|
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 2462571127 1 MQFIKLCTVSYGKVKLVLKHNRYFVESCHPDVIQHLLQDPVIRECRLRNSEGEatELITETFTSKSAHlplsqISKTAES 80
Cdd:TIGR00603 94 IEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKDPVIAPCRIDPTEEE--SLQTPTYGSKEDF-----IINKPGF 166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 81 SGGPSTSRVTDPQGKSDIPMDLFDFYEQMDKDEEEEEETQTVSFEVKQEMIEELQKRCIHLEYPLLAEYDFRNDSVNPDI 160
Cdd:TIGR00603 167 TGGASAGQLEANQGESAVPKDIADFYELEEEEEDEDEETATHSFEIDQEQVEEVKKRCIELDYPLLEEYDFRNDTVNPDL 246
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 161 NIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDD 240
Cdd:TIGR00603 247 NIDLKPTTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTSAVSVEQWKQQFKMWSTIDD 326
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 241 SQICRFTSDAKDKPIG-CSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLG 319
Cdd:TIGR00603 327 SQICRFTSDAKERFHGeAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAAMFRRVLTIVQAHCKLG 406
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 320 LTATLVREDDKIVDLNFLIGPKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNKFRACQ 399
Cdd:TIGR00603 407 LTATLVREDDKITDLNFLIGPKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKRMLLYVMNPNKFRACQ 486
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 400 FLIKFHERRNDKIIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSFDLPEANVLIQ 479
Cdd:TIGR00603 487 FLIRFHEQRGDKIIVFSDNVFALKEYAIKLGKPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTSIDLPEANVLIQ 566
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 480 ISSHGGSRRQEAQRLGRVLRAKKGMVAEEYNAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEE-DLAFS 558
Cdd:TIGR00603 567 ISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMYYSTKRQRFLVDQGYSFKVITHLPGMDNEsNLAYS 646
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 559 TKEEQQQLLQKVLAATDLDAEEEVVAGEFGSR-----------SSQASRRFGTMSSMSGADDTVYMEYHSSRSKAPSKHV 627
Cdd:TIGR00603 647 SKEEQLELLQKVLLAGDLDAELEVLEGEFGSRalgasrsmssaSGKAVRRGGSLSSLSGGDDMAYMEYRKPAIKKSKKEV 726
|
....*.
gi 2462571127 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 2462571127 350 LQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNKFRACQFLIKFHERRNDKIIVFADNVFALKEYAIRL 429
Cdd:pfam16203 1 LQEKGHIANVQCAEVWCPMTAEFYREYLRSKSRKKRLLYVMNPNKFRACQFLIRYHERRGDKIIVFSDNVFALKEYAKKL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 430 NKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEY 509
Cdd:pfam16203 81 NKPYIYGGTSQAERMRILQNFKHNPNVNTIFLSKVGDTSIDLPEANVLIQISSHFGSRRQEAQRLGRILRAKRRSNDEGF 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 510 NAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEE-EDLAFSTKEEQQQLLQKVLAATDLDAEEEVVAGEFG 588
Cdd:pfam16203 161 NAFFYSLVSKDTQEMYYSTKRQQFLVDQGYAFKVITNLAGMEDeENLAYSTKEEQLELLQKVLAANDTDAEEEVIADDLG 240
|
....*...
gi 2462571127 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 2462571127 162 IDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDS 241
Cdd:cd18029 1 IDLKPSTQLRPYQEKALSKMFGNGRARSGVIVLPCGAGKTLVGITAACTIKKSTLVLCTSAVSVEQWRRQFLDWTTIDDE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 242 QICRFTSDAKDKPIGCSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLT 321
Cdd:cd18029 81 QIGRFTSDKKEIFPEAGVTVSTYSMLANTRKRSPESEKFMEFITEREWGLIILDEVHVVPAPMFRRVLTLQKAHCKLGLT 160
|
....*....
gi 2462571127 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 2462571127 170 LRPYQEKSLRKMFGNGRA--RSGVIVLPCGAGKSLVGVTAACTVR--KRCLVLGNSAVSVEQWKAQFKMWSTIDDSqicr 245
Cdd:COG1061 81 LRPYQQEALEALLAALERggGRGLVVAPTGTGKTVLALALAAELLrgKRVLVLVPRRELLEQWAEELRRFLGDPLA---- 156
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 246 ftsDAKDKPIGCSVAISTYSMLGHttkrsweaeRVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLV 325
Cdd:COG1061 157 ---GGGKKDSDAPITVATYQSLAR---------RAHLDELGDRFGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPF 224
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 326 REDDKIVDLNFLIGpKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFyREYVAIKTKKRILLYTMNPNKFRACQFLIKFH 405
Cdd:COG1061 225 RSDGREILLFLFDG-IVYEYSLKEAIEDGYLAPPEYYGIRVDLTDER-AEYDALSERLREALAADAERKDKILRELLREH 302
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 406 eRRNDKIIVFADNVFALKEYAIRLNK-----PYIYGPTSQGERMQILQNFKHNpKINTIFISKVGDTSFDLPEANVLIQI 480
Cdd:COG1061 303 -PDDRKTLVFCSSVDHAEALAELLNEagiraAVVTGDTPKKEREEILEAFRDG-ELRILVTVDVLNEGVDVPRLDVAILL 380
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 481 SSHgGSRRQEAQRLGRVLRAKKGmvaEEYnAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEEDLAFSTK 560
Cdd:COG1061 381 RPT-GSPREFIQRLGRGLRPAPG---KED-ALVYDFVGNDVPVLEELAKDLRDLAGYRVEFLDEEESEELALLIAVKPAL 455
|
410 420
....*....|....*....|.
gi 2462571127 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 2462571127 162 IDLKPTAVLRPYQEKSLRKMFGNGRarSGVIVLPCGAGKSLVGVTAA-----CTVRKRCLVLGNSAVSVEQWKAQFKMWS 236
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGLR--DVILAAPTGSGKTLAALLPAlealkRGKGGRVLVLVPTRELAEQWAEELKKLG 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 237 T-IDDSQICRFTSDAKDKPI------GCSVAISTYSMLGHTTKRsweaervmEWLKTQEWGLMILDEVHTIPAKMFRRVL 309
Cdd:smart00487 79 PsLGLKVVGLYGGDSKREQLrklesgKTDILVTTPGRLLDLLEN--------DKLSLSNVDLVILDEAHRLLDGGFGDQL 150
|
170 180 190
....*....|....*....|....*....|..
gi 2462571127 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 2462571127 171 RPYQEKSLRKMFGNGRarsGVIVLPCGAGKSLVgvtAACTVR-------KRCLVLGNSAVSVEQWKAQFKMWSTIDDS-- 241
Cdd:PHA02558 116 HWYQYDAVYEGLKNNR---RLLNLPTSAGKSLI---QYLLSRyylenyeGKVLIIVPTTSLVTQMIDDFVDYRLFPREam 189
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 242 -QICRFTSDAKDKPIgcsvAISTYSMLGHTTKrsweaervmEWLktQEWGLMILDEVHTIPAKMFRRVLTIVqAHC--KL 318
Cdd:PHA02558 190 hKIYSGTAKDTDAPI----VVSTWQSAVKQPK---------EWF--DQFGMVIVDECHLFTGKSLTSIITKL-DNCkfKF 253
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 319 GLTATLVREDDKIVDLNFLIGP--KLYEANwmELQNNGYIAKVQCAEVWCPMSPEFyreyvaiktkkRILLytmnpnKFR 396
Cdd:PHA02558 254 GLTGSLRDGKANILQYVGLFGDifKPVTTS--QLMEEGQVTDLKINSIFLRYPDED-----------RVKL------KGE 314
|
250 260 270
....*....|....*....|....*....|....*....
gi 2462571127 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 2462571127 1 MQFIKLCTVSYGKVKLVLKHNRYFVESCHPDVIQHLLQDPVIRECRLRNSEGEatELITETFTSKSAHlplsqISKTAES 80
Cdd:TIGR00603 94 IEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKDPVIAPCRIDPTEEE--SLQTPTYGSKEDF-----IINKPGF 166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 81 SGGPSTSRVTDPQGKSDIPMDLFDFYEQMDKDEEEEEETQTVSFEVKQEMIEELQKRCIHLEYPLLAEYDFRNDSVNPDI 160
Cdd:TIGR00603 167 TGGASAGQLEANQGESAVPKDIADFYELEEEEEDEDEETATHSFEIDQEQVEEVKKRCIELDYPLLEEYDFRNDTVNPDL 246
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 161 NIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDD 240
Cdd:TIGR00603 247 NIDLKPTTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTSAVSVEQWKQQFKMWSTIDD 326
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 241 SQICRFTSDAKDKPIG-CSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLG 319
Cdd:TIGR00603 327 SQICRFTSDAKERFHGeAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAAMFRRVLTIVQAHCKLG 406
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 320 LTATLVREDDKIVDLNFLIGPKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNKFRACQ 399
Cdd:TIGR00603 407 LTATLVREDDKITDLNFLIGPKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKRMLLYVMNPNKFRACQ 486
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 400 FLIKFHERRNDKIIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSFDLPEANVLIQ 479
Cdd:TIGR00603 487 FLIRFHEQRGDKIIVFSDNVFALKEYAIKLGKPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTSIDLPEANVLIQ 566
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 480 ISSHGGSRRQEAQRLGRVLRAKKGMVAEEYNAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEE-DLAFS 558
Cdd:TIGR00603 567 ISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMYYSTKRQRFLVDQGYSFKVITHLPGMDNEsNLAYS 646
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 559 TKEEQQQLLQKVLAATDLDAEEEVVAGEFGSR-----------SSQASRRFGTMSSMSGADDTVYMEYHSSRSKAPSKHV 627
Cdd:TIGR00603 647 SKEEQLELLQKVLLAGDLDAELEVLEGEFGSRalgasrsmssaSGKAVRRGGSLSSLSGGDDMAYMEYRKPAIKKSKKEV 726
|
....*.
gi 2462571127 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 2462571127 350 LQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNKFRACQFLIKFHERRNDKIIVFADNVFALKEYAIRL 429
Cdd:pfam16203 1 LQEKGHIANVQCAEVWCPMTAEFYREYLRSKSRKKRLLYVMNPNKFRACQFLIRYHERRGDKIIVFSDNVFALKEYAKKL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 430 NKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEY 509
Cdd:pfam16203 81 NKPYIYGGTSQAERMRILQNFKHNPNVNTIFLSKVGDTSIDLPEANVLIQISSHFGSRRQEAQRLGRILRAKRRSNDEGF 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 510 NAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEE-EDLAFSTKEEQQQLLQKVLAATDLDAEEEVVAGEFG 588
Cdd:pfam16203 161 NAFFYSLVSKDTQEMYYSTKRQQFLVDQGYAFKVITNLAGMEDeENLAYSTKEEQLELLQKVLAANDTDAEEEVIADDLG 240
|
....*...
gi 2462571127 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 2462571127 162 IDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDS 241
Cdd:cd18029 1 IDLKPSTQLRPYQEKALSKMFGNGRARSGVIVLPCGAGKTLVGITAACTIKKSTLVLCTSAVSVEQWRRQFLDWTTIDDE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 242 QICRFTSDAKDKPIGCSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLT 321
Cdd:cd18029 81 QIGRFTSDKKEIFPEAGVTVSTYSMLANTRKRSPESEKFMEFITEREWGLIILDEVHVVPAPMFRRVLTLQKAHCKLGLT 160
|
....*....
gi 2462571127 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 2462571127 361 CAEVWCPMSPEFYREY-VAIKTKKRILLYTMNPNKFRACQFLIKFHERrNDKIIVFADNVFALKEYAIRLNKPYIYGPTS 439
Cdd:cd18789 1 CAEIRCPMTPEFYREYlGLGAHRKRRLLAAMNPNKLRALEELLKRHEQ-GDKIIVFTDNVEALYRYAKRLLKPFITGETP 79
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462571127 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 2462571127 170 LRPYQEKSLRKMFGNGRA--RSGVIVLPCGAGKSLVGVTAACTVR--KRCLVLGNSAVSVEQWKAQFKMWSTIDDSqicr 245
Cdd:COG1061 81 LRPYQQEALEALLAALERggGRGLVVAPTGTGKTVLALALAAELLrgKRVLVLVPRRELLEQWAEELRRFLGDPLA---- 156
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 246 ftsDAKDKPIGCSVAISTYSMLGHttkrsweaeRVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLV 325
Cdd:COG1061 157 ---GGGKKDSDAPITVATYQSLAR---------RAHLDELGDRFGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPF 224
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 326 REDDKIVDLNFLIGpKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFyREYVAIKTKKRILLYTMNPNKFRACQFLIKFH 405
Cdd:COG1061 225 RSDGREILLFLFDG-IVYEYSLKEAIEDGYLAPPEYYGIRVDLTDER-AEYDALSERLREALAADAERKDKILRELLREH 302
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 406 eRRNDKIIVFADNVFALKEYAIRLNK-----PYIYGPTSQGERMQILQNFKHNpKINTIFISKVGDTSFDLPEANVLIQI 480
Cdd:COG1061 303 -PDDRKTLVFCSSVDHAEALAELLNEagiraAVVTGDTPKKEREEILEAFRDG-ELRILVTVDVLNEGVDVPRLDVAILL 380
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 481 SSHgGSRRQEAQRLGRVLRAKKGmvaEEYnAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEEDLAFSTK 560
Cdd:COG1061 381 RPT-GSPREFIQRLGRGLRPAPG---KED-ALVYDFVGNDVPVLEELAKDLRDLAGYRVEFLDEEESEELALLIAVKPAL 455
|
410 420
....*....|....*....|.
gi 2462571127 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 2462571127 170 LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRK-RCLVLGNSAVSVEQWKAQFKMWSTidDSQICRFTS 248
Cdd:cd17926 1 LRPYQEEALEAWLAHKNNRRGILVLPTGSGKTLTALALIAYLKElRTLIVVPTDALLDQWKERFEDFLG--DSSIGLIGG 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462571127 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 2462571127 162 IDLKPTAVLRPYQEKSLRKMFGNGRarSGVIVLPCGAGKSLVGVTAA-----CTVRKRCLVLGNSAVSVEQWKAQFKMWS 236
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGLR--DVILAAPTGSGKTLAALLPAlealkRGKGGRVLVLVPTRELAEQWAEELKKLG 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 237 T-IDDSQICRFTSDAKDKPI------GCSVAISTYSMLGHTTKRsweaervmEWLKTQEWGLMILDEVHTIPAKMFRRVL 309
Cdd:smart00487 79 PsLGLKVVGLYGGDSKREQLrklesgKTDILVTTPGRLLDLLEN--------DKLSLSNVDLVILDEAHRLLDGGFGDQL 150
|
170 180 190
....*....|....*....|....*....|..
gi 2462571127 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 2462571127 169 VLRPYQE---KSLRKMFGNGRARsGVIVLPCGAGKSLVGVTAACTVRK-----RCLVLGNSAVSVEQWKAQFKMWsTIDD 240
Cdd:pfam04851 3 ELRPYQIeaiENLLESIKNGQKR-GLIVMATGSGKTLTAAKLIARLFKkgpikKVLFLVPRKDLLEQALEEFKKF-LPNY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 241 SQICRFTSDAKDKPI--GCSVAISTYSMLGHttkrswEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKL 318
Cdd:pfam04851 81 VEIGEIISGDKKDESvdDNKIVVTTIQSLYK------ALELASLELLPDFFDVIIIDEAHRSGASSYRNILEYFKPAFLL 154
|
....*...
gi 2462571127 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 2462571127 170 LRPYQEKSLRKMFGNGRARSGVIVLPC-GAGKSLVGVTAACTVRK------RCLVLGNSAVsVEQWKAQFKMWS------ 236
Cdd:cd17919 1 LRPYQLEGLNFLLELYENGPGGILADEmGLGKTLQAIAFLAYLLKegkergPVLVVCPLSV-LENWEREFEKWTpdlrvv 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 237 TIDDSQICRFTSDAKDKPIGCSVAISTYSMLghttkrsweaERVMEWLKTQEWGLMILDEVHTI---PAKMFRRVLTIvQ 313
Cdd:cd17919 80 VYHGSQRERAQIRAKEKLDKFDVVLTTYETL----------RRDKASLRKFRWDLVVVDEAHRLknpKSQLSKALKAL-R 148
|
170
....*....|
gi 2462571127 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 2462571127 167 TAVLRPYQEKSLRKMFGNGRARSGVI----VlpcGAGKSLVGVTAACTVR-----KRCLVLGNSAVsVEQWKAQFKmwst 237
Cdd:COG0553 239 KATLRPYQLEGAAWLLFLRRLGLGGLladdM---GLGKTIQALALLLELKerglaRPVLIVAPTSL-VGNWQRELA---- 310
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 238 iddsqicRFTSD-------------AKDKPIG-CSVAISTYSMLGhttkrsweaeRVMEWLKTQEWGLMILDEVHTI--- 300
Cdd:COG0553 311 -------KFAPGlrvlvldgtreraKGANPFEdADLVITSYGLLR----------RDIELLAAVDWDLVILDEAQHIknp 373
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 301 PAKMFRRVLTIvQAHCKLGLTATLV--REDD-----KIVDLNFLIGPKLYEANWMELQNNGYIA---------------- 357
Cdd:COG0553 374 ATKRAKAVRAL-KARHRLALTGTPVenRLEElwsllDFLNPGLLGSLKAFRERFARPIEKGDEEalerlrrllrpfllrr 452
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 358 -KVQCAE---------VWCPMSPE---FYREYVA-----------IKTKKRIL--------------LYTMNPN------ 393
Cdd:COG0553 453 tKEDVLKdlpekteetLYVELTPEqraLYEAVLEylrrelegaegIRRRGLILaaltrlrqicshpaLLLEEGAelsgrs 532
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 394 -KFRACQFLIKFHERRNDKIIVFADnvFA---------LKEYAIRLnkPYIYGPTSQGERMQILQNFKHNPKINTIFIS- 462
Cdd:COG0553 533 aKLEALLELLEELLAEGEKVLVFSQ--FTdtldlleerLEERGIEY--AYLHGGTSAEERDELVDRFQEGPEAPVFLISl 608
|
410
....*....|....*.
gi 2462571127 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 2462571127 393 NKFRACQFLIKFHerRNDKIIVFADNVFALKEYAIRLNKPY----IYGPTSQGERMQILQNFKhNPKINTIFISKVGDTS 468
Cdd:pfam00271 1 EKLEALLELLKKE--RGGKVLIFSQTKKTLEAELLLEKEGIkvarLHGDLSQEEREEILEDFR-KGKIDVLVATDVAERG 77
|
90 100 110
....*....|....*....|....*....|...
gi 2462571127 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 2462571127 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 2462571127 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 2462571127 170 LRPYQEKSLRKM---FGNGRARSGViVLPCGAGKSlvgVTAACTVR--------KRCLVLGNSAVSVEQWKAQFkmWSTI 238
Cdd:cd18032 1 PRYYQQEAIEALeeaREKGQRRALL-VMATGTGKT---YTAAFLIKrlleanrkKRILFLAHREELLEQAERSF--KEVL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 239 DDSQICRFTSDaKDKPIGCSVAISTYSmlghttkrSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLtivqAHCK- 317
Cdd:cd18032 75 PDGSFGNLKGG-KKKPDDARVVFATVQ--------TLNKRKRLEKFPPDYFDLIIIDEAHHAIASSYRKIL----EYFEp 141
|
170
....*....|....*.
gi 2462571127 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 2462571127 208 ACTVRKRCLVLGNSAVsVEQWKAQFKMWSTIDDSQicrFTSDAKD-------KPIGCSVAISTYSMLghttkrsweaERV 280
Cdd:cd18005 66 ASSAKKPVLIVAPLSV-LYNWKDELDTWGHFEVGV---YHGSRKDdelegrlKAGRLEVVVTTYDTL----------RRC 131
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|
gi 2462571127 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 2462571127 394 KFRACQFLIKFHERRNDKIIVFA---DNVFALKEYAIRLNKPY--IYGPTSQGERMQILQNFKHNPKINTIFIS-KVGDT 467
Cdd:cd18793 12 KLEALLELLEELREPGEKVLIFSqftDTLDILEEALRERGIKYlrLDGSTSSKERQKLVDRFNEDPDIRVFLLStKAGGV 91
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 2462571127 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 2462571127 172 PYQEKSLRKMFGNGRarSGVIVLPCGAGKSLVGVTAA----CTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDSQICRFT 247
Cdd:cd17921 4 PIQREALRALYLSGD--SVLVSAPTSSGKTLIAELAIlralATSGGKAVYIAPTRALVNQKEADLRERFGPLGKNVGLLT 81
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*.
gi 2462571127 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 2462571127 190 GVIVLPCGAGKSLVGVTAA-----CTVRKRCLVLGNSAVsVEQWKAQFKMWSTID--------DSQIC-RFTSDAKDKPI 255
Cdd:cd00046 4 VLITAPTGSGKTLAALLAAlllllKKGKKVLVLVPTKAL-ALQTAERLRELFGPGirvavlvgGSSAEeREKNKLGDADI 82
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462571127 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 2462571127 171 RPYQEKSLRKMFGNGRarsGVIVLPCGAGKSLVgvtAACTVR-------KRCLVLGNSAVSVEQWKAQFKMWSTIDDS-- 241
Cdd:PHA02558 116 HWYQYDAVYEGLKNNR---RLLNLPTSAGKSLI---QYLLSRyylenyeGKVLIIVPTTSLVTQMIDDFVDYRLFPREam 189
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 242 -QICRFTSDAKDKPIgcsvAISTYSMLGHTTKrsweaervmEWLktQEWGLMILDEVHTIPAKMFRRVLTIVqAHC--KL 318
Cdd:PHA02558 190 hKIYSGTAKDTDAPI----VVSTWQSAVKQPK---------EWF--DQFGMVIVDECHLFTGKSLTSIITKL-DNCkfKF 253
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 319 GLTATLVREDDKIVDLNFLIGP--KLYEANwmELQNNGYIAKVQCAEVWCPMSPEFyreyvaiktkkRILLytmnpnKFR 396
Cdd:PHA02558 254 GLTGSLRDGKANILQYVGLFGDifKPVTTS--QLMEEGQVTDLKINSIFLRYPDED-----------RVKL------KGE 314
|
250 260 270
....*....|....*....|....*....|....*....
gi 2462571127 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 2462571127 410 DKIIVFADNVFALKEYAirlnkpyiygptsqgERMQILqnfkhnpkINTifisKVGDTSFDLPEANVLIQISSHGgSRRQ 489
Cdd:cd18785 4 VKIIVFTNSIEHAEEIA---------------SSLEIL--------VAT----NVLGEGIDVPSLDTVIFFDPPS-SAAS 55
|
90 100
....*....|....*....|....*
gi 2462571127 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 2462571127 406 ERRNDKIIVFA---DNVFALKEYairLNKPYI-----------YGPT--SQGERMQILQNFKhNPKINTIFISKVGDTSF 469
Cdd:COG1111 350 TNPDSRIIVFTqyrDTAEMIVEF---LSEPGIkagrfvgqaskEGDKglTQKEQIEILERFR-AGEFNVLVATSVAEEGL 425
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 470 DLPEANVLI-------QISShggsrrqeAQRLGRVLRAKKGMVaeeynaffYSLVSQDTQEMAY---STKRQRFLVDQGY 539
Cdd:COG1111 426 DIPEVDLVIfyepvpsEIRS--------IQRKGRTGRKREGRV--------VVLIAKGTRDEAYywsSRRKEKKMKSILK 489
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 2462571127 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 2462571127 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 2462571127 171 RPYQEKSLRKMFGNgraRSGVIVLPCGAGKSLVGVTAACTV------RKRCLVLGNSAVSVEQWKAQFKMWSTIDDSQIC 244
Cdd:pfam00270 1 TPIQAEAIPAILEG---RDVLVQAPTGSGKTLAFLLPALEAldkldnGPQALVLAPTRELAEQIYEELKKLGKGLGLKVA 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462571127 245 RFTSDAKDKPI-----GCSVAISTYSMLGHTTKRSWEAERVmewlktqewGLMILDEVHTIPAKMFR----RVLTIVQAH 315
Cdd:pfam00270 78 SLLGGDSRKEQleklkGPDILVGTPGRLLDLLQERKLLKNL---------KLLVLDEAHRLLDMGFGpdleEILRRLPKK 148
|
170
....*....|...
gi 2462571127 316 CK-LGLTATLVRE 327
Cdd:pfam00270 149 RQiLLLSATLPRN 161
|
|
| |
