|
Name |
Accession |
Description |
Interval |
E-value |
| PRK04914 |
PRK04914 |
RNA polymerase-associated protein RapA; |
3-935 |
0e+00 |
|
RNA polymerase-associated protein RapA;
Pssm-ID: 235319 [Multi-domain] Cd Length: 956 Bit Score: 1457.36 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 3 EFALGQRWISDSESDLGLGTVVALNGRRISMLFPASGDQREYVIGSAPLTRVSFNPGDNVESAEGWSLAVKQVINEDGLN 82
Cdd:PRK04914 1 PFALGQRWISDTESELGLGTVVAVDGRTVTLLFPATGENRLYARNDAPLTRVMFNPGDTITSHEGWQLTVEEVEEENGLL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 83 IYLGIRSDNNEPEQLI-ETRINHHLKFNKPQDRLFTAQIDRNDWYTLRYEARKLQYEYQTHPLVGLAGARTALIPHQLHI 161
Cdd:PRK04914 81 TYHGTRLDTEEEGVALrETFLDSKIRFNKPQDRLFAGQIDRMDRFALRYRALKHQSEQFQSPLRGLRGARASLIPHQLYI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 162 AKEAGSRVAPRVLLSDEVGLGKTIEAGMIIHQQLLTGRASRILILLPESLQYQWLVEMLRRFNLQFAIFNEERCGEYDSS 241
Cdd:PRK04914 161 AHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTGRAERVLILVPETLQHQWLVEMLRRFNLRFSLFDEERYAEAQHD 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 242 EENPFETEQLIIAPVGLLADSDKRLEQASQAQWDLVVVDEAHHLDWHPDGASPAYLAVEKLSRICAGLLLLTATPDQLGH 321
Cdd:PRK04914 241 ADNPFETEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVWSEEAPSREYQVVEQLAEVIPGVLLLTATPEQLGQ 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 322 QSHFARLRLLDPERFYDYDKFVAEEAGYSQIAEQAKQITSNEDLSEAQIAEL---------------------------- 373
Cdd:PRK04914 321 ESHFARLRLLDPDRFHDYEAFVEEQQQYRPVADAVQALLAGEKLSDDALNALgellgeqdiepllqaansdseeaqaarq 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 374 ---KKLIDQHGTGRVLFRNTRASVKGFPVRCVLPVEMELPSEYQAAAdwwlsRHPDDASAKTvapLLTPEFLYEsAISGD 450
Cdd:PRK04914 401 eliSELLDRHGTGRVLFRNTRAAVKGFPKRELHPIPLPLPEQYQTAI-----KVSLEARARD---MLYPEQIYQ-EFEDN 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 451 IEWWKVDPRVEYLAELIKENKHEKFLIICARASTALTLEQAVRVKFGLNAAVFHEGMSIVERDRAAAWFADQDEGCQLLI 530
Cdd:PRK04914 472 ATWWNFDPRVEWLIDFLKSHRSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLL 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 531 CSEIGSEGRNFQFARHLVLFDIPLNPDLLEQRIGRLDRIGQRHDIQIHIPYFVNSASQTLFNWQHHGINAYANTCPAGIK 610
Cdd:PRK04914 552 CSEIGSEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHVPYLEGTAQERLFRWYHEGLNAFEHTCPTGRA 631
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 611 VFEQQQAELLQALAtNQYEQSQISGLIDTAKSQITELNTQLEQGRDILLELNSKGFDGA-AIAEQIEEMDDDTRLVAFML 689
Cdd:PRK04914 632 LYDEFGDELIPYLA-SPDDTDGLDELIAETREQHEALKAQLEQGRDRLLELNSCGGEKAqALAEAIAEQDDDTNLVNFAL 710
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 690 QIFDVYGVSQEDKGEQCIAVNPTEHMLEPHFPELHDDGMTITFDRETALSREDVRFISWDHPMVQGCFEMIAGGEVGNNA 769
Cdd:PRK04914 711 NLFDIIGINQEDRGENAIVLTPSDHMLVPDFPGLPEDGVTITFDRDQALSREDMQFLTWEHPLIRGGLDLILSGDTGSTA 790
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 770 VSILNNKALPEGTYLLELIYVVETSAPKQLQPGRFLPPTPIRLLLDKAGNNLAAKVGFDGLNKQLKPVNKQVASQLATAL 849
Cdd:PRK04914 791 VALLKNKALPAGTLLLELIYVVEAQAPKSLQLTRFLPPTPVRLLLDKNGNDLSAQVEFESLNRQLSAVNRHTASKLVKAV 870
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 850 QPQVHELIQQAEQKATAESVAIIDAAKEQVAKQLGEEISRLTELKAVNPNIRPIELESLLQQQKSLEEHLAQARVKLDAL 929
Cdd:PRK04914 871 QQDIHKLLQKAEAQAEAQARELIEQAKQEADEKLSAELSRLEALKAVNPNIRDDEIEALESQRQEVLEALDQAQLRLDAI 950
|
....*.
gi 515524197 930 RLIVVS 935
Cdd:PRK04914 951 RLIVVT 956
|
|
| RapA_C |
pfam12137 |
RNA polymerase recycling family C-terminal; This domain is found in bacteria. This domain is ... |
574-933 |
1.09e-168 |
|
RNA polymerase recycling family C-terminal; This domain is found in bacteria. This domain is about 360 amino acids in length. This domain is found associated with pfam00271, pfam00176. The function of this domain is not known, but structurally it forms an alpha-beta fold in nature with a central beta-sheet flanked by helices and loops, the beta-sheet being mainly antiparallel and flanked by four alpha helices, among which the two longer helices exhibit a coiled-coil arrangement.
Pssm-ID: 432354 Cd Length: 359 Bit Score: 495.52 E-value: 1.09e-168
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 574 DIQIHIPYFVNSASQTLFNWQHHGINAYANTCPAGIKVFEQQQAELLQALATNQYEQsqISGLIDTAKSQITELNTQLEQ 653
Cdd:pfam12137 1 DIQIHVPYLEGSAQEVLFRWYHEGLNAFEQTCPAGQAVYEEFGDRLLDLLAAPDEEA--LEALIAETRALREALKAELEQ 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 654 GRDILLELNSKGFD-GAAIAEQIEEMDDDTRLVAFMLQIFDVYGVSQEDKGEQCIAVNPTEHMLEPHFPELHDDGMTITF 732
Cdd:pfam12137 79 GRDRLLELNSCRPErAEALVEAIAEEDDDTELADFMERLFDAFGVDQEDHSEGSIVLRPSDHMLVPDFPGLPEDGMTVTF 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 733 DRETALSREDVRFISWDHPMVQGCFEMIAGGEVGNNAVSILNNKALPEGTYLLELIYVVETSAPKQLQPGRFLPPTPIRL 812
Cdd:pfam12137 159 DRDTALAREDLQFLTWEHPMVRGAMDLILSSDTGNAAVALLKNKALPAGTLLLELIFVVECVAPKALQLDRFLPPTPIRL 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 813 LLDKAGNNLAAKVGFDGLNKQLKPVNKQVASQLATALQPQVHELIQQAEQKATAESVAIIDAAKEQVAKQLGEEISRLTE 892
Cdd:pfam12137 239 LLDKKGNDLSAKVPFESLNRQLSPVNRHTARKLVKAQRDLIEKLLAKAEQLAEEQAEALIEQAKARMDQTLSAELERLEA 318
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 515524197 893 LKAVNPNIRPIELESLLQQQKSLEEHLAQARVKLDALRLIV 933
Cdd:pfam12137 319 LQAVNPNIRDDEIEALEEQRAQLLAALDQARLRLDAIRLIV 359
|
|
| HepA |
COG0553 |
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
1-605 |
2.14e-103 |
|
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];
Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 336.81 E-value: 2.14e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 1 MSEFALGQRWISDSESDLGLGTVVALNGRRISMLFPASGDQREYVIGSAPLTRVSFNPGDNVESAEGWSLAVKQVINEDG 80
Cdd:COG0553 108 LLLLALLGLLLSLALLLLLLLLLLLLLLALLLVLLAALLLLLLLLLLLALLLGRLLLLALLLLALEALLLLGLLLALALL 187
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 81 LNIYLGIRSDNNEPEQLIETRINHHLKFNKPQDRLftaqidrndwytlryEARKLQYEYQTHPlvglAGARTALIPHQLH 160
Cdd:COG0553 188 ALLELALLAAEAELLLLLELLLELELLAEAAVDAF---------------RLRRLREALESLP----AGLKATLRPYQLE 248
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 161 IAKEAG--SRVAPRVLLSDEVGLGKTIEAGMIIHQQLLTGRASRILILLPESLQYQWLVEMlRRFN--LQFAIFNEERcg 236
Cdd:COG0553 249 GAAWLLflRRLGLGGLLADDMGLGKTIQALALLLELKERGLARPVLIVAPTSLVGNWQREL-AKFApgLRVLVLDGTR-- 325
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 237 eYDSSEENPFETEQLIIAPVGLLAdsdKRLEQASQAQWDLVVVDEAHHLDwhpDGASPAYLAVEKLSriCAGLLLLTATP 316
Cdd:COG0553 326 -ERAKGANPFEDADLVITSYGLLR---RDIELLAAVDWDLVILDEAQHIK---NPATKRAKAVRALK--ARHRLALTGTP 396
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 317 DQLGHQSHFARLRLLDPERFYDYDKFVAEEAGYsqiaeqakqitsNEDLSEAQIAELKKLIdqhgtGRVLFRNTRASV-K 395
Cdd:COG0553 397 VENRLEELWSLLDFLNPGLLGSLKAFRERFARP------------IEKGDEEALERLRRLL-----RPFLLRRTKEDVlK 459
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 396 GFPVRCVLPVEMELPSE----YQA---AADWWLSRHPDDASAKTVAPLLT--------PEFLYESAISGDIEwwkvDPRV 460
Cdd:COG0553 460 DLPEKTEETLYVELTPEqralYEAvleYLRRELEGAEGIRRRGLILAALTrlrqicshPALLLEEGAELSGR----SAKL 535
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 461 EYLAELIKEN--KHEKFLIICARASTALTLEQAVRVKfGLNAAVFHEGMSIVERDRAAAWFADQDEGCQLLICSEIGSEG 538
Cdd:COG0553 536 EALLELLEELlaEGEKVLVFSQFTDTLDLLEERLEER-GIEYAYLHGGTSAEERDELVDRFQEGPEAPVFLISLKAGGEG 614
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 515524197 539 RNFQFARHLVLFDIPLNPDLLEQRIGRLDRIGQRHDIQIHIPYFVNSASQTLFNWQHHGINAYANTC 605
Cdd:COG0553 615 LNLTAADHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEEKILELLEEKRALAESVL 681
|
|
| DpdE |
NF041062 |
protein DpdE; |
14-935 |
4.08e-57 |
|
protein DpdE;
Pssm-ID: 468989 [Multi-domain] Cd Length: 1048 Bit Score: 213.68 E-value: 4.08e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 14 SESDLGLGTVVALNGRRISMLF---PASGDQREYVIGSAPLTRVSFNPGDNV----ESAEGWslAVKQVINEDGLNIYLg 86
Cdd:NF041062 6 SPGFPGIGKVVAIDGEEARVEFfesPAEPEAERQTVPLSDLRRVSLSPETRVyvrdPSSGRW--RAGRVIGSRPGNDYL- 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 87 IRSDNNEPEQLIETRInhHLKFNKPQD--------RLFTAQIdrndWYTLRYEARKLQYEyQ---THPLVGLAGARTALI 155
Cdd:NF041062 83 VRFPNGQDLDVPESEL--FVRWDRPVHdpvevlaaGGNESPF----FHDARSPFLESLIA-QraaCRGITALLSSAVELE 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 156 PHQLHIAKeagsRV----APRVLLSDEVGLGKTIEAGMIIHQQLLTGRASRILILLPESLQYQWLVEMLRRFNLqfaifn 231
Cdd:NF041062 156 PHQVAVVR----RVlqdpVQRYLLADEVGLGKTIEAGLVIRQHLLDNPDARVLVLVPDALVRQWRRELRDKFFL------ 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 232 eercgeydsseenpfetEQLIIAPVGLLADSDKRLEQASQAQWDLVVVDEAHHLDWHPDGASPAYLAV-EKLSRIC---A 307
Cdd:NF041062 226 -----------------DDFPGARVRVLSHEEPERWEPLLDAPDLLVVDEAHQLARLAWSGDPPERARyRELAALAhaaP 288
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 308 GLLLLTATPdQLGH-QSHFARLRLLDPERF--YDYDKF---VAEEAGYSQI-------------AEQAKQITSN----ED 364
Cdd:NF041062 289 RLLLLSATP-VLGNeETFLALLHLLDPDLYplDDLEAFrerLEEREELGRLvlgldpdnpnfllRQALDELRALfpedEE 367
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 365 LSEAqIAELKKLIDQHGTG------------------------RVLfRNTRASVKG--FPVRC-VLPVEMELPSEYQAAA 417
Cdd:NF041062 368 LQEL-AEELLPLLDEFDDEepeeraravsalrahisetyrlhrRMI-RNRRSSVLGadYLVPGrAGPRVLVWESPAREAA 445
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 418 D---------WWLSRHPDDASAKT---------VAPLLTPEFL---YESAISGDIEWWKVDPRVEYLAELIKE------- 469
Cdd:NF041062 446 DealedwreeAALLDAESDPAARAayaralawlVARLGGPDDLaalLRWRLRGDAASADLAGERELLEALIAAledeakd 525
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 470 ---------------NKHEKFLIICARASTALTLEQAVRVKFGLNAAVFHEGMSIVERDRAAAWFAdQDEGCQLLICSEI 534
Cdd:NF041062 526 adllaaladwllpllRGSGKAVVFCGDGSLADHLAAALARLGAGSVERHLSGQGADQAERAVRAFR-QDPSARVLVCDRS 604
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 535 GSEGRNFQFARHLVLFDIPLNPDLLEQRIGRLDRI---GQRHDIQIHIpyFVNSASQTLFN-WQ---HHGINAYANTCPA 607
Cdd:NF041062 605 GEEGLNLQGADRLVHLDLPWSPNRLEQRIGRLDRYaslRGGRPVESYV--LAPSDDDSLYSaWAdllREGFGVFDRSVAS 682
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 608 GIKVFEQQQAELLQALATNQYE-----QSQISGLIDTAKSQITELntqleqgrDILLELNSKGFDGAAIAEQIEEMDDD- 681
Cdd:NF041062 683 LQDALDEGLDEAWRALLEEGPEalleaIARLRGELARERRRIDEQ--------DALDSIEADAEEARSFAEALAEAEEDa 754
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 682 -------TRLVAFMLQiFDVYGVSQEDKGEQCIAVNPT---EHMLEPHFpeLHDDGMTITFDRETALSREDVRFISWDHP 751
Cdd:NF041062 755 delrdalLGWITKGLR-FRKRRDEVDDVFRFDFASRRTllpPRLLIRRF--LPGLDREGTFSRSVALRRPGVRLFRYGNP 831
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 752 MVQGCFEMIAGGEVGN-NAVSILNNKALPEGTYLLELIYVVETSAPKQLQPG-------------RFLPPTPIRLLLDKA 817
Cdd:NF041062 832 FVDALARLLRWDDRGQaFAMWRLDPSWRGEPRLYFRFDFLVEADLLPALALLdgaarralrrradRLFPPFTLRVWVDAD 911
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 818 GNNLAAKVGFDGLNkqlKPVNKQVASQ-----LATALQPQVHELIQQAEQKATAESVAiiDAAKEQVAKQ--LGEEIS-- 888
Cdd:NF041062 912 GEEVTDPELLAWLN---APYSKPGGVGgrdynLNGSRWEALLELFGADEWRELCRAAE--EAARALLRSRadLAEACAra 986
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 515524197 889 ----------RLTELKAVNPNIRPIE-LESLLQQQ---KSLEEHLAQARVKLDALRLIVVS 935
Cdd:NF041062 987 qararadlavRLAQLRARAAAGSLVEdAEELAREValaQALADGIRNPSVRLDAVGCVVLS 1047
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
154-346 |
9.35e-56 |
|
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: 191.73 E-value: 9.35e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 154 LIPHQLHIAKEAGSRVAPRVLLSDEVGLGKTIEAGMIIHQQLLTGRASRILILLPESLQYQWLVEMLRRFNLQFAIFNEE 233
Cdd:cd18011 1 PLPHQIDAVLRALRKPPVRLLLADEVGLGKTIEAGLIIKELLLRGDAKRVLILCPASLVEQWQDELQDKFGLPFLILDRE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 234 RCGEYDSSEENPFETEQLIIAPVGLLADSDKRLEQASQAQWDLVVVDEAHHLDWHPDGA-SPAYLAVEKLSRICAGLLLL 312
Cdd:cd18011 81 TAAQLRRLIGNPFEEFPIVIVSLDLLKRSEERRGLLLSEEWDLVVVDEAHKLRNSGGGKeTKRYKLGRLLAKRARHVLLL 160
|
170 180 190
....*....|....*....|....*....|....
gi 515524197 313 TATPDQLGHQSHFARLRLLDPERFYDYDKFVAEE 346
Cdd:cd18011 161 TATPHNGKEEDFRALLSLLDPGRFAVLGRFLRLD 194
|
|
| SF2_C_SNF |
cd18793 |
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
456-578 |
1.55e-28 |
|
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: 111.41 E-value: 1.55e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 456 VDPRVEYLAELIKENKH--EKFLIICARASTALTLEQAVRvKFGLNAAVFHEGMSIVERDRAAAWFADQDEGCQLLICSE 533
Cdd:cd18793 9 VSGKLEALLELLEELREpgEKVLIFSQFTDTLDILEEALR-ERGIKYLRLDGSTSSKERQKLVDRFNEDPDIRVFLLSTK 87
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 515524197 534 IGSEGRNFQFARHLVLFDIPLNPDLLEQRIGRLDRIGQRHDIQIH 578
Cdd:cd18793 88 AGGVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQKKPVVVY 132
|
|
| Tudor_1_RapA |
pfam18339 |
RapA N-terminal Tudor like domain 1; This is one of two Tudor-like domains found in the ... |
4-54 |
7.62e-26 |
|
RapA N-terminal Tudor like domain 1; This is one of two Tudor-like domains found in the N-terminal region of RapA proteins. RapA is an abundant RNAP-associated protein of 110-kDa molecular weight with ATPase activity. It forms a stable complex with the RNAP core enzyme, but not with the holoenzyme. The ATPase activity of RapA increases upon its binding to RNAP. The N-terminal region of RapA contains two copies of a Tudor-like domains, both folded as a highly bent antiparallel beta-sheet. This fold is also found in transcription factor NusG, ribosomal protein L24, human SMN (survival of motor neuron) protein, mammalian DNA repair factor 53BP1, putative fission yeast DNA repair factor Crb2 and bacterial transcription-repair coupling factor known as Mfd. The functional roles of the N-terminal region homologs in these proteins suggest that the Tudor-like domains of RapA may interact with both nucleic acids and RNAP.
Pssm-ID: 436422 [Multi-domain] Cd Length: 51 Bit Score: 100.63 E-value: 7.62e-26
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 515524197 4 FALGQRWISDSESDLGLGTVVALNGRRISMLFPASGDQREYVIGSAPLTRV 54
Cdd:pfam18339 1 FAPGQRWISDTEPELGLGIVVEVDGRTVTILFPASGETRTYATANAPLTRV 51
|
|
| Tudor_RapA |
pfam18337 |
RapA N-terminal Tudor like domain; This is one of two Tudor-like domains found in the ... |
56-117 |
8.84e-23 |
|
RapA N-terminal Tudor like domain; This is one of two Tudor-like domains found in the N-terminal region of RapA proteins. RapA is an abundant RNAP-associated protein of 110-kDa molecular weight with ATPase activity. It forms a stable complex with the RNAP core enzyme, but not with the holoenzyme. The ATPase activity of RapA increases upon its binding to RNAP. The N-terminal region of RapA contains two copies of a Tudor-like domains, both folded as a highly bent antiparallel beta-sheet. This fold is also found in transcription factor NusG, ribosomal protein L24, human SMN (survival of motor neuron) protein, mammalian DNA repair factor 53BP1, putative fission yeast DNA repair factor Crb2 and bacterial transcription-repair coupling factor known as Mfd. The functional roles of the N-terminal region homologs in these proteins suggest that the Tudor-like domains of RapA may interact with both nucleic acids and RNAP.
Pssm-ID: 465716 [Multi-domain] Cd Length: 62 Bit Score: 92.18 E-value: 8.84e-23
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 515524197 56 FNPGDNVESAEGWSLAVKQVINEDGLNIYLGIRSDNNEpEQLIETRINHHLKFNKPQDRLFT 117
Cdd:pfam18337 1 FNVGDTITSHEGWKLTVEEVEEENGLLIYLGTREDGEE-VSLPETELDHFIQFNKPQDRLFA 61
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
170-315 |
4.46e-22 |
|
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: 93.24 E-value: 4.46e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 170 APRVLLSDEVGLGKTIEAGMIIHQQLLTgRASRILILLPE-SLQYQWLVEMLRRF--NLQFAIFNeercGEYDSSE--EN 244
Cdd:cd00046 1 GENVLITAPTGSGKTLAALLAALLLLLK-KGKKVLVLVPTkALALQTAERLRELFgpGIRVAVLV----GGSSAEEreKN 75
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 515524197 245 PFETEQLIIAPVGLLADSDKRLEQASQAQWDLVVVDEAHHLDWHPDGASPAYLAVEKLSRICAGLLLLTAT 315
Cdd:cd00046 76 KLGDADIIIATPDMLLNLLLREDRLFLKDLKLIIVDEAHALLIDSRGALILDLAVRKAGLKNAQVILLSAT 146
|
|
| DEXHc_Snf |
cd17919 |
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
154-333 |
1.50e-20 |
|
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: 89.93 E-value: 1.50e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 154 LIPHQLHIAKEAGSRVA--PRVLLSDEVGLGKTIEAGMIIHQQLLTG-RASRILILLPESLQYQWLVEMLRRF-NLQFAI 229
Cdd:cd17919 1 LRPYQLEGLNFLLELYEngPGGILADEMGLGKTLQAIAFLAYLLKEGkERGPVLVVCPLSVLENWEREFEKWTpDLRVVV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 230 FNEERCGEYDSSEENPFETEQLIIAPVGLLADSDKRLEQASqaqWDLVVVDEAHHLDWhpdGASPAYLAVEKLSriCAGL 309
Cdd:cd17919 81 YHGSQRERAQIRAKEKLDKFDVVLTTYETLRRDKASLRKFR---WDLVVVDEAHRLKN---PKSQLSKALKALR--AKRR 152
|
170 180
....*....|....*....|....
gi 515524197 310 LLLTATPDQLGHQSHFARLRLLDP 333
Cdd:cd17919 153 LLLTGTPLQNNLEELWALLDFLDP 176
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
459-570 |
8.06e-20 |
|
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: 85.34 E-value: 8.06e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 459 RVEYLAELIKENKHEKFLIICARASTALtlEQAVRVKFGLNAAVFHEGMSIVERDRAAAWFADQDegCQLLICSEIGSEG 538
Cdd:pfam00271 2 KLEALLELLKKERGGKVLIFSQTKKTLE--AELLLEKEGIKVARLHGDLSQEEREEILEDFRKGK--IDVLVATDVAERG 77
|
90 100 110
....*....|....*....|....*....|..
gi 515524197 539 RNFQFARHLVLFDIPLNPDLLEQRIGRLDRIG 570
Cdd:pfam00271 78 LDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
156-337 |
1.41e-18 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 84.85 E-value: 1.41e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 156 PHQLHIAKEAGSRVaPRVLLSDEVGLGKTIEAGMIIHQQLLTGRASRILILLP-ESLQYQWLVEMLRRFNLQFAIFNEER 234
Cdd:smart00487 11 PYQKEAIEALLSGL-RDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPtRELAEQWAEELKKLGPSLGLKVVGLY 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 235 CGEYDSSEENPFETE--QLIIAPVGLLADsDKRLEQASQAQWDLVVVDEAHHLDwhPDGASPAYLAVEKLSRICAGLLLL 312
Cdd:smart00487 90 GGDSKREQLRKLESGktDILVTTPGRLLD-LLENDKLSLSNVDLVILDEAHRLL--DGGFGDQLEKLLKLLPKNVQLLLL 166
|
170 180
....*....|....*....|....*
gi 515524197 313 TATPDQLGHqsHFARLRLLDPERFY 337
Cdd:smart00487 167 SATPPEEIE--NLLELFLNDPVFID 189
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
495-570 |
4.85e-14 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 68.01 E-value: 4.85e-14
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 515524197 495 KFGLNAAVFHEGMSIVERDRAAAWFADQDegCQLLICSEIGSEGRNFQFARHLVLFDIPLNPDLLEQRIGRLDRIG 570
Cdd:smart00490 9 ELGIKVARLHGGLSQEEREEILDKFNNGK--IKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
76-566 |
3.41e-13 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 73.52 E-value: 3.41e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 76 INEDGLNIYLGIRSDNNEPEQLIETRINHHLKFNKPQDRLFTAQIDRNDWYTLRYEARKLQYEYQTHPLVGLAGARTA-- 153
Cdd:COG1061 1 VLLRGIAERGADKLRSSLLLLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEALEAGDEASGTSfe 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 154 LIPHQ---LHIAKEAGSRVAPRVLLSDEVGLGKTIEAGMIIHQqllTGRASRILILLP-ESLQYQWLVEMLRRFNLQFAI 229
Cdd:COG1061 81 LRPYQqeaLEALLAALERGGGRGLVVAPTGTGKTVLALALAAE---LLRGKRVLVLVPrRELLEQWAEELRRFLGDPLAG 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 230 FNEERcgeydsseenpfETEQLIIAPVGLLAdSDKRLEQASQAqWDLVVVDEAHHLdwhpdgASPAYLAVekLSRICAGL 309
Cdd:COG1061 158 GGKKD------------SDAPITVATYQSLA-RRAHLDELGDR-FGLVIIDEAHHA------GAPSYRRI--LEAFPAAY 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 310 LL-LTATPDQLGHQshfarlrlldPERFYDYDKFVAEeagYSqiaeqakqitsnedlseaqiaeLKKLIDQHgtgrVLfr 388
Cdd:COG1061 216 RLgLTATPFRSDGR----------EILLFLFDGIVYE---YS----------------------LKEAIEDG----YL-- 254
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 389 ntrasvkgFPVRCVlPVEMELPSEyqaaadwwlsRHPDDASAKTVAPLLTPEflyesaisgdiewwkvDPRVEY-LAELI 467
Cdd:COG1061 255 --------APPEYY-GIRVDLTDE----------RAEYDALSERLREALAAD----------------AERKDKiLRELL 299
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 468 KEN-KHEKFLIICARASTALTLEQAVRvKFGLNAAVFHEGMSIVERDRAAAWFADQDegCQLLICSEIGSEGRNFQFARH 546
Cdd:COG1061 300 REHpDDRKTLVFCSSVDHAEALAELLN-EAGIRAAVVTGDTPKKEREEILEAFRDGE--LRILVTVDVLNEGVDVPRLDV 376
|
490 500
....*....|....*....|
gi 515524197 547 LVLFDIPLNPDLLEQRIGRL 566
Cdd:COG1061 377 AILLRPTGSPREFIQRLGRG 396
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
156-316 |
4.12e-09 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 56.53 E-value: 4.12e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 156 PHQLHIAK---EAGSRVAPRVLLSDEVGLGKTIEAGMIIHQQLLTGRASRILILLP-ESLQYQWLvemlRRFNlQFAIFN 231
Cdd:pfam04851 6 PYQIEAIEnllESIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPrKDLLEQAL----EEFK-KFLPNY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 232 EERCGEYdSSEENPFETEQ---LIIAPVGLLADSDKRLEQASQAQWDLVVVDEAHHLdwhpdgASPAYLAVEKLSRiCAG 308
Cdd:pfam04851 81 VEIGEII-SGDKKDESVDDnkiVVTTIQSLYKALELASLELLPDFFDVIIIDEAHRS------GASSYRNILEYFK-PAF 152
|
....*...
gi 515524197 309 LLLLTATP 316
Cdd:pfam04851 153 LLGLTATP 160
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
172-317 |
4.02e-08 |
|
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: 53.72 E-value: 4.02e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 172 RVLLSDEVGLGKTIEAGMIIHQQLLTGRASRILILLP-ESLQYQwLVEMLRRFNLQFAIfneercGEYDSSEENPFETEQ 250
Cdd:cd18032 22 RALLVMATGTGKTYTAAFLIKRLLEANRKKRILFLAHrEELLEQ-AERSFKEVLPDGSF------GNLKGGKKKPDDARV 94
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 515524197 251 LIiAPVGLLAdSDKRLEQASQAQWDLVVVDEAHHldwhpdGASPAYLAVekLSRICAGLLL-LTATPD 317
Cdd:cd18032 95 VF-ATVQTLN-KRKRLEKFPPDYFDLIIIDEAHH------AIASSYRKI--LEYFEPAFLLgLTATPE 152
|
|
| DEXHc_CHD6_7_8_9 |
cd17995 |
DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; ... |
174-355 |
6.04e-08 |
|
DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; Chromodomain-helicase-DNA-binding protein 6-9 (CHD6, CHD7, CHD8, and CHD9) are members of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350753 [Multi-domain] Cd Length: 223 Bit Score: 54.18 E-value: 6.04e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 174 LLSDEVGLGKTIEAGMIIHQqLLTGRASR--ILILLPESLQYQWLVEMLRRFNL------------QFAIFNEERCGEYD 239
Cdd:cd17995 23 ILADEMGLGKTIQSIAFLEH-LYQVEGIRgpFLVIAPLSTIPNWQREFETWTDMnvvvyhgsgesrQIIQQYEMYFKDAQ 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 240 S-SEENPFETEQLIIAPVGLLADSDKRleqaSQAQWDLVVVDEAHHLDwhpdgaSPAYLAVEKLSRICAG-LLLLTATPD 317
Cdd:cd17995 102 GrKKKGVYKFDVLITTYEMVIADAEEL----RKIPWRVVVVDEAHRLK------NRNSKLLQGLKKLTLEhKLLLTGTPL 171
|
170 180 190
....*....|....*....|....*....|....*...
gi 515524197 318 QLGHQSHFARLRLLDPERFYDYDKFVaEEAGYSQIAEQ 355
Cdd:cd17995 172 QNNTEELWSLLNFLEPEKFPSSEEFL-EEFGDLKTAEQ 208
|
|
| SNF2-rel_dom |
pfam00176 |
SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
174-414 |
1.06e-07 |
|
SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.
Pssm-ID: 425504 [Multi-domain] Cd Length: 289 Bit Score: 54.61 E-value: 1.06e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 174 LLSDEVGLGKTIEA----GMIIHQQLLTGRAsrILILLPESLQYQWLVEMLRRFNLQ----FAIFNEERCGEYDSSEENP 245
Cdd:pfam00176 21 ILADEMGLGKTLQTisllLYLKHVDKNWGGP--TLIVVPLSLLHNWMNEFERWVSPPalrvVVLHGNKRPQERWKNDPNF 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 246 FETEQ-LIIAPVGLLadsdKRLEQASQAQWDLVVVDEAHHLDwhpDGASPAYLAVEKLS---RICaglllLTATPDQLGH 321
Cdd:pfam00176 99 LADFDvVITTYETLR----KHKELLKKVHWHRIVLDEGHRLK---NSKSKLSKALKSLKtrnRWI-----LTGTPLQNNL 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 322 QSHFARLRLLDPERFYDYDKFvaeeagysqiaEQAKQITSNEDLSEAQIAELKKLIDqhgtgRVLFRNTRASV-KGFPVR 400
Cdd:pfam00176 167 EELWALLNFLRPGPFGSLSTF-----------RNWFDRPIERGGGKKGVSRLHKLLK-----PFLLRRTKKDVeKSLPPK 230
|
250
....*....|....
gi 515524197 401 CVLPVEMELpSEYQ 414
Cdd:pfam00176 231 VEYILFCRL-SKLQ 243
|
|
| DEXQc_arch_SWI2_SNF2 |
cd18012 |
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ... |
175-316 |
1.19e-07 |
|
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging to SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprises a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. Archaeal SWI2 and SNF2 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: 350770 [Multi-domain] Cd Length: 218 Bit Score: 53.34 E-value: 1.19e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 175 LSDEVGLGKTIEAGMIIHQQLLTGRASRILILLPESLQYQWLVEmLRRFN--LQFAIF---NEERcgeydsSEENPFETE 249
Cdd:cd18012 28 LADDMGLGKTLQTLALLLSRKEEGRKGPSLVVAPTSLIYNWEEE-AAKFApeLKVLVIhgtKRKR------EKLRALEDY 100
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 515524197 250 QLIIAPVGLL-ADSDKRLEQasqaQWDLVVVDEAHHLDWHpdgASPAYLAVEKLS---RICaglllLTATP 316
Cdd:cd18012 101 DLVITSYGLLrRDIELLKEV----KFHYLVLDEAQNIKNP---QTKTAKAVKALKadhRLA-----LTGTP 159
|
|
| DEXHc_RAD54B |
cd18066 |
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ... |
166-377 |
1.23e-07 |
|
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as RDH54, binds to double-stranded DNA, displays ATPase activity in the presence of DNA, and may have a role in meiotic and mitotic recombination. RAD54B 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: 350824 [Multi-domain] Cd Length: 235 Bit Score: 53.70 E-value: 1.23e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 166 GSRVAPR--VLLSDEVGLGKTIEAGMIIHQQLLTGR------ASRILILLPESLQYQWLVEMLRRFNLQ----FAIFNEE 233
Cdd:cd18066 18 GMRVNERfgAILADEMGLGKTLQCISLIWTLLRQGPyggkpvIKRALIVTPGSLVKNWKKEFQKWLGSErikvFTVDQDH 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 234 RCGEYDSSeenPFETeQLIIAPVGLLadsdKRLEQASQAQWDLVVVDEAHHLDwhpDGASPAYLAVEKLSriCAGLLLLT 313
Cdd:cd18066 98 KVEEFIAS---PLYS-VLIISYEMLL----RSLDQISKLNFDLVICDEGHRLK---NTSIKTTTALTSLS--CERRIILT 164
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 515524197 314 ATPDQLGHQSHFARLRLLDPerfydydKFVAEEAGYSQIAEQ----AKQITSNE---DLSEAQIAELKKLI 377
Cdd:cd18066 165 GTPIQNDLQEFFALIDFVNP-------GILGSLSTYRKVYEEpivrSREPTATPeekKLGEARAAELTRLT 228
|
|
| DEXHc_CHD6 |
cd18058 |
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; ... |
174-361 |
2.29e-07 |
|
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; Chromodomain-helicase-DNA-binding protein 6 (CHD6) is a DNA-dependent ATPase that plays a role in chromatin remodeling. It regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin. It activates transcription of specific genes in response to oxidative stress through interaction with NFE2L2.2 and acts as a transcriptional repressor of different viruses including influenza virus or papillomavirus. During influenza virus infection, the viral polymerase complex localizes CHD6 to inactive chromatin where it gets degraded in a proteasome independent-manner. CHD6 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: 350816 [Multi-domain] Cd Length: 222 Bit Score: 52.74 E-value: 2.29e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 174 LLSDEVGLGKTIEAGMIIHQQLLTGRASRILILLPESLQYQWLVE----------------MLRRFNLQFAIFNEERCGE 237
Cdd:cd18058 23 ILADEMGLGKTIQSITFLSEIFLMGIRGPFLIIAPLSTITNWEREfrtwtemnaivyhgsqISRQMIQQYEMYYRDEQGN 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 238 YDSSEenpFETEQLIIAPVGLLADSdkrlEQASQAQWDLVVVDEAHHLDwhpdgaspaylavEKLSRICAGL-------- 309
Cdd:cd18058 103 PLSGI---FKFQVVITTFEMILADC----PELKKINWSCVIIDEAHRLK-------------NRNCKLLEGLklmalehk 162
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 515524197 310 LLLTATPDQLGHQSHFARLRLLDPERFYDYDKFVaEEAGYSQIAEQAKQITS 361
Cdd:cd18058 163 VLLTGTPLQNSVEELFSLLNFLEPSQFPSETTFL-EEFGDLKTEEQVKKLQS 213
|
|
| DEXHc_RAD54 |
cd18004 |
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ... |
154-342 |
8.09e-07 |
|
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. 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: 350762 [Multi-domain] Cd Length: 240 Bit Score: 51.13 E-value: 8.09e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 154 LIPHQ----------LHIAKEAGSRVAprvLLSDEVGLGKTIEAGMIIH---QQLLTGR--ASRILILLPESLQYQWLVE 218
Cdd:cd18004 1 LRPHQregvqflydcLTGRRGYGGGGA---ILADEMGLGKTLQAIALVWtllKQGPYGKptAKKALIVCPSSLVGNWKAE 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 219 M---LRRFNLQFAIFNEERCGEYDSSE-ENPFETEQLIIAPVGLLADSDKRLEQASqaQWDLVVVDEAHHLDwhpDGASP 294
Cdd:cd18004 78 FdkwLGLRRIKVVTADGNAKDVKASLDfFSSASTYPVLIISYETLRRHAEKLSKKI--SIDLLICDEGHRLK---NSESK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*...
gi 515524197 295 AYLAVEKLSriCAGLLLLTATPDQLGHQSHFARLRLLDPERFYDYDKF 342
Cdd:cd18004 153 TTKALNSLP--CRRRLLLTGTPIQNDLDEFFALVDFVNPGILGSLASF 198
|
|
| DEXHc_CHD1L |
cd18006 |
DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, ... |
154-336 |
2.71e-06 |
|
DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, also known as ALC1) is involved in DNA repair by regulating chromatin relaxation following DNA damage. CHD1L 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: 350764 [Multi-domain] Cd Length: 216 Bit Score: 49.36 E-value: 2.71e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 154 LIPHQLHIAKEAGSRVAPR--VLLSDEVGLGKTIEAgmIIHQQLLTGRASR---ILILLPESLQYQWlVEMLRRF--NLQ 226
Cdd:cd18006 1 LRPYQLEGVNWLLQCRAEQhgCILGDEMGLGKTCQT--ISLLWYLAGRLKLlgpFLVLCPLSVLDNW-KEELNRFapDLS 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 227 FAIF---NEER-CGEYDSSEENPFETeqliiapvgLLADSDKRLEQAS---QAQWDLVVVDEAHHLDwhpdgaSPAYLAV 299
Cdd:cd18006 78 VITYmgdKEKRlDLQQDIKSTNRFHV---------LLTTYEICLKDASflkSFPWASLVVDEAHRLK------NQNSLLH 142
|
170 180 190
....*....|....*....|....*....|....*...
gi 515524197 300 EKLSRICAGL-LLLTATPDQLGHQSHFARLRLLDPERF 336
Cdd:cd18006 143 KTLSEFSVDFrLLLTGTPIQNSLQELYALLSFIEPNVF 180
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
463-571 |
7.22e-06 |
|
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350174 [Multi-domain] Cd Length: 131 Bit Score: 46.35 E-value: 7.22e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 463 LAELIKENKHEKFLIICARASTALTLEQAVRvKFGLNAAVFHEGMSIVERDRAAAWFADQDegCQLLICSEIGSEGRNFQ 542
Cdd:cd18787 18 LLLLLEKLKPGKAIIFVNTKKRVDRLAELLE-ELGIKVAALHGDLSQEERERALKKFRSGK--VRVLVATDVAARGLDIP 94
|
90 100
....*....|....*....|....*....
gi 515524197 543 FARHLVLFDIPLNPDLLEQRIGRLDRIGQ 571
Cdd:cd18787 95 GVDHVINYDLPRDAEDYVHRIGRTGRAGR 123
|
|
| DEXHc_ERCC6L |
cd18001 |
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ... |
154-318 |
8.23e-06 |
|
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint helicase (ERCC6L, also known as RAD26L) is an essential component of the mitotic spindle assembly checkpoint, by acting as a tension sensor that associates with catenated DNA which is stretched under tension until it is resolved during anaphase. ERCC6L is proposed to stimulate cancer cell proliferation by promoting cell cycle through a way of RAB31-MAPK-CDK2. ERCC6L 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: 350759 [Multi-domain] Cd Length: 232 Bit Score: 48.14 E-value: 8.23e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 154 LIPHQ---------LHIAKEAGsrvaprvLLSDEVGLGKTIEAGMIIHQQLLTGRASRILILLPESLQYQWLVEMLR-RF 223
Cdd:cd18001 1 LYPHQregvawlwsLHDGGKGG-------ILADDMGLGKTVQICAFLSGMFDSGLIKSVLVVMPTSLIPHWVKEFAKwTP 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 224 NLQFAIFNEERCGEYDSSEENPFETEQLIIAPVGLLADSDKRLEQ--ASQAQWDLVVVDEAHHLDWHPDGASPAYLAVEK 301
Cdd:cd18001 74 GLRVKVFHGTSKKERERNLERIQRGGGVLLTTYGMVLSNTEQLSAddHDEFKWDYVILDEGHKIKNSKTKSAKSLREIPA 153
|
170
....*....|....*..
gi 515524197 302 LSRIcagllLLTATPDQ 318
Cdd:cd18001 154 KNRI-----ILTGTPIQ 165
|
|
| DEXHc_HARP_SMARCAL1 |
cd18010 |
DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin ... |
172-316 |
1.35e-05 |
|
DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1, also known as HARP) is recruited to stalled replication forks to promote repair and helps restart replication. It plays a role in DNA repair, telomere maintenance and replication fork stability in response to DNA replication stress. Mutations cause Schimke Immunoosseous Dysplasia. SMARCAL1 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: 350768 [Multi-domain] Cd Length: 213 Bit Score: 47.20 E-value: 1.35e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 172 RVLLSDEVGLGKTIEAgmiihqqLLTGRASR----ILILLPESLQYQWLVEMLRRF----NLQFAIFNEERCGEYDSSee 243
Cdd:cd18010 18 RVLIADEMGLGKTVQA-------IAIAAYYReewpLLIVCPSSLRLTWADEIERWLpslpPDDIQVIVKSKDGLRDGD-- 88
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 515524197 244 npfetEQLIIAPVGLLAdsdKRLEQASQAQWDLVVVDEAHHLDwhpDGASPAYLAVEKLSRICAGLLLLTATP 316
Cdd:cd18010 89 -----AKVVIVSYDLLR---RLEKQLLARKFKVVICDESHYLK---NSKAKRTKAALPLLKRAKRVILLSGTP 150
|
|
| DEXHc_ERCC6 |
cd18000 |
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ... |
174-318 |
5.32e-05 |
|
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, also known Cockayne syndrome group B (CSB), Rad26 in Saccharomyces cerevisiae, and Rhp26 in Schizosaccharomyces pombe) is a DNA-binding protein that is important in transcription-coupled excision repair. ERCC6 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350758 [Multi-domain] Cd Length: 193 Bit Score: 45.01 E-value: 5.32e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 174 LLSDEVGLGKTIEA----GMIIHQQLLTGRAsriLILLPESLQYQWLVEMLRRFNlQFAIFNEERCGEYDSSEE---NPF 246
Cdd:cd18000 23 ILGDEMGLGKTIQIiaflAALHHSKLGLGPS---LIVCPATVLKQWVKEFHRWWP-PFRVVVLHSSGSGTGSEEklgSIE 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 247 ETEQLII---APVGLLADSDKRLEQASQ----AQWDLVVVDEAHHLDwHPDGaspaylaveKLSRICAGL-----LLLTA 314
Cdd:cd18000 99 RKSQLIRkvvGDGGILITTYEGFRKHKDlllnHNWQYVILDEGHKIR-NPDA---------EITLACKQLrtphrLILSG 168
|
....
gi 515524197 315 TPDQ 318
Cdd:cd18000 169 TPIQ 172
|
|
| DEXHc_TTF2 |
cd18072 |
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ... |
174-339 |
1.61e-04 |
|
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called Forkhead-box E1/FOXE1 ) is a transcription termination factor that couples ATP hydrolysis with the removal of RNA polymerase II from the DNA template. Single nucleotide polymorphism (SNP) within the 5'-UTR of TTF2 is associated with thyroid cancer risk.TTF2 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: 350830 [Multi-domain] Cd Length: 241 Bit Score: 44.39 E-value: 1.61e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 174 LLSDEVGLGKTIEAGMIIHQQLLTGRASR-----------------------ILILLPESLQYQWLVEMLRRFN---LQF 227
Cdd:cd18072 24 ILADDMGLGKTLTMIALILAQKNTQNRKEeekekalteweskkdstlvpsagTLVVCPASLVHQWKNEVESRVAsnkLRV 103
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 228 AIF---NEERCGEYdsseenpFETEQLIIAPVGLLADSDKRLEQAS------QAQWDLVVVDEAHHLDWHPDGASpayLA 298
Cdd:cd18072 104 CLYhgpNRERIGEV-------LRDYDIVITTYSLVAKEIPTYKEESrssplfRIAWARIILDEAHNIKNPKVQAS---IA 173
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 515524197 299 VEKLSRICAglLLLTATPDQLGHQSHFARLRLLDPERFYDY 339
Cdd:cd18072 174 VCKLRAHAR--WALTGTPIQNNLLDMYSLLKFLRCSPFDDL 212
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
180-316 |
1.77e-04 |
|
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: 42.68 E-value: 1.77e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 180 GLGKTIEAGMIIhqQLLtgRASRILILLP-ESLQYQWlVEMLRRFNLQFAIfneercGEYDSSEENPFETEQLIIAPVGL 258
Cdd:cd17926 28 GSGKTLTALALI--AYL--KELRTLIVVPtDALLDQW-KERFEDFLGDSSI------GLIGGGKKKDFDDANVVVATYQS 96
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 515524197 259 LADSDKRlEQASQAQWDLVVVDEAHHLdwhpdgasPAYLAVEKLSRICAGLLL-LTATP 316
Cdd:cd17926 97 LSNLAEE-EKDLFDQFGLLIVDEAHHL--------PAKTFSEILKELNAKYRLgLTATP 146
|
|
| DEXHc_SMARCA5 |
cd18064 |
DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent ... |
174-342 |
1.29e-03 |
|
DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 (SMARCA5, also called SNF2H) is the catalytic subunit of the four known chromatin-remodeling complexes: CHRAC, RSF, ACF/WCRF, and WICH. SMARCA5 plays a major role organising arrays of nucleosomes adjacent to the binding sites for the architectural transcription factor CTCF sites and acts to promote CTCF binding SMARCA5 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: 350822 [Multi-domain] Cd Length: 244 Bit Score: 41.57 E-value: 1.29e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 174 LLSDEVGLGKTIEA----GMIIHQQLLTGRAsriLILLPESLQYQWLVEMLRRFNLQFAIfneerCGEYDSSEENPFETE 249
Cdd:cd18064 38 ILADEMGLGKTLQTisllGYMKHYRNIPGPH---MVLVPKSTLHNWMAEFKRWVPTLRAV-----CLIGDKDQRAAFVRD 109
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 250 QLIIAPVGLLADSDKRLEQASQA----QWDLVVVDEAHHLDWHPDGASPAYLAVEKLSRicaglLLLTATPDQLGHQSHF 325
Cdd:cd18064 110 VLLPGEWDVCVTSYEMLIKEKSVfkkfNWRYLVIDEAHRIKNEKSKLSEIVREFKTTNR-----LLLTGTPLQNNLHELW 184
|
170
....*....|....*..
gi 515524197 326 ARLRLLDPERFYDYDKF 342
Cdd:cd18064 185 ALLNFLLPDVFNSAEDF 201
|
|
| Cas3_I |
cd09696 |
CRISPR/Cas system-associated protein Cas3; Distinct Cas3 family with HD domain fused to ... |
524-581 |
2.42e-03 |
|
CRISPR/Cas system-associated protein Cas3; Distinct Cas3 family with HD domain fused to C-termus of Helicase domain; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DNA helicase Cas3; This protein includes both DEAH and HD motifs; signature gene for Type I
Pssm-ID: 187827 [Multi-domain] Cd Length: 843 Bit Score: 41.93 E-value: 2.42e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 515524197 524 EGCQLLICSEIGSEGRNFQFaRHLVLFDIPLnpDLLEQRIGRLDRIGQRHDIQIHIPY 581
Cdd:cd09696 334 QGTVYLVCTSAGEVGVNISA-DHLVCDLAPF--ESMQQRFGRVNRFGELQACQIAVVH 388
|
|
| DEXHc_Mot1 |
cd17999 |
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ... |
175-318 |
2.59e-03 |
|
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in eukaryotes) regulates transcription in association with TATA binding protein (TBP). Mot1, Ino80C, and NC2 function coordinately to regulate pervasive transcription in yeast and mammals. Mot1 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: 350757 [Multi-domain] Cd Length: 232 Bit Score: 40.41 E-value: 2.59e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 175 LSDEVGLGKTIEAGMII------HQQLLTGRASRILILLPESLQYQWLVEMLRRFNLQF-AIFNEERCGEYDSSEENPFE 247
Cdd:cd17999 24 LCDDMGLGKTLQTLCILasdhhkRANSFNSENLPSLVVCPPTLVGHWVAEIKKYFPNAFlKPLAYVGPPQERRRLREQGE 103
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 515524197 248 TEQLIIAPVG-LLADSDKRLEQasqaQWDLVVVDEAHHLDwhpDGASPAYLAVEKL---SRicaglLLLTATPDQ 318
Cdd:cd17999 104 KHNVIVASYDvLRNDIEVLTKI----EWNYCVLDEGHIIK---NSKTKLSKAVKQLkanHR-----LILSGTPIQ 166
|
|
| DEXHc_CHD3 |
cd18055 |
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; ... |
174-380 |
2.96e-03 |
|
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; Chromodomain-helicase-DNA-binding protein 3 (CHD3) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. It is required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity. CHD3 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: 350813 [Multi-domain] Cd Length: 232 Bit Score: 40.38 E-value: 2.96e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 174 LLSDEVGLGKTIEAGMIIHQQLLTGRAS-RILILLPESLQYQWLVEmLRRFNLQFAIFNeeRCGEYDSS---EENPFETE 249
Cdd:cd18055 23 ILADEMGLGKTIQTIVFLYSLYKEGHTKgPFLVSAPLSTIINWERE-FQMWAPDFYVVT--YTGDKDSRaiiRENEFSFD 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 250 QLII------------APVG---LLADSD-KRLEQAS--QAQWDLVVVDEAHHLDWHPdgaspaylavEKLSRICAGL-- 309
Cdd:cd18055 100 DNAVkggkkafkmkreAQVKfhvLLTSYElVTIDQAAlgSIRWACLVVDEAHRLKNNQ----------SKFFRVLNGYki 169
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 515524197 310 ---LLLTATPDQLGHQSHFARLRLLDPERFYDYDKFVAEEAGYSQiaeqakqitsnedlsEAQIAELKKLIDQH 380
Cdd:cd18055 170 dhkLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISK---------------EDQIKKLHDLLGPH 228
|
|
| DEXQc_INO80 |
cd18002 |
DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 ... |
174-342 |
4.49e-03 |
|
DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 chromatin remodeling complex. INO80 removes histone H3-containing nucleosomes from associated chromatin, promotes CENP-ACnp1 chromatin assembly at the centromere in a redundant manner with another chromatin-remodeling factor Chd1Hrp1. INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. INO80 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: 350760 [Multi-domain] Cd Length: 229 Bit Score: 39.80 E-value: 4.49e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 174 LLSDEVGLGKTIEA-GMIIHQQLLTGRASRILILLPESLQYQWLVEMlRRFNLQFAIF-----NEER-------CGEYDS 240
Cdd:cd18002 23 ILADEMGLGKTVQSiAVLAHLAEEHNIWGPFLVIAPASTLHNWQQEI-SRFVPQFKVLpywgnPKDRkvlrkfwDRKNLY 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 241 SEENPFeteQLIIAPVGLLADSDKRLEQAsqaQWDLVVVDEAHHLDwhpdgASPAYLAVEKLSRICAGLLLLTATPDQLG 320
Cdd:cd18002 102 TRDAPF---HVVITSYQLVVQDEKYFQRV---KWQYMVLDEAQAIK-----SSSSSRWKTLLSFHCRNRLLLTGTPIQNS 170
|
170 180
....*....|....*....|..
gi 515524197 321 HQSHFARLRLLDPERFYDYDKF 342
Cdd:cd18002 171 MAELWALLHFIMPTLFDSHDEF 192
|
|
| DEXHc_ATRX-like |
cd18007 |
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ... |
154-218 |
4.51e-03 |
|
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: 39.97 E-value: 4.51e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 515524197 154 LIPHQL--------HIAKEAGSRVAPR-VLLSDEVGLGKTIEAGMIIHQQL-LTGRASRILILLPESLQYQWLVE 218
Cdd:cd18007 1 LKPHQVegvrflwsNLVGTDVGSDEGGgCILAHTMGLGKTLQVITFLHTYLaAAPRRSRPLVLCPASTLYNWEDE 75
|
|
| DEXHc_CHD4 |
cd18056 |
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; ... |
174-365 |
7.28e-03 |
|
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. CHD4 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: 350814 [Multi-domain] Cd Length: 232 Bit Score: 39.28 E-value: 7.28e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 174 LLSDEVGLGKTIEAGMIIHQQLLTGRAS-RILILLPESLQYQWLvemlRRFNLQFA-IFNEERCGEYDSS---EENPFET 248
Cdd:cd18056 23 ILADEMGLGKTVQTAVFLYSLYKEGHSKgPFLVSAPLSTIINWE----REFEMWAPdMYVVTYVGDKDSRaiiRENEFSF 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 249 E----------------------------QLIIAPVGLLADSDkrleqasqaqWDLVVVDEAHHLDWHPdgaspaylavE 300
Cdd:cd18056 99 EdnairggkkasrmkkeasvkfhvlltsyELITIDMAILGSID----------WACLIVDEAHRLKNNQ----------S 158
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 301 KLSRICAGL-----LLLTATPDQLGHQSHFARLRLLDPERFYDYDKFVAEeagYSQIAEQaKQITSNEDL 365
Cdd:cd18056 159 KFFRVLNGYslqhkLLLTGTPLQNNLEELFHLLNFLTPERFHNLEGFLEE---FADIAKE-DQIKKLHDM 224
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| DEXHc_CHD3_4_5 |
cd17994 |
DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; ... |
274-380 |
9.99e-03 |
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DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; Chromodomain-helicase-DNA-binding protein 3 (CHD3) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. It is required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity. Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. It is thought to specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3 and plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. As a tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. CHD3, CHD4, and CHD5 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: 350752 [Multi-domain] Cd Length: 196 Bit Score: 38.19 E-value: 9.99e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515524197 274 WDLVVVDEAHHLDWHPdgaspaylavEKLSRICAGL-----LLLTATPDQLGHQSHFARLRLLDPERFYDYDKFVAEEAG 348
Cdd:cd17994 106 WAVLVVDEAHRLKNNQ----------SKFFRILNSYkigykLLLTGTPLQNNLEELFHLLNFLTPERFNNLQGFLEEFAD 175
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90 100 110
....*....|....*....|....*....|..
gi 515524197 349 YSQiaeqakqitsnedlsEAQIAELKKLIDQH 380
Cdd:cd17994 176 ISK---------------EDQIKKLHDLLGPH 192
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