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Conserved domains on  [gi|488884933|ref|WP_002797158|]
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MULTISPECIES: DEAD/DEAH box helicase [Microcystis]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 11437332)

DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
24-441 1.94e-99

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


:

Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 310.42  E-value: 1.94e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  24 WLDFATWDDRIERFRILAIHYRPLVETLQ--EEGINFQDEAKAFNNLELIASFEREPYPHQTEALIAWK----KSQRRGV 97
Cdd:COG1061   25 RLELSLLRNLVEARRLAIKEGTREDGRRLpeEDTERELAEAEALEAGDEASGTSFELRPYQQEALEALLaaleRGGGRGL 104
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  98 IVLPTAAGKTYLAQLALQS--TPRSTLIIVPTIDLMHQWYAQMLAAFPDAEVGllgGGSKDNSA-ILIATYQSAA--IYS 172
Cdd:COG1061  105 VVAPTGTGKTVLALALAAEllRGKRVLVLVPRRELLEQWAEELRRFLGDPLAG---GGKKDSDApITVATYQSLArrAHL 181
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 173 ETLGNRYAFLIFDECHHLPSDFFRKIAEDSIAPYRLGLTATPDRGDGSHQDLDYLIGaIVYQKSPQDL-SGKALADHEII 251
Cdd:COG1061  182 DELGDRFGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPFRSDGREILLFLFDG-IVYEYSLKEAiEDGYLAPPEYY 260
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 252 QIKVKLSaKEQEKYQEaikirndflrknnlslsgldgwqnfvmisarssegrramLAHRESKEISSGTQGKLRVLAELIC 331
Cdd:COG1061  261 GIRVDLT-DERAEYDA---------------------------------------LSERLREALAADAERKDKILRELLR 300
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 332 EH-HPEPILIFTNDNATVYRISESFL-----IPAITHQTPVKERHEILTRFRQGEYKILVTSHVLNEGVDVPEARIAIIL 405
Cdd:COG1061  301 EHpDDRKTLVFCSSVDHAEALAELLNeagirAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILL 380
                        410       420       430
                 ....*....|....*....|....*....|....*..
gi 488884933 406 SGTGSTREYIQRLGRVLRKgqQEDKR-AILYEVIAEN 441
Cdd:COG1061  381 RPTGSPREFIQRLGRGLRP--APGKEdALVYDFVGND 415
 
Name Accession Description Interval E-value
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
24-441 1.94e-99

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 310.42  E-value: 1.94e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  24 WLDFATWDDRIERFRILAIHYRPLVETLQ--EEGINFQDEAKAFNNLELIASFEREPYPHQTEALIAWK----KSQRRGV 97
Cdd:COG1061   25 RLELSLLRNLVEARRLAIKEGTREDGRRLpeEDTERELAEAEALEAGDEASGTSFELRPYQQEALEALLaaleRGGGRGL 104
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  98 IVLPTAAGKTYLAQLALQS--TPRSTLIIVPTIDLMHQWYAQMLAAFPDAEVGllgGGSKDNSA-ILIATYQSAA--IYS 172
Cdd:COG1061  105 VVAPTGTGKTVLALALAAEllRGKRVLVLVPRRELLEQWAEELRRFLGDPLAG---GGKKDSDApITVATYQSLArrAHL 181
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 173 ETLGNRYAFLIFDECHHLPSDFFRKIAEDSIAPYRLGLTATPDRGDGSHQDLDYLIGaIVYQKSPQDL-SGKALADHEII 251
Cdd:COG1061  182 DELGDRFGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPFRSDGREILLFLFDG-IVYEYSLKEAiEDGYLAPPEYY 260
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 252 QIKVKLSaKEQEKYQEaikirndflrknnlslsgldgwqnfvmisarssegrramLAHRESKEISSGTQGKLRVLAELIC 331
Cdd:COG1061  261 GIRVDLT-DERAEYDA---------------------------------------LSERLREALAADAERKDKILRELLR 300
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 332 EH-HPEPILIFTNDNATVYRISESFL-----IPAITHQTPVKERHEILTRFRQGEYKILVTSHVLNEGVDVPEARIAIIL 405
Cdd:COG1061  301 EHpDDRKTLVFCSSVDHAEALAELLNeagirAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILL 380
                        410       420       430
                 ....*....|....*....|....*....|....*..
gi 488884933 406 SGTGSTREYIQRLGRVLRKgqQEDKR-AILYEVIAEN 441
Cdd:COG1061  381 RPTGSPREFIQRLGRGLRP--APGKEdALVYDFVGND 415
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
308-438 9.26e-55

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


Pssm-ID: 350176 [Multi-domain]  Cd Length: 153  Bit Score: 180.52  E-value: 9.26e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 308 AHRESKEISSGTQGKLRVLAELICEHHP-EPILIFTNDNATVYRISESFLIPAITHQTPVKERHEILTRFRQGEYKILVT 386
Cdd:cd18789   21 AHRKRRLLAAMNPNKLRALEELLKRHEQgDKIIVFTDNVEALYRYAKRLLKPFITGETPQSEREEILQNFREGEYNTLVV 100
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 488884933 387 SHVLNEGVDVPEARIAIILSGT-GSTREYIQRLGRVLRKGQQEDKRAILYEVI 438
Cdd:cd18789  101 SKVGDEGIDLPEANVAIQISGHgGSRRQEAQRLGRILRPKKGGGKNAFFYSLV 153
ResIII pfam04851
Type III restriction enzyme, res subunit;
77-216 1.34e-31

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 119.31  E-value: 1.34e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933   77 EPYPHQTEALIAWKKS----QRRGVIVLPTAAGKTYLA-----QLALQSTPRSTLIIVPTIDLMHQWYAQMLAAFPDA-- 145
Cdd:pfam04851   3 ELRPYQIEAIENLLESikngQKRGLIVMATGSGKTLTAakliaRLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPNYve 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  146 EVGLLGGGSKD----NSAILIATYQSAAI-----YSETLGNRYAFLIFDECHHLPSDFFRKIAEDSIAPYRLGLTATPDR 216
Cdd:pfam04851  83 IGEIISGDKKDesvdDNKIVVTTIQSLYKalelaSLELLPDFFDVIIIDEAHRSGASSYRNILEYFKPAFLLGLTATPER 162
DEXDc smart00487
DEAD-like helicases superfamily;
70-214 1.61e-23

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 97.95  E-value: 1.61e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933    70 LIASFEREPYPHQTEALIAWKKSQRRGVIVLPTAAGKT-----YLAQLALQSTPRSTLIIVPTIDLMHQWYAQMLAAFPD 144
Cdd:smart00487   1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTlaallPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933   145 A---EVGLLGGGS---------KDNSAILIATYQSAAIYSE---TLGNRYAFLIFDECHHLPSDFFRKIAEDSI-----A 204
Cdd:smart00487  81 LglkVVGLYGGDSkreqlrkleSGKTDILVTTPGRLLDLLEndkLSLSNVDLVILDEAHRLLDGGFGDQLEKLLkllpkN 160
                          170
                   ....*....|
gi 488884933   205 PYRLGLTATP 214
Cdd:smart00487 161 VQLLLLSATP 170
rad25 TIGR00603
DNA repair helicase rad25; All proteins in this family for which functions are known are ...
94-471 7.04e-21

DNA repair helicase rad25; All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273168 [Multi-domain]  Cd Length: 732  Bit Score: 96.02  E-value: 7.04e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933   94 RRGVIVLPTAAGKTYLAQLALQSTPRSTLIIVPTIDLMHQWYAQ--MLAAFPDAEVGLLGGGSKD----NSAILIATY-- 165
Cdd:TIGR00603 274 RSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTSAVSVEQWKQQfkMWSTIDDSQICRFTSDAKErfhgEAGVVVSTYsm 353
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  166 ---------QSAAIYSETLGNRYAFLIFDECHHLPSDFFRKIAEDSIAPYRLGLTATPDRGDGSHQDLDYLIGAIVYQKS 236
Cdd:TIGR00603 354 vahtgkrsyESEKVMEWLTNREWGLILLDEVHVVPAAMFRRVLTIVQAHCKLGLTATLVREDDKITDLNFLIGPKLYEAN 433
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  237 PQDLSGKA-LADHEIIQIKVKLSAkeqEKYQEAIKIRNdflRKNNLSlsgldgwqnFVMisarssegrramlahreskei 315
Cdd:TIGR00603 434 WMELQKKGfIANVQCAEVWCPMTP---EFYREYLRENS---RKRMLL---------YVM--------------------- 477
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  316 ssgTQGKLRVLAELICEHHP--EPILIFTnDNatVYRISESFL---IPAITHQTPVKERHEILTRFRQGE-YKILVTSHV 389
Cdd:TIGR00603 478 ---NPNKFRACQFLIRFHEQrgDKIIVFS-DN--VFALKEYAIklgKPFIYGPTSQQERMQILQNFQHNPkVNTIFLSKV 551
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  390 LNEGVDVPEARIAI-ILSGTGSTREYIQRLGRVLRKGQQEDKR---AILYEVIAENTTEEKTSQRRRG------------ 453
Cdd:TIGR00603 552 GDTSIDLPEANVLIqISSHYGSRRQEAQRLGRILRAKKGSDAEeynAFFYSLVSKDTQEMYYSTKRQRflvdqgysfkvi 631
                         410       420
                  ....*....|....*....|....
gi 488884933  454 ------EQKNKTSYKTGNRQLELL 471
Cdd:TIGR00603 632 thlpgmDNESNLAYSSKEEQLELL 655
uvsW PHA02558
UvsW helicase; Provisional
42-438 3.39e-18

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 87.37  E-value: 3.39e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  42 IHYRPLVETLQEegINFQDEAKAFNNLELIASFER-EPYPHQTEALIAWKKsQRRGVIVLPTAAGKTYLAQLA----LQS 116
Cdd:PHA02558  80 IWVDPRIEENED--ISREDFDEWVSSLEIYSGNKKiEPHWYQYDAVYEGLK-NNRRLLNLPTSAGKSLIQYLLsryyLEN 156
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 117 TPRSTLIIVPTIDLMHQWYAQML--AAFPDAEV-GLLGGGSKDNSA-ILIATYQSAAIYSETLGNRYAFLIFDECHHLPS 192
Cdd:PHA02558 157 YEGKVLIIVPTTSLVTQMIDDFVdyRLFPREAMhKIYSGTAKDTDApIVVSTWQSAVKQPKEWFDQFGMVIVDECHLFTG 236
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 193 DFFRKIAEDSI-APYRLGLTATPDRGDGSHQDLDYLIGAIVYQKSPQDLSGKA-LADHEIIQIKVKLSAKEQEK-----Y 265
Cdd:PHA02558 237 KSLTSIITKLDnCKFKFGLTGSLRDGKANILQYVGLFGDIFKPVTTSQLMEEGqVTDLKINSIFLRYPDEDRVKlkgedY 316
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 266 QEAIKI------RNDFLRKNNLSLSGLDGwQNFVMIsarssegrramlahresKEISSGtqgklRVLAELICEHHPEpil 339
Cdd:PHA02558 317 QEEIKYitshtkRNKWIANLALKLAKKGE-NTFVMF-----------------KYVEHG-----KPLYEMLKKVYDK--- 370
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 340 iftndnatVYRISESflipaithqTPVKERHEILTRFRQGEYKILVTSH-VLNEGVDVPEARIAIILSGTGSTREYIQRL 418
Cdd:PHA02558 371 --------VYYVSGE---------VDTEDRNEMKKIAEGGKGIIIVASYgVFSTGISIKNLHHVIFAHPSKSKIIVLQSI 433
                        410       420
                 ....*....|....*....|
gi 488884933 419 GRVLRKGQQEDKrAILYEVI 438
Cdd:PHA02558 434 GRVLRKHGSKSI-ATVWDII 452
 
Name Accession Description Interval E-value
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
24-441 1.94e-99

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 310.42  E-value: 1.94e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  24 WLDFATWDDRIERFRILAIHYRPLVETLQ--EEGINFQDEAKAFNNLELIASFEREPYPHQTEALIAWK----KSQRRGV 97
Cdd:COG1061   25 RLELSLLRNLVEARRLAIKEGTREDGRRLpeEDTERELAEAEALEAGDEASGTSFELRPYQQEALEALLaaleRGGGRGL 104
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  98 IVLPTAAGKTYLAQLALQS--TPRSTLIIVPTIDLMHQWYAQMLAAFPDAEVGllgGGSKDNSA-ILIATYQSAA--IYS 172
Cdd:COG1061  105 VVAPTGTGKTVLALALAAEllRGKRVLVLVPRRELLEQWAEELRRFLGDPLAG---GGKKDSDApITVATYQSLArrAHL 181
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 173 ETLGNRYAFLIFDECHHLPSDFFRKIAEDSIAPYRLGLTATPDRGDGSHQDLDYLIGaIVYQKSPQDL-SGKALADHEII 251
Cdd:COG1061  182 DELGDRFGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPFRSDGREILLFLFDG-IVYEYSLKEAiEDGYLAPPEYY 260
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 252 QIKVKLSaKEQEKYQEaikirndflrknnlslsgldgwqnfvmisarssegrramLAHRESKEISSGTQGKLRVLAELIC 331
Cdd:COG1061  261 GIRVDLT-DERAEYDA---------------------------------------LSERLREALAADAERKDKILRELLR 300
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 332 EH-HPEPILIFTNDNATVYRISESFL-----IPAITHQTPVKERHEILTRFRQGEYKILVTSHVLNEGVDVPEARIAIIL 405
Cdd:COG1061  301 EHpDDRKTLVFCSSVDHAEALAELLNeagirAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILL 380
                        410       420       430
                 ....*....|....*....|....*....|....*..
gi 488884933 406 SGTGSTREYIQRLGRVLRKgqQEDKR-AILYEVIAEN 441
Cdd:COG1061  381 RPTGSPREFIQRLGRGLRP--APGKEdALVYDFVGND 415
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
308-438 9.26e-55

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


Pssm-ID: 350176 [Multi-domain]  Cd Length: 153  Bit Score: 180.52  E-value: 9.26e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 308 AHRESKEISSGTQGKLRVLAELICEHHP-EPILIFTNDNATVYRISESFLIPAITHQTPVKERHEILTRFRQGEYKILVT 386
Cdd:cd18789   21 AHRKRRLLAAMNPNKLRALEELLKRHEQgDKIIVFTDNVEALYRYAKRLLKPFITGETPQSEREEILQNFREGEYNTLVV 100
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 488884933 387 SHVLNEGVDVPEARIAIILSGT-GSTREYIQRLGRVLRKGQQEDKRAILYEVI 438
Cdd:cd18789  101 SKVGDEGIDLPEANVAIQISGHgGSRRQEAQRLGRILRPKKGGGKNAFFYSLV 153
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
78-214 1.06e-47

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


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 161.70  E-value: 1.06e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  78 PYPHQTEAL--IAWKKSQRRGVIVLPTAAGKTYLA-QLALQSTPRSTLIIVPTIDLMHQWYAQMLAAFPDAEVGLLGGGS 154
Cdd:cd17926    1 LRPYQEEALeaWLAHKNNRRGILVLPTGSGKTLTAlALIAYLKELRTLIVVPTDALLDQWKERFEDFLGDSSIGLIGGGK 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488884933 155 KD---NSAILIATYQSAAIYSET---LGNRYAFLIFDECHHLPSDFFRKIAEDSIAPYRLGLTATP 214
Cdd:cd17926   81 KKdfdDANVVVATYQSLSNLAEEekdLFDQFGLLIVDEAHHLPAKTFSEILKELNAKYRLGLTATP 146
ResIII pfam04851
Type III restriction enzyme, res subunit;
77-216 1.34e-31

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 119.31  E-value: 1.34e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933   77 EPYPHQTEALIAWKKS----QRRGVIVLPTAAGKTYLA-----QLALQSTPRSTLIIVPTIDLMHQWYAQMLAAFPDA-- 145
Cdd:pfam04851   3 ELRPYQIEAIENLLESikngQKRGLIVMATGSGKTLTAakliaRLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPNYve 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  146 EVGLLGGGSKD----NSAILIATYQSAAI-----YSETLGNRYAFLIFDECHHLPSDFFRKIAEDSIAPYRLGLTATPDR 216
Cdd:pfam04851  83 IGEIISGDKKDesvdDNKIVVTTIQSLYKalelaSLELLPDFFDVIIIDEAHRSGASSYRNILEYFKPAFLLGLTATPER 162
XPB_DRD pfam18458
Xeroderma pigmentosum group B helicase damage recognition domain; This domain is found in the ...
6-62 3.86e-27

Xeroderma pigmentosum group B helicase damage recognition domain; This domain is found in the N-terminal region of xeroderma pigmentosum group B (XPB) helicase present in Archaeoglobus fulgidus. XPB is essential for transcription, nucleotide excision repair, and TFIIH functional assembly. The domain is a damage recognition domain (DRD) which allows XPB to unwind damaged DNA as needed for nucleotide excision repair.


Pssm-ID: 465776  Cd Length: 57  Bit Score: 103.38  E-value: 3.86e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 488884933    6 LKYERGTLILHPPPKGKKWLDFATWDDRIERFRILAIHYRPLVETLQEEGINFQDEA 62
Cdd:pfam18458   1 LRYDRGTLILHGPPPGKAWLPFATWDDRVEKYRAPAYRYRDLVEALRAAGIEFEDRA 57
DEXDc smart00487
DEAD-like helicases superfamily;
70-214 1.61e-23

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 97.95  E-value: 1.61e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933    70 LIASFEREPYPHQTEALIAWKKSQRRGVIVLPTAAGKT-----YLAQLALQSTPRSTLIIVPTIDLMHQWYAQMLAAFPD 144
Cdd:smart00487   1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTlaallPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933   145 A---EVGLLGGGS---------KDNSAILIATYQSAAIYSE---TLGNRYAFLIFDECHHLPSDFFRKIAEDSI-----A 204
Cdd:smart00487  81 LglkVVGLYGGDSkreqlrkleSGKTDILVTTPGRLLDLLEndkLSLSNVDLVILDEAHRLLDGGFGDQLEKLLkllpkN 160
                          170
                   ....*....|
gi 488884933   205 PYRLGLTATP 214
Cdd:smart00487 161 VQLLLLSATP 170
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
321-425 3.34e-22

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


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 91.50  E-value: 3.34e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  321 GKLRVLAELICEHHPEPILIFTNDNATV----YRISESFLIPAITHQTPVKERHEILTRFRQGEYKILVTSHVLNEGVDV 396
Cdd:pfam00271   1 EKLEALLELLKKERGGKVLIFSQTKKTLeaelLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDL 80
                          90       100
                  ....*....|....*....|....*....
gi 488884933  397 PEARIAIILSGTGSTREYIQRLGRVLRKG 425
Cdd:pfam00271  81 PDVDLVINYDLPWNPASYIQRIGRAGRAG 109
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
78-221 4.12e-21

DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350790 [Multi-domain]  Cd Length: 163  Bit Score: 89.93  E-value: 4.12e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  78 PYPHQTEAL----IAWKKSQRRGVIVLPTAAGKTYLA-----QLALQSTPRSTLIIVPTIDLMHQWYAQMLAAFPDAEVG 148
Cdd:cd18032    1 PRYYQQEAIealeEAREKGQRRALLVMATGTGKTYTAaflikRLLEANRKKRILFLAHREELLEQAERSFKEVLPDGSFG 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488884933 149 LLGGGSKDNSA--ILIATYQS--AAIYSETLG-NRYAFLIFDECHHLPSDFFRKIAEDSIAPYRLGLTATPDRGDGSH 221
Cdd:cd18032   81 NLKGGKKKPDDarVVFATVQTlnKRKRLEKFPpDYFDLIIIDEAHHAIASSYRKILEYFEPAFLLGLTATPERTDGLD 158
rad25 TIGR00603
DNA repair helicase rad25; All proteins in this family for which functions are known are ...
94-471 7.04e-21

DNA repair helicase rad25; All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273168 [Multi-domain]  Cd Length: 732  Bit Score: 96.02  E-value: 7.04e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933   94 RRGVIVLPTAAGKTYLAQLALQSTPRSTLIIVPTIDLMHQWYAQ--MLAAFPDAEVGLLGGGSKD----NSAILIATY-- 165
Cdd:TIGR00603 274 RSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTSAVSVEQWKQQfkMWSTIDDSQICRFTSDAKErfhgEAGVVVSTYsm 353
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  166 ---------QSAAIYSETLGNRYAFLIFDECHHLPSDFFRKIAEDSIAPYRLGLTATPDRGDGSHQDLDYLIGAIVYQKS 236
Cdd:TIGR00603 354 vahtgkrsyESEKVMEWLTNREWGLILLDEVHVVPAAMFRRVLTIVQAHCKLGLTATLVREDDKITDLNFLIGPKLYEAN 433
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  237 PQDLSGKA-LADHEIIQIKVKLSAkeqEKYQEAIKIRNdflRKNNLSlsgldgwqnFVMisarssegrramlahreskei 315
Cdd:TIGR00603 434 WMELQKKGfIANVQCAEVWCPMTP---EFYREYLRENS---RKRMLL---------YVM--------------------- 477
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  316 ssgTQGKLRVLAELICEHHP--EPILIFTnDNatVYRISESFL---IPAITHQTPVKERHEILTRFRQGE-YKILVTSHV 389
Cdd:TIGR00603 478 ---NPNKFRACQFLIRFHEQrgDKIIVFS-DN--VFALKEYAIklgKPFIYGPTSQQERMQILQNFQHNPkVNTIFLSKV 551
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  390 LNEGVDVPEARIAI-ILSGTGSTREYIQRLGRVLRKGQQEDKR---AILYEVIAENTTEEKTSQRRRG------------ 453
Cdd:TIGR00603 552 GDTSIDLPEANVLIqISSHYGSRRQEAQRLGRILRAKKGSDAEeynAFFYSLVSKDTQEMYYSTKRQRflvdqgysfkvi 631
                         410       420
                  ....*....|....*....|....
gi 488884933  454 ------EQKNKTSYKTGNRQLELL 471
Cdd:TIGR00603 632 thlpgmDNESNLAYSSKEEQLELL 655
uvsW PHA02558
UvsW helicase; Provisional
42-438 3.39e-18

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 87.37  E-value: 3.39e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  42 IHYRPLVETLQEegINFQDEAKAFNNLELIASFER-EPYPHQTEALIAWKKsQRRGVIVLPTAAGKTYLAQLA----LQS 116
Cdd:PHA02558  80 IWVDPRIEENED--ISREDFDEWVSSLEIYSGNKKiEPHWYQYDAVYEGLK-NNRRLLNLPTSAGKSLIQYLLsryyLEN 156
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 117 TPRSTLIIVPTIDLMHQWYAQML--AAFPDAEV-GLLGGGSKDNSA-ILIATYQSAAIYSETLGNRYAFLIFDECHHLPS 192
Cdd:PHA02558 157 YEGKVLIIVPTTSLVTQMIDDFVdyRLFPREAMhKIYSGTAKDTDApIVVSTWQSAVKQPKEWFDQFGMVIVDECHLFTG 236
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 193 DFFRKIAEDSI-APYRLGLTATPDRGDGSHQDLDYLIGAIVYQKSPQDLSGKA-LADHEIIQIKVKLSAKEQEK-----Y 265
Cdd:PHA02558 237 KSLTSIITKLDnCKFKFGLTGSLRDGKANILQYVGLFGDIFKPVTTSQLMEEGqVTDLKINSIFLRYPDEDRVKlkgedY 316
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 266 QEAIKI------RNDFLRKNNLSLSGLDGwQNFVMIsarssegrramlahresKEISSGtqgklRVLAELICEHHPEpil 339
Cdd:PHA02558 317 QEEIKYitshtkRNKWIANLALKLAKKGE-NTFVMF-----------------KYVEHG-----KPLYEMLKKVYDK--- 370
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 340 iftndnatVYRISESflipaithqTPVKERHEILTRFRQGEYKILVTSH-VLNEGVDVPEARIAIILSGTGSTREYIQRL 418
Cdd:PHA02558 371 --------VYYVSGE---------VDTEDRNEMKKIAEGGKGIIIVASYgVFSTGISIKNLHHVIFAHPSKSKIIVLQSI 433
                        410       420
                 ....*....|....*....|
gi 488884933 419 GRVLRKGQQEDKrAILYEVI 438
Cdd:PHA02558 434 GRVLRKHGSKSI-ATVWDII 452
DEXHc_XPB cd18029
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ...
80-219 6.30e-18

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


Pssm-ID: 350787 [Multi-domain]  Cd Length: 169  Bit Score: 81.19  E-value: 6.30e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  80 PHQTEALIA-WKKSQ-RRGVIVLPTAAGKTYLAQLALQSTPRSTLIIVPTIDLMHQWYAQMLA--AFPDAEVGLLGGGSK 155
Cdd:cd18029   11 PYQEKALSKmFGNGRaRSGVIVLPCGAGKTLVGITAACTIKKSTLVLCTSAVSVEQWRRQFLDwtTIDDEQIGRFTSDKK 90
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488884933 156 D---NSAILIATYQ-----------SAAIYSETLGNRYAFLIFDECHHLPSDFFRKIAEDSIAPYRLGLTATPDRGDG 219
Cdd:cd18029   91 EifpEAGVTVSTYSmlantrkrspeSEKFMEFITEREWGLIILDEVHVVPAPMFRRVLTLQKAHCKLGLTATLVREDD 168
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
98-500 4.52e-17

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 84.40  E-value: 4.52e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  98 IVLPTAAGKTYLAQLA----LQSTPRSTLIIVPTIDLMHQWYAQMLAAF--PDAEVGLLGGGSK--------DNSAILIA 163
Cdd:COG1111   22 VVLPTGLGKTAVALLViaerLHKKGGKVLFLAPTKPLVEQHAEFFKEALniPEDEIVVFTGEVSpekrkelwEKARIIVA 101
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 164 TYQSaaIYSETLGNRY-----AFLIFDECHHLPSDF-----FRKIAEDSIAPYRLGLTATPdrgdGSHQD-----LDYLI 228
Cdd:COG1111  102 TPQV--IENDLIAGRIdlddvSLLIFDEAHRAVGNYayvyiAERYHEDAKDPLILGMTASP----GSDEEkieevCENLG 175
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 229 GAIVYQKSPQDLSGKA-LADHEIIQIKVKLSaKEQEK----YQEAIKIRNDFLRKN--------NLSLSGLDGWQNFVM- 294
Cdd:COG1111  176 IENVEVRTEEDPDVAPyVHDTEVEWIRVELP-EELKEirdlLNEVLDDRLKKLKELgvivstspDLSKKDLLALQKKLQr 254
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 295 -ISARSSEGRRAMLAH----------------------------RESKEISSGTQG------------------------ 321
Cdd:COG1111  255 rIREDDSEGYRAISILaealklrhalelletqgveallrylerlEEEARSSGGSKAskrlvsdprfrkamrlaeeadieh 334
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 322 -KLRVLAELICEH---HPEP-ILIFTNDNATVYRISEsFL----IPAITH-------------QtpvKERHEILTRFRQG 379
Cdd:COG1111  335 pKLSKLREILKEQlgtNPDSrIIVFTQYRDTAEMIVE-FLsepgIKAGRFvgqaskegdkgltQ---KEQIEILERFRAG 410
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 380 EYKILVTSHVLNEGVDVPEARIAIILSGTGSTREYIQRLGRVlrkGQQEDKRAILYevIAENTTEE---KTSQRRrgEQK 456
Cdd:COG1111  411 EFNVLVATSVAEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRT---GRKREGRVVVL--IAKGTRDEayyWSSRRK--EKK 483
                        490       500       510       520
                 ....*....|....*....|....*....|....*....|....
gi 488884933 457 NKTSYKTGNRQLEllpspPKKSFSFPKAAESSTPWVSSPESEEE 500
Cdd:COG1111  484 MKSILKKLKKLLD-----KQEKEKLKESAQATLDEFESIKELAE 522
HELICc smart00490
helicase superfamily c-terminal domain;
363-425 1.82e-16

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 74.17  E-value: 1.82e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488884933   363 QTPVKERHEILTRFRQGEYKILVTSHVLNEGVDVPEARIAIILSGTGSTREYIQRLGRVLRKG 425
Cdd:smart00490  20 GLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
PRK13766 PRK13766
Hef nuclease; Provisional
98-487 1.11e-15

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 79.92  E-value: 1.11e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  98 IVLPTAAGKTYLAQLA----LQSTPRSTLIIVPTIDLMHQWYA---QMLAAFPDAEVGLLGGGSKD-------NSAILIA 163
Cdd:PRK13766  34 VVLPTGLGKTAIALLViaerLHKKGGKVLILAPTKPLVEQHAEffrKFLNIPEEKIVVFTGEVSPEkraelweKAKVIVA 113
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 164 TYQsaAIYSETLGNRY-----AFLIFDECHHLPSDF--------FRKIAEDsiaPYRLGLTATPdrgdGSHQD-----LD 225
Cdd:PRK13766 114 TPQ--VIENDLIAGRIsledvSLLIFDEAHRAVGNYayvyiaerYHEDAKN---PLVLGLTASP----GSDEEkikevCE 184
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 226 YL-IGAIVYqKSPQDLSGKA-LADHEIIQIKVKLSAKEQEKY---QEAIKIRNDFLRKNNLSLSG--------LDGWQN- 291
Cdd:PRK13766 185 NLgIEHVEV-RTEDDPDVKPyVHKVKIEWVRVELPEELKEIRdllNEALKDRLKKLKELGVIVSIspdvskkeLLGLQKk 263
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 292 -FVMISARSSEGRRAMLAHRESKEISSG-----TQG-------------------------------------------- 321
Cdd:PRK13766 264 lQQEIANDDSEGYEAISILAEAMKLRHAvelleTQGvealrrylerlreearssggskaskrlvedprfrkavrkakeld 343
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 322 ----KLRVLAELICE---HHPEP-ILIFTNDNATVYRISESFLIPAITHQTPV-------------KERHEILTRFRQGE 380
Cdd:PRK13766 344 iehpKLEKLREIVKEqlgKNPDSrIIVFTQYRDTAEKIVDLLEKEGIKAVRFVgqaskdgdkgmsqKEQIEILDKFRAGE 423
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 381 YKILVTSHVLNEGVDVPEARIAIILSGTGSTREYIQRLGRVlrkGQQEDKRAILyeVIAENTTEEK---TSQRRrgEQKN 457
Cdd:PRK13766 424 FNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRT---GRQEEGRVVV--LIAKGTRDEAyywSSRRK--EKKM 496
                        490       500       510
                 ....*....|....*....|....*....|
gi 488884933 458 KTSYKTGNRQLELLPSPPKKSFSFPKAAES 487
Cdd:PRK13766 497 KEELKNLKGILNKKLQELDEEQKGEEEEKD 526
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
72-446 1.78e-14

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 76.03  E-value: 1.78e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  72 ASFEREPYPHQTEAL--IAWKKSQRRGVIVlptA----AGKT-----YLAQLALQSTPRSTLIIVPTIdLMHQWYAQMLA 140
Cdd:COG0553  236 AGLKATLRPYQLEGAawLLFLRRLGLGGLL---AddmgLGKTiqalaLLLELKERGLARPVLIVAPTS-LVGNWQRELAK 311
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 141 AFPDAEVGLLGGGSK--------DNSAILIATYQSAAIYSETLGN-RYAFLIFDECHHLP------SDFFRKIAedsiAP 205
Cdd:COG0553  312 FAPGLRVLVLDGTRErakganpfEDADLVITSYGLLRRDIELLAAvDWDLVILDEAQHIKnpatkrAKAVRALK----AR 387
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 206 YRLGLTATPDRgdGSHQDL---------DYLIGAIV----YQKSPQDLSGKALAD-HEIIQ------------------- 252
Cdd:COG0553  388 HRLALTGTPVE--NRLEELwslldflnpGLLGSLKAfrerFARPIEKGDEEALERlRRLLRpfllrrtkedvlkdlpekt 465
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 253 ---IKVKLSAKEQEKYQEaikIRNDFLRKnnlsLSGLDGWQNFVMISARSSEGRRA----MLAHRESKEISSGTqGKLRV 325
Cdd:COG0553  466 eetLYVELTPEQRALYEA---VLEYLRRE----LEGAEGIRRRGLILAALTRLRQIcshpALLLEEGAELSGRS-AKLEA 537
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 326 LAELICEH--HPEPILIFTNDNATVYRISEsFL------IPAITHQTPVKERHEILTRFRQGEYK--ILVTSHVLNEGVD 395
Cdd:COG0553  538 LLELLEELlaEGEKVLVFSQFTDTLDLLEE-RLeergieYAYLHGGTSAEERDELVDRFQEGPEApvFLISLKAGGEGLN 616
                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 488884933 396 VPEARIAIILSgtgstREY-----IQRLGRVLRKGQQEDkrAILYEVIAENTTEEK 446
Cdd:COG0553  617 LTAADHVIHYD-----LWWnpaveEQAIDRAHRIGQTRD--VQVYKLVAEGTIEEK 665
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
96-213 2.98e-13

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 67.04  E-value: 2.98e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  96 GVIVLPTAAGKTYLAQLA----LQSTPRSTLIIVPTIDLMHQWYAQMLAAF-PDAEVGLLGGGSK---------DNSAIL 161
Cdd:cd00046    4 VLITAPTGSGKTLAALLAalllLLKKGKKVLVLVPTKALALQTAERLRELFgPGIRVAVLVGGSSaeereknklGDADII 83
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488884933 162 IATYQSAAIYSETLG----NRYAFLIFDECHHLPSDFFRKIAEDSIA-------PYRLGLTAT 213
Cdd:cd00046   84 IATPDMLLNLLLREDrlflKDLKLIIVDEAHALLIDSRGALILDLAVrkaglknAQVILLSAT 146
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
339-424 8.08e-13

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


Pssm-ID: 350186 [Multi-domain]  Cd Length: 116  Bit Score: 64.89  E-value: 8.08e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 339 LIFTNDNATVYRISESFL-----IPAITHQTPVKER-HEILTRFRQGEYK--ILVTSHVLNEGVDVPEARIAIILSGTGS 410
Cdd:cd18799   10 LIFCVSIEHAEFMAEAFNeagidAVALNSDYSDRERgDEALILLFFGELKppILVTVDLLTTGVDIPEVDNVVFLRPTES 89
                         90
                 ....*....|....
gi 488884933 411 TREYIQRLGRVLRK 424
Cdd:cd18799   90 RTLFLQMLGRGLRL 103
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
337-435 1.98e-12

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


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 62.72  E-value: 1.98e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 337 PILIFTNDNATVYRISESFlipaithqtpvkerheiltrfrqgeyKILVTSHVLNEGVDVPEARIAIILSGTGSTREYIQ 416
Cdd:cd18785    5 KIIVFTNSIEHAEEIASSL--------------------------EILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQ 58
                         90
                 ....*....|....*....
gi 488884933 417 RLGRVLRKGQQEDkRAILY 435
Cdd:cd18785   59 RVGRAGRGGKDEG-EVILF 76
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
77-233 9.04e-12

DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350792 [Multi-domain]  Cd Length: 200  Bit Score: 64.21  E-value: 9.04e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  77 EPYPHQTEALIAWKKsqRRGVIVLPTAAGKTYLA----------QLALQSTPRSTLIIVPTIDLMHQwYAQMLAAFPDAE 146
Cdd:cd18034    2 TPRSYQLELFEAALK--RNTIVVLPTGSGKTLIAvmlikemgelNRKEKNPKKRAVFLVPTVPLVAQ-QAEAIRSHTDLK 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 147 VGLL-GGGSKDNSA------------ILIATYQsaaIYSETLGNRYA------FLIFDECHHLPSDF-FRKIAED----- 201
Cdd:cd18034   79 VGEYsGEMGVDKWTkerwkeelekydVLVMTAQ---ILLDALRHGFLslsdinLLIFDECHHATGDHpYARIMKEfyhle 155
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 488884933 202 --SIAPYRLGLTATPDRGDGSH-------QDLDYLIGAIVY 233
Cdd:cd18034  156 grTSRPRILGLTASPVNGKGDPksvekkiQQLEELLNSTIK 196
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
79-216 1.41e-11

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


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 62.65  E-value: 1.41e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933   79 YPHQTEALIAWKksQRRGVIVL-PTAAGKTYLAQLAL------QSTPRSTLIIVPTIDLMHQWYAQM--LAAFPDAEVGL 149
Cdd:pfam00270   1 TPIQAEAIPAIL--EGRDVLVQaPTGSGKTLAFLLPAlealdkLDNGPQALVLAPTRELAEQIYEELkkLGKGLGLKVAS 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  150 LGGGSK--------DNSAILIATYQSAAIYSETLG--NRYAFLIFDECHHLPSDFFRKIAEDSIA-----PYRLGLTATP 214
Cdd:pfam00270  79 LLGGDSrkeqleklKGPDILVGTPGRLLDLLQERKllKNLKLLVLDEAHRLLDMGFGPDLEEILRrlpkkRQILLLSATL 158

                  ..
gi 488884933  215 DR 216
Cdd:pfam00270 159 PR 160
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
322-426 2.54e-11

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


Pssm-ID: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 60.98  E-value: 2.54e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 322 KLRVLAELICEHHPEPILIFTNDNATVYRISESFL---IPAIT-H-QTPVKERHEILTRFRQGEYKILVTSHVLNEGVDV 396
Cdd:cd18787   14 KLLLLLLLLEKLKPGKAIIFVNTKKRVDRLAELLEelgIKVAAlHgDLSQEERERALKKFRSGKVRVLVATDVAARGLDI 93
                         90       100       110
                 ....*....|....*....|....*....|
gi 488884933 397 PEARIAIILSGTGSTREYIQRLGRVLRKGQ 426
Cdd:cd18787   94 PGVDHVINYDLPRDAEDYVHRIGRTGRAGR 123
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
78-214 4.48e-11

DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350677 [Multi-domain]  Cd Length: 182  Bit Score: 61.81  E-value: 4.48e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  78 PYPHQTEAL--IAWKKSQRRGVIVlptA----AGKT-----YLAQLALQS-TPRSTLIIVPTIdLMHQWYAQMLAAFPDA 145
Cdd:cd17919    1 LRPYQLEGLnfLLELYENGPGGIL---AdemgLGKTlqaiaFLAYLLKEGkERGPVLVVCPLS-VLENWEREFEKWTPDL 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 146 EVGLLGGGSKDNSA-----------ILIATYQSAAIYSETLGN-RYAFLIFDECHHL---PSDFFRKIaeDSI-APYRLG 209
Cdd:cd17919   77 RVVVYHGSQRERAQirakekldkfdVVLTTYETLRRDKASLRKfRWDLVVVDEAHRLknpKSQLSKAL--KALrAKRRLL 154

                 ....*
gi 488884933 210 LTATP 214
Cdd:cd17919  155 LTGTP 159
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
322-420 9.76e-09

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


Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 54.13  E-value: 9.76e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 322 KLRVLAELICEHHPEPI----LIFTNDNATVY--------------RISESFLI------PAITHQTPVKERHEILTRFR 377
Cdd:cd18802    8 KLQKLIEILREYFPKTPdfrgIIFVERRATAVvlsrllkehpstlaFIRCGFLIgrgnssQRKRSLMTQRKQKETLDKFR 87
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 488884933 378 QGEYKILVTSHVLNEGVDVPEARIAIILSGTGSTREYIQRLGR 420
Cdd:cd18802   88 DGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGR 130
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
332-439 1.29e-08

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 57.11  E-value: 1.29e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 332 EHHPEPILIFTNDnatvyRISESFLIPAITHQT-----------PVKERHEILTRFRQGEYKILVTSHVLNEGVDVPEAR 400
Cdd:PLN00206 364 QHFKPPAVVFVSS-----RLGADLLANAITVVTglkalsihgekSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVR 438
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 488884933 401 IAIILSGTGSTREYIQRLGRVLRKGQQ--------EDKRAILYEVIA 439
Cdd:PLN00206 439 QVIIFDMPNTIKEYIHQIGRASRMGEKgtaivfvnEEDRNLFPELVA 485
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
322-424 1.45e-08

C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350188 [Multi-domain]  Cd Length: 143  Bit Score: 53.51  E-value: 1.45e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 322 KLRVLAELICEH-------HPEPILIFTNdnatvYRISESFLIPAITHQTPV--------------------KERHEILT 374
Cdd:cd18801   10 KLEKLEEIVKEHfkkkqegSDTRVIIFSE-----FRDSAEEIVNFLSKIRPGiratrfigqasgksskgmsqKEQKEVIE 84
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 488884933 375 RFRQGEYKILVTSHVLNEGVDVPEARIAIILSGTGSTREYIQRLGRVLRK 424
Cdd:cd18801   85 QFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMIQRMGRTGRK 134
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
368-456 5.56e-08

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


Pssm-ID: 350177 [Multi-domain]  Cd Length: 171  Bit Score: 52.63  E-value: 5.56e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 368 ERHEILTRFRQGEYKILVTSHVLNEGVDVPEARIAIILSGTG-----STREYIQRLGRVLRkgqQEDKRAILYeviAENT 442
Cdd:cd18790   65 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKegflrSETSLIQTIGRAAR---NVNGKVILY---ADKI 138
                         90
                 ....*....|....*....
gi 488884933 443 TE--EKT---SQRRRGEQK 456
Cdd:cd18790  139 TDsmQKAieeTERRREIQM 157
DEXHc_UvsW cd18031
DEXH-box helicase domain of bacteriophage UvsW; Bacteriophage UvsW is part of the WXY system ...
78-214 6.67e-08

DEXH-box helicase domain of bacteriophage UvsW; Bacteriophage UvsW is part of the WXY system that repairs DNA damage by a process that involves homologous recombination. UvsW is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350789 [Multi-domain]  Cd Length: 161  Bit Score: 52.05  E-value: 6.67e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  78 PYPHQTEALIAWKKSQRRgVIVLPTAAGKTYLAQLA----LQSTPRSTLIIVPTIDLMHQWYAQML--AAFPDAEVGLLG 151
Cdd:cd18031    1 PHWYQKDAVFEGLVNRRR-ILNLPTSAGRSLIQALLaryyLENYEGKILIIVPTTALTTQMADDFVdyRLFSHAMIKKIG 79
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 152 GGSKDNSA------ILIATYQSAAIYSETLGNRYAFLIFDECHHLPSDFFRKIAED-SIAPYRLGLTATP 214
Cdd:cd18031   80 GGASKDDKykndapVVVGTWQTVVKQPKEWFSQFGMMMNDECHLATGKSISSIISGlNNCMFKFGLSGSL 149
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
86-214 1.01e-07

DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350793 [Multi-domain]  Cd Length: 181  Bit Score: 52.13  E-value: 1.01e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  86 LIAWKKSQRRGVIVLPTAAGKTYLAQLA----LQSTPRSTLIIVPTIDLMHQWYAQM--LAAFPDAEVGLLGGGSKDNSA 159
Cdd:cd18035    9 LIAAVALNGNTLIVLPTGLGKTIIAILVaadrLTKKGGKVLILAPSRPLVEQHAENLkrVLNIPDKITSLTGEVKPEERA 88
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488884933 160 -------ILIATYQSaaIYSETLGNRY-----AFLIFDECHHLPSDF--------FRKIAEDsiaPYRLGLTATP 214
Cdd:cd18035   89 erwdaskIIVATPQV--IENDLLAGRItlddvSLLIFDEAHHAVGNYayvyiahrYKREANN---PLILGLTASP 158
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
68-190 1.85e-07

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 53.75  E-value: 1.85e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  68 LELIASFEREP----YPHQTEALIAWKKSQRRGVIVLPTAAGKTYLAQLALQSTPRS---TLIIVPTIDLMHQWYAQMLA 140
Cdd:COG1204    9 EKVIEFLKERGieelYPPQAEALEAGLLEGKNLVVSAPTASGKTLIAELAILKALLNggkALYIVPLRALASEKYREFKR 88
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488884933 141 AFPDA--EVGLLGGGSKDNSA------ILIATYQSAAIYsetLGNRYAFL------IFDECHHL 190
Cdd:COG1204   89 DFEELgiKVGVSTGDYDSDDEwlgrydILVATPEKLDSL---LRNGPSWLrdvdlvVVDEAHLI 149
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
79-188 1.86e-07

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


Pssm-ID: 350679 [Multi-domain]  Cd Length: 181  Bit Score: 51.11  E-value: 1.86e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  79 YPHQTEALIAWKKSQRRGVIVLPTAAGKTYLAQLA----LQSTPRSTLIIVPTIDLMHQWYA---QMLAAFPDAEVGLLG 151
Cdd:cd17921    3 NPIQREALRALYLSGDSVLVSAPTSSGKTLIAELAilraLATSGGKAVYIAPTRALVNQKEAdlrERFGPLGKNVGLLTG 82
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 488884933 152 GGSKD-----NSAILIATYQSAAIYSETLGNRYAF----LIFDECH 188
Cdd:cd17921   83 DPSVNklllaEADILVATPEKLDLLLRNGGERLIQdvrlVVVDEAH 128
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
77-219 2.41e-07

DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350794 [Multi-domain]  Cd Length: 204  Bit Score: 51.32  E-value: 2.41e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  77 EPYPHQTEALIAWKKSqRRGVIVLPTAAGKTYLAQLAL---------QSTPRSTLIIVPTIDLMHQWYAQMLAAFPDA-E 146
Cdd:cd18036    2 ELRNYQLELVLPALRG-KNTIICAPTGSGKTRVAVYICrhhlekrrsAGEKGRVVVLVNKVPLVEQQLEKFFKYFRKGyK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 147 VGLLGGGSKDNSA----------------ILIATYQSAAIYSETLGNRYAFLIFDECHHLPSD------FFR----KIAE 200
Cdd:cd18036   81 VTGLSGDSSHKVSfgqivkasdviictpqILINNLLSGREEERVYLSDFSLLIFDECHHTQKEhpynkiMRMyldkKLSS 160
                        170
                 ....*....|....*....
gi 488884933 201 DSIAPYRLGLTATPDRGDG 219
Cdd:cd18036  161 QGPLPQILGLTASPGVGGA 179
ERCC3_RAD25_C pfam16203
ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 ...
358-452 7.57e-07

ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 and XPB helicases.


Pssm-ID: 406585  Cd Length: 248  Bit Score: 50.29  E-value: 7.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  358 PAITHQTPVKERHEILTRFRQG-EYKILVTSHVLNEGVDVPEARIAI-ILSGTGSTREYIQRLGRVLR---KGQQEDKRA 432
Cdd:pfam16203  83 PYIYGGTSQAERMRILQNFKHNpNVNTIFLSKVGDTSIDLPEANVLIqISSHFGSRRQEAQRLGRILRakrRSNDEGFNA 162
                          90       100
                  ....*....|....*....|
gi 488884933  433 ILYEVIAENTTEEKTSQRRR 452
Cdd:pfam16203 163 FFYSLVSKDTQEMYYSTKRQ 182
DEXHc_RecG cd17918
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ...
69-214 4.83e-06

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


Pssm-ID: 350676 [Multi-domain]  Cd Length: 180  Bit Score: 47.03  E-value: 4.83e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  69 ELIASFEREPYPHQTEALIAWKKSQRRG-----VIVLPTAAGKTYLAQLALQ---STPRSTLIIVPTIDLMHQWYAQMLA 140
Cdd:cd17918    7 ELCKSLPFSLTKDQAQAIKDIEKDLHSPepmdrLLSGDVGSGKTLVALGAALlayKNGKQVAILVPTEILAHQHYEEARK 86
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488884933 141 AFPDAEVGLLGGGSKDN----SAILIATyqSAAIYSETLGNRYAFLIFDECHHLPSDFFRKIAEDSiAPYRLGLTATP 214
Cdd:cd17918   87 FLPFINVELVTGGTKAQilsgISLLVGT--HALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLG-ATHFLEATATP 161
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
78-218 5.34e-06

DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350769 [Multi-domain]  Cd Length: 207  Bit Score: 47.28  E-value: 5.34e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  78 PYPHQTEAL---IAwkkSQRRGVIVlptA----AGKT-----YLAQLALQSTPRSTLIIVPTIdLMHQWYAQMLAAFPD- 144
Cdd:cd18011    1 PLPHQIDAVlraLR---KPPVRLLL---AdevgLGKTieaglIIKELLLRGDAKRVLILCPAS-LVEQWQDELQDKFGLp 73
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 145 ---------AEVGLLGGGSKDNSAILIATYQSAA--IYSETLGN--RYAFLIFDECHHL----------PSDFFRKIAEd 201
Cdd:cd18011   74 flildretaAQLRRLIGNPFEEFPIVIVSLDLLKrsEERRGLLLseEWDLVVVDEAHKLrnsgggketkRYKLGRLLAK- 152
                        170
                 ....*....|....*..
gi 488884933 202 sIAPYRLGLTATPDRGD 218
Cdd:cd18011  153 -RARHVLLLTATPHNGK 168
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
322-398 9.20e-06

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 47.83  E-value: 9.20e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 322 KLRVLAELICEHHPEPILIFTNDNATVYRISESFL---IPAIT-H----QtpvKERHEILTRFRQGEYKILVTSHVLNEG 393
Cdd:COG0513  228 KLELLRRLLRDEDPERAIVFCNTKRGADRLAEKLQkrgISAAAlHgdlsQ---GQRERALDAFRNGKIRVLVATDVAARG 304

                 ....*
gi 488884933 394 VDVPE 398
Cdd:COG0513  305 IDIDD 309
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
365-451 2.08e-05

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


Pssm-ID: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 44.64  E-value: 2.08e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 365 PVKERHEILTRFRQGEYKILVTSHVLNEGVDVPEARIAII-------LSGTGSTReyiqrlGRVLRKGQQEdkrailYEV 437
Cdd:cd18811   72 KSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPNATVMVIedaerfgLSQLHQLR------GRVGRGDHQS------YCL 139
                         90
                 ....*....|....
gi 488884933 438 IAENTTEEKTSQRR 451
Cdd:cd18811  140 LVYKDPLTETAKQR 153
HsdR COG4096
Type I site-specific restriction endonuclease, part of a restriction-modification system ...
30-398 4.98e-05

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


Pssm-ID: 443272 [Multi-domain]  Cd Length: 806  Bit Score: 45.99  E-value: 4.98e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  30 WDDR----IERfRILAIHyRPlvETLQEeginFQDEAKAFNNLELIA---SFEREPYPHQTEAlI-----AWKKSQRRGV 97
Cdd:COG4096  112 WDDRdpypRER-EVDGFP-SP--EELWE----LLKRRKGTARKRLATepyNDGIALRYYQIEA-IrrveeAIAKGQRRAL 182
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  98 IVLPTAAGKTYLA-QLA---LQSTP---------RSTLIivptidlmhqwyAQMLAAFPDAEVGL-----LGGGSKD--- 156
Cdd:COG4096  183 LVMATGTGKTRTAiALIyrlLKAGRakrilfladRNALV------------DQAKNAFKPFLPDLdaftkLYNKSKDidk 250
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 157 NSAILIATYQsaAIYSETLGNR------------YAFLIFDECHHlpSDF--FRKIAE--DSiapYRLGLTATPDRgDGS 220
Cdd:COG4096  251 SARVYFSTYQ--TMMNRIDGEEeepgyrqfppdfFDLIIIDECHR--GIYskWRAILDyfDA---LQIGLTATPKD-TID 322
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 221 HQDLDYLIGAIVYQKS-PQDLSGKALADHEIIQIKVKLSaKEQEKYQEAIKIRNDflRKNNLSLSGLDgwqnfvmisars 299
Cdd:COG4096  323 RNTYEYFNGNPVYTYSlEQAVADGFLVPYKVIRIDTKFD-REGIRYDAGEDLSDE--EGEEIELEELE------------ 387
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 300 segrramlahrESKEISSG-------TQGKLRVLAELICEHHPEPI-------LIFTNDNATVYRISESF--LIPA---- 359
Cdd:COG4096  388 -----------EDREYEAKdfnrkvvNEDTTRKVLEELMEYLDKPGgdrlgktIIFAKNDDHADRIVQALreLYPElggd 456
                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....*
gi 488884933 360 ----ITHQTPVKERHeiLTRFRQGEY--KILVTSHVLNEGVDVPE 398
Cdd:COG4096  457 fvkkITGDDDYGKSL--IDNFKNPEKypRIAVTVDMLDTGIDVPE 499
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
77-223 6.17e-05

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


Pssm-ID: 350685 [Multi-domain]  Cd Length: 201  Bit Score: 43.96  E-value: 6.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  77 EPYPHQTEALIAWKKSqRRGVIVLPTAAGKTYLAQLA----LQSTPRS----TLIIVPTIDLMHQwyaQMLAAF-----P 143
Cdd:cd17927    2 KPRNYQLELAQPALKG-KNTIICLPTGSGKTFVAVLIcehhLKKFPAGrkgkVVFLANKVPLVEQ---QKEVFRkhferP 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 144 DAEVGLLGGGSKDN---------SAILIATYQ-------SAAIYSETlgnRYAFLIFDECHHL----PSDFFRKIAEDSI 203
Cdd:cd17927   78 GYKVTGLSGDTSENvsveqivesSDVIIVTPQilvndlkSGTIVSLS---DFSLLVFDECHNTtknhPYNEIMFRYLDQK 154
                        170       180
                 ....*....|....*....|....*.
gi 488884933 204 A------PYRLGLTATPDRGDGSHQD 223
Cdd:cd17927  155 LgssgplPQILGLTASPGVGGAKNTE 180
PRK05298 PRK05298
excinuclease ABC subunit UvrB;
368-455 7.08e-05

excinuclease ABC subunit UvrB;


Pssm-ID: 235395 [Multi-domain]  Cd Length: 652  Bit Score: 45.42  E-value: 7.08e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 368 ERHEILTRFRQGEYKILVTSHVLNEGVDVPEARIAIILSG--TG---STREYIQRLGRVLRkgqQEDKRAILYeviAENT 442
Cdd:PRK05298 484 ERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDAdkEGflrSERSLIQTIGRAAR---NVNGKVILY---ADKI 557
                         90
                 ....*....|....*...
gi 488884933 443 TE--EKT---SQRRRGEQ 455
Cdd:PRK05298 558 TDsmQKAideTERRREIQ 575
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
359-451 1.35e-04

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


Pssm-ID: 350179 [Multi-domain]  Cd Length: 160  Bit Score: 42.25  E-value: 1.35e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 359 AITH-QTPVKERHEILTRFRQGEYKILVTSHVLNEGVDVPEARIAIIlsgtgstrEYIQRL---------GRVLRKGQQe 428
Cdd:cd18792   64 ALLHgKMTEDEKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMII--------EDADRFglsqlhqlrGRVGRGKHQ- 134
                         90       100
                 ....*....|....*....|...
gi 488884933 429 dkrAILYEVIAENTTEEKTSQRR 451
Cdd:cd18792  135 ---SYCYLLYPDPKKLTETAKKR 154
PRK04537 PRK04537
ATP-dependent RNA helicase RhlB; Provisional
322-429 1.90e-04

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235307 [Multi-domain]  Cd Length: 572  Bit Score: 44.17  E-value: 1.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 322 KLRVLAELICEHHPEPILIFTNDNATVYRISES-----FLIPAITHQTPVKERHEILTRFRQGEYKILVTSHVLNEGVDV 396
Cdd:PRK04537 244 KQTLLLGLLSRSEGARTMVFVNTKAFVERVARTlerhgYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHI 323
                         90       100       110
                 ....*....|....*....|....*....|...
gi 488884933 397 PEARIAIILSGTGSTREYIQRLGRVLRKGQQED 429
Cdd:PRK04537 324 DGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGD 356
DEXHc_ERCC6 cd18000
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ...
79-214 2.33e-04

DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, also known Cockayne syndrome group B (CSB), Rad26 in Saccharomyces cerevisiae, and Rhp26 in Schizosaccharomyces pombe) is a DNA-binding protein that is important in transcription-coupled excision repair. ERCC6 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: 350758 [Multi-domain]  Cd Length: 193  Bit Score: 42.31  E-value: 2.33e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  79 YPHQTEAL-IAWKKSQRR--GVIVLPTAAGKT-----YLAQLALQSTP-RSTLIIVPTiDLMHQWYAQMLAAFPDAEVGL 149
Cdd:cd18000    2 FKYQQTGVqWLWELHCQRvgGILGDEMGLGKTiqiiaFLAALHHSKLGlGPSLIVCPA-TVLKQWVKEFHRWWPPFRVVV 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 150 L-----GGGSKDNS-----------------AILIATYQSAAIYSETLGNR-YAFLIFDECHhlpsdffrKI----AEDS 202
Cdd:cd18000   81 LhssgsGTGSEEKLgsierksqlirkvvgdgGILITTYEGFRKHKDLLLNHnWQYVILDEGH--------KIrnpdAEIT 152
                        170
                 ....*....|....*...
gi 488884933 203 IA------PYRLGLTATP 214
Cdd:cd18000  153 LAckqlrtPHRLILSGTP 170
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
320-427 3.37e-04

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 42.98  E-value: 3.37e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 320 QGKLRVLAELICEHHPEPILIFTNDNATVYRISESFLIPAI-----THQTPVKERHEILTRFRQGEYKILVTSHVLNEGV 394
Cdd:PRK01297 320 SDKYKLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGInaaqlSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGI 399
                         90       100       110
                 ....*....|....*....|....*....|...
gi 488884933 395 DVPEARIAIILSGTGSTREYIQRLGRVLRKGQQ 427
Cdd:PRK01297 400 HIDGISHVINFTLPEDPDDYVHRIGRTGRAGAS 432
PTZ00424 PTZ00424
helicase 45; Provisional
367-427 3.84e-04

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 42.89  E-value: 3.84e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488884933 367 KERHEILTRFRQGEYKILVTSHVLNEGVDVPEARIAIILSGTGSTREYIQRLGRVLRKGQQ 427
Cdd:PTZ00424 304 KDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRK 364
ComFA COG4098
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ...
80-404 1.05e-03

Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair];


Pssm-ID: 443274 [Multi-domain]  Cd Length: 451  Bit Score: 41.40  E-value: 1.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933  80 PHQTEA---LIAWKKSQRRGVIVLPTAAGKT----YLAQLALQSTPRsTLIIVPTIDLMHQWYAQMLAAFPDAEVGLLGG 152
Cdd:COG4098  113 PAQQKAsdeLLEAIKKKEEHLVWAVCGAGKTemlfPAIAEALKQGGR-VCIATPRVDVVLELAPRLQQAFPGVDIAALYG 191
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 153 GSKD---NSAILIAT-------YQsaaiysetlgnryAF--LIFDEChhlpsDFFrkiaedsiaPYR------------- 207
Cdd:COG4098  192 GSEEkyrYAQLVIATthqllrfYQ-------------AFdlLIIDEV-----DAF---------PYSgdpmlqyavkrar 244
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 208 ------LGLTATPDRgdgsHQDLDYLIGAIVYQKSPQDLSGKALAdheIIQIKVklsakeQEKYQEAikirndfLRKNNL 281
Cdd:COG4098  245 kpdgklIYLTATPSK----ALQRQVKRGKLKVVKLPARYHGHPLP---VPKFKW------LGNWKKR-------LRRGKL 304
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 282 SLSgLDGWqnfvmISARSSEGRRAML--AHRESKEissgtqgklrVLAELICEHHPEPILiftndnATVYriSESflipa 359
Cdd:COG4098  305 PRK-LLKW-----LKKRLKEGRQLLIfvPTIELLE----------QLVALLQKLFPEERI------AGVH--AED----- 355
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*
gi 488884933 360 ithqtpvKERHEILTRFRQGEYKILVTSHVLNEGVDVPEARIAII 404
Cdd:COG4098  356 -------PERKEKVQAFRDGEIPILVTTTILERGVTFPNVDVAVL 393
PRK13767 PRK13767
ATP-dependent helicase; Provisional
307-420 1.08e-03

ATP-dependent helicase; Provisional


Pssm-ID: 237497 [Multi-domain]  Cd Length: 876  Bit Score: 41.80  E-value: 1.08e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 307 LAHRESKEISSGTqgkLRVLAELICEHhpEPILIFTND-NAT---VY----RISESFLIPAIT--HQTPVKE-RHEILTR 375
Cdd:PRK13767 261 LIHTPAEEISEAL---YETLHELIKEH--RTTLIFTNTrSGAervLYnlrkRFPEEYDEDNIGahHSSLSREvRLEVEEK 335
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 488884933 376 FRQGEYKILVTSHVLNEGVDVPEARIAIILSGTGSTREYIQRLGR 420
Cdd:PRK13767 336 LKRGELKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGR 380
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
321-429 1.86e-03

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


Pssm-ID: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 38.61  E-value: 1.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488884933 321 GKLRVLAELI--CEHHPEPILIFTNDNATVYRIsESFLIPA------ITHQTPVKERHEILTRFRQGEYK--ILVTSHVL 390
Cdd:cd18793   11 GKLEALLELLeeLREPGEKVLIFSQFTDTLDIL-EEALRERgikylrLDGSTSSKERQKLVDRFNEDPDIrvFLLSTKAG 89
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 488884933 391 NEGVDVPEARIAII--LSGTgSTREyIQRLGRVLRKGQQED 429
Cdd:cd18793   90 GVGLNLTAANRVILydPWWN-PAVE-EQAIDRAHRIGQKKP 128
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
359-404 5.88e-03

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 39.36  E-value: 5.88e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 488884933 359 AITH-QTPVKERHEILTRFRQGEYKILVTSHVLNEGVDVPEARIAII 404
Cdd:PRK10917 509 GLLHgRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVI 555
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
79-117 8.78e-03

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


Pssm-ID: 350786 [Multi-domain]  Cd Length: 177  Bit Score: 37.31  E-value: 8.78e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 488884933  79 YPHQTEALIAWKKSQRRGVIVLPTAAGKTYLAQLALQST 117
Cdd:cd18028    3 YPPQAEAVRAGLLKGENLLISIPTASGKTLIAEMAMVNT 41
 
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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