|
Name |
Accession |
Description |
Interval |
E-value |
| PRK04914 |
PRK04914 |
RNA polymerase-associated protein RapA; |
2-966 |
0e+00 |
|
RNA polymerase-associated protein RapA;
Pssm-ID: 235319 [Multi-domain] Cd Length: 956 Bit Score: 1904.19 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 2 PFTLGQRWISDTESELGLGTVVAVDARTVTLLFPSTGENRLYARSDSPVTRVMFNPGDTITSHDGWQMQVEEVKEENGLL 81
Cdd:PRK04914 1 PFALGQRWISDTESELGLGTVVAVDGRTVTLLFPATGENRLYARNDAPLTRVMFNPGDTITSHEGWQLTVEEVEEENGLL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 82 TYIGTRLDTEESGVALREVFLDSKLVFSKPQDRLFAGQIDRMDRFALRYRARKYSSEQFRMPYSGLRGQRTSLIPHQLNI 161
Cdd:PRK04914 81 TYHGTRLDTEEEGVALRETFLDSKIRFNKPQDRLFAGQIDRMDRFALRYRALKHQSEQFQSPLRGLRGARASLIPHQLYI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 162 AHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEMLRRFNLRFALFDDERYAEAQHD 241
Cdd:PRK04914 161 AHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTGRAERVLILVPETLQHQWLVEMLRRFNLRFSLFDEERYAEAQHD 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 242 AYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLAEHVPGVLLLTATPEQLGM 321
Cdd:PRK04914 241 ADNPFETEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVWSEEAPSREYQVVEQLAEVIPGVLLLTATPEQLGQ 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 322 ESHFARLRLLDPNRFHDFAQFVEEQKNYRPVADAVAMLLAGNKLSNDELNMLGEMIGEQDIEPLLQAANSDSEDAQSARQ 401
Cdd:PRK04914 321 ESHFARLRLLDPDRFHDYEAFVEEQQQYRPVADAVQALLAGEKLSDDALNALGELLGEQDIEPLLQAANSDSEEAQAARQ 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 402 ELVSMLMDRHGTSRVLFRNTRNGVKGFPKRELHTIKLPLPTQYQTAIKVSgimgarksAEDRARDMLYPERIYQEFEgDN 481
Cdd:PRK04914 401 ELISELLDRHGTGRVLFRNTRAAVKGFPKRELHPIPLPLPEQYQTAIKVS--------LEARARDMLYPEQIYQEFE-DN 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 482 ATWWNFDPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLL 561
Cdd:PRK04914 472 ATWWNFDPRVEWLIDFLKSHRSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLL 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 562 CSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRWYHEGLDAFEHTCPTGRT 641
Cdd:PRK04914 552 CSEIGSEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHVPYLEGTAQERLFRWYHEGLNAFEHTCPTGRA 631
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 642 IYDSVYNDLINYLASPDQTEGFDDLIKNCREQHEALKAQLEQGRDRLLEIHSNGGEKAQALAESIEEQDDDTNLIAFAMN 721
Cdd:PRK04914 632 LYDEFGDELIPYLASPDDTDGLDELIAETREQHEALKAQLEQGRDRLLELNSCGGEKAQALAEAIAEQDDDTNLVNFALN 711
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 722 LFDIIGINQDDRGDNMIVLTPSDHMLVPDFPGLSEDGITITFDREVALAREDAQFITWEHPLIRNGLDLILSGDTGSSTI 801
Cdd:PRK04914 712 LFDIIGINQEDRGENAIVLTPSDHMLVPDFPGLPEDGVTITFDRDQALSREDMQFLTWEHPLIRGGLDLILSGDTGSTAV 791
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 802 SLLKNKALPVGTLLVELIYVVEAQAPKQLQLNRFLPPTPVRMLLDKNGNNLAAQVEFETFNRQLNAVNRHTGSKLVNAVQ 881
Cdd:PRK04914 792 ALLKNKALPAGTLLLELIYVVEAQAPKSLQLTRFLPPTPVRLLLDKNGNDLSAQVEFESLNRQLSAVNRHTASKLVKAVQ 871
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 882 QDVHAILQLGEAQIEKSARALIDAARNEADEKLSAELSRLEALRAVNPNIRDDELTAIESNRQQVMESLDQAGWRLDALR 961
Cdd:PRK04914 872 QDIHKLLQKAEAQAEAQARELIEQAKQEADEKLSAELSRLEALKAVNPNIRDDEIEALESQRQEVLEALDQAQLRLDAIR 951
|
....*
gi 16128053 962 LIVVT 966
Cdd:PRK04914 952 LIVVT 956
|
|
| RapA_C |
pfam12137 |
RNA polymerase recycling family C-terminal; This domain is found in bacteria. This domain is ... |
605-964 |
0e+00 |
|
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: 590.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 605 DIQIHVPYLEKTAQSVLVRWYHEGLDAFEHTCPTGRTIYDSVYNDLINYLASPDQtEGFDDLIKNCREQHEALKAQLEQG 684
Cdd:pfam12137 1 DIQIHVPYLEGSAQEVLFRWYHEGLNAFEQTCPAGQAVYEEFGDRLLDLLAAPDE-EALEALIAETRALREALKAELEQG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 685 RDRLLEIHSNGGEKAQALAESIEEQDDDTNLIAFAMNLFDIIGINQDDRGDNMIVLTPSDHMLVPDFPGLSEDGITITFD 764
Cdd:pfam12137 80 RDRLLELNSCRPERAEALVEAIAEEDDDTELADFMERLFDAFGVDQEDHSEGSIVLRPSDHMLVPDFPGLPEDGMTVTFD 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 765 REVALAREDAQFITWEHPLIRNGLDLILSGDTGSSTISLLKNKALPVGTLLVELIYVVEAQAPKQLQLNRFLPPTPVRML 844
Cdd:pfam12137 160 RDTALAREDLQFLTWEHPMVRGAMDLILSSDTGNAAVALLKNKALPAGTLLLELIFVVECVAPKALQLDRFLPPTPIRLL 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 845 LDKNGNNLAAQVEFETFNRQLNAVNRHTGSKLVNAVQQDVHAILQLGEAQIEKSARALIDAARNEADEKLSAELSRLEAL 924
Cdd:pfam12137 240 LDKKGNDLSAKVPFESLNRQLSPVNRHTARKLVKAQRDLIEKLLAKAEQLAEEQAEALIEQAKARMDQTLSAELERLEAL 319
|
330 340 350 360
....*....|....*....|....*....|....*....|
gi 16128053 925 RAVNPNIRDDELTAIESNRQQVMESLDQAGWRLDALRLIV 964
Cdd:pfam12137 320 QAVNPNIRDDEIEALEEQRAQLLAALDQARLRLDAIRLIV 359
|
|
| HepA |
COG0553 |
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
1-636 |
1.28e-111 |
|
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];
Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 359.54 E-value: 1.28e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 1 MPFTLGQRWISDTESELGLGTVVAVDARTVTLLFPSTGENRLYARSDSPVTRVMFNPGDTITSHDGWQMQVEEVKEENGL 80
Cdd:COG0553 109 LLLALLGLLLSLALLLLLLLLLLLLLLALLLVLLAALLLLLLLLLLLALLLGRLLLLALLLLALEALLLLGLLLALALLA 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 81 LTYIGTRLDTEESGvALREVFLDSKLVFSKPQDRLfagqidrmdrfalryRARKYSSEQFRMPySGLRGQrtsLIPHQLN 160
Cdd:COG0553 189 LLELALLAAEAELL-LLLELLLELELLAEAAVDAF---------------RLRRLREALESLP-AGLKAT---LRPYQLE 248
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 161 IAHDVG--RRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEMlRRFN--LRFALFDDERya 236
Cdd:COG0553 249 GAAWLLflRRLGLGGLLADDMGLGKTIQALALLLELKERGLARPVLIVAPTSLVGNWQREL-AKFApgLRVLVLDGTR-- 325
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 237 eAQHDAYNPFDTEQLVICSLDFARRSkqrLEHLCEAEWDLLVVDEAHHLvwsEDAPSREYQAIEQLAehVPGVLLLTATP 316
Cdd:COG0553 326 -ERAKGANPFEDADLVITSYGLLRRD---IELLAAVDWDLVILDEAQHI---KNPATKRAKAVRALK--ARHRLALTGTP 396
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 317 EQLGMESHFARLRLLDPNRFHDFAQFVEEQKNYRPVADAVAMllagnklsnDELNmlgEMIGE-------QDIEPLL--- 386
Cdd:COG0553 397 VENRLEELWSLLDFLNPGLLGSLKAFRERFARPIEKGDEEAL---------ERLR---RLLRPfllrrtkEDVLKDLpek 464
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 387 --QAANSDSEDAQSARQELVSMLMDRHGTSRVLFRNtrngvkgfpkrelHTIKLPLptqyqtaikvsgIMGARKSAEDRA 464
Cdd:COG0553 465 teETLYVELTPEQRALYEAVLEYLRRELEGAEGIRR-------------RGLILAA------------LTRLRQICSHPA 519
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 465 rdmLYPERIyQEFEGDnatwwnfDPRVEWLMGYLTSHRS--QKVLVICAKAATALQLEQVLREReGIRAAVFHEGMSIIE 542
Cdd:COG0553 520 ---LLLEEG-AELSGR-------SAKLEALLELLEELLAegEKVLVFSQFTDTLDLLEERLEER-GIEYAYLHGGTSAEE 587
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 543 RDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLV 622
Cdd:COG0553 588 RDELVDRFQEGPEAPVFLISLKAGGEGLNLTAADHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEEKIL 667
|
650
....*....|....
gi 16128053 623 RWYHEGLDAFEHTC 636
Cdd:COG0553 668 ELLEEKRALAESVL 681
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
154-345 |
1.10e-73 |
|
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: 241.42 E-value: 1.10e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 154 LIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEMLRRFNLRFALFDDE 233
Cdd:cd18011 1 PLPHQIDAVLRALRKPPVRLLLADEVGLGKTIEAGLIIKELLLRGDAKRVLILCPASLVEQWQDELQDKFGLPFLILDRE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 234 RYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDA-PSREYQAIEQLAEHVPGVLLL 312
Cdd:cd18011 81 TAAQLRRLIGNPFEEFPIVIVSLDLLKRSEERRGLLLSEEWDLVVVDEAHKLRNSGGGkETKRYKLGRLLAKRARHVLLL 160
|
170 180 190
....*....|....*....|....*....|...
gi 16128053 313 TATPEQLGMESHFARLRLLDPNRFHDFAQFVEE 345
Cdd:cd18011 161 TATPHNGKEEDFRALLSLLDPGRFAVLGRFLRL 193
|
|
| DpdE |
NF041062 |
protein DpdE; |
154-966 |
2.80e-63 |
|
protein DpdE;
Pssm-ID: 468989 [Multi-domain] Cd Length: 1048 Bit Score: 232.94 E-value: 2.80e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 154 LIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEMLRRFNLrfalfDDe 233
Cdd:NF041062 154 LEPHQVAVVRRVLQDPVQRYLLADEVGLGKTIEAGLVIRQHLLDNPDARVLVLVPDALVRQWRRELRDKFFL-----DD- 227
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 234 ryaeaqhdaynpFDTEQLVICSLDFARRSKQRLEHLceaewDLLVVDEAHHLV---WSEDAPSRE-YQAIEQLAEHVPGV 309
Cdd:NF041062 228 ------------FPGARVRVLSHEEPERWEPLLDAP-----DLLVVDEAHQLArlaWSGDPPERArYRELAALAHAAPRL 290
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 310 LLLTATPEQLGMESHFARLRLLDPNRF-----HDFAQFVEEQKNYRPV-----ADAVAMLLAGNklsndeLNMLGEMIGE 379
Cdd:NF041062 291 LLLSATPVLGNEETFLALLHLLDPDLYplddlEAFRERLEEREELGRLvlgldPDNPNFLLRQA------LDELRALFPE 364
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 380 QD-----IEPLLQAANSDSEDAQSARQELVSMLM----DRHGTSRVLFRNTRNGVKG----FPKRE-LHTIKLPLPT--- 442
Cdd:NF041062 365 DEelqelAEELLPLLDEFDDEEPEERARAVSALRahisETYRLHRRMIRNRRSSVLGadylVPGRAgPRVLVWESPArea 444
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 443 ------QYQTAIKVSGI---------------------------------------MGARKSAEDRARDMLypERIYQEF 477
Cdd:NF041062 445 adealeDWREEAALLDAesdpaaraayaralawlvarlggpddlaallrwrlrgdaASADLAGERELLEAL--IAALEDE 522
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 478 EGDNATwwnFDPRVEWLMGYLTSHRsqKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFaEEDTGA 557
Cdd:NF041062 523 AKDADL---LAALADWLLPLLRGSG--KAVVFCGDGSLADHLAAALARLGAGSVERHLSGQGADQAERAVRAF-RQDPSA 596
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 558 QVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQI--HVPYLEKTAQSVLVRWY---HEGLDAF 632
Cdd:NF041062 597 RVLVCDRSGEEGLNLQGADRLVHLDLPWSPNRLEQRIGRLDRYASLRGGRPveSYVLAPSDDDSLYSAWAdllREGFGVF 676
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 633 EHTCPTGRTIYDSVYNDLINYLASpDQTEGFDDLIkncreqhEALKAQLEQGR------DRLLEIHsNGGEKAQALAESI 706
Cdd:NF041062 677 DRSVASLQDALDEGLDEAWRALLE-EGPEALLEAI-------ARLRGELARERrrideqDALDSIE-ADAEEARSFAEAL 747
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 707 EEQDDDTNLIAFAMN--LFDIIGINQDDRGDNMIV---------LTPSDHmLVPDF-PGLSEDGitiTFDREVALAREDA 774
Cdd:NF041062 748 AEAEEDADELRDALLgwITKGLRFRKRRDEVDDVFrfdfasrrtLLPPRL-LIRRFlPGLDREG---TFSRSVALRRPGV 823
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 775 QFITWEHPLIRNGLDLILSGDTGSST--ISLLKNKALPvGTLLVELIYVVEAQAPKQLQLN-------------RFLPPT 839
Cdd:NF041062 824 RLFRYGNPFVDALARLLRWDDRGQAFamWRLDPSWRGE-PRLYFRFDFLVEADLLPALALLdgaarralrrradRLFPPF 902
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 840 PVRMLLDKNGNnlaaQVEFETFNRQLNAVNRHTGSKL---VNAVQQDVHAILQLGEAQ--------IEKSARAL------ 902
Cdd:NF041062 903 TLRVWVDADGE----EVTDPELLAWLNAPYSKPGGVGgrdYNLNGSRWEALLELFGADewrelcraAEEAARALlrsrad 978
|
890 900 910 920 930 940
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16128053 903 ----IDAARNEADEKLSAELSRLEALRAVNPNIRDDELTAIESNRQQVM-ESLDQAGWRLDALRLIVVT 966
Cdd:NF041062 979 laeaCARAQARARADLAVRLAQLRARAAAGSLVEDAEELAREVALAQALaDGIRNPSVRLDAVGCVVLS 1047
|
|
| DEXHc_Snf |
cd17919 |
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
154-333 |
7.13e-40 |
|
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: 145.40 E-value: 7.13e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 154 LIPHQLNIAHDVGRR--HAPRVLLADEVGLGKTIEAGMILHQQLLSGA-AERVLIIVPETLQHQWLVEMLRRF-NLRFAL 229
Cdd:cd17919 1 LRPYQLEGLNFLLELyeNGPGGILADEMGLGKTLQAIAFLAYLLKEGKeRGPVLVVCPLSVLENWEREFEKWTpDLRVVV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 230 FDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKqrlEHLCEAEWDLLVVDEAHHLVWSEdapSREYQAIEQLAEHVpgV 309
Cdd:cd17919 81 YHGSQRERAQIRAKEKLDKFDVVLTTYETLRRDK---ASLRKFRWDLVVVDEAHRLKNPK---SQLSKALKALRAKR--R 152
|
170 180
....*....|....*....|....
gi 16128053 310 LLLTATPEQLGMESHFARLRLLDP 333
Cdd:cd17919 153 LLLTGTPLQNNLEELWALLDFLDP 176
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
170-315 |
1.38e-31 |
|
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: 120.59 E-value: 1.38e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 170 APRVLLADEVGLGKTIEAGMILHQQLLSgAAERVLIIVPE-TLQHQWLVEMLRRF--NLRFALFDDERYAEaqHDAYNPF 246
Cdd:cd00046 1 GENVLITAPTGSGKTLAALLAALLLLLK-KGKKVLVLVPTkALALQTAERLRELFgpGIRVAVLVGGSSAE--EREKNKL 77
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16128053 247 DTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLAEHVPGVLLLTAT 315
Cdd:cd00046 78 GDADIIIATPDMLLNLLLREDRLFLKDLKLIIVDEAHALLIDSRGALILDLAVRKAGLKNAQVILLSAT 146
|
|
| Tudor_RapA |
pfam18337 |
RapA N-terminal Tudor like domain; This is one of two Tudor-like domains found in the ... |
55-118 |
4.95e-30 |
|
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: 112.98 E-value: 4.95e-30
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16128053 55 FNPGDTITSHDGWQMQVEEVKEENGLLTYIGTRLDTEEsgVALREVFLDSKLVFSKPQDRLFAG 118
Cdd:pfam18337 1 FNVGDTITSHEGWKLTVEEVEEENGLLIYLGTREDGEE--VSLPETELDHFIQFNKPQDRLFAG 62
|
|
| SF2_C_SNF |
cd18793 |
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
488-609 |
2.13e-29 |
|
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: 113.73 E-value: 2.13e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 488 DPRVEWLMGYLTSHRS--QKVLVICAKAATALQLEQVLREReGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEI 565
Cdd:cd18793 10 SGKLEALLELLEELREpgEKVLIFSQFTDTLDILEEALRER-GIKYLRLDGSTSSKERQKLVDRFNEDPDIRVFLLSTKA 88
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 16128053 566 GSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIH 609
Cdd:cd18793 89 GGVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQKKPVVVY 132
|
|
| Tudor_1_RapA |
pfam18339 |
RapA N-terminal Tudor like domain 1; This is one of two Tudor-like domains found in the ... |
3-53 |
7.93e-27 |
|
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: 103.33 E-value: 7.93e-27
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 16128053 3 FTLGQRWISDTESELGLGTVVAVDARTVTLLFPSTGENRLYARSDSPVTRV 53
Cdd:pfam18339 1 FAPGQRWISDTEPELGLGIVVEVDGRTVTILFPASGETRTYATANAPLTRV 51
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
490-601 |
7.87e-22 |
|
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: 91.12 E-value: 7.87e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 490 RVEWLMGYLTSHRSQKVLVICAKAATALqlEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTgaQVLLCSEIGSEG 569
Cdd:pfam00271 2 KLEALLELLKKERGGKVLIFSQTKKTLE--AELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKI--DVLVATDVAERG 77
|
90 100 110
....*....|....*....|....*....|..
gi 16128053 570 RNFQFASHMVMFDLPFNPDLLEQRIGRLDRIG 601
Cdd:pfam00271 78 LDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
152-336 |
3.04e-18 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 84.08 E-value: 3.04e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 152 TSLIPHQLNIAHDVgRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVP-ETLQHQWLVEMLRRF----NLR 226
Cdd:smart00487 7 EPLRPYQKEAIEAL-LSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPtRELAEQWAEELKKLGpslgLKV 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 227 FALFDDERYAEAQHDAYNpfDTEQLVICSLDFARRSKQRlEHLCEAEWDLLVVDEAHHLvwSEDAPSREYQAIEQLAEHV 306
Cdd:smart00487 86 VGLYGGDSKREQLRKLES--GKTDILVTTPGRLLDLLEN-DKLSLSNVDLVILDEAHRL--LDGGFGDQLEKLLKLLPKN 160
|
170 180 190
....*....|....*....|....*....|
gi 16128053 307 PGVLLLTATPEQLGMEshFARLRLLDPNRF 336
Cdd:smart00487 161 VQLLLLSATPPEEIEN--LLELFLNDPVFI 188
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
518-601 |
7.19e-17 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 76.10 E-value: 7.19e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 518 QLEQVLREReGIRAAVFHEGMSIIERDRAAAWFAEEDTgaQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRL 597
Cdd:smart00490 2 ELAELLKEL-GIKVARLHGGLSQEEREEILDKFNNGKI--KVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
|
....
gi 16128053 598 DRIG 601
Cdd:smart00490 79 GRAG 82
|
|
| DEXHc_CHD6_7_8_9 |
cd17995 |
DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; ... |
174-345 |
8.55e-16 |
|
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: 77.67 E-value: 8.55e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEAGMILHQQLLSGAAER-VLIIVP-ETLQHqWLVEMLRRFNLRFALFDDERYAEA---QHDAYNPFD- 247
Cdd:cd17995 23 ILADEMGLGKTIQSIAFLEHLYQVEGIRGpFLVIAPlSTIPN-WQREFETWTDMNVVVYHGSGESRQiiqQYEMYFKDAq 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 248 ---------------TEQLVICSLDFARRskqrlehlceAEWDLLVVDEAHHLvwsEDAPSREYQAIEQLA-EHVpgvLL 311
Cdd:cd17995 102 grkkkgvykfdvlitTYEMVIADAEELRK----------IPWRVVVVDEAHRL---KNRNSKLLQGLKKLTlEHK---LL 165
|
170 180 190
....*....|....*....|....*....|....
gi 16128053 312 LTATPEQLGMESHFARLRLLDPNRFHDFAQFVEE 345
Cdd:cd17995 166 LTGTPLQNNTEELWSLLNFLEPEKFPSSEEFLEE 199
|
|
| DEXHc_RAD54 |
cd18004 |
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ... |
166-375 |
1.94e-15 |
|
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: 76.94 E-value: 1.94e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 166 GRRHAPR--VLLADEVGLGKTIEAGMILHQQLLSGA-----AERVLIIVPETLQHQWLVEMLRRFNLRF----ALFDDER 234
Cdd:cd18004 18 GRRGYGGggAILADEMGLGKTLQAIALVWTLLKQGPygkptAKKALIVCPSSLVGNWKAEFDKWLGLRRikvvTADGNAK 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 235 YAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLceAEWDLLVVDEAHHLvwsEDAPSREYQAIEQLAehVPGVLLLTA 314
Cdd:cd18004 98 DVKASLDFFSSASTYPVLIISYETLRRHAEKLSKK--ISIDLLICDEGHRL---KNSESKTTKALNSLP--CRRRLLLTG 170
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 16128053 315 TPEQLGMESHFARLRLLDPNRFHDFAQFveeQKNY-RPVadavamLLAGNKLSNDELNMLGE 375
Cdd:cd18004 171 TPIQNDLDEFFALVDFVNPGILGSLASF---RKVFeEPI------LRSRDPDASEEDKELGA 223
|
|
| DEXQc_arch_SWI2_SNF2 |
cd18012 |
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ... |
175-344 |
6.68e-15 |
|
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: 74.91 E-value: 6.68e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 175 LADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEmLRRFN--LRFALFDDERYAEAQHDAYNPFDteqLV 252
Cdd:cd18012 28 LADDMGLGKTLQTLALLLSRKEEGRKGPSLVVAPTSLIYNWEEE-AAKFApeLKVLVIHGTKRKREKLRALEDYD---LV 103
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 253 ICSLDFARRSkqrLEHLCEAEWDLLVVDEAHHLvwsEDAPSREYQAIEQL-AEHvpgVLLLTATPeqlgMESHFARL--- 328
Cdd:cd18012 104 ITSYGLLRRD---IELLKEVKFHYLVLDEAQNI---KNPQTKTAKAVKALkADH---RLALTGTP----IENHLGELwsi 170
|
170
....*....|....*..
gi 16128053 329 -RLLDPNRFHDFAQFVE 344
Cdd:cd18012 171 fDFLNPGLLGSYKRFKK 187
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
81-759 |
4.39e-14 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 76.22 E-value: 4.39e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 81 LTYIGTRLDTEESGVALREVFLDSKLVFSKPQDRLFAGQIDRMDRFALRYRARKYSSEQFRMPYSGLRGQRTSLIPHQ-- 158
Cdd:COG1061 8 ERGADKLRSSLLLLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEALEAGDEASGTSFELRPYQqe 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 159 -LNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGaaeRVLIIVP-ETLQHQWlVEMLRRFNLRFALFDDERYA 236
Cdd:COG1061 88 aLEALLAALERGGGRGLVVAPTGTGKTVLALALAAELLRGK---RVLVLVPrRELLEQW-AEELRRFLGDPLAGGGKKDS 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 237 EAQHdaynpfdteqlVICSLDFARRSKQRleHLCEAEWDLLVVDEAHHlvwsedAPSREYQAIeqlAEHVPG--VLLLTA 314
Cdd:COG1061 164 DAPI-----------TVATYQSLARRAHL--DELGDRFGLVIIDEAHH------AGAPSYRRI---LEAFPAayRLGLTA 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 315 TPEQLGMEshfarlrlldPNRFHDFAQFVEEqknyRPVADAVAmllagnklsndelnmlGEMIGEQDIEPLLQAANSDSE 394
Cdd:COG1061 222 TPFRSDGR----------EILLFLFDGIVYE----YSLKEAIE----------------DGYLAPPEYYGIRVDLTDERA 271
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 395 DAQSARQELVSMLMdrhgtsrvlfrntrngvkgfpkrelhtiklplptqyqtaikvsgimgarkSAEDRARDMLypERIY 474
Cdd:COG1061 272 EYDALSERLREALA--------------------------------------------------ADAERKDKIL--RELL 299
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 475 QEFEGDnatwwnfdprvewlmgyltshrsQKVLVICAKAATALQLEQVLREReGIRAAVFHEGMSIIERDRAAAWFAEED 554
Cdd:COG1061 300 REHPDD-----------------------RKTLVFCSSVDHAEALAELLNEA-GIRAAVVTGDTPKKEREEILEAFRDGE 355
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 555 TgaQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHD-------IQIHVPYLEKTAQSVLVRWYHE 627
Cdd:COG1061 356 L--RILVTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGRGLRPAPGKEdalvydfVGNDVPVLEELAKDLRDLAGYR 433
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 628 GLDAFEHTCPTGRTIYDSVYNDLINYLASPDQTEGFDDLIKNCREQHEALKAQLEQGRDRLLEIHSNGGEKAQALAESIE 707
Cdd:COG1061 434 VEFLDEEESEELALLIAVKPALEVKGELEEELLEELELLEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKE 513
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|..
gi 16128053 708 EQDDDTNLIAFAMNLFDIIGINQDDRGDNMIVLTPSDHMLVPDFPGLSEDGI 759
Cdd:COG1061 514 LLLLLALAKLLKLLLLLLLLLLLELLELLAALLRLEELAALLLKELLRAALA 565
|
|
| DEXHc_HARP_SMARCAL1 |
cd18010 |
DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin ... |
168-340 |
1.21e-13 |
|
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: 71.08 E-value: 1.21e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 168 RHAPRVLLADEVGLGKTIEAGMILHqqllsgaAER----VLIIVPETLQHQWlVEMLRRFnLRFALFDDERYAEAQHDAY 243
Cdd:cd18010 14 RRGGRVLIADEMGLGKTVQAIAIAA-------YYReewpLLIVCPSSLRLTW-ADEIERW-LPSLPPDDIQVIVKSKDGL 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 244 NPFDTeQLVICSLDFARRSKqrlEHLCEAEWDLLVVDEAHHLvwsEDAPSREYQAIEQLAEHVPGVLLLTATP-----EQ 318
Cdd:cd18010 85 RDGDA-KVVIVSYDLLRRLE---KQLLARKFKVVICDESHYL---KNSKAKRTKAALPLLKRAKRVILLSGTPalsrpIE 157
|
170 180
....*....|....*....|....*
gi 16128053 319 LgmeshFARLRLLDP---NRFHDFA 340
Cdd:cd18010 158 L-----FTQLDALDPklfGRFHDFG 177
|
|
| SNF2-rel_dom |
pfam00176 |
SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
174-342 |
4.47e-13 |
|
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: 70.79 E-value: 4.47e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEA----GMILHQQLLSGAAerVLIIVPETLQHQWLVEMLRRFNL----RFALFDDERYAEAQHDAYNP 245
Cdd:pfam00176 21 ILADEMGLGKTLQTisllLYLKHVDKNWGGP--TLIVVPLSLLHNWMNEFERWVSPpalrVVVLHGNKRPQERWKNDPNF 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 246 FDTEQLVICSLDFARRSKqrlEHLCEAEWDLLVVDEAHHLvwsEDAPSREYQAIEQLAEHvpGVLLLTATPEQLGMESHF 325
Cdd:pfam00176 99 LADFDVVITTYETLRKHK---ELLKKVHWHRIVLDEGHRL---KNSKSKLSKALKSLKTR--NRWILTGTPLQNNLEELW 170
|
170
....*....|....*..
gi 16128053 326 ARLRLLDPNRFHDFAQF 342
Cdd:pfam00176 171 ALLNFLRPGPFGSLSTF 187
|
|
| DEXHc_CHD1L |
cd18006 |
DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, ... |
154-360 |
7.55e-12 |
|
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: 65.92 E-value: 7.55e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 154 LIPHQLN----IAHDVGRRHAprVLLADEVGLGKTIEAgmilhQQLLSGAAERV------LIIVPETLQHQWlVEMLRRF 223
Cdd:cd18006 1 LRPYQLEgvnwLLQCRAEQHG--CILGDEMGLGKTCQT-----ISLLWYLAGRLkllgpfLVLCPLSVLDNW-KEELNRF 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 224 --NLRFALF--DDERYAEAQHDAY--NPFD----TEQLVICSLDFARRSKqrlehlceaeWDLLVVDEAHHLvwsEDAPS 293
Cdd:cd18006 73 apDLSVITYmgDKEKRLDLQQDIKstNRFHvlltTYEICLKDASFLKSFP----------WASLVVDEAHRL---KNQNS 139
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 16128053 294 REYQAIEQLAehVPGVLLLTATPEQLGMESHFARLRLLDPNRF-----HDFAQFVEEQKNYRPVADAVAMLL 360
Cdd:cd18006 140 LLHKTLSEFS--VDFRLLLTGTPIQNSLQELYALLSFIEPNVFpkdklDDFIKAYSETDDESETVEELHLLL 209
|
|
| DEXHc_CHD1_2 |
cd17993 |
DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and ... |
173-346 |
7.43e-10 |
|
DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and similar proteins; Chromodomain-helicase-DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin-remodeling factor which functions as the substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. It is not only involved in transcription-related chromatin-remodeling, but is also required to maintain a specific chromatin configuration across the genome. CHD1 is also associated with histone deacetylase (HDAC) activity. Chromodomain-helicase-DNA-binding protein 2 (CHD2) is a DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. It is involved in myogenesis via interaction with MYOD1; it binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression. Both 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: 350751 [Multi-domain] Cd Length: 218 Bit Score: 60.06 E-value: 7.43e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 173 VLLADEVGLGKTIEA----GMILHQQLLSGAaerVLIIVP--------ETLQhQWLVEMlrrfNLRFALFDDE-----RY 235
Cdd:cd17993 23 GILADEMGLGKTVQTisflSYLFHSQQQYGP---FLVVVPlstmpawqREFA-KWAPDM----NVIVYLGDIKsrdtiRE 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 236 AEAQHDAYNPFDTEQLvICSLDFARRSKQRLEHLceaEWDLLVVDEAHHLVWSEdapSREYQAIEQLaeHVPGVLLLTAT 315
Cdd:cd17993 95 YEFYFSQTKKLKFNVL-LTTYEIILKDKAFLGSI---KWQYLAVDEAHRLKNDE---SLLYEALKEF--KTNNRLLITGT 165
|
170 180 190
....*....|....*....|....*....|.
gi 16128053 316 PEQLGMESHFARLRLLDPNRFHDFAQFVEEQ 346
Cdd:cd17993 166 PLQNSLKELWALLHFLMPGKFDIWEEFEEEH 196
|
|
| DEXHc_Mot1 |
cd17999 |
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ... |
175-318 |
1.56e-09 |
|
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: 59.29 E-value: 1.56e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 175 LADEVGLGKTIEAGMIL------HQQLLSGAAERVLIIVPETLQHQWLVEMLRRFNLRFaLFDDERYAEAQHDAYNP--F 246
Cdd:cd17999 24 LCDDMGLGKTLQTLCILasdhhkRANSFNSENLPSLVVCPPTLVGHWVAEIKKYFPNAF-LKPLAYVGPPQERRRLReqG 102
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16128053 247 DTEQLVICSLDFARRSkqrLEHLCEAEWDLLVVDEAHHLvwsEDAPSREYQAIEQL-AEHvpgVLLLTATPEQ 318
Cdd:cd17999 103 EKHNVIVASYDVLRND---IEVLTKIEWNYCVLDEGHII---KNSKTKLSKAVKQLkANH---RLILSGTPIQ 166
|
|
| DEXHc_CHD6 |
cd18058 |
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; ... |
174-345 |
8.18e-09 |
|
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: 56.97 E-value: 8.18e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEMLRRFNLRFALFDDERYAEA---QHDAY------N 244
Cdd:cd18058 23 ILADEMGLGKTIQSITFLSEIFLMGIRGPFLIIAPLSTITNWEREFRTWTEMNAIVYHGSQISRQmiqQYEMYyrdeqgN 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 245 PFDTE---QLVICSLDFARRSKQRLEHLceaEWDLLVVDEAHHLvwsedaPSREYQAIEQLA----EHvpgVLLLTATPE 317
Cdd:cd18058 103 PLSGIfkfQVVITTFEMILADCPELKKI---NWSCVIIDEAHRL------KNRNCKLLEGLKlmalEH---KVLLTGTPL 170
|
170 180
....*....|....*....|....*...
gi 16128053 318 QLGMESHFARLRLLDPNRFHDFAQFVEE 345
Cdd:cd18058 171 QNSVEELFSLLNFLEPSQFPSETTFLEE 198
|
|
| DEXHc_ERCC6L2 |
cd18005 |
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ... |
173-342 |
1.12e-08 |
|
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: 57.00 E-value: 1.12e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 173 VLLADEVGLGKTIEA----GMILH-----------------QQLLSGAAERVLIIVPETLQHQWLVEMLRRFNLRFALF- 230
Cdd:cd18005 22 GILGDDMGLGKTVQViaflAAVLGktgtrrdrennrprfkkKPPASSAKKPVLIVAPLSVLYNWKDELDTWGHFEVGVYh 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 231 ----DDERYAEAQHDAYnpfdteQLVICSLDFARRSKQRLEHLceaEWDLLVVDEAHHLvwsEDAPSREYQAIEQL-AEH 305
Cdd:cd18005 102 gsrkDDELEGRLKAGRL------EVVVTTYDTLRRCIDSLNSI---NWSAVIADEAHRI---KNPKSKLTQAMKELkCKV 169
|
170 180 190
....*....|....*....|....*....|....*..
gi 16128053 306 VPGvllLTATPEQLGMESHFARLRLLDPNRFHDFAQF 342
Cdd:cd18005 170 RIG---LTGTLLQNNMKELWCLLDWAVPGALGSRSQF 203
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
172-317 |
1.92e-08 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 54.60 E-value: 1.92e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 172 RVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLqhqwLVE-MLRRFNlRFALFDDERYAEAQHDAYNP-FDTE 249
Cdd:pfam04851 25 RGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRKD----LLEqALEEFK-KFLPNYVEIGEIISGDKKDEsVDDN 99
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 16128053 250 QLVICSLD-FARRSKQRLEHLCEAEWDLLVVDEAHHLVwsedapsreYQAIEQLAEHVPGVLLL--TATPE 317
Cdd:pfam04851 100 KIVVTTIQsLYKALELASLELLPDFFDVIIIDEAHRSG---------ASSYRNILEYFKPAFLLglTATPE 161
|
|
| DEXHc_CHD8 |
cd18060 |
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; ... |
174-345 |
7.60e-08 |
|
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; Chromodomain-helicase-DNA-binding protein 8 (CHD8) is a DNA helicase that acts as a chromatin remodeling factor and regulates transcription. It also acts as a transcription repressor by remodeling chromatin structure and recruiting histone H1 to target genes. It suppresses p53/TP53-mediated apoptosis by recruiting histone H1 and preventing p53/TP53 transactivation activity and of STAT3 activity by suppressing the LIF-induced STAT3 transcriptional activity. It also acts as a negative regulator of Wnt signaling pathway and CTNNB1-targeted gene expression. CHD8 is also involved in both enhancer blocking and epigenetic remodeling at chromatin boundary via its interaction with CTCF. It also acts as a transcription activator via its interaction with ZNF143 by participating in efficient U6 RNA polymerase III transcription. CHD8 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: 350818 [Multi-domain] Cd Length: 222 Bit Score: 54.29 E-value: 7.60e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEMLRRFNLRFALFDDE---RYAEAQHDAYNPFDTEQ 250
Cdd:cd18060 23 ILADEMGLGKTIQSIAFLQEVYNVGIHGPFLVIAPLSTITNWEREFNTWTEMNTIVYHGSlasRQMIQQYEMYCKDSRGR 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 251 LVICSLDFA------RRSKQRLEHLCEAEWDLLVVDEAHHLvwsedaPSREYQAIEQLA----EHVpgvLLLTATPEQLG 320
Cdd:cd18060 103 LIPGAYKFDalittfEMILSDCPELREIEWRCVIIDEAHRL------KNRNCKLLDSLKhmdlEHK---VLLTGTPLQNT 173
|
170 180
....*....|....*....|....*
gi 16128053 321 MESHFARLRLLDPNRFHDFAQFVEE 345
Cdd:cd18060 174 VEELFSLLHFLEPSQFPSESEFLKD 198
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
494-602 |
8.34e-08 |
|
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: 51.74 E-value: 8.34e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 494 LMGYLTSHRSQKVLVICAKAATALQLEQVLREReGIRAAVFHEGMSIIERDRAAAWFAEEDTGaqVLLCSEIGSEGRNFQ 573
Cdd:cd18787 18 LLLLLEKLKPGKAIIFVNTKKRVDRLAELLEEL-GIKVAALHGDLSQEERERALKKFRSGKVR--VLVATDVAARGLDIP 94
|
90 100
....*....|....*....|....*....
gi 16128053 574 FASHMVMFDLPFNPDLLEQRIGRLDRIGQ 602
Cdd:cd18787 95 GVDHVINYDLPRDAEDYVHRIGRTGRAGR 123
|
|
| DEXHc_CHD7 |
cd18059 |
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; ... |
174-345 |
1.09e-07 |
|
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; Chromodomain-helicase-DNA-binding protein 7 (CHD7) is a probable transcription regulator. It may be involved in the 45S precursor rRNA production. CHD7 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: 350817 [Multi-domain] Cd Length: 222 Bit Score: 53.50 E-value: 1.09e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEMLRRFNLRFALFDDERYAEAQHDAYNPF--DTE-- 249
Cdd:cd18059 23 ILADEMGLGKTIQSITFLYEIYLKGIHGPFLVIAPLSTIPNWEREFRTWTELNVVVYHGSQASRRTIQLYEMYfkDPQgr 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 250 --------QLVICSLDFARRSKQRLEHLceaEWDLLVVDEAHHLvwsedaPSREYQAIEQLA----EHvpgVLLLTATPE 317
Cdd:cd18059 103 vikgsykfHAIITTFEMILTDCPELRNI---PWRCVVIDEAHRL------KNRNCKLLEGLKmmdlEH---KVLLTGTPL 170
|
170 180
....*....|....*....|....*...
gi 16128053 318 QLGMESHFARLRLLDPNRFHDFAQFVEE 345
Cdd:cd18059 171 QNTVEELFSLLHFLEPSRFPSETTFMQE 198
|
|
| DEXHc_ERCC6L |
cd18001 |
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ... |
154-318 |
1.87e-07 |
|
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: 53.14 E-value: 1.87e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 154 LIPHQLNIAHDVGRRHAPRV--LLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEMLR-RFNLRFALF 230
Cdd:cd18001 1 LYPHQREGVAWLWSLHDGGKggILADDMGLGKTVQICAFLSGMFDSGLIKSVLVVMPTSLIPHWVKEFAKwTPGLRVKVF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 231 DDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLC--EAEWDLLVVDEAHHLvwsEDAPSREYQAIEQL-AEHvp 307
Cdd:cd18001 81 HGTSKKERERNLERIQRGGGVLLTTYGMVLSNTEQLSADDhdEFKWDYVILDEGHKI---KNSKTKSAKSLREIpAKN-- 155
|
170
....*....|.
gi 16128053 308 gVLLLTATPEQ 318
Cdd:cd18001 156 -RIILTGTPIQ 165
|
|
| DEXHc_HELLS_SMARCA6 |
cd18009 |
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ... |
174-342 |
6.26e-07 |
|
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: 51.62 E-value: 6.26e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEmLRRFN-----LRFALFDDERYAEAQHDAYNPFDT 248
Cdd:cd18009 26 ILADEMGLGKTIQTIALLAHLRERGVWGPFLVIAPLSTLPNWVNE-FARFTpsvpvLLYHGTKEERERLRKKIMKREGTL 104
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 249 EQ--LVICSLDFARRSKQRLEHLceaEWDLLVVDEAHHLvwsEDAPSREYQAIEQLAEhvPGVLLLTATPEQLGMESHFA 326
Cdd:cd18009 105 QDfpVVVTSYEIAMRDRKALQHY---AWKYLIVDEGHRL---KNLNCRLIQELKTFNS--DNRLLLTGTPLQNNLSELWS 176
|
170
....*....|....*.
gi 16128053 327 RLRLLDPNRFHDFAQF 342
Cdd:cd18009 177 LLNFLLPDVFDDLSSF 192
|
|
| DEXHc_CHD3_4_5 |
cd17994 |
DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; ... |
173-345 |
6.66e-07 |
|
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: 50.90 E-value: 6.66e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 173 VLLADEVGLGKTIEAGMILHQQLLSGAAE-RVLIIVPETLQHQWLVEmlrrfnlrFALFDDERYAEAQHDAYNPFDTEQL 251
Cdd:cd17994 22 TILADEMGLGKTIQTIVFLYSLYKEGHSKgPFLVSAPLSTIINWERE--------FEMWAPDFYVVTYVGDHVLLTSYEL 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 252 VicSLDFARrskqrlehLCEAEWDLLVVDEAHHLvwsEDAPSREYQAIEQLaeHVPGVLLLTATPEQLGMESHFARLRLL 331
Cdd:cd17994 94 I--SIDQAI--------LGSIDWAVLVVDEAHRL---KNNQSKFFRILNSY--KIGYKLLLTGTPLQNNLEELFHLLNFL 158
|
170
....*....|....
gi 16128053 332 DPNRFHDFAQFVEE 345
Cdd:cd17994 159 TPERFNNLQGFLEE 172
|
|
| DEXHc_SMARCA1_SMARCA5 |
cd17997 |
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ... |
174-342 |
7.43e-07 |
|
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 and 5 (SMARCA1 and SMARCA5) 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: 350755 [Multi-domain] Cd Length: 222 Bit Score: 51.17 E-value: 7.43e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEA----GMILHQQLLSGAAervLIIVPETLQHQWLVEMLR---RFNLRFALFDDERYAEAQHDA--YN 244
Cdd:cd17997 26 ILADEMGLGKTLQTisllGYLKHYKNINGPH---LIIVPKSTLDNWMREFKRwcpSLRVVVLIGDKEERADIIRDVllPG 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 245 PFDteqLVICSLDFARRSKQrleHLCEAEWDLLVVDEAHHLvwsEDAPSREYQAIEQLaeHVPGVLLLTATPEQLGMESH 324
Cdd:cd17997 103 KFD---VCITSYEMVIKEKT---VLKKFNWRYIIIDEAHRI---KNEKSKLSQIVRLF--NSRNRLLLTGTPLQNNLHEL 171
|
170
....*....|....*...
gi 16128053 325 FARLRLLDPNRFHDFAQF 342
Cdd:cd17997 172 WALLNFLLPDVFTSSEDF 189
|
|
| DEXHc_SMARCA5 |
cd18064 |
DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent ... |
174-342 |
2.52e-06 |
|
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: 50.05 E-value: 2.52e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEA----GMILHQQLLSGAAervLIIVPETLQHQWLVEMLRRF-NLRFALF--DDERYAEAQHDAYNPF 246
Cdd:cd18064 38 ILADEMGLGKTLQTisllGYMKHYRNIPGPH---MVLVPKSTLHNWMAEFKRWVpTLRAVCLigDKDQRAAFVRDVLLPG 114
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 247 DTEqLVICSLDFARRSKQRLEHLceaEWDLLVVDEAHHLVWSEDAPS---REYQAIEQlaehvpgvLLLTATPEQLGMES 323
Cdd:cd18064 115 EWD-VCVTSYEMLIKEKSVFKKF---NWRYLVIDEAHRIKNEKSKLSeivREFKTTNR--------LLLTGTPLQNNLHE 182
|
170
....*....|....*....
gi 16128053 324 HFARLRLLDPNRFHDFAQF 342
Cdd:cd18064 183 LWALLNFLLPDVFNSAEDF 201
|
|
| DEXHc_RAD54A |
cd18067 |
DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as ... |
174-349 |
3.15e-06 |
|
DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as RAD54L or RAD54, plays a role in homologous recombination related repair of DNA double-strand breaks. RAD54A 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: 350825 [Multi-domain] Cd Length: 243 Bit Score: 49.39 E-value: 3.15e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEAGMILHQQLLSG-----AAERVLIIVPETLQHQWLVEMLRRFNLRFALF--------DDERYAEAQH 240
Cdd:cd18067 28 IMADEMGLGKTLQCITLMWTLLRQSpqckpEIDKAIVVSPSSLVKNWANELGKWLGGRLQPLaidggskkEIDRKLVQWA 107
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 241 DAYNPFDTEQLVICSLDFARRSkqrLEHLCEAEWDLLVVDEAHHLVWSEdapSREYQAIEQLaeHVPGVLLLTATPEQLG 320
Cdd:cd18067 108 SQQGRRVSTPVLIISYETFRLH---VEVLQKGEVGLVICDEGHRLKNSD---NQTYQALDSL--NTQRRVLLSGTPIQND 179
|
170 180
....*....|....*....|....*....
gi 16128053 321 MESHFARLRLLDPNRFHDFAQFveeQKNY 349
Cdd:cd18067 180 LSEYFSLVNFVNPGILGTAAEF---KKNF 205
|
|
| DEXHc_SMARCA1 |
cd18065 |
DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent ... |
174-342 |
3.83e-06 |
|
DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 (SMARCA1, also called SNF2L) is a component of NURF (nucleosome-remodeling factor) and CERF (CECR2-containing-remodeling factor) complexes which promote the perturbation of chromatin structure in an ATP-dependent manner. SMARCA1 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: 350823 [Multi-domain] Cd Length: 233 Bit Score: 49.25 E-value: 3.83e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEA----GMILHQQLLSGAAervLIIVPETLQHQWLVEMLRRF-NLRFALFDDERYAEAQ--HDAYNPF 246
Cdd:cd18065 38 ILADEMGLGKTLQTiallGYLKHYRNIPGPH---MVLVPKSTLHNWMNEFKRWVpSLRAVCLIGDKDARAAfiRDVMMPG 114
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 247 DTEqLVICSLDFARRSKQRLEHLceaEWDLLVVDEAHHLVWSEDAPS---REYQAIEQlaehvpgvLLLTATPEQLGMES 323
Cdd:cd18065 115 EWD-VCVTSYEMVIKEKSVFKKF---NWRYLVIDEAHRIKNEKSKLSeivREFKTTNR--------LLLTGTPLQNNLHE 182
|
170
....*....|....*....
gi 16128053 324 HFARLRLLDPNRFHDFAQF 342
Cdd:cd18065 183 LWALLNFLLPDVFNSADDF 201
|
|
| DEXHc_ERCC6 |
cd18000 |
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ... |
174-283 |
8.60e-06 |
|
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: 47.32 E-value: 8.60e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEAGMIL----HQQLLSGaaeRVLIIVPETLQHQWLVEMLRRF-NLRFALFDD-------------ERY 235
Cdd:cd18000 23 ILGDEMGLGKTIQIIAFLaalhHSKLGLG---PSLIVCPATVLKQWVKEFHRWWpPFRVVVLHSsgsgtgseeklgsIER 99
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 16128053 236 AEAQHDAYNPfdTEQLVICSLDFARRSKQrleHLCEAEWDLLVVDEAH 283
Cdd:cd18000 100 KSQLIRKVVG--DGGILITTYEGFRKHKD---LLLNHNWQYVILDEGH 142
|
|
| DEXHc_SMARCAD1 |
cd17998 |
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ... |
174-318 |
9.24e-06 |
|
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (SMARCAD1, also known as ATP-dependent helicase 1 or Hel1) possesses intrinsic ATP-dependent nucleosome-remodeling activity and is required for both DNA repair and heterochromatin organization. SMARCAD1 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: 350756 [Multi-domain] Cd Length: 187 Bit Score: 47.38 E-value: 9.24e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEmLRRF--NLRFALF---DDERyAEAQHDAYNPFDT 248
Cdd:cd17998 23 ILADEMGLGKTIQVIAFLAYLKEIGIPGPHLVVVPSSTLDNWLRE-FKRWcpSLKVEPYygsQEER-KHLRYDILKGLED 100
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 16128053 249 EQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLvwsEDAPSREYQAIEQL-AEHvpgVLLLTATPEQ 318
Cdd:cd17998 101 FDVIVTTYNLATSNPDDRSFFKRLKLNYVVYDEGHML---KNMTSERYRHLMTInANF---RLLLTGTPLQ 165
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
180-316 |
1.39e-05 |
|
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: 45.76 E-value: 1.39e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 180 GLGKTIEagMILHQQLLSgaAERVLIIVPET-LQHQWlVEMLRRFNLRFALFddERYAEAQHDaynpFDTEQLVICSLDF 258
Cdd:cd17926 28 GSGKTLT--ALALIAYLK--ELRTLIVVPTDaLLDQW-KERFEDFLGDSSIG--LIGGGKKKD----FDDANVVVATYQS 96
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 259 ARRSKQRLEHLcEAEWDLLVVDEAHHLvwsedaPSREYqaiEQLAEHVPG--VLLLTATP 316
Cdd:cd17926 97 LSNLAEEEKDL-FDQFGLLIVDEAHHL------PAKTF---SEILKELNAkyRLGLTATP 146
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
166-317 |
1.78e-05 |
|
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: 46.02 E-value: 1.78e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 166 GRRhapRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVP-ETLQHQwLVEMLRRFNLRFALFDDERyaeaqhDAYN 244
Cdd:cd18032 19 GQR---RALLVMATGTGKTYTAAFLIKRLLEANRKKRILFLAHrEELLEQ-AERSFKEVLPDGSFGNLKG------GKKK 88
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16128053 245 PFDTEQlVICSLD-FARRSkqRLEHLCEAEWDLLVVDEAHHlvwsedAPSREYQAIeqLAEHVPGVLL-LTATPE 317
Cdd:cd18032 89 PDDARV-VFATVQtLNKRK--RLEKFPPDYFDLIIIDEAHH------AIASSYRKI--LEYFEPAFLLgLTATPE 152
|
|
| DEXHc_CHD4 |
cd18056 |
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; ... |
174-345 |
2.07e-05 |
|
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: 46.98 E-value: 2.07e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEAGMILHQQLLSG--------AAERVLIIVPETLQHQWLVEMlrrFNLRFALFDDERYAEAQhdayNP 245
Cdd:cd18056 23 ILADEMGLGKTVQTAVFLYSLYKEGhskgpflvSAPLSTIINWEREFEMWAPDM---YVVTYVGDKDSRAIIRE----NE 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 246 FDTEQLVICSLDFARRSKQR------------------LEHLCEAEWDLLVVDEAHHLvwsEDAPSREYQAIEQLAehVP 307
Cdd:cd18056 96 FSFEDNAIRGGKKASRMKKEasvkfhvlltsyelitidMAILGSIDWACLIVDEAHRL---KNNQSKFFRVLNGYS--LQ 170
|
170 180 190
....*....|....*....|....*....|....*...
gi 16128053 308 GVLLLTATPEQLGMESHFARLRLLDPNRFHDFAQFVEE 345
Cdd:cd18056 171 HKLLLTGTPLQNNLEELFHLLNFLTPERFHNLEGFLEE 208
|
|
| DEXQc_SHPRH |
cd18070 |
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ... |
174-341 |
4.10e-05 |
|
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously expressed protein that contains motifs characteristic of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 and is involved in DNA repair. SHPRH 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: 350828 [Multi-domain] Cd Length: 257 Bit Score: 46.18 E-value: 4.10e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEA-GMILHQQLLS-------------------GAAERV------LIIVPETLQHQWLVEMLR--RFNL 225
Cdd:cd18070 18 ILADEMGLGKTVEVlALILLHPRPDndldaadddsdemvccpdcLVAETPvsskatLIVCPSAILAQWLDEINRhvPSSL 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 226 RFALFDDERYAEAQHDAYnPFD--TEQLVICSLD-------FARRSKQRLEH------------LCEAEWDLLVVDEAhH 284
Cdd:cd18070 98 KVLTYQGVKKDGALASPA-PEIlaEYDIVVTTYDvlrtelhYAEANRSNRRRrrqkryeappspLVLVEWWRVCLDEA-Q 175
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*..
gi 16128053 285 LVWSEDAPSREyQAIEQLAEHVPGVlllTATPEQLGMESHFARLRLLdpnRFHDFAQ 341
Cdd:cd18070 176 MVESSTSKAAE-MARRLPRVNRWCV---SGTPIQRGLDDLFGLLSFL---GVEPFCD 225
|
|
| DEXQc_SRCAP |
cd18003 |
DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or ... |
174-344 |
4.75e-05 |
|
DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or DOMO1) is the core catalytic component of the multiprotein chromatin-remodeling SRCAP complex, that is necessary for the incorporation of the histone variant H2A.Z into nucleosomes. SRCAP 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: 350761 [Multi-domain] Cd Length: 223 Bit Score: 45.81 E-value: 4.75e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEAGMIL-HQQLLSGAAERVLIIVPETLQHQWLVEmLRRFNLRFALF-----DDERYAE----AQHDAY 243
Cdd:cd18003 23 ILADEMGLGKTIQTIALLaHLACEKGNWGPHLIVVPTSVMLNWEME-FKRWCPGFKILtyygsAKERKLKrqgwMKPNSF 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 244 NPFDTE-QLVICSLDFARRSKqrlehlceaeWDLLVVDEAHHLvwsEDAPSREYQAIeqLAEHVPGVLLLTATPEQLGME 322
Cdd:cd18003 102 HVCITSyQLVVQDHQVFKRKK----------WKYLILDEAHNI---KNFKSQRWQTL--LNFNTQRRLLLTGTPLQNSLM 166
|
170 180
....*....|....*....|..
gi 16128053 323 SHFARLRLLDPNRFHDFAQFVE 344
Cdd:cd18003 167 ELWSLMHFLMPHIFQSHQEFKE 188
|
|
| DEXHc_CHD5 |
cd18057 |
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; ... |
174-345 |
6.80e-05 |
|
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; 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. CHD5 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: 350815 [Multi-domain] Cd Length: 232 Bit Score: 45.44 E-value: 6.80e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEAGMILHQQLLSGAAE-RVLIIVPETLQHQWLvemlRRFNLRFALFDDERYAEAQHDAY----NPFDT 248
Cdd:cd18057 23 ILADEMGLGKTVQTIVFLYSLYKEGHSKgPYLVSAPLSTIINWE----REFEMWAPDFYVVTYTGDKESRSvireNEFSF 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 249 EQLVICSLDFARRSKQRLE---H---------------LCEAEWDLLVVDEAHHLvwsEDAPSREYQAIEqlAEHVPGVL 310
Cdd:cd18057 99 EDNAIRSGKKVFRMKKEAQikfHvlltsyelitidqaiLGSIEWACLVVDEAHRL---KNNQSKFFRVLN--SYKIDYKL 173
|
170 180 190
....*....|....*....|....*....|....*
gi 16128053 311 LLTATPEQLGMESHFARLRLLDPNRFHDFAQFVEE 345
Cdd:cd18057 174 LLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEE 208
|
|
| DEXHc_RAD54B |
cd18066 |
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ... |
165-333 |
7.83e-05 |
|
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: 45.22 E-value: 7.83e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 165 VGRRHAPR--VLLADEVGLGKTIEAGMILHQQLLSG------AAERVLIIVPETLQHQWLVEMLRRFNL-RFALFDDERY 235
Cdd:cd18066 17 MGMRVNERfgAILADEMGLGKTLQCISLIWTLLRQGpyggkpVIKRALIVTPGSLVKNWKKEFQKWLGSeRIKVFTVDQD 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 236 AEAQHDAYNPFDTeqLVICSLDFARRSKQRLEHLceaEWDLLVVDEAHHLvwsEDAPSREYQAIEQLAehVPGVLLLTAT 315
Cdd:cd18066 97 HKVEEFIASPLYS--VLIISYEMLLRSLDQISKL---NFDLVICDEGHRL---KNTSIKTTTALTSLS--CERRIILTGT 166
|
170
....*....|....*...
gi 16128053 316 PEQLGMESHFARLRLLDP 333
Cdd:cd18066 167 PIQNDLQEFFALIDFVNP 184
|
|
| DEXHc_CHD1 |
cd18053 |
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; ... |
174-350 |
1.10e-04 |
|
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; Chromodomain-helicase-DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. It is not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome. CHD1 is also associated with histone deacetylase (HDAC) activity. It 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: 350811 [Multi-domain] Cd Length: 237 Bit Score: 44.66 E-value: 1.10e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEA----GMILHQQLLSGAaerVLIIVPETLQHQWLVEM---LRRFNLRFALFD-DERYAEAQHDAYNP 245
Cdd:cd18053 43 ILADEMGLGKTIQTisflNYLFHEHQLYGP---FLLVVPLSTLTSWQREIqtwAPQMNAVVYLGDiNSRNMIRTHEWMHP 119
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 246 fDTEQL----VICSLDFARRSKQRLEHLceaEWDLLVVDEAHHLvwsEDAPSREYQA-IEQLAEHVpgvLLLTATPEQLG 320
Cdd:cd18053 120 -QTKRLkfniLLTTYEILLKDKSFLGGL---NWAFIGVDEAHRL---KNDDSLLYKTlIDFKSNHR---LLITGTPLQNS 189
|
170 180 190
....*....|....*....|....*....|
gi 16128053 321 MESHFARLRLLDPNRFHDFAQFVEEQKNYR 350
Cdd:cd18053 190 LKELWSLLHFIMPEKFSSWEDFEEEHGKGR 219
|
|
| DEXDc_SHPRH-like |
cd18008 |
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ... |
174-365 |
1.34e-04 |
|
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to 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: 350766 [Multi-domain] Cd Length: 241 Bit Score: 44.59 E-value: 1.34e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEA-GMIL--HQQLLSGAAERV---------------LIIVPETLQHQWLVEMLRRFN---LRFALFDD 232
Cdd:cd18008 18 ILADEMGLGKTIQAlALILatRPQDPKIPEELEenssdpkklylskttLIVVPLSLLSQWKDEIEKHTKpgsLKVYVYHG 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 233 ERYAE-----AQHD----AYNPFDTEQLVicSLDFARRSKQRLEH--LCEAEWDLLVVDEAH----------HLVWSEDA 291
Cdd:cd18008 98 SKRIKsieelSDYDivitTYGTLASEFPK--NKKGGGRDSKEKEAspLHRIRWYRVILDEAHniknrstktsRAVCALKA 175
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16128053 292 PSReyqaieqlaehvpgvLLLTATPEQLGMESHFARLRLLDPNRFHDFAQFVEE-----QKNYRPVADAVAMLLAGNKL 365
Cdd:cd18008 176 ERR---------------WCLTGTPIQNSLDDLYSLLRFLRVEPFGDYPWFNSDiskpfSKNDRKALERLQALLKPILL 239
|
|
| DEXHc_CHD3 |
cd18055 |
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; ... |
273-345 |
2.20e-04 |
|
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: 43.85 E-value: 2.20e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16128053 273 EWDLLVVDEAHHLvwsEDAPSREYQAIEQLaeHVPGVLLLTATPEQLGMESHFARLRLLDPNRFHDFAQFVEE 345
Cdd:cd18055 141 RWACLVVDEAHRL---KNNQSKFFRVLNGY--KIDHKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEE 208
|
|
| PRK10590 |
PRK10590 |
ATP-dependent RNA helicase RhlE; Provisional |
504-599 |
6.50e-04 |
|
ATP-dependent RNA helicase RhlE; Provisional
Pssm-ID: 236722 [Multi-domain] Cd Length: 456 Bit Score: 43.26 E-value: 6.50e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 504 QKVLVICAKAATALQLEQVLrEREGIRAAVFHEGMSIIERDRAAAWFaeEDTGAQVLLCSEIGSEGRNFQFASHMVMFDL 583
Cdd:PRK10590 246 QQVLVFTRTKHGANHLAEQL-NKDGIRSAAIHGNKSQGARTRALADF--KSGDIRVLVATDIAARGLDIEELPHVVNYEL 322
|
90
....*....|....*.
gi 16128053 584 PFNPDLLEQRIGRLDR 599
Cdd:PRK10590 323 PNVPEDYVHRIGRTGR 338
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
173-316 |
1.39e-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: 40.30 E-value: 1.39e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 173 VLLADEVGLGKTiEAGMI--LHQQLLSGAAERVLIIVPET-LQHQwlveMLRRFNLRFALFDDERYAE----AQHDAYNP 245
Cdd:pfam00270 17 VLVQAPTGSGKT-LAFLLpaLEALDKLDNGPQALVLAPTReLAEQ----IYEELKKLGKGLGLKVASLlggdSRKEQLEK 91
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16128053 246 FDTEQLVICS----LDFARRSKqRLEHLceaewDLLVVDEAHHLVwsedapSREYQA-IEQLAEHVPG---VLLLTATP 316
Cdd:pfam00270 92 LKGPDILVGTpgrlLDLLQERK-LLKNL-----KLLVLDEAHRLL------DMGFGPdLEEILRRLPKkrqILLLSATL 158
|
|
| PLN03142 |
PLN03142 |
Probable chromatin-remodeling complex ATPase chain; Provisional |
174-344 |
1.63e-03 |
|
Probable chromatin-remodeling complex ATPase chain; Provisional
Pssm-ID: 215601 [Multi-domain] Cd Length: 1033 Bit Score: 42.48 E-value: 1.63e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 174 LLADEVGLGKTIEAGMI---LHQqlLSGAAERVLIIVPETLQHQWLVEmLRRFN--LRFALF---DDERyaEAQHDAY-- 243
Cdd:PLN03142 192 ILADEMGLGKTLQTISLlgyLHE--YRGITGPHMVVAPKSTLGNWMNE-IRRFCpvLRAVKFhgnPEER--AHQREELlv 266
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 244 -NPFDteqlvICSLDFARRSKQRlEHLCEAEWDLLVVDEAHHLvwsEDAPSREYQAIEQLAEHVPgvLLLTATPEQLGME 322
Cdd:PLN03142 267 aGKFD-----VCVTSFEMAIKEK-TALKRFSWRYIIIDEAHRI---KNENSLLSKTMRLFSTNYR--LLITGTPLQNNLH 335
|
170 180
....*....|....*....|..
gi 16128053 323 SHFARLRLLDPNRFHDFAQFVE 344
Cdd:PLN03142 336 ELWALLNFLLPEIFSSAETFDE 357
|
|
| Cas3_I |
cd09696 |
CRISPR/Cas system-associated protein Cas3; Distinct Cas3 family with HD domain fused to ... |
560-614 |
3.89e-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: 41.16 E-value: 3.89e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 16128053 560 LLCSEIGSEGRNFQFaSHMVMFDLPFnpDLLEQRIGRLDRIGQAHDIQIHVPYLE 614
Cdd:cd09696 339 LVCTSAGEVGVNISA-DHLVCDLAPF--ESMQQRFGRVNRFGELQACQIAVVHLD 390
|
|
| PRK11192 |
PRK11192 |
ATP-dependent RNA helicase SrmB; Provisional |
519-608 |
4.29e-03 |
|
ATP-dependent RNA helicase SrmB; Provisional
Pssm-ID: 236877 [Multi-domain] Cd Length: 434 Bit Score: 40.70 E-value: 4.29e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 519 LEQVLREReGIRAAvFHEG-MSIIERDRAAAWFaeEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRL 597
Cdd:PRK11192 261 LAGWLRKA-GINCC-YLEGeMVQAKRNEAIKRL--TDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRT 336
|
90 100
....*....|....*....|
gi 16128053 598 DRIGQ---------AHDIQI 608
Cdd:PRK11192 337 GRAGRkgtaislveAHDHLL 356
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
266-348 |
4.92e-03 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 40.51 E-value: 4.92e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128053 266 LEHLCEAEWDLLVVDEAHHLV-WSED-APsrEYQAIEQLAEHVPGVLLL----TATP-------EQLGME------SHFA 326
Cdd:COG0514 124 LELLRRLKISLFAIDEAHCISqWGHDfRP--DYRRLGELRERLPNVPVLaltaTATPrvradiaEQLGLEdprvfvGSFD 201
|
90 100
....*....|....*....|....*....
gi 16128053 327 R-------LRLLDPNRFHDFAQFVEEQKN 348
Cdd:COG0514 202 RpnlrlevVPKPPDDKLAQLLDFLKEHPG 230
|
|
| |
