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Conserved domains on  [gi|742068541|ref|NP_001290345|]
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general transcription and DNA repair factor IIH helicase/translocase subunit XPB isoform b [Homo sapiens]

Protein Classification

rad25 family protein( domain architecture ID 11489419)

rad25 family protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
rad25 TIGR00603
DNA repair helicase rad25; All proteins in this family for which functions are known are ...
1-715 0e+00

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: 1377.19  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541    1 MPLKDDHTSRPLWVAPDGHIFLEAFSPVYKYAQDFLVAIAEPVCRPTHVHEYKLTAYSLYAAVSVGLQTSDITEYLRKLS 80
Cdd:TIGR00603   6 LELKPDHGSRPLWVAPDGHIFLESFSPLYKQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEVLGRLS 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541   81 KTGVPDGIMQFIKLCTVSYGKVKLVLKHNRYFVESCHPDVIQHLLQDPVIRECRLRNSEGEatELITETFTSKSAISKTA 160
Cdd:TIGR00603  86 KTPIPKGIIEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKDPVIAPCRIDPTEEE--SLQTPTYGSKEDFIINK 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  161 ES-SGGPSTSRVTDPQGKSDIPMDLFDFYEQMDKDEEEEEETQTVSFEVKQEMIEELQKRCIHLEYPLLAEYDFRNDSVN 239
Cdd:TIGR00603 164 PGfTGGASAGQLEANQGESAVPKDIADFYELEEEEEDEDEETATHSFEIDQEQVEEVKKRCIELDYPLLEEYDFRNDTVN 243
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  240 PDINIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWST 319
Cdd:TIGR00603 244 PDLNIDLKPTTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTSAVSVEQWKQQFKMWST 323
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  320 IDDSQICRFTSDAKDKPIG-CSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHC 398
Cdd:TIGR00603 324 IDDSQICRFTSDAKERFHGeAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAAMFRRVLTIVQAHC 403
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  399 KLGLTATLVREDDKIVDLNFLIGPKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNKFR 478
Cdd:TIGR00603 404 KLGLTATLVREDDKITDLNFLIGPKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKRMLLYVMNPNKFR 483
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  479 ACQFLIKFHERRNDKIIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSFDLPEANV 558
Cdd:TIGR00603 484 ACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLGKPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTSIDLPEANV 563
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  559 LIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEYNAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEE-DL 637
Cdd:TIGR00603 564 LIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMYYSTKRQRFLVDQGYSFKVITHLPGMDNEsNL 643
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  638 AFSTKEEQQQLLQKVLAATDLDAEEEVVAGEFGSR-----------SSQASRRFGTMSSMSGADDTVYMEYHSSRSKAPS 706
Cdd:TIGR00603 644 AYSSKEEQLELLQKVLLAGDLDAELEVLEGEFGSRalgasrsmssaSGKAVRRGGSLSSLSGGDDMAYMEYRKPAIKKSK 723

                  ....*....
gi 742068541  707 KHVHPLFKR 715
Cdd:TIGR00603 724 KEVHPLFKK 732
 
Name Accession Description Interval E-value
rad25 TIGR00603
DNA repair helicase rad25; All proteins in this family for which functions are known are ...
1-715 0e+00

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: 1377.19  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541    1 MPLKDDHTSRPLWVAPDGHIFLEAFSPVYKYAQDFLVAIAEPVCRPTHVHEYKLTAYSLYAAVSVGLQTSDITEYLRKLS 80
Cdd:TIGR00603   6 LELKPDHGSRPLWVAPDGHIFLESFSPLYKQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEVLGRLS 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541   81 KTGVPDGIMQFIKLCTVSYGKVKLVLKHNRYFVESCHPDVIQHLLQDPVIRECRLRNSEGEatELITETFTSKSAISKTA 160
Cdd:TIGR00603  86 KTPIPKGIIEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKDPVIAPCRIDPTEEE--SLQTPTYGSKEDFIINK 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  161 ES-SGGPSTSRVTDPQGKSDIPMDLFDFYEQMDKDEEEEEETQTVSFEVKQEMIEELQKRCIHLEYPLLAEYDFRNDSVN 239
Cdd:TIGR00603 164 PGfTGGASAGQLEANQGESAVPKDIADFYELEEEEEDEDEETATHSFEIDQEQVEEVKKRCIELDYPLLEEYDFRNDTVN 243
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  240 PDINIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWST 319
Cdd:TIGR00603 244 PDLNIDLKPTTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTSAVSVEQWKQQFKMWST 323
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  320 IDDSQICRFTSDAKDKPIG-CSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHC 398
Cdd:TIGR00603 324 IDDSQICRFTSDAKERFHGeAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAAMFRRVLTIVQAHC 403
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  399 KLGLTATLVREDDKIVDLNFLIGPKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNKFR 478
Cdd:TIGR00603 404 KLGLTATLVREDDKITDLNFLIGPKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKRMLLYVMNPNKFR 483
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  479 ACQFLIKFHERRNDKIIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSFDLPEANV 558
Cdd:TIGR00603 484 ACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLGKPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTSIDLPEANV 563
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  559 LIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEYNAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEE-DL 637
Cdd:TIGR00603 564 LIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMYYSTKRQRFLVDQGYSFKVITHLPGMDNEsNL 643
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  638 AFSTKEEQQQLLQKVLAATDLDAEEEVVAGEFGSR-----------SSQASRRFGTMSSMSGADDTVYMEYHSSRSKAPS 706
Cdd:TIGR00603 644 AYSSKEEQLELLQKVLLAGDLDAELEVLEGEFGSRalgasrsmssaSGKAVRRGGSLSSLSGGDDMAYMEYRKPAIKKSK 723

                  ....*....
gi 742068541  707 KHVHPLFKR 715
Cdd:TIGR00603 724 KEVHPLFKK 732
ERCC3_RAD25_C pfam16203
ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 ...
432-678 0e+00

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: 531.02  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  432 LQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNKFRACQFLIKFHERRNDKIIVFADNVFALKEYAIRL 511
Cdd:pfam16203   1 LQEKGHIANVQCAEVWCPMTAEFYREYLRSKSRKKRLLYVMNPNKFRACQFLIRYHERRGDKIIVFSDNVFALKEYAKKL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  512 NKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEY 591
Cdd:pfam16203  81 NKPYIYGGTSQAERMRILQNFKHNPNVNTIFLSKVGDTSIDLPEANVLIQISSHFGSRRQEAQRLGRILRAKRRSNDEGF 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  592 NAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEE-EDLAFSTKEEQQQLLQKVLAATDLDAEEEVVAGEFG 670
Cdd:pfam16203 161 NAFFYSLVSKDTQEMYYSTKRQQFLVDQGYAFKVITNLAGMEDeENLAYSTKEEQLELLQKVLAANDTDAEEEVIADDLG 240

                  ....*...
gi 742068541  671 SRSSQASR 678
Cdd:pfam16203 241 KDRKGGVR 248
DEXHc_XPB cd18029
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ...
244-412 1.88e-110

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: 331.57  E-value: 1.88e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 244 IDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDS 323
Cdd:cd18029    1 IDLKPSTQLRPYQEKALSKMFGNGRARSGVIVLPCGAGKTLVGITAACTIKKSTLVLCTSAVSVEQWRRQFLDWTTIDDE 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 324 QICRFTSDAKDKPIGCSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLT 403
Cdd:cd18029   81 QIGRFTSDKKEIFPEAGVTVSTYSMLANTRKRSPESEKFMEFITEREWGLIILDEVHVVPAPMFRRVLTLQKAHCKLGLT 160

                 ....*....
gi 742068541 404 ATLVREDDK 412
Cdd:cd18029  161 ATLVREDDK 169
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
252-663 4.24e-65

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 226.06  E-value: 4.24e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 252 LRPYQEKSLRKMFGNGRA--RSGVIVLPCGAGKSLVGVTAACTVR--KRCLVLGNSAVSVEQWKAQFKMWSTIDDSqicr 327
Cdd:COG1061   81 LRPYQQEALEALLAALERggGRGLVVAPTGTGKTVLALALAAELLrgKRVLVLVPRRELLEQWAEELRRFLGDPLA---- 156
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 328 ftsDAKDKPIGCSVAISTYSMLGHttkrsweaeRVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLV 407
Cdd:COG1061  157 ---GGGKKDSDAPITVATYQSLAR---------RAHLDELGDRFGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPF 224
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 408 REDDKIVDLNFLIGpKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFyREYVAIKTKKRILLYTMNPNKFRACQFLIKFH 487
Cdd:COG1061  225 RSDGREILLFLFDG-IVYEYSLKEAIEDGYLAPPEYYGIRVDLTDER-AEYDALSERLREALAADAERKDKILRELLREH 302
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 488 eRRNDKIIVFADNVFALKEYAIRLNK-----PYIYGPTSQGERMQILQNFKHNpKINTIFISKVGDTSFDLPEANVLIQI 562
Cdd:COG1061  303 -PDDRKTLVFCSSVDHAEALAELLNEagiraAVVTGDTPKKEREEILEAFRDG-ELRILVTVDVLNEGVDVPRLDVAILL 380
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 563 SSHgGSRRQEAQRLGRVLRAKKGmvaEEYnAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEEDLAFSTK 642
Cdd:COG1061  381 RPT-GSPREFIQRLGRGLRPAPG---KED-ALVYDFVGNDVPVLEELAKDLRDLAGYRVEFLDEEESEELALLIAVKPAL 455
                        410       420
                 ....*....|....*....|.
gi 742068541 643 EEQQQLLQKVLAATDLDAEEE 663
Cdd:COG1061  456 EVKGELEEELLEELELLEDAL 476
DEXDc smart00487
DEAD-like helicases superfamily;
244-418 3.87e-17

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 80.23  E-value: 3.87e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541   244 IDLKPTAVLRPYQEKSLRKMFGNGRarSGVIVLPCGAGKSLVGVTAA-----CTVRKRCLVLGNSAVSVEQWKAQFKMWS 318
Cdd:smart00487   1 IEKFGFEPLRPYQKEAIEALLSGLR--DVILAAPTGSGKTLAALLPAlealkRGKGGRVLVLVPTRELAEQWAEELKKLG 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541   319 T-IDDSQICRFTSDAKDKPI------GCSVAISTYSMLGHTTKRsweaervmEWLKTQEWGLMILDEVHTIPAKMFRRVL 391
Cdd:smart00487  79 PsLGLKVVGLYGGDSKREQLrklesgKTDILVTTPGRLLDLLEN--------DKLSLSNVDLVILDEAHRLLDGGFGDQL 150
                          170       180       190
                   ....*....|....*....|....*....|..
gi 742068541   392 TIV-----QAHCKLGLTATLVREDDKIVDLNF 418
Cdd:smart00487 151 EKLlkllpKNVQLLLLSATPPEEIENLLELFL 182
uvsW PHA02558
UvsW helicase; Provisional
253-507 9.80e-04

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 42.30  E-value: 9.80e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 253 RPYQEKSLRKMFGNGRarsGVIVLPCGAGKSLVgvtAACTVR-------KRCLVLGNSAVSVEQWKAQFKMWSTIDDS-- 323
Cdd:PHA02558 116 HWYQYDAVYEGLKNNR---RLLNLPTSAGKSLI---QYLLSRyylenyeGKVLIIVPTTSLVTQMIDDFVDYRLFPREam 189
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 324 -QICRFTSDAKDKPIgcsvAISTYSMLGHTTKrsweaervmEWLktQEWGLMILDEVHTIPAKMFRRVLTIVqAHC--KL 400
Cdd:PHA02558 190 hKIYSGTAKDTDAPI----VVSTWQSAVKQPK---------EWF--DQFGMVIVDECHLFTGKSLTSIITKL-DNCkfKF 253
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 401 GLTATLVREDDKIVDLNFLIGP--KLYEANwmELQNNGYIAKVQCAEVWCPMSPEFyreyvaiktkkRILLytmnpnKFR 478
Cdd:PHA02558 254 GLTGSLRDGKANILQYVGLFGDifKPVTTS--QLMEEGQVTDLKINSIFLRYPDED-----------RVKL------KGE 314
                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 742068541 479 ACQFLIKF---HERRNDKIIVFA-------DNVFALKEY 507
Cdd:PHA02558 315 DYQEEIKYitsHTKRNKWIANLAlklakkgENTFVMFKY 353
 
Name Accession Description Interval E-value
rad25 TIGR00603
DNA repair helicase rad25; All proteins in this family for which functions are known are ...
1-715 0e+00

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: 1377.19  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541    1 MPLKDDHTSRPLWVAPDGHIFLEAFSPVYKYAQDFLVAIAEPVCRPTHVHEYKLTAYSLYAAVSVGLQTSDITEYLRKLS 80
Cdd:TIGR00603   6 LELKPDHGSRPLWVAPDGHIFLESFSPLYKQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEVLGRLS 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541   81 KTGVPDGIMQFIKLCTVSYGKVKLVLKHNRYFVESCHPDVIQHLLQDPVIRECRLRNSEGEatELITETFTSKSAISKTA 160
Cdd:TIGR00603  86 KTPIPKGIIEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKDPVIAPCRIDPTEEE--SLQTPTYGSKEDFIINK 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  161 ES-SGGPSTSRVTDPQGKSDIPMDLFDFYEQMDKDEEEEEETQTVSFEVKQEMIEELQKRCIHLEYPLLAEYDFRNDSVN 239
Cdd:TIGR00603 164 PGfTGGASAGQLEANQGESAVPKDIADFYELEEEEEDEDEETATHSFEIDQEQVEEVKKRCIELDYPLLEEYDFRNDTVN 243
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  240 PDINIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWST 319
Cdd:TIGR00603 244 PDLNIDLKPTTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTSAVSVEQWKQQFKMWST 323
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  320 IDDSQICRFTSDAKDKPIG-CSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHC 398
Cdd:TIGR00603 324 IDDSQICRFTSDAKERFHGeAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAAMFRRVLTIVQAHC 403
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  399 KLGLTATLVREDDKIVDLNFLIGPKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNKFR 478
Cdd:TIGR00603 404 KLGLTATLVREDDKITDLNFLIGPKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKRMLLYVMNPNKFR 483
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  479 ACQFLIKFHERRNDKIIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSFDLPEANV 558
Cdd:TIGR00603 484 ACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLGKPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTSIDLPEANV 563
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  559 LIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEYNAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEE-DL 637
Cdd:TIGR00603 564 LIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMYYSTKRQRFLVDQGYSFKVITHLPGMDNEsNL 643
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  638 AFSTKEEQQQLLQKVLAATDLDAEEEVVAGEFGSR-----------SSQASRRFGTMSSMSGADDTVYMEYHSSRSKAPS 706
Cdd:TIGR00603 644 AYSSKEEQLELLQKVLLAGDLDAELEVLEGEFGSRalgasrsmssaSGKAVRRGGSLSSLSGGDDMAYMEYRKPAIKKSK 723

                  ....*....
gi 742068541  707 KHVHPLFKR 715
Cdd:TIGR00603 724 KEVHPLFKK 732
ERCC3_RAD25_C pfam16203
ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 ...
432-678 0e+00

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: 531.02  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  432 LQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNKFRACQFLIKFHERRNDKIIVFADNVFALKEYAIRL 511
Cdd:pfam16203   1 LQEKGHIANVQCAEVWCPMTAEFYREYLRSKSRKKRLLYVMNPNKFRACQFLIRYHERRGDKIIVFSDNVFALKEYAKKL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  512 NKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEY 591
Cdd:pfam16203  81 NKPYIYGGTSQAERMRILQNFKHNPNVNTIFLSKVGDTSIDLPEANVLIQISSHFGSRRQEAQRLGRILRAKRRSNDEGF 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  592 NAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEE-EDLAFSTKEEQQQLLQKVLAATDLDAEEEVVAGEFG 670
Cdd:pfam16203 161 NAFFYSLVSKDTQEMYYSTKRQQFLVDQGYAFKVITNLAGMEDeENLAYSTKEEQLELLQKVLAANDTDAEEEVIADDLG 240

                  ....*...
gi 742068541  671 SRSSQASR 678
Cdd:pfam16203 241 KDRKGGVR 248
DEXHc_XPB cd18029
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ...
244-412 1.88e-110

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: 331.57  E-value: 1.88e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 244 IDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDS 323
Cdd:cd18029    1 IDLKPSTQLRPYQEKALSKMFGNGRARSGVIVLPCGAGKTLVGITAACTIKKSTLVLCTSAVSVEQWRRQFLDWTTIDDE 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 324 QICRFTSDAKDKPIGCSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLT 403
Cdd:cd18029   81 QIGRFTSDKKEIFPEAGVTVSTYSMLANTRKRSPESEKFMEFITEREWGLIILDEVHVVPAPMFRRVLTLQKAHCKLGLT 160

                 ....*....
gi 742068541 404 ATLVREDDK 412
Cdd:cd18029  161 ATLVREDDK 169
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
443-599 2.44e-88

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: 273.36  E-value: 2.44e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 443 CAEVWCPMSPEFYREY-VAIKTKKRILLYTMNPNKFRACQFLIKFHERrNDKIIVFADNVFALKEYAIRLNKPYIYGPTS 521
Cdd:cd18789    1 CAEIRCPMTPEFYREYlGLGAHRKRRLLAAMNPNKLRALEELLKRHEQ-GDKIIVFTDNVEALYRYAKRLLKPFITGETP 79
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 742068541 522 QGERMQILQNFKHNPkINTIFISKVGDTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGMvaeEYNAFFYSLV 599
Cdd:cd18789   80 QSEREEILQNFREGE-YNTLVVSKVGDEGIDLPEANVAIQISGHGGSRRQEAQRLGRILRPKKGG---GKNAFFYSLV 153
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
252-663 4.24e-65

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 226.06  E-value: 4.24e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 252 LRPYQEKSLRKMFGNGRA--RSGVIVLPCGAGKSLVGVTAACTVR--KRCLVLGNSAVSVEQWKAQFKMWSTIDDSqicr 327
Cdd:COG1061   81 LRPYQQEALEALLAALERggGRGLVVAPTGTGKTVLALALAAELLrgKRVLVLVPRRELLEQWAEELRRFLGDPLA---- 156
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 328 ftsDAKDKPIGCSVAISTYSMLGHttkrsweaeRVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLV 407
Cdd:COG1061  157 ---GGGKKDSDAPITVATYQSLAR---------RAHLDELGDRFGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPF 224
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 408 REDDKIVDLNFLIGpKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFyREYVAIKTKKRILLYTMNPNKFRACQFLIKFH 487
Cdd:COG1061  225 RSDGREILLFLFDG-IVYEYSLKEAIEDGYLAPPEYYGIRVDLTDER-AEYDALSERLREALAADAERKDKILRELLREH 302
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 488 eRRNDKIIVFADNVFALKEYAIRLNK-----PYIYGPTSQGERMQILQNFKHNpKINTIFISKVGDTSFDLPEANVLIQI 562
Cdd:COG1061  303 -PDDRKTLVFCSSVDHAEALAELLNEagiraAVVTGDTPKKEREEILEAFRDG-ELRILVTVDVLNEGVDVPRLDVAILL 380
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 563 SSHgGSRRQEAQRLGRVLRAKKGmvaEEYnAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEEDLAFSTK 642
Cdd:COG1061  381 RPT-GSPREFIQRLGRGLRPAPG---KED-ALVYDFVGNDVPVLEELAKDLRDLAGYRVEFLDEEESEELALLIAVKPAL 455
                        410       420
                 ....*....|....*....|.
gi 742068541 643 EEQQQLLQKVLAATDLDAEEE 663
Cdd:COG1061  456 EVKGELEEELLEELELLEDAL 476
Helicase_C_3 pfam13625
Helicase conserved C-terminal domain; This domain family is found in a wide variety of ...
12-136 1.84e-47

Helicase conserved C-terminal domain; This domain family is found in a wide variety of helicases and helicase-related proteins.


Pssm-ID: 463939 [Multi-domain]  Cd Length: 121  Bit Score: 163.44  E-value: 1.84e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541   12 LWVAPDGHIFLEAfsPVYKYAQDFLVAIAEPVCRpTHVHEYKLTAYSLYAAVSVGLQTSDITEYLRKLSKTGVPDGIMQF 91
Cdd:pfam13625   1 LIVQADLTILLPG--PLAPEARDFLAAFAELESR-GHAHTYRLTPLSLRRALDAGLTAEDILDFLERHSKYPVPQALEYL 77
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 742068541   92 IKLCTVSYGKVKLVLkHNRYFVESCHPDVIQHLLQDPVIRECRLR 136
Cdd:pfam13625  78 IRDVARRHGRLRLGL-GASSYLRSDDPAVLAELLADPRIAPLGLR 121
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
252-406 1.18e-44

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: 156.70  E-value: 1.18e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 252 LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRK-RCLVLGNSAVSVEQWKAQFKMWSTidDSQICRFTS 330
Cdd:cd17926    1 LRPYQEEALEAWLAHKNNRRGILVLPTGSGKTLTALALIAYLKElRTLIVVPTDALLDQWKERFEDFLG--DSSIGLIGG 78
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 742068541 331 DAKDKPIGCSVAISTYSmlghttKRSWEAERVMewLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATL 406
Cdd:cd17926   79 GKKKDFDDANVVVATYQ------SLSNLAEEEK--DLFDQFGLLIVDEAHHLPAKTFSEILKELNAKYRLGLTATP 146
DEXDc smart00487
DEAD-like helicases superfamily;
244-418 3.87e-17

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 80.23  E-value: 3.87e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541   244 IDLKPTAVLRPYQEKSLRKMFGNGRarSGVIVLPCGAGKSLVGVTAA-----CTVRKRCLVLGNSAVSVEQWKAQFKMWS 318
Cdd:smart00487   1 IEKFGFEPLRPYQKEAIEALLSGLR--DVILAAPTGSGKTLAALLPAlealkRGKGGRVLVLVPTRELAEQWAEELKKLG 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541   319 T-IDDSQICRFTSDAKDKPI------GCSVAISTYSMLGHTTKRsweaervmEWLKTQEWGLMILDEVHTIPAKMFRRVL 391
Cdd:smart00487  79 PsLGLKVVGLYGGDSKREQLrklesgKTDILVTTPGRLLDLLEN--------DKLSLSNVDLVILDEAHRLLDGGFGDQL 150
                          170       180       190
                   ....*....|....*....|....*....|..
gi 742068541   392 TIV-----QAHCKLGLTATLVREDDKIVDLNF 418
Cdd:smart00487 151 EKLlkllpKNVQLLLLSATPPEEIENLLELFL 182
ResIII pfam04851
Type III restriction enzyme, res subunit;
251-408 2.12e-15

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 74.25  E-value: 2.12e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  251 VLRPYQE---KSLRKMFGNGRARsGVIVLPCGAGKSLVGVTAACTVRK-----RCLVLGNSAVSVEQWKAQFKMWsTIDD 322
Cdd:pfam04851   3 ELRPYQIeaiENLLESIKNGQKR-GLIVMATGSGKTLTAAKLIARLFKkgpikKVLFLVPRKDLLEQALEEFKKF-LPNY 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  323 SQICRFTSDAKDKPI--GCSVAISTYSMLGHttkrswEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKL 400
Cdd:pfam04851  81 VEIGEIISGDKKDESvdDNKIVVTTIQSLYK------ALELASLELLPDFFDVIIIDEAHRSGASSYRNILEYFKPAFLL 154

                  ....*...
gi 742068541  401 GLTATLVR 408
Cdd:pfam04851 155 GLTATPER 162
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
252-405 1.93e-12

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: 66.44  E-value: 1.93e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 252 LRPYQEKSLRKMFGNGRARSGVIVLPC-GAGKSLVGVTAACTVRK------RCLVLGNSAVsVEQWKAQFKMWS------ 318
Cdd:cd17919    1 LRPYQLEGLNFLLELYENGPGGILADEmGLGKTLQAIAFLAYLLKegkergPVLVVCPLSV-LENWEREFEKWTpdlrvv 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 319 TIDDSQICRFTSDAKDKPIGCSVAISTYSMLghttkrsweaERVMEWLKTQEWGLMILDEVHTI---PAKMFRRVLTIvQ 395
Cdd:cd17919   80 VYHGSQRERAQIRAKEKLDKFDVVLTTYETL----------RRDKASLRKFRWDLVVVDEAHRLknpKSQLSKALKAL-R 148
                        170
                 ....*....|
gi 742068541 396 AHCKLGLTAT 405
Cdd:cd17919  149 AKRRLLLTGT 158
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
249-560 3.27e-12

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 69.87  E-value: 3.27e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 249 TAVLRPYQEKSLRKMFGNGRARSGVI----VlpcGAGKSLVGVTAACTVR-----KRCLVLGNSAVsVEQWKAQFKmwst 319
Cdd:COG0553  239 KATLRPYQLEGAAWLLFLRRLGLGGLladdM---GLGKTIQALALLLELKerglaRPVLIVAPTSL-VGNWQRELA---- 310
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 320 iddsqicRFTSD-------------AKDKPIG-CSVAISTYSMLGhttkrsweaeRVMEWLKTQEWGLMILDEVHTI--- 382
Cdd:COG0553  311 -------KFAPGlrvlvldgtreraKGANPFEdADLVITSYGLLR----------RDIELLAAVDWDLVILDEAQHIknp 373
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 383 PAKMFRRVLTIvQAHCKLGLTATLV--REDD-----KIVDLNFLIGPKLYEANWMELQNNGYIA---------------- 439
Cdd:COG0553  374 ATKRAKAVRAL-KARHRLALTGTPVenRLEElwsllDFLNPGLLGSLKAFRERFARPIEKGDEEalerlrrllrpfllrr 452
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 440 -KVQCAE---------VWCPMSPE---FYREYVA-----------IKTKKRIL--------------LYTMNPN------ 475
Cdd:COG0553  453 tKEDVLKdlpekteetLYVELTPEqraLYEAVLEylrrelegaegIRRRGLILaaltrlrqicshpaLLLEEGAelsgrs 532
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 476 -KFRACQFLIKFHERRNDKIIVFADnvFA---------LKEYAIRLnkPYIYGPTSQGERMQILQNFKHNPKINTIFIS- 544
Cdd:COG0553  533 aKLEALLELLEELLAEGEKVLVFSQ--FTdtldlleerLEERGIEY--AYLHGGTSAEERDELVDRFQEGPEAPVFLISl 608
                        410
                 ....*....|....*.
gi 742068541 545 KVGDTSFDLPEANVLI 560
Cdd:COG0553  609 KAGGEGLNLTAADHVI 624
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
475-583 6.11e-12

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: 62.61  E-value: 6.11e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541  475 NKFRACQFLIKFHerRNDKIIVFADNVFALKEYAIRLNKPY----IYGPTSQGERMQILQNFKhNPKINTIFISKVGDTS 550
Cdd:pfam00271   1 EKLEALLELLKKE--RGGKVLIFSQTKKTLEAELLLEKEGIkvarLHGDLSQEEREEILEDFR-KGKIDVLVATDVAERG 77
                          90       100       110
                  ....*....|....*....|....*....|...
gi 742068541  551 FDLPEANVLIQISSHgGSRRQEAQRLGRVLRAK 583
Cdd:pfam00271  78 LDLPDVDLVINYDLP-WNPASYIQRIGRAGRAG 109
HELICc smart00490
helicase superfamily c-terminal domain;
515-583 1.41e-10

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 57.99  E-value: 1.41e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 742068541   515 YIYGPTSQGERMQILQNFKhNPKINTIFISKVGDTSFDLPEANVLIQISSHgGSRRQEAQRLGRVLRAK 583
Cdd:smart00490  16 RLHGGLSQEEREEILDKFN-NGKIKVLVATDVAERGLDLPGVDLVIIYDLP-WSPASYIQRIGRAGRAG 82
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
252-412 1.65e-09

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: 57.19  E-value: 1.65e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 252 LRPYQEKSLRKM---FGNGRARSGViVLPCGAGKSlvgVTAACTVR--------KRCLVLGNSAVSVEQWKAQFkmWSTI 320
Cdd:cd18032    1 PRYYQQEAIEALeeaREKGQRRALL-VMATGTGKT---YTAAFLIKrlleanrkKRILFLAHREELLEQAERSF--KEVL 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 321 DDSQICRFTSDaKDKPIGCSVAISTYSmlghttkrSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLtivqAHCK- 399
Cdd:cd18032   75 PDGSFGNLKGG-KKKPDDARVVFATVQ--------TLNKRKRLEKFPPDYFDLIIIDEAHHAIASSYRKIL----EYFEp 141
                        170
                 ....*....|....*.
gi 742068541 400 ---LGLTATLVREDDK 412
Cdd:cd18032  142 aflLGLTATPERTDGL 157
DEXHc_ERCC6L2 cd18005
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
290-410 8.42e-06

DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as RAD26L) may play a role in DNA repair and mitochondrial function. In humans, mutations in the ERCC6L2 gene are associated with bone marrow failure syndrome 2. ERCC6L2 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: 350763 [Multi-domain]  Cd Length: 245  Bit Score: 47.76  E-value: 8.42e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 290 ACTVRKRCLVLGNSAVsVEQWKAQFKMWSTIDDSQicrFTSDAKD-------KPIGCSVAISTYSMLghttkrsweaERV 362
Cdd:cd18005   66 ASSAKKPVLIVAPLSV-LYNWKDELDTWGHFEVGV---YHGSRKDdelegrlKAGRLEVVVTTYDTL----------RRC 131
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 742068541 363 MEWLKTQEWGLMILDEVHTI--PAKMFRRVLTIVQAHCKLGLTATLVRED 410
Cdd:cd18005  132 IDSLNSINWSAVIADEAHRIknPKSKLTQAMKELKCKVRIGLTGTLLQNN 181
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
476-581 1.46e-05

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: 45.16  E-value: 1.46e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 476 KFRACQFLIKFHERRNDKIIVFA---DNVFALKEYAIRLNKPY--IYGPTSQGERMQILQNFKHNPKINTIFIS-KVGDT 549
Cdd:cd18793   12 KLEALLELLEELREPGEKVLIFSqftDTLDILEEALRERGIKYlrLDGSTSSKERQKLVDRFNEDPDIRVFLLStKAGGV 91
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 742068541 550 SFDLPEANVLI--------QIsshggsrrqEAQRLGRVLR 581
Cdd:cd18793   92 GLNLTAANRVIlydpwwnpAV---------EEQAIDRAHR 122
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
254-382 4.02e-05

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: 44.95  E-value: 4.02e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 254 PYQEKSLRKMFGNGRarSGVIVLPCGAGKSLVGVTAA----CTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDSQICRFT 329
Cdd:cd17921    4 PIQREALRALYLSGD--SVLVSAPTSSGKTLIAELAIlralATSGGKAVYIAPTRALVNQKEADLRERFGPLGKNVGLLT 81
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 742068541 330 SD---AKDKPIGCSVAISTYSMLGHTTKRSWEaervmewLKTQEWGLMILDEVHTI 382
Cdd:cd17921   82 GDpsvNKLLLAEADILVATPEKLDLLLRNGGE-------RLIQDVRLVVVDEAHLI 130
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
272-405 2.72e-04

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: 41.62  E-value: 2.72e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 272 GVIVLPCGAGKSLVGVTAA-----CTVRKRCLVLGNSAVsVEQWKAQFKMWSTID--------DSQIC-RFTSDAKDKPI 337
Cdd:cd00046    4 VLITAPTGSGKTLAALLAAlllllKKGKKVLVLVPTKAL-ALQTAERLRELFGPGirvavlvgGSSAEeREKNKLGDADI 82
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 742068541 338 gcsvAISTYSMLGhttkRSWEAERvmeWLKTQEWGLMILDEVHTIPAKMfRRVLTIVQAHCKL--------GLTAT 405
Cdd:cd00046   83 ----IIATPDMLL----NLLLRED---RLFLKDLKLIIVDEAHALLIDS-RGALILDLAVRKAglknaqviLLSAT 146
uvsW PHA02558
UvsW helicase; Provisional
253-507 9.80e-04

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 42.30  E-value: 9.80e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 253 RPYQEKSLRKMFGNGRarsGVIVLPCGAGKSLVgvtAACTVR-------KRCLVLGNSAVSVEQWKAQFKMWSTIDDS-- 323
Cdd:PHA02558 116 HWYQYDAVYEGLKNNR---RLLNLPTSAGKSLI---QYLLSRyylenyeGKVLIIVPTTSLVTQMIDDFVDYRLFPREam 189
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 324 -QICRFTSDAKDKPIgcsvAISTYSMLGHTTKrsweaervmEWLktQEWGLMILDEVHTIPAKMFRRVLTIVqAHC--KL 400
Cdd:PHA02558 190 hKIYSGTAKDTDAPI----VVSTWQSAVKQPK---------EWF--DQFGMVIVDECHLFTGKSLTSIITKL-DNCkfKF 253
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 401 GLTATLVREDDKIVDLNFLIGP--KLYEANwmELQNNGYIAKVQCAEVWCPMSPEFyreyvaiktkkRILLytmnpnKFR 478
Cdd:PHA02558 254 GLTGSLRDGKANILQYVGLFGDifKPVTTS--QLMEEGQVTDLKINSIFLRYPDED-----------RVKL------KGE 314
                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 742068541 479 ACQFLIKF---HERRNDKIIVFA-------DNVFALKEY 507
Cdd:PHA02558 315 DYQEEIKYitsHTKRNKWIANLAlklakkgENTFVMFKY 353
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
492-596 1.35e-03

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: 38.07  E-value: 1.35e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 492 DKIIVFADNVFALKEYAirlnkpyiygptsqgERMQILqnfkhnpkINTifisKVGDTSFDLPEANVLIQISSHGgSRRQ 571
Cdd:cd18785    4 VKIIVFTNSIEHAEEIA---------------SSLEIL--------VAT----NVLGEGIDVPSLDTVIFFDPPS-SAAS 55
                         90       100
                 ....*....|....*....|....*
gi 742068541 572 EAQRLGRVLRAKKgmvaEEYNAFFY 596
Cdd:cd18785   56 YIQRVGRAGRGGK----DEGEVILF 76
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
488-674 2.32e-03

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 41.25  E-value: 2.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 488 ERRNDKIIVFA---DNVFALKEYairLNKPYI-----------YGPT--SQGERMQILQNFKhNPKINTIFISKVGDTSF 551
Cdd:COG1111  350 TNPDSRIIVFTqyrDTAEMIVEF---LSEPGIkagrfvgqaskEGDKglTQKEQIEILERFR-AGEFNVLVATSVAEEGL 425
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742068541 552 DLPEANVLI-------QISShggsrrqeAQRLGRVLRAKKGMVaeeynaffYSLVSQDTQEMAY---STKRQRFLVDQGY 621
Cdd:COG1111  426 DIPEVDLVIfyepvpsEIRS--------IQRKGRTGRKREGRV--------VVLIAKGTRDEAYywsSRRKEKKMKSILK 489
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 742068541 622 sfkvitKLAGMEEEDLAFSTKEEQQQLLQKVLAATDLDAEEEVVAGEFGSRSS 674
Cdd:COG1111  490 ------KLKKLLDKQEKEKLKESAQATLDEFESIKELAEDEINEKDLDEIESS 536
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
375-406 3.96e-03

CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 440816 [Multi-domain]  Cd Length: 535  Bit Score: 40.45  E-value: 3.96e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 742068541 375 ILDEVHTIPAKMFRRVLTIVQAHCKLG-----LTATL 406
Cdd:COG1203  273 ILDEVQAYPPYMLALLLRLLEWLKNLGgsvilMTATL 309
 
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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