKIRVMLDVQYR 466
Cdd:cd18044   142 RCILAGDHKQLPPTILSDKAARGGLGVTLFERLVNLYGESVVRMLTVQYR 191
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 467-654 2.71e-64

C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350195 [Multi-domain]  Cd Length: 184  Bit Score: 210.55  E-value: 2.71e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 467 MNDAIAEFPGKEFYDGKLRADESVKKHNLFDLLPESKlidedaKPFLFIDTGGserfKERTRRGSTSKENAGEAKLVEEI 546
Cdd:cd18808     1 MHPEISEFPSKLFYEGKLKAGVSVAARLNPPPLPGPS------KPLVFVDVSG----GEEREESGTSKSNEAEAELVVEL 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 547 AERLLSLGVKPEDIAVISPYDDQVALIRKELR-----VEGLEIKTVDGFQGREKEVVIVSFVRSNKSRE-IGFLRDLRRL 620
Cdd:cd18808    71 VKYLLKSGVKPSSIGVITPYRAQVALIRELLRkrgglLEDVEVGTVDNFQGREKDVIILSLVRSNESGGsIGFLSDPRRL 150

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1899282647 621 NVSITRAKRKLVLIGDSHTLEREGCYKRLVALAK 654
Cdd:cd18808   151 NVALTRAKRGLIIVGNPDTLSKDPLWKKLLEYLE 184
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 182-434 8.03e-62

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.


Pssm-ID: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 206.43  E-value: 8.03e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 182 SQREAVLRSLAARDFFLIHGPPGTGKTITCIEIIAQLVE-HGREHERSYNILAAADSNVAVDNLVERL----DKIGVNVV 256
Cdd:pfam13086   1 SQREAIRSALSSSHFTLIQGPPGTGKTTTIVELIRQLLSyPATSAAAGPRILVCAPSNAAVDNILERLlrkgQKYGPKIV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 257 RIGHPARVIPSLRKRSLDYLIQEEPE-YIKAQELRENAYEIKERMKSfivpemrwRRGLSDEAIMQLAREGRTIRgipkh 335
Cdd:pfam13086  81 RIGHPAAISEAVLPVSLDYLVESKLNnEEDAQIVKDISKELEKLAKA--------LRAFEKEIIVEKLLKSRNKD----- 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 336 KIEGMRKWLDLKHGIDKLFGDARELEEKAVKRIILEAEVICATNSTVGSEILKG-AKFDLAVIDEATQSTEPSSLISVLK 414
Cdd:pfam13086 148 KSKLEQERRKLRSERKELRKELRRREQSLEREILDEAQIVCSTLSGAGSRLLSSlANFDVVIIDEAAQALEPSTLIPLLR 227

                         250       260
                  ....*....|....*....|.
gi 1899282647 415 -TKRFIMAGDHKQLPPTILNE 434
Cdd:pfam13086 228 gPKKVVLVGDPKQLPPTVISK 248
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 178-466 1.95e-53

DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of Nonsense Transcripts, or ATP-Dependent Helicase RENT1) is an RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. It is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. It is recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) located downstream from the termination codon through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Diseases associated with UPF1 include juvenile amyotrophic lateral sclerosis and epidermolysis bullosa, junctional, non-Herlitz type. UPF1 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: 350797 [Multi-domain]  Cd Length: 234  Bit Score: 183.22  E-value: 1.95e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 178 ELNKSQREAVLRSLAARdFFLIHGPPGTGKTITCIEIIAQLVEHGREhersyNILAAADSNVAVDNLVERLDKIGVNVVR 257
Cdd:cd18039     1 ELNHSQVDAVKTALQRP-LSLIQGPPGTGKTVTSATIVYHLVKQGNG-----PVLVCAPSNVAVDQLTEKIHQTGLKVVR 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 258 IGHPAR--VIPSLRKRSLDYLIQEepeYIKAQELRENAYEIKERmksfivpemrwrRGLSDEAimqlaregrtirgipkh 335
Cdd:cd18039    75 LCAKSReaVESPVSFLALHNQVRN---LDSAEKLELLKLLKLET------------GELSSAD----------------- 122

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 336 kiegmrkwldlkhgiDKLFgdaRELEEKAVKRIILEAEVICATNSTVGSEILKGAKFDLAVIDEATQSTEPSSLIS-VLK 414
Cdd:cd18039   123 ---------------EKRY---RKLKRKAERELLRNADVICCTCVGAGDPRLSKMKFRTVLIDEATQATEPECLIPlVHG 184

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1899282647 415 TKRFIMAGDHKQLPPTILNENAARGNLSRSLFERLLEMygdKIR-VMLDVQYR 466
Cdd:cd18039   185 AKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQL---GIRpIRLQVQYR 234
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 179-466 2.47e-43

DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5-3 helicase, and endonuclease activities, and is involved in DNA replication and DNA repair in the nucleus and mitochondrion. It is involved in Okazaki fragment processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. It is also involved in 5-end resection of DNA during double-strand break (DSB) repair; it is recruited by BLM and mediates the cleavage of 5-ssDNA, while the 3-ssDNA cleavage is prevented by the presence of RPA. DNA2 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: 350799 [Multi-domain]  Cd Length: 203  Bit Score: 154.70  E-value: 2.47e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 179 LNKSQREAVLRSLAARDFFLIHGPPGTGKTITCIEIIAQLVEHGRehersyNILAAADSNVAVDNLVERLDKIGVNVVRI 258
Cdd:cd18041     2 LNKDQRQAIKKVLNAKDYALILGMPGTGKTTTIAALVRILVALGK------SVLLTSYTHSAVDNILLKLKKFGVNFLRL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 259 GHPARVIPSLRKRSLDyliqeepeyikaqelrenayEIKERMKSFivpemrwrrglsdeaimqlaregrtirgipkhkie 338
Cdd:cd18041    76 GRLKKIHPDVQEFTLE--------------------AILKSCKSV----------------------------------- 100

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 339 gmrkwldlkhgidklfgdareleeKAVKRIILEAEVICATNSTVGSEILKGAKFDLAVIDEATQSTEPSSLISVLKTKRF 418
Cdd:cd18041   101 ------------------------EELESKYESVSVVATTCLGINHPIFRRRTFDYCIVDEASQITLPICLGPLRLAKKF 156

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1899282647 419 IMAGDHKQLPPTILNENAARGNLSRSLFERLLEMYGDKIrVMLDVQYR 466
Cdd:cd18041   157 VLVGDHYQLPPLVKSREARELGMDESLFKRLSEAHPDAV-VQLTIQYR 203
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 179-466 2.88e-41

DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX 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: 438712 [Multi-domain]  Cd Length: 218  Bit Score: 149.67  E-value: 2.88e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 179 LNKSQREAVLRSLAA-RDFFLIHGPPGTGKTITCIEIIAQLveHGREHERSYN---------------------ILAAAD 236
Cdd:cd18042     1 LNESQLEAIASALQNsPGITLIQGPPGTGKTKTIVGILSVL--LAGKYRKYYEkvkkklrklqrnlnnkkkknrILVCAP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 237 SNVAVDNLVERLdkigvnvvrighparvipsLRKRSLDYLIqeepeyikaqelreNAYEIKermksfivpemrwrrglsd 316
Cdd:cd18042    79 SNAAVDEIVLRL-------------------LSEGFLDGDG--------------RSYKPN------------------- 106

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 317 eaimqLAREGRtirgipkhkiegmrkwldlkhgidklfgdareleEKAVKRIILEAEVICATNSTVGSEILK--GAKFDL 394
Cdd:cd18042   107 -----VVRVGR----------------------------------QELRASILNEADIVCTTLSSSGSDLLEslPRGFDT 147

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1899282647 395 AVIDEATQSTEPSSLISV-LKTKRFIMAGDHKQLPPTILNENAARGNLSRSLFERLLEmYGDKIrVMLDVQYR 466
Cdd:cd18042   148 VIIDEAAQAVELSTLIPLrLGCKRLILVGDPKQLPATVFSKVAQKLGYDRSLFERLQL-AGYPV-LMLTTQYR 218
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
 178-451 1.39e-30

DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and similar proteins. Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. All 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: 350796 [Multi-domain]  Cd Length: 229  Bit Score: 120.03  E-value: 1.39e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 178 ELNKSQREAVLRSLAARDF---FLIHGPPGTGKTITCIEIIAQLVEHGREHersyNILAAADSNVAVDNLVERLdkigvn 254
Cdd:cd18038     1 ELNDEQKLAVRNIVTGTSRpppYIIFGPPGTGKTVTLVEAILQVLRQPPEA----RILVCAPSNSAADLLAERL------ 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 255 vvrighpARVIPSlrkrsldyliqeepeyiKAQELRENAYEikermksfivpemrwrrglsdeaimqlaregRTIRGIPK 334
Cdd:cd18038    71 -------LNALVT-----------------KREILRLNAPS-------------------------------RDRASVPP 95

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 335 HkiegmrkWLDLKHGIDKLFGDARELEEKAVKRIileaeVICATNStvgSEILKGAK-----FDLAVIDEATQSTEPSSL 409
Cdd:cd18038    96 E-------LLPYCNSKAEGTFRLPSLEELKKYRI-----VVCTLMT---AGRLVQAGvpnghFTHIFIDEAGQATEPEAL 160

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1899282647 410 I--SVLKTK--RFIMAGDHKQLPPTILNENAARGNLSRSLFERLLE 451
Cdd:cd18038   161 IplSELASKntQIVLAGDPKQLGPVVRSPLARKYGLGKSLLERLME 206
DEXXc_HELZ2-C cd18040
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 179-466 1.13e-25

C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB and RXRA. It belongs to 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: 350798 [Multi-domain]  Cd Length: 271  Bit Score: 106.84  E-value: 1.13e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 179 LNKSQREAVLRSLAaRDFFLIHGPPGTGKTITCIEIIAQLVEHGREHERSYN-------ILAAADSNVAVDNLVERLDKI 251
Cdd:cd18040     2 LNPSQNHAVRTALT-KPFTLIQGPPGTGKTVTGVHIAYWFAKQNREIQSVSGegdggpcVLYCGPSNKSVDVVAELLLKV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 252 -GVNVVRIghparviPSLRKRSLDYLIQEEPEYIKAQELRENayEIKERMKSFIVpEMRWRRGLSDEAIMQLAREGRTIR 330
Cdd:cd18040    81 pGLKILRV-------YSEQIETTEYPIPNEPRHPNKKSERES--KPNSELSSITL-HHRIRQPSNPHSQQIKAFEARFER 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 331 giPKHKI-EGMRKWLDlkhgidKLFGDARELEEKAVkriileaEVICATNSTVGSEILKG-AKFDLAVIDEATQSTEPSS 408
Cdd:cd18040   151 --TQEKItEEDIKTYK------ILIWEARFEELETV-------DVILCTCSEAASQKMRThANVKQCIVDECGMCTEPES 215

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1899282647 409 LI---SVLKTKRFIMAGDHKQLPPTILNENAARGNLSRSLFERLLEMygdkiRVMLDVQYR 466
Cdd:cd18040   216 LIpivSAPRAEQVVLIGDHKQLRPVVQNKEAQKLGLGRSLFERYAEK-----ACMLDTQYR 271
DEXXQc_Mov10L1 cd18078
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ...
 179-451 2.62e-22

DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. Mov10L1 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: 350836 [Multi-domain]  Cd Length: 230  Bit Score: 95.90  E-value: 2.62e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 179 LNKSQREAVLRSLA--ARDF-FLIHGPPGTGKTITCIEIIAQLVehgREHERSyNILAAADSNVAVDNLVERLdkIGVNV 255
Cdd:cd18078     2 LNELQKEAVKRILGgeCRPLpYILFGPPGTGKTVTIIEAILQVV---YNLPRS-RILVCAPSNSAADLVTSRL--HESKV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 256 VRIGHPARVipslrkrsldyliqeepeyikaqelreNAYEIKERMksfiVPEMRWRRGLSDEaimqlaregrtirgipkh 335
Cdd:cd18078    76 LKPGDMVRL---------------------------NAVNRFEST----VIDARKLYCRLGE------------------ 106

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 336 kiegmRKWLDLKHgidklfgdareleekavkRIILEAeviCATNSTVGSEILKGAKFDLAVIDEATQSTEPSSLISV--- 412
Cdd:cd18078   107 -----DLSKASRH------------------RIVIST---CSTAGLLYQMGLPVGHFTHVFVDEAGQATEPESLIPLgli 160

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 1899282647 413 -LKTKRFIMAGDHKQLPPTILNENAARGNLSRSLFERLLE 451
Cdd:cd18078   161 sSRDGQIILAGDPMQLGPVIKSRLASAYGLGVSFLERLMN 200
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 360-466 1.10e-20

DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to 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: 438708 [Multi-domain]  Cd Length: 121  Bit Score: 88.06  E-value: 1.10e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 360 LEEKAVKRIileaeVICA-TNSTVGSeilkgakFDLAVIDEATQSTEPSSLISVLKTKRFIMAGDHKQLPPTILNENAA- 437
Cdd:cd17934    24 LKGLRGKRV-----LVTAqSNVAVDN-------VDVVIIDEASQITEPELLIALIRAKKVVLVGDPKQLPPVVQEDHAAl 91

                          90       100       110
                  ....*....|....*....|....*....|
gi 1899282647 438 -RGNLSRSLFERLLEMYGDKIRVMLDVQYR 466
Cdd:cd17934    92 lGLSFILSLLLLFRLLLPGSPKVMLDTQYR 121
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 179-465 1.43e-13

EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that represses class II MHC (major histocompatibility complex) gene expression. NFX1 binds a conserved cis-acting element, termed the X-box, in promoters of human class II MHC genes. The Cys-rich region contains several NFX1-type zinc finger domains. Frequently, a R3H domain is present in the C-terminus, and a RING finger domain and a PAM2 motif are present in the N-terminus. The lack of R3H and PAM2 motifs in the plant proteins indicates functional differences. Plant NFX1-like proteins are proposed to modulate growth and survival by coordinating reactive oxygen species, salicylic acid, further biotic stress and abscisic acid responses. A common feature of all members may be E3 ubiquitin ligase, due to the presence of a RING finger domain, as well as DNA binding. NFX1 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: 350694 [Multi-domain]  Cd Length: 178  Bit Score: 69.50  E-value: 1.43e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 179 LNKSQREAVLRSLAaRDFFLIHGPPGTGKTITCIEIIAQLVEHGREHERSyNILAAADSNVAVDNLVERLDKIGV-NVVR 257
Cdd:cd17936     2 LDPSQLEALKHALT-SELALIQGPPGTGKTFLGVKLVRALLQNQDLSITG-PILVVCYTNHALDQFLEGLLDFGPtKIVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 258 IGhpARVIpslrkrsldyliqeepeyikaqelrenayeikermksfivpemrwrrglsdeaimqlareGRTIRGIPKHKi 337
Cdd:cd17936    80 LG--ARVI------------------------------------------------------------GMTTTGAAKYR- 96

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 338 egmrkwldlkhgidklfgdareleekavkriileaevicatnstvgsEILKGAKFDLAVIDEATQSTEpSSLISVL--KT 415
Cdd:cd17936    97 -----------------------------------------------ELLQALGPKVVIVEEAAEVLE-AHILAALtpST 128

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1899282647 416 KRFIMAGDHKQLPPTILNEN--AARGNLSRSLFERLLEMygdKIR-VMLDVQY 465
Cdd:cd17936   129 EHLILIGDHKQLRPKVNVYEltAKKYNLDVSLFERLVKN---GLPfVTLNVQR 178
EEXXQc_AQR cd17935
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ...
 348-473 3.44e-11

EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds precursor-mRNA introns at a defined position and is part of a pentameric intron-binding complex (IBC). It is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350693 [Multi-domain]  Cd Length: 207  Bit Score: 63.21  E-value: 3.44e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 348 HGIDKLFG--DARELEEKAVKRIILEAEVI---CATNSTVGSEILK-GAKFDLAVIDEATQSTEPSSLISVL-------- 413
Cdd:cd17935    61 QALNQLFEkiMALDIDERHLLRLGHGAKIIamtCTHAALKRGELVElGFKYDNILMEEAAQILEIETFIPLLlqnpedgp 140

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1899282647 414 -KTKRFIMAGDHKQLPPTILNENAAR-GNLSRSLFERLLEMygdKIR-VMLDVQYRMNDAIAE 473
Cdd:cd17935   141 nRLKRLIMIGDHHQLPPVIKNMAFQKySNMEQSLFTRLVRL---GVPtVDLDAQGRARASISS 200
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 559-635 7.71e-11

C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 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: 350173 [Multi-domain]  Cd Length: 89  Bit Score: 58.99  E-value: 7.71e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 559 DIAVISPYDDQVALIRKELRVEGL--------EIKTVDGFQGREKEVVIVSFVRSNksreigfLRDLRRLNVSITRAKRK 630
Cdd:cd18786    12 KGVVLTPYHRDRAYLNQYLQGLSLdefdlqlvGAITIDSSQGLTFDVVTLYLPTAN-------SLTPRRLYVALTRARKR 84


                  ....*
gi 1899282647 631 LVLIG 635
Cdd:cd18786    85 LVIYD 89
CoV_Nsp13-helicase cd21718
helicase domain of coronavirus non-structural protein 13; This model represents the helicase ...
 380-634 9.58e-11

helicase domain of coronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from alpha-, beta-, gamma-, and deltacoronavirus, including pathogenic human viruses such as Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.


Pssm-ID: 409652 [Multi-domain]  Cd Length: 341  Bit Score: 63.70  E-value: 9.58e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 380 STVGSeiLKGAKFDLAVIDEATQST--EPSSLISVLKTKRFIMAGDHKQLP-PTILnenAARGNLSRSLFERLLE-MYGD 455
Cdd:cd21718   108 STINA--LPECSADIVVVDEVSMCTnyDLSVVNARLKYKHIVYVGDPAQLPaPRTL---LTEGSLEPKDYNVVTRlMVGS 182

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 456 KIRVMLDVQYRMNDAIAEFPGKEFYDGKLRAdesvkkHNlfdllPESkliDEDAKPFLfidtggserfkertrRGSTSKE 535
Cdd:cd21718   183 GPDVFLSKCYRCPKEIVDTVSKLVYDNKLKA------IK-----PKS---RQCFKTFG---------------KGDVRHD 233

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 536 NAGEAKLVE-EIAERLLSLGVKPEDIAVISPYDDQVAlirKELRVEGLEIKTVDGFQGREKEVVIvsFVRSNKSREIgfl 614
Cdd:cd21718   234 NGSAINRPQlEFVKRFLDRNPRWRKAVFISPYNAMNN---RASRLLGLSTQTVDSSQGSEYDYVI--FCQTTDTAHA--- 305

                         250       260
                  ....*....|....*....|
gi 1899282647 615 RDLRRLNVSITRAKRKLVLI 634
Cdd:cd21718   306 LNINRFNVAITRAKHGILVI 325
betaCoV_Nsp13-helicase cd21722
helicase domain of betacoronavirus non-structural protein 13; This model represents the ...
 393-640 1.26e-09

helicase domain of betacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from betacoronavirus, including pathogenic human viruses such as Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.


Pssm-ID: 409655 [Multi-domain]  Cd Length: 340  Bit Score: 60.20  E-value: 1.26e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 393 DLAVIDEATQST--EPSSLISVLKTKRFIMAGDHKQLP-PTILnenAARGNLSRSLFE---RLLEMYGDKIrvMLDVQYR 466
Cdd:cd21722   119 DILVVDEVSMCTnyDLSVINARVRAKHIVYIGDPAQLPaPRTL---LTKGTLEPEYFNsvtRLMCCLGPDI--FLGTCYR 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 467 MNDAIAEFPGKEFYDGKLRADEsvkkhnlfdllpeskliDEDAKPFLFIdtggserFKERTRRGSTSKENAGEAKLVEEi 546
Cdd:cd21722   194 CPKEIVDTVSALVYDNKLKAKK-----------------DNSGQCFKVY-------YKGSVTHDSSSAINRPQIYLVKK- 248

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 547 aerLLSLGVKPEDIAVISPYDDQVALIRKELrveGLEIKTVDGFQGREKEVVIVSfvrsnKSREIGFLRDLRRLNVSITR 626
Cdd:cd21722   249 ---FLKANPAWSKAVFISPYNSQNAVARRVL---GLQTQTVDSSQGSEYDYVIYC-----QTAETAHSVNVNRFNVAITR 317

                         250
                  ....*....|....
gi 1899282647 627 AKRKLVLIGDSHTL 640
Cdd:cd21722   318 AKKGILCVMSSMQL 331
DEXXQc_HELZ cd18077
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ...
 179-466 1.04e-08

DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. HELZ is a member of the family I class of RNA helicases 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: 350835 [Multi-domain]  Cd Length: 226  Bit Score: 56.34  E-value: 1.04e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 179 LNKSQREAVLRSLAARDF----FLIHGPPGTGKTITcieiIAQLVEHGREHERSyNILAAADSNVAVDNLVErldkigvn 254
Cdd:cd18077     2 LNAKQKEAVLAITTPLSIqlppVLLIGPFGTGKTFT----LAQAVKHILQQPET-RILICTHSNSAADLYIK-------- 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 255 vvrighparvipslrkrslDYL-IQEEPEYIKAQELRenayeikermksfIVPEMRWRRGLsdEAIMQ---LAREGRTIR 330
Cdd:cd18077    69 -------------------EYLhPYVETGNPRARPLR-------------VYYRNRWVKTV--HPVVQkycLIDEHGTFR 114

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 331 GIPKHKIegmrkwldLKHgidklfgdareleekavkRIILeaeVICATNSTVGSEILKGAKFDLAVIDEATQSTEPSSLI 410
Cdd:cd18077   115 MPTREDV--------MRH------------------RVVV---VTLSTSQYLCQLDLEPGFFTHILLDEAAQAMECEAIM 165

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1899282647 411 SV---LKTKRFIMAGDHKQLPPTILNENAARGNLSRSLFERLLEMYGDK--IRVMLDVQYR 466
Cdd:cd18077   166 PLalaTKSTRIVLAGDHMQLSPEVYSEFARERNLHISLLERLYEHYPSEhpCRILLCENYR 226
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 137-250 1.15e-07

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 54.98  E-value: 1.15e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 137 FQRMIEALKKFKRLPRRRKDKLLGNAAPDFEKVGEIEFFNQELNKSQREAVLRSLAARDFFLIHGPPGTGKTITCIEIIA 216
Cdd:COG0507    83 LTRLLEAEQRLARRLRRLARPALDEADVEAALAALEPRAGITLSDEQREAVALALTTRRVSVLTGGAGTGKTTTLRALLA 162

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1899282647 217 QLVEHGrehersYNILAAADSNVAVDNLVERLDK 250
Cdd:COG0507   163 ALEALG------LRVALAAPTGKAAKRLSESTGI 190
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 391-435 1.30e-07

DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases 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: 350801 [Multi-domain]  Cd Length: 127  Bit Score: 50.66  E-value: 1.30e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1899282647 391 KFDLAVIDEATQSTEPSSLISVLKTKRFIMAGDHKQLPPTI-LNEN 435
Cdd:cd18043    80 LFDLVIFDEASQIPIEEALPALFRGKQVVVVGDDKQLPPSIlLREH 125
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 374-465 5.11e-07

DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. 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. SF1 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: 438706 [Multi-domain]  Cd Length: 121  Bit Score: 49.02  E-value: 5.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 374 VICATNSTVgseilkgAKFDLAVIDEATQSTEPSSLIS---VLKTKRFIMAGDHKQLPPTILNENAARGNLSRSLFERLL 450
Cdd:cd17914    36 LVTPTNKAA-------AQLDNILVDEAAQILEPETSRLidlALDQGRVILVGDHDQLGPVWRGAVLAKICNEQSLFTRLV 108

                          90
                  ....*....|....*
gi 1899282647 451 EMYGDKIRvmLDVQY 465
Cdd:cd17914   109 RLGVSLIR--LQVQY 121
AAA_19 pfam13245
AAA domain;
183-268 9.58e-06

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 45.67  E-value: 9.58e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 183 QREAVlRSLAARDFFLIHGPPGTGKTITCIEIIAQLVehgREHERSYNILAAADSNVAVDNLVERLdkigvnvvriGHPA 262
Cdd:pfam13245   1 QREAV-RTALPSKVVLLTGGPGTGKTTTIRHIVALLV---ALGGVSFPILLAAPTGRAAKRLSERT----------GLPA 66


                  ....*.
gi 1899282647 263 RVIPSL 268
Cdd:pfam13245  67 STIHRL 72
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 178-268 1.37e-05

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.


Pssm-ID: 433343 [Multi-domain]  Cd Length: 191  Bit Score: 46.40  E-value: 1.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 178 ELNKSQREAVLRSLAARD-FFLIHGPPGTGKTiTCIEIIAQLVEhgrehERSYNILAAADSNVAVDNLVERLdkigvnvv 256
Cdd:pfam13604   1 TLNAEQAAAVRALLTSGDrVAVLVGPAGTGKT-TALKALREAWE-----AAGYRVIGLAPTGRAAKVLGEEL-------- 66

                          90
                  ....*....|..
gi 1899282647 257 riGHPARVIPSL 268
Cdd:pfam13604  67 --GIPADTIAKL 76
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 198-244 1.80e-05

DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. 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. SF1 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: 438706 [Multi-domain]  Cd Length: 121  Bit Score: 44.40  E-value: 1.80e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1899282647 198 LIHGPPGTGKTITCIEIIAQLVEHgrEHERSYNILAAADSNVAVDNL 244
Cdd:cd17914     3 LIQGPPGTGKTRVLVKIVAALMQN--KNGEPGRILLVTPTNKAAAQL 47
gammaCoV_Nsp13-helicase cd21720
helicase domain of gammacoronavirus non-structural protein 13; This model represents the ...
 393-634 3.71e-05

helicase domain of gammacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from gammacoronavirus, including Avian infectious bronchitis virus. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Coronavirus (CoV) Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.


Pssm-ID: 409653 [Multi-domain]  Cd Length: 343  Bit Score: 46.45  E-value: 3.71e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 393 DLAVIDEATQST--EPSSLISVLKTKRFIMAGDHKQLPP--TILNenaarGNLSRSLFERLLE-MYGDKIRVMLDVQYRM 467
Cdd:cd21720   119 DILLVDEVSMLTnyELSFINGKINYQYVVYVGDPAQLPAprTLLN-----GSLSPKDYNVVTNlMVCVKPDIFLAKCYRC 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 468 NDAIAEFPGKEFYDGKLRADesvkkhnlfdlLPESKLIDEdakpfLFIDTGGSERFKErtrrgSTSKENAGEAKLVEEIA 547
Cdd:cd21720   194 PKEIVDTVSTLVYDGKFIAN-----------NPESRQCFK-----VIVNNGNSDVGHE-----SGSAYNTTQLEFVKDFV 252

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 548 ERllslgvKPE--DIAVISPYDdqvALIRKELRVEGLEIKTVDGFQGREKEVVIVSfVRSNKSREIgflrDLRRLNVSIT 625
Cdd:cd21720   253 CR------NKEwrEATFISPYN---AMNQRAYRMLGLNVQTVDSSQGSEYDYVIFC-VTADSQHAL----NINRFNVALT 318


                  ....*....
gi 1899282647 626 RAKRKLVLI 634
Cdd:cd21720   319 RAKRGILVV 327
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
123-223 7.08e-05

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 45.79  E-value: 7.08e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 123 RKDLRIDLFVNDITFQRMIEALKKFKRLPRRRKDKLLGNAAPDFEKVGEIEFFNQELNKSQREAVLRSLAAR----DFFL 198
Cdd:COG1061    25 RLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEALEAGDEASGTSFELRPYQQEALEALLAALerggGRGL 104

                          90       100
                  ....*....|....*....|....*
gi 1899282647 199 IHGPPGTGKTITCIEIIAQLVEHGR 223
Cdd:COG1061   105 VVAPTGTGKTVLALALAAELLRGKR 129
alphaCoV_Nsp13-helicase cd21723
helicase domain of alphacoronavirus non-structural protein 13; This model represents the ...
 563-629 9.47e-05

helicase domain of alphacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from alphacoronavirus, including Porcine epidemic diarrhea virus and Human coronavirus (CoV) NL63. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.


Pssm-ID: 409656 [Multi-domain]  Cd Length: 340  Bit Score: 45.11  E-value: 9.47e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1899282647 563 ISPYDDQVALIRkelRVEGLEIKTVDGFQGREKEVVIVSfvrsnKSREIGFLRDLRRLNVSITRAKR 629
Cdd:cd21723   262 ISPYNSQNYVAS---RVLGLQIQTVDSSQGSEYDYVIYT-----QTSDTAHACNVNRFNVAITRAKK 320
SF1_C_UvrD cd18807
C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase ...
 534-635 1.19e-04

C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. This family also includes ATP-dependent helicase/nuclease AddA and helicase/nuclease RecBCD subunit RecB, among others. UvrD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350194 [Multi-domain]  Cd Length: 150  Bit Score: 42.60  E-value: 1.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 534 KENAGEAKLV-EEIAERLLSLGVKPEDIAVISPYDDQVALIRKELRVeglEIKTVDGFQGREKEVVIVSFV--------- 603
Cdd:cd18807    40 KDEADEAKAIaDEIKRLIESGPVQYSDIAILVRTNRQARVIEEALRV---TLMTIHASKGLEFPVVFIVGLgegfipsda 116

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1899282647 604 --RSNKSREIGFLRDLRRLNVSITRAKRKLVLIG 635
Cdd:cd18807   117 syHAAKEDEERLEEERRLLYVALTRAKKELYLVG 150
DEXQc_UvrD cd17932
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ...
 180-251 1.62e-04

DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. UvrD 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: 350690 [Multi-domain]  Cd Length: 189  Bit Score: 42.89  E-value: 1.62e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1899282647 180 NKSQREAVLrslaardffLIHGP------PGTGKTITCIEIIAQLVEHGREHERsyNILAAADSNVAVDNLVERLDKI 251
Cdd:cd17932     1 NPEQREAVT---------HPDGPllvlagAGSGKTRVLTHRIAYLILEGGVPPE--RILAVTFTNKAAKEMRERLRKL 67
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 183-268 3.02e-04

DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD 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: 350691 [Multi-domain]  Cd Length: 155  Bit Score: 41.77  E-value: 3.02e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 183 QREAVLRSLAARdFFLIHGPPGTGKTITCIEIIAQLVEHGrehersYNILAAADSNVAVDNLVErldkigvnvvRIGHPA 262
Cdd:cd17933     2 QKAAVRLVLRNR-VSVLTGGAGTGKTTTLKALLAALEAEG------KRVVLAAPTGKAAKRLSE----------STGIEA 64


                  ....*.
gi 1899282647 263 RVIPSL 268
Cdd:cd17933    65 STIHRL 70
ResIII pfam04851
Type III restriction enzyme, res subunit;
178-224 7.73e-04

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 40.73  E-value: 7.73e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1899282647 178 ELNKSQREAVLRSLAARDF----FLIHGPPGTGKTITCIEIIAQLVEHGRE 224
Cdd:pfam04851   3 ELRPYQIEAIENLLESIKNgqkrGLIVMATGSGKTLTAAKLIARLFKKGPI 53
UvrD COG0210
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
177-251 2.14e-03

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


Pssm-ID: 439980 [Multi-domain]  Cd Length: 721  Bit Score: 41.46  E-value: 2.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899282647 177 QELNKSQREAVLrslaardffLIHGP------PGTGKTITCIEIIAQLVEHGRehERSYNILAAADSNVAVDNLVERLDK 250
Cdd:COG0210     5 AGLNPEQRAAVE---------HPEGPllvlagAGSGKTRVLTHRIAYLIAEGG--VDPEQILAVTFTNKAAREMRERIEA 73


                  .
gi 1899282647 251 I 251
Cdd:COG0210    74 L 74
UvrD_C_2 pfam13538
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ...
 586-634 2.90e-03

UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.


Pssm-ID: 463913 [Multi-domain]  Cd Length: 52  Bit Score: 36.01  E-value: 2.90e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1899282647 586 TVDGFQGREKEVVIVSFVRSNKSREIGFLRdlRRLNVSITRAKRKLVLI 634
Cdd:pfam13538   6 TVHKAQGSEFPAVFLVDPDLTAHYHSMLRR--RLLYTAVTRARKKLVLV 52
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 574-635 5.79e-03

Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.


Pssm-ID: 366646 [Multi-domain]  Cd Length: 227  Bit Score: 38.90  E-value: 5.79e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1899282647 574 RKELRVEGLEIKTVDGFQGREKEVVivSFVRSNKSREIGFLRDLRRLNVSITRAKRKLVLIG 635
Cdd:pfam01443 168 QALKESLGVRVTTVHEVQGLTFDSV--TLVLDTDTDLLIISDSPEHLYVALTRHRKSLHILT 227
 
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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