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Conserved domains on  [gi|19075869|ref|NP_588369|]
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DNA polymerase alpha-associated DNA helicase A [Schizosaccharomyces pombe]

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 ...
 33-651 3.78e-174

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: 510.51  E-value: 3.78e-174
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869    33 EVDETEKSIKRFPLSVLQRKGLALINLRiGVVKTGFGGKTIIDFEKDPAFsngeelpANSFSPGDVVSIRqdfqsskkkR 112
Cdd:TIGR00376   6 EISAMMNEIRRLSLKQRERRGRAILNLQ-GKIRGGLLGFLLVRFGRRKAI-------ATEISVGDIVLVS---------R 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   113 PNETDISVEGVVTRVHERHISVALksEEDIPS-SVTRLSVVKLVNRVTYERMRHTMLEFKRsipeYRNSLFYTLIGRKKA 191
Cdd:TIGR00376  69 GNPLQSDLTGVVTRVGKRFITVAL--EESVPQwSLKRVRIDLYANDVTFKRMKEALRALTE----NHSRLLEFLLGREAP 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   192 DVSIDqklIGDIKYFNKELNASQKKAVKFSIAVKELSLIHGPPGTGKTHTLVEIIQQLVLRNKRILVCGASNLAVDNIVD 271
Cdd:TIGR00376 143 SKASE---IHDFQFFDPNLNESQKEAVLFALSSKDLFLIHGPPGTGKTRTVVELIRQLVKRGLRVLVTAPSNIAVDNLLE 219

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   272 RLSSSGIPMVRLGHPARLLPSILDHSLDVLSRTGDNGDVIRGISEDIDVCLSKITK-TKNGRERREIYKNIRELRKDYRK 350
Cdd:TIGR00376 220 RLALCDQKIVRLGHPARLLKSNKQHSLDYLIENHPKYQIVADIREKIDELIEERNKkTKPSPQKRRGLSDIKILRKALKK 299

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   351 YEAKTVANIVSASKVVFCTLHG------------------------------AGSRQLKGQRFDAVIIDEASQALEPQCW 400
Cdd:TIGR00376 300 REARGIESLKIASMAEWIETNKsidrllkllpeseerimneilaesdatnsmAGSEILNGQYFDVAVIDEASQAMEPSCL 379

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   401 IPLLGMNKVILAGDHMQLSPNVQSKRPY---ISMFERLVKSQGDLVKcFLNIQYRMHELISKFPSDTFYDSKLVPAEEVK 477
Cdd:TIGR00376 380 IPLLKARKLILAGDHKQLPPTILSHDAEelsLTLFERLIKEYPERSR-TLNVQYRMNQKIMEFPSREFYNGKLTAHESVA 458

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   478 KRLLMDLENVEETELTDS-----PIYFYDTLGNYQEDDRSEDMQnfyqdSKSNHWEAQIVSYHISGLLEAGLEAKDIAVV 552
Cdd:TIGR00376 459 NILLRDLPKVEATESEDDletgiPLLFIDTSGCELFELKEADST-----SKYNPGEAELVSEIIQALVKMGVPANDIGVI 533

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   553 TPYNAQVALIRQLLKEKGIEVEMGSVDKVQGREKEAIIFSLVRSNDVREVGFLAEKRRLNVAITRPKRHLCVIGDSNTVK 632
Cdd:TIGR00376 534 TPYDAQVDLLRQLLEHRHIDIEVSSVDGFQGREKEVIIISFVRSNRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLS 613

                         650
                  ....*....|....*....
gi 19075869   633 wASEFFHQWVDFLEENAIV 651
Cdd:TIGR00376 614 -NHKFYKRLIEWCKQHGEV 631
 
Name Accession Description Interval E-value
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 33-651 3.78e-174

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: 510.51  E-value: 3.78e-174
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869    33 EVDETEKSIKRFPLSVLQRKGLALINLRiGVVKTGFGGKTIIDFEKDPAFsngeelpANSFSPGDVVSIRqdfqsskkkR 112
Cdd:TIGR00376   6 EISAMMNEIRRLSLKQRERRGRAILNLQ-GKIRGGLLGFLLVRFGRRKAI-------ATEISVGDIVLVS---------R 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   113 PNETDISVEGVVTRVHERHISVALksEEDIPS-SVTRLSVVKLVNRVTYERMRHTMLEFKRsipeYRNSLFYTLIGRKKA 191
Cdd:TIGR00376  69 GNPLQSDLTGVVTRVGKRFITVAL--EESVPQwSLKRVRIDLYANDVTFKRMKEALRALTE----NHSRLLEFLLGREAP 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   192 DVSIDqklIGDIKYFNKELNASQKKAVKFSIAVKELSLIHGPPGTGKTHTLVEIIQQLVLRNKRILVCGASNLAVDNIVD 271
Cdd:TIGR00376 143 SKASE---IHDFQFFDPNLNESQKEAVLFALSSKDLFLIHGPPGTGKTRTVVELIRQLVKRGLRVLVTAPSNIAVDNLLE 219

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   272 RLSSSGIPMVRLGHPARLLPSILDHSLDVLSRTGDNGDVIRGISEDIDVCLSKITK-TKNGRERREIYKNIRELRKDYRK 350
Cdd:TIGR00376 220 RLALCDQKIVRLGHPARLLKSNKQHSLDYLIENHPKYQIVADIREKIDELIEERNKkTKPSPQKRRGLSDIKILRKALKK 299

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   351 YEAKTVANIVSASKVVFCTLHG------------------------------AGSRQLKGQRFDAVIIDEASQALEPQCW 400
Cdd:TIGR00376 300 REARGIESLKIASMAEWIETNKsidrllkllpeseerimneilaesdatnsmAGSEILNGQYFDVAVIDEASQAMEPSCL 379

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   401 IPLLGMNKVILAGDHMQLSPNVQSKRPY---ISMFERLVKSQGDLVKcFLNIQYRMHELISKFPSDTFYDSKLVPAEEVK 477
Cdd:TIGR00376 380 IPLLKARKLILAGDHKQLPPTILSHDAEelsLTLFERLIKEYPERSR-TLNVQYRMNQKIMEFPSREFYNGKLTAHESVA 458

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   478 KRLLMDLENVEETELTDS-----PIYFYDTLGNYQEDDRSEDMQnfyqdSKSNHWEAQIVSYHISGLLEAGLEAKDIAVV 552
Cdd:TIGR00376 459 NILLRDLPKVEATESEDDletgiPLLFIDTSGCELFELKEADST-----SKYNPGEAELVSEIIQALVKMGVPANDIGVI 533

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   553 TPYNAQVALIRQLLKEKGIEVEMGSVDKVQGREKEAIIFSLVRSNDVREVGFLAEKRRLNVAITRPKRHLCVIGDSNTVK 632
Cdd:TIGR00376 534 TPYDAQVDLLRQLLEHRHIDIEVSSVDGFQGREKEVIIISFVRSNRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLS 613

                         650
                  ....*....|....*....
gi 19075869   633 wASEFFHQWVDFLEENAIV 651
Cdd:TIGR00376 614 -NHKFYKRLIEWCKQHGEV 631
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 209-452 8.38e-101

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: 305.69  E-value: 8.38e-101
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 209 ELNASQKKAVKFSIAVKELSLIHGPPGTGKTHTLVEIIQQLVLRNKRILVCGASNLAVDNIVDRLSSSGIPMVRLGHPAR 288
Cdd:cd18044   1 NLNDSQKEAVKFALSQKDVALIHGPPGTGKTTTVVEIILQAVKRGEKVLACAPSNIAVDNLVERLVALKVKVVRIGHPAR 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 289 LLPSILDHSLDVLsrtgdngdvirgisedidvclskitktkngrerreiyknirelrkdyrkyeaktvanivSASKVVFC 368
Cdd:cd18044  81 LLESVLDHSLDAL-----------------------------------------------------------VAAQVVLA 101

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 369 TLHGAGSRQLK-GQRFDAVIIDEASQALEPQCWIPLLGMNKVILAGDHMQLSPNVQS-----KRPYISMFERLVKSQGDL 442
Cdd:cd18044 102 TNTGAGSRQLLpNELFDVVVIDEAAQALEASCWIPLLKARRCILAGDHKQLPPTILSdkaarGGLGVTLFERLVNLYGES 181

                       250
                ....*....|
gi 19075869 443 VKCFLNIQYR 452
Cdd:cd18044 182 VVRMLTVQYR 191
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
332-648 7.78e-73

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 251.20  E-value: 7.78e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 332 RERREIYKNIRELRKDYRKYEAKTVANIVSASKVVFCTLHGAGS-RQLKGQRFDAVIIDEASQALEPQCWIPLLGMNKVI 410
Cdd:COG1112 504 REAARLRRALRRELKKRRELRKLLWDALLELAPVVGMTPASVARlLPLGEGSFDLVIIDEASQATLAEALGALARAKRVV 583

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 411 LAGDHMQLSPNVQSKRPY--------ISMFERLVKSQGDlVKCFLNIQYRMHELISKFPSDTFYDSKLVPAEEVKKRLLm 482
Cdd:COG1112 584 LVGDPKQLPPVVFGEEAEevaeegldESLLDRLLARLPE-RGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSPKARRL- 661

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 483 dlenveetELTDSPIYFYDTLGNYQEDDRSedmqnfyqdsKSNHWEAQIVSYHISGLLEAGLEAKDIAVVTPYNAQVALI 562
Cdd:COG1112 662 --------ADPDSPLVFIDVDGVYERRGGS----------RTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALI 723

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 563 RQLLKE----KGIEVEMGSVDKVQGREKEAIIFSLVRSND---VREVGFLAEK-RRLNVAITRPKRHLCVIGDSNTvkWA 634
Cdd:COG1112 724 RELLREalgdGLEPVFVGTVDRFQGDERDVIIFSLVYSNDedvPRNFGFLNGGpRRLNVAVSRARRKLIVVGSREL--LD 801

                       330
                ....*....|....*...
gi 19075869 635 SE----FFHQWVDFLEEN 648
Cdd:COG1112 802 SDpstpALKRLLEYLERA 819
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 429-629 8.81e-73

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: 233.21  E-value: 8.81e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   429 ISMFERLVKsQGDLVKCFLNIQYRMHELISKFPSDTFYDSKLVPAEEVKKRLLMDLENVEETeltDSPIYFYDTlgnyqe 508
Cdd:pfam13087   3 RSLFERLQE-LGPSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPDDFHLPDP---LGPLVFIDV------ 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   509 dDRSEDMQNFYQDSKSNHWEAQIVSYHISGLLEAGLEA-KDIAVVTPYNAQVALIRQLLKEKG---IEVEMGSVDKVQGR 584
Cdd:pfam13087  73 -DGSEEEESDGGTSYSNEAEAELVVQLVEKLIKSGPEEpSDIGVITPYRAQVRLIRKLLKRKLggkLEIEVNTVDGFQGR 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 19075869   585 EKEAIIFSLVRSNDVREVGFLAEKRRLNVAITRPKRHLCVIGDSN 629
Cdd:pfam13087 152 EKDVIIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 229-273 2.35e-04

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 41.98  E-value: 2.35e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 19075869    229 LIHGPPGTGKTHTLVEIIQQLVLRNKRILVCGASNLAVDNIVDRL 273
Cdd:smart00382   6 LIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLL 50
 
Name Accession Description Interval E-value
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 33-651 3.78e-174

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: 510.51  E-value: 3.78e-174
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869    33 EVDETEKSIKRFPLSVLQRKGLALINLRiGVVKTGFGGKTIIDFEKDPAFsngeelpANSFSPGDVVSIRqdfqsskkkR 112
Cdd:TIGR00376   6 EISAMMNEIRRLSLKQRERRGRAILNLQ-GKIRGGLLGFLLVRFGRRKAI-------ATEISVGDIVLVS---------R 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   113 PNETDISVEGVVTRVHERHISVALksEEDIPS-SVTRLSVVKLVNRVTYERMRHTMLEFKRsipeYRNSLFYTLIGRKKA 191
Cdd:TIGR00376  69 GNPLQSDLTGVVTRVGKRFITVAL--EESVPQwSLKRVRIDLYANDVTFKRMKEALRALTE----NHSRLLEFLLGREAP 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   192 DVSIDqklIGDIKYFNKELNASQKKAVKFSIAVKELSLIHGPPGTGKTHTLVEIIQQLVLRNKRILVCGASNLAVDNIVD 271
Cdd:TIGR00376 143 SKASE---IHDFQFFDPNLNESQKEAVLFALSSKDLFLIHGPPGTGKTRTVVELIRQLVKRGLRVLVTAPSNIAVDNLLE 219

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   272 RLSSSGIPMVRLGHPARLLPSILDHSLDVLSRTGDNGDVIRGISEDIDVCLSKITK-TKNGRERREIYKNIRELRKDYRK 350
Cdd:TIGR00376 220 RLALCDQKIVRLGHPARLLKSNKQHSLDYLIENHPKYQIVADIREKIDELIEERNKkTKPSPQKRRGLSDIKILRKALKK 299

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   351 YEAKTVANIVSASKVVFCTLHG------------------------------AGSRQLKGQRFDAVIIDEASQALEPQCW 400
Cdd:TIGR00376 300 REARGIESLKIASMAEWIETNKsidrllkllpeseerimneilaesdatnsmAGSEILNGQYFDVAVIDEASQAMEPSCL 379

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   401 IPLLGMNKVILAGDHMQLSPNVQSKRPY---ISMFERLVKSQGDLVKcFLNIQYRMHELISKFPSDTFYDSKLVPAEEVK 477
Cdd:TIGR00376 380 IPLLKARKLILAGDHKQLPPTILSHDAEelsLTLFERLIKEYPERSR-TLNVQYRMNQKIMEFPSREFYNGKLTAHESVA 458

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   478 KRLLMDLENVEETELTDS-----PIYFYDTLGNYQEDDRSEDMQnfyqdSKSNHWEAQIVSYHISGLLEAGLEAKDIAVV 552
Cdd:TIGR00376 459 NILLRDLPKVEATESEDDletgiPLLFIDTSGCELFELKEADST-----SKYNPGEAELVSEIIQALVKMGVPANDIGVI 533

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   553 TPYNAQVALIRQLLKEKGIEVEMGSVDKVQGREKEAIIFSLVRSNDVREVGFLAEKRRLNVAITRPKRHLCVIGDSNTVK 632
Cdd:TIGR00376 534 TPYDAQVDLLRQLLEHRHIDIEVSSVDGFQGREKEVIIISFVRSNRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLS 613

                         650
                  ....*....|....*....
gi 19075869   633 wASEFFHQWVDFLEENAIV 651
Cdd:TIGR00376 614 -NHKFYKRLIEWCKQHGEV 631
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 209-452 8.38e-101

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: 305.69  E-value: 8.38e-101
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 209 ELNASQKKAVKFSIAVKELSLIHGPPGTGKTHTLVEIIQQLVLRNKRILVCGASNLAVDNIVDRLSSSGIPMVRLGHPAR 288
Cdd:cd18044   1 NLNDSQKEAVKFALSQKDVALIHGPPGTGKTTTVVEIILQAVKRGEKVLACAPSNIAVDNLVERLVALKVKVVRIGHPAR 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 289 LLPSILDHSLDVLsrtgdngdvirgisedidvclskitktkngrerreiyknirelrkdyrkyeaktvanivSASKVVFC 368
Cdd:cd18044  81 LLESVLDHSLDAL-----------------------------------------------------------VAAQVVLA 101

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 369 TLHGAGSRQLK-GQRFDAVIIDEASQALEPQCWIPLLGMNKVILAGDHMQLSPNVQS-----KRPYISMFERLVKSQGDL 442
Cdd:cd18044 102 TNTGAGSRQLLpNELFDVVVIDEAAQALEASCWIPLLKARRCILAGDHKQLPPTILSdkaarGGLGVTLFERLVNLYGES 181

                       250
                ....*....|
gi 19075869 443 VKCFLNIQYR 452
Cdd:cd18044 182 VVRMLTVQYR 191
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
332-648 7.78e-73

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 251.20  E-value: 7.78e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 332 RERREIYKNIRELRKDYRKYEAKTVANIVSASKVVFCTLHGAGS-RQLKGQRFDAVIIDEASQALEPQCWIPLLGMNKVI 410
Cdd:COG1112 504 REAARLRRALRRELKKRRELRKLLWDALLELAPVVGMTPASVARlLPLGEGSFDLVIIDEASQATLAEALGALARAKRVV 583

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 411 LAGDHMQLSPNVQSKRPY--------ISMFERLVKSQGDlVKCFLNIQYRMHELISKFPSDTFYDSKLVPAEEVKKRLLm 482
Cdd:COG1112 584 LVGDPKQLPPVVFGEEAEevaeegldESLLDRLLARLPE-RGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSPKARRL- 661

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 483 dlenveetELTDSPIYFYDTLGNYQEDDRSedmqnfyqdsKSNHWEAQIVSYHISGLLEAGLEAKDIAVVTPYNAQVALI 562
Cdd:COG1112 662 --------ADPDSPLVFIDVDGVYERRGGS----------RTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALI 723

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 563 RQLLKE----KGIEVEMGSVDKVQGREKEAIIFSLVRSND---VREVGFLAEK-RRLNVAITRPKRHLCVIGDSNTvkWA 634
Cdd:COG1112 724 RELLREalgdGLEPVFVGTVDRFQGDERDVIIFSLVYSNDedvPRNFGFLNGGpRRLNVAVSRARRKLIVVGSREL--LD 801

                       330
                ....*....|....*...
gi 19075869 635 SE----FFHQWVDFLEEN 648
Cdd:COG1112 802 SDpstpALKRLLEYLERA 819
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 429-629 8.81e-73

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: 233.21  E-value: 8.81e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   429 ISMFERLVKsQGDLVKCFLNIQYRMHELISKFPSDTFYDSKLVPAEEVKKRLLMDLENVEETeltDSPIYFYDTlgnyqe 508
Cdd:pfam13087   3 RSLFERLQE-LGPSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPDDFHLPDP---LGPLVFIDV------ 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   509 dDRSEDMQNFYQDSKSNHWEAQIVSYHISGLLEAGLEA-KDIAVVTPYNAQVALIRQLLKEKG---IEVEMGSVDKVQGR 584
Cdd:pfam13087  73 -DGSEEEESDGGTSYSNEAEAELVVQLVEKLIKSGPEEpSDIGVITPYRAQVRLIRKLLKRKLggkLEIEVNTVDGFQGR 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 19075869   585 EKEAIIFSLVRSNDVREVGFLAEKRRLNVAITRPKRHLCVIGDSN 629
Cdd:pfam13087 152 EKDVIIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 213-425 3.90e-70

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: 228.00  E-value: 3.90e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   213 SQKKAVKFSIAVKELSLIHGPPGTGKTHTLVEIIQQLVLRN-------KRILVCGASNLAVDNIVDRLSSSG----IPMV 281
Cdd:pfam13086   1 SQREAIRSALSSSHFTLIQGPPGTGKTTTIVELIRQLLSYPatsaaagPRILVCAPSNAAVDNILERLLRKGqkygPKIV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   282 RLGHPARLLPSILDHSLDVL-----------SRTGDNGDVIRGISEDIDVCLSKITKT-----------KNGRERREIYK 339
Cdd:pfam13086  81 RIGHPAAISEAVLPVSLDYLvesklnneedaQIVKDISKELEKLAKALRAFEKEIIVEkllksrnkdksKLEQERRKLRS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   340 NIRELRKDYRKYEAKTVANIVSASKVVFCTLHGAGSRQLKGQ-RFDAVIIDEASQALEPQCWIPLL-GMNKVILAGDHMQ 417
Cdd:pfam13086 161 ERKELRKELRRREQSLEREILDEAQIVCSTLSGAGSRLLSSLaNFDVVIIDEAAQALEPSTLIPLLrGPKKVVLVGDPKQ 240


                  ....*...
gi 19075869   418 LSPNVQSK 425
Cdd:pfam13086 241 LPPTVISK 248
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 453-646 2.38e-60

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: 199.77  E-value: 2.38e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 453 MHELISKFPSDTFYDSKLVPAEEVKKRllmdlENVEETELTDSPIYFYDTLGNYQEDDRSedmqnfyqDSKSNHWEAQIV 532
Cdd:cd18808   1 MHPEISEFPSKLFYEGKLKAGVSVAAR-----LNPPPLPGPSKPLVFVDVSGGEEREESG--------TSKSNEAEAELV 67

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 533 SYHISGLLEAGLEAKDIAVVTPYNAQVALIRQLLKEKGI---EVEMGSVDKVQGREKEAIIFSLVRSNDVRE-VGFLAEK 608
Cdd:cd18808  68 VELVKYLLKSGVKPSSIGVITPYRAQVALIRELLRKRGGlleDVEVGTVDNFQGREKDVIILSLVRSNESGGsIGFLSDP 147

                       170       180       190
                ....*....|....*....|....*....|....*...
gi 19075869 609 RRLNVAITRPKRHLCVIGDSNTVKwASEFFHQWVDFLE 646
Cdd:cd18808 148 RRLNVALTRAKRGLIIVGNPDTLS-KDPLWKKLLEYLE 184
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 209-452 8.14e-50

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: 173.59  E-value: 8.14e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 209 ELNASQKKAVKFSIAvKELSLIHGPPGTGKTHTLVEIIQQLV-LRNKRILVCGASNLAVDNIVDRLSSSGIPMVRLGHPA 287
Cdd:cd18039   1 ELNHSQVDAVKTALQ-RPLSLIQGPPGTGKTVTSATIVYHLVkQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKS 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 288 R-LLPSILDH-SLDvlsrtgdngDVIRGISEDIDVCLSKITKTKNGRERREIYKNIRELRkdyRKYEAKtvanIVSASKV 365
Cdd:cd18039  80 ReAVESPVSFlALH---------NQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLK---RKAERE----LLRNADV 143

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 366 VFCTLHGAGSRQLKGQRFDAVIIDEASQALEPQCWIPL-LGMNKVILAGDHMQLSPNVQSKRPY-----ISMFERLVKSq 439
Cdd:cd18039 144 ICCTCVGAGDPRLSKMKFRTVLIDEATQATEPECLIPLvHGAKQVILVGDHCQLGPVVMCKKAAkaglsQSLFERLVQL- 222

                       250
                ....*....|...
gi 19075869 440 gDLVKCFLNIQYR 452
Cdd:cd18039 223 -GIRPIRLQVQYR 234
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 210-452 3.89e-48

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: 167.80  E-value: 3.89e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 210 LNASQKKAVKFSIAVKELSLIHGPPGTGKTHTLVEIIQQLVLRNKRILVCGASNLAVDNIVDRLSSSGIPMVRLGHPARL 289
Cdd:cd18041   2 LNKDQRQAIKKVLNAKDYALILGMPGTGKTTTIAALVRILVALGKSVLLTSYTHSAVDNILLKLKKFGVNFLRLGRLKKI 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 290 LPSILDHSLDvlsrtgdngdvirgisedidvclSKITKTKNGRERREIYKNIrelrkdyrkyeaktvanivsasKVVFCT 369
Cdd:cd18041  82 HPDVQEFTLE-----------------------AILKSCKSVEELESKYESV----------------------SVVATT 116

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 370 LHGAGSRQLKGQRFDAVIIDEASQALEPQCWIPLLGMNKVILAGDHMQLSPNVQSKRPY-----ISMFERLVKSQGDLVK 444
Cdd:cd18041 117 CLGINHPIFRRRTFDYCIVDEASQITLPICLGPLRLAKKFVLVGDHYQLPPLVKSREARelgmdESLFKRLSEAHPDAVV 196


                ....*...
gi 19075869 445 cFLNIQYR 452
Cdd:cd18041 197 -QLTIQYR 203
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 210-452 5.56e-42

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: 151.60  E-value: 5.56e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 210 LNASQKKAVKFS-IAVKELSLIHGPPGTGKTHTLVEIIQQLVLRN-------------------------KRILVCGASN 263
Cdd:cd18042   1 LNESQLEAIASAlQNSPGITLIQGPPGTGKTKTIVGILSVLLAGKyrkyyekvkkklrklqrnlnnkkkkNRILVCAPSN 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 264 LAVDNIVDRLSSSGIPMVRlghparllpsildhsldvlsRTGDNGDVIR-GISEDidvclskitktkngreRREIYKNir 342
Cdd:cd18042  81 AAVDEIVLRLLSEGFLDGD--------------------GRSYKPNVVRvGRQEL----------------RASILNE-- 122

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 343 elrkdyrkyeaktvanivsaSKVVFCTLHGAGSRQLK--GQRFDAVIIDEASQALEPQCWIPL-LGMNKVILAGDHMQLS 419
Cdd:cd18042 123 --------------------ADIVCTTLSSSGSDLLEslPRGFDTVIIDEAAQAVELSTLIPLrLGCKRLILVGDPKQLP 182

                       250       260       270       280
                ....*....|....*....|....*....|....*....|.
gi 19075869 420 PNVQSK--------RpyiSMFERLVKSqgDLVKCFLNIQYR 452
Cdd:cd18042 183 ATVFSKvaqklgydR---SLFERLQLA--GYPVLMLTTQYR 218
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
 209-438 6.46e-39

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: 143.14  E-value: 6.46e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 209 ELNASQKKAVKFSIAVKELS---LIHGPPGTGKTHTLVEIIQQLV--LRNKRILVCGASNLAVDNIVDRLSSSgipmvrL 283
Cdd:cd18038   1 ELNDEQKLAVRNIVTGTSRPppyIIFGPPGTGKTVTLVEAILQVLrqPPEARILVCAPSNSAADLLAERLLNA------L 74

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 284 GHPARLLpsildhslDVLSRTgdngdvirgisedidvclskitktkngRERREIYKNIREL--RKDYRKYEAKTVANIVS 361
Cdd:cd18038  75 VTKREIL--------RLNAPS---------------------------RDRASVPPELLPYcnSKAEGTFRLPSLEELKK 119

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 362 AsKVVFCTLHGAG---SRQLKGQRFDAVIIDEASQALEPQCWIPLLGMNK----VILAGDHMQLSPNVQSKRP-----YI 429
Cdd:cd18038 120 Y-RIVVCTLMTAGrlvQAGVPNGHFTHIFIDEAGQATEPEALIPLSELASkntqIVLAGDPKQLGPVVRSPLArkyglGK 198


                ....*....
gi 19075869 430 SMFERLVKS 438
Cdd:cd18038 199 SLLERLMER 207
DEXXQc_Mov10L1 cd18078
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ...
 210-471 2.36e-27

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: 110.54  E-value: 2.36e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 210 LNASQKKAVKfSIAVKELS----LIHGPPGTGKTHTLVEIIQQLV--LRNKRILVCGASNLAVDNIVDRLSSSGIpmVRL 283
Cdd:cd18078   2 LNELQKEAVK-RILGGECRplpyILFGPPGTGKTVTIIEAILQVVynLPRSRILVCAPSNSAADLVTSRLHESKV--LKP 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 284 GHPARlLPSILDHSLDVlsrtgdngdvirgISEDIDVCLSKITKTKNGRERreiyknirelrkdyrkyeaktvanIVSAS 363
Cdd:cd18078  79 GDMVR-LNAVNRFESTV-------------IDARKLYCRLGEDLSKASRHR------------------------IVIST 120

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 364 kvvfCTLhgAGSRQLKGQR---FDAVIIDEASQALEPQCWIPL----LGMNKVILAGDHMQLSPNVQSKRPY-----ISM 431
Cdd:cd18078 121 ----CST--AGLLYQMGLPvghFTHVFVDEAGQATEPESLIPLglisSRDGQIILAGDPMQLGPVIKSRLASayglgVSF 194

                       250       260       270       280
                ....*....|....*....|....*....|....*....|
gi 19075869 432 FERLVksqgdlvkcfLNIQYRMHEliSKFPSDTFYDSKLV 471
Cdd:cd18078 195 LERLM----------NRPLYLRDP--NRFGESGGYNPLLV 222
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 227-452 2.05e-26

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: 104.24  E-value: 2.05e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 227 LSLIHGPPGTGKTHTLVEIIQQLV--LRNKRILVCGASNLAVDNIvdrlsssgipmvrlghparllpsildhsldvlsrt 304
Cdd:cd17934   1 ISLIQGPPGTGKTTTIAAIVLQLLkgLRGKRVLVTAQSNVAVDNV----------------------------------- 45

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 305 gdngdvirgisedidvclskitktkngrerreiyknirelrkdyrkyeaktvanivsaskvvfctlhgagsrqlkgqrfD 384
Cdd:cd17934  46 -------------------------------------------------------------------------------D 46

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19075869 385 AVIIDEASQALEPQCWIPLLGMNKVILAGDHMQLSPNVQSKRP-------YISMFERLVKSQGDLVKCFLNIQYR 452
Cdd:cd17934  47 VVIIDEASQITEPELLIALIRAKKVVLVGDPKQLPPVVQEDHAallglsfILSLLLLFRLLLPGSPKVMLDTQYR 121
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 210-451 1.91e-24

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: 100.70  E-value: 1.91e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 210 LNASQKKAVKfSIAVKELSLIHGPPGTGKTHTLVEIIQQLV-----LRNKRILVCGASNLAVDNIVDRLSSSGIP-MVRL 283
Cdd:cd17936   2 LDPSQLEALK-HALTSELALIQGPPGTGKTFLGVKLVRALLqnqdlSITGPILVVCYTNHALDQFLEGLLDFGPTkIVRL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 284 GHparllpsildhsldvlsrtgdngdvirgisedidvclskitktkngrerreiyknirelrkdyrkyeaktvanivsas 363
Cdd:cd17936  81 GA------------------------------------------------------------------------------ 82

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 364 KVVFCTLHGAGSRQ--LKGQRFDAVIIDEASQALEPQ---CWIPLLgmNKVILAGDHMQLSPNVQSK----RPY---ISM 431
Cdd:cd17936  83 RVIGMTTTGAAKYRelLQALGPKVVIVEEAAEVLEAHilaALTPST--EHLILIGDHKQLRPKVNVYeltaKKYnldVSL 160

                       250       260
                ....*....|....*....|
gi 19075869 432 FERLVKSQGDLVkcFLNIQY 451
Cdd:cd17936 161 FERLVKNGLPFV--TLNVQR 178
DEXXc_HELZ2-C cd18040
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 210-452 8.19e-24

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: 101.45  E-value: 8.19e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 210 LNASQKKAVKFSIAvKELSLIHGPPGTGKTHTLVEIIQQLVLRNKR-------------ILVCGASNLAVDNIVDRL-SS 275
Cdd:cd18040   2 LNPSQNHAVRTALT-KPFTLIQGPPGTGKTVTGVHIAYWFAKQNREiqsvsgegdggpcVLYCGPSNKSVDVVAELLlKV 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 276 SGIPMVRL-GHPARLL----PSILDHSLDVLSRTGDNGDVIRGI-------------SEDIDVCLSKITKTKNGRERREI 337
Cdd:cd18040  81 PGLKILRVySEQIETTeypiPNEPRHPNKKSERESKPNSELSSItlhhrirqpsnphSQQIKAFEARFERTQEKITEEDI 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 338 YKNIRELRKDyRKYEAKTVanivsasKVVFCTLHGAGSRQLKGQ-RFDAVIIDEASQALEPQCWIPLLG---MNKVILAG 413
Cdd:cd18040 161 KTYKILIWEA-RFEELETV-------DVILCTCSEAASQKMRTHaNVKQCIVDECGMCTEPESLIPIVSaprAEQVVLIG 232

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....
gi 19075869 414 DHMQLSPNVQSKRPY-----ISMFERLVKSqgdlvKCFLNIQYR 452
Cdd:cd18040 233 DHKQLRPVVQNKEAQklglgRSLFERYAEK-----ACMLDTQYR 271
DEXXQc_HELZ cd18077
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ...
 210-435 8.08e-16

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: 77.14  E-value: 8.08e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 210 LNASQKKAV-----KFSIAVKELSLIhGPPGTGKTHTLVEIIQQLVLR-NKRILVCGASNLAVD-NIVDRLSssgiPMVR 282
Cdd:cd18077   2 LNAKQKEAVlaittPLSIQLPPVLLI-GPFGTGKTFTLAQAVKHILQQpETRILICTHSNSAADlYIKEYLH----PYVE 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 283 LGHPaRLLPsildhsLDVLSRTgdngdvirgisedidvclskitktkngRERREIYKNIRE--LRKDYRKYEAKTVANIV 360
Cdd:cd18077  77 TGNP-RARP------LRVYYRN---------------------------RWVKTVHPVVQKycLIDEHGTFRMPTREDVM 122

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 361 SAsKVVFCTLhgAGSR---QLKGQR--FDAVIIDEASQALEPQCWIPLLGMNK---VILAGDHMQLSPNVQS-----KRP 427
Cdd:cd18077 123 RH-RVVVVTL--STSQylcQLDLEPgfFTHILLDEAAQAMECEAIMPLALATKstrIVLAGDHMQLSPEVYSefareRNL 199


                ....*...
gi 19075869 428 YISMFERL 435
Cdd:cd18077 200 HISLLERL 207
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 211-422 1.31e-13

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: 67.99  E-value: 1.31e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 211 NASQKKAVKfSIAVKELSLIHGPPGTGKTHTLVEIIQQLVLRNKRILVCGASNLAvdnivdrlsssgipmvrlghparll 290
Cdd:cd18043   1 DSSQEAAII-SARNGKNVVIQGPPGTGKSQTIANIIANALARGKRVLFVSEKKAA------------------------- 54

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 291 psildhsLDVLsrtgdngdvirgisedidvclskitktkngrerreiYKNIrelrkdyrkyeakTVANIVSASKVVfctl 370
Cdd:cd18043  55 -------LDVV------------------------------------RFPC-------------WIMSPLSVSQYL---- 74

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|...
gi 19075869 371 hgagsrQLKGQRFDAVIIDEASQAlEPQCWIPLL-GMNKVILAGDHMQLSPNV 422
Cdd:cd18043  75 ------PLNRNLFDLVIFDEASQI-PIEEALPALfRGKQVVVVGDDKQLPPSI 120
EEXXQc_AQR cd17935
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ...
 227-459 1.53e-13

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: 70.15  E-value: 1.53e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 227 LSLIHGPPGTGKTHTLVEIIQQLV--LRNKRILVCGASNLAVDNIVDRLSSSGIP---MVRLGHPARLLpsildhsldvl 301
Cdd:cd17935  22 LTMVVGPPGTGKTDVAVQIISNLYhnFPNQRTLIVTHSNQALNQLFEKIMALDIDerhLLRLGHGAKII----------- 90

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 302 srtgdngdvirgisedidvclsKITKTKNGRERREIYKnirelrkdyrkyeaktvanivsaskvvfctlhgagsrqlKGQ 381
Cdd:cd17935  91 ----------------------AMTCTHAALKRGELVE---------------------------------------LGF 109

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 382 RFDAVIIDEASQALEPQCWIPLL---------GMNKVILAGDHMQLSPNVQSK--RPYI----SMFERLVKSQGDLVKcf 446
Cdd:cd17935 110 KYDNILMEEAAQILEIETFIPLLlqnpedgpnRLKRLIMIGDHHQLPPVIKNMafQKYSnmeqSLFTRLVRLGVPTVD-- 187

                       250
                ....*....|...
gi 19075869 447 LNIQYRMHELISK 459
Cdd:cd17935 188 LDAQGRARASISS 200
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 548-627 1.84e-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: 60.53  E-value: 1.84e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 548 DIAVVTPYNAQVALIRQLLKEKGI------EVEMGSVDKVQGREKEAIIFSLVRSNDVrevgflaEKRRLNVAITRPKRH 621
Cdd:cd18786  12 KGVVLTPYHRDRAYLNQYLQGLSLdefdlqLVGAITIDSSQGLTFDVVTLYLPTANSL-------TPRRLYVALTRARKR 84


                ....*.
gi 19075869 622 LcVIGD 627
Cdd:cd18786  85 L-VIYD 89
DEXXQc_HELZ2-N cd18076
N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 210-435 2.73e-11

N-terminal DEXXQ-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: 350834 [Multi-domain]  Cd Length: 230  Bit Score: 63.76  E-value: 2.73e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 210 LNASQKKAVKFsIAVKELS-------LIHGPPGTGKTHTLVEIIQQLVLR-NKRILVCGASNLAVDNIVDRLSSsgiPMV 281
Cdd:cd18076   2 GNNKQQLAFNF-IAGKPSEarfvpplLIYGPFGTGKTFTLAMAALEVIREpGTKVLICTHTNSAADIYIREYFH---PYV 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 282 RLGHP-ARLLPSIL-DHSLDVLSRTgdngdvirgisEDIDVCLSKitktkngrerreiyknirelrkDYRKYEAKTVANI 359
Cdd:cd18076  78 DKGHPeARPLRIKAtDRPNAITDPD-----------TITYCCLTK----------------------DRQCFRLPTRDEL 124

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 360 VSASKVVFCTLHGAGSRQLKGqRFDAVIIDEASQALEPQCWIPLLGMN---KVILAGDHMQLSPNVQS----KRPYISMF 432
Cdd:cd18076 125 DFHNIVITTTAMAFNLHVLSG-FFTHIFIDEAAQMLECEALIPLSYAGpktRVVLAGDHMQMTPKLFSvadyNRANHTLL 203


                ...
gi 19075869 433 ERL 435
Cdd:cd18076 204 NRL 206
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 209-259 5.32e-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: 52.67  E-value: 5.32e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 19075869 209 ELNASQKKAVKFSIAVKELSLIHGPPGTGKTHTLVEIIQQLVLRNKRILVC 259
Cdd:COG0507 124 TLSDEQREAVALALTTRRVSVLTGGAGTGKTTTLRALLAALEALGLRVALA 174
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 227-267 4.39e-06

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: 46.33  E-value: 4.39e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 19075869 227 LSLIHGPPGTGKTHTLVEIIQQLVlRNK-----RILVCGASNLAVD 267
Cdd:cd17914   1 LSLIQGPPGTGKTRVLVKIVAALM-QNKngepgRILLVTPTNKAAA 45
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 382-451 4.47e-06

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: 46.33  E-value: 4.47e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19075869 382 RFDAVIIDEASQALEPQCWIP---LLGMNKVILAGDHMQLSP-----NVQSKRPYISMFERLVKSQGDLVKcfLNIQY 451
Cdd:cd17914  46 QLDNILVDEAAQILEPETSRLidlALDQGRVILVGDHDQLGPvwrgaVLAKICNEQSLFTRLVRLGVSLIR--LQVQY 121
AAA_19 pfam13245
AAA domain;
214-273 1.08e-05

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 45.29  E-value: 1.08e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19075869   214 QKKAVkFSIAVKELSLIHGPPGTGKTHTLVEIIQQLVLR---NKRILVCGASNLAVDNIVDRL 273
Cdd:pfam13245   1 QREAV-RTALPSKVVLLTGGPGTGKTTTIRHIVALLVALggvSFPILLAAPTGRAAKRLSERT 62
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 214-290 1.31e-05

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: 45.62  E-value: 1.31e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19075869 214 QKKAVKfsIAVKE-LSLIHGPPGTGKTHTLVEIIQQLVLRNKRILVCGASNLAvdniVDRLS-SSGIPMVRLghpARLL 290
Cdd:cd17933   2 QKAAVR--LVLRNrVSVLTGGAGTGKTTTLKALLAALEAEGKRVVLAAPTGKA----AKRLSeSTGIEASTI---HRLL 71
UvrD COG0210
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
209-364 4.78e-05

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


Pssm-ID: 439980 [Multi-domain]  Cd Length: 721  Bit Score: 46.47  E-value: 4.78e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 209 ELNASQKKAVKFsiavkelslIHGP------PGTGKTHTLVEIIQQLVLRN----KRILVCGASNLAVDNIVDRLSSsgi 278
Cdd:COG0210   6 GLNPEQRAAVEH---------PEGPllvlagAGSGKTRVLTHRIAYLIAEGgvdpEQILAVTFTNKAAREMRERIEA--- 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 279 pmvRLGHPARLLP-SILdHSL--DVLSRtgdNGDVIrGISED---IDvclskitktknGRERREIYKNI-RELRKDYRKY 351
Cdd:COG0210  74 ---LLGRLARGLWvGTF-HSLalRILRR---HAELL-GLPPNftiLD-----------GDDQLRLIKELlKELGLDEKRF 134

                       170
                ....*....|...
gi 19075869 352 EAKTVANIVSASK 364
Cdd:COG0210 135 PPRELLSLISRAK 147
CoV_Nsp13-helicase cd21718
helicase domain of coronavirus non-structural protein 13; This model represents the helicase ...
 222-638 1.72e-04

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: 44.06  E-value: 1.72e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 222 IAVKELSLIHGPPGTGKTHTLVEIiqQLVLRNKRILVCGASNLAVDNIVDRLSssgipmvrlghpaRLLPsildhsldvl 301
Cdd:cd21718  22 IGKQKYTTVQGPPGTGKSHFAIGL--ALYYPGARIVYTACSHAAVDALCEKAS-------------KWLP---------- 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 302 srtgdngdvirgisedIDVClSKITKTkngRERREIYKNIRelrkdyrkyeaktvANIVSAsKVVFCTLHGagsrqLKGQ 381
Cdd:cd21718  77 ----------------NDKC-SRIVPQ---RARVECFDGFK--------------VNNTNA-QYIFSTINA-----LPEC 116

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 382 RFDAVIIDEASQALEPQCWI--PLLGMNKVILAGDHMQL-SPNVQ------SKRPYISMFERLVKSQGDLvkcFLNIQYR 452
Cdd:cd21718 117 SADIVVVDEVSMCTNYDLSVvnARLKYKHIVYVGDPAQLpAPRTLltegslEPKDYNVVTRLMVGSGPDV---FLSKCYR 193

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 453 MHELISKFPSDTFYDSKLVPAEEVKKRLlmdlenveeteltdspiyfYDTLGNyqeddrsedmQNFYQDSKSNHWEAQIv 532
Cdd:cd21718 194 CPKEIVDTVSKLVYDNKLKAIKPKSRQC-------------------FKTFGK----------GDVRHDNGSAINRPQL- 243

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 533 sYHISGLLEAGLEAKDIAVVTPYNAQVALIRQLLkekGIEVEmgSVDKVQGREKEAIIFSLVRSNDvrevgFLAEKRRLN 612
Cdd:cd21718 244 -EFVKRFLDRNPRWRKAVFISPYNAMNNRASRLL---GLSTQ--TVDSSQGSEYDYVIFCQTTDTA-----HALNINRFN 312

                       410       420
                ....*....|....*....|....*..
gi 19075869 613 VAITRPKRH-LCVIGDSNTVKWASEFF 638
Cdd:cd21718 313 VAITRAKHGiLVIMRDENDLYNALQFK 339
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 229-273 2.35e-04

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 41.98  E-value: 2.35e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 19075869    229 LIHGPPGTGKTHTLVEIIQQLVLRNKRILVCGASNLAVDNIVDRL 273
Cdd:smart00382   6 LIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLL 50
DEXQc_UvrD cd17932
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ...
 211-312 2.92e-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: 42.12  E-value: 2.92e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 211 NASQKKAVkfsIAVKELSLIHGPPGTGKTHTLVEIIQQLVLRNK----RILVCGASNLAVDNIVDRLSSsgipmvRLGHP 286
Cdd:cd17932   1 NPEQREAV---THPDGPLLVLAGAGSGKTRVLTHRIAYLILEGGvppeRILAVTFTNKAAKEMRERLRK------LLGEQ 71

                        90       100
                ....*....|....*....|....*....
gi 19075869 287 ARLLPSILD-HSL--DVLSRTGDNGDVIR 312
Cdd:cd17932  72 LASGVWIGTfHSFalRILRRYGDFDDLLL 100
betaCoV_Nsp13-helicase cd21722
helicase domain of betacoronavirus non-structural protein 13; This model represents the ...
 534-629 3.61e-04

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: 43.25  E-value: 3.61e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869 534 YHISGLLEAGLEAKDIAVVTPYNAQVALIRQLLkekGIEVEmgSVDKVQGREKEAIIFS----LVRSNDVRevgflaekr 609
Cdd:cd21722 244 YLVKKFLKANPAWSKAVFISPYNSQNAVARRVL---GLQTQ--TVDSSQGSEYDYVIYCqtaeTAHSVNVN--------- 309

                        90       100
                ....*....|....*....|.
gi 19075869 610 RLNVAITRPKRH-LCVIGDSN 629
Cdd:cd21722 310 RFNVAITRAKKGiLCVMSSMQ 330
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 229-273 4.68e-04

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 40.98  E-value: 4.68e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 19075869 229 LIHGPPGTGKTHTLVEIIQQLVLRNKRILVCGASNLAVDNIVDRL 273
Cdd:cd00009  23 LLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAEL 67
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 209-290 2.39e-03

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: 39.47  E-value: 2.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   209 ELNASQKKAVKfSIAVKE--LSLIHGPPGTGKTHTLVEIIQQLVLRNKRILVCGASNLAvdniVDRLS-SSGIPMVRLgh 285
Cdd:pfam13604   1 TLNAEQAAAVR-ALLTSGdrVAVLVGPAGTGKTTALKALREAWEAAGYRVIGLAPTGRA----AKVLGeELGIPADTI-- 73


                  ....*
gi 19075869   286 pARLL 290
Cdd:pfam13604  74 -AKLL 77
ResIII pfam04851
Type III restriction enzyme, res subunit;
207-391 5.47e-03

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 38.04  E-value: 5.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   207 NKELNASQKKAVK----FSIAVKELSLIHGPPGTGKTHTLVEIIQQL--VLRNKRILVcgasnlavdnIVDRLsssgipm 280
Cdd:pfam04851   1 KLELRPYQIEAIEnlleSIKNGQKRGLIVMATGSGKTLTAAKLIARLfkKGPIKKVLF----------LVPRK------- 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075869   281 vrlghparllpSILDHSLDVLSRTGDNGDvirgisedidvclsKITKTKNGRERREIYKNIrelrkdyrkyeaktvaniv 360
Cdd:pfam04851  64 -----------DLLEQALEEFKKFLPNYV--------------EIGEIISGDKKDESVDDN------------------- 99

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 19075869   361 sasKVVFCTLHGAGS------RQLKGQRFDAVIIDEA 391
Cdd:pfam04851 100 ---KIVVTTIQSLYKalelasLELLPDFFDVIIIDEA 133
DEXDc smart00487
DEAD-like helicases superfamily;
204-280 9.18e-03

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 37.86  E-value: 9.18e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19075869    204 KYFNKELNASQKKAVKFSIAVKELSLIHGPPGTGKTHTLVEIIQQLVLRN--KRILVCGASNLAVDNIVDRLSSSGIPM 280
Cdd:smart00487   3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGkgGRVLVLVPTRELAEQWAEELKKLGPSL 81
 
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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