|
Name |
Accession |
Description |
Interval |
E-value |
| rad25 |
TIGR00603 |
DNA repair helicase rad25; All proteins in this family for which functions are known are ... |
70-795 |
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: 1354.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 70 DYRSQMQLRPDHGNRPLWVAPNGHVFLESFSPVYKHAHDFLIAISEPVCRPEHIHEYKLTAYSLYAAVSVGLQTHDIVEY 149
Cdd:TIGR00603 1 DYSKQLELKPDHGSRPLWVAPDGHIFLESFSPLYKQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 150 LKRLSKTSIPEGILEFIRLCTLSYGKVKLVLKHNKYFIESPHPEVLQKLLKDPVIQKCRLIRSEGEdfiqgtldgKAITQ 229
Cdd:TIGR00603 81 LGRLSKTPIPKGIIEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKDPVIAPCRIDPTEEE---------SLQTP 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 230 FGTKLPPGATDKPTPD----PAAAAGADGTTAVPEDITDFYEKIDKEEEDEDeaNLKTVSFEVAQEKIEVIQKRCIEIEH 305
Cdd:TIGR00603 152 TYGSKEDFIINKPGFTggasAGQLEANQGESAVPKDIADFYELEEEEEDEDE--ETATHSFEIDQEQVEEVKKRCIELDY 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 306 PLLAEYDFRNDTNNPDINIDLKPAAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGV 385
Cdd:TIGR00603 230 PLLEEYDFRNDTVNPDLNIDLKPTTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTSAV 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 386 SVEQWKQQFKMWSTADDSMICRFTSEAKDKPMG-CGILVTTYSMITHTQKRSWEAEQTMRWLQEQEWGIMVLDEVHTIPA 464
Cdd:TIGR00603 310 SVEQWKQQFKMWSTIDDSQICRFTSDAKERFHGeAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPA 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 465 KMFRRVLTIVQSHCKLGLTATLLREDDKIADLNFLIGPKLYEANWLELQKKGYIARVQCAEVWCPMSPEFYREYLTTKTS 544
Cdd:TIGR00603 390 AMFRRVLTIVQAHCKLGLTATLVREDDKITDLNFLIGPKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSR 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 545 KKMLLYVMNPSKFRSCQFLIKYHEQRGDKTIVFSDNVFALKHYAIKMNKPFIYGPTSQNERIQILQNFKFNSKVNTIFVS 624
Cdd:TIGR00603 470 KRMLLYVMNPNKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLGKPFIYGPTSQQERMQILQNFQHNPKVNTIFLS 549
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 625 KVADTSFDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKGAIAEEYNAFFYTLVSQDTMEMSYSRKRQRFLVNQGYSYK 704
Cdd:TIGR00603 550 KVGDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMYYSTKRQRFLVDQGYSFK 629
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 705 VITHLKGMDTDSDLMYGTQEEQGQLLQLVLSASDLDCEDEKLPGEPGYRPSG--------SGGAVRRVGGLSSMSGGDDA 776
Cdd:TIGR00603 630 VITHLPGMDNESNLAYSSKEEQLELLQKVLLAGDLDAELEVLEGEFGSRALGasrsmssaSGKAVRRGGSLSSLSGGDDM 709
|
730 740
....*....|....*....|...
gi 24662247 777 IYYEHRKKNIGS----VHPLFKK 795
Cdd:TIGR00603 710 AYMEYRKPAIKKskkeVHPLFKK 732
|
|
| ERCC3_RAD25_C |
pfam16203 |
ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 ... |
512-757 |
7.04e-178 |
|
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: 509.83 E-value: 7.04e-178
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 512 LQKKGYIARVQCAEVWCPMSPEFYREYLTTKTSKKMLLYVMNPSKFRSCQFLIKYHEQRGDKTIVFSDNVFALKHYAIKM 591
Cdd:pfam16203 1 LQEKGHIANVQCAEVWCPMTAEFYREYLRSKSRKKRLLYVMNPNKFRACQFLIRYHERRGDKIIVFSDNVFALKEYAKKL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 592 NKPFIYGPTSQNERIQILQNFKFNSKVNTIFVSKVADTSFDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKGAIAEEY 671
Cdd:pfam16203 81 NKPYIYGGTSQAERMRILQNFKHNPNVNTIFLSKVGDTSIDLPEANVLIQISSHFGSRRQEAQRLGRILRAKRRSNDEGF 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 672 NAFFYTLVSQDTMEMSYSRKRQRFLVNQGYSYKVITHLKGMDTDSDLMYGTQEEQGQLLQLVLSASDLDCEDEKLPGEPG 751
Cdd:pfam16203 161 NAFFYSLVSKDTQEMYYSTKRQQFLVDQGYAFKVITNLAGMEDEENLAYSTKEEQLELLQKVLAANDTDAEEEVIADDLG 240
|
....*.
gi 24662247 752 YRPSGS 757
Cdd:pfam16203 241 KDRKGG 246
|
|
| DEXHc_XPB |
cd18029 |
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ... |
324-492 |
1.29e-109 |
|
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription factor complex helicase XPB subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350787 [Multi-domain] Cd Length: 169 Bit Score: 331.57 E-value: 1.29e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 324 IDLKPAAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVSVEQWKQQFKMWSTADDS 403
Cdd:cd18029 1 IDLKPSTQLRPYQEKALSKMFGNGRARSGVIVLPCGAGKTLVGITAACTIKKSTLVLCTSAVSVEQWRRQFLDWTTIDDE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 404 MICRFTSEAKDKPMGCGILVTTYSMITHTQKRSWEAEQTMRWLQEQEWGIMVLDEVHTIPAKMFRRVLTIVQSHCKLGLT 483
Cdd:cd18029 81 QIGRFTSDKKEIFPEAGVTVSTYSMLANTRKRSPESEKFMEFITEREWGLIILDEVHVVPAPMFRRVLTLQKAHCKLGLT 160
|
....*....
gi 24662247 484 ATLLREDDK 492
Cdd:cd18029 161 ATLVREDDK 169
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
332-705 |
1.70e-58 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 209.11 E-value: 1.70e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 332 LRPYQEKSLRKMFGNGRA--RSGVIVLPCGAGKSLVGVTACCTVR--KRALVLCNSGVSVEQWKQQFKMWSTaddsmicR 407
Cdd:COG1061 81 LRPYQQEALEALLAALERggGRGLVVAPTGTGKTVLALALAAELLrgKRVLVLVPRRELLEQWAEELRRFLG-------D 153
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 408 FTSEAKDKPMGCGILVTTYSMITHtqkrsweaEQTMRWLQEqEWGIMVLDEVHTIPAKMFRRVLTIVQSHCKLGLTATLL 487
Cdd:COG1061 154 PLAGGGKKDSDAPITVATYQSLAR--------RAHLDELGD-RFGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPF 224
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 488 REDDKIADLNFLIGpKLYEANWLELQKKGYIARVQCAEVWCPMSPEFyREYlttKTSKKMLLYVMNPSKFRSCQFLIKYH 567
Cdd:COG1061 225 RSDGREILLFLFDG-IVYEYSLKEAIEDGYLAPPEYYGIRVDLTDER-AEY---DALSERLREALAADAERKDKILRELL 299
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 568 EQRGD--KTIVFSDNVFALKHYA-----IKMNKPFIYGPTSQNERIQILQNFKfNSKVNTIFVSKVADTSFDLPEANVLI 640
Cdd:COG1061 300 REHPDdrKTLVFCSSVDHAEALAellneAGIRAAVVTGDTPKKEREEILEAFR-DGELRILVTVDVLNEGVDVPRLDVAI 378
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24662247 641 QISSHgGSRRQEAQRLGRILRAKKGaiaEEYnAFFYTLVSQDTMEMSYSRKRQRFLVnqGYSYKV 705
Cdd:COG1061 379 LLRPT-GSPREFIQRLGRGLRPAPG---KED-ALVYDFVGNDVPVLEELAKDLRDLA--GYRVEF 436
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
324-498 |
1.30e-18 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 84.85 E-value: 1.30e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 324 IDLKPAAVLRPYQEKSLRKMFGNGRarSGVIVLPCGAGKSLVGVTAC-----CTVRKRALVLCNSGVSVEQWKQQFKMWS 398
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGLR--DVILAAPTGSGKTLAALLPAlealkRGKGGRVLVLVPTRELAEQWAEELKKLG 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 399 TADDSM-ICRFTSEAKDKPM------GCGILVTTYSMITHtqkrsweaEQTMRWLQEQEWGIMVLDEVHTIPAKMFRRVL 471
Cdd:smart00487 79 PSLGLKvVGLYGGDSKREQLrklesgKTDILVTTPGRLLD--------LLENDKLSLSNVDLVILDEAHRLLDGGFGDQL 150
|
170 180 190
....*....|....*....|....*....|..
gi 24662247 472 TIVQSHCK-----LGLTATLLREDDKIADLNF 498
Cdd:smart00487 151 EKLLKLLPknvqlLLLSATPPEEIENLLELFL 182
|
|
| uvsW |
PHA02558 |
UvsW helicase; Provisional |
333-570 |
7.68e-03 |
|
UvsW helicase; Provisional
Pssm-ID: 222875 [Multi-domain] Cd Length: 501 Bit Score: 39.61 E-value: 7.68e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 333 RPYQEKSLRKMFGNGRarsGVIVLPCGAGKSLVgvtACCTVR-------KRALVLCNSGVSVEQWKQQFKMWSTADDS-- 403
Cdd:PHA02558 116 HWYQYDAVYEGLKNNR---RLLNLPTSAGKSLI---QYLLSRyylenyeGKVLIIVPTTSLVTQMIDDFVDYRLFPREam 189
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 404 -MICRFTSEAKDKPmgcgILVTTYSMItHTQKRSWeaeqtmrwlqEQEWGIMVLDEVHTIPAKMFRRVLTIVqSHC--KL 480
Cdd:PHA02558 190 hKIYSGTAKDTDAP----IVVSTWQSA-VKQPKEW----------FDQFGMVIVDECHLFTGKSLTSIITKL-DNCkfKF 253
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 481 GLTATLlrEDDKIADLNF--LIGP--KLYEANwlELQKKGYIARVQCAEVWCPMSPEFyreylttktSKKMllyvmnpsK 556
Cdd:PHA02558 254 GLTGSL--RDGKANILQYvgLFGDifKPVTTS--QLMEEGQVTDLKINSIFLRYPDED---------RVKL--------K 312
|
250
....*....|....*..
gi 24662247 557 FRSCQFLIKY---HEQR 570
Cdd:PHA02558 313 GEDYQEEIKYitsHTKR 329
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rad25 |
TIGR00603 |
DNA repair helicase rad25; All proteins in this family for which functions are known are ... |
70-795 |
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: 1354.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 70 DYRSQMQLRPDHGNRPLWVAPNGHVFLESFSPVYKHAHDFLIAISEPVCRPEHIHEYKLTAYSLYAAVSVGLQTHDIVEY 149
Cdd:TIGR00603 1 DYSKQLELKPDHGSRPLWVAPDGHIFLESFSPLYKQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 150 LKRLSKTSIPEGILEFIRLCTLSYGKVKLVLKHNKYFIESPHPEVLQKLLKDPVIQKCRLIRSEGEdfiqgtldgKAITQ 229
Cdd:TIGR00603 81 LGRLSKTPIPKGIIEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKDPVIAPCRIDPTEEE---------SLQTP 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 230 FGTKLPPGATDKPTPD----PAAAAGADGTTAVPEDITDFYEKIDKEEEDEDeaNLKTVSFEVAQEKIEVIQKRCIEIEH 305
Cdd:TIGR00603 152 TYGSKEDFIINKPGFTggasAGQLEANQGESAVPKDIADFYELEEEEEDEDE--ETATHSFEIDQEQVEEVKKRCIELDY 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 306 PLLAEYDFRNDTNNPDINIDLKPAAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGV 385
Cdd:TIGR00603 230 PLLEEYDFRNDTVNPDLNIDLKPTTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTSAV 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 386 SVEQWKQQFKMWSTADDSMICRFTSEAKDKPMG-CGILVTTYSMITHTQKRSWEAEQTMRWLQEQEWGIMVLDEVHTIPA 464
Cdd:TIGR00603 310 SVEQWKQQFKMWSTIDDSQICRFTSDAKERFHGeAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPA 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 465 KMFRRVLTIVQSHCKLGLTATLLREDDKIADLNFLIGPKLYEANWLELQKKGYIARVQCAEVWCPMSPEFYREYLTTKTS 544
Cdd:TIGR00603 390 AMFRRVLTIVQAHCKLGLTATLVREDDKITDLNFLIGPKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSR 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 545 KKMLLYVMNPSKFRSCQFLIKYHEQRGDKTIVFSDNVFALKHYAIKMNKPFIYGPTSQNERIQILQNFKFNSKVNTIFVS 624
Cdd:TIGR00603 470 KRMLLYVMNPNKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLGKPFIYGPTSQQERMQILQNFQHNPKVNTIFLS 549
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 625 KVADTSFDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKGAIAEEYNAFFYTLVSQDTMEMSYSRKRQRFLVNQGYSYK 704
Cdd:TIGR00603 550 KVGDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMYYSTKRQRFLVDQGYSFK 629
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 705 VITHLKGMDTDSDLMYGTQEEQGQLLQLVLSASDLDCEDEKLPGEPGYRPSG--------SGGAVRRVGGLSSMSGGDDA 776
Cdd:TIGR00603 630 VITHLPGMDNESNLAYSSKEEQLELLQKVLLAGDLDAELEVLEGEFGSRALGasrsmssaSGKAVRRGGSLSSLSGGDDM 709
|
730 740
....*....|....*....|...
gi 24662247 777 IYYEHRKKNIGS----VHPLFKK 795
Cdd:TIGR00603 710 AYMEYRKPAIKKskkeVHPLFKK 732
|
|
| ERCC3_RAD25_C |
pfam16203 |
ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 ... |
512-757 |
7.04e-178 |
|
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: 509.83 E-value: 7.04e-178
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 512 LQKKGYIARVQCAEVWCPMSPEFYREYLTTKTSKKMLLYVMNPSKFRSCQFLIKYHEQRGDKTIVFSDNVFALKHYAIKM 591
Cdd:pfam16203 1 LQEKGHIANVQCAEVWCPMTAEFYREYLRSKSRKKRLLYVMNPNKFRACQFLIRYHERRGDKIIVFSDNVFALKEYAKKL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 592 NKPFIYGPTSQNERIQILQNFKFNSKVNTIFVSKVADTSFDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKGAIAEEY 671
Cdd:pfam16203 81 NKPYIYGGTSQAERMRILQNFKHNPNVNTIFLSKVGDTSIDLPEANVLIQISSHFGSRRQEAQRLGRILRAKRRSNDEGF 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 672 NAFFYTLVSQDTMEMSYSRKRQRFLVNQGYSYKVITHLKGMDTDSDLMYGTQEEQGQLLQLVLSASDLDCEDEKLPGEPG 751
Cdd:pfam16203 161 NAFFYSLVSKDTQEMYYSTKRQQFLVDQGYAFKVITNLAGMEDEENLAYSTKEEQLELLQKVLAANDTDAEEEVIADDLG 240
|
....*.
gi 24662247 752 YRPSGS 757
Cdd:pfam16203 241 KDRKGG 246
|
|
| DEXHc_XPB |
cd18029 |
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ... |
324-492 |
1.29e-109 |
|
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription factor complex helicase XPB subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350787 [Multi-domain] Cd Length: 169 Bit Score: 331.57 E-value: 1.29e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 324 IDLKPAAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVSVEQWKQQFKMWSTADDS 403
Cdd:cd18029 1 IDLKPSTQLRPYQEKALSKMFGNGRARSGVIVLPCGAGKTLVGITAACTIKKSTLVLCTSAVSVEQWRRQFLDWTTIDDE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 404 MICRFTSEAKDKPMGCGILVTTYSMITHTQKRSWEAEQTMRWLQEQEWGIMVLDEVHTIPAKMFRRVLTIVQSHCKLGLT 483
Cdd:cd18029 81 QIGRFTSDKKEIFPEAGVTVSTYSMLANTRKRSPESEKFMEFITEREWGLIILDEVHVVPAPMFRRVLTLQKAHCKLGLT 160
|
....*....
gi 24662247 484 ATLLREDDK 492
Cdd:cd18029 161 ATLVREDDK 169
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
523-679 |
2.47e-87 |
|
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: 2.47e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 523 CAEVWCPMSPEFYREYLTTK-TSKKMLLYVMNPSKFRSCQFLIKYHEQrGDKTIVFSDNVFALKHYAIKMNKPFIYGPTS 601
Cdd:cd18789 1 CAEIRCPMTPEFYREYLGLGaHRKRRLLAAMNPNKLRALEELLKRHEQ-GDKIIVFTDNVEALYRYAKRLLKPFITGETP 79
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24662247 602 QNERIQILQNFKFNsKVNTIFVSKVADTSFDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKGAiaeEYNAFFYTLV 679
Cdd:cd18789 80 QSEREEILQNFREG-EYNTLVVSKVGDEGIDLPEANVAIQISGHGGSRRQEAQRLGRILRPKKGG---GKNAFFYSLV 153
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
332-705 |
1.70e-58 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 209.11 E-value: 1.70e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 332 LRPYQEKSLRKMFGNGRA--RSGVIVLPCGAGKSLVGVTACCTVR--KRALVLCNSGVSVEQWKQQFKMWSTaddsmicR 407
Cdd:COG1061 81 LRPYQQEALEALLAALERggGRGLVVAPTGTGKTVLALALAAELLrgKRVLVLVPRRELLEQWAEELRRFLG-------D 153
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 408 FTSEAKDKPMGCGILVTTYSMITHtqkrsweaEQTMRWLQEqEWGIMVLDEVHTIPAKMFRRVLTIVQSHCKLGLTATLL 487
Cdd:COG1061 154 PLAGGGKKDSDAPITVATYQSLAR--------RAHLDELGD-RFGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPF 224
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 488 REDDKIADLNFLIGpKLYEANWLELQKKGYIARVQCAEVWCPMSPEFyREYlttKTSKKMLLYVMNPSKFRSCQFLIKYH 567
Cdd:COG1061 225 RSDGREILLFLFDG-IVYEYSLKEAIEDGYLAPPEYYGIRVDLTDER-AEY---DALSERLREALAADAERKDKILRELL 299
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 568 EQRGD--KTIVFSDNVFALKHYA-----IKMNKPFIYGPTSQNERIQILQNFKfNSKVNTIFVSKVADTSFDLPEANVLI 640
Cdd:COG1061 300 REHPDdrKTLVFCSSVDHAEALAellneAGIRAAVVTGDTPKKEREEILEAFR-DGELRILVTVDVLNEGVDVPRLDVAI 378
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24662247 641 QISSHgGSRRQEAQRLGRILRAKKGaiaEEYnAFFYTLVSQDTMEMSYSRKRQRFLVnqGYSYKV 705
Cdd:COG1061 379 LLRPT-GSPREFIQRLGRGLRPAPG---KED-ALVYDFVGNDVPVLEELAKDLRDLA--GYRVEF 436
|
|
| Helicase_C_3 |
pfam13625 |
Helicase conserved C-terminal domain; This domain family is found in a wide variety of ... |
86-209 |
4.07e-46 |
|
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: 160.36 E-value: 4.07e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 86 LWVAPNGHVFLESfsPVYKHAHDFLIAISEPVCRpEHIHEYKLTAYSLYAAVSVGLQTHDIVEYLKRLSKTSIPEGILEF 165
Cdd:pfam13625 1 LIVQADLTILLPG--PLAPEARDFLAAFAELESR-GHAHTYRLTPLSLRRALDAGLTAEDILDFLERHSKYPVPQALEYL 77
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 24662247 166 IRLCTLSYGKVKLVLkHNKYFIESPHPEVLQKLLKDPVIQKCRL 209
Cdd:pfam13625 78 IRDVARRHGRLRLGL-GASSYLRSDDPAVLAELLADPRIAPLGL 120
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
332-486 |
1.41e-39 |
|
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: 142.83 E-value: 1.41e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 332 LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRK-RALVLCNSGVSVEQWKQQFKMWSTadDSMICRFTS 410
Cdd:cd17926 1 LRPYQEEALEAWLAHKNNRRGILVLPTGSGKTLTALALIAYLKElRTLIVVPTDALLDQWKERFEDFLG--DSSIGLIGG 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24662247 411 EAKDKPMGCGILVTTYsmithtQKRSWEAEQTMRWLqeQEWGIMVLDEVHTIPAKMFRRVLTIVQSHCKLGLTATL 486
Cdd:cd17926 79 GKKKDFDDANVVVATY------QSLSNLAEEEKDLF--DQFGLLIVDEAHHLPAKTFSEILKELNAKYRLGLTATP 146
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
324-498 |
1.30e-18 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 84.85 E-value: 1.30e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 324 IDLKPAAVLRPYQEKSLRKMFGNGRarSGVIVLPCGAGKSLVGVTAC-----CTVRKRALVLCNSGVSVEQWKQQFKMWS 398
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGLR--DVILAAPTGSGKTLAALLPAlealkRGKGGRVLVLVPTRELAEQWAEELKKLG 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 399 TADDSM-ICRFTSEAKDKPM------GCGILVTTYSMITHtqkrsweaEQTMRWLQEQEWGIMVLDEVHTIPAKMFRRVL 471
Cdd:smart00487 79 PSLGLKvVGLYGGDSKREQLrklesgKTDILVTTPGRLLD--------LLENDKLSLSNVDLVILDEAHRLLDGGFGDQL 150
|
170 180 190
....*....|....*....|....*....|..
gi 24662247 472 TIVQSHCK-----LGLTATLLREDDKIADLNF 498
Cdd:smart00487 151 EKLLKLLPknvqlLLLSATPPEEIENLLELFL 182
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
331-488 |
1.07e-15 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 75.40 E-value: 1.07e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 331 VLRPYQE---KSLRKMFGNGRARsGVIVLPCGAGKSLVGVTACCTVRK-----RALVLCNSGVSVEQWKQQFKMWSTADD 402
Cdd:pfam04851 3 ELRPYQIeaiENLLESIKNGQKR-GLIVMATGSGKTLTAAKLIARLFKkgpikKVLFLVPRKDLLEQALEEFKKFLPNYV 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 403 SmICRFTSEAKDKPM--GCGILVTTYSMIThtqkrSWEAEQTMRWLQEQeWGIMVLDEVHTIPAKMFRRVLTIVQSHCKL 480
Cdd:pfam04851 82 E-IGEIISGDKKDESvdDNKIVVTTIQSLY-----KALELASLELLPDF-FDVIIIDEAHRSGASSYRNILEYFKPAFLL 154
|
....*...
gi 24662247 481 GLTATLLR 488
Cdd:pfam04851 155 GLTATPER 162
|
|
| DEXHc_Snf |
cd17919 |
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
332-485 |
1.61e-13 |
|
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: 69.52 E-value: 1.61e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 332 LRPYQEKSLRKMFGNGRARSGVIVLPC-GAGKSLVGVTACCTVRK------RALVLC-NSgvSVEQWKQQFKMWstADDS 403
Cdd:cd17919 1 LRPYQLEGLNFLLELYENGPGGILADEmGLGKTLQAIAFLAYLLKegkergPVLVVCpLS--VLENWEREFEKW--TPDL 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 404 MICRFTSEAKD--------KPMGCGILVTTYSMIthtqkrSWEAEqtmrWLQEQEWGIMVLDEVHTI---PAKMFRRVLT 472
Cdd:cd17919 77 RVVVYHGSQREraqirakeKLDKFDVVLTTYETL------RRDKA----SLRKFRWDLVVVDEAHRLknpKSQLSKALKA 146
|
170
....*....|...
gi 24662247 473 IvQSHCKLGLTAT 485
Cdd:cd17919 147 L-RAKRRLLLTGT 158
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
561-663 |
9.24e-13 |
|
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: 65.31 E-value: 9.24e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 561 QFLIKYHE-QRGDKTIVFSDNVFALKHYAIKMNKPF----IYGPTSQNERIQILQNFKfNSKVNTIFVSKVADTSFDLPE 635
Cdd:pfam00271 4 EALLELLKkERGGKVLIFSQTKKTLEAELLLEKEGIkvarLHGDLSQEEREEILEDFR-KGKIDVLVATDVAERGLDLPD 82
|
90 100
....*....|....*....|....*...
gi 24662247 636 ANVLIQISSHgGSRRQEAQRLGRILRAK 663
Cdd:pfam00271 83 VDLVINYDLP-WNPASYIQRIGRAGRAG 109
|
|
| HepA |
COG0553 |
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
330-695 |
4.26e-11 |
|
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];
Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 66.40 E-value: 4.26e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 330 AVLRPYQEKSLRKMFGNGRARSGVI----VlpcGAGKSLVGVTACCTVR-----KRALVLCNSGVsVEQWKQQFKMWSTA 400
Cdd:COG0553 240 ATLRPYQLEGAAWLLFLRRLGLGGLladdM---GLGKTIQALALLLELKerglaRPVLIVAPTSL-VGNWQRELAKFAPG 315
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 401 DDSMICRFTSEAKDKP---MGCGILVTTYSMIthtqkRSWEAEqtmrwLQEQEWGIMVLDEVHTI---PAKMFRRVLTIv 474
Cdd:COG0553 316 LRVLVLDGTRERAKGAnpfEDADLVITSYGLL-----RRDIEL-----LAAVDWDLVILDEAQHIknpATKRAKAVRAL- 384
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 475 QSHCKLGLTAT-----------LLR------------------------EDDKIADLNFLIGPKLY----EANWLELQKK 515
Cdd:COG0553 385 KARHRLALTGTpvenrleelwsLLDflnpgllgslkafrerfarpiekgDEEALERLRRLLRPFLLrrtkEDVLKDLPEK 464
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 516 gyiaRVQcaEVWCPMSPE---FYREYL---------TTKTSKKMLL-----------------------YVMNPSKFRSC 560
Cdd:COG0553 465 ----TEE--TLYVELTPEqraLYEAVLeylrrelegAEGIRRRGLIlaaltrlrqicshpallleegaeLSGRSAKLEAL 538
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 561 QFLIKYHEQRGDKTIVFS---DNVFALKHYAIKMNKP--FIYGPTSQNERIQILQNFKFNSKVNTIFVS-KVADTSFDLP 634
Cdd:COG0553 539 LELLEELLAEGEKVLVFSqftDTLDLLEERLEERGIEyaYLHGGTSAEERDELVDRFQEGPEAPVFLISlKAGGEGLNLT 618
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24662247 635 EANVLIQISshggsrR-----QEAQRLGRILRakkgaIAEEYNAFFYTLVSQDT-----MEMsYSRKRQRF 695
Cdd:COG0553 619 AADHVIHYD------LwwnpaVEEQAIDRAHR-----IGQTRDVQVYKLVAEGTieekiLEL-LEEKRALA 677
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
332-492 |
8.13e-11 |
|
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: 61.04 E-value: 8.13e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 332 LRPYQEKSLRKM---FGNGRARSGViVLPCGAGKSLVGVTAC-----CTVRKRALVLCNSGVSVEQWKQQFKmwsTA--D 401
Cdd:cd18032 1 PRYYQQEAIEALeeaREKGQRRALL-VMATGTGKTYTAAFLIkrlleANRKKRILFLAHREELLEQAERSFK---EVlpD 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 402 DSMIcrFTSEAKDKPMGCGILVTTYsmithtqkrsweaeQTM--RWLQEQ----EWGIMVLDEVHTIPAKMFRRVLTIVQ 475
Cdd:cd18032 77 GSFG--NLKGGKKKPDDARVVFATV--------------QTLnkRKRLEKfppdYFDLIIIDEAHHAIASSYRKILEYFE 140
|
170
....*....|....*..
gi 24662247 476 SHCKLGLTATLLREDDK 492
Cdd:cd18032 141 PAFLLGLTATPERTDGL 157
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
595-663 |
3.52e-10 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 56.84 E-value: 3.52e-10
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24662247 595 FIYGPTSQNERIQILQNFKfNSKVNTIFVSKVADTSFDLPEANVLIQISSHgGSRRQEAQRLGRILRAK 663
Cdd:smart00490 16 RLHGGLSQEEREEILDKFN-NGKIKVLVATDVAERGLDLPGVDLVIIYDLP-WSPASYIQRIGRAGRAG 82
|
|
| DEXHc_ATRX-like |
cd18007 |
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ... |
332-487 |
4.16e-06 |
|
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) which is involved in transcriptional regulation and chromatin remodeling, and ARIP4 (also called androgen receptor-interacting protein 4, RAD54 like 2 or RAD54L2) which modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. They 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: 350765 [Multi-domain] Cd Length: 239 Bit Score: 48.83 E-value: 4.16e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 332 LRPYQEKSLRKM----FGNGRARS---GVIVLPC-GAGKSLVGVT------ACCTVRKRALVLCNSGVsVEQWKQQFKMW 397
Cdd:cd18007 1 LKPHQVEGVRFLwsnlVGTDVGSDeggGCILAHTmGLGKTLQVITflhtylAAAPRRSRPLVLCPAST-LYNWEDEFKKW 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 398 --STADDSMICRFTSEAKdKPMGC-----------GILVTTYSM----ITHTQKRSWEAEQTMRWLQEQEWGIMVLDEVH 460
Cdd:cd18007 80 lpPDLRPLLVLVSLSASK-RADARlrkinkwhkegGVLLIGYELfrnlASNATTDPRLKQEFIAALLDPGPDLLVLDEGH 158
|
170 180
....*....|....*....|....*....
gi 24662247 461 TI--PAKMFRRVLTIVQSHCKLGLTATLL 487
Cdd:cd18007 159 RLknEKSQLSKALSKVKTKRRILLTGTPL 187
|
|
| DEXHc_ERCC6L2 |
cd18005 |
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ... |
371-490 |
1.48e-05 |
|
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: 47.37 E-value: 1.48e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 371 CTVRKRALVLCNSGVsVEQWKQQFKMW----------STADDSMICRFtseakdKPMGCGILVTTYSMIthtqKRSWEAe 440
Cdd:cd18005 67 SSAKKPVLIVAPLSV-LYNWKDELDTWghfevgvyhgSRKDDELEGRL------KAGRLEVVVTTYDTL----RRCIDS- 134
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|..
gi 24662247 441 qtmrwLQEQEWGIMVLDEVHTI--PAKMFRRVLTIVQSHCKLGLTATLLRED 490
Cdd:cd18005 135 -----LNSINWSAVIADEAHRIknPKSKLTQAMKELKCKVRIGLTGTLLQNN 181
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
352-485 |
2.44e-05 |
|
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: 45.09 E-value: 2.44e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 352 GVIVLPCGAGKSLVG----VTACCTVRKRALVLCNSGVSVEQWKQQFKMWST--ADDSMICRFTSEAKDKPMGCG---IL 422
Cdd:cd00046 4 VLITAPTGSGKTLAAllaaLLLLLKKGKKVLVLVPTKALALQTAERLRELFGpgIRVAVLVGGSSAEEREKNKLGdadII 83
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24662247 423 VTTYSMIThtqkRSWEAEqtmRWLQEQEWGIMVLDEVHTIPAKMfRRVLTIVQSHCKL--------GLTAT 485
Cdd:cd00046 84 IATPDMLL----NLLLRE---DRLFLKDLKLIIVDEAHALLIDS-RGALILDLAVRKAglknaqviLLSAT 146
|
|
| SF2_C_SNF |
cd18793 |
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
555-661 |
3.79e-04 |
|
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: 41.31 E-value: 3.79e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 555 SKFRSCQFLIKYHEQRGDKTIVFS---DNVFALKHYAIKMNKPF--IYGPTSQNERIQILQNFKFNSKVNTIFVS-KVAD 628
Cdd:cd18793 11 GKLEALLELLEELREPGEKVLIFSqftDTLDILEEALRERGIKYlrLDGSTSSKERQKLVDRFNEDPDIRVFLLStKAGG 90
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 24662247 629 TSFDLPEANVLI--------QIsshggsrrqEAQRLGRILR 661
Cdd:cd18793 91 VGLNLTAANRVIlydpwwnpAV---------EEQAIDRAHR 122
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
334-462 |
6.31e-04 |
|
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: 41.48 E-value: 6.31e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 334 PYQEKSLRKMFGNGRarSGVIVLPCGAGKSLVG----VTACCTVRKRALVLCNSGVSVEQ----WKQQFKMwSTADDSMI 405
Cdd:cd17921 4 PIQREALRALYLSGD--SVLVSAPTSSGKTLIAelaiLRALATSGGKAVYIAPTRALVNQkeadLRERFGP-LGKNVGLL 80
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 24662247 406 CRFTSEAKDKPMGCGILVTTYsMITHTQKRSWEAeqtmRWLQEQewGIMVLDEVHTI 462
Cdd:cd17921 81 TGDPSVNKLLLAEADILVATP-EKLDLLLRNGGE----RLIQDV--RLVVVDEAHLI 130
|
|
| DEXHc_HELLS_SMARCA6 |
cd18009 |
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ... |
331-500 |
2.02e-03 |
|
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or SMARCA6) is a major epigenetic regulator crucial for normal heterochromatin structure and function. HELLS is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350767 [Multi-domain] Cd Length: 236 Bit Score: 40.45 E-value: 2.02e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 331 VLRPYQEKS---LRKMFGNGRarSGVIVLPCGAGKSLVGVTACCTVRKRAL----VLCNSGVSVEQWKQQFKMWSTADDS 403
Cdd:cd18009 3 VMRPYQLEGmewLRMLWENGI--NGILADEMGLGKTIQTIALLAHLRERGVwgpfLVIAPLSTLPNWVNEFARFTPSVPV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 404 MICRFTSEAKDK-----------PMGCGILVTTYSMITHTQKRsweaeqtmrwLQEQEWGIMVLDEVHTIPAKMFR--RV 470
Cdd:cd18009 81 LLYHGTKEERERlrkkimkregtLQDFPVVVTSYEIAMRDRKA----------LQHYAWKYLIVDEGHRLKNLNCRliQE 150
|
170 180 190
....*....|....*....|....*....|..
gi 24662247 471 LTIVQSHCKLGLTATLLREDDK--IADLNFLI 500
Cdd:cd18009 151 LKTFNSDNRLLLTGTPLQNNLSelWSLLNFLL 182
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
374-521 |
2.08e-03 |
|
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350769 [Multi-domain] Cd Length: 207 Bit Score: 40.35 E-value: 2.08e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 374 RKRALVLCNSGVsVEQWKQQfkMWS-------TADDSMICRFTSEAKDKPMGCGILVTTYSMIthtqkRSWEAEQtmRWL 446
Cdd:cd18011 47 AKRVLILCPASL-VEQWQDE--LQDkfglpflILDRETAAQLRRLIGNPFEEFPIVIVSLDLL-----KRSEERR--GLL 116
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 447 QEQEWGIMVLDEVH-------TIPAKMFRRVLTIVQ-SHCKLGLTAT--LLREDDkIADLNFLIGPKLYEANWLELQKKG 516
Cdd:cd18011 117 LSEEWDLVVVDEAHklrnsggGKETKRYKLGRLLAKrARHVLLLTATphNGKEED-FRALLSLLDPGRFAVLGRFLRLDG 195
|
....*
gi 24662247 517 YIARV 521
Cdd:cd18011 196 LREVL 200
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
621-677 |
2.74e-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: 37.30 E-value: 2.74e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 24662247 621 IFVSKVADTSFDLPEANVLIQISSHGgSRRQEAQRLGRILRAKKgaiaEEYNAFFYT 677
Cdd:cd18785 26 LVATNVLGEGIDVPSLDTVIFFDPPS-SAASYIQRVGRAGRGGK----DEGEVILFV 77
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
333-486 |
3.81e-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: 38.76 E-value: 3.81e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 333 RPYQEKSLRKMFGNgraRSGVIVLPCGAGKSLV-GVTACCTVRK-----RALVLCNSGVSVEQWKQQFKMWSTADDSMIC 406
Cdd:pfam00270 1 TPIQAEAIPAILEG---RDVLVQAPTGSGKTLAfLLPALEALDKldngpQALVLAPTRELAEQIYEELKKLGKGLGLKVA 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 407 RFTSEAKDKPM-----GCGILVTTYSMI-THTQKRsweaeqtmRWLQEQEWgiMVLDEVHTIPAKMFRRVLTIVQSHCK- 479
Cdd:pfam00270 78 SLLGGDSRKEQleklkGPDILVGTPGRLlDLLQER--------KLLKNLKL--LVLDEAHRLLDMGFGPDLEEILRRLPk 147
|
170
....*....|.
gi 24662247 480 ----LGLTATL 486
Cdd:pfam00270 148 krqiLLLSATL 158
|
|
| uvsW |
PHA02558 |
UvsW helicase; Provisional |
333-570 |
7.68e-03 |
|
UvsW helicase; Provisional
Pssm-ID: 222875 [Multi-domain] Cd Length: 501 Bit Score: 39.61 E-value: 7.68e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 333 RPYQEKSLRKMFGNGRarsGVIVLPCGAGKSLVgvtACCTVR-------KRALVLCNSGVSVEQWKQQFKMWSTADDS-- 403
Cdd:PHA02558 116 HWYQYDAVYEGLKNNR---RLLNLPTSAGKSLI---QYLLSRyylenyeGKVLIIVPTTSLVTQMIDDFVDYRLFPREam 189
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 404 -MICRFTSEAKDKPmgcgILVTTYSMItHTQKRSWeaeqtmrwlqEQEWGIMVLDEVHTIPAKMFRRVLTIVqSHC--KL 480
Cdd:PHA02558 190 hKIYSGTAKDTDAP----IVVSTWQSA-VKQPKEW----------FDQFGMVIVDECHLFTGKSLTSIITKL-DNCkfKF 253
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24662247 481 GLTATLlrEDDKIADLNF--LIGP--KLYEANwlELQKKGYIARVQCAEVWCPMSPEFyreylttktSKKMllyvmnpsK 556
Cdd:PHA02558 254 GLTGSL--RDGKANILQYvgLFGDifKPVTTS--QLMEEGQVTDLKINSIFLRYPDED---------RVKL--------K 312
|
250
....*....|....*..
gi 24662247 557 FRSCQFLIKY---HEQR 570
Cdd:PHA02558 313 GEDYQEEIKYitsHTKR 329
|
|
| |
