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Conserved domains on  [gi|1958747478|ref|XP_038953982|]
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chromodomain-helicase-DNA-binding protein 9 isoform X1 [Rattus norvegicus]

Protein Classification

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
858-1479 2.30e-150

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: 497.79  E-value: 2.30e-150
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  858 QLREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSIT---FLYEvlLTGIRGPFLIIAPLSTIANWEREFRTWTD-IN 933
Cdd:PLN03142   169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISllgYLHE--YRGITGPHMVVAPKSTLGNWMNEIRRFCPvLR 246
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  934 VVVYHGSLISRQMIQQYEMYfrdsqgriirgAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLK 1013
Cdd:PLN03142   247 AVKFHGNPEERAHQREELLV-----------AGKFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNENSLLSKTMR 315
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1014 LMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEF---GDLKTEEQVQKLQAILKPMMLRRLKEDVEKRLA 1090
Cdd:PLN03142   316 LFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFqisGENDQQEVVQQLHKVLRPFLLRRLKSDVEKGLP 395
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1091 PKEETIIEVELTNIQKKYYRAILEKNFSFLSKGAGQTNvpnLVNTMMELRKCCNHPYLIKGAEEKiigefrdtyNPSASD 1170
Cdd:PLN03142   396 PKKETILKVGMSQMQKQYYKALLQKDLDVVNAGGERKR---LLNIAMQLRKCCNHPYLFQGAEPG---------PPYTTG 463
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1171 FHLqamIQSAGKLVLIDKLLPKMKAGGHKVLIFSQMVRCLDILEDYLIHKRYLYERIDGRVRGNLRQAAIDRFSKPDSDR 1250
Cdd:PLN03142   464 EHL---VENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEK 540
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1251 FVFLLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAVKVYRLVTRNSYEREMFDRASLKLGLDKAVL 1330
Cdd:PLN03142   541 FVFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVI 620
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1331 QsmSGRdsnvsgIQQLSKKEIEDLLRRGAYGAIMEEEDEGSKFCEEDIDQILLR-RTKTITIESEGCGSTFAKASFVASG 1409
Cdd:PLN03142   621 Q--QGR------LAEQKTVNKDELLQMVRYGAEMVFSSKDSTITDEDIDRIIAKgEEATAELDAKMKKFTEDAIKFKMDD 692
                          570       580       590       600       610       620       630
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958747478 1410 NRTDISLDDpnfwQKWAKKAELDLDAISGRNSlvIDTPRiRKQTRPFSAT---KDELAELSEAESEGEEKPKL 1479
Cdd:PLN03142   693 TAELYDFDD----EDDKDENKLDFKKIVSDNW--IDPPK-RERKRNYSESeyfKQAMRQGAPAKPKEPRIPRM 758
CD2_tandem_CHD5-9_like cd18663
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ...
769-827 2.69e-34

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: 126.25  E-value: 2.69e-34
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958747478  769 PDYVEVDRILEVSFCEDKDTGESVVYYLVKWCSLPYEDSTWELKEDVDLAKIEEFEQLQ 827
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, ...
685-749 1.91e-29

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: 112.82  E-value: 1.91e-29
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958747478  685 EEDAAIVDKILACRTVKKEVSPGV-MLDIEEFFVKYKNYSYLHCEWATEQQLLK-DKRIQQKIKRFK 749
Cdd:cd18668      1 EEDTMIIEKILASRKKKKEKEEGAeEIEVEEYLVKYKNFSYLHCEWKTEEELEKgDKRIKQKIKRFK 67
BRK smart00592
domain in transcription and CHROMO domain helicases;
2549-2593 4.38e-15

domain in transcription and CHROMO domain helicases;


:

Pssm-ID: 197800  Cd Length: 45  Bit Score: 71.22  E-value: 4.38e-15
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*
gi 1958747478  2549 TGEERVQLINRRNARKVGGAFAPPLKDLCRFLKENSEYGVAPEWG 2593
Cdd:smart00592    1 DGEERVPVINRETGKKLTGDDAPKAKDLERWLEENPEYEVAPRSA 45
BRK pfam07533
BRK domain; The function of this domain is unknown. It is often found associated with ...
2475-2515 1.34e-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: 1.34e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1958747478 2475 DTESPVPVINLKDGTRLAGDDAPKRKDLDRWLKEHPGYVED 2515
Cdd:pfam07533    2 TGDERVPVVNRKTGKKLTGDKAPKLKDLEEWLEENPGYEVD 42
PTZ00121 super family cl31754
MAEBL; Provisional
510-765 1.01e-04

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 48.21  E-value: 1.01e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  510 KKPRKKAESESKQEKANRIISEAIARAKERGERNIPRVMSPENFPSSSVDGK--EEKRAQRVKSKPKDRdnrkpKACSKL 587
Cdd:PTZ00121  1401 EEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKaeEAKKAEEAKKKAEEA-----KKADEA 1475
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  588 KEKTKIGKLIITLGKNHKRRSESSDELSDAEQMPQHTFKEQHSQKRRSNRQVKRKKYAEDAEGRQCEEEVRGSLKVKRTS 667
Cdd:PTZ00121  1476 KKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAE 1555
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  668 APPPGEQPLQLFVENPSEEDAAIVDKI--LACRTVKKEVSPGVMLDIEEFFVKYKNYSYLHCEWATEQQLLKDKRIQQKI 745
Cdd:PTZ00121  1556 ELKKAEEKKKAEEAKKAEEDKNMALRKaeEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKV 1635
                          250       260
                   ....*....|....*....|...
gi 1958747478  746 KRFKLRQAQ---RAHFLADMEEE 765
Cdd:PTZ00121  1636 EQLKKKEAEekkKAEELKKAEEE 1658
KLF3_N super family cl40586
N-terminal domain of Kruppel-like factor 3; Kruppel-like factor 3 (KLF3; also called ...
217-375 2.35e-03

N-terminal domain of Kruppel-like factor 3; Kruppel-like factor 3 (KLF3; also called Krueppel-like factor 3 and originally called Basic Kruppel-like Factor/BKLF), was the third member of the KLF family of zinc finger transcription factors to be discovered. KLF3 possesses a wide range of biological impacts on regulating apoptosis, differentiation, and proliferation in various tissues during the entire progression process. It has been proposed as a tumor suppressor in colorectal cancer. It appears to function predominantly as a repressor of transcription, turning genes off by recruiting the C-terminal Binding Protein co-repressors CtBP1 and CtBP2. CtBP docks onto a short motif (residues 61-65) in the N-terminus of KLF3, through the Proline-X-Aspartate-Leucine-Serine (PXDLS) motif. CtBP in turn recruits histone modifying enzymes to alter chromatin and repress gene expression. KLF3 belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF3.


The actual alignment was detected with superfamily member cd21577:

Pssm-ID: 410554 [Multi-domain]  Cd Length: 214  Bit Score: 41.95  E-value: 2.35e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  217 SAPSSQQTLPVQFSPTANPPAHFLKCSSQQDGSYNRPSPSMTSCSVSNSQPFPAHYSFSSGHVSPSSLLQSPAGLTPSHS 296
Cdd:cd21577     37 SSSSSSSSSSSSPSSRASPPSPYSKSSPPSPPQQRPLSPPLSLPPPVAPPPLSPGSVPGGLPVISPVMVQPVPVLYPPHL 116
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  297 NQALsdfagSNSFSPHRGMKQEPTPHILNPTPSLNSNNFQIL-------HSSHPQGNYSNSKLSPMhMdfpdpadSGPPM 369
Cdd:cd21577    117 HQPI-----MVSSSPPPDDDHHHHKASSMKPSELGGDNHELHkpiktepRPEHAQDPYSEEMSSSV-I-------SSPPE 183

                   ....*.
gi 1958747478  370 GHFNDH 375
Cdd:cd21577    184 YESNTP 189
 
Name Accession Description Interval E-value
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
858-1479 2.30e-150

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 497.79  E-value: 2.30e-150
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  858 QLREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSIT---FLYEvlLTGIRGPFLIIAPLSTIANWEREFRTWTD-IN 933
Cdd:PLN03142   169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISllgYLHE--YRGITGPHMVVAPKSTLGNWMNEIRRFCPvLR 246
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  934 VVVYHGSLISRQMIQQYEMYfrdsqgriirgAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLK 1013
Cdd:PLN03142   247 AVKFHGNPEERAHQREELLV-----------AGKFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNENSLLSKTMR 315
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1014 LMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEF---GDLKTEEQVQKLQAILKPMMLRRLKEDVEKRLA 1090
Cdd:PLN03142   316 LFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFqisGENDQQEVVQQLHKVLRPFLLRRLKSDVEKGLP 395
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1091 PKEETIIEVELTNIQKKYYRAILEKNFSFLSKGAGQTNvpnLVNTMMELRKCCNHPYLIKGAEEKiigefrdtyNPSASD 1170
Cdd:PLN03142   396 PKKETILKVGMSQMQKQYYKALLQKDLDVVNAGGERKR---LLNIAMQLRKCCNHPYLFQGAEPG---------PPYTTG 463
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1171 FHLqamIQSAGKLVLIDKLLPKMKAGGHKVLIFSQMVRCLDILEDYLIHKRYLYERIDGRVRGNLRQAAIDRFSKPDSDR 1250
Cdd:PLN03142   464 EHL---VENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEK 540
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1251 FVFLLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAVKVYRLVTRNSYEREMFDRASLKLGLDKAVL 1330
Cdd:PLN03142   541 FVFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVI 620
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1331 QsmSGRdsnvsgIQQLSKKEIEDLLRRGAYGAIMEEEDEGSKFCEEDIDQILLR-RTKTITIESEGCGSTFAKASFVASG 1409
Cdd:PLN03142   621 Q--QGR------LAEQKTVNKDELLQMVRYGAEMVFSSKDSTITDEDIDRIIAKgEEATAELDAKMKKFTEDAIKFKMDD 692
                          570       580       590       600       610       620       630
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958747478 1410 NRTDISLDDpnfwQKWAKKAELDLDAISGRNSlvIDTPRiRKQTRPFSAT---KDELAELSEAESEGEEKPKL 1479
Cdd:PLN03142   693 TAELYDFDD----EDDKDENKLDFKKIVSDNW--IDPPK-RERKRNYSESeyfKQAMRQGAPAKPKEPRIPRM 758
DEXHc_CHD9 cd18061
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; ...
859-1080 3.54e-150

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: 464.86  E-value: 3.54e-150
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLTGIRGPFLIIAPLSTIANWEREFRTWTDINVVVYH 938
Cdd:cd18061      1 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEILLTGIRGPFLIIAPLSTIANWEREFRTWTDLNVVVYH 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  939 GSLISRQMIQQYEMYFRDSQGRIIRGAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLE 1018
Cdd:cd18061     81 GSLISRQMIQQYEMYFRDSQGRIIRGAYRFQAIITTFEMILGGCPELNAIDWRCVIIDEAHRLKNKNCKLLEGLKLMNLE 160
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958747478 1019 HKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 1080
Cdd:cd18061    161 HKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 222
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
858-1331 1.93e-122

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 404.22  E-value: 1.93e-122
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  858 QLREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLTGIRGPFLIIAPLSTIANWEREFRTWT-DINVVV 936
Cdd:COG0553    241 TLRPYQLEGAAWLLFLRRLGLGGLLADDMGLGKTIQALALLLELKERGLARPVLIVAPTSLVGNWQRELAKFApGLRVLV 320
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  937 YHGSLISRQMIQQYEmyfrdsqgriirgayRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMN 1016
Cdd:COG0553    321 LDGTRERAKGANPFE---------------DADLVITSYGLLRRDIELLAAVDWDLVILDEAQHIKNPATKRAKAVRALK 385
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1017 LEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKT---EEQVQKLQAILKPMMLRRLKEDVEKRLAPKE 1093
Cdd:COG0553    386 ARHRLALTGTPVENRLEELWSLLDFLNPGLLGSLKAFRERFARPIEkgdEEALERLRRLLRPFLLRRTKEDVLKDLPEKT 465
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1094 ETIIEVELTNIQKKYYRAILEKNFSFLSKGAGQTNVPNLVNTMMELRKCCNHPYLIKGAEEKIIGEfrdtynpsasdfhl 1173
Cdd:COG0553    466 EETLYVELTPEQRALYEAVLEYLRRELEGAEGIRRRGLILAALTRLRQICSHPALLLEEGAELSGR-------------- 531
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1174 qamiqsAGKLVLIDKLLPKMKAGGHKVLIFSQMVRCLDILEDYLIHKRYLYERIDGRVRGNLRQAAIDRFSKpDSDRFVF 1253
Cdd:COG0553    532 ------SAKLEALLELLEELLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQE-GPEAPVF 604
                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958747478 1254 LLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAVKVYRLVTRNSYEREMFDRASLKLGLDKAVLQ 1331
Cdd:COG0553    605 LISLKAGGEGLNLTAADHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEEKILELLEEKRALAESVLG 682
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
862-1149 7.55e-84

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: 277.64  E-value: 7.55e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  862 YQLEGLNWLLFNWYNR-RNCILADEMGLGKTIQSITFLYEVLLTGI--RGPFLIIAPLSTIANWEREFRTWT---DINVV 935
Cdd:pfam00176    1 YQIEGVNWMLSLENNLgRGGILADEMGLGKTLQTISLLLYLKHVDKnwGGPTLIVVPLSLLHNWMNEFERWVsppALRVV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  936 VYHGSLISRQMIQQYEMYFRDsqgriirgayrFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLM 1015
Cdd:pfam00176   81 VLHGNKRPQERWKNDPNFLAD-----------FDVVITTYETLRKHKELLKKVHWHRIVLDEGHRLKNSKSKLSKALKSL 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1016 NLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFG----DLKTEEQVQKLQAILKPMMLRRLKEDVEKRLAP 1091
Cdd:pfam00176  150 KTRNRWILTGTPLQNNLEELWALLNFLRPGPFGSLSTFRNWFDrpieRGGGKKGVSRLHKLLKPFLLRRTKKDVEKSLPP 229
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1092 KEETIIEVELTNIQKKYY-RAILEKNFSFLSKG-AGQTNVPNLVNTMMELRKCCNHPYLI 1149
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, ...
769-827 2.69e-34

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: 126.25  E-value: 2.69e-34
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958747478  769 PDYVEVDRILEVSFCEDKDTGESVVYYLVKWCSLPYEDSTWELKEDVDLAKIEEFEQLQ 827
Cdd:cd18663      1 PDYVEVDRILDVSVSTDPNTGEPVTHYLVKWCSLPYEDSTWELEEDVDPAKIEEFEKLR 59
DEXDc smart00487
DEAD-like helicases superfamily;
852-1050 3.54e-31

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 122.99  E-value: 3.54e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478   852 EYKNGNQLREYQLEGLNWLLFNWynrRNCILADEMGLGKTIQSITFLYEVLLTGIRGPFLIIAPLSTIA-NWEREFRTW- 929
Cdd:smart00487    2 EKFGFEPLRPYQKEAIEALLSGL---RDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAeQWAEELKKLg 78
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478   930 --TDINVVVYHGSLISRQMIQQyemyfrdsqgrIIRGayRFQAIITTFEMIL--GGCGELNAIEWRCVIIDEAHRLKNKN 1005
Cdd:smart00487   79 psLGLKVVGLYGGDSKREQLRK-----------LESG--KTDILVTTPGRLLdlLENDKLSLSNVDLVILDEAHRLLDGG 145
                           170       180       190       200       210
                    ....*....|....*....|....*....|....*....|....*....|.
gi 1958747478  1006 --CKLLEGLKLMNLE-HKVLLTGTP---LQNTVEELFSLLHFLEPLRFPSE 1050
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, ...
685-749 1.91e-29

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: 112.82  E-value: 1.91e-29
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958747478  685 EEDAAIVDKILACRTVKKEVSPGV-MLDIEEFFVKYKNYSYLHCEWATEQQLLK-DKRIQQKIKRFK 749
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 ...
881-1345 6.78e-24

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: 110.54  E-value: 6.78e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  881 ILADEMGLGKTIQSITFLYEVLLTGIRgPFLIIAPLSTIANWEREFRTWTDINVVVyhgslISRQMIQQYemyfRDSQGR 960
Cdd:NF038318    51 ILADEVGLGKTIEAGLVLKYVLESGAK-KILIILPANLRKQWEIELEEKFDLESLI-----LDSLTVEKD----AKKWNK 120
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  961 IIRGAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKN--KNCKLLEGL-KLMNLEHKVLLTGTPLQNTVEELFS 1037
Cdd:NF038318   121 RLTDNKKVRIVITSYDYASKLMKRFPKVKWDFIIIDEAHNLRNvhKGGKRAKNLyELTKGIPKILLTATPLQNSLLDLYG 200
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1038 LLHFLEPLRFPSESTFM------QEFGDLKTEeqvqklqaiLKPMMLRRLKEDVEKRLAPKEETIIEV--ELTNIQKKYY 1109
Cdd:NF038318   201 LVSFIDPRIFGSEKVFSkryikdEDYSDLKRE---------LSPVLYRTLRKDVADYMQFKKRKCITVdfELSPDEIELY 271
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1110 RAI---LEKNFSFlskgagqtNVPN--------------------LVNTMMELRKCCNHPY---LIKGAEEKI--IGEFR 1161
Cdd:NF038318   272 VRVnnfLKRDILY--------SIPTsnrtliilvirkllasssfaLAETFEVLKKRLEKLKegtRSANAQEGFdlFWSFV 343
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1162 DTYNpSASDFHL---------QAMIQSAGKLV--LID-----KLLPKMKAG----------------GHKVLIFSQMVRC 1209
Cdd:NF038318   344 EDEI-DESGFEEkqdelytrqKEFIQHEIDEVdaIIDvakriKTNAKVTALktaleiafeyqreegiAQKVVVFTESKRT 422
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1210 LDILEDYLIHKRYLYERI---DG--------------RVR--GN--------LRQAAIDRFSkpdsDRFVFLLCTRAGGL 1262
Cdd:NF038318   423 QKYIAEELRKSGYEGEDIllfNGdfddamtkeiyrawQVKnyGKanygrsveYKHAIVDYFK----NNAKILIVTDAGSE 498
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1263 GINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAVKVYRLV-TRNSYEREMFDRASLKLGL--------DKA--VLQ 1331
Cdd:NF038318   499 GLNLQFCNTVINYDLPWNPQKIEQRIGRCHRYGQKNDVVAINLLnTQNVADKRVYEILSEKFELfegvfgasDIAlgLLE 578
                          570
                   ....*....|....
gi 1958747478 1332 SMSGRDSNVSGIQQ 1345
Cdd:NF038318   579 SGTDFEKRVLQIYQ 592
BRK smart00592
domain in transcription and CHROMO domain helicases;
2549-2593 4.38e-15

domain in transcription and CHROMO domain helicases;


Pssm-ID: 197800  Cd Length: 45  Bit Score: 71.22  E-value: 4.38e-15
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*
gi 1958747478  2549 TGEERVQLINRRNARKVGGAFAPPLKDLCRFLKENSEYGVAPEWG 2593
Cdd:smart00592    1 DGEERVPVINRETGKKLTGDDAPKAKDLERWLEENPEYEVAPRSA 45
BRK pfam07533
BRK domain; The function of this domain is unknown. It is often found associated with ...
2475-2515 1.34e-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: 1.34e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1958747478 2475 DTESPVPVINLKDGTRLAGDDAPKRKDLDRWLKEHPGYVED 2515
Cdd:pfam07533    2 TGDERVPVVNRKTGKKLTGDKAPKLKDLEEWLEENPGYEVD 42
BRK smart00592
domain in transcription and CHROMO domain helicases;
2475-2522 2.09e-14

domain in transcription and CHROMO domain helicases;


Pssm-ID: 197800  Cd Length: 45  Bit Score: 69.30  E-value: 2.09e-14
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 1958747478  2475 DTESPVPVINLKDGTRLAGDDAPKRKDLDRWLKEHPGYvedlgAFIPR 2522
Cdd:smart00592    1 DGEERVPVINRETGKKLTGDDAPKAKDLERWLEENPEY-----EVAPR 43
BRK pfam07533
BRK domain; The function of this domain is unknown. It is often found associated with ...
2548-2591 2.29e-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: 66.38  E-value: 2.29e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1958747478 2548 LTGEERVQLINRRNARKVGGAFAPPLKDLCRFLKENSEYGVAPE 2591
Cdd:pfam07533    1 LTGDERVPVVNRKTGKKLTGDKAPKLKDLEEWLEENPGYEVDPR 44
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
773-825 1.55e-09

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 55.66  E-value: 1.55e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1958747478  773 EVDRILEVSFCEDKdtgesVVYYLVKWCSLPYEDSTWELKEDVDLAK--IEEFEQ 825
Cdd:pfam00385    2 EVERILDHRKDKGG-----KEEYLVKWKGYPYDENTWEPEENLSKCPelIEEFKD 51
CHROMO smart00298
Chromatin organization modifier domain;
691-753 2.94e-09

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 54.91  E-value: 2.94e-09
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958747478   691 VDKILACRTVKKEVspgvmldiEEFFVKYKNYSYLHCEWATEQQLLKDKRiqqKIKRFKLRQA 753
Cdd:smart00298    4 VEKILDHRWKKKGE--------LEYLVKWKGYSYSEDTWEPEENLLNCSK---KLDNYKKKER 55
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
690-749 2.42e-08

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 52.19  E-value: 2.42e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  690 IVDKILACRTVKKEVspgvmldiEEFFVKYKNYSYLHCEWATEQQLLKDKRIqqkIKRFK 749
Cdd:pfam00385    2 EVERILDHRKDKGGK--------EEYLVKWKGYPYDENTWEPEENLSKCPEL---IEEFK 50
CHROMO smart00298
Chromatin organization modifier domain;
773-828 1.97e-05

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 44.13  E-value: 1.97e-05
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958747478   773 EVDRILEVSFcedkdTGESVVYYLVKWCSLPYEDSTWELKEDVDLA--KIEEFEQLQA 828
Cdd:smart00298    3 EVEKILDHRW-----KKKGELEYLVKWKGYSYSEDTWEPEENLLNCskKLDNYKKKER 55
PTZ00121 PTZ00121
MAEBL; Provisional
510-765 1.01e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 48.21  E-value: 1.01e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  510 KKPRKKAESESKQEKANRIISEAIARAKERGERNIPRVMSPENFPSSSVDGK--EEKRAQRVKSKPKDRdnrkpKACSKL 587
Cdd:PTZ00121  1401 EEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKaeEAKKAEEAKKKAEEA-----KKADEA 1475
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  588 KEKTKIGKLIITLGKNHKRRSESSDELSDAEQMPQHTFKEQHSQKRRSNRQVKRKKYAEDAEGRQCEEEVRGSLKVKRTS 667
Cdd:PTZ00121  1476 KKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAE 1555
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  668 APPPGEQPLQLFVENPSEEDAAIVDKI--LACRTVKKEVSPGVMLDIEEFFVKYKNYSYLHCEWATEQQLLKDKRIQQKI 745
Cdd:PTZ00121  1556 ELKKAEEKKKAEEAKKAEEDKNMALRKaeEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKV 1635
                          250       260
                   ....*....|....*....|...
gi 1958747478  746 KRFKLRQAQ---RAHFLADMEEE 765
Cdd:PTZ00121  1636 EQLKKKEAEekkKAEELKKAEEE 1658
CDC27 pfam09507
DNA polymerase subunit Cdc27; This protein forms the C subunit of DNA polymerase delta. It ...
484-675 1.62e-04

DNA polymerase subunit Cdc27; This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif.


Pssm-ID: 462819 [Multi-domain]  Cd Length: 427  Bit Score: 47.12  E-value: 1.62e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  484 PPSSKK--SDGSGTYSRLQNTQVRVMSEKKPRK----KAESESKQEKANRIISEAIARAKERGERNIPRVMSPENFPSSS 557
Cdd:pfam09507  203 APSLKRspSAKSNIMSAFFKAKPKNKKKKTSASeqkvQEESAEESGKEDVTLEDDSAAEEEEDEQLPTKKDKRRQKRGES 282
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  558 VDGKEEKRAQRvksKPKDRDNRKPKACSKLKEKTKIgklIITLGKNHKRRSESSDELSDAEQMPQHTFKEQHSQKRRSNR 637
Cdd:pfam09507  283 SDSEESTRESR---KEKRERLKKMMEDDSDDDEMED---VPESPVATEEEETGSPPPLLKKEVEKEEVTESGDGRRRKRR 356
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 1958747478  638 QVKRKKYAEDAEGRQCEEEVRGS---------LKVKRTSAPPPGEQP 675
Cdd:pfam09507  357 KVMKKKTFKDEEGYMVTEKVYEWesfsededePPVKPKPAVSTPASP 403
KLF3_N cd21577
N-terminal domain of Kruppel-like factor 3; Kruppel-like factor 3 (KLF3; also called ...
217-375 2.35e-03

N-terminal domain of Kruppel-like factor 3; Kruppel-like factor 3 (KLF3; also called Krueppel-like factor 3 and originally called Basic Kruppel-like Factor/BKLF), was the third member of the KLF family of zinc finger transcription factors to be discovered. KLF3 possesses a wide range of biological impacts on regulating apoptosis, differentiation, and proliferation in various tissues during the entire progression process. It has been proposed as a tumor suppressor in colorectal cancer. It appears to function predominantly as a repressor of transcription, turning genes off by recruiting the C-terminal Binding Protein co-repressors CtBP1 and CtBP2. CtBP docks onto a short motif (residues 61-65) in the N-terminus of KLF3, through the Proline-X-Aspartate-Leucine-Serine (PXDLS) motif. CtBP in turn recruits histone modifying enzymes to alter chromatin and repress gene expression. KLF3 belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF3.


Pssm-ID: 410554 [Multi-domain]  Cd Length: 214  Bit Score: 41.95  E-value: 2.35e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  217 SAPSSQQTLPVQFSPTANPPAHFLKCSSQQDGSYNRPSPSMTSCSVSNSQPFPAHYSFSSGHVSPSSLLQSPAGLTPSHS 296
Cdd:cd21577     37 SSSSSSSSSSSSPSSRASPPSPYSKSSPPSPPQQRPLSPPLSLPPPVAPPPLSPGSVPGGLPVISPVMVQPVPVLYPPHL 116
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  297 NQALsdfagSNSFSPHRGMKQEPTPHILNPTPSLNSNNFQIL-------HSSHPQGNYSNSKLSPMhMdfpdpadSGPPM 369
Cdd:cd21577    117 HQPI-----MVSSSPPPDDDHHHHKASSMKPSELGGDNHELHkpiktepRPEHAQDPYSEEMSSSV-I-------SSPPE 183

                   ....*.
gi 1958747478  370 GHFNDH 375
Cdd:cd21577    184 YESNTP 189
ROM1 COG5422
RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction ...
203-363 5.23e-03

RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms];


Pssm-ID: 227709 [Multi-domain]  Cd Length: 1175  Bit Score: 42.57  E-value: 5.23e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  203 NVSGAHRVNVNHLTSAPSSQQTLpvQFSPTANPPAHFLKCSSQQDGSYNRPSPSMTSCSVSNSQP---FPAHYSFSSGHV 279
Cdd:COG5422     65 KYALGHQIFSSFSSSPKLFQRRN--SAGPITHSPSATSSTSSLNSNDGDQFSPASDSLSFNPSSTqsrKDSGPGDGSPVQ 142
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  280 SPSSLLQSPAGLTPSHSNQALSDFAGSNSFSPHRGMKQEpTPHILNPTPSLNSNNFQILHSSHPQGN---YSNSKLSPMH 356
Cdd:COG5422    143 KRKNPLLPSSSTHGTHPPIVFTDNNGSHAGAPNARSRKE-IPSLGSQSMQLPSPHFRQKFSSSDTSNgfsYPSIRKNSRH 221

                   ....*..
gi 1958747478  357 MDFPDPA 363
Cdd:COG5422    222 SSNSMPS 228
 
Name Accession Description Interval E-value
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
858-1479 2.30e-150

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 497.79  E-value: 2.30e-150
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  858 QLREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSIT---FLYEvlLTGIRGPFLIIAPLSTIANWEREFRTWTD-IN 933
Cdd:PLN03142   169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISllgYLHE--YRGITGPHMVVAPKSTLGNWMNEIRRFCPvLR 246
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  934 VVVYHGSLISRQMIQQYEMYfrdsqgriirgAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLK 1013
Cdd:PLN03142   247 AVKFHGNPEERAHQREELLV-----------AGKFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNENSLLSKTMR 315
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1014 LMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEF---GDLKTEEQVQKLQAILKPMMLRRLKEDVEKRLA 1090
Cdd:PLN03142   316 LFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFqisGENDQQEVVQQLHKVLRPFLLRRLKSDVEKGLP 395
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1091 PKEETIIEVELTNIQKKYYRAILEKNFSFLSKGAGQTNvpnLVNTMMELRKCCNHPYLIKGAEEKiigefrdtyNPSASD 1170
Cdd:PLN03142   396 PKKETILKVGMSQMQKQYYKALLQKDLDVVNAGGERKR---LLNIAMQLRKCCNHPYLFQGAEPG---------PPYTTG 463
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1171 FHLqamIQSAGKLVLIDKLLPKMKAGGHKVLIFSQMVRCLDILEDYLIHKRYLYERIDGRVRGNLRQAAIDRFSKPDSDR 1250
Cdd:PLN03142   464 EHL---VENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEK 540
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1251 FVFLLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAVKVYRLVTRNSYEREMFDRASLKLGLDKAVL 1330
Cdd:PLN03142   541 FVFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVI 620
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1331 QsmSGRdsnvsgIQQLSKKEIEDLLRRGAYGAIMEEEDEGSKFCEEDIDQILLR-RTKTITIESEGCGSTFAKASFVASG 1409
Cdd:PLN03142   621 Q--QGR------LAEQKTVNKDELLQMVRYGAEMVFSSKDSTITDEDIDRIIAKgEEATAELDAKMKKFTEDAIKFKMDD 692
                          570       580       590       600       610       620       630
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958747478 1410 NRTDISLDDpnfwQKWAKKAELDLDAISGRNSlvIDTPRiRKQTRPFSAT---KDELAELSEAESEGEEKPKL 1479
Cdd:PLN03142   693 TAELYDFDD----EDDKDENKLDFKKIVSDNW--IDPPK-RERKRNYSESeyfKQAMRQGAPAKPKEPRIPRM 758
DEXHc_CHD9 cd18061
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; ...
859-1080 3.54e-150

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: 464.86  E-value: 3.54e-150
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLTGIRGPFLIIAPLSTIANWEREFRTWTDINVVVYH 938
Cdd:cd18061      1 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEILLTGIRGPFLIIAPLSTIANWEREFRTWTDLNVVVYH 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  939 GSLISRQMIQQYEMYFRDSQGRIIRGAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLE 1018
Cdd:cd18061     81 GSLISRQMIQQYEMYFRDSQGRIIRGAYRFQAIITTFEMILGGCPELNAIDWRCVIIDEAHRLKNKNCKLLEGLKLMNLE 160
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958747478 1019 HKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 1080
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; ...
859-1080 1.15e-144

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: 449.01  E-value: 1.15e-144
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLT-GIRGPFLIIAPLSTIANWEREFRTWTDINVVVY 937
Cdd:cd17995      1 LRDYQLEGVNWLLFNWYNRRNCILADEMGLGKTIQSIAFLEHLYQVeGIRGPFLVIAPLSTIPNWQREFETWTDMNVVVY 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  938 HGSLISRQMIQQYEMYFRDSQGRIIRGAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNL 1017
Cdd:cd17995     81 HGSGESRQIIQQYEMYFKDAQGRKKKGVYKFDVLITTYEMVIADAEELRKIPWRVVVVDEAHRLKNRNSKLLQGLKKLTL 160
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958747478 1018 EHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 1080
Cdd:cd17995    161 EHKLLLTGTPLQNNTEELWSLLNFLEPEKFPSSEEFLEEFGDLKTAEQVEKLQALLKPYMLRR 223
DEXHc_CHD6 cd18058
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; ...
859-1080 8.97e-138

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: 429.46  E-value: 8.97e-138
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLTGIRGPFLIIAPLSTIANWEREFRTWTDINVVVYH 938
Cdd:cd18058      1 LREYQLEGMNWLLFNWYNRKNCILADEMGLGKTIQSITFLSEIFLMGIRGPFLIIAPLSTITNWEREFRTWTEMNAIVYH 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  939 GSLISRQMIQQYEMYFRDSQGRIIRGAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLE 1018
Cdd:cd18058     81 GSQISRQMIQQYEMYYRDEQGNPLSGIFKFQVVITTFEMILADCPELKKINWSCVIIDEAHRLKNRNCKLLEGLKLMALE 160
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958747478 1019 HKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 1080
Cdd:cd18058    161 HKVLLTGTPLQNSVEELFSLLNFLEPSQFPSETTFLEEFGDLKTEEQVKKLQSILKPMMLRR 222
DEXHc_CHD7 cd18059
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; ...
859-1080 2.15e-132

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: 414.04  E-value: 2.15e-132
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLTGIRGPFLIIAPLSTIANWEREFRTWTDINVVVYH 938
Cdd:cd18059      1 LREYQLEGVNWLLFNWYNTRNCILADEMGLGKTIQSITFLYEIYLKGIHGPFLVIAPLSTIPNWEREFRTWTELNVVVYH 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  939 GSLISRQMIQQYEMYFRDSQGRIIRGAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLE 1018
Cdd:cd18059     81 GSQASRRTIQLYEMYFKDPQGRVIKGSYKFHAIITTFEMILTDCPELRNIPWRCVVIDEAHRLKNRNCKLLEGLKMMDLE 160
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958747478 1019 HKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 1080
Cdd:cd18059    161 HKVLLTGTPLQNTVEELFSLLHFLEPSRFPSETTFMQEFGDLKTEEQVQKLQAILKPMMLRR 222
DEXHc_CHD8 cd18060
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; ...
859-1080 9.50e-132

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: 412.14  E-value: 9.50e-132
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLTGIRGPFLIIAPLSTIANWEREFRTWTDINVVVYH 938
Cdd:cd18060      1 LREYQLEGVNWLLFNWYNRQNCILADEMGLGKTIQSIAFLQEVYNVGIHGPFLVIAPLSTITNWEREFNTWTEMNTIVYH 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  939 GSLISRQMIQQYEMYFRDSQGRIIRGAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLE 1018
Cdd:cd18060     81 GSLASRQMIQQYEMYCKDSRGRLIPGAYKFDALITTFEMILSDCPELREIEWRCVIIDEAHRLKNRNCKLLDSLKHMDLE 160
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958747478 1019 HKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 1080
Cdd:cd18060    161 HKVLLTGTPLQNTVEELFSLLHFLEPSQFPSESEFLKDFGDLKTEEQVQKLQAILKPMMLRR 222
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
858-1331 1.93e-122

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 404.22  E-value: 1.93e-122
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  858 QLREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLTGIRGPFLIIAPLSTIANWEREFRTWT-DINVVV 936
Cdd:COG0553    241 TLRPYQLEGAAWLLFLRRLGLGGLLADDMGLGKTIQALALLLELKERGLARPVLIVAPTSLVGNWQRELAKFApGLRVLV 320
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  937 YHGSLISRQMIQQYEmyfrdsqgriirgayRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMN 1016
Cdd:COG0553    321 LDGTRERAKGANPFE---------------DADLVITSYGLLRRDIELLAAVDWDLVILDEAQHIKNPATKRAKAVRALK 385
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1017 LEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKT---EEQVQKLQAILKPMMLRRLKEDVEKRLAPKE 1093
Cdd:COG0553    386 ARHRLALTGTPVENRLEELWSLLDFLNPGLLGSLKAFRERFARPIEkgdEEALERLRRLLRPFLLRRTKEDVLKDLPEKT 465
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1094 ETIIEVELTNIQKKYYRAILEKNFSFLSKGAGQTNVPNLVNTMMELRKCCNHPYLIKGAEEKIIGEfrdtynpsasdfhl 1173
Cdd:COG0553    466 EETLYVELTPEQRALYEAVLEYLRRELEGAEGIRRRGLILAALTRLRQICSHPALLLEEGAELSGR-------------- 531
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1174 qamiqsAGKLVLIDKLLPKMKAGGHKVLIFSQMVRCLDILEDYLIHKRYLYERIDGRVRGNLRQAAIDRFSKpDSDRFVF 1253
Cdd:COG0553    532 ------SAKLEALLELLEELLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQE-GPEAPVF 604
                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958747478 1254 LLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAVKVYRLVTRNSYEREMFDRASLKLGLDKAVLQ 1331
Cdd:COG0553    605 LISLKAGGEGLNLTAADHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEEKILELLEEKRALAESVLG 682
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
862-1149 7.55e-84

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: 277.64  E-value: 7.55e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  862 YQLEGLNWLLFNWYNR-RNCILADEMGLGKTIQSITFLYEVLLTGI--RGPFLIIAPLSTIANWEREFRTWT---DINVV 935
Cdd:pfam00176    1 YQIEGVNWMLSLENNLgRGGILADEMGLGKTLQTISLLLYLKHVDKnwGGPTLIVVPLSLLHNWMNEFERWVsppALRVV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  936 VYHGSLISRQMIQQYEMYFRDsqgriirgayrFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLM 1015
Cdd:pfam00176   81 VLHGNKRPQERWKNDPNFLAD-----------FDVVITTYETLRKHKELLKKVHWHRIVLDEGHRLKNSKSKLSKALKSL 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1016 NLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFG----DLKTEEQVQKLQAILKPMMLRRLKEDVEKRLAP 1091
Cdd:pfam00176  150 KTRNRWILTGTPLQNNLEELWALLNFLRPGPFGSLSTFRNWFDrpieRGGGKKGVSRLHKLLKPFLLRRTKKDVEKSLPP 229
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1092 KEETIIEVELTNIQKKYY-RAILEKNFSFLSKG-AGQTNVPNLVNTMMELRKCCNHPYLI 1149
Cdd:pfam00176  230 KVEYILFCRLSKLQRKLYqTFLLKKDLNAIKTGeGGREIKASLLNILMRLRKICNHPGLI 289
DEXHc_CHD1_2 cd17993
DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and ...
858-1080 7.77e-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: 266.14  E-value: 7.77e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  858 QLREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLT-GIRGPFLIIAPLSTIANWEREFRTWT-DINVV 935
Cdd:cd17993      1 ELRDYQLTGLNWLAHSWCKGNNGILADEMGLGKTVQTISFLSYLFHSqQQYGPFLVVVPLSTMPAWQREFAKWApDMNVI 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  936 VYHGSLISRQMIQQYEMYFrdSQGRIIRgayrFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLM 1015
Cdd:cd17993     81 VYLGDIKSRDTIREYEFYF--SQTKKLK----FNVLLTTYEIILKDKAFLGSIKWQYLAVDEAHRLKNDESLLYEALKEF 154
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958747478 1016 NLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFmQEFGDLKTEEQVQKLQAILKPMMLRR 1080
Cdd:cd17993    155 KTNNRLLITGTPLQNSLKELWALLHFLMPGKFDIWEEF-EEEHDEEQEKGIADLHKELEPFILRR 218
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
859-1046 3.96e-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: 245.17  E-value: 3.96e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLTG-IRGPFLIIAPLSTIANWEREFRTWT-DINVVV 936
Cdd:cd17919      1 LRPYQLEGLNFLLELYENGPGGILADEMGLGKTLQAIAFLAYLLKEGkERGPVLVVCPLSVLENWEREFEKWTpDLRVVV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  937 YHGSLISRQMIQQYEmyfrdsqgriirGAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMN 1016
Cdd:cd17919     81 YHGSQRERAQIRAKE------------KLDKFDVVLTTYETLRRDKASLRKFRWDLVVVDEAHRLKNPKSQLSKALKALR 148
                          170       180       190
                   ....*....|....*....|....*....|...
gi 1958747478 1017 LEHKVLLTGTPLQNTVEELFSLLHFLEP---LR 1046
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; ...
859-1080 9.71e-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: 233.10  E-value: 9.71e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLTG-IRGPFLIIAPLSTIANWEREFRTWT-DINVVV 936
Cdd:cd17994      1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTIQTIVFLYSLYKEGhSKGPFLVSAPLSTIINWEREFEMWApDFYVVT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  937 YHGSlisrqmiqqyemyfrdsqgriirgayrfQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMN 1016
Cdd:cd17994     81 YVGD----------------------------HVLLTSYELISIDQAILGSIDWAVLVVDEAHRLKNNQSKFFRILNSYK 132
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958747478 1017 LEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 1080
Cdd:cd17994    133 IGYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLQGFLEEFADISKEDQIKKLHDLLGPHMLRR 196
DEXHc_HELLS_SMARCA6 cd18009
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ...
856-1082 2.19e-69

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: 233.82  E-value: 2.19e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  856 GNQLREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLTGIRGPFLIIAPLSTIANWEREFRTWT-DINV 934
Cdd:cd18009      1 GGVMRPYQLEGMEWLRMLWENGINGILADEMGLGKTIQTIALLAHLRERGVWGPFLVIAPLSTLPNWVNEFARFTpSVPV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  935 VVYHGSLISRQMIQQyEMYFRDSQGRIirgayrFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKL 1014
Cdd:cd18009     81 LLYHGTKEERERLRK-KIMKREGTLQD------FPVVVTSYEIAMRDRKALQHYAWKYLIVDEGHRLKNLNCRLIQELKT 153
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1015 MNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFG-----------DLKTEEQ----VQKLQAILKPMMLR 1079
Cdd:cd18009    154 FNSDNRLLLTGTPLQNNLSELWSLLNFLLPDVFDDLSSFESWFDfsslsdnaadiSNLSEEReqniVHMLHAILKPFLLR 233

                   ...
gi 1958747478 1080 RLK 1082
Cdd:cd18009    234 RLK 236
DEXHc_SMARCA1_SMARCA5 cd17997
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ...
856-1082 5.76e-67

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: 226.43  E-value: 5.76e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  856 GNQLREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFL-YEVLLTGIRGPFLIIAPLSTIANWEREFRTWT-DIN 933
Cdd:cd17997      1 GGTMRDYQIRGLNWLISLFENGINGILADEMGLGKTLQTISLLgYLKHYKNINGPHLIIVPKSTLDNWMREFKRWCpSLR 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  934 VVVYHGSLISRQMIqqyemyFRDsqgRIIRGayRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLK 1013
Cdd:cd17997     81 VVVLIGDKEERADI------IRD---VLLPG--KFDVCITSYEMVIKEKTVLKKFNWRYIIIDEAHRIKNEKSKLSQIVR 149
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958747478 1014 LMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEF----GDLKTEEQVQKLQAILKPMMLRRLK 1082
Cdd:cd17997    150 LFNSRNRLLLTGTPLQNNLHELWALLNFLLPDVFTSSEDFDEWFnvnnCDDDNQEVVQRLHKVLRPFLLRRIK 222
DEXHc_CHD3 cd18055
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; ...
859-1080 7.65e-66

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: 223.73  E-value: 7.65e-66
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLTG-IRGPFLIIAPLSTIANWEREFRTWT-DINVVV 936
Cdd:cd18055      1 LHMYQLEGLNWLRFSWAQGTDTILADEMGLGKTIQTIVFLYSLYKEGhTKGPFLVSAPLSTIINWEREFQMWApDFYVVT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  937 YHGSLISRQMIQQYEMYFRDSQGRIIRGAYR--------FQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKL 1008
Cdd:cd18055     81 YTGDKDSRAIIRENEFSFDDNAVKGGKKAFKmkreaqvkFHVLLTSYELVTIDQAALGSIRWACLVVDEAHRLKNNQSKF 160
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958747478 1009 LEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 1080
Cdd:cd18055    161 FRVLNGYKIDHKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLLGPHMLRR 232
DEXHc_CHD5 cd18057
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; ...
859-1080 4.80e-65

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: 221.48  E-value: 4.80e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLTG-IRGPFLIIAPLSTIANWEREFRTWT-DINVVV 936
Cdd:cd18057      1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGhSKGPYLVSAPLSTIINWEREFEMWApDFYVVT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  937 YHGSLISRQMIQQYEMYFRDSQGRIIRGAYR--------FQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKL 1008
Cdd:cd18057     81 YTGDKESRSVIRENEFSFEDNAIRSGKKVFRmkkeaqikFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 160
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958747478 1009 LEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 1080
Cdd:cd18057    161 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLLGPHMLRR 232
DEXHc_CHD2 cd18054
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; ...
830-1080 8.34e-65

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: 220.65  E-value: 8.34e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  830 RPDTRQLDRPPSNIWKKidqsreyknGNQLREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFL-YEVLLTGIRG 908
Cdd:cd18054      1 RPRFVALKKQPSYIGGE---------NLELRDYQLEGLNWLAHSWCKNNSVILADEMGLGKTIQTISFLsYLFHQHQLYG 71
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  909 PFLIIAPLSTIANWEREFRTWT-DINVVVYHGSLISRQMIQQYEMYFRDSQgRIirgayRFQAIITTFEMILGGCGELNA 987
Cdd:cd18054     72 PFLLVVPLSTLTSWQREFEIWApEINVVVYIGDLMSRNTIREYEWIHSQTK-RL-----KFNALITTYEILLKDKTVLGS 145
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  988 IEWRCVIIDEAHRLKNKNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKtEEQVQ 1067
Cdd:cd18054    146 INWAFLGVDEAHRLKNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGR-ENGYQ 224
                          250
                   ....*....|...
gi 1958747478 1068 KLQAILKPMMLRR 1080
Cdd:cd18054    225 SLHKVLEPFLLRR 237
DEXHc_CHD4 cd18056
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; ...
859-1080 1.43e-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: 219.94  E-value: 1.43e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLTG-IRGPFLIIAPLSTIANWEREFRTWT-DINVVV 936
Cdd:cd18056      1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTAVFLYSLYKEGhSKGPFLVSAPLSTIINWEREFEMWApDMYVVT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  937 YHGSLISRQMIQQYEMYFRDSQGRIIRGAYR--------FQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKL 1008
Cdd:cd18056     81 YVGDKDSRAIIRENEFSFEDNAIRGGKKASRmkkeasvkFHVLLTSYELITIDMAILGSIDWACLIVDEAHRLKNNQSKF 160
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958747478 1009 LEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 1080
Cdd:cd18056    161 FRVLNGYSLQHKLLLTGTPLQNNLEELFHLLNFLTPERFHNLEGFLEEFADIAKEDQIKKLHDMLGPHMLRR 232
DEXHc_SMARCA2_SMARCA4 cd17996
DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin ...
856-1082 4.80e-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: 218.39  E-value: 4.80e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  856 GNQLREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSI---TFLYEVllTGIRGPFLIIAPLSTIANWEREFRTWT-D 931
Cdd:cd17996      1 GGTLKEYQLKGLQWMVSLYNNNLNGILADEMGLGKTIQTIsliTYLMEK--KKNNGPYLVIVPLSTLSNWVSEFEKWApS 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  932 INVVVYHGSLISRQMIQQYEMyfrdsqgriirgAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEG 1011
Cdd:cd17996     79 VSKIVYKGTPDVRKKLQSQIR------------AGKFNVLLTTYEYIIKDKPLLSKIKWKYMIIDEGHRMKNAQSKLTQT 146
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1012 LKLM-NLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFG------------DLKTEEQV---QKLQAILKP 1075
Cdd:cd17996    147 LNTYyHARYRLLLTGTPLQNNLPELWALLNFLLPKIFKSCKTFEQWFNtpfantgeqvkiELNEEETLliiRRLHKVLRP 226

                   ....*..
gi 1958747478 1076 MMLRRLK 1082
Cdd:cd17996    227 FLLRRLK 233
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
1181-1306 5.49e-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: 191.15  E-value: 5.49e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1181 GKLVLIDKLLPKMKAGGHKVLIFSQMVRCLDILEDYLIHKRYLYERIDGRVRGNLRQAAIDRFSKPDSDrFVFLLCTRAG 1260
Cdd:cd18793     11 GKLEALLELLEELREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPDI-RVFLLSTKAG 89
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1958747478 1261 GLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAVKVYRLV 1306
Cdd:cd18793     90 GVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQKKPVVVYRLI 135
DEXQc_arch_SWI2_SNF2 cd18012
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ...
857-1082 2.11e-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: 193.17  E-value: 2.11e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  857 NQLREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLTGIRGPFLIIAPLSTIANWEREFRTWT-DINVV 935
Cdd:cd18012      3 ATLRPYQKEGFNWLSFLRHYGLGGILADDMGLGKTLQTLALLLSRKEEGRKGPSLVVAPTSLIYNWEEEAAKFApELKVL 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  936 VYHGSLISRQMIQQYEMYfrdsqgriirgayrfQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLM 1015
Cdd:cd18012     83 VIHGTKRKREKLRALEDY---------------DLVITSYGLLRRDIELLKEVKFHYLVLDEAQNIKNPQTKTAKAVKAL 147
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958747478 1016 NLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFG----DLKTEEQVQKLQAILKPMMLRRLK 1082
Cdd:cd18012    148 KADHRLALTGTPIENHLGELWSIFDFLNPGLLGSYKRFKKRFAkpieKDGDEEALEELKKLISPFILRRLK 218
DEXHc_CHD1L cd18006
DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, ...
859-1080 7.16e-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: 188.42  E-value: 7.16e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFL-YEVLLTGIRGPFLIIAPLSTIANWEREFRTWT-DINVVV 936
Cdd:cd18006      1 LRPYQLEGVNWLLQCRAEQHGCILGDEMGLGKTCQTISLLwYLAGRLKLLGPFLVLCPLSVLDNWKEELNRFApDLSVIT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  937 YHGSLISRQMIQQYemyfrdsqgriIRGAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMN 1016
Cdd:cd18006     81 YMGDKEKRLDLQQD-----------IKSTNRFHVLLTTYEICLKDASFLKSFPWASLVVDEAHRLKNQNSLLHKTLSEFS 149
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958747478 1017 LEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSEST--FMQEFGDLKTE-EQVQKLQAILKPMMLRR 1080
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 ...
859-1080 4.98e-52

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: 183.71  E-value: 4.98e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFL-YEVLLTGIRGPFLIIAPLSTIANWEREFRTWTD-INVVV 936
Cdd:cd18003      1 LREYQHIGLDWLATLYEKNLNGILADEMGLGKTIQTIALLaHLACEKGNWGPHLIVVPTSVMLNWEMEFKRWCPgFKILT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  937 YHGSLISRQMIQQyEMYFRDSqgriirgayrFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMN 1016
Cdd:cd18003     81 YYGSAKERKLKRQ-GWMKPNS----------FHVCITSYQLVVQDHQVFKRKKWKYLILDEAHNIKNFKSQRWQTLLNFN 149
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958747478 1017 LEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTF----------MQEFGDLKTEEQVQKLQAILKPMMLRR 1080
Cdd:cd18003    150 TQRRLLLTGTPLQNSLMELWSLMHFLMPHIFQSHQEFkewfsnpltaMSEGSQEENEELVRRLHKVLRPFLLRR 223
DEXHc_ERCC6L2 cd18005
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
859-1080 1.67e-51

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: 182.96  E-value: 1.67e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLlFNWY-NRRNCILADEMGLGKTIQSITFLYEVL-LTGIR--------------------GPFLIIAPL 916
Cdd:cd18005      1 LRDYQREGVEFM-YDLYkNGRGGILGDDMGLGKTVQVIAFLAAVLgKTGTRrdrennrprfkkkppassakKPVLIVAPL 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  917 STIANWEREFRTWTDINVVVYHGSLISRqmiqqyemyfrDSQGRIIRGAYrfQAIITTFEMILGGCGELNAIEWRCVIID 996
Cdd:cd18005     80 SVLYNWKDELDTWGHFEVGVYHGSRKDD-----------ELEGRLKAGRL--EVVVTTYDTLRRCIDSLNSINWSAVIAD 146
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  997 EAHRLKNKNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGD---------------LK 1061
Cdd:cd18005    147 EAHRIKNPKSKLTQAMKELKCKVRIGLTGTLLQNNMKELWCLLDWAVPGALGSRSQFKKHFSEpikrgqrhtatarelRL 226
                          250
                   ....*....|....*....
gi 1958747478 1062 TEEQVQKLQAILKPMMLRR 1080
Cdd:cd18005    227 GRKRKQELAVKLSKFFLRR 245
DEXHc_CHD1 cd18053
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; ...
856-1080 6.70e-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: 181.02  E-value: 6.70e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  856 GNQLREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFL-YEVLLTGIRGPFLIIAPLSTIANWEREFRTWTD-IN 933
Cdd:cd18053     18 GLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLnYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWAPqMN 97
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  934 VVVYHGSLISRQMIQQYEmYFRDSQGRIirgayRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLK 1013
Cdd:cd18053     98 AVVYLGDINSRNMIRTHE-WMHPQTKRL-----KFNILLTTYEILLKDKSFLGGLNWAFIGVDEAHRLKNDDSLLYKTLI 171
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958747478 1014 LMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKtEEQVQKLQAILKPMMLRR 1080
Cdd:cd18053    172 DFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGR-EYGYASLHKELEPFLLRR 237
DEXQc_INO80 cd18002
DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 ...
859-1080 6.20e-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: 175.00  E-value: 6.20e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLfNWYNRR-NCILADEMGLGKTIQSITFL-YEVLLTGIRGPFLIIAPLSTIANWEREF-RTWTDINVV 935
Cdd:cd18002      1 LKEYQLKGLNWLA-NLYEQGiNGILADEMGLGKTVQSIAVLaHLAEEHNIWGPFLVIAPASTLHNWQQEIsRFVPQFKVL 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  936 VYHGSLISRQMIQQY----EMYFRDSQgriirgayrFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEG 1011
Cdd:cd18002     80 PYWGNPKDRKVLRKFwdrkNLYTRDAP---------FHVVITSYQLVVQDEKYFQRVKWQYMVLDEAQAIKSSSSSRWKT 150
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958747478 1012 LKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFG-DLKT---------EEQVQKLQAILKPMMLRR 1080
Cdd:cd18002    151 LLSFHCRNRLLLTGTPIQNSMAELWALLHFIMPTLFDSHDEFNEWFSkDIEShaenktglnEHQLKRLHMILKPFMLRR 229
DEXHc_SMARCAD1 cd17998
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ...
859-1047 7.86e-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: 172.95  E-value: 7.86e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLTGIRGPFLIIAPLSTIANWEREFRTWT-DINVVVY 937
Cdd:cd17998      1 LKDYQLIGLNWLNLLYQKKLSGILADEMGLGKTIQVIAFLAYLKEIGIPGPHLVVVPSSTLDNWLREFKRWCpSLKVEPY 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  938 HGSLISRqmiqqyemyfRDSQGRIIRGAYRFQAIITTFEMILGGCGE---LNAIEWRCVIIDEAHRLKNKNCKLLEGLKL 1014
Cdd:cd17998     81 YGSQEER----------KHLRYDILKGLEDFDVIVTTYNLATSNPDDrsfFKRLKLNYVVYDEGHMLKNMTSERYRHLMT 150
                          170       180       190
                   ....*....|....*....|....*....|...
gi 1958747478 1015 MNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRF 1047
Cdd:cd17998    151 INANFRLLLTGTPLQNNLLELMSLLNFIMPKPF 183
DEXHc_SMARCA4 cd18062
DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent ...
843-1082 3.44e-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: 167.91  E-value: 3.44e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  843 IWKKIDQSREYKNGNQLREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFL-YEVLLTGIRGPFLIIAPLSTIAN 921
Cdd:cd18062      8 VTEKVEKQSSLLVNGVLKQYQIKGLEWLVSLYNNNLNGILADEMGLGKTIQTIALItYLMEHKRINGPFLIIVPLSTLSN 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  922 WEREFRTWTDINV-VVYHGSLISRQMIQQyemyfrdsqgrIIRGAyRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHR 1000
Cdd:cd18062     88 WVYEFDKWAPSVVkVSYKGSPAARRAFVP-----------QLRSG-KFNVLLTTYEYIIKDKQILAKIRWKYMIVDEGHR 155
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1001 LKNKNCKLLEGLKLMNLE-HKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFG----------DLKTEEQ---V 1066
Cdd:cd18062    156 MKNHHCKLTQVLNTHYVApRRLLLTGTPLQNKLPELWALLNFLLPTIFKSCSTFEQWFNapfamtgekvDLNEEETiliI 235
                          250
                   ....*....|....*.
gi 1958747478 1067 QKLQAILKPMMLRRLK 1082
Cdd:cd18062    236 RRLHKVLRPFLLRRLK 251
DEXHc_SMARCA5 cd18064
DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent ...
846-1093 3.09e-45

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: 164.84  E-value: 3.09e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  846 KIDQSREYKNGNQLREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFL-YEVLLTGIRGPFLIIAPLSTIANWER 924
Cdd:cd18064      3 RFEDSPSYVKWGKLRDYQVRGLNWLISLYENGINGILADEMGLGKTLQTISLLgYMKHYRNIPGPHMVLVPKSTLHNWMA 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  925 EFRTWTDINVVVyhgSLISRQmiQQYEMYFRDSqgrIIRGAYrfQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNK 1004
Cdd:cd18064     83 EFKRWVPTLRAV---CLIGDK--DQRAAFVRDV---LLPGEW--DVCVTSYEMLIKEKSVFKKFNWRYLVIDEAHRIKNE 152
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1005 NCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGD---LKTEEQVQKLQAILKPMMLRRL 1081
Cdd:cd18064    153 KSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALLNFLLPDVFNSAEDFDSWFDTnncLGDQKLVERLHMVLRPFLLRRI 232
                          250
                   ....*....|..
gi 1958747478 1082 KEDVEKRLAPKE 1093
Cdd:cd18064    233 KADVEKSLPPKK 244
DEXHc_SMARCA2 cd18063
DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent ...
849-1082 1.03e-43

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: 160.61  E-value: 1.03e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  849 QSREYKNGNqLREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFL-YEVLLTGIRGPFLIIAPLSTIANWEREFR 927
Cdd:cd18063     15 QSSLLINGT-LKHYQLQGLEWMVSLYNNNLNGILADEMGLGKTIQTIALItYLMEHKRLNGPYLIIVPLSTLSNWTYEFD 93
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  928 TWT-DINVVVYHGS-LISRQMIQQYEmyfrdsqgriirgAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKN 1005
Cdd:cd18063     94 KWApSVVKISYKGTpAMRRSLVPQLR-------------SGKFNVLLTTYEYIIKDKHILAKIRWKYMIVDEGHRMKNHH 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1006 CKLLEGLKLMNLE-HKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFG----------DLKTEEQ---VQKLQA 1071
Cdd:cd18063    161 CKLTQVLNTHYVApRRILLTGTPLQNKLPELWALLNFLLPTIFKSCSTFEQWFNapfamtgervDLNEEETiliIRRLHK 240
                          250
                   ....*....|.
gi 1958747478 1072 ILKPMMLRRLK 1082
Cdd:cd18063    241 VLRPFLLRRLK 251
DEXDc_SHPRH-like cd18008
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ...
859-1080 1.54e-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: 159.76  E-value: 1.54e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFnwynrRNCILADEMGLGKTIQSI----------------TFLYEVLLTGIR--GPFLIIAPLSTIA 920
Cdd:cd18008      1 LLPYQKQGLAWMLP-----RGGILADEMGLGKTIQALalilatrpqdpkipeeLEENSSDPKKLYlsKTTLIVVPLSLLS 75
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  921 NWEREFRTWTD---INVVVYHGSlisrqmiqqyemyfrdSQGRIIRGAYRFQAIITTFEMI----------------LGG 981
Cdd:cd18008     76 QWKDEIEKHTKpgsLKVYVYHGS----------------KRIKSIEELSDYDIVITTYGTLasefpknkkgggrdskEKE 139
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  982 CGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLK 1061
Cdd:cd18008    140 ASPLHRIRWYRVILDEAHNIKNRSTKTSRAVCALKAERRWCLTGTPIQNSLDDLYSLLRFLRVEPFGDYPWFNSDISKPF 219
                          250       260
                   ....*....|....*....|..
gi 1958747478 1062 TE---EQVQKLQAILKPMMLRR 1080
Cdd:cd18008    220 SKndrKALERLQALLKPILLRR 241
DEXHc_SMARCA1 cd18065
DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent ...
846-1082 7.60e-42

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: 154.79  E-value: 7.60e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  846 KIDQSREYKNGNQLREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFL-YEVLLTGIRGPFLIIAPLSTIANWER 924
Cdd:cd18065      3 RFEESPSYVKGGTLRDYQVRGLNWMISLYENGVNGILADEMGLGKTLQTIALLgYLKHYRNIPGPHMVLVPKSTLHNWMN 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  925 EFRTWT-DINVVVYHGSLISRQMIQQYEMYfrdsqgriirgAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKN 1003
Cdd:cd18065     83 EFKRWVpSLRAVCLIGDKDARAAFIRDVMM-----------PGEWDVCVTSYEMVIKEKSVFKKFNWRYLVIDEAHRIKN 151
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1004 KNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGD---LKTEEQVQKLQAILKPMMLRR 1080
Cdd:cd18065    152 EKSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALLNFLLPDVFNSADDFDSWFDTkncLGDQKLVERLHAVLKPFLLRR 231

                   ..
gi 1958747478 1081 LK 1082
Cdd:cd18065    232 IK 233
DEXHc_ERCC6L cd18001
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ...
859-1080 1.90e-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: 153.68  E-value: 1.90e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLTGIRGPFLIIAPLSTIANWEREFRTWT-DINVVVY 937
Cdd:cd18001      1 LYPHQREGVAWLWSLHDGGKGGILADDMGLGKTVQICAFLSGMFDSGLIKSVLVVMPTSLIPHWVKEFAKWTpGLRVKVF 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  938 HGSLISRQmiqqyemyfRDSQGRIIRGayrFQAIITTFEMILGGCGELNAIE-----WRCVIIDEAHRLKNKNCKLLEGL 1012
Cdd:cd18001     81 HGTSKKER---------ERNLERIQRG---GGVLLTTYGMVLSNTEQLSADDhdefkWDYVILDEGHKIKNSKTKSAKSL 148
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1013 KLMNLEHKVLLTGTPLQNTVEELFSLLHFLEP-LRFPSESTFMQEF------GDLKTEEQVQK---------LQAILKPM 1076
Cdd:cd18001    149 REIPAKNRIILTGTPIQNNLKELWALFDFACNgSLLGTRKTFKMEFenpitrGRDKDATQGEKalgsevaenLRQIIKPY 228

                   ....
gi 1958747478 1077 MLRR 1080
Cdd:cd18001    229 FLRR 232
DEXHc_RAD54 cd18004
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ...
859-1080 1.88e-38

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: 145.12  E-value: 1.88e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLL-----FNWYNRRNCILADEMGLGKTIQSITFLYEVLLTGIRGP-----FLIIAPLSTIANWEREFRT 928
Cdd:cd18004      1 LRPHQREGVQFLYdcltgRRGYGGGGAILADEMGLGKTLQAIALVWTLLKQGPYGKptakkALIVCPSSLVGNWKAEFDK 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  929 W---TDINVVVYHGSLISRQMIQQYEMYFRdsqgriirgayRFQAIITTFEMILGGCGELNAIEwRC--VIIDEAHRLKN 1003
Cdd:cd18004     81 WlglRRIKVVTADGNAKDVKASLDFFSSAS-----------TYPVLIISYETLRRHAEKLSKKI-SIdlLICDEGHRLKN 148
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1004 KNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGD--LK------TEEQV-------QK 1068
Cdd:cd18004    149 SESKTTKALNSLPCRRRLLLTGTPIQNDLDEFFALVDFVNPGILGSLASFRKVFEEpiLRsrdpdaSEEDKelgaersQE 228
                          250
                   ....*....|..
gi 1958747478 1069 LQAILKPMMLRR 1080
Cdd:cd18004    229 LSELTSRFILRR 240
DEXHc_ERCC6 cd18000
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ...
859-1044 2.70e-36

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: 137.07  E-value: 2.70e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLfnWYNRRNC--ILADEMGLGKTIQSITFLYEVLLTGI-RGPFLIIAPLSTIANWEREFRTW-TDINV 934
Cdd:cd18000      1 LFKYQQTGVQWLW--ELHCQRVggILGDEMGLGKTIQIIAFLAALHHSKLgLGPSLIVCPATVLKQWVKEFHRWwPPFRV 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  935 VVYHGSLISRQMIQQYEMYFRDSQgRIIRGAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKL 1014
Cdd:cd18000     79 VVLHSSGSGTGSEEKLGSIERKSQ-LIRKVVGDGGILITTYEGFRKHKDLLLNHNWQYVILDEGHKIRNPDAEITLACKQ 157
                          170       180       190
                   ....*....|....*....|....*....|
gi 1958747478 1015 MNLEHKVLLTGTPLQNTVEELFSLLHFLEP 1044
Cdd:cd18000    158 LRTPHRLILSGTPIQNNLKELWSLFDFVFP 187
CD2_tandem_CHD5-9_like cd18663
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ...
769-827 2.69e-34

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: 126.25  E-value: 2.69e-34
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958747478  769 PDYVEVDRILEVSFCEDKDTGESVVYYLVKWCSLPYEDSTWELKEDVDLAKIEEFEQLQ 827
Cdd:cd18663      1 PDYVEVDRILDVSVSTDPNTGEPVTHYLVKWCSLPYEDSTWELEEDVDPAKIEEFEKLR 59
DEXHc_Mot1 cd17999
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ...
859-1080 6.50e-33

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: 129.01  E-value: 6.50e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLF-NWYNRRNcILADEMGLGKTIQSITFLY------EVLLTGIRGPFLIIAPLSTIANWEREFRTWTD 931
Cdd:cd17999      1 LRPYQQEGINWLAFlNKYNLHG-ILCDDMGLGKTLQTLCILAsdhhkrANSFNSENLPSLVVCPPTLVGHWVAEIKKYFP 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  932 ---INVVVYHGSLISRQMIQQYemyfrdsqgriirgAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKL 1008
Cdd:cd17999     80 nafLKPLAYVGPPQERRRLREQ--------------GEKHNVIVASYDVLRNDIEVLTKIEWNYCVLDEGHIIKNSKTKL 145
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1009 LEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFG-------DLK-----TEEQVQKLQAILK-- 1074
Cdd:cd17999    146 SKAVKQLKANHRLILSGTPIQNNVLELWSLFDFLMPGYLGTEKQFQRRFLkpilasrDSKasakeQEAGALALEALHKqv 225

                   ....*..
gi 1958747478 1075 -PMMLRR 1080
Cdd:cd17999    226 lPFLLRR 232
DEXHc_ATRX-like cd18007
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ...
859-1057 1.09e-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: 128.56  E-value: 1.09e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNwllFNWYN----------RRNCILADEMGLGKTIQSITFLYEVLLTGIRGP-FLIIAPLSTIANWEREFR 927
Cdd:cd18007      1 LKPHQVEGVR---FLWSNlvgtdvgsdeGGGCILAHTMGLGKTLQVITFLHTYLAAAPRRSrPLVLCPASTLYNWEDEFK 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  928 TWT------DINVVVYHGSLISRQ---MIQQ-----------YEMyFRDSQGRIIRGAYRFQAIITtfEMILGGCGelna 987
Cdd:cd18007     78 KWLppdlrpLLVLVSLSASKRADArlrKINKwhkeggvlligYEL-FRNLASNATTDPRLKQEFIA--ALLDPGPD---- 150
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  988 iewrCVIIDEAHRLKNKNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEF 1057
Cdd:cd18007    151 ----LLVLDEGHRLKNEKSQLSKALSKVKTKRRILLTGTPLQNNLKEYWTMVDFARPKYLGTLKEFKKKF 216
DEXDc smart00487
DEAD-like helicases superfamily;
852-1050 3.54e-31

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 122.99  E-value: 3.54e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478   852 EYKNGNQLREYQLEGLNWLLFNWynrRNCILADEMGLGKTIQSITFLYEVLLTGIRGPFLIIAPLSTIA-NWEREFRTW- 929
Cdd:smart00487    2 EKFGFEPLRPYQKEAIEALLSGL---RDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAeQWAEELKKLg 78
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478   930 --TDINVVVYHGSLISRQMIQQyemyfrdsqgrIIRGayRFQAIITTFEMIL--GGCGELNAIEWRCVIIDEAHRLKNKN 1005
Cdd:smart00487   79 psLGLKVVGLYGGDSKREQLRK-----------LESG--KTDILVTTPGRLLdlLENDKLSLSNVDLVILDEAHRLLDGG 145
                           170       180       190       200       210
                    ....*....|....*....|....*....|....*....|....*....|.
gi 1958747478  1006 --CKLLEGLKLMNLE-HKVLLTGTP---LQNTVEELFSLLHFLEPLRFPSE 1050
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, ...
685-749 1.91e-29

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: 112.82  E-value: 1.91e-29
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958747478  685 EEDAAIVDKILACRTVKKEVSPGV-MLDIEEFFVKYKNYSYLHCEWATEQQLLK-DKRIQQKIKRFK 749
Cdd:cd18668      1 EEDTMIIEKILASRKKKKEKEEGAeEIEVEEYLVKYKNFSYLHCEWKTEEELEKgDKRIKQKIKRFK 67
DEXHc_RAD54B cd18066
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ...
859-1057 9.24e-29

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: 116.87  E-value: 9.24e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLnwlLFNWY--------NRRNCILADEMGLGKTIQSITFLYEVLLTGIRGP------FLIIAPLSTIANWER 924
Cdd:cd18066      1 LRPHQREGI---EFLYEcvmgmrvnERFGAILADEMGLGKTLQCISLIWTLLRQGPYGGkpvikrALIVTPGSLVKNWKK 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  925 EFRTWtdinvvvyhgslISRQMIQQYEMYfRDSQGRIIRGAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNK 1004
Cdd:cd18066     78 EFQKW------------LGSERIKVFTVD-QDHKVEEFIASPLYSVLIISYEMLLRSLDQISKLNFDLVICDEGHRLKNT 144
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958747478 1005 NCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEF 1057
Cdd:cd18066    145 SIKTTTALTSLSCERRIILTGTPIQNDLQEFFALIDFVNPGILGSLSTYRKVY 197
DEXHc_HARP_SMARCAL1 cd18010
DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin ...
859-1080 1.21e-27

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: 113.07  E-value: 1.21e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLfnwynRRN--CILADEMGLGKTIQSITFLY----EvlltgirGPFLIIAPLSTIANWEREFRTW--- 929
Cdd:cd18010      1 LLPFQREGVCFAL-----RRGgrVLIADEMGLGKTVQAIAIAAyyreE-------WPLLIVCPSSLRLTWADEIERWlps 68
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  930 ---TDINVVVyHGSlisrqmiqqyeMYFRDSQGRIirgayrfqaIITTFEMILGGCGELNAIEWRCVIIDEAHRLKN--- 1003
Cdd:cd18010     69 lppDDIQVIV-KSK-----------DGLRDGDAKV---------VIVSYDLLRRLEKQLLARKFKVVICDESHYLKNska 127
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1004 KNCKLLEGLkLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTF--------MQEFG-DLKTEEQVQKLQAIL- 1073
Cdd:cd18010    128 KRTKAALPL-LKRAKRVILLSGTPALSRPIELFTQLDALDPKLFGRFHDFgrrycaakQGGFGwDYSGSSNLEELHLLLl 206

                   ....*..
gi 1958747478 1074 KPMMLRR 1080
Cdd:cd18010    207 ATIMIRR 213
DEXHc_RAD54A cd18067
DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as ...
859-1080 2.84e-26

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: 110.25  E-value: 2.84e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFNWYNRRN-----CILADEMGLGKTIQSITFLYEVLLTGIRGPFLI-----IAPLSTIANWEREFRT 928
Cdd:cd18067      1 LRPHQREGVKFLYRCVTGRRIrgshgCIMADEMGLGKTLQCITLMWTLLRQSPQCKPEIdkaivVSPSSLVKNWANELGK 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  929 WTDINVVVYHGSLISRQMIQQYEMYFRDSQGRIIRGAyrfqAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKNKNCKL 1008
Cdd:cd18067     81 WLGGRLQPLAIDGGSKKEIDRKLVQWASQQGRRVSTP----VLIISYETFRLHVEVLQKGEVGLVICDEGHRLKNSDNQT 156
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1009 LEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEF---------GD------LKTEEQVQKLQAIL 1073
Cdd:cd18067    157 YQALDSLNTQRRVLLSGTPIQNDLSEYFSLVNFVNPGILGTAAEFKKNFelpilkgrdADasekerQLGEEKLQELISIV 236

                   ....*..
gi 1958747478 1074 KPMMLRR 1080
Cdd:cd18067    237 NRCIIRR 243
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
1181-1295 8.96e-26

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: 103.83  E-value: 8.96e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1181 GKLVLIDKLLPKMKagGHKVLIFSQMVRCLDilEDYLIHKR-YLYERIDGRVRGNLRQAAIDRFSKPDSDrfvFLLCTRA 1259
Cdd:pfam00271    1 EKLEALLELLKKER--GGKVLIFSQTKKTLE--AELLLEKEgIKVARLHGDLSQEEREEILEDFRKGKID---VLVATDV 73
                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1958747478 1260 GGLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIG 1295
Cdd:pfam00271   74 AERGLDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
DISARM_DrmD_b NF038318
DISARM system SNF2-like helicase DrmD, short form; DrmD, a SNF2-like helicase, is a component ...
881-1345 6.78e-24

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: 110.54  E-value: 6.78e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  881 ILADEMGLGKTIQSITFLYEVLLTGIRgPFLIIAPLSTIANWEREFRTWTDINVVVyhgslISRQMIQQYemyfRDSQGR 960
Cdd:NF038318    51 ILADEVGLGKTIEAGLVLKYVLESGAK-KILIILPANLRKQWEIELEEKFDLESLI-----LDSLTVEKD----AKKWNK 120
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  961 IIRGAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAHRLKN--KNCKLLEGL-KLMNLEHKVLLTGTPLQNTVEELFS 1037
Cdd:NF038318   121 RLTDNKKVRIVITSYDYASKLMKRFPKVKWDFIIIDEAHNLRNvhKGGKRAKNLyELTKGIPKILLTATPLQNSLLDLYG 200
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1038 LLHFLEPLRFPSESTFM------QEFGDLKTEeqvqklqaiLKPMMLRRLKEDVEKRLAPKEETIIEV--ELTNIQKKYY 1109
Cdd:NF038318   201 LVSFIDPRIFGSEKVFSkryikdEDYSDLKRE---------LSPVLYRTLRKDVADYMQFKKRKCITVdfELSPDEIELY 271
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1110 RAI---LEKNFSFlskgagqtNVPN--------------------LVNTMMELRKCCNHPY---LIKGAEEKI--IGEFR 1161
Cdd:NF038318   272 VRVnnfLKRDILY--------SIPTsnrtliilvirkllasssfaLAETFEVLKKRLEKLKegtRSANAQEGFdlFWSFV 343
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1162 DTYNpSASDFHL---------QAMIQSAGKLV--LID-----KLLPKMKAG----------------GHKVLIFSQMVRC 1209
Cdd:NF038318   344 EDEI-DESGFEEkqdelytrqKEFIQHEIDEVdaIIDvakriKTNAKVTALktaleiafeyqreegiAQKVVVFTESKRT 422
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1210 LDILEDYLIHKRYLYERI---DG--------------RVR--GN--------LRQAAIDRFSkpdsDRFVFLLCTRAGGL 1262
Cdd:NF038318   423 QKYIAEELRKSGYEGEDIllfNGdfddamtkeiyrawQVKnyGKanygrsveYKHAIVDYFK----NNAKILIVTDAGSE 498
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1263 GINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAVKVYRLV-TRNSYEREMFDRASLKLGL--------DKA--VLQ 1331
Cdd:NF038318   499 GLNLQFCNTVINYDLPWNPQKIEQRIGRCHRYGQKNDVVAINLLnTQNVADKRVYEILSEKFELfegvfgasDIAlgLLE 578
                          570
                   ....*....|....
gi 1958747478 1332 SMSGRDSNVSGIQQ 1345
Cdd:NF038318   579 SGTDFEKRVLQIYQ 592
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
859-1080 1.73e-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: 1.73e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFNWYNRrnCILADEMGLGKTIQSITFLYEVLLTGIRGPFLIIAPLSTIANWEREFRTWTDINVVVyh 938
Cdd:cd18011      1 PLPHQIDAVLRALRKPPVR--LLLADEVGLGKTIEAGLIIKELLLRGDAKRVLILCPASLVEQWQDELQDKFGLPFLI-- 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  939 gslISRQMIQQyemyfrdSQGRIIRGAYRFQAIITTFEMILGG---CGELNAIEWRCVIIDEAHRLKNKNCKLLEGL-KL 1014
Cdd:cd18011     77 ---LDRETAAQ-------LRRLIGNPFEEFPIVIVSLDLLKRSeerRGLLLSEEWDLVVVDEAHKLRNSGGGKETKRyKL 146
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958747478 1015 MNL-----EHKVLLTGTPLQNTVEELFSLLHFLEPLRFpsesTFMQEFGDLKTEEQVqklqaiLKPMMLRR 1080
Cdd:cd18011    147 GRLlakraRHVLLLTATPHNGKEEDFRALLSLLDPGRF----AVLGRFLRLDGLREV------LAKVLLRR 207
DEXHc_HLTF1_SMARC3 cd18071
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ...
881-1080 3.61e-23

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: 101.01  E-value: 3.61e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  881 ILADEMGLGKTIQSITFlyeVLLTgirgPFLIIAPLSTIANWEREFRTWTD---INVVVYHGSlisrqmiqqyemyfrdS 957
Cdd:cd18071     52 ILADDMGLGKTLTTISL---ILAN----FTLIVCPLSVLSNWETQFEEHVKpgqLKVYTYHGG----------------E 108
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  958 QGRIIRGAYRFQAIITTFEMILG-----GCGELNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLEHKVLLTGTPLQNTV 1032
Cdd:cd18071    109 RNRDPKLLSKYDIVLTTYNTLASdfgakGDSPLHTINWLRVVLDEGHQIRNPNAQQTKAVLNLSSERRWVLTGTPIQNSP 188
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1958747478 1033 EELFSLLHFLEPLRFPSESTFMQEFG---DLKTEEQVQKLQAILKPMMLRR 1080
Cdd:cd18071    189 KDLGSLLSFLHLKPFSNPEYWRRLIQrplTMGDPTGLKRLQVLMKQITLRR 239
DEXHc_ATRX cd18068
DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha ...
880-1057 2.68e-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: 98.81  E-value: 2.68e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  880 CILADEMGLGKTIQSITFLYEVLLTGIRGPF---LIIAPLSTIANWEREFRTWTDIN-----VVVYHGSLISRQ------ 945
Cdd:cd18068     31 CILAHCMGLGKTLQVVTFLHTVLLCEKLENFsrvLVVCPLNTVLNWLNEFEKWQEGLkdeekIEVNELATYKRPqersyk 110
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  946 ----------MIQQYEMYFRDSQGRIIRGAYRFQAiitTFEMILGGCGElnaiewRCVIIDEAHRLKNKNCKLLEGLKLM 1015
Cdd:cd18068    111 lqrwqeeggvMIIGYDMYRILAQERNVKSREKLKE---IFNKALVDPGP------DFVVCDEGHILKNEASAVSKAMNSI 181
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1958747478 1016 NLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEF 1057
Cdd:cd18068    182 RTKRRIVLTGTPLQNNLIEYHCMVNFVKPNLLGTIKEFRNRF 223
HELICc smart00490
helicase superfamily c-terminal domain;
1211-1295 4.03e-20

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 86.88  E-value: 4.03e-20
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  1211 DILEDYLIHKRYLYERIDGRVRGNLRQAAIDRFSKPDSDrfvFLLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQAQAR 1290
Cdd:smart00490    1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIK---VLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGR 77

                    ....*
gi 1958747478  1291 CHRIG 1295
Cdd:smart00490   78 AGRAG 82
DEXHc_TTF2 cd18072
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ...
859-1080 3.50e-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: 86.38  E-value: 3.50e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLfnWYNRRNC---ILADEMGLGKTIQSITFLY--------------EVLLTGI---------RGPFLI 912
Cdd:cd18072      1 LLLHQKQALAWLL--WRERQKPrggILADDMGLGKTLTMIALILaqkntqnrkeeekeKALTEWEskkdstlvpSAGTLV 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  913 IAPLSTIANWEREFRTWTD---INVVVYHGSlisrqmiqqyemyFRDSQGRIIRgayRFQAIITTFEMI---LGGCGE-- 984
Cdd:cd18072     79 VCPASLVHQWKNEVESRVAsnkLRVCLYHGP-------------NRERIGEVLR---DYDIVITTYSLVakeIPTYKEes 142
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  985 ----LNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFgDL 1060
Cdd:cd18072    143 rsspLFRIAWARIILDEAHNIKNPKVQASIAVCKLRAHARWALTGTPIQNNLLDMYSLLKFLRCSPFDDLKVWKKQV-DN 221
                          250       260
                   ....*....|....*....|
gi 1958747478 1061 KTEEQVQKLQAILKPMMLRR 1080
Cdd:cd18072    222 KSRKGGERLNILTKSLLLRR 241
DEXHc_ARIP4 cd18069
DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called ...
880-1057 5.43e-17

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: 82.56  E-value: 5.43e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  880 CILADEMGLGKTIQSITFLYEVLLTGIRGPFLIIAPLSTIANWEREFRTWtdinvvVYHGSLISRQMIQQYEMYFRDSQG 959
Cdd:cd18069     31 CILAHSMGLGKTLQVISFLDVLLRHTGAKTVLAIVPVNTLQNWLSEFNKW------LPPPEALPNVRPRPFKVFILNDEH 104
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  960 RiirgAYRFQAIITTFEMILGGCGELNAIEWR------CVIIDEAHRLKNKNCKLLEGLKLMNLEHKVLLTGTPLQNTVE 1033
Cdd:cd18069    105 K----TTAARAKVIEDWVKDGGVLLMGYEMFRlrpgpdVVICDEGHRIKNCHASTSQALKNIRSRRRIVLTGYPLQNNLI 180
                          170       180
                   ....*....|....*....|....
gi 1958747478 1034 ELFSLLHFLEPLRFPSESTFMQEF 1057
Cdd:cd18069    181 EYWCMVDFVRPDFLGTRQEFSNMF 204
CD2_tandem cd18659
repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier ...
770-825 6.36e-16

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: 73.76  E-value: 6.36e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958747478  770 DYVEVDRILEVSfcedkDTGESVVYYLVKWCSLPYEDSTWELKEDV---DLAKIEEFEQ 825
Cdd:cd18659      1 EYTIVERIIAHR-----EDDEGVTEYLVKWKGLPYDECTWESEEDIsdiFQEAIDEYKK 54
BRK smart00592
domain in transcription and CHROMO domain helicases;
2549-2593 4.38e-15

domain in transcription and CHROMO domain helicases;


Pssm-ID: 197800  Cd Length: 45  Bit Score: 71.22  E-value: 4.38e-15
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*
gi 1958747478  2549 TGEERVQLINRRNARKVGGAFAPPLKDLCRFLKENSEYGVAPEWG 2593
Cdd:smart00592    1 DGEERVPVINRETGKKLTGDDAPKAKDLERWLEENPEYEVAPRSA 45
BRK pfam07533
BRK domain; The function of this domain is unknown. It is often found associated with ...
2475-2515 1.34e-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: 1.34e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1958747478 2475 DTESPVPVINLKDGTRLAGDDAPKRKDLDRWLKEHPGYVED 2515
Cdd:pfam07533    2 TGDERVPVVNRKTGKKLTGDKAPKLKDLEEWLEENPGYEVD 42
BRK smart00592
domain in transcription and CHROMO domain helicases;
2475-2522 2.09e-14

domain in transcription and CHROMO domain helicases;


Pssm-ID: 197800  Cd Length: 45  Bit Score: 69.30  E-value: 2.09e-14
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 1958747478  2475 DTESPVPVINLKDGTRLAGDDAPKRKDLDRWLKEHPGYvedlgAFIPR 2522
Cdd:smart00592    1 DGEERVPVINRETGKKLTGDDAPKAKDLERWLEENPEY-----EVAPR 43
BRK pfam07533
BRK domain; The function of this domain is unknown. It is often found associated with ...
2548-2591 2.29e-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: 66.38  E-value: 2.29e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1958747478 2548 LTGEERVQLINRRNARKVGGAFAPPLKDLCRFLKENSEYGVAPE 2591
Cdd:pfam07533    1 LTGDERVPVVNRKTGKKLTGDKAPKLKDLEEWLEENPGYEVDPR 44
CD1_tandem cd18660
repeat 1 of paired tandem chromodomains; Repeat 1 of tandem CHRomatin Organization Modifier ...
687-749 5.64e-12

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: 63.15  E-value: 5.64e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958747478  687 DAAIVDKILACRtVKKEVSPGVMLDIE--------EFFVKYKNYSYLHCEWATEQQlLKDKRIQQKIKRFK 749
Cdd:cd18660      1 DEDKIEKILDHR-PKGPVEEASLDLTDpdepwderEFLVKWKGKSYLHCTWVTEET-LEQLRGKKKLKNYI 69
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
805-1389 4.80e-11

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 68.51  E-value: 4.80e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  805 EDSTWELKEDVDLAKIEEFEQLQASRPDTRQLDRPPSNIWKKIDQSREYKNGN-------QLREYQLEGLN-WLLFNWYN 876
Cdd:COG1061     20 LLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEALEAGDeasgtsfELRPYQQEALEaLLAALERG 99
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  877 RRNCILADEMGLGKTIQSITFLYEVLLtgiRGPFLIIAPLSTIAN-WEREFRTWTDiNVVVYHGSlisrqmiqqyemyfR 955
Cdd:COG1061    100 GGRGLVVAPTGTGKTVLALALAAELLR---GKRVLVLVPRRELLEqWAEELRRFLG-DPLAGGGK--------------K 161
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  956 DSQGRIIrgayrfqaiITTFEmILGGCGELNAI--EWRCVIIDEAHRLKNKncKLLEGLKLMNLEHKVLLTGTPlqntve 1033
Cdd:COG1061    162 DSDAPIT---------VATYQ-SLARRAHLDELgdRFGLVIIDEAHHAGAP--SYRRILEAFPAAYRLGLTATP------ 223
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1034 elfsllhfleplrfpsestfmqEFGDLKTEEqVQKLQAILKPMMLRRLKEDveKRLAPKEETIIEVELTNIQKKYyrAIL 1113
Cdd:COG1061    224 ----------------------FRSDGREIL-LFLFDGIVYEYSLKEAIED--GYLAPPEYYGIRVDLTDERAEY--DAL 276
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1114 EKNFsflskgagqtnvpnlvntmmelrkccnhpylikgaEEKIIGEfrdtynpsasdfhlqamiqSAGKLVLIDKLLPKM 1193
Cdd:COG1061    277 SERL-----------------------------------REALAAD-------------------AERKDKILRELLREH 302
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1194 kAGGHKVLIFSQMVRCLDILEDYLIHKRYLYERIDGRVRGNLRQAAIDRFSkpdSDRFVFLLCTRAGGLGINLTAADTCI 1273
Cdd:COG1061    303 -PDDRKTLVFCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFR---DGELRILVTVDVLNEGVDVPRLDVAI 378
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1274 IFDSDWNPQNDLQAQARCHRIGQNK-AVKVYRLVTRNSYEREMFDRASLKLGLDKavLQSMSGRDSNVSGIQQLSKKEIE 1352
Cdd:COG1061    379 LLRPTGSPREFIQRLGRGLRPAPGKeDALVYDFVGNDVPVLEELAKDLRDLAGYR--VEFLDEEESEELALLIAVKPALE 456
                          570       580       590
                   ....*....|....*....|....*....|....*..
gi 1958747478 1353 DLLRRGAYGAIMEEEDEGSKFCEEDIDQILLRRTKTI 1389
Cdd:COG1061    457 VKGELEEELLEELELLEDALLLVLAELLLLELLALAL 493
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
859-1042 8.31e-11

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: 65.06  E-value: 8.31e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLFnwynrRNCILADEMGLGKTIQSITFL---------YEVLLTGIR-----------------GPFLI 912
Cdd:cd18070      1 LLPYQRRAVNWMLV-----PGGILADEMGLGKTVEVLALIllhprpdndLDAADDDSDemvccpdclvaetpvssKATLI 75
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  913 IAPLSTIANWEREFRTWTDINVVVYHGSLISRQMIQQYEMYFRDSQGRIIRGAY---RFQ-AIITTFEMILGGCGE---- 984
Cdd:cd18070     76 VCPSAILAQWLDEINRHVPSSLKVLTYQGVKKDGALASPAPEILAEYDIVVTTYdvlRTElHYAEANRSNRRRRRQkrye 155
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958747478  985 -----LNAIEWRCVIIDEAHRLKNKNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFL 1042
Cdd:cd18070    156 appspLVLVEWWRVCLDEAQMVESSTSKAAEMARRLPRVNRWCVSGTPIQRGLDDLFGLLSFL 218
DEXQc_bact_SNF2 cd18013
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ...
859-1043 5.24e-10

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: 61.98  E-value: 5.24e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  859 LREYQLEGLNWLLfnwYNRRNCILADeMGLGKTIQSITFLYEVLLTGIRGPFLIIAPLSTIAN-WEREFRTW-----TDI 932
Cdd:cd18013      1 PHPYQKVAINFII---EHPYCGLFLD-MGLGKTVTTLTALSDLQLDDFTRRVLVIAPLRVARStWPDEVEKWnhlrnLTV 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  933 NVVVYHGSLISRQMIQQYEMYfrdsqgriirgayrfqaiITTFEMILGGCGELNaIEW--RCVIIDEAHRLKNKNCKllE 1010
Cdd:cd18013     77 SVAVGTERQRSKAANTPADLY------------------VINRENLKWLVNKSG-DPWpfDMVVIDELSSFKSPRSK--R 135
                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1958747478 1011 GLKLMNLEHKV----LLTGTPLQNTVEELFSLLHFLE 1043
Cdd:cd18013    136 FKALRKVRPVIkrliGLTGTPSPNGLMDLWAQIALLD 172
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
773-825 1.55e-09

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 55.66  E-value: 1.55e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1958747478  773 EVDRILEVSFCEDKdtgesVVYYLVKWCSLPYEDSTWELKEDVDLAK--IEEFEQ 825
Cdd:pfam00385    2 EVERILDHRKDKGG-----KEEYLVKWKGYPYDENTWEPEENLSKCPelIEEFKD 51
CHROMO smart00298
Chromatin organization modifier domain;
691-753 2.94e-09

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 54.91  E-value: 2.94e-09
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958747478   691 VDKILACRTVKKEVspgvmldiEEFFVKYKNYSYLHCEWATEQQLLKDKRiqqKIKRFKLRQA 753
Cdd:smart00298    4 VEKILDHRWKKKGE--------LEYLVKWKGYSYSEDTWEPEENLLNCSK---KLDNYKKKER 55
CD2_tandem_CHD3-4_like cd18662
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and ...
769-823 1.54e-08

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: 53.04  E-value: 1.54e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1958747478  769 PDYVEVDRILEVSfcEDKDTGesvVYYLVKWCSLPYEDSTWElKEDVDLAKIEEF 823
Cdd:cd18662      1 PEWLQIHRIINHR--VDKDGN---TWYLVKWRDLPYDQSTWE-SEDDDIPDYEKH 49
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
879-1026 1.57e-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: 55.87  E-value: 1.57e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  879 NCILADEMGLGKTIQSITFLYEVLLTGiRGPFLIIAPLSTIAN-WEREFRTW--TDINVVVYHGsliSRQMIQQYEMYFR 955
Cdd:cd00046      3 NVLITAPTGSGKTLAALLAALLLLLKK-GKKVLVLVPTKALALqTAERLRELfgPGIRVAVLVG---GSSAEEREKNKLG 78
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958747478  956 DSqgriirgayrfQAIITTFEMILGGCGELNAI---EWRCVIIDEAHRL----KNKNCKLLEGLKLMNLEHK-VLLTGT 1026
Cdd:cd00046     79 DA-----------DIIIATPDMLLNLLLREDRLflkDLKLIIVDEAHALlidsRGALILDLAVRKAGLKNAQvILLSAT 146
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
690-749 2.42e-08

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 52.19  E-value: 2.42e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  690 IVDKILACRTVKKEVspgvmldiEEFFVKYKNYSYLHCEWATEQQLLKDKRIqqkIKRFK 749
Cdd:pfam00385    2 EVERILDHRKDKGGK--------EEYLVKWKGYPYDENTWEPEENLSKCPEL---IEEFK 50
CD1_tandem_CHD3-4_like cd18667
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and ...
714-735 3.99e-06

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: 46.95  E-value: 3.99e-06
                           10        20
                   ....*....|....*....|..
gi 1958747478  714 EFFVKYKNYSYLHCEWATEQQL 735
Cdd:cd18667     45 EFFVKWHGMSYWHCEWVSELQL 66
ResIII pfam04851
Type III restriction enzyme, res subunit;
858-1027 5.12e-06

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 48.82  E-value: 5.12e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  858 QLREYQLEGL-NWLLFNWYNRRNCILADEMGLGKTIQSITFLYEVLLTGIRGPFLIIAP-LSTIANWEREFRTWTDINVV 935
Cdd:pfam04851    3 ELRPYQIEAIeNLLESIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPrKDLLEQALEEFKKFLPNYVE 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  936 vyHGSLIS----RQMIQQYEMYF--RDSQGRIIRGAYRfQAIITTFEMIlggcgelnaiewrcvIIDEAHRL-------- 1001
Cdd:pfam04851   83 --IGEIISgdkkDESVDDNKIVVttIQSLYKALELASL-ELLPDFFDVI---------------IIDEAHRSgassyrni 144
                          170       180
                   ....*....|....*....|....*...
gi 1958747478 1002 --KNKNCKLLEglklmnlehkvlLTGTP 1027
Cdd:pfam04851  145 leYFKPAFLLG------------LTATP 160
CD_CSD cd00024
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
773-825 7.34e-06

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: 45.16  E-value: 7.34e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1958747478  773 EVDRILevsfceDKDTGESVVYYLVKWCSLPYEDSTWELKEDVDLAK--IEEFEQ 825
Cdd:cd00024      2 EVEKIL------DHRVRKGKLEYLVKWKGYPPEENTWEPEENLTNAPelIKEYEK 50
CHROMO smart00298
Chromatin organization modifier domain;
773-828 1.97e-05

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 44.13  E-value: 1.97e-05
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958747478   773 EVDRILEVSFcedkdTGESVVYYLVKWCSLPYEDSTWELKEDVDLA--KIEEFEQLQA 828
Cdd:smart00298    3 EVEKILDHRW-----KKKGELEYLVKWKGYSYSEDTWEPEENLLNCskKLDNYKKKER 55
CD2_tandem cd18659
repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier ...
687-749 2.35e-05

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: 44.10  E-value: 2.35e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958747478  687 DAAIVDKILACRTVKKEVspgvmldiEEFFVKYKNYSYLHCEWATEQQLLkdKRIQQKIKRFK 749
Cdd:cd18659      1 EYTIVERIIAHREDDEGV--------TEYLVKWKGLPYDECTWESEEDIS--DIFQEAIDEYK 53
PTZ00121 PTZ00121
MAEBL; Provisional
510-765 1.01e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 48.21  E-value: 1.01e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  510 KKPRKKAESESKQEKANRIISEAIARAKERGERNIPRVMSPENFPSSSVDGK--EEKRAQRVKSKPKDRdnrkpKACSKL 587
Cdd:PTZ00121  1401 EEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKaeEAKKAEEAKKKAEEA-----KKADEA 1475
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  588 KEKTKIGKLIITLGKNHKRRSESSDELSDAEQMPQHTFKEQHSQKRRSNRQVKRKKYAEDAEGRQCEEEVRGSLKVKRTS 667
Cdd:PTZ00121  1476 KKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAE 1555
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  668 APPPGEQPLQLFVENPSEEDAAIVDKI--LACRTVKKEVSPGVMLDIEEFFVKYKNYSYLHCEWATEQQLLKDKRIQQKI 745
Cdd:PTZ00121  1556 ELKKAEEKKKAEEAKKAEEDKNMALRKaeEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKV 1635
                          250       260
                   ....*....|....*....|...
gi 1958747478  746 KRFKLRQAQ---RAHFLADMEEE 765
Cdd:PTZ00121  1636 EQLKKKEAEekkKAEELKKAEEE 1658
CDC27 pfam09507
DNA polymerase subunit Cdc27; This protein forms the C subunit of DNA polymerase delta. It ...
484-675 1.62e-04

DNA polymerase subunit Cdc27; This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif.


Pssm-ID: 462819 [Multi-domain]  Cd Length: 427  Bit Score: 47.12  E-value: 1.62e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  484 PPSSKK--SDGSGTYSRLQNTQVRVMSEKKPRK----KAESESKQEKANRIISEAIARAKERGERNIPRVMSPENFPSSS 557
Cdd:pfam09507  203 APSLKRspSAKSNIMSAFFKAKPKNKKKKTSASeqkvQEESAEESGKEDVTLEDDSAAEEEEDEQLPTKKDKRRQKRGES 282
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  558 VDGKEEKRAQRvksKPKDRDNRKPKACSKLKEKTKIgklIITLGKNHKRRSESSDELSDAEQMPQHTFKEQHSQKRRSNR 637
Cdd:pfam09507  283 SDSEESTRESR---KEKRERLKKMMEDDSDDDEMED---VPESPVATEEEETGSPPPLLKKEVEKEEVTESGDGRRRKRR 356
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 1958747478  638 QVKRKKYAEDAEGRQCEEEVRGS---------LKVKRTSAPPPGEQP 675
Cdd:pfam09507  357 KVMKKKTFKDEEGYMVTEKVYEWesfsededePPVKPKPAVSTPASP 403
HDA2-3 pfam11496
Class II histone deacetylase complex subunits 2 and 3; This family of class II histone ...
1139-1312 2.21e-04

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: 45.78  E-value: 2.21e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1139 LRKCC---NHPYLIKgaeekiigefrDTYNPSASDF-----HLqamIQSAGKLV----LIDKLLPKMKAGGHKVLIFSQM 1206
Cdd:pfam11496   54 LENLSlvaTHPYLLV-----------DHYMPKSLLLkdepeKL---AYTSGKFLvlndLVNLLIERDRKEPINVAIVARS 119
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478 1207 VRCLDILEDYLIHKRYLYERIDG-RVRGNLRQAAIDRFSKPDSDRFVFL----LCTRAGGLGINlTAADTCIIFDSDWNP 1281
Cdd:pfam11496  120 GKTLDLVEALLLGKGLSYKRYSGeMLYGENKKVSDSGNKKIHSTTCHLLsstgQLTNDDSLLEN-YKFDLIIAFDSSVDT 198
                          170       180       190
                   ....*....|....*....|....*....|.
gi 1958747478 1282 QNDLQAQARCHRIGQNKAVKVYRLVTRNSYE 1312
Cdd:pfam11496  199 SSPSVEHLRTQNRRKGNLAPIIRLVVINSIE 229
chromodomain cd18966
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
773-816 5.02e-04

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: 39.96  E-value: 5.02e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1958747478  773 EVDRILevsfCEDKDTGEsvVYYLVKWCSLPYEDSTWELKEDVD 816
Cdd:cd18966      2 EVERIL----AERRDDGG--KRYLVKWEGYPLEEATWEPEENIG 39
CD1_tandem_CHD1-2_like cd18666
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ...
713-749 7.81e-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: 40.74  E-value: 7.81e-04
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1958747478  713 EEFFVKYKNYSYLHCEWATEQQLLkdkriQQKIKRFK 749
Cdd:cd18666     47 IQYLIKWKGWSHIHNTWESEESLK-----DQNVKGMK 78
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
1248-1300 1.14e-03

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


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 39.99  E-value: 1.14e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958747478 1248 SDRFVFLLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQNKAV 1300
Cdd:cd18785     20 ASSLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGGKDEGE 72
CD2_tandem_ScCHD1_like cd18664
repeat 2 of the paired tandem chromodomains of yeast chromodomain helicase DNA-binding protein ...
770-815 1.73e-03

repeat 2 of the paired tandem chromodomains of yeast chromodomain helicase DNA-binding protein 1, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as 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: 349311  Cd Length: 59  Bit Score: 38.79  E-value: 1.73e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1958747478  770 DYVEVDRILEVSFCEDKDtGESVVYYLVKWCSLPYEDSTWELKEDV 815
Cdd:cd18664      1 EFHVVERIIASQRASLED-GTSQLQYLVKWRRLNYDECTWEDATLI 45
KLF3_N cd21577
N-terminal domain of Kruppel-like factor 3; Kruppel-like factor 3 (KLF3; also called ...
217-375 2.35e-03

N-terminal domain of Kruppel-like factor 3; Kruppel-like factor 3 (KLF3; also called Krueppel-like factor 3 and originally called Basic Kruppel-like Factor/BKLF), was the third member of the KLF family of zinc finger transcription factors to be discovered. KLF3 possesses a wide range of biological impacts on regulating apoptosis, differentiation, and proliferation in various tissues during the entire progression process. It has been proposed as a tumor suppressor in colorectal cancer. It appears to function predominantly as a repressor of transcription, turning genes off by recruiting the C-terminal Binding Protein co-repressors CtBP1 and CtBP2. CtBP docks onto a short motif (residues 61-65) in the N-terminus of KLF3, through the Proline-X-Aspartate-Leucine-Serine (PXDLS) motif. CtBP in turn recruits histone modifying enzymes to alter chromatin and repress gene expression. KLF3 belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF3.


Pssm-ID: 410554 [Multi-domain]  Cd Length: 214  Bit Score: 41.95  E-value: 2.35e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  217 SAPSSQQTLPVQFSPTANPPAHFLKCSSQQDGSYNRPSPSMTSCSVSNSQPFPAHYSFSSGHVSPSSLLQSPAGLTPSHS 296
Cdd:cd21577     37 SSSSSSSSSSSSPSSRASPPSPYSKSSPPSPPQQRPLSPPLSLPPPVAPPPLSPGSVPGGLPVISPVMVQPVPVLYPPHL 116
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  297 NQALsdfagSNSFSPHRGMKQEPTPHILNPTPSLNSNNFQIL-------HSSHPQGNYSNSKLSPMhMdfpdpadSGPPM 369
Cdd:cd21577    117 HQPI-----MVSSSPPPDDDHHHHKASSMKPSELGGDNHELHkpiktepRPEHAQDPYSEEMSSSV-I-------SSPPE 183

                   ....*.
gi 1958747478  370 GHFNDH 375
Cdd:cd21577    184 YESNTP 189
CD3_cpSRP43_like cd18628
chromodomain 3 of chloroplast signal recognition particle 43 kDa protein, and similar proteins; ...
770-824 2.71e-03

chromodomain 3 of chloroplast signal recognition particle 43 kDa protein, and similar proteins; This subgroup includes the chromodomain 3 of chloroplast SRP43 (cpSRP43), and similar proteins. CpSRP43 is a component of the chloroplast signal recognition particle (SRP) pathway. It forms a stable complex with cpSRP54 (cpSRP complex) which is required for the efficient posttranslational transport of members of the nuclearly encoded light harvesting chlorophyll-a/b-binding proteins (LHCPs) to the thylakoid membrane. Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromodomain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followed by a related chromo shadow domain.


Pssm-ID: 349278  Cd Length: 51  Bit Score: 38.13  E-value: 2.71e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1958747478  770 DYVEVDRILEVSFCEDKDTGEsvvyYLVKWcsLPYEDSTWELKEDVDLAKIEEFE 824
Cdd:cd18628      2 EYAVAESVIGKRVGDDGKTIE----YLVKW--TDMSDATWEPQDNVDSTLVLLYQ 50
chromodomain cd18964
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
784-825 2.94e-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: 38.08  E-value: 2.94e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1958747478  784 EDKDTGESVVYYLVKWCSLPYEDSTWELKEDV-DLAK-IEEFEQ 825
Cdd:cd18964     11 PSARDGPGKFLWLVKWDGYPIEDATWEPPENLgEHAKlIEDFEK 54
CD_CMT3_like cd18635
chromodomain of chromomethylase 3, and similar proteins; CHRomatin Organization Modifier ...
773-823 3.01e-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: 38.06  E-value: 3.01e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958747478  773 EVDRILEVSFCEDKDTGESVVYYLVKWCSLPYEDSTWELKEDVD--LAKIEEF 823
Cdd:cd18635      3 EVEKLVGICYGDPKKTGERGLYFKVRWKGYGPEEDTWEPIEGLSncPEKIKEF 55
CD_SUV39H1_like cd18639
chromodomain of histone methyltransferase SUV39H1, and similar proteins; CHRomatin ...
779-820 5.21e-03

chromodomain of histone methyltransferase SUV39H1, and similar proteins; CHRomatin Organization Modifier (chromo) domain of human SUV39H1, a histone lysine methyltransferase (HMT) which catalyzes di- and tri-methylation of lysine 9 of histone H3 (H3K9me2/3), leading to heterochromatin formation and gene silencing. H3K9me2/3 represents a specific mark for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3, and/or CBX5) proteins to methylated histones. SUV39H1 mainly functions in heterochromatin regions. The human SUV39H1/2, histone H3K9 methyltransferases, are the mammalian homologs of Drosophila Su(var)3-9 and Schizosaccharomyces pombe Clr4. SUV39H1 contains a chromodomain at its N-terminus and a SET domain at its C-terminus. Although the SET domain performs the catalytic activity, the chromodomain of SUV39H1 is essential for the catalytic activity of SUV39H1. 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: 349289  Cd Length: 49  Bit Score: 37.11  E-value: 5.21e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1958747478  779 EVSFCEDKDTGESVVYYLVKWCSLPYEDSTWELKEDVDLAKI 820
Cdd:cd18639      2 EVEYLCDYKKIREQEYYLVKWKGYPDSENTWEPRQNLKCSRL 43
ROM1 COG5422
RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction ...
203-363 5.23e-03

RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms];


Pssm-ID: 227709 [Multi-domain]  Cd Length: 1175  Bit Score: 42.57  E-value: 5.23e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  203 NVSGAHRVNVNHLTSAPSSQQTLpvQFSPTANPPAHFLKCSSQQDGSYNRPSPSMTSCSVSNSQP---FPAHYSFSSGHV 279
Cdd:COG5422     65 KYALGHQIFSSFSSSPKLFQRRN--SAGPITHSPSATSSTSSLNSNDGDQFSPASDSLSFNPSSTqsrKDSGPGDGSPVQ 142
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  280 SPSSLLQSPAGLTPSHSNQALSDFAGSNSFSPHRGMKQEpTPHILNPTPSLNSNNFQILHSSHPQGN---YSNSKLSPMH 356
Cdd:COG5422    143 KRKNPLLPSSSTHGTHPPIVFTDNNGSHAGAPNARSRKE-IPSLGSQSMQLPSPHFRQKFSSSDTSNgfsYPSIRKNSRH 221

                   ....*..
gi 1958747478  357 MDFPDPA 363
Cdd:COG5422    222 SSNSMPS 228
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
860-1035 7.69e-03

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 39.92  E-value: 7.69e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  860 REYQLEGLNWLLfnwyNRRNCILADEMGLGKTIQSITFLYEVLLTGIRGP-FLIIAPLSTIAN-WEREFRTW---TDINV 934
Cdd:pfam00270    1 TPIQAEAIPAIL----EGRDVLVQAPTGSGKTLAFLLPALEALDKLDNGPqALVLAPTRELAEqIYEELKKLgkgLGLKV 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747478  935 V-VYHGSLISRQMiqqyemyfrdsqgRIIRGAyrfQAIITTFEMI---LGGCGELNAIewRCVIIDEAHRLKNKN--CKL 1008
Cdd:pfam00270   77 AsLLGGDSRKEQL-------------EKLKGP---DILVGTPGRLldlLQERKLLKNL--KLLVLDEAHRLLDMGfgPDL 138
                          170       180
                   ....*....|....*....|....*...
gi 1958747478 1009 LEGLKLMNLEHK-VLLTGTPLQNtVEEL 1035
Cdd:pfam00270  139 EEILRRLPKKRQiLLLSATLPRN-LEDL 165
 
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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