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Conserved domains on  [gi|545493356|ref|XP_005618381|]
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Protein Classification

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List of domain hits

Name Accession Description Interval E-value
DEXHc_CHD2 cd18054
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; ...
477-713 0e+00

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: 547.30  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  477 RPRFVALKKQPTYLGGENLELRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLS 556
Cdd:cd18054     1 RPRFVALKKQPSYIGGENLELRDYQLEGLNWLAHSWCKNNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLLVVPLS 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  557 TLTSWQREFEIWAPEINVVVYIGDLMSRNTIREYEWIHSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLK 636
Cdd:cd18054    81 TLTSWQREFEIWAPEINVVVYIGDLMSRNTIREYEWIHSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLK 160
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 545493356  637 NDDSLLYKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGRENGYQSLHKVLEPFLLRR 713
Cdd:cd18054   161 NDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGRENGYQSLHKVLEPFLLRR 237
PLN03142 super family cl33647
Probable chromatin-remodeling complex ATPase chain; Provisional
481-1034 1.21e-168

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: 540.54  E-value: 1.21e-168
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  481 VALKKQPTYLGGEnleLRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTS 560
Cdd:PLN03142  157 TRLLVQPSCIKGK---MRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPKSTLGN 233
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  561 WQREFEIWAPEINVVVYIGDLMSRNTIREYewihsQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDS 640
Cdd:PLN03142  234 WMNEIRRFCPVLRAVKFHGNPEERAHQREE-----LLVAGKFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNENS 308
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  641 LLYKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGRENG----YQSLHKVLEPFLLRRVKK 716
Cdd:PLN03142  309 LLSKTMRLFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDqqevVQQLHKVLRPFLLRRLKS 388
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  717 DVEKSLPAKVEQILRVEMSALQKQYYKWILTRNYKALAKGtrGSTSGFLNIVMELKKCCNHCYLIKPPEENERENGQEvl 796
Cdd:PLN03142  389 DVEKGLPPKKETILKVGMSQMQKQYYKALLQKDLDVVNAG--GERKRLLNIAMQLRKCCNHPYLFQGAEPGPPYTTGE-- 464
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  797 lSLIRSSGKLILLDKLLTRLRERGNRVLIFSQMVRMLDILAEYLTIKHYPFQRLDGSIKGEIRKQALDHFNADGSEDFCF 876
Cdd:PLN03142  465 -HLVENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVF 543
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  877 LLSTRAGGLGINLASADTVVIFDSDWNPQNDLQAQARAHRIGQKKQVNIYRLVTKGTVEEEIIERAKKKMVLDHLVIQRm 956
Cdd:PLN03142  544 LLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVIQQ- 622
                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 545493356  957 dttGRtVLENNSgrsnsnpFNKEELTAILKFGAEDLFkelEGEESEPQEMDIDEILrlaetRENEVSTSATDELLSQF 1034
Cdd:PLN03142  623 ---GR-LAEQKT-------VNKDELLQMVRYGAEMVF---SSKDSTITDEDIDRII-----AKGEEATAELDAKMKKF 681
CD1_tandem_CHD1-2_like cd18666
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ...
272-356 4.30e-47

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: 163.23  E-value: 4.30e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  272 NSETIEKVLDSRLGKKGATGASTTVYAIEANGDPSGDFDTEKDESEVQYLIKWKGWSYIHSTWESEESLQQQKVKGLKKL 351
Cdd:cd18666     1 EFETIERVLDHRIGRKGATGASTTIYAVEADGDPNAGFDPEDEETEIQYLIKWKGWSHIHNTWESEESLKDQNVKGMKKL 80

                  ....*
gi 545493356  352 ENFKK 356
Cdd:cd18666    81 ENYKK 85
CDH1_2_SANT_HL1 pfam18375
CDH1/2 SANT-Helical linker 1; CDH1 is an ATP-dependent chromatin-remodelling factor and plays ...
1143-1231 1.78e-37

CDH1/2 SANT-Helical linker 1; CDH1 is an ATP-dependent chromatin-remodelling factor and plays an important role in regulating nucleosome assembly and mobilization. CHD1 consists of double chromodomain, SNF2-related ATPase domain, and a C-terminal DNA-binding domain. The DNA-binding domain contains SANT (Swi3, Ada2, N-CoR, TFIIIB) and SLIDE (SANT-like ISWI) domains in its C-terminal region. SANT domains are structurally related to Myb-like domains are common motifs found in chromatin interacting proteins. Deletion of individual SANT or SLIDE domains in CDH1 does not significantly affect nucleosome binding, but combined deletion of both domains severely compromise binding, suggesting that the SANT-SLIDE motif recognizes DNA/nucleosomes as a single cooperative unit. SANT sequences of Chd1 proteins are the most distantly relation group of sequences relation to other SANT/Myb sequences, and are more diverse than other SANT proteins. The SANT and SLIDE regions are well conserved in both Chd1 and ISWI (imitation switch) remodelling enzymes. This domain comprises the SANT region and the helical linker region 1 (HL1).


:

Pssm-ID: 408175  Cd Length: 90  Bit Score: 135.92  E-value: 1.78e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  1143 GFTDAEIRRFIKAYKKFGLPLERLECIARDAELVDKSVADLKRLGELIHNSCVSAMQEYEEQLKENasEGKGPGKK--RG 1220
Cdd:pfam18375    2 GFTDAEIRRFVKSYKKFPAPLKRLDAIACDAELQEKPLSDLKRLGELLHERCEEAMEEYEEKEDEN--PGADGGKKriRG 79
                           90
                   ....*....|.
gi 545493356  1221 PTIKISGVQVN 1231
Cdd:pfam18375   80 PTFKLGGVSVN 90
CD2_tandem_CHD1-2_like cd18661
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ...
389-460 2.50e-30

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


:

Pssm-ID: 349308  Cd Length: 58  Bit Score: 114.32  E-value: 2.50e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 545493356  389 QYQIVERVIAVKTSKStlgqtdfpahsrkpAPSNEPEYLCKWMGLPYSECSWEDEALIGKKFQSCIDSFHSR 460
Cdd:cd18661     1 QYQIVERIIAHSPQKS--------------AASGYPDYLCKWQGLPYSECTWEDGALISKKFQACIDEYHSR 58
DUF4208 pfam13907
Domain of unknown function (DUF4208); This domain is found at the C-terminus of ...
1437-1519 1.58e-29

Domain of unknown function (DUF4208); This domain is found at the C-terminus of chromodomain-helicase-DNA-binding proteins. The exact function of the domain is undetermined.


:

Pssm-ID: 404744  Cd Length: 93  Bit Score: 113.46  E-value: 1.58e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  1437 ICKERMRPVKKALKQLDKPDKGLNVQEQLEHTRNCLLKIGDRIAECLKAYSDqEHIKLWRRNLWIFVSKFTE--FDARKL 1514
Cdd:pfam13907   10 ECKELMRPVKKSLKRLKKGTKGLSRKERAKILKKELLKIGDFIDSILKEYKD-EKIEKLRKHLWSFVSKFWPnkVSGKKL 88

                   ....*
gi 545493356  1515 HKLYK 1519
Cdd:pfam13907   89 REMYK 93
 
Name Accession Description Interval E-value
DEXHc_CHD2 cd18054
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; ...
477-713 0e+00

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: 547.30  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  477 RPRFVALKKQPTYLGGENLELRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLS 556
Cdd:cd18054     1 RPRFVALKKQPSYIGGENLELRDYQLEGLNWLAHSWCKNNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLLVVPLS 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  557 TLTSWQREFEIWAPEINVVVYIGDLMSRNTIREYEWIHSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLK 636
Cdd:cd18054    81 TLTSWQREFEIWAPEINVVVYIGDLMSRNTIREYEWIHSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLK 160
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 545493356  637 NDDSLLYKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGRENGYQSLHKVLEPFLLRR 713
Cdd:cd18054   161 NDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGRENGYQSLHKVLEPFLLRR 237
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
481-1034 1.21e-168

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 540.54  E-value: 1.21e-168
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  481 VALKKQPTYLGGEnleLRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTS 560
Cdd:PLN03142  157 TRLLVQPSCIKGK---MRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPKSTLGN 233
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  561 WQREFEIWAPEINVVVYIGDLMSRNTIREYewihsQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDS 640
Cdd:PLN03142  234 WMNEIRRFCPVLRAVKFHGNPEERAHQREE-----LLVAGKFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNENS 308
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  641 LLYKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGRENG----YQSLHKVLEPFLLRRVKK 716
Cdd:PLN03142  309 LLSKTMRLFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDqqevVQQLHKVLRPFLLRRLKS 388
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  717 DVEKSLPAKVEQILRVEMSALQKQYYKWILTRNYKALAKGtrGSTSGFLNIVMELKKCCNHCYLIKPPEENERENGQEvl 796
Cdd:PLN03142  389 DVEKGLPPKKETILKVGMSQMQKQYYKALLQKDLDVVNAG--GERKRLLNIAMQLRKCCNHPYLFQGAEPGPPYTTGE-- 464
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  797 lSLIRSSGKLILLDKLLTRLRERGNRVLIFSQMVRMLDILAEYLTIKHYPFQRLDGSIKGEIRKQALDHFNADGSEDFCF 876
Cdd:PLN03142  465 -HLVENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVF 543
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  877 LLSTRAGGLGINLASADTVVIFDSDWNPQNDLQAQARAHRIGQKKQVNIYRLVTKGTVEEEIIERAKKKMVLDHLVIQRm 956
Cdd:PLN03142  544 LLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVIQQ- 622
                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 545493356  957 dttGRtVLENNSgrsnsnpFNKEELTAILKFGAEDLFkelEGEESEPQEMDIDEILrlaetRENEVSTSATDELLSQF 1034
Cdd:PLN03142  623 ---GR-LAEQKT-------VNKDELLQMVRYGAEMVF---SSKDSTITDEDIDRII-----AKGEEATAELDAKMKKF 681
SNF2_N pfam00176
SNF2 family N-terminal domain; This domain is found in proteins involved in a variety of ...
500-781 1.01e-105

SNF2 family N-terminal 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).


Pssm-ID: 395124 [Multi-domain]  Cd Length: 305  Bit Score: 340.13  E-value: 1.01e-105
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356   500 YQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFL---SYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVVV 576
Cdd:pfam00176    1 YQIEGVNWMPELYQNGRGGILADEMGLGKTLQTISLLltlKYLYHIKKLAGPTLIVVPLSLLDNWMNEFERWVPSLRLVV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356   577 YIGDLMSRntiREYEWIHSQTKRL-KFNALITTYEILLKDK---TVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFKSH 652
Cdd:pfam00176   81 LVGDGGSR---MDKMNVRLLPKVLaDYDVVITTYETLRRDKkfrSLLKKLKWHRVILDEGHRLKNSKSKLSEALSKLRTR 157
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356   653 HRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFE-----EDHGKGRENGYQSLHKVLEPFLLRRVKKDVEKSLPAKVE 727
Cdd:pfam00176  158 NRWILTGTPIQNNLEELWALLNFLRPGPFGSLQTFDkwfvrPIEREGGEKGVARLHKLLKPFLLRRTKKDVEKSLPPKVE 237
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 545493356   728 QILRVEMSALQKQYYK------------WILTRNYKALAKGTRG--STSGFLNIVMELKKCCNHCYLI 781
Cdd:pfam00176  238 EILFCRLSKGQRKLYQtalqalrgngilKLLIRNRAATKFSSKSfrGKPGLLNILLRLRKICNHPDLF 305
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and ...
496-970 9.16e-105

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


Pssm-ID: 223627 [Multi-domain]  Cd Length: 866  Bit Score: 357.12  E-value: 9.16e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  496 ELRDYQLEGLNWLAHS-WCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLY-GPFLIVVPLSTLTSWQREFEIWAPEIN 573
Cdd:COG0553   338 ELRPYQLEGVNWLSELlRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYlGPALIVVPASLLSNWKREFEKFAPDLR 417
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  574 VVVyIGDLMSRNTIREYEWIH---SQTKRLKFNALITTYEIL---LKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLI 647
Cdd:COG0553   418 LVL-VYHGEKSELDKKREALRdllKLHLVIIFDVVITTYELLrrfLVDHGGLKKIEWDRVVLDEAHRIKNDQSSEGKALQ 496
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  648 DFKSHHRLLITGTPLQNSLKELWSLL-HFIMPEKF-----EFWEDFEE--------DHGKGRENGYQSLHKVLEPFLLRR 713
Cdd:COG0553   497 FLKALNRLDLTGTPLENRLGELWSLLqEFLNPGLLgtsfaIFTRLFEKpiqaeediGPLEARELGIELLRKLLSPFILRR 576
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  714 VKKDVE--KSLPAKVEQILRVEMSALQKQYYKWILTRNYKALAKGTRGSTSG------------FLNIVMELKKCCNHCY 779
Cdd:COG0553   577 TKEDVEvlKELPPKIEKVLECELSEEQRELYEALLEGAEKNQQLLEDLEKADsdenrigdselnILALLTRLRQICNHPA 656
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  780 LIKPPEENERENGQEVLLSLI-----------RSSGKLILLDKLL-TRLRERGN--RVLIFSQMVRMLDILAEYLTIKHY 845
Cdd:COG0553   657 LVDEGLEATFDRIVLLLREDKdfdylkkpliqLSKGKLQALDELLlDKLLEEGHyhKVLIFSQFTPVLDLLEDYLKALGI 736
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  846 PFQRLDGSIKGEIRKQALDHFNADGSEdFCFLLSTRAGGLGINLASADTVVIFDSDWNPQNDLQAQARAHRIGQKKQVNI 925
Cdd:COG0553   737 KYVRLDGSTPAKRRQELIDRFNADEEE-KVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQKRPVKV 815
                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*
gi 545493356  926 YRLVTKGTVEEEIIERAKKKMVLDHLVIQRMDTTGRTVLENNSGR 970
Cdd:COG0553   816 YRLITRGTIEEKILELQEKKQELLDSLIDAEGEKELSKLSIEDLL 860
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
803-929 1.39e-57

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: 195.00  E-value: 1.39e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  803 SGKLILLDKLLTRLRERGNRVLIFSQMVRMLDILAEYLTIKHYPFQRLDGSIKGEIRKQALDHFNADgSEDFCFLLSTRA 882
Cdd:cd18793    10 SGKLEALLELLEELREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNED-PDIRVFLLSTKA 88
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 545493356  883 GGLGINLASADTVVIFDSDWNPQNDLQAQARAHRIGQKKQVNIYRLV 929
Cdd:cd18793    89 GGVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQKKPVVVYRLI 135
CD1_tandem_CHD1-2_like cd18666
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ...
272-356 4.30e-47

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: 163.23  E-value: 4.30e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  272 NSETIEKVLDSRLGKKGATGASTTVYAIEANGDPSGDFDTEKDESEVQYLIKWKGWSYIHSTWESEESLQQQKVKGLKKL 351
Cdd:cd18666     1 EFETIERVLDHRIGRKGATGASTTIYAVEADGDPNAGFDPEDEETEIQYLIKWKGWSHIHNTWESEESLKDQNVKGMKKL 80

                  ....*
gi 545493356  352 ENFKK 356
Cdd:cd18666    81 ENYKK 85
CDH1_2_SANT_HL1 pfam18375
CDH1/2 SANT-Helical linker 1; CDH1 is an ATP-dependent chromatin-remodelling factor and plays ...
1143-1231 1.78e-37

CDH1/2 SANT-Helical linker 1; CDH1 is an ATP-dependent chromatin-remodelling factor and plays an important role in regulating nucleosome assembly and mobilization. CHD1 consists of double chromodomain, SNF2-related ATPase domain, and a C-terminal DNA-binding domain. The DNA-binding domain contains SANT (Swi3, Ada2, N-CoR, TFIIIB) and SLIDE (SANT-like ISWI) domains in its C-terminal region. SANT domains are structurally related to Myb-like domains are common motifs found in chromatin interacting proteins. Deletion of individual SANT or SLIDE domains in CDH1 does not significantly affect nucleosome binding, but combined deletion of both domains severely compromise binding, suggesting that the SANT-SLIDE motif recognizes DNA/nucleosomes as a single cooperative unit. SANT sequences of Chd1 proteins are the most distantly relation group of sequences relation to other SANT/Myb sequences, and are more diverse than other SANT proteins. The SANT and SLIDE regions are well conserved in both Chd1 and ISWI (imitation switch) remodelling enzymes. This domain comprises the SANT region and the helical linker region 1 (HL1).


Pssm-ID: 408175  Cd Length: 90  Bit Score: 135.92  E-value: 1.78e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  1143 GFTDAEIRRFIKAYKKFGLPLERLECIARDAELVDKSVADLKRLGELIHNSCVSAMQEYEEQLKENasEGKGPGKK--RG 1220
Cdd:pfam18375    2 GFTDAEIRRFVKSYKKFPAPLKRLDAIACDAELQEKPLSDLKRLGELLHERCEEAMEEYEEKEDEN--PGADGGKKriRG 79
                           90
                   ....*....|.
gi 545493356  1221 PTIKISGVQVN 1231
Cdd:pfam18375   80 PTFKLGGVSVN 90
CD2_tandem_CHD1-2_like cd18661
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ...
389-460 2.50e-30

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


Pssm-ID: 349308  Cd Length: 58  Bit Score: 114.32  E-value: 2.50e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 545493356  389 QYQIVERVIAVKTSKStlgqtdfpahsrkpAPSNEPEYLCKWMGLPYSECSWEDEALIGKKFQSCIDSFHSR 460
Cdd:cd18661     1 QYQIVERIIAHSPQKS--------------AASGYPDYLCKWQGLPYSECTWEDGALISKKFQACIDEYHSR 58
DEXDc smart00487
DEAD-like helicases superfamily;
495-680 3.65e-30

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 119.13  E-value: 3.65e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356    495 LELRDYQLEGLNWLAHSWcksNSVILADEMGLGKTIQTISFLSYLFHQHQlYGPFLIVVPLSTLT-SWQREFEIWAPE-- 571
Cdd:smart00487    7 EPLRPYQKEAIEALLSGL---RDVILAAPTGSGKTLAALLPALEALKRGK-GGRVLVLVPTRELAeQWAEELKKLGPSlg 82
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356    572 INVVVYIGDLMSRNTIREYewihsqtKRLKFNALITTYEILLKD--KTVLGSINWAFLGVDEAHRLKND---DSLLYKTL 646
Cdd:smart00487   83 LKVVGLYGGDSKREQLRKL-------ESGKTDILVTTPGRLLDLleNDKLSLSNVDLVILDEAHRLLDGgfgDQLEKLLK 155
                           170       180       190
                    ....*....|....*....|....*....|....*..
gi 545493356    647 IDFKSHHRLLITGTP---LQNSLKELWSLLHFIMPEK 680
Cdd:smart00487  156 LLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGF 192
DUF4208 pfam13907
Domain of unknown function (DUF4208); This domain is found at the C-terminus of ...
1437-1519 1.58e-29

Domain of unknown function (DUF4208); This domain is found at the C-terminus of chromodomain-helicase-DNA-binding proteins. The exact function of the domain is undetermined.


Pssm-ID: 404744  Cd Length: 93  Bit Score: 113.46  E-value: 1.58e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  1437 ICKERMRPVKKALKQLDKPDKGLNVQEQLEHTRNCLLKIGDRIAECLKAYSDqEHIKLWRRNLWIFVSKFTE--FDARKL 1514
Cdd:pfam13907   10 ECKELMRPVKKSLKRLKKGTKGLSRKERAKILKKELLKIGDFIDSILKEYKD-EKIEKLRKHLWSFVSKFWPnkVSGKKL 88

                   ....*
gi 545493356  1515 HKLYK 1519
Cdd:pfam13907   89 REMYK 93
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
804-918 5.87e-28

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: 395209 [Multi-domain]  Cd Length: 109  Bit Score: 109.61  E-value: 5.87e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356   804 GKLILLDKLLTRlrERGNRVLIFSQMVRMLDilAEYLTIKH-YPFQRLDGSIKGEIRKQALDHFNadgSEDFCFLLSTRA 882
Cdd:pfam00271    1 EKLEALLELLKK--ERGGKVLIFSQTKKTLE--AELLLEKEgIKVARLHGDLSQEEREEILEDFR---KGKIDVLVATDV 73
                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 545493356   883 GGLGINLASADTVVIFDSDWNPQNDLQAQARAHRIG 918
Cdd:pfam00271   74 AERGLDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
HELICc smart00490
helicase superfamily c-terminal domain;
834-918 3.42e-22

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 91.89  E-value: 3.42e-22
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356    834 DILAEYLTIKHYPFQRLDGSIKGEIRKQALDHFNADgseDFCFLLSTRAGGLGINLASADTVVIFDSDWNPQNDLQAQAR 913
Cdd:smart00490    1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNG---KIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGR 77

                    ....*
gi 545493356    914 AHRIG 918
Cdd:smart00490   78 AGRAG 82
Chromo pfam00385
Chromo (CHRromatin Organisation MOdifier) domain;
392-460 9.17e-10

Chromo (CHRromatin Organisation MOdifier) domain;


Pssm-ID: 395309 [Multi-domain]  Cd Length: 52  Bit Score: 55.67  E-value: 9.17e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 545493356   392 IVERVIAVKTSKSTLGqtdfpahsrkpapsnepEYLCKWMGLPYSECSWEDEALIgKKFQSCIDSFHSR 460
Cdd:pfam00385    2 EVERILDHRKDKGGKE-----------------EYLVKWKGYPYDENTWEPEENL-SKCPELIEEFEDR 52
CHROMO smart00298
Chromatin organization modifier domain;
313-359 5.22e-09

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 53.76  E-value: 5.22e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 545493356    313 KDESEVQYLIKWKGWSYIHSTWESEESLQQqkvkGLKKLENFKKKED 359
Cdd:smart00298   13 KKKGELEYLVKWKGYSYSEDTWEPEENLLN----CSKKLDNYKKKER 55
Chromo pfam00385
Chromo (CHRromatin Organisation MOdifier) domain;
313-357 4.47e-07

Chromo (CHRromatin Organisation MOdifier) domain;


Pssm-ID: 395309 [Multi-domain]  Cd Length: 52  Bit Score: 47.96  E-value: 4.47e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 545493356   313 KDESEVQYLIKWKGWSYIHSTWESEESLQQQKvkglKKLENFKKK 357
Cdd:pfam00385   12 DKGGKEEYLVKWKGYPYDENTWEPEENLSKCP----ELIEEFEDR 52
CHROMO smart00298
Chromatin organization modifier domain;
393-462 1.69e-06

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 46.44  E-value: 1.69e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356    393 VERVIAVKTSKStlgqtdfpahsrkpapsNEPEYLCKWMGLPYSECSWEDEALIgKKFQSCIDSFHSRNN 462
Cdd:smart00298    4 VEKILDHRWKKK-----------------GELEYLVKWKGYSYSEDTWEPEENL-LNCSKKLDNYKKKER 55
 
Name Accession Description Interval E-value
DEXHc_CHD2 cd18054
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; ...
477-713 0e+00

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: 547.30  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  477 RPRFVALKKQPTYLGGENLELRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLS 556
Cdd:cd18054     1 RPRFVALKKQPSYIGGENLELRDYQLEGLNWLAHSWCKNNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLLVVPLS 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  557 TLTSWQREFEIWAPEINVVVYIGDLMSRNTIREYEWIHSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLK 636
Cdd:cd18054    81 TLTSWQREFEIWAPEINVVVYIGDLMSRNTIREYEWIHSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLK 160
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 545493356  637 NDDSLLYKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGRENGYQSLHKVLEPFLLRR 713
Cdd:cd18054   161 NDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGRENGYQSLHKVLEPFLLRR 237
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
481-1034 1.21e-168

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 540.54  E-value: 1.21e-168
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  481 VALKKQPTYLGGEnleLRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTS 560
Cdd:PLN03142  157 TRLLVQPSCIKGK---MRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPKSTLGN 233
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  561 WQREFEIWAPEINVVVYIGDLMSRNTIREYewihsQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDS 640
Cdd:PLN03142  234 WMNEIRRFCPVLRAVKFHGNPEERAHQREE-----LLVAGKFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNENS 308
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  641 LLYKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGRENG----YQSLHKVLEPFLLRRVKK 716
Cdd:PLN03142  309 LLSKTMRLFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDqqevVQQLHKVLRPFLLRRLKS 388
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  717 DVEKSLPAKVEQILRVEMSALQKQYYKWILTRNYKALAKGtrGSTSGFLNIVMELKKCCNHCYLIKPPEENERENGQEvl 796
Cdd:PLN03142  389 DVEKGLPPKKETILKVGMSQMQKQYYKALLQKDLDVVNAG--GERKRLLNIAMQLRKCCNHPYLFQGAEPGPPYTTGE-- 464
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  797 lSLIRSSGKLILLDKLLTRLRERGNRVLIFSQMVRMLDILAEYLTIKHYPFQRLDGSIKGEIRKQALDHFNADGSEDFCF 876
Cdd:PLN03142  465 -HLVENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVF 543
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  877 LLSTRAGGLGINLASADTVVIFDSDWNPQNDLQAQARAHRIGQKKQVNIYRLVTKGTVEEEIIERAKKKMVLDHLVIQRm 956
Cdd:PLN03142  544 LLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVIQQ- 622
                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 545493356  957 dttGRtVLENNSgrsnsnpFNKEELTAILKFGAEDLFkelEGEESEPQEMDIDEILrlaetRENEVSTSATDELLSQF 1034
Cdd:PLN03142  623 ---GR-LAEQKT-------VNKDELLQMVRYGAEMVF---SSKDSTITDEDIDRII-----AKGEEATAELDAKMKKF 681
DEXHc_CHD1_2 cd17993
DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and ...
496-713 2.70e-152

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: 465.68  E-value: 2.70e-152
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  496 ELRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVV 575
Cdd:cd17993     1 ELRDYQLTGLNWLAHSWCKGNNGILADEMGLGKTVQTISFLSYLFHSQQQYGPFLVVVPLSTMPAWQREFAKWAPDMNVI 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  576 VYIGDLMSRNTIREYEWIHSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFKSHHRL 655
Cdd:cd17993    81 VYLGDIKSRDTIREYEFYFSQTKKLKFNVLLTTYEIILKDKAFLGSIKWQYLAVDEAHRLKNDESLLYEALKEFKTNNRL 160
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 545493356  656 LITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGRENGYQSLHKVLEPFLLRR 713
Cdd:cd17993   161 LITGTPLQNSLKELWALLHFLMPGKFDIWEEFEEEHDEEQEKGIADLHKELEPFILRR 218
DEXHc_CHD1 cd18053
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; ...
478-713 1.15e-135

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: 421.00  E-value: 1.15e-135
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  478 PRFVALKKQPTYLGG-ENLELRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLS 556
Cdd:cd18053     1 PRFVALKKQPSYIGGhEGLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLS 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  557 TLTSWQREFEIWAPEINVVVYIGDLMSRNTIREYEWIHSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLK 636
Cdd:cd18053    81 TLTSWQREIQTWAPQMNAVVYLGDINSRNMIRTHEWMHPQTKRLKFNILLTTYEILLKDKSFLGGLNWAFIGVDEAHRLK 160
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 545493356  637 NDDSLLYKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGRENGYQSLHKVLEPFLLRR 713
Cdd:cd18053   161 NDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYGYASLHKELEPFLLRR 237
SNF2_N pfam00176
SNF2 family N-terminal domain; This domain is found in proteins involved in a variety of ...
500-781 1.01e-105

SNF2 family N-terminal 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).


Pssm-ID: 395124 [Multi-domain]  Cd Length: 305  Bit Score: 340.13  E-value: 1.01e-105
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356   500 YQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFL---SYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVVV 576
Cdd:pfam00176    1 YQIEGVNWMPELYQNGRGGILADEMGLGKTLQTISLLltlKYLYHIKKLAGPTLIVVPLSLLDNWMNEFERWVPSLRLVV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356   577 YIGDLMSRntiREYEWIHSQTKRL-KFNALITTYEILLKDK---TVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFKSH 652
Cdd:pfam00176   81 LVGDGGSR---MDKMNVRLLPKVLaDYDVVITTYETLRRDKkfrSLLKKLKWHRVILDEGHRLKNSKSKLSEALSKLRTR 157
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356   653 HRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFE-----EDHGKGRENGYQSLHKVLEPFLLRRVKKDVEKSLPAKVE 727
Cdd:pfam00176  158 NRWILTGTPIQNNLEELWALLNFLRPGPFGSLQTFDkwfvrPIEREGGEKGVARLHKLLKPFLLRRTKKDVEKSLPPKVE 237
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 545493356   728 QILRVEMSALQKQYYK------------WILTRNYKALAKGTRG--STSGFLNIVMELKKCCNHCYLI 781
Cdd:pfam00176  238 EILFCRLSKGQRKLYQtalqalrgngilKLLIRNRAATKFSSKSfrGKPGLLNILLRLRKICNHPDLF 305
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and ...
496-970 9.16e-105

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


Pssm-ID: 223627 [Multi-domain]  Cd Length: 866  Bit Score: 357.12  E-value: 9.16e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  496 ELRDYQLEGLNWLAHS-WCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLY-GPFLIVVPLSTLTSWQREFEIWAPEIN 573
Cdd:COG0553   338 ELRPYQLEGVNWLSELlRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYlGPALIVVPASLLSNWKREFEKFAPDLR 417
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  574 VVVyIGDLMSRNTIREYEWIH---SQTKRLKFNALITTYEIL---LKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLI 647
Cdd:COG0553   418 LVL-VYHGEKSELDKKREALRdllKLHLVIIFDVVITTYELLrrfLVDHGGLKKIEWDRVVLDEAHRIKNDQSSEGKALQ 496
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  648 DFKSHHRLLITGTPLQNSLKELWSLL-HFIMPEKF-----EFWEDFEE--------DHGKGRENGYQSLHKVLEPFLLRR 713
Cdd:COG0553   497 FLKALNRLDLTGTPLENRLGELWSLLqEFLNPGLLgtsfaIFTRLFEKpiqaeediGPLEARELGIELLRKLLSPFILRR 576
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  714 VKKDVE--KSLPAKVEQILRVEMSALQKQYYKWILTRNYKALAKGTRGSTSG------------FLNIVMELKKCCNHCY 779
Cdd:COG0553   577 TKEDVEvlKELPPKIEKVLECELSEEQRELYEALLEGAEKNQQLLEDLEKADsdenrigdselnILALLTRLRQICNHPA 656
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  780 LIKPPEENERENGQEVLLSLI-----------RSSGKLILLDKLL-TRLRERGN--RVLIFSQMVRMLDILAEYLTIKHY 845
Cdd:COG0553   657 LVDEGLEATFDRIVLLLREDKdfdylkkpliqLSKGKLQALDELLlDKLLEEGHyhKVLIFSQFTPVLDLLEDYLKALGI 736
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  846 PFQRLDGSIKGEIRKQALDHFNADGSEdFCFLLSTRAGGLGINLASADTVVIFDSDWNPQNDLQAQARAHRIGQKKQVNI 925
Cdd:COG0553   737 KYVRLDGSTPAKRRQELIDRFNADEEE-KVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQKRPVKV 815
                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*
gi 545493356  926 YRLVTKGTVEEEIIERAKKKMVLDHLVIQRMDTTGRTVLENNSGR 970
Cdd:COG0553   816 YRLITRGTIEEKILELQEKKQELLDSLIDAEGEKELSKLSIEDLL 860
DEXHc_CHD6_7_8_9 cd17995
DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; ...
497-713 5.68e-90

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: 291.46  E-value: 5.68e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPeINVVV 576
Cdd:cd17995     1 LRDYQLEGVNWLLFNWYNRRNCILADEMGLGKTIQSIAFLEHLYQVEGIRGPFLVIAPLSTIPNWQREFETWTD-MNVVV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  577 YIGDLMSRNTIREYEWIHSQTKRL------KFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFK 650
Cdd:cd17995    80 YHGSGESRQIIQQYEMYFKDAQGRkkkgvyKFDVLITTYEMVIADAEELRKIPWRVVVVDEAHRLKNRNSKLLQGLKKLT 159
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 545493356  651 SHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGRENG-YQSLHKVLEPFLLRR 713
Cdd:cd17995   160 LEHKLLLTGTPLQNNTEELWSLLNFLEPEKFPSSEEFLEEFGDLKTAEqVEKLQALLKPYMLRR 223
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
497-678 3.12e-80

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: 262.12  E-value: 3.12e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVVV 576
Cdd:cd17919     1 LRPYQLEGLNFLLELYENGPGGILADEMGLGKTLQAIAFLAYLLKEGKERGPVLVVCPLSVLENWEREFEKWTPDLRVVV 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  577 YIGDLMSRNTIREYEWihsqtkRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFKSHHRLL 656
Cdd:cd17919    81 YHGSQRERAQIRAKEK------LDKFDVVLTTYETLRRDKASLRKFRWDLVVVDEAHRLKNPKSQLSKALKALRAKRRLL 154
                         170       180
                  ....*....|....*....|..
gi 545493356  657 ITGTPLQNSLKELWSLLHFIMP 678
Cdd:cd17919   155 LTGTPLQNNLEELWALLDFLDP 176
DEXHc_SMARCA1_SMARCA5 cd17997
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ...
496-715 6.87e-80

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: 262.64  E-value: 6.87e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  496 ELRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVV 575
Cdd:cd17997     3 TMRDYQIRGLNWLISLFENGINGILADEMGLGKTLQTISLLGYLKHYKNINGPHLIIVPKSTLDNWMREFKRWCPSLRVV 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  576 VYIGDLMSRNTIreyewIHSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFKSHHRL 655
Cdd:cd17997    83 VLIGDKEERADI-----IRDVLLPGKFDVCITSYEMVIKEKTVLKKFNWRYIIIDEAHRIKNEKSKLSQIVRLFNSRNRL 157
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 545493356  656 LITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEE-----DHGKGRENGYQSLHKVLEPFLLRRVK 715
Cdd:cd17997   158 LLTGTPLQNNLHELWALLNFLLPDVFTSSEDFDEwfnvnNCDDDNQEVVQRLHKVLRPFLLRRIK 222
DEXHc_HELLS_SMARCA6 cd18009
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ...
497-715 8.22e-74

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: 245.76  E-value: 8.22e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFhQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVVV 576
Cdd:cd18009     4 MRPYQLEGMEWLRMLWENGINGILADEMGLGKTIQTIALLAHLR-ERGVWGPFLVIAPLSTLPNWVNEFARFTPSVPVLL 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  577 YIGDLMSRNTIREYEWIHSQTKRlKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFKSHHRLL 656
Cdd:cd18009    83 YHGTKEERERLRKKIMKREGTLQ-DFPVVVTSYEIAMRDRKALQHYAWKYLIVDEGHRLKNLNCRLIQELKTFNSDNRLL 161
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 545493356  657 ITGTPLQNSLKELWSLLHFIMPE------KFEFW----------EDFEEDHGKGRENGYQSLHKVLEPFLLRRVK 715
Cdd:cd18009   162 LTGTPLQNNLSELWSLLNFLLPDvfddlsSFESWfdfsslsdnaADISNLSEEREQNIVHMLHAILKPFLLRRLK 236
DEXHc_SMARCA2_SMARCA4 cd17996
DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin ...
494-715 1.01e-73

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: 245.36  E-value: 1.01e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  494 NLELRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEIN 573
Cdd:cd17996     1 GGTLKEYQLKGLQWMVSLYNNNLNGILADEMGLGKTIQTISLITYLMEKKKNNGPYLVIVPLSTLSNWVSEFEKWAPSVS 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  574 VVVYIGDLMSRNTIreyewiHSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLID-FKSH 652
Cdd:cd17996    81 KIVYKGTPDVRKKL------QSQIRAGKFNVLLTTYEYIIKDKPLLSKIKWKYMIIDEGHRMKNAQSKLTQTLNTyYHAR 154
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 545493356  653 HRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEE------DHGKGRENGY----------QSLHKVLEPFLLRRVK 715
Cdd:cd17996   155 YRLLLTGTPLQNNLPELWALLNFLLPKIFKSCKTFEQwfntpfANTGEQVKIElneeetlliiRRLHKVLRPFLLRRLK 233
DEXHc_CHD3_4_5 cd17994
DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; ...
497-713 5.67e-72

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: 238.88  E-value: 5.67e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVVV 576
Cdd:cd17994     1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTIQTIVFLYSLYKEGHSKGPFLVSAPLSTIINWEREFEMWAPDFYVVT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  577 YIGDlmsrntireyewihsqtkrlkfNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFKSHHRLL 656
Cdd:cd17994    81 YVGD----------------------HVLLTSYELISIDQAILGSIDWAVLVVDEAHRLKNNQSKFFRILNSYKIGYKLL 138
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 545493356  657 ITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGK-GRENGYQSLHKVLEPFLLRR 713
Cdd:cd17994   139 LTGTPLQNNLEELFHLLNFLTPERFNNLQGFLEEFADiSKEDQIKKLHDLLGPHMLRR 196
DEXHc_CHD1L cd18006
DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, ...
497-713 2.65e-70

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: 235.02  E-value: 2.65e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVVV 576
Cdd:cd18006     1 LRPYQLEGVNWLLQCRAEQHGCILGDEMGLGKTCQTISLLWYLAGRLKLLGPFLVLCPLSVLDNWKEELNRFAPDLSVIT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  577 YIGDLMSRNTIREyewihSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFKSHHRLL 656
Cdd:cd18006    81 YMGDKEKRLDLQQ-----DIKSTNRFHVLLTTYEICLKDASFLKSFPWASLVVDEAHRLKNQNSLLHKTLSEFSVDFRLL 155
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 545493356  657 ITGTPLQNSLKELWSLLHFIMPEKF--EFWEDF---EEDHGKGRENgYQSLHKVLEPFLLRR 713
Cdd:cd18006   156 LTGTPIQNSLQELYALLSFIEPNVFpkDKLDDFikaYSETDDESET-VEELHLLLQPFLLRR 216
DEXQc_SRCAP cd18003
DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or ...
497-713 5.77e-68

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: 228.39  E-value: 5.77e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVVV 576
Cdd:cd18003     1 LREYQHIGLDWLATLYEKNLNGILADEMGLGKTIQTIALLAHLACEKGNWGPHLIVVPTSVMLNWEMEFKRWCPGFKILT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  577 YIGDLMSRNTIREyEWihsqTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFKSHHRLL 656
Cdd:cd18003    81 YYGSAKERKLKRQ-GW----MKPNSFHVCITSYQLVVQDHQVFKRKKWKYLILDEAHNIKNFKSQRWQTLLNFNTQRRLL 155
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 545493356  657 ITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHG-------KGRENGYQS----LHKVLEPFLLRR 713
Cdd:cd18003   156 LTGTPLQNSLMELWSLMHFLMPHIFQSHQEFKEWFSnpltamsEGSQEENEElvrrLHKVLRPFLLRR 223
DEXHc_CHD3 cd18055
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; ...
497-713 1.80e-65

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; Chromodomain-helicase-DNA-binding protein 3 (CHD3) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. It is required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity. CHD3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350813 [Multi-domain]  Cd Length: 232  Bit Score: 221.81  E-value: 1.80e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVVV 576
Cdd:cd18055     1 LHMYQLEGLNWLRFSWAQGTDTILADEMGLGKTIQTIVFLYSLYKEGHTKGPFLVSAPLSTIINWEREFQMWAPDFYVVT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  577 YIGDLMSRNTIREYEWIHSQT--------------KRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLL 642
Cdd:cd18055    81 YTGDKDSRAIIRENEFSFDDNavkggkkafkmkreAQVKFHVLLTSYELVTIDQAALGSIRWACLVVDEAHRLKNNQSKF 160
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 545493356  643 YKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGK-GRENGYQSLHKVLEPFLLRR 713
Cdd:cd18055   161 FRVLNGYKIDHKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADiSKEDQIKKLHDLLGPHMLRR 232
DEXHc_CHD5 cd18057
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; ...
497-713 7.72e-64

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. It is thought to specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3 and plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. As a tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. CHD5 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350815 [Multi-domain]  Cd Length: 232  Bit Score: 217.24  E-value: 7.72e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVVV 576
Cdd:cd18057     1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  577 YIGDLMSRNTIREYEW------IHSQTK--------RLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLL 642
Cdd:cd18057    81 YTGDKESRSVIRENEFsfednaIRSGKKvfrmkkeaQIKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 160
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 545493356  643 YKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGK-GRENGYQSLHKVLEPFLLRR 713
Cdd:cd18057   161 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADiSKEDQIKKLHDLLGPHMLRR 232
DEXHc_CHD4 cd18056
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; ...
497-713 1.07e-62

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: 213.77  E-value: 1.07e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVVV 576
Cdd:cd18056     1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTAVFLYSLYKEGHSKGPFLVSAPLSTIINWEREFEMWAPDMYVVT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  577 YIGDLMSRNTIREYEWIH-----------SQTKR---LKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLL 642
Cdd:cd18056    81 YVGDKDSRAIIRENEFSFednairggkkaSRMKKeasVKFHVLLTSYELITIDMAILGSIDWACLIVDEAHRLKNNQSKF 160
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 545493356  643 YKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGK-GRENGYQSLHKVLEPFLLRR 713
Cdd:cd18056   161 FRVLNGYSLQHKLLLTGTPLQNNLEELFHLLNFLTPERFHNLEGFLEEFADiAKEDQIKKLHDMLGPHMLRR 232
DEXQc_INO80 cd18002
DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 ...
497-713 2.83e-62

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: 212.36  E-value: 2.83e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVVV 576
Cdd:cd18002     1 LKEYQLKGLNWLANLYEQGINGILADEMGLGKTVQSIAVLAHLAEEHNIWGPFLVIAPASTLHNWQQEISRFVPQFKVLP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  577 YIGDLMSRNTIREYeW--IHSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFKSHHR 654
Cdd:cd18002    81 YWGNPKDRKVLRKF-WdrKNLYTRDAPFHVVITSYQLVVQDEKYFQRVKWQYMVLDEAQAIKSSSSSRWKTLLSFHCRNR 159
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  655 LLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGRENGYQS-----------LHKVLEPFLLRR 713
Cdd:cd18002   160 LLLTGTPIQNSMAELWALLHFIMPTLFDSHDEFNEWFSKDIESHAENktglnehqlkrLHMILKPFMLRR 229
DEXHc_CHD6 cd18058
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; ...
497-713 1.55e-60

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: 207.20  E-value: 1.55e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQhQLYGPFLIVVPLSTLTSWQREFEIWApEINVVV 576
Cdd:cd18058     1 LREYQLEGMNWLLFNWYNRKNCILADEMGLGKTIQSITFLSEIFLM-GIRGPFLIIAPLSTITNWEREFRTWT-EMNAIV 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  577 YIGDLMSRNTIREYEWIHSQTK------RLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFK 650
Cdd:cd18058    79 YHGSQISRQMIQQYEMYYRDEQgnplsgIFKFQVVITTFEMILADCPELKKINWSCVIIDEAHRLKNRNCKLLEGLKLMA 158
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 545493356  651 SHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGR-ENGYQSLHKVLEPFLLRR 713
Cdd:cd18058   159 LEHKVLLTGTPLQNSVEELFSLLNFLEPSQFPSETTFLEEFGDLKtEEQVKKLQSILKPMMLRR 222
DEXHc_SMARCA5 cd18064
DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent ...
496-725 3.46e-60

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: 207.21  E-value: 3.46e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  496 ELRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVV 575
Cdd:cd18064    15 KLRDYQVRGLNWLISLYENGINGILADEMGLGKTLQTISLLGYMKHYRNIPGPHMVLVPKSTLHNWMAEFKRWVPTLRAV 94
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  576 VYIGD-----LMSRNTIREYEWihsqtkrlkfNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFK 650
Cdd:cd18064    95 CLIGDkdqraAFVRDVLLPGEW----------DVCVTSYEMLIKEKSVFKKFNWRYLVIDEAHRIKNEKSKLSEIVREFK 164
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 545493356  651 SHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEE----DHGKGRENGYQSLHKVLEPFLLRRVKKDVEKSLPAK 725
Cdd:cd18064   165 TTNRLLLTGTPLQNNLHELWALLNFLLPDVFNSAEDFDSwfdtNNCLGDQKLVERLHMVLRPFLLRRIKADVEKSLPPK 243
DEXHc_CHD8 cd18060
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; ...
497-713 6.06e-60

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: 205.67  E-value: 6.06e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQhQLYGPFLIVVPLSTLTSWQREFEIWApEINVVV 576
Cdd:cd18060     1 LREYQLEGVNWLLFNWYNRQNCILADEMGLGKTIQSIAFLQEVYNV-GIHGPFLVIAPLSTITNWEREFNTWT-EMNTIV 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  577 YIGDLMSRNTIREYEWIHSQTK-RL-----KFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFK 650
Cdd:cd18060    79 YHGSLASRQMIQQYEMYCKDSRgRLipgayKFDALITTFEMILSDCPELREIEWRCVIIDEAHRLKNRNCKLLDSLKHMD 158
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 545493356  651 SHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGR-ENGYQSLHKVLEPFLLRR 713
Cdd:cd18060   159 LEHKVLLTGTPLQNTVEELFSLLHFLEPSQFPSESEFLKDFGDLKtEEQVQKLQAILKPMMLRR 222
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
803-929 1.39e-57

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: 195.00  E-value: 1.39e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  803 SGKLILLDKLLTRLRERGNRVLIFSQMVRMLDILAEYLTIKHYPFQRLDGSIKGEIRKQALDHFNADgSEDFCFLLSTRA 882
Cdd:cd18793    10 SGKLEALLELLEELREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNED-PDIRVFLLSTKA 88
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 545493356  883 GGLGINLASADTVVIFDSDWNPQNDLQAQARAHRIGQKKQVNIYRLV 929
Cdd:cd18793    89 GGVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQKKPVVVYRLI 135
DEXHc_SMARCAD1 cd17998
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ...
497-681 6.48e-57

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: 195.30  E-value: 6.48e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFhQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVVV 576
Cdd:cd17998     1 LKDYQLIGLNWLNLLYQKKLSGILADEMGLGKTIQVIAFLAYLK-EIGIPGPHLVVVPSSTLDNWLREFKRWCPSLKVEP 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  577 YIGDLMSRNTIREYEwihsQTKRLKFNALITTYEILL---KDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFKSHH 653
Cdd:cd17998    80 YYGSQEERKHLRYDI----LKGLEDFDVIVTTYNLATsnpDDRSFFKRLKLNYVVYDEGHMLKNMTSERYRHLMTINANF 155
                         170       180
                  ....*....|....*....|....*...
gi 545493356  654 RLLITGTPLQNSLKELWSLLHFIMPEKF 681
Cdd:cd17998   156 RLLLTGTPLQNNLLELMSLLNFIMPKPF 183
DEXHc_SMARCA1 cd18065
DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent ...
481-715 1.12e-56

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: 196.78  E-value: 1.12e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  481 VALKKQPTYLGGENLelRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTS 560
Cdd:cd18065     2 VRFEESPSYVKGGTL--RDYQVRGLNWMISLYENGVNGILADEMGLGKTLQTIALLGYLKHYRNIPGPHMVLVPKSTLHN 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  561 WQREFEIWAPEINVVVYIGDLMSRNTireyeWIHSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDS 640
Cdd:cd18065    80 WMNEFKRWVPSLRAVCLIGDKDARAA-----FIRDVMMPGEWDVCVTSYEMVIKEKSVFKKFNWRYLVIDEAHRIKNEKS 154
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 545493356  641 LLYKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEE----DHGKGRENGYQSLHKVLEPFLLRRVK 715
Cdd:cd18065   155 KLSEIVREFKTTNRLLLTGTPLQNNLHELWALLNFLLPDVFNSADDFDSwfdtKNCLGDQKLVERLHAVLKPFLLRRIK 233
DEXHc_CHD7 cd18059
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; ...
497-713 1.57e-56

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: 195.64  E-value: 1.57e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLsYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWApEINVVV 576
Cdd:cd18059     1 LREYQLEGVNWLLFNWYNTRNCILADEMGLGKTIQSITFL-YEIYLKGIHGPFLVIAPLSTIPNWEREFRTWT-ELNVVV 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  577 YIGDLMSRNTIREYEWIHSQTK------RLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFK 650
Cdd:cd18059    79 YHGSQASRRTIQLYEMYFKDPQgrvikgSYKFHAIITTFEMILTDCPELRNIPWRCVVIDEAHRLKNRNCKLLEGLKMMD 158
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 545493356  651 SHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGR-ENGYQSLHKVLEPFLLRR 713
Cdd:cd18059   159 LEHKVLLTGTPLQNTVEELFSLLHFLEPSRFPSETTFMQEFGDLKtEEQVQKLQAILKPMMLRR 222
DEXQc_arch_SWI2_SNF2 cd18012
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ...
496-715 1.46e-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: 192.78  E-value: 1.46e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  496 ELRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLyGPFLIVVPLSTLTSWQREFEIWAPEINVV 575
Cdd:cd18012     4 TLRPYQKEGFNWLSFLRHYGLGGILADDMGLGKTLQTLALLLSRKEEGRK-GPSLVVAPTSLIYNWEEEAAKFAPELKVL 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  576 VYIGDLMSRNTIREYEwihsqtkrlKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFKSHHRL 655
Cdd:cd18012    83 VIHGTKRKREKLRALE---------DYDLVITSYGLLRRDIELLKEVKFHYLVLDEAQNIKNPQTKTAKAVKALKADHRL 153
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 545493356  656 LITGTPLQNSLKELWSLLHFIMP------EKF-EFWEDFEEDHgkGRENGYQSLHKVLEPFLLRRVK 715
Cdd:cd18012   154 ALTGTPIENHLGELWSIFDFLNPgllgsyKRFkKRFAKPIEKD--GDEEALEELKKLISPFILRRLK 218
DEXHc_CHD9 cd18061
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; ...
497-713 6.39e-55

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: 190.99  E-value: 6.39e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLsYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWApEINVVV 576
Cdd:cd18061     1 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFL-YEILLTGIRGPFLIIAPLSTIANWEREFRTWT-DLNVVV 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  577 YIGDLMSRNTIREYE-WIHSQTKRL-----KFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFK 650
Cdd:cd18061    79 YHGSLISRQMIQQYEmYFRDSQGRIirgayRFQAIITTFEMILGGCPELNAIDWRCVIIDEAHRLKNKNCKLLEGLKLMN 158
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 545493356  651 SHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGR-ENGYQSLHKVLEPFLLRR 713
Cdd:cd18061   159 LEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKtEEQVQKLQAILKPMMLRR 222
DEXHc_SMARCA4 cd18062
DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent ...
494-715 1.91e-52

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: 185.25  E-value: 1.91e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  494 NLELRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEIN 573
Cdd:cd18062    21 NGVLKQYQIKGLEWLVSLYNNNLNGILADEMGLGKTIQTIALITYLMEHKRINGPFLIIVPLSTLSNWVYEFDKWAPSVV 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  574 VVVYIGDLMSRNTIReyewihSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTL-IDFKSH 652
Cdd:cd18062   101 KVSYKGSPAARRAFV------PQLRSGKFNVLLTTYEYIIKDKQILAKIRWKYMIVDEGHRMKNHHCKLTQVLnTHYVAP 174
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 545493356  653 HRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFE-----------EDHGKGRENGY---QSLHKVLEPFLLRRVK 715
Cdd:cd18062   175 RRLLLTGTPLQNKLPELWALLNFLLPTIFKSCSTFEqwfnapfamtgEKVDLNEEETIliiRRLHKVLRPFLLRRLK 251
DEXHc_SMARCA2 cd18063
DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent ...
494-715 5.54e-52

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: 183.73  E-value: 5.54e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  494 NLELRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEIN 573
Cdd:cd18063    21 NGTLKHYQLQGLEWMVSLYNNNLNGILADEMGLGKTIQTIALITYLMEHKRLNGPYLIIVPLSTLSNWTYEFDKWAPSVV 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  574 VVVYIGDLMSRNTIReyewihSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTL-IDFKSH 652
Cdd:cd18063   101 KISYKGTPAMRRSLV------PQLRSGKFNVLLTTYEYIIKDKHILAKIRWKYMIVDEGHRMKNHHCKLTQVLnTHYVAP 174
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 545493356  653 HRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFE-----------EDHGKGRENGY---QSLHKVLEPFLLRRVK 715
Cdd:cd18063   175 RRILLTGTPLQNKLPELWALLNFLLPTIFKSCSTFEqwfnapfamtgERVDLNEEETIliiRRLHKVLRPFLLRRLK 251
CD1_tandem_CHD1-2_like cd18666
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ...
272-356 4.30e-47

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: 163.23  E-value: 4.30e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  272 NSETIEKVLDSRLGKKGATGASTTVYAIEANGDPSGDFDTEKDESEVQYLIKWKGWSYIHSTWESEESLQQQKVKGLKKL 351
Cdd:cd18666     1 EFETIERVLDHRIGRKGATGASTTIYAVEADGDPNAGFDPEDEETEIQYLIKWKGWSHIHNTWESEESLKDQNVKGMKKL 80

                  ....*
gi 545493356  352 ENFKK 356
Cdd:cd18666    81 ENYKK 85
DEXHc_ERCC6 cd18000
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ...
497-678 2.49e-46

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: 165.19  E-value: 2.49e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEINVVV 576
Cdd:cd18000     1 LFKYQQTGVQWLWELHCQRVGGILGDEMGLGKTIQIIAFLAALHHSKLGLGPSLIVCPATVLKQWVKEFHRWWPPFRVVV 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  577 Y---IGDLMSRNTIREYEWIHSQTKRLKFNA--LITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFKS 651
Cdd:cd18000    81 LhssGSGTGSEEKLGSIERKSQLIRKVVGDGgiLITTYEGFRKHKDLLLNHNWQYVILDEGHKIRNPDAEITLACKQLRT 160
                         170       180
                  ....*....|....*....|....*..
gi 545493356  652 HHRLLITGTPLQNSLKELWSLLHFIMP 678
Cdd:cd18000   161 PHRLILSGTPIQNNLKELWSLFDFVFP 187
DEXHc_ERCC6L cd18001
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ...
497-713 6.28e-45

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: 162.93  E-value: 6.28e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQhQLYGPFLIVVPLSTLTSWQREFEIWAPEINVVV 576
Cdd:cd18001     1 LYPHQREGVAWLWSLHDGGKGGILADDMGLGKTVQICAFLSGMFDS-GLIKSVLVVMPTSLIPHWVKEFAKWTPGLRVKV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  577 YIGdlmSRNTIREY--EWIHSqtkrlKFNALITTYEILLKDKTVLGSIN-----WAFLGVDEAHRLKNDDSLLYKTLIDF 649
Cdd:cd18001    80 FHG---TSKKERERnlERIQR-----GGGVLLTTYGMVLSNTEQLSADDhdefkWDYVILDEGHKIKNSKTKSAKSLREI 151
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  650 KSHHRLLITGTPLQNSLKELWSLLHFIMP-----EKFEFWEDFEEDHGKGRENG------------YQSLHKVLEPFLLR 712
Cdd:cd18001   152 PAKNRIILTGTPIQNNLKELWALFDFACNgsllgTRKTFKMEFENPITRGRDKDatqgekalgsevAENLRQIIKPYFLR 231

                  .
gi 545493356  713 R 713
Cdd:cd18001   232 R 232
DEXHc_ERCC6L2 cd18005
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
497-713 1.72e-43

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: 159.08  E-value: 1.72e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQ--------------------HQLYGPFLIVVPLS 556
Cdd:cd18005     1 LRDYQREGVEFMYDLYKNGRGGILGDDMGLGKTVQVIAFLAAVLGKtgtrrdrennrprfkkkppaSSAKKPVLIVAPLS 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  557 TLTSWQREFEIWApEINVVVYIG-----DLMSRNTIREYEwihsqtkrlkfnALITTYEILLKDKTVLGSINWAFLGVDE 631
Cdd:cd18005    81 VLYNWKDELDTWG-HFEVGVYHGsrkddELEGRLKAGRLE------------VVVTTYDTLRRCIDSLNSINWSAVIADE 147
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  632 AHRLKNDDSLLYKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDF-----------------EEDHGKG 694
Cdd:cd18005   148 AHRIKNPKSKLTQAMKELKCKVRIGLTGTLLQNNMKELWCLLDWAVPGALGSRSQFkkhfsepikrgqrhtatARELRLG 227
                         250
                  ....*....|....*....
gi 545493356  695 RENGyQSLHKVLEPFLLRR 713
Cdd:cd18005   228 RKRK-QELAVKLSKFFLRR 245
DEXHc_Mot1 cd17999
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ...
497-713 3.48e-42

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: 154.82  E-value: 3.48e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLA-------HSwcksnsvILADEMGLGKTIQTISFLSYLFHQHQLYG-----PFLIVVPlSTLTS-WQR 563
Cdd:cd17999     1 LRPYQQEGINWLAflnkynlHG-------ILCDDMGLGKTLQTLCILASDHHKRANSFnsenlPSLVVCP-PTLVGhWVA 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  564 EFEIWAPE--INVVVYIGDLMSRNTIREyewihsqtKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSL 641
Cdd:cd17999    73 EIKKYFPNafLKPLAYVGPPQERRRLRE--------QGEKHNVIVASYDVLRNDIEVLTKIEWNYCVLDEGHIIKNSKTK 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  642 LYKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMP-----EKfEFWEDF---------EEDHGKGRENGYQS---LHK 704
Cdd:cd17999   145 LSKAVKQLKANHRLILSGTPIQNNVLELWSLFDFLMPgylgtEK-QFQRRFlkpilasrdSKASAKEQEAGALAleaLHK 223

                  ....*....
gi 545493356  705 VLEPFLLRR 713
Cdd:cd17999   224 QVLPFLLRR 232
DEXDc_SHPRH-like cd18008
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ...
497-713 5.49e-39

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: 145.89  E-value: 5.49e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLahswcKSNSVILADEMGLGKTIQTIS---------------FLSYLFHQHQLY--GPFLIVVPLSTLT 559
Cdd:cd18008     1 LLPYQKQGLAWM-----LPRGGILADEMGLGKTIQALAlilatrpqdpkipeeLEENSSDPKKLYlsKTTLIVVPLSLLS 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  560 SWQREFE--IWAPEINVVVYIGdlmSRNTIREYEWihsqtkrLKFNALITTYEILLKD----------------KTVLGS 621
Cdd:cd18008    76 QWKDEIEkhTKPGSLKVYVYHG---SKRIKSIEEL-------SDYDIVITTYGTLASEfpknkkgggrdskekeASPLHR 145
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  622 INWAFLGVDEAHRLKNDDSLLYKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEED----HGKGREN 697
Cdd:cd18008   146 IRWYRVILDEAHNIKNRSTKTSRAVCALKAERRWCLTGTPIQNSLDDLYSLLRFLRVEPFGDYPWFNSDiskpFSKNDRK 225
                         250
                  ....*....|....*.
gi 545493356  698 GYQSLHKVLEPFLLRR 713
Cdd:cd18008   226 ALERLQALLKPILLRR 241
CDH1_2_SANT_HL1 pfam18375
CDH1/2 SANT-Helical linker 1; CDH1 is an ATP-dependent chromatin-remodelling factor and plays ...
1143-1231 1.78e-37

CDH1/2 SANT-Helical linker 1; CDH1 is an ATP-dependent chromatin-remodelling factor and plays an important role in regulating nucleosome assembly and mobilization. CHD1 consists of double chromodomain, SNF2-related ATPase domain, and a C-terminal DNA-binding domain. The DNA-binding domain contains SANT (Swi3, Ada2, N-CoR, TFIIIB) and SLIDE (SANT-like ISWI) domains in its C-terminal region. SANT domains are structurally related to Myb-like domains are common motifs found in chromatin interacting proteins. Deletion of individual SANT or SLIDE domains in CDH1 does not significantly affect nucleosome binding, but combined deletion of both domains severely compromise binding, suggesting that the SANT-SLIDE motif recognizes DNA/nucleosomes as a single cooperative unit. SANT sequences of Chd1 proteins are the most distantly relation group of sequences relation to other SANT/Myb sequences, and are more diverse than other SANT proteins. The SANT and SLIDE regions are well conserved in both Chd1 and ISWI (imitation switch) remodelling enzymes. This domain comprises the SANT region and the helical linker region 1 (HL1).


Pssm-ID: 408175  Cd Length: 90  Bit Score: 135.92  E-value: 1.78e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  1143 GFTDAEIRRFIKAYKKFGLPLERLECIARDAELVDKSVADLKRLGELIHNSCVSAMQEYEEQLKENasEGKGPGKK--RG 1220
Cdd:pfam18375    2 GFTDAEIRRFVKSYKKFPAPLKRLDAIACDAELQEKPLSDLKRLGELLHERCEEAMEEYEEKEDEN--PGADGGKKriRG 79
                           90
                   ....*....|.
gi 545493356  1221 PTIKISGVQVN 1231
Cdd:pfam18375   80 PTFKLGGVSVN 90
DEXHc_ATRX-like cd18007
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ...
497-687 9.05e-35

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: 133.96  E-value: 9.05e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLN--W--LAHSWCKSNS---VILADEMGLGKTIQTISFLsylfHQHQLYGP----FLIVVPLSTLTSWQREF 565
Cdd:cd18007     1 LKPHQVEGVRflWsnLVGTDVGSDEgggCILAHTMGLGKTLQVITFL----HTYLAAAPrrsrPLVLCPASTLYNWEDEF 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  566 EIWAPEINVVVYIGDLMSRntireyewIHSQTKRL-KFNA-------LITTYEI---LLKDKTVLGSINWAF-------- 626
Cdd:cd18007    77 KKWLPPDLRPLLVLVSLSA--------SKRADARLrKINKwhkeggvLLIGYELfrnLASNATTDPRLKQEFiaalldpg 148
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 545493356  627 ---LGVDEAHRLKNDDSLLYKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDF 687
Cdd:cd18007   149 pdlLVLDEGHRLKNEKSQLSKALSKVKTKRRILLTGTPLQNNLKEYWTMVDFARPKYLGTLKEF 212
DEXHc_RAD54 cd18004
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ...
497-713 1.94e-34

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: 132.79  E-value: 1.94e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWL-----AHSWCKSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGP----FLIVVPLSTLTSWQREFEI 567
Cdd:cd18004     1 LRPHQREGVQFLydcltGRRGYGGGGAILADEMGLGKTLQAIALVWTLLKQGPYGKPtakkALIVCPSSLVGNWKAEFDK 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  568 WAPEINVVVYIgdlMSRNTIREYEWIHSQTKRLKFNALITTYEILLKDKTVLGS-INWAFLGVDEAHRLKNDDSLLYKTL 646
Cdd:cd18004    81 WLGLRRIKVVT---ADGNAKDVKASLDFFSSASTYPVLIISYETLRRHAEKLSKkISIDLLICDEGHRLKNSESKTTKAL 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  647 IDFKSHHRLLITGTPLQNSLKELWSLLHFIMPEKF----EFWEDFEEDHGKGRENGY------------QSLHKVLEPFL 710
Cdd:cd18004   158 NSLPCRRRLLLTGTPIQNDLDEFFALVDFVNPGILgslaSFRKVFEEPILRSRDPDAseedkelgaersQELSELTSRFI 237

                  ...
gi 545493356  711 LRR 713
Cdd:cd18004   238 LRR 240
CD2_tandem_CHD1-2_like cd18661
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ...
389-460 2.50e-30

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


Pssm-ID: 349308  Cd Length: 58  Bit Score: 114.32  E-value: 2.50e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 545493356  389 QYQIVERVIAVKTSKStlgqtdfpahsrkpAPSNEPEYLCKWMGLPYSECSWEDEALIGKKFQSCIDSFHSR 460
Cdd:cd18661     1 QYQIVERIIAHSPQKS--------------AASGYPDYLCKWQGLPYSECTWEDGALISKKFQACIDEYHSR 58
DEXDc smart00487
DEAD-like helicases superfamily;
495-680 3.65e-30

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 119.13  E-value: 3.65e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356    495 LELRDYQLEGLNWLAHSWcksNSVILADEMGLGKTIQTISFLSYLFHQHQlYGPFLIVVPLSTLT-SWQREFEIWAPE-- 571
Cdd:smart00487    7 EPLRPYQKEAIEALLSGL---RDVILAAPTGSGKTLAALLPALEALKRGK-GGRVLVLVPTRELAeQWAEELKKLGPSlg 82
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356    572 INVVVYIGDLMSRNTIREYewihsqtKRLKFNALITTYEILLKD--KTVLGSINWAFLGVDEAHRLKND---DSLLYKTL 646
Cdd:smart00487   83 LKVVGLYGGDSKREQLRKL-------ESGKTDILVTTPGRLLDLleNDKLSLSNVDLVILDEAHRLLDGgfgDQLEKLLK 155
                           170       180       190
                    ....*....|....*....|....*....|....*..
gi 545493356    647 IDFKSHHRLLITGTP---LQNSLKELWSLLHFIMPEK 680
Cdd:smart00487  156 LLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGF 192
DUF4208 pfam13907
Domain of unknown function (DUF4208); This domain is found at the C-terminus of ...
1437-1519 1.58e-29

Domain of unknown function (DUF4208); This domain is found at the C-terminus of chromodomain-helicase-DNA-binding proteins. The exact function of the domain is undetermined.


Pssm-ID: 404744  Cd Length: 93  Bit Score: 113.46  E-value: 1.58e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  1437 ICKERMRPVKKALKQLDKPDKGLNVQEQLEHTRNCLLKIGDRIAECLKAYSDqEHIKLWRRNLWIFVSKFTE--FDARKL 1514
Cdd:pfam13907   10 ECKELMRPVKKSLKRLKKGTKGLSRKERAKILKKELLKIGDFIDSILKEYKD-EKIEKLRKHLWSFVSKFWPnkVSGKKL 88

                   ....*
gi 545493356  1515 HKLYK 1519
Cdd:pfam13907   89 REMYK 93
DEXHc_RAD54A cd18067
DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as ...
497-713 1.88e-28

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: 115.64  E-value: 1.88e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHswC-------KSNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFL----IVVPLSTLTSWQREF 565
Cdd:cd18067     1 LRPHQREGVKFLYR--CvtgrrirGSHGCIMADEMGLGKTLQCITLMWTLLRQSPQCKPEIdkaiVVSPSSLVKNWANEL 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  566 EIW-APEINVVVYIGDLMSRNTIREYEWIHSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYK 644
Cdd:cd18067    79 GKWlGGRLQPLAIDGGSKKEIDRKLVQWASQQGRRVSTPVLIISYETFRLHVEVLQKGEVGLVICDEGHRLKNSDNQTYQ 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  645 TLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMPE----KFEFWEDFEEDHGKGR------------ENGYQSLHKVLEP 708
Cdd:cd18067   159 ALDSLNTQRRVLLSGTPIQNDLSEYFSLVNFVNPGilgtAAEFKKNFELPILKGRdadasekerqlgEEKLQELISIVNR 238

                  ....*
gi 545493356  709 FLLRR 713
Cdd:cd18067   239 CIIRR 243
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
804-918 5.87e-28

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: 395209 [Multi-domain]  Cd Length: 109  Bit Score: 109.61  E-value: 5.87e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356   804 GKLILLDKLLTRlrERGNRVLIFSQMVRMLDilAEYLTIKH-YPFQRLDGSIKGEIRKQALDHFNadgSEDFCFLLSTRA 882
Cdd:pfam00271    1 EKLEALLELLKK--ERGGKVLIFSQTKKTLE--AELLLEKEgIKVARLHGDLSQEEREEILEDFR---KGKIDVLVATDV 73
                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 545493356   883 GGLGINLASADTVVIFDSDWNPQNDLQAQARAHRIG 918
Cdd:pfam00271   74 AERGLDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
DEXHc_HARP_SMARCAL1 cd18010
DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin ...
497-687 1.07e-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: 112.68  E-value: 1.07e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNW-LAHSwcksNSVILADEMGLGKTIQTISFLSYLFHqhqlYGPFLIVVPLSTLTSWQREFEIWAP----- 570
Cdd:cd18010     1 LLPFQREGVCFaLRRG----GRVLIADEMGLGKTVQAIAIAAYYRE----EWPLLIVCPSSLRLTWADEIERWLPslppd 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  571 EINVVVyigdlMSRNTIReyewiHSQTKrlkfnALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDF- 649
Cdd:cd18010    73 DIQVIV-----KSKDGLR-----DGDAK-----VVIVSYDLLRRLEKQLLARKFKVVICDESHYLKNSKAKRTKAALPLl 137
                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 545493356  650 -KSHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDF 687
Cdd:cd18010   138 kRAKRVILLSGTPALSRPIELFTQLDALDPKLFGRFHDF 176
DEXHc_HLTF1_SMARC3 cd18071
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ...
519-713 3.07e-27

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: 112.18  E-value: 3.07e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  519 ILADEMGLGKTIQTISFLsylfhqhqLYGPFLIVVPLSTLTSWQREFE--IWAPEINVVVYIGDlmsrntireyEWIHSQ 596
Cdd:cd18071    52 ILADDMGLGKTLTTISLI--------LANFTLIVCPLSVLSNWETQFEehVKPGQLKVYTYHGG----------ERNRDP 113
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  597 TKRLKFNALITTYEILL-----KDKTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFKSHHRLLITGTPLQNSLKELWS 671
Cdd:cd18071   114 KLLSKYDIVLTTYNTLAsdfgaKGDSPLHTINWLRVVLDEGHQIRNPNAQQTKAVLNLSSERRWVLTGTPIQNSPKDLGS 193
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 545493356  672 LLHFIMPEKF---EFWED-FEEDHGKGRENGYQSLHKVLEPFLLRR 713
Cdd:cd18071   194 LLSFLHLKPFsnpEYWRRlIQRPLTMGDPTGLKRLQVLMKQITLRR 239
DEXHc_RAD54B cd18066
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ...
497-678 5.18e-24

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: 102.62  E-value: 5.18e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKSNSV-----ILADEMGLGKTIQTISFLSYLFHQHQlYGP------FLIVVPLSTLTSWQREF 565
Cdd:cd18066     1 LRPHQREGIEFLYECVMGMRVNerfgaILADEMGLGKTLQCISLIWTLLRQGP-YGGkpvikrALIVTPGSLVKNWKKEF 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  566 EIWAPEINVVVYIGDlmSRNTIREYewihsqTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLKNDDSLLYKT 645
Cdd:cd18066    80 QKWLGSERIKVFTVD--QDHKVEEF------IASPLYSVLIISYEMLLRSLDQISKLNFDLVICDEGHRLKNTSIKTTTA 151
                         170       180       190
                  ....*....|....*....|....*....|...
gi 545493356  646 LIDFKSHHRLLITGTPLQNSLKELWSLLHFIMP 678
Cdd:cd18066   152 LTSLSCERRIILTGTPIQNDLQEFFALIDFVNP 184
HELICc smart00490
helicase superfamily c-terminal domain;
834-918 3.42e-22

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 91.89  E-value: 3.42e-22
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356    834 DILAEYLTIKHYPFQRLDGSIKGEIRKQALDHFNADgseDFCFLLSTRAGGLGINLASADTVVIFDSDWNPQNDLQAQAR 913
Cdd:smart00490    1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNG---KIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGR 77

                    ....*
gi 545493356    914 AHRIG 918
Cdd:smart00490   78 AGRAG 82
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
497-713 6.66e-21

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: 92.74  E-value: 6.66e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNW-LAHswcKSNSVILADEMGLGKTIQTISFLSYLFHQHqLYGPFLIVVPLSTLTSWQRE----FEIWAPe 571
Cdd:cd18011     1 PLPHQIDAVLRaLRK---PPVRLLLADEVGLGKTIEAGLIIKELLLRG-DAKRVLILCPASLVEQWQDElqdkFGLPFL- 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  572 invvvyigdLMSRNTIREYEWIHSQTKRLkFNALITTYEiLLKDKT----VLGSINWAFLGVDEAHRLKN----DDSLLY 643
Cdd:cd18011    76 ---------ILDRETAAQLRRLIGNPFEE-FPIVIVSLD-LLKRSEerrgLLLSEEWDLVVVDEAHKLRNsgggKETKRY 144
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 545493356  644 KT---LIDfKSHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGkgrengyqsLHKVLEPFLLRR 713
Cdd:cd18011   145 KLgrlLAK-RARHVLLLTATPHNGKEEDFRALLSLLDPGRFAVLGRFLRLDG---------LREVLAKVLLRR 207
DEXHc_ATRX cd18068
DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha ...
497-678 1.16e-19

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  Cd Length: 246  Bit Score: 90.33  E-value: 1.16e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSWCKS---------NSVILADEMGLGKTIQTISFLSYLFHQHQLYG--PFLIVVPLSTLTSWQREF 565
Cdd:cd18068     1 LKPHQVDGVQFMWDCCCESlkktkkspgSGCILAHCMGLGKTLQVVTFLHTVLLCEKLENfsRVLVVCPLNTVLNWLNEF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  566 EIWapeinvvvyIGDLMSRNTIREYE---WIHSQTKRLKFN-------ALITTYE---ILLKDKTV-------------L 619
Cdd:cd18068    81 EKW---------QEGLKDEEKIEVNElatYKRPQERSYKLQrwqeeggVMIIGYDmyrILAQERNVksreklkeifnkaL 151
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 545493356  620 GSINWAFLGVDEAHRLKNDDSLLYKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMP 678
Cdd:cd18068   152 VDPGPDFVVCDEGHILKNEASAVSKAMNSIRTKRRIVLTGTPLQNNLIEYHCMVNFVKP 210
DEXHc_ARIP4 cd18069
DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called ...
519-688 3.33e-19

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  Cd Length: 227  Bit Score: 88.33  E-value: 3.33e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  519 ILADEMGLGKTIQTISFLsYLFHQHQLYGPFLIVVPLSTLTSWQREFEIWAPEinvvvYIGDLMSRNTIREYEWIHSQTK 598
Cdd:cd18069    32 ILAHSMGLGKTLQVISFL-DVLLRHTGAKTVLAIVPVNTLQNWLSEFNKWLPP-----PEALPNVRPRPFKVFILNDEHK 105
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  599 RLKFNA-LITTYEillKDKTVL--GSINWAF------LGVDEAHRLKNDDSLLYKTLIDFKSHHRLLITGTPLQNSLKEL 669
Cdd:cd18069   106 TTAARAkVIEDWV---KDGGVLlmGYEMFRLrpgpdvVICDEGHRIKNCHASTSQALKNIRSRRRIVLTGYPLQNNLIEY 182
                         170       180
                  ....*....|....*....|...
gi 545493356  670 WSLLHFIMPE----KFEFWEDFE 688
Cdd:cd18069   183 WCMVDFVRPDflgtRQEFSNMFE 205
CD1_tandem cd18660
repeat 1 of paired tandem chromodomains; Repeat 1 of tandem CHRomatin Organization Modifier ...
272-356 5.00e-18

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: 79.71  E-value: 5.00e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  272 NSETIEKVLDSRLGKKGATgasttvyaieangDPSGDFDTEKDESEVQYLIKWKGWSYIHSTWESEESLQQQkvKGLKKL 351
Cdd:cd18660     1 DEDKIEKILDHRPKGPVEE-------------ASLDLTDPDEPWDEREFLVKWKGKSYLHCTWVTEETLEQL--RGKKKL 65

                  ....*
gi 545493356  352 ENFKK 356
Cdd:cd18660    66 KNYIK 70
CD2_tandem cd18659
repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier ...
389-459 2.34e-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: 74.53  E-value: 2.34e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 545493356  389 QYQIVERVIAVKTSKSTlgqtdfpahsrkpapsnEPEYLCKWMGLPYSECSWEDEALIGKKFQSCIDSFHS 459
Cdd:cd18659     1 EYTIVERIIAHREDDEG-----------------VTEYLVKWKGLPYDECTWESEEDISDIFQEAIDEYKK 54
DEXHc_TTF2 cd18072
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ...
497-713 2.35e-16

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: 80.60  E-value: 2.35e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLahSWCKSNSV---ILADEMGLGKTIQTISFLSYLFHQHQL----------------------YGPFLI 551
Cdd:cd18072     1 LLLHQKQALAWL--LWRERQKPrggILADDMGLGKTLTMIALILAQKNTQNRkeeekekalteweskkdstlvpSAGTLV 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  552 VVPLSTLTSWQREFEIWAPEINVVVYIGDLMSRNTIREYewihsqtkRLKFNALITTYEILLKD---------KTVLGSI 622
Cdd:cd18072    79 VCPASLVHQWKNEVESRVASNKLRVCLYHGPNRERIGEV--------LRDYDIVITTYSLVAKEiptykeesrSSPLFRI 150
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  623 NWAFLGVDEAHRLKNDDSLLYKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGRENGYQSL 702
Cdd:cd18072   151 AWARIILDEAHNIKNPKVQASIAVCKLRAHARWALTGTPIQNNLLDMYSLLKFLRCSPFDDLKVWKKQVDNKSRKGGERL 230
                         250
                  ....*....|.
gi 545493356  703 HKVLEPFLLRR 713
Cdd:cd18072   231 NILTKSLLLRR 241
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
497-712 5.55e-12

DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously expressed protein that contains motifs characteristic of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 and is involved in DNA repair. SHPRH is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350828 [Multi-domain]  Cd Length: 257  Bit Score: 67.75  E-value: 5.55e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNWLAHSwcksnSVILADEMGLGKTIQTISFLsyLFHQHQL---------------------------YGPF 549
Cdd:cd18070     1 LLPYQRRAVNWMLVP-----GGILADEMGLGKTVEVLALI--LLHPRPDndldaadddsdemvccpdclvaetpvsSKAT 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  550 LIVVPLSTLTSWQREFEIWAPE-INVVVYIGdlmsrntIREYEWIHSQT-KRL-KFNALITTYEILLKD----------- 615
Cdd:cd18070    74 LIVCPSAILAQWLDEINRHVPSsLKVLTYQG-------VKKDGALASPApEILaEYDIVVTTYDVLRTElhyaeanrsnr 146
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  616 -----------KTVLGSINWAFLGVDEAHRLKNDDSLLYKTLIDFKSHHRLLITGTPLQNSLKELWSLLHFIMPEKF--E 682
Cdd:cd18070   147 rrrrqkryeapPSPLVLVEWWRVCLDEAQMVESSTSKAAEMARRLPRVNRWCVSGTPIQRGLDDLFGLLSFLGVEPFcdS 226
                         250       260       270
                  ....*....|....*....|....*....|
gi 545493356  683 FWEDFEEDHGKGRENGYQSLHKVLEPFLLR 712
Cdd:cd18070   227 DWWARVLIRPQGRNKAREPLAALLKELLWR 256
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination and repair];
493-941 1.56e-10

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


Pssm-ID: 223989 [Multi-domain]  Cd Length: 442  Bit Score: 65.54  E-value: 1.56e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  493 ENLELRDYQLEGLNWLAHSWCKSNSVILADEMGLGKTIqTISFLSylfhqHQLYGPFLIVVPLSTL-TSWQREFEIWAPE 571
Cdd:COG1061    33 FEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTV-VAAEAI-----AELKRSTLVLVPTKELlDQWAEALKKFLLL 106
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  572 INVVVYIGdlmsrntireyewihSQTKRLKFNA-LITTYEILLKDKTVLGSIN--WAFLGVDEAHRLKNDDsllYKTLID 648
Cdd:COG1061   107 NDEIGIYG---------------GGEKELEPAKvTVATVQTLARRQLLDEFLGneFGLIIFDEVHHLPAPS---YRRILE 168
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  649 FKSHHRLLI--TGTPLQNSLKELWSLLHFIMPEKFEF-WEDFEEDhgkgrengyqslhKVLEPFLLRRVKkdvekslpak 725
Cdd:COG1061   169 LLSAAYPRLglTATPEREDGGRIGDLFDLIGPIVYEVsLKELIDE-------------GYLAPYKYVEIK---------- 225
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  726 veqilrVEMSAL-QKQYYKwiltrNYKALAKGTRGSTSGFLNIVMELKkccnhcylikppeenerengqevllsLIRSSG 804
Cdd:COG1061   226 ------VTLTEDeEREYAK-----ESARFRELLRARGTLRAENEARRI--------------------------AIASER 268
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  805 KLILLDKLLtRLRERGNRVLIFSQMVRMLDILAEYLTIKHYPfQRLDGSIKGEIRKQALDHFNADGSEdfcFLLSTRAGG 884
Cdd:COG1061   269 KIAAVRGLL-LKHARGDKTLIFASDVEHAYEIAKLFLAPGIV-EAITGETPKEEREAILERFRTGGIK---VLVTVKVLD 343
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  885 LGINLASADTVVIFDSDWNPQNDLQAQARAHR-IGQKKQVNI--YRLVTKGTVEEEIIER 941
Cdd:COG1061   344 EGVDIPDADVLIILRPTGSRRLFIQRLGRGLRpAEGKEDTLAldYSLVPDDLGEEDIARR 403
ResIII pfam04851
Type III restriction enzyme, res subunit;
494-661 2.23e-10

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 61.15  E-value: 2.23e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356   494 NLELRDYQLEGL-NWLAHSWCKSNSVILADEMGLGKTIqTISFLSYLFHQHQLYGPFLIVVP-LSTLTSWQREFEIWAPe 571
Cdd:pfam04851    1 KLELRPYQIEAIeNLLESIKNGQKRGLIVMATGSGKTL-TAAKLIARLFKKGPIKKVLFLVPrKDLLEQALEEFKKFLP- 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356   572 iNVVVYIGDLMSRNTIREYewihsQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRLkNDDSllYKTLID-FK 650
Cdd:pfam04851   79 -NYVEIGEIISGDKKDESV-----DDNKIVVTTIQSLYKALELASLELLPDFFDVIIIDEAHRS-GASS--YRNILEyFK 149
                          170
                   ....*....|.
gi 545493356   651 SHHRLLITGTP 661
Cdd:pfam04851  150 PAFLLGLTATP 160
Chromo pfam00385
Chromo (CHRromatin Organisation MOdifier) domain;
392-460 9.17e-10

Chromo (CHRromatin Organisation MOdifier) domain;


Pssm-ID: 395309 [Multi-domain]  Cd Length: 52  Bit Score: 55.67  E-value: 9.17e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 545493356   392 IVERVIAVKTSKSTLGqtdfpahsrkpapsnepEYLCKWMGLPYSECSWEDEALIgKKFQSCIDSFHSR 460
Cdd:pfam00385    2 EVERILDHRKDKGGKE-----------------EYLVKWKGYPYDENTWEPEENL-SKCPELIEEFEDR 52
DEXQc_bact_SNF2 cd18013
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ...
497-676 1.83e-09

DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprise a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. The bacterial SNF2 present in this family are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350771 [Multi-domain]  Cd Length: 218  Bit Score: 59.67  E-value: 1.83e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGLNW-LAHSWCKsnsvILADeMGLGKTIQTISFLSYLFHQhQLYGPFLIVVPLSTLTS-WQREFEIWAPEINV 574
Cdd:cd18013     1 PHPYQKVAINFiIEHPYCG----LFLD-MGLGKTVTTLTALSDLQLD-DFTRRVLVIAPLRVARStWPDEVEKWNHLRNL 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  575 VVYIGDlmsrNTIREyewihsQTKRLKFNALITTYEI-LLKDKTVLGSINWAFLGV--DEAHRLKNDDSLLYKTLidfKS 651
Cdd:cd18013    75 TVSVAV----GTERQ------RSKAANTPADLYVINReNLKWLVNKSGDPWPFDMVviDELSSFKSPRSKRFKAL---RK 141
                         170       180       190
                  ....*....|....*....|....*....|
gi 545493356  652 HHR-----LLITGTPLQNSLKELWSLLHFI 676
Cdd:cd18013   142 VRPvikrlIGLTGTPSPNGLMDLWAQIALL 171
CD1_tandem_CHD1_yeast_like cd18665
repeat 1 of the paired tandem chromodomains of yeast chromodomain helicase DNA-binding protein ...
302-356 2.90e-09

repeat 1 of the paired tandem chromodomains of yeast chromodomain helicase DNA-binding protein 1, and similar proteins; Repeat 1 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: 349312  Cd Length: 65  Bit Score: 54.70  E-value: 2.90e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 545493356  302 NGDPSGDFDTEKDESEvqYLIKWKGWSYIHSTWESEESLQQqkVKGLKKLENFKK 356
Cdd:cd18665    15 EGLEEGELDDPKENYE--FLIKWTDESHLHNTWETYESLKQ--VRGLKKVDNYIK 65
CHROMO smart00298
Chromatin organization modifier domain;
313-359 5.22e-09

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 53.76  E-value: 5.22e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 545493356    313 KDESEVQYLIKWKGWSYIHSTWESEESLQQqkvkGLKKLENFKKKED 359
Cdd:smart00298   13 KKKGELEYLVKWKGYSYSEDTWEPEENLLN----CSKKLDNYKKKER 55
Chromo pfam00385
Chromo (CHRromatin Organisation MOdifier) domain;
313-357 4.47e-07

Chromo (CHRromatin Organisation MOdifier) domain;


Pssm-ID: 395309 [Multi-domain]  Cd Length: 52  Bit Score: 47.96  E-value: 4.47e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 545493356   313 KDESEVQYLIKWKGWSYIHSTWESEESLQQQKvkglKKLENFKKK 357
Cdd:pfam00385   12 DKGGKEEYLVKWKGYPYDENTWEPEENLSKCP----ELIEEFEDR 52
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
497-661 5.44e-07

DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 50.77  E-value: 5.44e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  497 LRDYQLEGL-NWLAHSWCKSNSVILAdeMGLGKTIQTISFLSYLFHQhqlygPFLIVVP-LSTLTSWQREFEIWAPEINV 574
Cdd:cd17926     1 LRPYQEEALeAWLAHKNNRRGILVLP--TGSGKTLTALALIAYLKEL-----RTLIVVPtDALLDQWKERFEDFLGDSSI 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  575 -VVYIGDLMSRNTIreyewihsqtkrlkfNALITTYEILLKDKTVLGSI--NWAFLGVDEAHRLkndDSLLYKTLID-FK 650
Cdd:cd17926    74 gLIGGGKKKDFDDA---------------NVVVATYQSLSNLAEEEKDLfdQFGLLIVDEAHHL---PAKTFSEILKeLN 135
                         170
                  ....*....|.
gi 545493356  651 SHHRLLITGTP 661
Cdd:cd17926   136 AKYRLGLTATP 146
CD2_tandem_ScCHD1_like cd18664
repeat 2 of the paired tandem chromodomains of yeast chromodomain helicase DNA-binding protein ...
389-460 7.74e-07

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: 47.65  E-value: 7.74e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 545493356  389 QYQIVERVIAVKTSKSTLGQTDFpahsrkpapsnepEYLCKWMGLPYSECSWEDEALIGKKFQSCIDSFHSR 460
Cdd:cd18664     1 EFHVVERIIASQRASLEDGTSQL-------------QYLVKWRRLNYDECTWEDATLIAKLAPEQVDHFQNR 59
CHROMO smart00298
Chromatin organization modifier domain;
393-462 1.69e-06

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 46.44  E-value: 1.69e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356    393 VERVIAVKTSKStlgqtdfpahsrkpapsNEPEYLCKWMGLPYSECSWEDEALIgKKFQSCIDSFHSRNN 462
Cdd:smart00298    4 VEKILDHRWKKK-----------------GELEYLVKWKGYSYSEDTWEPEENL-LNCSKKLDNYKKKER 55
CD2_tandem cd18659
repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier ...
312-343 4.69e-06

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: 45.26  E-value: 4.69e-06
                          10        20        30
                  ....*....|....*....|....*....|..
gi 545493356  312 EKDESEVQYLIKWKGWSYIHSTWESEESLQQQ 343
Cdd:cd18659    13 EDDEGVTEYLVKWKGLPYDECTWESEEDISDI 44
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
822-921 6.92e-06

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: 45.39  E-value: 6.92e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  822 RVLIFSQMVRMLDILAEYLTIkhypfqrldgsikgeirkqaldhfnadgsedfcfLLSTRAGGLGINLASADTVVIFDSD 901
Cdd:cd18785     5 KIIVFTNSIEHAEEIASSLEI----------------------------------LVATNVLGEGIDVPSLDTVIFFDPP 50
                          90       100
                  ....*....|....*....|
gi 545493356  902 WNPQNDLQAQARAHRIGQKK 921
Cdd:cd18785    51 SSAASYIQRVGRAGRGGKDE 70
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
489-1000 1.01e-05

ERCC4-related helicase [Replication, recombination and repair];


Pssm-ID: 224036 [Multi-domain]  Cd Length: 542  Bit Score: 50.42  E-value: 1.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  489 YLGGENLELRDYQLEglnwLAHSWCKSNSVILAdEMGLGKTIQTISFLSYLFHQHQlyGPFLIVVPLSTLTSWQREF--E 566
Cdd:COG1111     8 LIKPNTIEPRLYQLN----IAAKALFKNTLVVL-PTGLGKTFIAAMVIANRLRWFG--GKVLFLAPTKPLVLQHAEFcrK 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  567 IWA-PEINVVVYIGDlmSRNTIREYEWIHSQ----TKRLKFNALITTyeILLKDKTVLgsinwafLGVDEAHRLKNDDSL 641
Cdd:COG1111    81 VTGiPEDEIAALTGE--VRPEEREELWAKKKvfvaTPQVVENDLKAG--RIDLDDVSL-------LIFDEAHRAVGNYAY 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  642 LY--KTLIDFKSHHRLL-ITGTP--LQNSLKELWSLLHFimpEKFEFWEDFEED---HGKGREngyQSLHKVLEPFLLRR 713
Cdd:COG1111   150 VFvaKEYLRSAKNPLILgLTASPgsDLEKIQEVVENLGI---EKVEVRTEEDPDvrpYVKKIK---VEWIKVDLPEEIKE 223
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  714 VKKDVEKSL-----PAKVEQILRVEMSALQKQYYKWILTRnyKALAKGTRGSTSGFLNIVMELKKCcNHC---------- 778
Cdd:COG1111   224 IRDLLRDALkprlkPLKELGVIESSSPVSKKDLLELRQIR--LIMAKNEDSDKFRLLSVLAEAIKL-AHAlelletqgir 300
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  779 ----YLIKPPEENERENGQ---------------EVLLSLIRSS---GKLILLDKLLTR--LRERGNRVLIFSQMVRMLD 834
Cdd:COG1111   301 pfyqYLEKLEEEATKGGSKaakslladpyfkralRLLIRADESGvehPKLEKLREILKEqlEKNGDSRVIVFTEYRDTAE 380
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  835 ILAEYLTiKHYPFQRL----------DGSIKGEIRKQALDHFNADgseDFCFLLSTRAGGLGINLASADTVVIFDSDWNP 904
Cdd:COG1111   381 EIVNFLK-KIGIKARVrfigqasregDKGMSQKEQKEIIDQFRKG---EYNVLVATSVGEEGLDIPEVDLVIFYEPVPSE 456
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  905 QNDLQaqaRAHRIGQKKQVNIYRLVTKGTVEEEIIERAKKKmvldhlvIQRMDTTGRTVlennSGRSNSNPFNKEELT-- 982
Cdd:COG1111   457 IRSIQ---RKGRTGRKRKGRVVVLVTEGTRDEAYYYSSRRK-------EQKMIESIRGL----SLELKVRLPEKEEPSgd 522
                         570
                  ....*....|....*....
gi 545493356  983 -AILKFGAEDLfKELEGEE 1000
Cdd:COG1111   523 gQKIPEDAETL-LEVVGEE 540
CD_CSD cd00024
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
310-342 1.28e-05

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: 44.00  E-value: 1.28e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 545493356  310 DTEKDESEVQYLIKWKGWSYIHSTWESEESLQQ 342
Cdd:cd00024     8 DHRVRKGKLEYLVKWKGYPPEENTWEPEENLTN 40
CD1_tandem_CHD5-9_like cd18668
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ...
271-346 1.80e-05

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: 44.25  E-value: 1.80e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  271 DNSETIEKVLDSRLGKKGAtgasttvyaieangdpsgdfDTEKDESEVQ-YLIKWKGWSYIHSTWESEESLQ------QQ 343
Cdd:cd18668     2 EDTMIIEKILASRKKKKEK--------------------EEGAEEIEVEeYLVKYKNFSYLHCEWKTEEELEkgdkriKQ 61

                  ...
gi 545493356  344 KVK 346
Cdd:cd18668    62 KIK 64
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
803-918 3.49e-05

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


Pssm-ID: 223587 [Multi-domain]  Cd Length: 513  Bit Score: 48.63  E-value: 3.49e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  803 SGKLILLDKLLTRLRERgnRVLIFSQMVRMLDILAEYLTIKHYPFQRLDGSIKGEIRKQALDHFNaDGSEDfcFLLSTRA 882
Cdd:COG0513   258 EEKLELLLKLLKDEDEG--RVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFK-DGELR--VLVATDV 332
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 545493356  883 GGLGINLASADTVVIFDSDWNPQNDLqaqaraHRIG 918
Cdd:COG0513   333 AARGLDIPDVSHVINYDLPLDPEDYV------HRIG 362
CD_polycomb cd18644
chromodomain of polycomb; CHRomatin Organization Modifier (chromo) domain of the PcG ...
318-358 6.63e-05

chromodomain of polycomb; CHRomatin Organization Modifier (chromo) domain of the PcG (polycomb-group) chromodomain protein Polycomb (Pc) from Drosophila melanogaster, anthropod, worm, and sea cucumber, and similar proteins. Pc is a component of the Polycomb-group (PcG) multiprotein PRC1 complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. The core subunits of PRC1 are polycomb (Pc), polyhomeotic (Ph), posterior sex combs (Psc), and sex comb extra (Sce, also known as dRing). Polycomb (Pc) plays a role in modulating life span in flies, it negatively regulates longevity.


Pssm-ID: 349291  Cd Length: 54  Bit Score: 42.07  E-value: 6.63e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 545493356  318 VQYLIKWKGWSYIHSTWESEESLQQQKVkglkkLENFKKKE 358
Cdd:cd18644    19 VEYLVKWKGWSNKHNTWEPEENILDRRL-----IEIFERTN 54
CD_polycomb_like cd18627
chromodomain of polycomb and chromobox family proteins; CHRomatin Organization Modifier ...
318-340 9.11e-05

chromodomain of polycomb and chromobox family proteins; CHRomatin Organization Modifier (chromo) domain of Polycomb and Polycomb-group (PcG) chromobox (CBX) family proteins such as CBX2, CBX4, CBX6, CBX7, and CBX8. These CBX proteins are components of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells.


Pssm-ID: 349277  Cd Length: 49  Bit Score: 41.61  E-value: 9.11e-05
                          10        20
                  ....*....|....*....|...
gi 545493356  318 VQYLIKWKGWSYIHSTWESEESL 340
Cdd:cd18627    16 VEYLVKWKGWSQKYNTWEPEENI 38
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
518-652 9.13e-05

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 44.32  E-value: 9.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545493356  518 VILADEMGLGKTIQ-TISFLSYLFHQHqlyGPFLIVVPLSTLT-SWQREFEIWAPEINVVVYIGDLMS-----RNTIREY 590
Cdd:cd00046     4 VLITAPTGSGKTLAaLLAALLLLLKKG---KKVLVLVPTKALAlQTAERLRELFGPGIRVAVLVGGSSaeereKNKLGDA 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 545493356  591 EWIhsqtkrlkfnalITTYEILLKDKTVLGSI---NWAFLGVDEAHR-LKNDDSLLYKTLIDFKSH 652
Cdd:cd00046    81 DII------------IATPDMLLNLLLREDRLflkDLKLIIVDEAHAlLIDSRGALILDLAVRKAG 134
CD2_tandem_CHD3-4_like cd18662
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and ...
416-458 2.47e-04

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: 40.33  E-value: 2.47e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 545493356  416 RKPAPSNEpEYLCKWMGLPYSECSWEDEALIGKKFQSCIDSFH 458
Cdd:cd18662    13 RVDKDGNT-WYLVKWRDLPYDQSTWESEDDDIPDYEKHIQEYW 54
CD2_tandem_CHD5-9_like cd18663
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ...
390-444 5.41e-04

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: 39.58  E-value: 5.41e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 545493356  390 YQIVERVIAVKTSKStlgqtdfpahsrkpAPSNEP--EYLCKWMGLPYSECSWEDEA 444
Cdd:cd18663     3 YVEVDRILDVSVSTD--------------PNTGEPvtHYLVKWCSLPYEDSTWELEE 45
chromodomain cd18968
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
319-340 6.57e-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: 349324  Cd Length: 57  Bit Score: 39.25  E-value: 6.57e-04
                          10        20
                  ....*....|....*....|..
gi 545493356  319 QYLIKWKGWSYIHSTWESEESL 340
Cdd:cd18968    24 KYLVKWAGYPDEENTWEPEESF 45
CD_Cbx2 cd18647
chromodomain of chromobox homolog 2; CHRomatin Organization Modifier (chromo) domain of ...
315-340 1.26e-03

chromodomain of chromobox homolog 2; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 2 (CBX2), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells.


Pssm-ID: 349294  Cd Length: 53  Bit Score: 38.50  E-value: 1.26e-03
                          10        20
                  ....*....|....*....|....*.
gi 545493356  315 ESEVQYLIKWKGWSYIHSTWESEESL 340
Cdd:cd18647    16 KGKLEYLVKWRGWSSKHNSWEPEENI 41
CD_Cbx6 cd18648
chromodomain of chromobox homolog 6; CHRomatin Organization Modifier (chromo) domain of ...
315-360 1.89e-03

chromodomain of chromobox homolog 6; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 6 (CBX6), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells.


Pssm-ID: 349295  Cd Length: 58  Bit Score: 38.11  E-value: 1.89e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 545493356  315 ESEVQYLIKWKGWSYIHSTWESEESLQQQKVkglkkLENFKKKEDE 360
Cdd:cd18648    16 KGRIEYLVKWKGWAIKYSTWEPEENILDSRL-----IAAFEQKERE 56
CD2_tandem_CHD5-9_like cd18663
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ...
310-352 1.95e-03

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: 38.04  E-value: 1.95e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 545493356  310 DTEKDESEVQYLIKWKGWSYIHSTWESEESLQQQKVKGLKKLE 352
Cdd:cd18663    17 DPNTGEPVTHYLVKWCSLPYEDSTWELEEDVDPAKIEEFEKLR 59
CD_Cbx8 cd18649
chromodomain of chromobox homolog 8; CHRomatin Organization Modifier (chromo) domain of ...
315-340 2.36e-03

chromodomain of chromobox homolog 8; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 8 (CBX8), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells. CBX proteins may act as an oncogene or tumor suppressor in a cell-type-dependent manner, CBX8 for example promotes proliferation while suppressing metastasis, in colorectal carcinoma progression.


Pssm-ID: 349296  Cd Length: 55  Bit Score: 37.78  E-value: 2.36e-03
                          10        20
                  ....*....|....*....|....*.
gi 545493356  315 ESEVQYLIKWKGWSYIHSTWESEESL 340
Cdd:cd18649    17 KGRMEYLVKWKGWSQKYSTWEPEENI 42
CD_HP1alpha_Cbx5 cd18651
chromodomain of heterochromatin protein 1 homolog alpha; CHRomatin Organization Modifier ...
315-340 6.53e-03

chromodomain of heterochromatin protein 1 homolog alpha; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog alpha (also known as HP1alpha, Cbx5, and Chromobox 5), and related proteins. HP1alpha has diverse functions in heterochromatin formation, gene regulation, and mitotic progression, and forms complex networks of gene, RNA, and protein interactions. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha, HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3).


Pssm-ID: 349298  Cd Length: 50  Bit Score: 36.51  E-value: 6.53e-03
                          10        20
                  ....*....|....*....|....*.
gi 545493356  315 ESEVQYLIKWKGWSYIHSTWESEESL 340
Cdd:cd18651    14 KGQVEYLLKWKGFSEEHNTWEPEKNL 39
CD_MarY1_POL_like cd18975
chromodomain of Tricholoma matsutake polyprotein, and similar proteins; This subgroup includes ...
310-345 6.81e-03

chromodomain of Tricholoma matsutake polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in the polyprotein from the MarY1 Ty3/Gypsy long terminal repeat (LTR) retroelement from the from the Ectomycorrhizal Basidiomycete Tricholoma matsutake. The pol gene in TY3/gypsy elements generally encodes domains in the following order: prt-reverse transcriptase-RNase H-integrase, in marY1 POL the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and 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: 349331  Cd Length: 49  Bit Score: 36.37  E-value: 6.81e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 545493356  310 DTEKDESEVQYLIKWKGWSYIHSTWESEESLQQQKV 345
Cdd:cd18975     8 NSRLHRGKLQYLIQWKGYPLEEASWELEDNIKNPRL 43
CD_HP1beta_Cbx1 cd18650
chromodomain of heterochromatin protein 1 homolog beta; CHRomatin Organization Modifier ...
315-340 7.09e-03

chromodomain of heterochromatin protein 1 homolog beta; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog beta (also known as HP1beta, CBX1, and chromobox 1), and related proteins. HP1beta is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta, and HP1gamma (also known as Cbx3).


Pssm-ID: 349297  Cd Length: 50  Bit Score: 36.08  E-value: 7.09e-03
                          10        20
                  ....*....|....*....|....*.
gi 545493356  315 ESEVQYLIKWKGWSYIHSTWESEESL 340
Cdd:cd18650    14 KGKVEYLLKWKGFSDEDNTWEPEENL 39
CD2_tandem_CHD3-4_like cd18662
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and ...
315-339 8.30e-03

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: 36.09  E-value: 8.30e-03
                          10        20
                  ....*....|....*....|....*
gi 545493356  315 ESEVQYLIKWKGWSYIHSTWESEES 339
Cdd:cd18662    17 DGNTWYLVKWRDLPYDQSTWESEDD 41
CD_POL_like cd18974
chromodomain of Penicillium solitum protein PENSOL_c198G03123; This subgroup includes the ...
310-356 9.53e-03

chromodomain of Penicillium solitum protein PENSOL_c198G03123; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Penicillium solitum protein PENSOL_c198G03123 a putative polyprotein from a Ty3/Gypsy long terminal repeat (LTR) retroelement. The pol gene in TY3/gypsy elements generally encodes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and 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: 349330  Cd Length: 50  Bit Score: 35.92  E-value: 9.53e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 545493356  310 DTEKDESEVQYLIKWKGWSYIHSTWESEESLQQQKvkglKKLENFKK 356
Cdd:cd18974     8 DEKMIDDELHYLVKWKGWPAEYNQWEPEDDMENAP----KAIQSYEK 50
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.19
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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