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Conserved domains on  [gi|2117983367|ref|XP_044283679|]
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chromodomain-helicase-DNA-binding protein 9 isoform X9 [Varanus komodoensis]

Protein Classification

chromo domain-containing DEAD/DEAH box helicase( domain architecture ID 13036674)

chromo (chromatin organization modifier) domain-containing DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA; similar to chromodomain helicase DNA-binding (CHD) family of ATP-dependent chromatin remodelers

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PLN03142 super family cl33647
Probable chromatin-remodeling complex ATPase chain; Provisional
354-880 7.09e-145

Probable chromatin-remodeling complex ATPase chain; Provisional


The actual alignment was detected with superfamily member PLN03142:

Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 480.84  E-value: 7.09e-145
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  354 QLREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSIT---FLYEilLTGLRGPFLIIAPLSTIANWEREFRTWTD-LN 429
Cdd:PLN03142   169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISllgYLHE--YRGITGPHMVVAPKSTLGNWMNEIRRFCPvLR 246
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  430 VVVYHGSMISRqmiqqfeMYFRDSQgrIIRGtyKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLK 509
Cdd:PLN03142   247 AVKFHGNPEER-------AHQREEL--LVAG--KFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNENSLLSKTMR 315
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  510 LMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEF---GDLKTEEQVQKLQAILKPMMLRRLKEDVEKKLA 586
Cdd:PLN03142   316 LFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFqisGENDQQEVVQQLHKVLRPFLLRRLKSDVEKGLP 395
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  587 PKEETIIEVELTNIQKKYYRAILEKNFAFLSKGAGQANvpnLVNTMMELRKCCNHPYLIKGAEEKilgefretySPAAQD 666
Cdd:PLN03142   396 PKKETILKVGMSQMQKQYYKALLQKDLDVVNAGGERKR---LLNIAMQLRKCCNHPYLFQGAEPG---------PPYTTG 463
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  667 FHLqamIQSAGKLVLIDKLLPKMKAGGHKVLIFSQMVRCLDILEDYLIHKRYLYERIDGRVRGNLRQAAIDRFSKPDSDR 746
Cdd:PLN03142   464 EHL---VENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEK 540
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  747 FVFLLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAVKVYRLITRNSYEREMFDRASLKLGLDKAVL 826
Cdd:PLN03142   541 FVFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVI 620
                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2117983367  827 QSmsgrensvGGIQQLSKKEIEDLLRKGAYGAIMDEEDEGSKFCEEDIDQILQR 880
Cdd:PLN03142   621 QQ--------GRLAEQKTVNKDELLQMVRYGAEMVFSSKDSTITDEDIDRIIAK 666
CD2_tandem_CHD5-9_like cd18663
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ...
265-323 6.38e-35

repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


:

Pssm-ID: 349310 [Multi-domain]  Cd Length: 59  Bit Score: 127.79  E-value: 6.38e-35
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2117983367  265 PDYIEVDRVLEVSFCEDKDTGEPVTYYLVKWCSLPYEDSTWELKEDVDQGKIEEFEQLQ 323
Cdd:cd18663      1 PDYVEVDRILDVSVSTDPNTGEPVTHYLVKWCSLPYEDSTWELEEDVDPAKIEEFEKLR 59
CD1_tandem_CHD5-9_like cd18668
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ...
181-245 4.64e-27

repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


:

Pssm-ID: 349315 [Multi-domain]  Cd Length: 68  Bit Score: 105.88  E-value: 4.64e-27
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2117983367  181 EEDAAIVDKILSSRIIKKEI-TGGVTVEAEEFYVKYKNYSYLHCEWATEQQLLK-DKRIQQKIKRFK 245
Cdd:cd18668      1 EEDTMIIEKILASRKKKKEKeEGAEEIEVEEYLVKYKNFSYLHCEWKTEEELEKgDKRIKQKIKRFK 67
BRK smart00592
domain in transcription and CHROMO domain helicases;
2054-2098 1.89e-15

domain in transcription and CHROMO domain helicases;


:

Pssm-ID: 197800  Cd Length: 45  Bit Score: 72.00  E-value: 1.89e-15
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*
gi 2117983367  2054 TGEERVQLINRRNARKVGGAFAPPLKDLCRFLKENSEYGVAPEWA 2098
Cdd:smart00592    1 DGEERVPVINRETGKKLTGDDAPKAKDLERWLEENPEYEVAPRSA 45
BRK pfam07533
BRK domain; The function of this domain is unknown. It is often found associated with ...
1980-2020 1.01e-14

BRK domain; The function of this domain is unknown. It is often found associated with helicases and transcription factors.


:

Pssm-ID: 462196  Cd Length: 44  Bit Score: 69.85  E-value: 1.01e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2117983367 1980 DAESPVPVINLKDGTRLAGDDAPKRKDLEKWLNEHPGYVED 2020
Cdd:pfam07533    2 TGDERVPVVNRKTGKKLTGDKAPKLKDLEEWLEENPGYEVD 42
 
Name Accession Description Interval E-value
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
354-880 7.09e-145

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 480.84  E-value: 7.09e-145
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  354 QLREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSIT---FLYEilLTGLRGPFLIIAPLSTIANWEREFRTWTD-LN 429
Cdd:PLN03142   169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISllgYLHE--YRGITGPHMVVAPKSTLGNWMNEIRRFCPvLR 246
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  430 VVVYHGSMISRqmiqqfeMYFRDSQgrIIRGtyKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLK 509
Cdd:PLN03142   247 AVKFHGNPEER-------AHQREEL--LVAG--KFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNENSLLSKTMR 315
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  510 LMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEF---GDLKTEEQVQKLQAILKPMMLRRLKEDVEKKLA 586
Cdd:PLN03142   316 LFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFqisGENDQQEVVQQLHKVLRPFLLRRLKSDVEKGLP 395
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  587 PKEETIIEVELTNIQKKYYRAILEKNFAFLSKGAGQANvpnLVNTMMELRKCCNHPYLIKGAEEKilgefretySPAAQD 666
Cdd:PLN03142   396 PKKETILKVGMSQMQKQYYKALLQKDLDVVNAGGERKR---LLNIAMQLRKCCNHPYLFQGAEPG---------PPYTTG 463
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  667 FHLqamIQSAGKLVLIDKLLPKMKAGGHKVLIFSQMVRCLDILEDYLIHKRYLYERIDGRVRGNLRQAAIDRFSKPDSDR 746
Cdd:PLN03142   464 EHL---VENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEK 540
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  747 FVFLLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAVKVYRLITRNSYEREMFDRASLKLGLDKAVL 826
Cdd:PLN03142   541 FVFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVI 620
                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2117983367  827 QSmsgrensvGGIQQLSKKEIEDLLRKGAYGAIMDEEDEGSKFCEEDIDQILQR 880
Cdd:PLN03142   621 QQ--------GRLAEQKTVNKDELLQMVRYGAEMVFSSKDSTITDEDIDRIIAK 666
DEXHc_CHD9 cd18061
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; ...
355-576 7.98e-145

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; Chromodomain-helicase-DNA-binding protein 9 (CHD9) acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors. It is proposed to be a ATP-dependent chromatin remodeling protein. CHD9 has DNA-dependent ATPase activity and binds to A/T-rich DNA. It also associates with A/T-rich regulatory regions in promoters of genes that participate in the differentiation of progenitors during osteogenesis. CHD9 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: 350819 [Multi-domain]  Cd Length: 222  Bit Score: 449.07  E-value: 7.98e-145
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLTGLRGPFLIIAPLSTIANWEREFRTWTDLNVVVYH 434
Cdd:cd18061      1 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEILLTGIRGPFLIIAPLSTIANWEREFRTWTDLNVVVYH 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  435 GSMISRQMIQQFEMYFRDSQGRIIRGTYKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLE 514
Cdd:cd18061     81 GSLISRQMIQQYEMYFRDSQGRIIRGAYRFQAIITTFEMILGGCPELNAIDWRCVIIDEAHRLKNKNCKLLEGLKLMNLE 160
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2117983367  515 HKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 576
Cdd:cd18061    161 HKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 222
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
354-827 1.80e-121

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 401.14  E-value: 1.80e-121
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  354 QLREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLTGLRGPFLIIAPLSTIANWEREFRTWT-DLNVVV 432
Cdd:COG0553    241 TLRPYQLEGAAWLLFLRRLGLGGLLADDMGLGKTIQALALLLELKERGLARPVLIVAPTSLVGNWQRELAKFApGLRVLV 320
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  433 YHGSMISRQMIQQFEmyfrdsqgriirgtyKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMN 512
Cdd:COG0553    321 LDGTRERAKGANPFE---------------DADLVITSYGLLRRDIELLAAVDWDLVILDEAQHIKNPATKRAKAVRALK 385
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  513 LEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGDLKT---EEQVQKLQAILKPMMLRRLKEDVEKKLAPKE 589
Cdd:COG0553    386 ARHRLALTGTPVENRLEELWSLLDFLNPGLLGSLKAFRERFARPIEkgdEEALERLRRLLRPFLLRRTKEDVLKDLPEKT 465
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  590 ETIIEVELTNIQKKYYRAILEKNFAFLSKGAGQANVPNLVNTMMELRKCCNHPYLIKGAEEKILGEfretyspaaqdfhl 669
Cdd:COG0553    466 EETLYVELTPEQRALYEAVLEYLRRELEGAEGIRRRGLILAALTRLRQICSHPALLLEEGAELSGR-------------- 531
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  670 qamiqsAGKLVLIDKLLPKMKAGGHKVLIFSQMVRCLDILEDYLIHKRYLYERIDGRVRGNLRQAAIDRFSKpDSDRFVF 749
Cdd:COG0553    532 ------SAKLEALLELLEELLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQE-GPEAPVF 604
                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2117983367  750 LLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAVKVYRLITRNSYEREMFDRASLKLGLDKAVLQ 827
Cdd:COG0553    605 LISLKAGGEGLNLTAADHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEEKILELLEEKRALAESVLG 682
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
358-645 4.16e-83

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: 275.33  E-value: 4.16e-83
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  358 YQLEGLNWLLFNWYNRQ-NCILADEMGLGKTIQSITFLYEILL--TGLRGPFLIIAPLSTIANWEREFRTWT---DLNVV 431
Cdd:pfam00176    1 YQIEGVNWMLSLENNLGrGGILADEMGLGKTLQTISLLLYLKHvdKNWGGPTLIVVPLSLLHNWMNEFERWVsppALRVV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  432 VYHGSMISRQMIQQFEMYFRDsqgriirgtykFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLM 511
Cdd:pfam00176   81 VLHGNKRPQERWKNDPNFLAD-----------FDVVITTYETLRKHKELLKKVHWHRIVLDEGHRLKNSKSKLSKALKSL 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  512 NLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFG----DLKTEEQVQKLQAILKPMMLRRLKEDVEKKLAP 587
Cdd:pfam00176  150 KTRNRWILTGTPLQNNLEELWALLNFLRPGPFGSLSTFRNWFDrpieRGGGKKGVSRLHKLLKPFLLRRTKKDVEKSLPP 229
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  588 KEETIIEVELTNIQKKYY-RAILEKNFAFLSKGAGQANVP-NLVNTMMELRKCCNHPYLI 645
Cdd:pfam00176  230 KVEYILFCRLSKLQRKLYqTFLLKKDLNAIKTGEGGREIKaSLLNILMRLRKICNHPGLI 289
CD2_tandem_CHD5-9_like cd18663
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ...
265-323 6.38e-35

repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349310 [Multi-domain]  Cd Length: 59  Bit Score: 127.79  E-value: 6.38e-35
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2117983367  265 PDYIEVDRVLEVSFCEDKDTGEPVTYYLVKWCSLPYEDSTWELKEDVDQGKIEEFEQLQ 323
Cdd:cd18663      1 PDYVEVDRILDVSVSTDPNTGEPVTHYLVKWCSLPYEDSTWELEEDVDPAKIEEFEKLR 59
DEXDc smart00487
DEAD-like helicases superfamily;
348-546 1.23e-30

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 121.06  E-value: 1.23e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367   348 EYKNGNQLREYQLEGLNWLLFNWynrQNCILADEMGLGKTIQSITFLYEILLTGLRGPFLIIAPLSTIA-NWEREFRTW- 425
Cdd:smart00487    2 EKFGFEPLRPYQKEAIEALLSGL---RDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAeQWAEELKKLg 78
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367   426 --TDLNVVVYHGSMISRQMIQQFEmyfrdsqgriirgTYKFQAIITTFEMILGGCPE--LNAIEWRCVIIDEAHRLKNKN 501
Cdd:smart00487   79 psLGLKVVGLYGGDSKREQLRKLE-------------SGKTDILVTTPGRLLDLLENdkLSLSNVDLVILDEAHRLLDGG 145
                           170       180       190       200       210
                    ....*....|....*....|....*....|....*....|....*....|.
gi 2117983367   502 --CKLLEGLKLMNLE-HKVLLTGTP---LQNTVEELFSLLHFLEPLRFPAE 546
Cdd:smart00487  146 fgDQLEKLLKLLPKNvQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLE 196
CD1_tandem_CHD5-9_like cd18668
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ...
181-245 4.64e-27

repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349315 [Multi-domain]  Cd Length: 68  Bit Score: 105.88  E-value: 4.64e-27
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2117983367  181 EEDAAIVDKILSSRIIKKEI-TGGVTVEAEEFYVKYKNYSYLHCEWATEQQLLK-DKRIQQKIKRFK 245
Cdd:cd18668      1 EEDTMIIEKILASRKKKKEKeEGAEEIEVEEYLVKYKNFSYLHCEWKTEEELEKgDKRIKQKIKRFK 67
DISARM_DrmD_b NF038318
DISARM system SNF2-like helicase DrmD, short form; DrmD, a SNF2-like helicase, is a component ...
377-841 1.62e-21

DISARM system SNF2-like helicase DrmD, short form; DrmD, a SNF2-like helicase, is a component of class 1 DISARM (Defence Island System Associated with Restriction Modification), which contains a DNA adenine N6 methyltransferase. This HMM describes a distinct form that is somewhat shorter than the majority of DrmD proteins.


Pssm-ID: 468472 [Multi-domain]  Cd Length: 868  Bit Score: 102.84  E-value: 1.62e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  377 ILADEMGLGKTIQSITFLYEILLTGLRgPFLIIAPLSTIANWEREFRTWTDLNVVVyhgsmISRQMIQqfemYFRDSQGR 456
Cdd:NF038318    51 ILADEVGLGKTIEAGLVLKYVLESGAK-KILIILPANLRKQWEIELEEKFDLESLI-----LDSLTVE----KDAKKWNK 120
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  457 IIRGTYKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKN--KNCKLLEGL-KLMNLEHKVLLTGTPLQNTVEELFS 533
Cdd:NF038318   121 RLTDNKKVRIVITSYDYASKLMKRFPKVKWDFIIIDEAHNLRNvhKGGKRAKNLyELTKGIPKILLTATPLQNSLLDLYG 200
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  534 LLHFLEPLRFPAESTFM------QEFGDLKTEeqvqklqaiLKPMMLRRLKEDVEKKLAPKEETIIEV--ELTNIQKKYY 605
Cdd:NF038318   201 LVSFIDPRIFGSEKVFSkryikdEDYSDLKRE---------LSPVLYRTLRKDVADYMQFKKRKCITVdfELSPDEIELY 271
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  606 RAIlekNfAFLSKGAGQAnVPN--------------------LVNTMMELRKCCNHPY-------LIKG--------AEE 650
Cdd:NF038318   272 VRV---N-NFLKRDILYS-IPTsnrtliilvirkllasssfaLAETFEVLKKRLEKLKegtrsanAQEGfdlfwsfvEDE 346
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  651 KILGEFRETYSP--AAQDFHLQAMIQSAGKLVLIDKLL---PKMKAG----------------GHKVLIFSQMVRCLDIL 709
Cdd:NF038318   347 IDESGFEEKQDElyTRQKEFIQHEIDEVDAIIDVAKRIktnAKVTALktaleiafeyqreegiAQKVVVFTESKRTQKYI 426
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  710 EDYLIHKRYLYERI---DG--------------RVR--GN--------LRQAAIDRFSkpdsDRFVFLLCTRAGGLGINL 762
Cdd:NF038318   427 AEELRKSGYEGEDIllfNGdfddamtkeiyrawQVKnyGKanygrsveYKHAIVDYFK----NNAKILIVTDAGSEGLNL 502
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  763 TAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAVKVYRLI-TRNSYEREMFDRASLKLGL--------DKA--VLQSMSG 831
Cdd:NF038318   503 QFCNTVINYDLPWNPQKIEQRIGRCHRYGQKNDVVAINLLnTQNVADKRVYEILSEKFELfegvfgasDIAlgLLESGTD 582
                          570
                   ....*....|
gi 2117983367  832 RENSVGGIQQ 841
Cdd:NF038318   583 FEKRVLQIYQ 592
BRK smart00592
domain in transcription and CHROMO domain helicases;
2054-2098 1.89e-15

domain in transcription and CHROMO domain helicases;


Pssm-ID: 197800  Cd Length: 45  Bit Score: 72.00  E-value: 1.89e-15
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*
gi 2117983367  2054 TGEERVQLINRRNARKVGGAFAPPLKDLCRFLKENSEYGVAPEWA 2098
Cdd:smart00592    1 DGEERVPVINRETGKKLTGDDAPKAKDLERWLEENPEYEVAPRSA 45
BRK pfam07533
BRK domain; The function of this domain is unknown. It is often found associated with ...
1980-2020 1.01e-14

BRK domain; The function of this domain is unknown. It is often found associated with helicases and transcription factors.


Pssm-ID: 462196  Cd Length: 44  Bit Score: 69.85  E-value: 1.01e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2117983367 1980 DAESPVPVINLKDGTRLAGDDAPKRKDLEKWLNEHPGYVED 2020
Cdd:pfam07533    2 TGDERVPVVNRKTGKKLTGDKAPKLKDLEEWLEENPGYEVD 42
BRK smart00592
domain in transcription and CHROMO domain helicases;
1980-2029 1.04e-14

domain in transcription and CHROMO domain helicases;


Pssm-ID: 197800  Cd Length: 45  Bit Score: 70.07  E-value: 1.04e-14
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|
gi 2117983367  1980 DAESPVPVINLKDGTRLAGDDAPKRKDLEKWLNEHPGYvedlgAFIPKMQ 2029
Cdd:smart00592    1 DGEERVPVINRETGKKLTGDDAPKAKDLERWLEENPEY-----EVAPRSA 45
BRK pfam07533
BRK domain; The function of this domain is unknown. It is often found associated with ...
2053-2096 2.38e-13

BRK domain; The function of this domain is unknown. It is often found associated with helicases and transcription factors.


Pssm-ID: 462196  Cd Length: 44  Bit Score: 65.99  E-value: 2.38e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 2117983367 2053 LTGEERVQLINRRNARKVGGAFAPPLKDLCRFLKENSEYGVAPE 2096
Cdd:pfam07533    1 LTGDERVPVVNRKTGKKLTGDKAPKLKDLEEWLEENPGYEVDPR 44
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
269-321 6.77e-09

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 53.74  E-value: 6.77e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2117983367  269 EVDRVLEVSFCEDKdtgepVTYYLVKWCSLPYEDSTWELKEDVD--QGKIEEFEQ 321
Cdd:pfam00385    2 EVERILDHRKDKGG-----KEEYLVKWKGYPYDENTWEPEENLSkcPELIEEFKD 51
CHROMO smart00298
Chromatin organization modifier domain;
187-249 8.68e-08

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 50.68  E-value: 8.68e-08
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2117983367   187 VDKILSSRIIKKEitggvtveAEEFYVKYKNYSYLHCEWATEQQLLKDKRiqqKIKRFKLRQA 249
Cdd:smart00298    4 VEKILDHRWKKKG--------ELEYLVKWKGYSYSEDTWEPEENLLNCSK---KLDNYKKKER 55
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
186-245 5.30e-07

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 48.34  E-value: 5.30e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  186 IVDKILSSRIIKKEitggvtveAEEFYVKYKNYSYLHCEWATEQQLLKDKRIqqkIKRFK 245
Cdd:pfam00385    2 EVERILDHRKDKGG--------KEEYLVKWKGYPYDENTWEPEENLSKCPEL---IEEFK 50
CHROMO smart00298
Chromatin organization modifier domain;
269-324 1.76e-03

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 38.35  E-value: 1.76e-03
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 2117983367   269 EVDRVLEVSFcedkdTGEPVTYYLVKWCSLPYEDSTWELKEDVDQG--KIEEFEQLQA 324
Cdd:smart00298    3 EVEKILDHRW-----KKKGELEYLVKWKGYSYSEDTWEPEENLLNCskKLDNYKKKER 55
 
Name Accession Description Interval E-value
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
354-880 7.09e-145

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 480.84  E-value: 7.09e-145
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  354 QLREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSIT---FLYEilLTGLRGPFLIIAPLSTIANWEREFRTWTD-LN 429
Cdd:PLN03142   169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISllgYLHE--YRGITGPHMVVAPKSTLGNWMNEIRRFCPvLR 246
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  430 VVVYHGSMISRqmiqqfeMYFRDSQgrIIRGtyKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLK 509
Cdd:PLN03142   247 AVKFHGNPEER-------AHQREEL--LVAG--KFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNENSLLSKTMR 315
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  510 LMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEF---GDLKTEEQVQKLQAILKPMMLRRLKEDVEKKLA 586
Cdd:PLN03142   316 LFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFqisGENDQQEVVQQLHKVLRPFLLRRLKSDVEKGLP 395
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  587 PKEETIIEVELTNIQKKYYRAILEKNFAFLSKGAGQANvpnLVNTMMELRKCCNHPYLIKGAEEKilgefretySPAAQD 666
Cdd:PLN03142   396 PKKETILKVGMSQMQKQYYKALLQKDLDVVNAGGERKR---LLNIAMQLRKCCNHPYLFQGAEPG---------PPYTTG 463
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  667 FHLqamIQSAGKLVLIDKLLPKMKAGGHKVLIFSQMVRCLDILEDYLIHKRYLYERIDGRVRGNLRQAAIDRFSKPDSDR 746
Cdd:PLN03142   464 EHL---VENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEK 540
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  747 FVFLLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAVKVYRLITRNSYEREMFDRASLKLGLDKAVL 826
Cdd:PLN03142   541 FVFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVI 620
                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2117983367  827 QSmsgrensvGGIQQLSKKEIEDLLRKGAYGAIMDEEDEGSKFCEEDIDQILQR 880
Cdd:PLN03142   621 QQ--------GRLAEQKTVNKDELLQMVRYGAEMVFSSKDSTITDEDIDRIIAK 666
DEXHc_CHD9 cd18061
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; ...
355-576 7.98e-145

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; Chromodomain-helicase-DNA-binding protein 9 (CHD9) acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors. It is proposed to be a ATP-dependent chromatin remodeling protein. CHD9 has DNA-dependent ATPase activity and binds to A/T-rich DNA. It also associates with A/T-rich regulatory regions in promoters of genes that participate in the differentiation of progenitors during osteogenesis. CHD9 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: 350819 [Multi-domain]  Cd Length: 222  Bit Score: 449.07  E-value: 7.98e-145
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLTGLRGPFLIIAPLSTIANWEREFRTWTDLNVVVYH 434
Cdd:cd18061      1 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEILLTGIRGPFLIIAPLSTIANWEREFRTWTDLNVVVYH 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  435 GSMISRQMIQQFEMYFRDSQGRIIRGTYKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLE 514
Cdd:cd18061     81 GSLISRQMIQQYEMYFRDSQGRIIRGAYRFQAIITTFEMILGGCPELNAIDWRCVIIDEAHRLKNKNCKLLEGLKLMNLE 160
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2117983367  515 HKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 576
Cdd:cd18061    161 HKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 222
DEXHc_CHD6_7_8_9 cd17995
DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; ...
355-576 2.14e-140

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: 436.68  E-value: 2.14e-140
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLT-GLRGPFLIIAPLSTIANWEREFRTWTDLNVVVY 433
Cdd:cd17995      1 LRDYQLEGVNWLLFNWYNRRNCILADEMGLGKTIQSIAFLEHLYQVeGIRGPFLVIAPLSTIPNWQREFETWTDMNVVVY 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  434 HGSMISRQMIQQFEMYFRDSQGRIIRGTYKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNL 513
Cdd:cd17995     81 HGSGESRQIIQQYEMYFKDAQGRKKKGVYKFDVLITTYEMVIADAEELRKIPWRVVVVDEAHRLKNRNSKLLQGLKKLTL 160
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2117983367  514 EHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 576
Cdd:cd17995    161 EHKLLLTGTPLQNNTEELWSLLNFLEPEKFPSSEEFLEEFGDLKTAEQVEKLQALLKPYMLRR 223
DEXHc_CHD6 cd18058
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; ...
355-576 2.90e-137

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: 427.54  E-value: 2.90e-137
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLTGLRGPFLIIAPLSTIANWEREFRTWTDLNVVVYH 434
Cdd:cd18058      1 LREYQLEGMNWLLFNWYNRKNCILADEMGLGKTIQSITFLSEIFLMGIRGPFLIIAPLSTITNWEREFRTWTEMNAIVYH 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  435 GSMISRQMIQQFEMYFRDSQGRIIRGTYKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLE 514
Cdd:cd18058     81 GSQISRQMIQQYEMYYRDEQGNPLSGIFKFQVVITTFEMILADCPELKKINWSCVIIDEAHRLKNRNCKLLEGLKLMALE 160
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2117983367  515 HKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 576
Cdd:cd18058    161 HKVLLTGTPLQNSVEELFSLLNFLEPSQFPSETTFLEEFGDLKTEEQVKKLQSILKPMMLRR 222
DEXHc_CHD7 cd18059
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; ...
355-576 2.21e-131

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: 410.96  E-value: 2.21e-131
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLTGLRGPFLIIAPLSTIANWEREFRTWTDLNVVVYH 434
Cdd:cd18059      1 LREYQLEGVNWLLFNWYNTRNCILADEMGLGKTIQSITFLYEIYLKGIHGPFLVIAPLSTIPNWEREFRTWTELNVVVYH 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  435 GSMISRQMIQQFEMYFRDSQGRIIRGTYKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLE 514
Cdd:cd18059     81 GSQASRRTIQLYEMYFKDPQGRVIKGSYKFHAIITTFEMILTDCPELRNIPWRCVVIDEAHRLKNRNCKLLEGLKMMDLE 160
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2117983367  515 HKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 576
Cdd:cd18059    161 HKVLLTGTPLQNTVEELFSLLHFLEPSRFPSETTFMQEFGDLKTEEQVQKLQAILKPMMLRR 222
DEXHc_CHD8 cd18060
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; ...
355-576 9.21e-131

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: 409.06  E-value: 9.21e-131
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLTGLRGPFLIIAPLSTIANWEREFRTWTDLNVVVYH 434
Cdd:cd18060      1 LREYQLEGVNWLLFNWYNRQNCILADEMGLGKTIQSIAFLQEVYNVGIHGPFLVIAPLSTITNWEREFNTWTEMNTIVYH 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  435 GSMISRQMIQQFEMYFRDSQGRIIRGTYKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLE 514
Cdd:cd18060     81 GSLASRQMIQQYEMYCKDSRGRLIPGAYKFDALITTFEMILSDCPELREIEWRCVIIDEAHRLKNRNCKLLDSLKHMDLE 160
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2117983367  515 HKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 576
Cdd:cd18060    161 HKVLLTGTPLQNTVEELFSLLHFLEPSQFPSESEFLKDFGDLKTEEQVQKLQAILKPMMLRR 222
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
354-827 1.80e-121

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 401.14  E-value: 1.80e-121
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  354 QLREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLTGLRGPFLIIAPLSTIANWEREFRTWT-DLNVVV 432
Cdd:COG0553    241 TLRPYQLEGAAWLLFLRRLGLGGLLADDMGLGKTIQALALLLELKERGLARPVLIVAPTSLVGNWQRELAKFApGLRVLV 320
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  433 YHGSMISRQMIQQFEmyfrdsqgriirgtyKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMN 512
Cdd:COG0553    321 LDGTRERAKGANPFE---------------DADLVITSYGLLRRDIELLAAVDWDLVILDEAQHIKNPATKRAKAVRALK 385
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  513 LEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGDLKT---EEQVQKLQAILKPMMLRRLKEDVEKKLAPKE 589
Cdd:COG0553    386 ARHRLALTGTPVENRLEELWSLLDFLNPGLLGSLKAFRERFARPIEkgdEEALERLRRLLRPFLLRRTKEDVLKDLPEKT 465
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  590 ETIIEVELTNIQKKYYRAILEKNFAFLSKGAGQANVPNLVNTMMELRKCCNHPYLIKGAEEKILGEfretyspaaqdfhl 669
Cdd:COG0553    466 EETLYVELTPEQRALYEAVLEYLRRELEGAEGIRRRGLILAALTRLRQICSHPALLLEEGAELSGR-------------- 531
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  670 qamiqsAGKLVLIDKLLPKMKAGGHKVLIFSQMVRCLDILEDYLIHKRYLYERIDGRVRGNLRQAAIDRFSKpDSDRFVF 749
Cdd:COG0553    532 ------SAKLEALLELLEELLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQE-GPEAPVF 604
                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2117983367  750 LLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAVKVYRLITRNSYEREMFDRASLKLGLDKAVLQ 827
Cdd:COG0553    605 LISLKAGGEGLNLTAADHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEEKILELLEEKRALAESVLG 682
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
358-645 4.16e-83

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: 275.33  E-value: 4.16e-83
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  358 YQLEGLNWLLFNWYNRQ-NCILADEMGLGKTIQSITFLYEILL--TGLRGPFLIIAPLSTIANWEREFRTWT---DLNVV 431
Cdd:pfam00176    1 YQIEGVNWMLSLENNLGrGGILADEMGLGKTLQTISLLLYLKHvdKNWGGPTLIVVPLSLLHNWMNEFERWVsppALRVV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  432 VYHGSMISRQMIQQFEMYFRDsqgriirgtykFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLM 511
Cdd:pfam00176   81 VLHGNKRPQERWKNDPNFLAD-----------FDVVITTYETLRKHKELLKKVHWHRIVLDEGHRLKNSKSKLSKALKSL 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  512 NLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFG----DLKTEEQVQKLQAILKPMMLRRLKEDVEKKLAP 587
Cdd:pfam00176  150 KTRNRWILTGTPLQNNLEELWALLNFLRPGPFGSLSTFRNWFDrpieRGGGKKGVSRLHKLLKPFLLRRTKKDVEKSLPP 229
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  588 KEETIIEVELTNIQKKYY-RAILEKNFAFLSKGAGQANVP-NLVNTMMELRKCCNHPYLI 645
Cdd:pfam00176  230 KVEYILFCRLSKLQRKLYqTFLLKKDLNAIKTGEGGREIKaSLLNILMRLRKICNHPGLI 289
DEXHc_CHD1_2 cd17993
DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and ...
354-576 8.69e-81

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: 265.76  E-value: 8.69e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  354 QLREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLT-GLRGPFLIIAPLSTIANWEREFRTWT-DLNVV 431
Cdd:cd17993      1 ELRDYQLTGLNWLAHSWCKGNNGILADEMGLGKTVQTISFLSYLFHSqQQYGPFLVVVPLSTMPAWQREFAKWApDMNVI 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  432 VYHGSMISRQMIQQFEMYFrdSQGRIIrgtyKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLM 511
Cdd:cd17993     81 VYLGDIKSRDTIREYEFYF--SQTKKL----KFNVLLTTYEIILKDKAFLGSIKWQYLAVDEAHRLKNDESLLYEALKEF 154
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2117983367  512 NLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFmQEFGDLKTEEQVQKLQAILKPMMLRR 576
Cdd:cd17993    155 KTNNRLLITGTPLQNSLKELWALLHFLMPGKFDIWEEF-EEEHDEEQEKGIADLHKELEPFILRR 218
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
355-542 2.15e-74

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: 245.55  E-value: 2.15e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLTGL-RGPFLIIAPLSTIANWEREFRTWT-DLNVVV 432
Cdd:cd17919      1 LRPYQLEGLNFLLELYENGPGGILADEMGLGKTLQAIAFLAYLLKEGKeRGPVLVVCPLSVLENWEREFEKWTpDLRVVV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  433 YHGSMISRQMIQqfemyfrdsqgrIIRGTYKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMN 512
Cdd:cd17919     81 YHGSQRERAQIR------------AKEKLDKFDVVLTTYETLRRDKASLRKFRWDLVVVDEAHRLKNPKSQLSKALKALR 148
                          170       180       190
                   ....*....|....*....|....*....|...
gi 2117983367  513 LEHKVLLTGTPLQNTVEELFSLLHFLEP---LR 542
Cdd:cd17919    149 AKRRLLLTGTPLQNNLEELWALLDFLDPpflLR 181
DEXHc_CHD3_4_5 cd17994
DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; ...
355-576 2.55e-70

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: 234.64  E-value: 2.55e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLTG-LRGPFLIIAPLSTIANWEREFRTWT-DLNVVV 432
Cdd:cd17994      1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTIQTIVFLYSLYKEGhSKGPFLVSAPLSTIINWEREFEMWApDFYVVT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  433 YHGSMIsrqmiqqfemyfrdsqgriirgtykfqaIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMN 512
Cdd:cd17994     81 YVGDHV----------------------------LLTSYELISIDQAILGSIDWAVLVVDEAHRLKNNQSKFFRILNSYK 132
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2117983367  513 LEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 576
Cdd:cd17994    133 IGYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLQGFLEEFADISKEDQIKKLHDLLGPHMLRR 196
DEXHc_HELLS_SMARCA6 cd18009
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ...
352-578 8.20e-70

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: 234.97  E-value: 8.20e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  352 GNQLREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLTGLRGPFLIIAPLSTIANWEREFRTWT-DLNV 430
Cdd:cd18009      1 GGVMRPYQLEGMEWLRMLWENGINGILADEMGLGKTIQTIALLAHLRERGVWGPFLVIAPLSTLPNWVNEFARFTpSVPV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  431 VVYHGSMISRQMIQQfEMYFRDSQGRiirgtyKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKL 510
Cdd:cd18009     81 LLYHGTKEERERLRK-KIMKREGTLQ------DFPVVVTSYEIAMRDRKALQHYAWKYLIVDEGHRLKNLNCRLIQELKT 153
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  511 MNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFG-----------DLKTEEQ----VQKLQAILKPMMLR 575
Cdd:cd18009    154 FNSDNRLLLTGTPLQNNLSELWSLLNFLLPDVFDDLSSFESWFDfsslsdnaadiSNLSEEReqniVHMLHAILKPFLLR 233

                   ...
gi 2117983367  576 RLK 578
Cdd:cd18009    234 RLK 236
DEXHc_CHD3 cd18055
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; ...
355-576 7.73e-65

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: 220.65  E-value: 7.73e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLTG-LRGPFLIIAPLSTIANWEREFRTWT-DLNVVV 432
Cdd:cd18055      1 LHMYQLEGLNWLRFSWAQGTDTILADEMGLGKTIQTIVFLYSLYKEGhTKGPFLVSAPLSTIINWEREFQMWApDFYVVT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  433 YHGSMISRQMIQQFEMYFRDSQGRIIRGTYK--------FQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKL 504
Cdd:cd18055     81 YTGDKDSRAIIRENEFSFDDNAVKGGKKAFKmkreaqvkFHVLLTSYELVTIDQAALGSIRWACLVVDEAHRLKNNQSKF 160
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2117983367  505 LEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 576
Cdd:cd18055    161 FRVLNGYKIDHKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLLGPHMLRR 232
DEXHc_SMARCA1_SMARCA5 cd17997
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ...
352-578 9.42e-65

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: 219.89  E-value: 9.42e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  352 GNQLREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFL-YEILLTGLRGPFLIIAPLSTIANWEREFRTWT-DLN 429
Cdd:cd17997      1 GGTMRDYQIRGLNWLISLFENGINGILADEMGLGKTLQTISLLgYLKHYKNINGPHLIIVPKSTLDNWMREFKRWCpSLR 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  430 VVVYHGSMISRQMIqqfemyFRDsqgRIIRGtyKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLK 509
Cdd:cd17997     81 VVVLIGDKEERADI------IRD---VLLPG--KFDVCITSYEMVIKEKTVLKKFNWRYIIIDEAHRIKNEKSKLSQIVR 149
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2117983367  510 LMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEF----GDLKTEEQVQKLQAILKPMMLRRLK 578
Cdd:cd17997    150 LFNSRNRLLLTGTPLQNNLHELWALLNFLLPDVFTSSEDFDEWFnvnnCDDDNQEVVQRLHKVLRPFLLRRIK 222
DEXHc_CHD4 cd18056
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; ...
355-576 1.94e-64

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: 219.17  E-value: 1.94e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLTG-LRGPFLIIAPLSTIANWEREFRTWT-DLNVVV 432
Cdd:cd18056      1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTAVFLYSLYKEGhSKGPFLVSAPLSTIINWEREFEMWApDMYVVT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  433 YHGSMISRQMIQQFEMYFRDSQgriIRG-----------TYKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKN 501
Cdd:cd18056     81 YVGDKDSRAIIRENEFSFEDNA---IRGgkkasrmkkeaSVKFHVLLTSYELITIDMAILGSIDWACLIVDEAHRLKNNQ 157
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2117983367  502 CKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 576
Cdd:cd18056    158 SKFFRVLNGYSLQHKLLLTGTPLQNNLEELFHLLNFLTPERFHNLEGFLEEFADIAKEDQIKKLHDMLGPHMLRR 232
DEXHc_CHD5 cd18057
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; ...
355-576 3.43e-64

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: 218.78  E-value: 3.43e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLTG-LRGPFLIIAPLSTIANWEREFRTWT-DLNVVV 432
Cdd:cd18057      1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGhSKGPYLVSAPLSTIINWEREFEMWApDFYVVT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  433 YHGSMISRQMIQQFEMYFRDSQGRIIRGTY--------KFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKL 504
Cdd:cd18057     81 YTGDKESRSVIRENEFSFEDNAIRSGKKVFrmkkeaqiKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 160
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2117983367  505 LEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 576
Cdd:cd18057    161 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLLGPHMLRR 232
DEXHc_SMARCA2_SMARCA4 cd17996
DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin ...
352-578 5.10e-64

DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, members 2 and 4 (SMARCA2 and SMARCA4) 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: 350754 [Multi-domain]  Cd Length: 233  Bit Score: 218.01  E-value: 5.10e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  352 GNQLREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSI---TFLYEIllTGLRGPFLIIAPLSTIANWEREFRTWT-D 427
Cdd:cd17996      1 GGTLKEYQLKGLQWMVSLYNNNLNGILADEMGLGKTIQTIsliTYLMEK--KKNNGPYLVIVPLSTLSNWVSEFEKWApS 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  428 LNVVVYHGSMISRQMIQqfemyfrdsqgRIIRGTyKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEG 507
Cdd:cd17996     79 VSKIVYKGTPDVRKKLQ-----------SQIRAG-KFNVLLTTYEYIIKDKPLLSKIKWKYMIIDEGHRMKNAQSKLTQT 146
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  508 LKLM-NLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFG------------DLKTEEQV---QKLQAILKP 571
Cdd:cd17996    147 LNTYyHARYRLLLTGTPLQNNLPELWALLNFLLPKIFKSCKTFEQWFNtpfantgeqvkiELNEEETLliiRRLHKVLRP 226

                   ....*..
gi 2117983367  572 MMLRRLK 578
Cdd:cd17996    227 FLLRRLK 233
DEXHc_CHD2 cd18054
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; ...
352-576 9.01e-64

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; 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. CHD2 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: 350812 [Multi-domain]  Cd Length: 237  Bit Score: 217.57  E-value: 9.01e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  352 GNQLREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFL-YEILLTGLRGPFLIIAPLSTIANWEREFRTWT-DLN 429
Cdd:cd18054     18 NLELRDYQLEGLNWLAHSWCKNNSVILADEMGLGKTIQTISFLsYLFHQHQLYGPFLLVVPLSTLTSWQREFEIWApEIN 97
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  430 VVVYHGSMISRQMIQQFEMYFRDSQgRIirgtyKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLK 509
Cdd:cd18054     98 VVVYIGDLMSRNTIREYEWIHSQTK-RL-----KFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLI 171
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2117983367  510 LMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGDLKtEEQVQKLQAILKPMMLRR 576
Cdd:cd18054    172 DFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGR-ENGYQSLHKVLEPFLLRR 237
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
677-802 3.80e-56

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: 191.54  E-value: 3.80e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  677 GKLVLIDKLLPKMKAGGHKVLIFSQMVRCLDILEDYLIHKRYLYERIDGRVRGNLRQAAIDRFSKPDSDrFVFLLCTRAG 756
Cdd:cd18793     11 GKLEALLELLEELREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPDI-RVFLLSTKAG 89
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 2117983367  757 GLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAVKVYRLI 802
Cdd:cd18793     90 GVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQKKPVVVYRLI 135
DEXQc_arch_SWI2_SNF2 cd18012
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ...
353-578 1.13e-55

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: 193.55  E-value: 1.13e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  353 NQLREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLTGLRGPFLIIAPLSTIANWEREFRTWT-DLNVV 431
Cdd:cd18012      3 ATLRPYQKEGFNWLSFLRHYGLGGILADDMGLGKTLQTLALLLSRKEEGRKGPSLVVAPTSLIYNWEEEAAKFApELKVL 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  432 VYHGSMISRQMIQQFEmyfrdsqgriirgtyKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLM 511
Cdd:cd18012     83 VIHGTKRKREKLRALE---------------DYDLVITSYGLLRRDIELLKEVKFHYLVLDEAQNIKNPQTKTAKAVKAL 147
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2117983367  512 NLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFG----DLKTEEQVQKLQAILKPMMLRRLK 578
Cdd:cd18012    148 KADHRLALTGTPIENHLGELWSIFDFLNPGLLGSYKRFKKRFAkpieKDGDEEALEELKKLISPFILRRLK 218
DEXHc_CHD1L cd18006
DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, ...
355-576 1.49e-54

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: 190.34  E-value: 1.49e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLT-GLRGPFLIIAPLSTIANWEREFRTWT-DLNVVV 432
Cdd:cd18006      1 LRPYQLEGVNWLLQCRAEQHGCILGDEMGLGKTCQTISLLWYLAGRlKLLGPFLVLCPLSVLDNWKEELNRFApDLSVIT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  433 YHGSMISRQMIQQfemyfrdsqgrIIRGTYKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMN 512
Cdd:cd18006     81 YMGDKEKRLDLQQ-----------DIKSTNRFHVLLTTYEICLKDASFLKSFPWASLVVDEAHRLKNQNSLLHKTLSEFS 149
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2117983367  513 LEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAEST--FMQEFGDLKTE-EQVQKLQAILKPMMLRR 576
Cdd:cd18006    150 VDFRLLLTGTPIQNSLQELYALLSFIEPNVFPKDKLddFIKAYSETDDEsETVEELHLLLQPFLLRR 216
DEXQc_SRCAP cd18003
DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or ...
355-576 1.50e-51

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: 181.78  E-value: 1.50e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFL-YEILLTGLRGPFLIIAPLSTIANWEREFRTWTD-LNVVV 432
Cdd:cd18003      1 LREYQHIGLDWLATLYEKNLNGILADEMGLGKTIQTIALLaHLACEKGNWGPHLIVVPTSVMLNWEMEFKRWCPgFKILT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  433 YHGSMISRQMIQQfemyfrdsqgriirGTYK---FQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLK 509
Cdd:cd18003     81 YYGSAKERKLKRQ--------------GWMKpnsFHVCITSYQLVVQDHQVFKRKKWKYLILDEAHNIKNFKSQRWQTLL 146
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2117983367  510 LMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTF----------MQEFGDLKTEEQVQKLQAILKPMMLRR 576
Cdd:cd18003    147 NFNTQRRLLLTGTPLQNSLMELWSLMHFLMPHIFQSHQEFkewfsnpltaMSEGSQEENEELVRRLHKVLRPFLLRR 223
DEXHc_CHD1 cd18053
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; ...
352-576 2.85e-51

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: 181.79  E-value: 2.85e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  352 GNQLREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFL-YEILLTGLRGPFLIIAPLSTIANWEREFRTWTDL-N 429
Cdd:cd18053     18 GLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLnYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWAPQmN 97
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  430 VVVYHGSMISRQMIQQFEmYFRDSQGRIirgtyKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLK 509
Cdd:cd18053     98 AVVYLGDINSRNMIRTHE-WMHPQTKRL-----KFNILLTTYEILLKDKSFLGGLNWAFIGVDEAHRLKNDDSLLYKTLI 171
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2117983367  510 LMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGDLKtEEQVQKLQAILKPMMLRR 576
Cdd:cd18053    172 DFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGR-EYGYASLHKELEPFLLRR 237
DEXHc_ERCC6L2 cd18005
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
355-576 3.25e-50

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: 179.11  E-value: 3.25e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLlFNWY-NRQNCILADEMGLGKTIQSITFLYEIL-LTGLR--------------------GPFLIIAPL 412
Cdd:cd18005      1 LRDYQREGVEFM-YDLYkNGRGGILGDDMGLGKTVQVIAFLAAVLgKTGTRrdrennrprfkkkppassakKPVLIVAPL 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  413 STIANWEREFRTWTDLNVVVYHGSMISRqmiqqfemyfrDSQGRIIRGTYkfQAIITTFEMILGGCPELNAIEWRCVIID 492
Cdd:cd18005     80 SVLYNWKDELDTWGHFEVGVYHGSRKDD-----------ELEGRLKAGRL--EVVVTTYDTLRRCIDSLNSINWSAVIAD 146
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  493 EAHRLKNKNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGD---------------LK 557
Cdd:cd18005    147 EAHRIKNPKSKLTQAMKELKCKVRIGLTGTLLQNNMKELWCLLDWAVPGALGSRSQFKKHFSEpikrgqrhtatarelRL 226
                          250
                   ....*....|....*....
gi 2117983367  558 TEEQVQKLQAILKPMMLRR 576
Cdd:cd18005    227 GRKRKQELAVKLSKFFLRR 245
DEXHc_SMARCAD1 cd17998
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ...
355-543 7.69e-49

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: 172.57  E-value: 7.69e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLTGLRGPFLIIAPLSTIANWEREFRTWT-DLNVVVY 433
Cdd:cd17998      1 LKDYQLIGLNWLNLLYQKKLSGILADEMGLGKTIQVIAFLAYLKEIGIPGPHLVVVPSSTLDNWLREFKRWCpSLKVEPY 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  434 HGSMISRqmiqqfemyfRDSQGRIIRGTYKFQAIITTFEMIlGGCPE----LNAIEWRCVIIDEAHRLKNKNCKLLEGLK 509
Cdd:cd17998     81 YGSQEER----------KHLRYDILKGLEDFDVIVTTYNLA-TSNPDdrsfFKRLKLNYVVYDEGHMLKNMTSERYRHLM 149
                          170       180       190
                   ....*....|....*....|....*....|....
gi 2117983367  510 LMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRF 543
Cdd:cd17998    150 TINANFRLLLTGTPLQNNLLELMSLLNFIMPKPF 183
DEXQc_INO80 cd18002
DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 ...
355-576 9.33e-49

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: 174.23  E-value: 9.33e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLfNWYNRQ-NCILADEMGLGKTIQSITFLYEILLT-GLRGPFLIIAPLSTIANWEREF-RTWTDLNVV 431
Cdd:cd18002      1 LKEYQLKGLNWLA-NLYEQGiNGILADEMGLGKTVQSIAVLAHLAEEhNIWGPFLVIAPASTLHNWQQEIsRFVPQFKVL 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  432 VYHGSMISRQMIQQF----EMYFRDSqgriirgtyKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEG 507
Cdd:cd18002     80 PYWGNPKDRKVLRKFwdrkNLYTRDA---------PFHVVITSYQLVVQDEKYFQRVKWQYMVLDEAQAIKSSSSSRWKT 150
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2117983367  508 LKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFG-DLKT---------EEQVQKLQAILKPMMLRR 576
Cdd:cd18002    151 LLSFHCRNRLLLTGTPIQNSMAELWALLHFIMPTLFDSHDEFNEWFSkDIEShaenktglnEHQLKRLHMILKPFMLRR 229
DEXHc_SMARCA4 cd18062
DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent ...
341-578 9.94e-46

DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 (SMARCA4, also known as transcription activator BRG1) is a component of the CREST-BRG1 complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders. SMARCA4 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: 350820 [Multi-domain]  Cd Length: 251  Bit Score: 166.37  E-value: 9.94e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  341 KKIEQSREYKNGNQLREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFL-YEILLTGLRGPFLIIAPLSTIANWE 419
Cdd:cd18062     10 EKVEKQSSLLVNGVLKQYQIKGLEWLVSLYNNNLNGILADEMGLGKTIQTIALItYLMEHKRINGPFLIIVPLSTLSNWV 89
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  420 REFRTWTDLNV-VVYHGSMISRqmiQQFEMYFRDSqgriirgtyKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLK 498
Cdd:cd18062     90 YEFDKWAPSVVkVSYKGSPAAR---RAFVPQLRSG---------KFNVLLTTYEYIIKDKQILAKIRWKYMIVDEGHRMK 157
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  499 NKNCKLLEGLKLMNLE-HKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFG----------DLKTEEQ---VQK 564
Cdd:cd18062    158 NHHCKLTQVLNTHYVApRRLLLTGTPLQNKLPELWALLNFLLPTIFKSCSTFEQWFNapfamtgekvDLNEEETiliIRR 237
                          250
                   ....*....|....
gi 2117983367  565 LQAILKPMMLRRLK 578
Cdd:cd18062    238 LHKVLRPFLLRRLK 251
DEXHc_SMARCA5 cd18064
DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent ...
342-589 1.30e-44

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: 162.91  E-value: 1.30e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  342 KIEQSREYKNGNQLREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFL-YEILLTGLRGPFLIIAPLSTIANWER 420
Cdd:cd18064      3 RFEDSPSYVKWGKLRDYQVRGLNWLISLYENGINGILADEMGLGKTLQTISLLgYMKHYRNIPGPHMVLVPKSTLHNWMA 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  421 EFRTWT-DLNVVVYHGSMisrqmiQQFEMYFRDSqgrIIRGtyKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKN 499
Cdd:cd18064     83 EFKRWVpTLRAVCLIGDK------DQRAAFVRDV---LLPG--EWDVCVTSYEMLIKEKSVFKKFNWRYLVIDEAHRIKN 151
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  500 KNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGD---LKTEEQVQKLQAILKPMMLRR 576
Cdd:cd18064    152 EKSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALLNFLLPDVFNSAEDFDSWFDTnncLGDQKLVERLHMVLRPFLLRR 231
                          250
                   ....*....|...
gi 2117983367  577 LKEDVEKKLAPKE 589
Cdd:cd18064    232 IKADVEKSLPPKK 244
DEXHc_SMARCA2 cd18063
DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent ...
344-578 3.33e-44

DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 (SMARCA2, also known as brahma homolog) is a component of the BAF complex. SMARCA2 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: 350821 [Multi-domain]  Cd Length: 251  Bit Score: 161.77  E-value: 3.33e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  344 EQSREYKNGNqLREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFL-YEILLTGLRGPFLIIAPLSTIANWEREF 422
Cdd:cd18063     14 KQSSLLINGT-LKHYQLQGLEWMVSLYNNNLNGILADEMGLGKTIQTIALItYLMEHKRLNGPYLIIVPLSTLSNWTYEF 92
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  423 RTWTDLNV-VVYHGS-MISRQMIQQFEmyfrdsqgriirgTYKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNK 500
Cdd:cd18063     93 DKWAPSVVkISYKGTpAMRRSLVPQLR-------------SGKFNVLLTTYEYIIKDKHILAKIRWKYMIVDEGHRMKNH 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  501 NCKLLEGLKLMNLE-HKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFG----------DLKTEEQ---VQKLQ 566
Cdd:cd18063    160 HCKLTQVLNTHYVApRRILLTGTPLQNKLPELWALLNFLLPTIFKSCSTFEQWFNapfamtgervDLNEEETiliIRRLH 239
                          250
                   ....*....|..
gi 2117983367  567 AILKPMMLRRLK 578
Cdd:cd18063    240 KVLRPFLLRRLK 251
DEXDc_SHPRH-like cd18008
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ...
355-576 2.04e-43

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: 159.38  E-value: 2.04e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLFnwynrqnC--ILADEMGLGKTIQSI------------------TFLYEILLTGLRGPFLIIAPLST 414
Cdd:cd18008      1 LLPYQKQGLAWMLP-------RggILADEMGLGKTIQALalilatrpqdpkipeeleENSSDPKKLYLSKTTLIVVPLSL 73
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  415 IANWEREFRTWTD---LNVVVYHGSM-------ISRQMI-----QQFEMYFRDSQGRIIRGTYKFQAiittfemilggcP 479
Cdd:cd18008     74 LSQWKDEIEKHTKpgsLKVYVYHGSKriksieeLSDYDIvittyGTLASEFPKNKKGGGRDSKEKEA------------S 141
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  480 ELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGDLKTE 559
Cdd:cd18008    142 PLHRIRWYRVILDEAHNIKNRSTKTSRAVCALKAERRWCLTGTPIQNSLDDLYSLLRFLRVEPFGDYPWFNSDISKPFSK 221
                          250       260
                   ....*....|....*....|
gi 2117983367  560 ---EQVQKLQAILKPMMLRR 576
Cdd:cd18008    222 ndrKALERLQALLKPILLRR 241
DEXHc_SMARCA1 cd18065
DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent ...
342-578 1.15e-41

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: 154.02  E-value: 1.15e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  342 KIEQSREYKNGNQLREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFL-YEILLTGLRGPFLIIAPLSTIANWER 420
Cdd:cd18065      3 RFEESPSYVKGGTLRDYQVRGLNWMISLYENGVNGILADEMGLGKTLQTIALLgYLKHYRNIPGPHMVLVPKSTLHNWMN 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  421 EFRTWT-DLNVVVYHGSMISRQMIQQFEMYfrdsqgriirgTYKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKN 499
Cdd:cd18065     83 EFKRWVpSLRAVCLIGDKDARAAFIRDVMM-----------PGEWDVCVTSYEMVIKEKSVFKKFNWRYLVIDEAHRIKN 151
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  500 KNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGD---LKTEEQVQKLQAILKPMMLRR 576
Cdd:cd18065    152 EKSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALLNFLLPDVFNSADDFDSWFDTkncLGDQKLVERLHAVLKPFLLRR 231

                   ..
gi 2117983367  577 LK 578
Cdd:cd18065    232 IK 233
DEXHc_ERCC6L cd18001
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ...
355-576 3.44e-41

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: 152.53  E-value: 3.44e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLFNWYNRQNCILADEMGLGKTIQSITFLYEILLTGLRGPFLIIAPLSTIANWEREFRTWT-DLNVVVY 433
Cdd:cd18001      1 LYPHQREGVAWLWSLHDGGKGGILADDMGLGKTVQICAFLSGMFDSGLIKSVLVVMPTSLIPHWVKEFAKWTpGLRVKVF 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  434 HGSMISRQmiqqfemyfRDSQGRIIRGtykFQAIITTFEMILGGCPELNAIE-----WRCVIIDEAHRLKNKNCKLLEGL 508
Cdd:cd18001     81 HGTSKKER---------ERNLERIQRG---GGVLLTTYGMVLSNTEQLSADDhdefkWDYVILDEGHKIKNSKTKSAKSL 148
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  509 KLMNLEHKVLLTGTPLQNTVEELFSLLHFLEP-LRFPAESTFMQEF------GDLKTEEQVQK---------LQAILKPM 572
Cdd:cd18001    149 REIPAKNRIILTGTPIQNNLKELWALFDFACNgSLLGTRKTFKMEFenpitrGRDKDATQGEKalgsevaenLRQIIKPY 228

                   ....
gi 2117983367  573 MLRR 576
Cdd:cd18001    229 FLRR 232
DEXHc_ERCC6 cd18000
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ...
355-540 2.42e-38

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: 142.85  E-value: 2.42e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLfnWYNRQNC--ILADEMGLGKTIQSITFLYEILLTG-LRGPFLIIAPLSTIANWEREFRTW-TDLNV 430
Cdd:cd18000      1 LFKYQQTGVQWLW--ELHCQRVggILGDEMGLGKTIQIIAFLAALHHSKlGLGPSLIVCPATVLKQWVKEFHRWwPPFRV 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  431 VVYHGSMISRQMIQQFEMYFRDSQgRIIRGTYKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKL 510
Cdd:cd18000     79 VVLHSSGSGTGSEEKLGSIERKSQ-LIRKVVGDGGILITTYEGFRKHKDLLLNHNWQYVILDEGHKIRNPDAEITLACKQ 157
                          170       180       190
                   ....*....|....*....|....*....|
gi 2117983367  511 MNLEHKVLLTGTPLQNTVEELFSLLHFLEP 540
Cdd:cd18000    158 LRTPHRLILSGTPIQNNLKELWSLFDFVFP 187
DEXHc_RAD54 cd18004
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ...
355-576 6.76e-37

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: 140.50  E-value: 6.76e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLL-----FNWYNRQNCILADEMGLGKTIQSITFLYeILLTglRGPF--------LIIAPLSTIANWERE 421
Cdd:cd18004      1 LRPHQREGVQFLYdcltgRRGYGGGGAILADEMGLGKTLQAIALVW-TLLK--QGPYgkptakkaLIVCPSSLVGNWKAE 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  422 FRTW---TDLNVVVYHGSMISRQMIQQFEMYFRDsqgriirgtykFQAIITTFEMILGGCPELNAIEwRC--VIIDEAHR 496
Cdd:cd18004     78 FDKWlglRRIKVVTADGNAKDVKASLDFFSSAST-----------YPVLIISYETLRRHAEKLSKKI-SIdlLICDEGHR 145
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  497 LKNKNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGD--LK------TEEQV------ 562
Cdd:cd18004    146 LKNSESKTTKALNSLPCRRRLLLTGTPIQNDLDEFFALVDFVNPGILGSLASFRKVFEEpiLRsrdpdaSEEDKelgaer 225
                          250
                   ....*....|....*
gi 2117983367  563 -QKLQAILKPMMLRR 576
Cdd:cd18004    226 sQELSELTSRFILRR 240
CD2_tandem_CHD5-9_like cd18663
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ...
265-323 6.38e-35

repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349310 [Multi-domain]  Cd Length: 59  Bit Score: 127.79  E-value: 6.38e-35
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2117983367  265 PDYIEVDRVLEVSFCEDKDTGEPVTYYLVKWCSLPYEDSTWELKEDVDQGKIEEFEQLQ 323
Cdd:cd18663      1 PDYVEVDRILDVSVSTDPNTGEPVTHYLVKWCSLPYEDSTWELEEDVDPAKIEEFEKLR 59
DEXHc_Mot1 cd17999
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ...
355-576 2.01e-34

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: 132.86  E-value: 2.01e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLF-NWYNRQNcILADEMGLGKTIQSITFLY--------EILLTGLrgPFLIIAPLSTIANWEREFRTW 425
Cdd:cd17999      1 LRPYQQEGINWLAFlNKYNLHG-ILCDDMGLGKTLQTLCILAsdhhkranSFNSENL--PSLVVCPPTLVGHWVAEIKKY 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  426 TD---LNVVVYHGSMISRQMIQQFemyfrdsqgriirgTYKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNC 502
Cdd:cd17999     78 FPnafLKPLAYVGPPQERRRLREQ--------------GEKHNVIVASYDVLRNDIEVLTKIEWNYCVLDEGHIIKNSKT 143
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  503 KLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFG-------DLK-----TEEQVQKLQAILK 570
Cdd:cd17999    144 KLSKAVKQLKANHRLILSGTPIQNNVLELWSLFDFLMPGYLGTEKQFQRRFLkpilasrDSKasakeQEAGALALEALHK 223

                   ....*....
gi 2117983367  571 ---PMMLRR 576
Cdd:cd17999    224 qvlPFLLRR 232
DEXHc_ATRX-like cd18007
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ...
355-553 3.06e-32

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: 127.02  E-value: 3.06e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLN--W--LLFNWYNRQN---CILADEMGLGKTIQSITFLYEILLTGLRGP-FLIIAPLSTIANWEREFRTWT 426
Cdd:cd18007      1 LKPHQVEGVRflWsnLVGTDVGSDEgggCILAHTMGLGKTLQVITFLHTYLAAAPRRSrPLVLCPASTLYNWEDEFKKWL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  427 ------DLNVVVYHGSMISRQ---MIQQ-----------FEMYFR-----DSQGRIIRGTYKFQAIITtfemilggcPEL 481
Cdd:cd18007     81 ppdlrpLLVLVSLSASKRADArlrKINKwhkeggvlligYELFRNlasnaTTDPRLKQEFIAALLDPG---------PDL 151
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2117983367  482 naiewrcVIIDEAHRLKNKNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEF 553
Cdd:cd18007    152 -------LVLDEGHRLKNEKSQLSKALSKVKTKRRILLTGTPLQNNLKEYWTMVDFARPKYLGTLKEFKKKF 216
DEXDc smart00487
DEAD-like helicases superfamily;
348-546 1.23e-30

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 121.06  E-value: 1.23e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367   348 EYKNGNQLREYQLEGLNWLLFNWynrQNCILADEMGLGKTIQSITFLYEILLTGLRGPFLIIAPLSTIA-NWEREFRTW- 425
Cdd:smart00487    2 EKFGFEPLRPYQKEAIEALLSGL---RDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAeQWAEELKKLg 78
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367   426 --TDLNVVVYHGSMISRQMIQQFEmyfrdsqgriirgTYKFQAIITTFEMILGGCPE--LNAIEWRCVIIDEAHRLKNKN 501
Cdd:smart00487   79 psLGLKVVGLYGGDSKREQLRKLE-------------SGKTDILVTTPGRLLDLLENdkLSLSNVDLVILDEAHRLLDGG 145
                           170       180       190       200       210
                    ....*....|....*....|....*....|....*....|....*....|.
gi 2117983367   502 --CKLLEGLKLMNLE-HKVLLTGTP---LQNTVEELFSLLHFLEPLRFPAE 546
Cdd:smart00487  146 fgDQLEKLLKLLPKNvQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLE 196
DEXHc_RAD54B cd18066
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ...
355-553 1.31e-28

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: 116.48  E-value: 1.31e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLnwlLFNWY--------NRQNCILADEMGLGKTIQSITFLYEILLTGLRGP------FLIIAPLSTIANWER 420
Cdd:cd18066      1 LRPHQREGI---EFLYEcvmgmrvnERFGAILADEMGLGKTLQCISLIWTLLRQGPYGGkpvikrALIVTPGSLVKNWKK 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  421 EFRTWtdlnvvvyhgsmISRQMIQQFEMYfRDSQGRIIRGTYKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNK 500
Cdd:cd18066     78 EFQKW------------LGSERIKVFTVD-QDHKVEEFIASPLYSVLIISYEMLLRSLDQISKLNFDLVICDEGHRLKNT 144
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2117983367  501 NCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEF 553
Cdd:cd18066    145 SIKTTTALTSLSCERRIILTGTPIQNDLQEFFALIDFVNPGILGSLSTYRKVY 197
CD1_tandem_CHD5-9_like cd18668
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ...
181-245 4.64e-27

repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349315 [Multi-domain]  Cd Length: 68  Bit Score: 105.88  E-value: 4.64e-27
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2117983367  181 EEDAAIVDKILSSRIIKKEI-TGGVTVEAEEFYVKYKNYSYLHCEWATEQQLLK-DKRIQQKIKRFK 245
Cdd:cd18668      1 EEDTMIIEKILASRKKKKEKeEGAEEIEVEEYLVKYKNFSYLHCEWKTEEELEKgDKRIKQKIKRFK 67
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
677-791 2.09e-25

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: 102.67  E-value: 2.09e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  677 GKLVLIDKLLPKMKagGHKVLIFSQMVRCLDilEDYLIHKR-YLYERIDGRVRGNLRQAAIDRFSKPDSDrfvFLLCTRA 755
Cdd:pfam00271    1 EKLEALLELLKKER--GGKVLIFSQTKKTLE--AELLLEKEgIKVARLHGDLSQEEREEILEDFRKGKID---VLVATDV 73
                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 2117983367  756 GGLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIG 791
Cdd:pfam00271   74 AERGLDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
DEXHc_HLTF1_SMARC3 cd18071
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ...
355-576 4.72e-25

DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as HIP116 or SMARCA3) has both helicase and E3 ubiquitin ligase activities and ATP-dependent nucleosome-remodeling activity. HLTF1 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: 350829 [Multi-domain]  Cd Length: 239  Bit Score: 106.01  E-value: 4.72e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLFN----------------WYN-----RQNC--------ILADEMGLGKTIQSITFLyeilltgLRGP 405
Cdd:cd18071      1 LLPHQKQALAWMVSRensqdlppfweeavglFLNtitnfSQKKrpelvrggILADDMGLGKTLTTISLI-------LANF 73
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  406 FLIIAPLSTIANWEREFRTWTD---LNVVVYHGSmisrqmiqqfemyfrdSQGRIIRGTYKFQAIITTFEMILG-----G 477
Cdd:cd18071     74 TLIVCPLSVLSNWETQFEEHVKpgqLKVYTYHGG----------------ERNRDPKLLSKYDIVLTTYNTLASdfgakG 137
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  478 CPELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFG--- 554
Cdd:cd18071    138 DSPLHTINWLRVVLDEGHQIRNPNAQQTKAVLNLSSERRWVLTGTPIQNSPKDLGSLLSFLHLKPFSNPEYWRRLIQrpl 217
                          250       260
                   ....*....|....*....|..
gi 2117983367  555 DLKTEEQVQKLQAILKPMMLRR 576
Cdd:cd18071    218 TMGDPTGLKRLQVLMKQITLRR 239
DEXHc_HARP_SMARCAL1 cd18010
DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin ...
355-576 8.13e-25

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: 104.59  E-value: 8.13e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLfnwynRQN--CILADEMGLGKTIQSITFLYEilltgLR--GPFLIIAPLSTIANWEREFRTW----- 425
Cdd:cd18010      1 LLPFQREGVCFAL-----RRGgrVLIADEMGLGKTVQAIAIAAY-----YReeWPLLIVCPSSLRLTWADEIERWlpslp 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  426 -TDLNVVVyHGSmisrqmiqqfeMYFRDSQGRIirgtykfqaIITTFEMILGGCPELNAIEWRCVIIDEAHRLKN---KN 501
Cdd:cd18010     71 pDDIQVIV-KSK-----------DGLRDGDAKV---------VIVSYDLLRRLEKQLLARKFKVVICDESHYLKNskaKR 129
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  502 CKLLEGLkLMNLEHKVLLTGTPLQNTVEELFSLLHFLEP--LRFPAEST------FMQEFG-DLKTEEQVQKLQAIL-KP 571
Cdd:cd18010    130 TKAALPL-LKRAKRVILLSGTPALSRPIELFTQLDALDPklFGRFHDFGrrycaaKQGGFGwDYSGSSNLEELHLLLlAT 208

                   ....*
gi 2117983367  572 MMLRR 576
Cdd:cd18010    209 IMIRR 213
DEXHc_RAD54A cd18067
DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as ...
355-576 1.17e-24

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: 105.24  E-value: 1.17e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLL-----FNWYNRQNCILADEMGLGKTIQSITFLYEILLTGLRGPFLI-----IAPLSTIANWEREFRT 424
Cdd:cd18067      1 LRPHQREGVKFLYrcvtgRRIRGSHGCIMADEMGLGKTLQCITLMWTLLRQSPQCKPEIdkaivVSPSSLVKNWANELGK 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  425 WTDLNVVVYHGSMISRQMIQQFEMYFRDSQGRIIRGTykfqAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKNKNCKL 504
Cdd:cd18067     81 WLGGRLQPLAIDGGSKKEIDRKLVQWASQQGRRVSTP----VLIISYETFRLHVEVLQKGEVGLVICDEGHRLKNSDNQT 156
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  505 LEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFGD---------------LKTEEQVQKLQAIL 569
Cdd:cd18067    157 YQALDSLNTQRRVLLSGTPIQNDLSEYFSLVNFVNPGILGTAAEFKKNFELpilkgrdadasekerQLGEEKLQELISIV 236

                   ....*..
gi 2117983367  570 KPMMLRR 576
Cdd:cd18067    237 NRCIIRR 243
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
373-576 1.58e-23

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: 100.83  E-value: 1.58e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  373 RQNCILADEMGLGKTIQSITFLYEILLTGLRGPFLIIAPLSTIANWEREFRTWTDLNVVVYHGSMIS--RQMIQQFEMYF 450
Cdd:cd18011     17 PVRLLLADEVGLGKTIEAGLIIKELLLRGDAKRVLILCPASLVEQWQDELQDKFGLPFLILDRETAAqlRRLIGNPFEEF 96
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  451 RD---SQGRIIRGTYKFQAiittfemilggcpeLNAIEWRCVIIDEAHRLKNKNCKLLEGL-KLMNL-----EHKVLLTG 521
Cdd:cd18011     97 PIvivSLDLLKRSEERRGL--------------LLSEEWDLVVVDEAHKLRNSGGGKETKRyKLGRLlakraRHVLLLTA 162
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2117983367  522 TPLQNTVEELFSLLHFLEPLRFPAestfMQEFGDLKTEEQVqklqaiLKPMMLRR 576
Cdd:cd18011    163 TPHNGKEEDFRALLSLLDPGRFAV----LGRFLRLDGLREV------LAKVLLRR 207
DEXHc_ATRX cd18068
DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha ...
376-553 9.05e-22

DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) is involved in transcriptional regulation and chromatin remodeling. Mutations in humans cause mental retardation, X-linked, syndromic, with hypotonic facies 1 (MRXSHF1) and alpha-thalassemia myelodysplasia syndrome (ATMDS). ATRX is part of the a 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: 350826 [Multi-domain]  Cd Length: 246  Bit Score: 96.88  E-value: 9.05e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  376 CILADEMGLGKTIQSITFLYEILLTGLRGPF---LIIAPLSTIANWEREFRTWTDLN-----VVVYHGSMISRQ------ 441
Cdd:cd18068     31 CILAHCMGLGKTLQVVTFLHTVLLCEKLENFsrvLVVCPLNTVLNWLNEFEKWQEGLkdeekIEVNELATYKRPqersyk 110
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  442 ----------MIQQFEMYFRDSQGRIIRGTYKFQAIITTFEMILGgcPELnaiewrcVIIDEAHRLKNKNCKLLEGLKLM 511
Cdd:cd18068    111 lqrwqeeggvMIIGYDMYRILAQERNVKSREKLKEIFNKALVDPG--PDF-------VVCDEGHILKNEASAVSKAMNSI 181
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 2117983367  512 NLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEF 553
Cdd:cd18068    182 RTKRRIVLTGTPLQNNLIEYHCMVNFVKPNLLGTIKEFRNRF 223
DISARM_DrmD_b NF038318
DISARM system SNF2-like helicase DrmD, short form; DrmD, a SNF2-like helicase, is a component ...
377-841 1.62e-21

DISARM system SNF2-like helicase DrmD, short form; DrmD, a SNF2-like helicase, is a component of class 1 DISARM (Defence Island System Associated with Restriction Modification), which contains a DNA adenine N6 methyltransferase. This HMM describes a distinct form that is somewhat shorter than the majority of DrmD proteins.


Pssm-ID: 468472 [Multi-domain]  Cd Length: 868  Bit Score: 102.84  E-value: 1.62e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  377 ILADEMGLGKTIQSITFLYEILLTGLRgPFLIIAPLSTIANWEREFRTWTDLNVVVyhgsmISRQMIQqfemYFRDSQGR 456
Cdd:NF038318    51 ILADEVGLGKTIEAGLVLKYVLESGAK-KILIILPANLRKQWEIELEEKFDLESLI-----LDSLTVE----KDAKKWNK 120
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  457 IIRGTYKFQAIITTFEMILGGCPELNAIEWRCVIIDEAHRLKN--KNCKLLEGL-KLMNLEHKVLLTGTPLQNTVEELFS 533
Cdd:NF038318   121 RLTDNKKVRIVITSYDYASKLMKRFPKVKWDFIIIDEAHNLRNvhKGGKRAKNLyELTKGIPKILLTATPLQNSLLDLYG 200
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  534 LLHFLEPLRFPAESTFM------QEFGDLKTEeqvqklqaiLKPMMLRRLKEDVEKKLAPKEETIIEV--ELTNIQKKYY 605
Cdd:NF038318   201 LVSFIDPRIFGSEKVFSkryikdEDYSDLKRE---------LSPVLYRTLRKDVADYMQFKKRKCITVdfELSPDEIELY 271
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  606 RAIlekNfAFLSKGAGQAnVPN--------------------LVNTMMELRKCCNHPY-------LIKG--------AEE 650
Cdd:NF038318   272 VRV---N-NFLKRDILYS-IPTsnrtliilvirkllasssfaLAETFEVLKKRLEKLKegtrsanAQEGfdlfwsfvEDE 346
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  651 KILGEFRETYSP--AAQDFHLQAMIQSAGKLVLIDKLL---PKMKAG----------------GHKVLIFSQMVRCLDIL 709
Cdd:NF038318   347 IDESGFEEKQDElyTRQKEFIQHEIDEVDAIIDVAKRIktnAKVTALktaleiafeyqreegiAQKVVVFTESKRTQKYI 426
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  710 EDYLIHKRYLYERI---DG--------------RVR--GN--------LRQAAIDRFSkpdsDRFVFLLCTRAGGLGINL 762
Cdd:NF038318   427 AEELRKSGYEGEDIllfNGdfddamtkeiyrawQVKnyGKanygrsveYKHAIVDYFK----NNAKILIVTDAGSEGLNL 502
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  763 TAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAVKVYRLI-TRNSYEREMFDRASLKLGL--------DKA--VLQSMSG 831
Cdd:NF038318   503 QFCNTVINYDLPWNPQKIEQRIGRCHRYGQKNDVVAINLLnTQNVADKRVYEILSEKFELfegvfgasDIAlgLLESGTD 582
                          570
                   ....*....|
gi 2117983367  832 RENSVGGIQQ 841
Cdd:NF038318   583 FEKRVLQIYQ 592
HELICc smart00490
helicase superfamily c-terminal domain;
707-791 4.64e-20

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 86.50  E-value: 4.64e-20
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367   707 DILEDYLIHKRYLYERIDGRVRGNLRQAAIDRFSKPDSDrfvFLLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQAQAR 786
Cdd:smart00490    1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIK---VLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGR 77

                    ....*
gi 2117983367   787 CHRIG 791
Cdd:smart00490   78 AGRAG 82
DEXHc_ARIP4 cd18069
DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called ...
376-540 1.64e-18

DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called RAD54 like 2 or RAD54L2 ) modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. ARIP4 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: 350827 [Multi-domain]  Cd Length: 227  Bit Score: 86.79  E-value: 1.64e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  376 CILADEMGLGKTIQSITFLYEIL-LTGLRgPFLIIAPLSTIANWEREFRTWtdlnvvVYHGSMISRQMIQQFEMYFRDSQ 454
Cdd:cd18069     31 CILAHSMGLGKTLQVISFLDVLLrHTGAK-TVLAIVPVNTLQNWLSEFNKW------LPPPEALPNVRPRPFKVFILNDE 103
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  455 GRIIRGTYKFQA--------IITTFEMI-LGGCPELnaiewrcVIIDEAHRLKNKNCKLLEGLKLMNLEHKVLLTGTPLQ 525
Cdd:cd18069    104 HKTTAARAKVIEdwvkdggvLLMGYEMFrLRPGPDV-------VICDEGHRIKNCHASTSQALKNIRSRRRIVLTGYPLQ 176
                          170
                   ....*....|....*
gi 2117983367  526 NTVEELFSLLHFLEP 540
Cdd:cd18069    177 NNLIEYWCMVDFVRP 191
DEXHc_TTF2 cd18072
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ...
355-576 2.60e-18

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: 86.77  E-value: 2.60e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLfnWYNRQNC---ILADEMGLGKTIQSITFLY--------------EILLTGL---------RGPFLI 408
Cdd:cd18072      1 LLLHQKQALAWLL--WRERQKPrggILADDMGLGKTLTMIALILaqkntqnrkeeekeKALTEWEskkdstlvpSAGTLV 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  409 IAPLSTIANWEREFRTWTD---LNVVVYHGSMisrqmiqqfemyfRDSQGRIIRgtyKFQAIITTFEMILGGCPE----- 480
Cdd:cd18072     79 VCPASLVHQWKNEVESRVAsnkLRVCLYHGPN-------------RERIGEVLR---DYDIVITTYSLVAKEIPTykees 142
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  481 ----LNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPAESTFMQEFgDL 556
Cdd:cd18072    143 rsspLFRIAWARIILDEAHNIKNPKVQASIAVCKLRAHARWALTGTPIQNNLLDMYSLLKFLRCSPFDDLKVWKKQV-DN 221
                          250       260
                   ....*....|....*....|
gi 2117983367  557 KTEEQVQKLQAILKPMMLRR 576
Cdd:cd18072    222 KSRKGGERLNILTKSLLLRR 241
BRK smart00592
domain in transcription and CHROMO domain helicases;
2054-2098 1.89e-15

domain in transcription and CHROMO domain helicases;


Pssm-ID: 197800  Cd Length: 45  Bit Score: 72.00  E-value: 1.89e-15
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*
gi 2117983367  2054 TGEERVQLINRRNARKVGGAFAPPLKDLCRFLKENSEYGVAPEWA 2098
Cdd:smart00592    1 DGEERVPVINRETGKKLTGDDAPKAKDLERWLEENPEYEVAPRSA 45
BRK pfam07533
BRK domain; The function of this domain is unknown. It is often found associated with ...
1980-2020 1.01e-14

BRK domain; The function of this domain is unknown. It is often found associated with helicases and transcription factors.


Pssm-ID: 462196  Cd Length: 44  Bit Score: 69.85  E-value: 1.01e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2117983367 1980 DAESPVPVINLKDGTRLAGDDAPKRKDLEKWLNEHPGYVED 2020
Cdd:pfam07533    2 TGDERVPVVNRKTGKKLTGDKAPKLKDLEEWLEENPGYEVD 42
BRK smart00592
domain in transcription and CHROMO domain helicases;
1980-2029 1.04e-14

domain in transcription and CHROMO domain helicases;


Pssm-ID: 197800  Cd Length: 45  Bit Score: 70.07  E-value: 1.04e-14
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|
gi 2117983367  1980 DAESPVPVINLKDGTRLAGDDAPKRKDLEKWLNEHPGYvedlgAFIPKMQ 2029
Cdd:smart00592    1 DGEERVPVINRETGKKLTGDDAPKAKDLERWLEENPEY-----EVAPRSA 45
CD2_tandem cd18659
repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier ...
266-321 1.82e-14

repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 to CHD9, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349306 [Multi-domain]  Cd Length: 54  Bit Score: 69.53  E-value: 1.82e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2117983367  266 DYIEVDRVLEVSfcedkDTGEPVTYYLVKWCSLPYEDSTWELKEDV---DQGKIEEFEQ 321
Cdd:cd18659      1 EYTIVERIIAHR-----EDDEGVTEYLVKWKGLPYDECTWESEEDIsdiFQEAIDEYKK 54
BRK pfam07533
BRK domain; The function of this domain is unknown. It is often found associated with ...
2053-2096 2.38e-13

BRK domain; The function of this domain is unknown. It is often found associated with helicases and transcription factors.


Pssm-ID: 462196  Cd Length: 44  Bit Score: 65.99  E-value: 2.38e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 2117983367 2053 LTGEERVQLINRRNARKVGGAFAPPLKDLCRFLKENSEYGVAPE 2096
Cdd:pfam07533    1 LTGDERVPVVNRKTGKKLTGDKAPKLKDLEEWLEENPGYEVDPR 44
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
355-538 1.47e-12

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: 70.07  E-value: 1.47e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLfnwyNRQNcILADEMGLGKTIQSI----------------------TFLYEILLTGLR----GPFLI 408
Cdd:cd18070      1 LLPYQRRAVNWML----VPGG-ILADEMGLGKTVEVLalillhprpdndldaadddsdeMVCCPDCLVAETpvssKATLI 75
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  409 IAPLSTIANWEREFRTWTDLNVVVYHGSMISRQMIQQFEMYFRDSQGRIIRGTY---KFQ-AIITTFEMILGGCPE---- 480
Cdd:cd18070     76 VCPSAILAQWLDEINRHVPSSLKVLTYQGVKKDGALASPAPEILAEYDIVVTTYdvlRTElHYAEANRSNRRRRRQkrye 155
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2117983367  481 -----LNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFL 538
Cdd:cd18070    156 appspLVLVEWWRVCLDEAQMVESSTSKAAEMARRLPRVNRWCVSGTPIQRGLDDLFGLLSFL 218
CD1_tandem cd18660
repeat 1 of paired tandem chromodomains; Repeat 1 of tandem CHRomatin Organization Modifier ...
183-245 7.70e-11

repeat 1 of paired tandem chromodomains; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 to CHD9, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349307 [Multi-domain]  Cd Length: 70  Bit Score: 59.68  E-value: 7.70e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  183 DAAIVDKILSSRIIKKEITGG-------VTVEAEEFYVKYKNYSYLHCEWATEQQlLKDKRIQQKIKRFK 245
Cdd:cd18660      1 DEDKIEKILDHRPKGPVEEASldltdpdEPWDEREFLVKWKGKSYLHCTWVTEET-LEQLRGKKKLKNYI 69
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
301-875 1.07e-10

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 66.97  E-value: 1.07e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  301 EDSTWELKEDVDQGKIEEFEQLQALRPDSRRLDRPPPNSWKKIEQSREYKNGN-------QLREYQLEGLN-WLLFNWYN 372
Cdd:COG1061     20 LLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEALEAGDeasgtsfELRPYQQEALEaLLAALERG 99
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  373 RQNCILADEMGLGKTIqsiTFLYEILLTGLRGPFLIIAPLSTIAN-WEREFRTWTDlNVVVYHGSmisrqmiqqfemyfR 451
Cdd:COG1061    100 GGRGLVVAPTGTGKTV---LALALAAELLRGKRVLVLVPRRELLEqWAEELRRFLG-DPLAGGGK--------------K 161
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  452 DSQGRIIrgtykfqaiITTFEmILGGCPELNAI--EWRCVIIDEAHRLKNKncKLLEGLKLMNLEHKVLLTGTPlqntve 529
Cdd:COG1061    162 DSDAPIT---------VATYQ-SLARRAHLDELgdRFGLVIIDEAHHAGAP--SYRRILEAFPAAYRLGLTATP------ 223
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  530 elfsllhfleplrfpaestfmqEFGDLKTEEqVQKLQAILKPMMLRRLKEDveKKLAPKEETIIEVELTNIQKKY--YRA 607
Cdd:COG1061    224 ----------------------FRSDGREIL-LFLFDGIVYEYSLKEAIED--GYLAPPEYYGIRVDLTDERAEYdaLSE 278
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  608 ILEKNFAFLSKGAgqanvpnlvntmmelrkccnhpylikgaeEKILGEFRETYspaaqdfhlqamiqsagklvlidkllp 687
Cdd:COG1061    279 RLREALAADAERK-----------------------------DKILRELLREH--------------------------- 302
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  688 kmkAGGHKVLIFSQMVRCLDILEDYLIHKRYLYERIDGRVRGNLRQAAIDRFSkpdSDRFVFLLCTRAGGLGINLTAADT 767
Cdd:COG1061    303 ---PDDRKTLVFCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFR---DGELRILVTVDVLNEGVDVPRLDV 376
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  768 CIIFDSDWNPQNDLQAQARCHRIGQNK-AVKVYRLITRNSYEREMFDRASLKLGLDKAVLQSMSGRENSVGGIQQLSKKE 846
Cdd:COG1061    377 AILLRPTGSPREFIQRLGRGLRPAPGKeDALVYDFVGNDVPVLEELAKDLRDLAGYRVEFLDEEESEELALLIAVKPALE 456
                          570       580
                   ....*....|....*....|....*....
gi 2117983367  847 IEDLLRKGAYGAIMDEEDEGSKFCEEDID 875
Cdd:COG1061    457 VKGELEEELLEELELLEDALLLVLAELLL 485
DEXQc_bact_SNF2 cd18013
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ...
355-539 1.51e-09

DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the 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 comprise a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. The bacterial SNF2 present in this family 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: 350771 [Multi-domain]  Cd Length: 218  Bit Score: 60.44  E-value: 1.51e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGLNWLLfnwYNRQNCILADeMGLGKTIQSITFLYEILLTGLRGPFLIIAPLSTIAN-WEREFRTWT---DLNV 430
Cdd:cd18013      1 PHPYQKVAINFII---EHPYCGLFLD-MGLGKTVTTLTALSDLQLDDFTRRVLVIAPLRVARStWPDEVEKWNhlrNLTV 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  431 VVYHGSmiSRQmiqqfemyfrdsqgRIIRGTYKFQAIITTFEMILGGCPELNaIEW--RCVIIDEAHRLKNKNCKllEGL 508
Cdd:cd18013     77 SVAVGT--ERQ--------------RSKAANTPADLYVINRENLKWLVNKSG-DPWpfDMVVIDELSSFKSPRSK--RFK 137
                          170       180       190
                   ....*....|....*....|....*....|....*
gi 2117983367  509 KLMNLEHKV----LLTGTPLQNTVEELFSLLHFLE 539
Cdd:cd18013    138 ALRKVRPVIkrliGLTGTPSPNGLMDLWAQIALLD 172
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
269-321 6.77e-09

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 53.74  E-value: 6.77e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2117983367  269 EVDRVLEVSFCEDKdtgepVTYYLVKWCSLPYEDSTWELKEDVD--QGKIEEFEQ 321
Cdd:pfam00385    2 EVERILDHRKDKGG-----KEEYLVKWKGYPYDENTWEPEENLSkcPELIEEFKD 51
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
375-522 3.08e-08

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: 54.72  E-value: 3.08e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  375 NCILADEMGLGKTIQSITFLYEILLTGlRGPFLIIAPLSTIAN-WEREFRTWTDLNVVVyhgSMISRqmiqqfemyFRDS 453
Cdd:cd00046      3 NVLITAPTGSGKTLAALLAALLLLLKK-GKKVLVLVPTKALALqTAERLRELFGPGIRV---AVLVG---------GSSA 69
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2117983367  454 QGRIIRGTYKFQAIITTFEMILGGCPELNAI---EWRCVIIDEAHRL----KNKNCKLLEGLKLMNLEHK-VLLTGT 522
Cdd:cd00046     70 EEREKNKLGDADIIIATPDMLLNLLLREDRLflkDLKLIIVDEAHALlidsRGALILDLAVRKAGLKNAQvILLSAT 146
CHROMO smart00298
Chromatin organization modifier domain;
187-249 8.68e-08

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 50.68  E-value: 8.68e-08
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2117983367   187 VDKILSSRIIKKEitggvtveAEEFYVKYKNYSYLHCEWATEQQLLKDKRiqqKIKRFKLRQA 249
Cdd:smart00298    4 VEKILDHRWKKKG--------ELEYLVKWKGYSYSEDTWEPEENLLNCSK---KLDNYKKKER 55
CD2_tandem_CHD3-4_like cd18662
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and ...
265-320 1.44e-07

repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD3 and CHD4, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. Human CHD3 (also named Mi-2 alpha) and CHD4 (also named Mi-2 beta) are coexpressed in many cell lines and tissues and may act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). The proteins form distinct CHD3- and CHD4-NuRD complexes that repress, as well as activate gene transcription of overlapping and specific target genes. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349309 [Multi-domain]  Cd Length: 55  Bit Score: 49.96  E-value: 1.44e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  265 PDYIEVDRVLEVSfcEDKDTGepvTYYLVKWCSLPYEDSTWElKEDVD----QGKIEEFE 320
Cdd:cd18662      1 PEWLQIHRIINHR--VDKDGN---TWYLVKWRDLPYDQSTWE-SEDDDipdyEKHIQEYW 54
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
186-245 5.30e-07

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 48.34  E-value: 5.30e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  186 IVDKILSSRIIKKEitggvtveAEEFYVKYKNYSYLHCEWATEQQLLKDKRIqqkIKRFK 245
Cdd:pfam00385    2 EVERILDHRKDKGG--------KEEYLVKWKGYPYDENTWEPEENLSKCPEL---IEEFK 50
ResIII pfam04851
Type III restriction enzyme, res subunit;
354-523 3.90e-05

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 46.13  E-value: 3.90e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  354 QLREYQLEGLNWLLFNWYNRQNCILAdEM--GLGKTIQSITFLYEILLTGLRGPFLIIAP-LSTIANWEREFRTWTDlnv 430
Cdd:pfam04851    3 ELRPYQIEAIENLLESIKNGQKRGLI-VMatGSGKTLTAAKLIARLFKKGPIKKVLFLVPrKDLLEQALEEFKKFLP--- 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  431 vVYHGSMISrqmIQQFEMYFRDSQGRIIRGTY-KFQAIITTFEMilggcpELNAIEWRCVIIDEAHRL----------KN 499
Cdd:pfam04851   79 -NYVEIGEI---ISGDKKDESVDDNKIVVTTIqSLYKALELASL------ELLPDFFDVIIIDEAHRSgassyrnileYF 148
                          170       180
                   ....*....|....*....|....
gi 2117983367  500 KNCKLLEglklmnlehkvlLTGTP 523
Cdd:pfam04851  149 KPAFLLG------------LTATP 160
CD1_tandem_CHD3-4_like cd18667
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and ...
210-231 4.78e-05

repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD3 and CHD4. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. Human CHD3 (also named Mi-2 alpha) and CHD4 (also named Mi-2 beta) are coexpressed in many cell lines and tissues and may act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). The proteins form distinct CHD3- and CHD4-NuRD complexes that repress, as well as activate gene transcription of overlapping and specific target genes. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349314 [Multi-domain]  Cd Length: 79  Bit Score: 43.87  E-value: 4.78e-05
                           10        20
                   ....*....|....*....|..
gi 2117983367  210 EFYVKYKNYSYLHCEWATEQQL 231
Cdd:cd18667     45 EFFVKWHGMSYWHCEWVSELQL 66
CD_CSD cd00024
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
269-321 1.24e-04

CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this group are chromodomains or chromo shadow domains; these are SH3-fold-beta-barrel domains of the chromo-like superfamily. Chromodomains lack the first strand of the SH3-fold-beta-barrel, this first strand is altered by insertion in the chromo shadow domains. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. Chromodomain-containing proteins include: i) those having an N-terminal chromodomain followed by a related chromo shadow domain, such as Drosophila and human heterochromatin protein Su(var)205 (HP1), and mammalian modifier 1 and 2; ii) those having a single chromodomain, such as Drosophila protein Polycomb (Pc), mammalian modifier 3, human Mi-2 autoantigen, and several yeast and Caenorhabditis elegans proteins of unknown function; iii) those having paired tandem chromodomains, such as mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1; (iv) and elongation factor eEF3, a member of the ATP-binding cassette (ABC) family of proteins, that serves an essential function in the translation cycle of fungi. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain.


Pssm-ID: 349274 [Multi-domain]  Cd Length: 50  Bit Score: 41.69  E-value: 1.24e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2117983367  269 EVDRVLevsfceDKDTGEPVTYYLVKWCSLPYEDSTWELKEDVDQGK--IEEFEQ 321
Cdd:cd00024      2 EVEKIL------DHRVRKGKLEYLVKWKGYPPEENTWEPEENLTNAPelIKEYEK 50
CD1_tandem_CHD1-2_like cd18666
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ...
183-245 2.02e-04

repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 and CHD2. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349313  Cd Length: 85  Bit Score: 42.28  E-value: 2.02e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  183 DAAIVDKILSSRIIKKEITGGVT----VEAEE----------------FYVKYKNYSYLHCEWATEQQLLkdkriQQKIK 242
Cdd:cd18666      1 EFETIERVLDHRIGRKGATGASTtiyaVEADGdpnagfdpedeeteiqYLIKWKGWSHIHNTWESEESLK-----DQNVK 75

                   ...
gi 2117983367  243 RFK 245
Cdd:cd18666     76 GMK 78
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
744-796 9.42e-04

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 39.99  E-value: 9.42e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2117983367  744 SDRFVFLLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAV 796
Cdd:cd18785     20 ASSLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGGKDEGE 72
CD_CMT3_like cd18635
chromodomain of chromomethylase 3, and similar proteins; CHRomatin Organization Modifier ...
269-319 1.57e-03

chromodomain of chromomethylase 3, and similar proteins; CHRomatin Organization Modifier (chromo) domain of DNA (cytosine-5)-methyltransferase chromomethylase 3 (CMT3, EC:2.1.1.37), and similar proteins. CMT3 is primarily a CHG (where H is either A, T or C) methyltransferase and is predominantly expressed in actively replicating cells. The protein is involved in preferentially methylating transposon-related sequences, reducing their mobility. Studies suggest that in order to target DNA methylation, CMT3 associates with H3K9me2-containing nucleosomes through binding of its BAH- and chromo-domains to H3K9me2. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349285  Cd Length: 57  Bit Score: 38.83  E-value: 1.57e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2117983367  269 EVDRVLEVSFCEDKDTGEPVTYYLVKWCSLPYEDSTWELKEDVD--QGKIEEF 319
Cdd:cd18635      3 EVEKLVGICYGDPKKTGERGLYFKVRWKGYGPEEDTWEPIEGLSncPEKIKEF 55
CHROMO smart00298
Chromatin organization modifier domain;
269-324 1.76e-03

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 38.35  E-value: 1.76e-03
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 2117983367   269 EVDRVLEVSFcedkdTGEPVTYYLVKWCSLPYEDSTWELKEDVDQG--KIEEFEQLQA 324
Cdd:smart00298    3 EVEKILDHRW-----KKKGELEYLVKWKGYSYSEDTWEPEENLLNCskKLDNYKKKER 55
chromodomain cd18966
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
269-312 2.70e-03

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.


Pssm-ID: 349322  Cd Length: 49  Bit Score: 37.65  E-value: 2.70e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 2117983367  269 EVDRVLevsfCEDKDTGEpvTYYLVKWCSLPYEDSTWELKEDVD 312
Cdd:cd18966      2 EVERIL----AERRDDGG--KRYLVKWEGYPLEEATWEPEENIG 39
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
355-523 3.36e-03

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: 40.37  E-value: 3.36e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  355 LREYQLEGL-NWLLFNWYNRQNCILAdeMGLGKTIqsiTFLYEILLTGlRGPFLIIAPlsTIAnwerefrtwtdlnvvvy 433
Cdd:cd17926      1 LRPYQEEALeAWLAHKNNRRGILVLP--TGSGKTL---TALALIAYLK-ELRTLIVVP--TDA----------------- 55
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  434 hgsmISRQMIQQFEMYFRDSQGRIIRGTYK-----FQAIITTFEmILGGCPELNAI---EWRCVIIDEAHRLknkNCKLL 505
Cdd:cd17926     56 ----LLDQWKERFEDFLGDSSIGLIGGGKKkdfddANVVVATYQ-SLSNLAEEEKDlfdQFGLLIVDEAHHL---PAKTF 127
                          170
                   ....*....|....*....
gi 2117983367  506 EGLKLMNLEHKVL-LTGTP 523
Cdd:cd17926    128 SEILKELNAKYRLgLTATP 146
CD2_tandem cd18659
repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier ...
183-245 3.61e-03

repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 to CHD9, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349306 [Multi-domain]  Cd Length: 54  Bit Score: 37.56  E-value: 3.61e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2117983367  183 DAAIVDKILSSRIIKKEITggvtveaeEFYVKYKNYSYLHCEWATEQQLLkdKRIQQKIKRFK 245
Cdd:cd18659      1 EYTIVERIIAHREDDEGVT--------EYLVKWKGLPYDECTWESEEDIS--DIFQEAIDEYK 53
CD2_tandem_CHD1-2_like cd18661
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ...
267-321 3.86e-03

repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 and CHD2. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349308  Cd Length: 58  Bit Score: 37.67  E-value: 3.86e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2117983367  267 YIEVDRVLEVSFCEDKDTGEPvtYYLVKWCSLPYEDSTWE---LKEDVDQGKIEEFEQ 321
Cdd:cd18661      2 YQIVERIIAHSPQKSAASGYP--DYLCKWQGLPYSECTWEdgaLISKKFQACIDEYHS 57
HDA2-3 pfam11496
Class II histone deacetylase complex subunits 2 and 3; This family of class II histone ...
635-840 5.66e-03

Class II histone deacetylase complex subunits 2 and 3; This family of class II histone deacetylase complex subunits HDA2 and HDA3 is found in fungi, The member from S. pombe is referred to as Ccq1 in Swiss:Q10432. These proteins associate with HDA1 to generate the activity of the HDA1 histone deacetylase complex. HDA1 interacts with itself and with the HDA2-HDA3 subcomplex to form a probable tetramer and these interactions are necessary for catalytic activity. The HDA1 histone deacetylase complex is responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. HDA2 and HDA3 have a conserved coiled-coil domain towards their C-terminus.


Pssm-ID: 402894  Cd Length: 281  Bit Score: 41.16  E-value: 5.66e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  635 LRKCC---NHPYLIKgaeekilgefrETYSPAAQDF-----HLqamIQSAGKLV----LIDKLLPKMKAGGHKVLIFSQM 702
Cdd:pfam11496   54 LENLSlvaTHPYLLV-----------DHYMPKSLLLkdepeKL---AYTSGKFLvlndLVNLLIERDRKEPINVAIVARS 119
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2117983367  703 VRCLDILEDYLIHKRYLYERIDG-RVRGNLRQAAIDRFSKPDSDRFVFL----LCTRAGGLGINlTAADTCIIFDSDWNP 777
Cdd:pfam11496  120 GKTLDLVEALLLGKGLSYKRYSGeMLYGENKKVSDSGNKKIHSTTCHLLsstgQLTNDDSLLEN-YKFDLIIAFDSSVDT 198
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2117983367  778 QNDLQAQARCHRIGQNKAVKVYRLITRNSYEREMFDRASLKLGLD--KAVLQSMSGRENSVGGIQ 840
Cdd:pfam11496  199 SSPSVEHLRTQNRRKGNLAPIIRLVVINSIEHVELCFPKPPDSPDylYKVIAAIVVLRDVVGDLP 263
chromodomain cd18964
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
280-321 8.85e-03

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.


Pssm-ID: 349320  Cd Length: 54  Bit Score: 36.54  E-value: 8.85e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 2117983367  280 EDKDTGEPVTYYLVKWCSLPYEDSTWELKEDV-DQGK-IEEFEQ 321
Cdd:cd18964     11 PSARDGPGKFLWLVKWDGYPIEDATWEPPENLgEHAKlIEDFEK 54
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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