NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|767917183|ref|XP_011509097|]
View 

general transcription and DNA repair factor IIH helicase subunit XPB isoform X2 [Homo sapiens]

Protein Classification

Ercc3/Rad25/XPB family helicase( domain architecture ID 1004556)

Ercc3/Rad25/XPB family helicase (also known as RepB/Ssl2/haywire) is a core subunit of the eukaryotic basal transcription factor complex TFIIH and is involved in nucleotide excision repair (NER) of DNA and in RNA transcription by RNA polymerase II

CATH:  3.40.50.300
EC:  3.6.4.12
Gene Ontology:  GO:0003677|GO:0003678|GO:0005524
PubMed:  8202161
SCOP:  4000282

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
rad25 super family cl36703
DNA repair helicase rad25; All proteins in this family for which functions are known are ...
 1-633 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]


The actual alignment was detected with superfamily member TIGR00603:

Pssm-ID: 273168 [Multi-domain]  Cd Length: 732  Bit Score: 1185.36  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183    1 MQFIKLCTVSYGKVKLVLKHNRYFVESCHPDVIQHLLQDPVIRECRLRNSEGEatELITETFTSKSAHlplsqISKTAES 80
Cdd:TIGR00603  94 IEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKDPVIAPCRIDPTEEE--SLQTPTYGSKEDF-----IINKPGF 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183   81 SGGPSTSRVTDPQGKSDIPMDLFDFYEQMDKDEEEEEETQTVSFEVKQEMIEELQKRCIHLEYPLLAEYDFRNDSVNPDI 160
Cdd:TIGR00603 167 TGGASAGQLEANQGESAVPKDIADFYELEEEEEDEDEETATHSFEIDQEQVEEVKKRCIELDYPLLEEYDFRNDTVNPDL 246

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  161 NIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDD 240
Cdd:TIGR00603 247 NIDLKPTTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTSAVSVEQWKQQFKMWSTIDD 326

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  241 SQICRFTSDAKDKPIG-CSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLG 319
Cdd:TIGR00603 327 SQICRFTSDAKERFHGeAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAAMFRRVLTIVQAHCKLG 406

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  320 LTATLVREDDKIVDLNFLIGPKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNKFRACQ 399
Cdd:TIGR00603 407 LTATLVREDDKITDLNFLIGPKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKRMLLYVMNPNKFRACQ 486

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  400 FLIKFHERRNDKIIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSFDLPEANVLIQ 479
Cdd:TIGR00603 487 FLIRFHEQRGDKIIVFSDNVFALKEYAIKLGKPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTSIDLPEANVLIQ 566

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  480 ISSHGGSRRQEAQRLGRVLRAKKGMVAEEYNAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEE-DLAFS 558
Cdd:TIGR00603 567 ISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMYYSTKRQRFLVDQGYSFKVITHLPGMDNEsNLAYS 646

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  559 TKEEQQQLLQKVLAATDLDAEEEVVAGEFGSR-----------SSQASRRFGTMSSMSGADDTVYMEYHSSRSKAPSKHV 627
Cdd:TIGR00603 647 SKEEQLELLQKVLLAGDLDAELEVLEGEFGSRalgasrsmssaSGKAVRRGGSLSSLSGGDDMAYMEYRKPAIKKSKKEV 726


                  ....*.
gi 767917183  628 HPLFKR 633
Cdd:TIGR00603 727 HPLFKK 732
 
Name Accession Description Interval E-value
rad25 TIGR00603
DNA repair helicase rad25; All proteins in this family for which functions are known are ...
 1-633 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: 1185.36  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183    1 MQFIKLCTVSYGKVKLVLKHNRYFVESCHPDVIQHLLQDPVIRECRLRNSEGEatELITETFTSKSAHlplsqISKTAES 80
Cdd:TIGR00603  94 IEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKDPVIAPCRIDPTEEE--SLQTPTYGSKEDF-----IINKPGF 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183   81 SGGPSTSRVTDPQGKSDIPMDLFDFYEQMDKDEEEEEETQTVSFEVKQEMIEELQKRCIHLEYPLLAEYDFRNDSVNPDI 160
Cdd:TIGR00603 167 TGGASAGQLEANQGESAVPKDIADFYELEEEEEDEDEETATHSFEIDQEQVEEVKKRCIELDYPLLEEYDFRNDTVNPDL 246

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  161 NIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDD 240
Cdd:TIGR00603 247 NIDLKPTTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTSAVSVEQWKQQFKMWSTIDD 326

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  241 SQICRFTSDAKDKPIG-CSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLG 319
Cdd:TIGR00603 327 SQICRFTSDAKERFHGeAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAAMFRRVLTIVQAHCKLG 406

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  320 LTATLVREDDKIVDLNFLIGPKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNKFRACQ 399
Cdd:TIGR00603 407 LTATLVREDDKITDLNFLIGPKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKRMLLYVMNPNKFRACQ 486

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  400 FLIKFHERRNDKIIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSFDLPEANVLIQ 479
Cdd:TIGR00603 487 FLIRFHEQRGDKIIVFSDNVFALKEYAIKLGKPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTSIDLPEANVLIQ 566

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  480 ISSHGGSRRQEAQRLGRVLRAKKGMVAEEYNAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEE-DLAFS 558
Cdd:TIGR00603 567 ISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMYYSTKRQRFLVDQGYSFKVITHLPGMDNEsNLAYS 646

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  559 TKEEQQQLLQKVLAATDLDAEEEVVAGEFGSR-----------SSQASRRFGTMSSMSGADDTVYMEYHSSRSKAPSKHV 627
Cdd:TIGR00603 647 SKEEQLELLQKVLLAGDLDAELEVLEGEFGSRalgasrsmssaSGKAVRRGGSLSSLSGGDDMAYMEYRKPAIKKSKKEV 726


                  ....*.
gi 767917183  628 HPLFKR 633
Cdd:TIGR00603 727 HPLFKK 732
ERCC3_RAD25_C pfam16203
ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 ...
 350-596 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: 528.32  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  350 LQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNKFRACQFLIKFHERRNDKIIVFADNVFALKEYAIRL 429
Cdd:pfam16203   1 LQEKGHIANVQCAEVWCPMTAEFYREYLRSKSRKKRLLYVMNPNKFRACQFLIRYHERRGDKIIVFSDNVFALKEYAKKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  430 NKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEY 509
Cdd:pfam16203  81 NKPYIYGGTSQAERMRILQNFKHNPNVNTIFLSKVGDTSIDLPEANVLIQISSHFGSRRQEAQRLGRILRAKRRSNDEGF 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  510 NAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEE-EDLAFSTKEEQQQLLQKVLAATDLDAEEEVVAGEFG 588
Cdd:pfam16203 161 NAFFYSLVSKDTQEMYYSTKRQQFLVDQGYAFKVITNLAGMEDeENLAYSTKEEQLELLQKVLAANDTDAEEEVIADDLG 240


                  ....*...
gi 767917183  589 SRSSQASR 596
Cdd:pfam16203 241 KDRKGGVR 248
DEXHc_XPB cd18029
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ...
 162-330 3.79e-111

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: 330.80  E-value: 3.79e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 162 IDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDS 241
Cdd:cd18029    1 IDLKPSTQLRPYQEKALSKMFGNGRARSGVIVLPCGAGKTLVGITAACTIKKSTLVLCTSAVSVEQWRRQFLDWTTIDDE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 242 QICRFTSDAKDKPIGCSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLT 321
Cdd:cd18029   81 QIGRFTSDKKEIFPEAGVTVSTYSMLANTRKRSPESEKFMEFITEREWGLIILDEVHVVPAPMFRRVLTLQKAHCKLGLT 160


                 ....*....
gi 767917183 322 ATLVREDDK 330
Cdd:cd18029  161 ATLVREDDK 169
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
170-581 5.13e-66

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 226.44  E-value: 5.13e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 170 LRPYQEKSLRKMFGNGRA--RSGVIVLPCGAGKSLVGVTAACTVR--KRCLVLGNSAVSVEQWKAQFKMWSTIDDSqicr 245
Cdd:COG1061   81 LRPYQQEALEALLAALERggGRGLVVAPTGTGKTVLALALAAELLrgKRVLVLVPRRELLEQWAEELRRFLGDPLA---- 156

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 246 ftsDAKDKPIGCSVAISTYSMLGHttkrsweaeRVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLV 325
Cdd:COG1061  157 ---GGGKKDSDAPITVATYQSLAR---------RAHLDELGDRFGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPF 224

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 326 REDDKIVDLNFLIGpKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFyREYVAIKTKKRILLYTMNPNKFRACQFLIKFH 405
Cdd:COG1061  225 RSDGREILLFLFDG-IVYEYSLKEAIEDGYLAPPEYYGIRVDLTDER-AEYDALSERLREALAADAERKDKILRELLREH 302

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 406 eRRNDKIIVFADNVFALKEYAIRLNK-----PYIYGPTSQGERMQILQNFKHNpKINTIFISKVGDTSFDLPEANVLIQI 480
Cdd:COG1061  303 -PDDRKTLVFCSSVDHAEALAELLNEagiraAVVTGDTPKKEREEILEAFRDG-ELRILVTVDVLNEGVDVPRLDVAILL 380

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 481 SSHgGSRRQEAQRLGRVLRAKKGmvaEEYnAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEEDLAFSTK 560
Cdd:COG1061  381 RPT-GSPREFIQRLGRGLRPAPG---KED-ALVYDFVGNDVPVLEELAKDLRDLAGYRVEFLDEEESEELALLIAVKPAL 455

                        410       420
                 ....*....|....*....|.
gi 767917183 561 EEQQQLLQKVLAATDLDAEEE 581
Cdd:COG1061  456 EVKGELEEELLEELELLEDAL 476
DEXDc smart00487
DEAD-like helicases superfamily;
162-336 3.53e-17

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 80.23  E-value: 3.53e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183   162 IDLKPTAVLRPYQEKSLRKMFGNGRarSGVIVLPCGAGKSLVGVTAA-----CTVRKRCLVLGNSAVSVEQWKAQFKMWS 236
Cdd:smart00487   1 IEKFGFEPLRPYQKEAIEALLSGLR--DVILAAPTGSGKTLAALLPAlealkRGKGGRVLVLVPTRELAEQWAEELKKLG 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183   237 T-IDDSQICRFTSDAKDKPI------GCSVAISTYSMLGHTTKRsweaervmEWLKTQEWGLMILDEVHTIPAKMFRRVL 309
Cdd:smart00487  79 PsLGLKVVGLYGGDSKREQLrklesgKTDILVTTPGRLLDLLEN--------DKLSLSNVDLVILDEAHRLLDGGFGDQL 150

                          170       180       190
                   ....*....|....*....|....*....|..
gi 767917183   310 TIV-----QAHCKLGLTATLVREDDKIVDLNF 336
Cdd:smart00487 151 EKLlkllpKNVQLLLLSATPPEEIENLLELFL 182
uvsW PHA02558
UvsW helicase; Provisional
 171-425 8.45e-04

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 42.30  E-value: 8.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 171 RPYQEKSLRKMFGNGRarsGVIVLPCGAGKSLVgvtAACTVR-------KRCLVLGNSAVSVEQWKAQFKMWSTIDDS-- 241
Cdd:PHA02558 116 HWYQYDAVYEGLKNNR---RLLNLPTSAGKSLI---QYLLSRyylenyeGKVLIIVPTTSLVTQMIDDFVDYRLFPREam 189

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 242 -QICRFTSDAKDKPIgcsvAISTYSMLGHTTKrsweaervmEWLktQEWGLMILDEVHTIPAKMFRRVLTIVqAHC--KL 318
Cdd:PHA02558 190 hKIYSGTAKDTDAPI----VVSTWQSAVKQPK---------EWF--DQFGMVIVDECHLFTGKSLTSIITKL-DNCkfKF 253

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 319 GLTATLVREDDKIVDLNFLIGP--KLYEANwmELQNNGYIAKVQCAEVWCPMSPEFyreyvaiktkkRILLytmnpnKFR 396
Cdd:PHA02558 254 GLTGSLRDGKANILQYVGLFGDifKPVTTS--QLMEEGQVTDLKINSIFLRYPDED-----------RVKL------KGE 314

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 767917183 397 ACQFLIKF---HERRNDKIIVFA-------DNVFALKEY 425
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 ...
 1-633 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: 1185.36  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183    1 MQFIKLCTVSYGKVKLVLKHNRYFVESCHPDVIQHLLQDPVIRECRLRNSEGEatELITETFTSKSAHlplsqISKTAES 80
Cdd:TIGR00603  94 IEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKDPVIAPCRIDPTEEE--SLQTPTYGSKEDF-----IINKPGF 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183   81 SGGPSTSRVTDPQGKSDIPMDLFDFYEQMDKDEEEEEETQTVSFEVKQEMIEELQKRCIHLEYPLLAEYDFRNDSVNPDI 160
Cdd:TIGR00603 167 TGGASAGQLEANQGESAVPKDIADFYELEEEEEDEDEETATHSFEIDQEQVEEVKKRCIELDYPLLEEYDFRNDTVNPDL 246

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  161 NIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDD 240
Cdd:TIGR00603 247 NIDLKPTTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTSAVSVEQWKQQFKMWSTIDD 326

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  241 SQICRFTSDAKDKPIG-CSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLG 319
Cdd:TIGR00603 327 SQICRFTSDAKERFHGeAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAAMFRRVLTIVQAHCKLG 406

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  320 LTATLVREDDKIVDLNFLIGPKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNKFRACQ 399
Cdd:TIGR00603 407 LTATLVREDDKITDLNFLIGPKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKRMLLYVMNPNKFRACQ 486

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  400 FLIKFHERRNDKIIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSFDLPEANVLIQ 479
Cdd:TIGR00603 487 FLIRFHEQRGDKIIVFSDNVFALKEYAIKLGKPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTSIDLPEANVLIQ 566

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  480 ISSHGGSRRQEAQRLGRVLRAKKGMVAEEYNAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEE-DLAFS 558
Cdd:TIGR00603 567 ISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMYYSTKRQRFLVDQGYSFKVITHLPGMDNEsNLAYS 646

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  559 TKEEQQQLLQKVLAATDLDAEEEVVAGEFGSR-----------SSQASRRFGTMSSMSGADDTVYMEYHSSRSKAPSKHV 627
Cdd:TIGR00603 647 SKEEQLELLQKVLLAGDLDAELEVLEGEFGSRalgasrsmssaSGKAVRRGGSLSSLSGGDDMAYMEYRKPAIKKSKKEV 726


                  ....*.
gi 767917183  628 HPLFKR 633
Cdd:TIGR00603 727 HPLFKK 732
ERCC3_RAD25_C pfam16203
ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 ...
 350-596 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: 528.32  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  350 LQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNKFRACQFLIKFHERRNDKIIVFADNVFALKEYAIRL 429
Cdd:pfam16203   1 LQEKGHIANVQCAEVWCPMTAEFYREYLRSKSRKKRLLYVMNPNKFRACQFLIRYHERRGDKIIVFSDNVFALKEYAKKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  430 NKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEY 509
Cdd:pfam16203  81 NKPYIYGGTSQAERMRILQNFKHNPNVNTIFLSKVGDTSIDLPEANVLIQISSHFGSRRQEAQRLGRILRAKRRSNDEGF 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  510 NAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEE-EDLAFSTKEEQQQLLQKVLAATDLDAEEEVVAGEFG 588
Cdd:pfam16203 161 NAFFYSLVSKDTQEMYYSTKRQQFLVDQGYAFKVITNLAGMEDeENLAYSTKEEQLELLQKVLAANDTDAEEEVIADDLG 240


                  ....*...
gi 767917183  589 SRSSQASR 596
Cdd:pfam16203 241 KDRKGGVR 248
DEXHc_XPB cd18029
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ...
 162-330 3.79e-111

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: 330.80  E-value: 3.79e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 162 IDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDS 241
Cdd:cd18029    1 IDLKPSTQLRPYQEKALSKMFGNGRARSGVIVLPCGAGKTLVGITAACTIKKSTLVLCTSAVSVEQWRRQFLDWTTIDDE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 242 QICRFTSDAKDKPIGCSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLT 321
Cdd:cd18029   81 QIGRFTSDKKEIFPEAGVTVSTYSMLANTRKRSPESEKFMEFITEREWGLIILDEVHVVPAPMFRRVLTLQKAHCKLGLT 160


                 ....*....
gi 767917183 322 ATLVREDDK 330
Cdd:cd18029  161 ATLVREDDK 169
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
 361-517 9.38e-89

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: 272.59  E-value: 9.38e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 361 CAEVWCPMSPEFYREY-VAIKTKKRILLYTMNPNKFRACQFLIKFHERrNDKIIVFADNVFALKEYAIRLNKPYIYGPTS 439
Cdd:cd18789    1 CAEIRCPMTPEFYREYlGLGAHRKRRLLAAMNPNKLRALEELLKRHEQ-GDKIIVFTDNVEALYRYAKRLLKPFITGETP 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767917183 440 QGERMQILQNFKHNPkINTIFISKVGDTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGMvaeEYNAFFYSLV 517
Cdd:cd18789   80 QSEREEILQNFREGE-YNTLVVSKVGDEGIDLPEANVAIQISGHGGSRRQEAQRLGRILRPKKGG---GKNAFFYSLV 153
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
170-581 5.13e-66

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 226.44  E-value: 5.13e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 170 LRPYQEKSLRKMFGNGRA--RSGVIVLPCGAGKSLVGVTAACTVR--KRCLVLGNSAVSVEQWKAQFKMWSTIDDSqicr 245
Cdd:COG1061   81 LRPYQQEALEALLAALERggGRGLVVAPTGTGKTVLALALAAELLrgKRVLVLVPRRELLEQWAEELRRFLGDPLA---- 156

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 246 ftsDAKDKPIGCSVAISTYSMLGHttkrsweaeRVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLV 325
Cdd:COG1061  157 ---GGGKKDSDAPITVATYQSLAR---------RAHLDELGDRFGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPF 224

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 326 REDDKIVDLNFLIGpKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFyREYVAIKTKKRILLYTMNPNKFRACQFLIKFH 405
Cdd:COG1061  225 RSDGREILLFLFDG-IVYEYSLKEAIEDGYLAPPEYYGIRVDLTDER-AEYDALSERLREALAADAERKDKILRELLREH 302

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 406 eRRNDKIIVFADNVFALKEYAIRLNK-----PYIYGPTSQGERMQILQNFKHNpKINTIFISKVGDTSFDLPEANVLIQI 480
Cdd:COG1061  303 -PDDRKTLVFCSSVDHAEALAELLNEagiraAVVTGDTPKKEREEILEAFRDG-ELRILVTVDVLNEGVDVPRLDVAILL 380

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 481 SSHgGSRRQEAQRLGRVLRAKKGmvaEEYnAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEEDLAFSTK 560
Cdd:COG1061  381 RPT-GSPREFIQRLGRGLRPAPG---KED-ALVYDFVGNDVPVLEELAKDLRDLAGYRVEFLDEEESEELALLIAVKPAL 455

                        410       420
                 ....*....|....*....|.
gi 767917183 561 EEQQQLLQKVLAATDLDAEEE 581
Cdd:COG1061  456 EVKGELEEELLEELELLEDAL 476
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 170-324 5.68e-45

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: 5.68e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 170 LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRK-RCLVLGNSAVSVEQWKAQFKMWSTidDSQICRFTS 248
Cdd:cd17926    1 LRPYQEEALEAWLAHKNNRRGILVLPTGSGKTLTALALIAYLKElRTLIVVPTDALLDQWKERFEDFLG--DSSIGLIGG 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767917183 249 DAKDKPIGCSVAISTYSmlghttKRSWEAERVMewLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATL 324
Cdd:cd17926   79 GKKKDFDDANVVVATYQ------SLSNLAEEEK--DLFDQFGLLIVDEAHHLPAKTFSEILKELNAKYRLGLTATP 146
DEXDc smart00487
DEAD-like helicases superfamily;
162-336 3.53e-17

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 80.23  E-value: 3.53e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183   162 IDLKPTAVLRPYQEKSLRKMFGNGRarSGVIVLPCGAGKSLVGVTAA-----CTVRKRCLVLGNSAVSVEQWKAQFKMWS 236
Cdd:smart00487   1 IEKFGFEPLRPYQKEAIEALLSGLR--DVILAAPTGSGKTLAALLPAlealkRGKGGRVLVLVPTRELAEQWAEELKKLG 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183   237 T-IDDSQICRFTSDAKDKPI------GCSVAISTYSMLGHTTKRsweaervmEWLKTQEWGLMILDEVHTIPAKMFRRVL 309
Cdd:smart00487  79 PsLGLKVVGLYGGDSKREQLrklesgKTDILVTTPGRLLDLLEN--------DKLSLSNVDLVILDEAHRLLDGGFGDQL 150

                          170       180       190
                   ....*....|....*....|....*....|..
gi 767917183   310 TIV-----QAHCKLGLTATLVREDDKIVDLNF 336
Cdd:smart00487 151 EKLlkllpKNVQLLLLSATPPEEIENLLELFL 182
ResIII pfam04851
Type III restriction enzyme, res subunit;
169-326 2.20e-15

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 73.86  E-value: 2.20e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  169 VLRPYQE---KSLRKMFGNGRARsGVIVLPCGAGKSLVGVTAACTVRK-----RCLVLGNSAVSVEQWKAQFKMWsTIDD 240
Cdd:pfam04851   3 ELRPYQIeaiENLLESIKNGQKR-GLIVMATGSGKTLTAAKLIARLFKkgpikKVLFLVPRKDLLEQALEEFKKF-LPNY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  241 SQICRFTSDAKDKPI--GCSVAISTYSMLGHttkrswEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKL 318
Cdd:pfam04851  81 VEIGEIISGDKKDESvdDNKIVVTTIQSLYK------ALELASLELLPDFFDVIIIDEAHRSGASSYRNILEYFKPAFLL 154


                  ....*...
gi 767917183  319 GLTATLVR 326
Cdd:pfam04851 155 GLTATPER 162
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
 170-323 1.84e-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: 66.05  E-value: 1.84e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 170 LRPYQEKSLRKMFGNGRARSGVIVLPC-GAGKSLVGVTAACTVRK------RCLVLGNSAVsVEQWKAQFKMWS------ 236
Cdd:cd17919    1 LRPYQLEGLNFLLELYENGPGGILADEmGLGKTLQAIAFLAYLLKegkergPVLVVCPLSV-LENWEREFEKWTpdlrvv 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 237 TIDDSQICRFTSDAKDKPIGCSVAISTYSMLghttkrsweaERVMEWLKTQEWGLMILDEVHTI---PAKMFRRVLTIvQ 313
Cdd:cd17919   80 VYHGSQRERAQIRAKEKLDKFDVVLTTYETL----------RRDKASLRKFRWDLVVVDEAHRLknpKSQLSKALKAL-R 148

                        170
                 ....*....|
gi 767917183 314 AHCKLGLTAT 323
Cdd:cd17919  149 AKRRLLLTGT 158
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 167-478 3.00e-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: 3.00e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 167 TAVLRPYQEKSLRKMFGNGRARSGVI----VlpcGAGKSLVGVTAACTVR-----KRCLVLGNSAVsVEQWKAQFKmwst 237
Cdd:COG0553  239 KATLRPYQLEGAAWLLFLRRLGLGGLladdM---GLGKTIQALALLLELKerglaRPVLIVAPTSL-VGNWQRELA---- 310

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 238 iddsqicRFTSD-------------AKDKPIG-CSVAISTYSMLGhttkrsweaeRVMEWLKTQEWGLMILDEVHTI--- 300
Cdd:COG0553  311 -------KFAPGlrvlvldgtreraKGANPFEdADLVITSYGLLR----------RDIELLAAVDWDLVILDEAQHIknp 373

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 301 PAKMFRRVLTIvQAHCKLGLTATLV--REDD-----KIVDLNFLIGPKLYEANWMELQNNGYIA---------------- 357
Cdd:COG0553  374 ATKRAKAVRAL-KARHRLALTGTPVenRLEElwsllDFLNPGLLGSLKAFRERFARPIEKGDEEalerlrrllrpfllrr 452

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 358 -KVQCAE---------VWCPMSPE---FYREYVA-----------IKTKKRIL--------------LYTMNPN------ 393
Cdd:COG0553  453 tKEDVLKdlpekteetLYVELTPEqraLYEAVLEylrrelegaegIRRRGLILaaltrlrqicshpaLLLEEGAelsgrs 532

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 394 -KFRACQFLIKFHERRNDKIIVFADnvFA---------LKEYAIRLnkPYIYGPTSQGERMQILQNFKHNPKINTIFIS- 462
Cdd:COG0553  533 aKLEALLELLEELLAEGEKVLVFSQ--FTdtldlleerLEERGIEY--AYLHGGTSAEERDELVDRFQEGPEAPVFLISl 608

                        410
                 ....*....|....*.
gi 767917183 463 KVGDTSFDLPEANVLI 478
Cdd:COG0553  609 KAGGEGLNLTAADHVI 624
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 393-501 7.45e-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: 62.23  E-value: 7.45e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  393 NKFRACQFLIKFHerRNDKIIVFADNVFALKEYAIRLNKPY----IYGPTSQGERMQILQNFKhNPKINTIFISKVGDTS 468
Cdd:pfam00271   1 EKLEALLELLKKE--RGGKVLIFSQTKKTLEAELLLEKEGIkvarLHGDLSQEEREEILEDFR-KGKIDVLVATDVAERG 77

                          90       100       110
                  ....*....|....*....|....*....|...
gi 767917183  469 FDLPEANVLIQISSHgGSRRQEAQRLGRVLRAK 501
Cdd:pfam00271  78 LDLPDVDLVINYDLP-WNPASYIQRIGRAGRAG 109
Helicase_C_3 pfam13625
Helicase conserved C-terminal domain; This domain family is found in a wide variety of ...
 2-48 1.46e-11

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: 61.75  E-value: 1.46e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767917183    2 QFIKLCTVSYGKVKLVLkHNRYFVESCHPDVIQHLLQDPVIRECRLR 48
Cdd:pfam13625  76 YLIRDVARRHGRLRLGL-GASSYLRSDDPAVLAELLADPRIAPLGLR 121
HELICc smart00490
helicase superfamily c-terminal domain;
433-501 1.46e-10

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 57.61  E-value: 1.46e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767917183   433 YIYGPTSQGERMQILQNFKhNPKINTIFISKVGDTSFDLPEANVLIQISSHgGSRRQEAQRLGRVLRAK 501
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 ...
 170-330 1.30e-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: 57.57  E-value: 1.30e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 170 LRPYQEKSLRKM---FGNGRARSGViVLPCGAGKSlvgVTAACTVR--------KRCLVLGNSAVSVEQWKAQFkmWSTI 238
Cdd:cd18032    1 PRYYQQEAIEALeeaREKGQRRALL-VMATGTGKT---YTAAFLIKrlleanrkKRILFLAHREELLEQAERSF--KEVL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 239 DDSQICRFTSDaKDKPIGCSVAISTYSmlghttkrSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLtivqAHCK- 317
Cdd:cd18032   75 PDGSFGNLKGG-KKKPDDARVVFATVQ--------TLNKRKRLEKFPPDYFDLIIIDEAHHAIASSYRKIL----EYFEp 141

                        170
                 ....*....|....*.
gi 767917183 318 ---LGLTATLVREDDK 330
Cdd:cd18032  142 aflLGLTATPERTDGL 157
DEXHc_ERCC6L2 cd18005
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
 208-328 7.23e-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: 7.23e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 208 ACTVRKRCLVLGNSAVsVEQWKAQFKMWSTIDDSQicrFTSDAKD-------KPIGCSVAISTYSMLghttkrsweaERV 280
Cdd:cd18005   66 ASSAKKPVLIVAPLSV-LYNWKDELDTWGHFEVGV---YHGSRKDdelegrlKAGRLEVVVTTYDTL----------RRC 131

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 767917183 281 MEWLKTQEWGLMILDEVHTI--PAKMFRRVLTIVQAHCKLGLTATLVRED 328
Cdd:cd18005  132 IDSLNSINWSAVIADEAHRIknPKSKLTQAMKELKCKVRIGLTGTLLQNN 181
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 394-499 1.58e-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: 44.77  E-value: 1.58e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 394 KFRACQFLIKFHERRNDKIIVFA---DNVFALKEYAIRLNKPY--IYGPTSQGERMQILQNFKHNPKINTIFIS-KVGDT 467
Cdd:cd18793   12 KLEALLELLEELREPGEKVLIFSqftDTLDILEEALRERGIKYlrLDGSTSSKERQKLVDRFNEDPDIRVFLLStKAGGV 91

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 767917183 468 SFDLPEANVLI--------QIsshggsrrqEAQRLGRVLR 499
Cdd:cd18793   92 GLNLTAANRVIlydpwwnpAV---------EEQAIDRAHR 122
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 172-300 3.52e-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: 3.52e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 172 PYQEKSLRKMFGNGRarSGVIVLPCGAGKSLVGVTAA----CTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDSQICRFT 247
Cdd:cd17921    4 PIQREALRALYLSGD--SVLVSAPTSSGKTLIAELAIlralATSGGKAVYIAPTRALVNQKEADLRERFGPLGKNVGLLT 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 767917183 248 SD---AKDKPIGCSVAISTYSMLGHTTKRSWEaervmewLKTQEWGLMILDEVHTI 300
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 ...
 190-323 2.37e-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: 2.37e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 190 GVIVLPCGAGKSLVGVTAA-----CTVRKRCLVLGNSAVsVEQWKAQFKMWSTID--------DSQIC-RFTSDAKDKPI 255
Cdd:cd00046    4 VLITAPTGSGKTLAALLAAlllllKKGKKVLVLVPTKAL-ALQTAERLRELFGPGirvavlvgGSSAEeREKNKLGDADI 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767917183 256 gcsvAISTYSMLGhttkRSWEAERvmeWLKTQEWGLMILDEVHTIPAKMfRRVLTIVQAHCKL--------GLTAT 323
Cdd:cd00046   83 ----IIATPDMLL----NLLLRED---RLFLKDLKLIIVDEAHALLIDS-RGALILDLAVRKAglknaqviLLSAT 146
uvsW PHA02558
UvsW helicase; Provisional
 171-425 8.45e-04

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 42.30  E-value: 8.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 171 RPYQEKSLRKMFGNGRarsGVIVLPCGAGKSLVgvtAACTVR-------KRCLVLGNSAVSVEQWKAQFKMWSTIDDS-- 241
Cdd:PHA02558 116 HWYQYDAVYEGLKNNR---RLLNLPTSAGKSLI---QYLLSRyylenyeGKVLIIVPTTSLVTQMIDDFVDYRLFPREam 189

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 242 -QICRFTSDAKDKPIgcsvAISTYSMLGHTTKrsweaervmEWLktQEWGLMILDEVHTIPAKMFRRVLTIVqAHC--KL 318
Cdd:PHA02558 190 hKIYSGTAKDTDAPI----VVSTWQSAVKQPK---------EWF--DQFGMVIVDECHLFTGKSLTSIITKL-DNCkfKF 253

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 319 GLTATLVREDDKIVDLNFLIGP--KLYEANwmELQNNGYIAKVQCAEVWCPMSPEFyreyvaiktkkRILLytmnpnKFR 396
Cdd:PHA02558 254 GLTGSLRDGKANILQYVGLFGDifKPVTTS--QLMEEGQVTDLKINSIFLRYPDED-----------RVKL------KGE 314

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 767917183 397 ACQFLIKF---HERRNDKIIVFA-------DNVFALKEY 425
Cdd:PHA02558 315 DYQEEIKYitsHTKRNKWIANLAlklakkgENTFVMFKY 353
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 410-514 1.14e-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: 1.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 410 DKIIVFADNVFALKEYAirlnkpyiygptsqgERMQILqnfkhnpkINTifisKVGDTSFDLPEANVLIQISSHGgSRRQ 489
Cdd:cd18785    4 VKIIVFTNSIEHAEEIA---------------SSLEIL--------VAT----NVLGEGIDVPSLDTVIFFDPPS-SAAS 55

                         90       100
                 ....*....|....*....|....*
gi 767917183 490 EAQRLGRVLRAKKgmvaEEYNAFFY 514
Cdd:cd18785   56 YIQRVGRAGRGGK----DEGEVILF 76
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
406-592 2.45e-03

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 40.87  E-value: 2.45e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 406 ERRNDKIIVFA---DNVFALKEYairLNKPYI-----------YGPT--SQGERMQILQNFKhNPKINTIFISKVGDTSF 469
Cdd:COG1111  350 TNPDSRIIVFTqyrDTAEMIVEF---LSEPGIkagrfvgqaskEGDKglTQKEQIEILERFR-AGEFNVLVATSVAEEGL 425

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183 470 DLPEANVLI-------QISShggsrrqeAQRLGRVLRAKKGMVaeeynaffYSLVSQDTQEMAY---STKRQRFLVDQGY 539
Cdd:COG1111  426 DIPEVDLVIfyepvpsEIRS--------IQRKGRTGRKREGRV--------VVLIAKGTRDEAYywsSRRKEKKMKSILK 489

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 767917183 540 sfkvitKLAGMEEEDLAFSTKEEQQQLLQKVLAATDLDAEEEVVAGEFGSRSS 592
Cdd:COG1111  490 ------KLKKLLDKQEKEKLKESAQATLDEFESIKELAEDEINEKDLDEIESS 536
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 293-324 3.40e-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: 3.40e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 767917183 293 ILDEVHTIPAKMFRRVLTIVQAHCKLG-----LTATL 324
Cdd:COG1203  273 ILDEVQAYPPYMLALLLRLLEWLKNLGgsvilMTATL 309
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 171-327 9.76e-03

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: 37.22  E-value: 9.76e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  171 RPYQEKSLRKMFGNgraRSGVIVLPCGAGKSLVGVTAACTV------RKRCLVLGNSAVSVEQWKAQFKMWSTIDDSQIC 244
Cdd:pfam00270   1 TPIQAEAIPAILEG---RDVLVQAPTGSGKTLAFLLPALEAldkldnGPQALVLAPTRELAEQIYEELKKLGKGLGLKVA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767917183  245 RFTSDAKDKPI-----GCSVAISTYSMLGHTTKRSWEAERVmewlktqewGLMILDEVHTIPAKMFR----RVLTIVQAH 315
Cdd:pfam00270  78 SLLGGDSRKEQleklkGPDILVGTPGRLLDLLQERKLLKNL---------KLLVLDEAHRLLDMGFGpdleEILRRLPKK 148

                         170
                  ....*....|...
gi 767917183  316 CK-LGLTATLVRE 327
Cdd:pfam00270 149 RQiLLLSATLPRN 161
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH