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Conserved domains on  [gi|1622945983|ref|XP_028705438|]
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chromodomain-helicase-DNA-binding protein 1 isoform X1 [Macaca mulatta]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
466-703 2.79e-162

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


The actual alignment was detected with superfamily member cd18054:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 237  Bit Score: 493.75  E-value: 2.79e-162
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  466 RPRFVALKKQPSYIGGhEGLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPL 545
Cdd:cd18054      1 RPRFVALKKQPSYIGG-ENLELRDYQLEGLNWLAHSWCKNNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLLVVPL 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  546 STLTSWQREIQTWASQMNAVVYLGDINSRNMIRTHEWTHHQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRL 625
Cdd:cd18054     80 STLTSWQREFEIWAPEINVVVYIGDLMSRNTIREYEWIHSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRL 159
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622945983  626 KNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYGYASLHKELEPFLLRR 703
Cdd:cd18054    160 KNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGRENGYQSLHKVLEPFLLRR 237
PLN03142 super family cl33647
Probable chromatin-remodeling complex ATPase chain; Provisional
470-1006 9.29e-160

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: 516.66  E-value: 9.29e-160
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  470 VALKKQPSYIGGheglELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLT 549
Cdd:PLN03142   157 TRLLVQPSCIKG----KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPKSTLG 232
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  550 SWQREIQTWASQMNAVVYLGDINSRNMIRthewtHHQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDD 629
Cdd:PLN03142   233 NWMNEIRRFCPVLRAVKFHGNPEERAHQR-----EELLVAGKFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNEN 307
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  630 SLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYGYAS----LHKELEPFLLRRVK 705
Cdd:PLN03142   308 SLLSKTMRLFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDQQEvvqqLHKVLRPFLLRRLK 387
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  706 KDVEKSLPAKVEQILRMEMSALQKQYYKWILTRNYKALSKGskGSTSGFLNIMMELKKCCNHCYLIKPPDNNEFYNKQEa 785
Cdd:PLN03142   388 SDVEKGLPPKKETILKVGMSQMQKQYYKALLQKDLDVVNAG--GERKRLLNIAMQLRKCCNHPYLFQGAEPGPPYTTGE- 464
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  786 lqHLIRSSGKLILLDKLLIRLRERGNRVLIFSQMVRMLDILAEYLKYRQFPFQRLDGSIKGELRKQALDHFNAEGSEDFC 865
Cdd:PLN03142   465 --HLVENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFV 542
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  866 FLLSTRAGGLGINLASADTVVIFDSDWNPQNDLQAQARAHRIGQKKQVNIYRLVTKGSVEEDILERAKKKMVLDHLVIQ- 944
Cdd:PLN03142   543 FLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVIQq 622
                          490       500       510       520       530       540
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1622945983  945 -RMdTTGKTVlhtgsapssstpfNKEELSAILKFGAEELFKEPEGEEQEPqemDIDEILKRAE 1006
Cdd:PLN03142   623 gRL-AEQKTV-------------NKDELLQMVRYGAEMVFSSKDSTITDE---DIDRIIAKGE 668
CD1_tandem_CHD1-2_like cd18666
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ...
282-360 1.63e-45

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: 158.61  E-value: 1.63e-45
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1622945983  282 RFMDCRIGRKGATGATTTIYAVEADGDPNAGFEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKK 360
Cdd:cd18666      7 RVLDHRIGRKGATGASTTIYAVEADGDPNAGFDPEDEETEIQYLIKWKGWSHIHNTWESEESLKDQNVKGMKKLENYKK 85
CD2_tandem_CHD1-2_like cd18661
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ...
393-449 2.28e-34

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: 125.88  E-value: 2.28e-34
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622945983  393 QYQIVERIIAHSNQKSA-AGYPDYYCKWQGLPYSECSWEDGALISKKFQACIDEYFSR 449
Cdd:cd18661      1 QYQIVERIIAHSPQKSAaSGYPDYLCKWQGLPYSECTWEDGALISKKFQACIDEYHSR 58
CDH1_2_SANT_HL1 super family cl39715
CDH1/2 SANT-Helical linker 1; CDH1 is an ATP-dependent chromatin-remodelling factor and plays ...
1130-1216 2.69e-33

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).


The actual alignment was detected with superfamily member pfam18375:

Pssm-ID: 477096  Cd Length: 90  Bit Score: 124.00  E-value: 2.69e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983 1130 KGFSDAEIRRFIKSYKKFGGPLERLDAIARDAELVDKSETDLRRLGELVHNGCIKALKD----SSSGTERTGGRlGKVKG 1205
Cdd:pfam18375    1 KGFTDAEIRRFVKSYKKFSAPLKRLDAIACDAELQEKPLSDLRRLGELLKERCDEAMEEytekEDENPGADGGK-KRIRG 79
                           90
                   ....*....|.
gi 1622945983 1206 PTFRISGVQVN 1216
Cdd:pfam18375   80 PSFKLGGVSVN 90
DUF4208 pfam13907
Domain of unknown function (DUF4208); This domain is found at the C-terminus of ...
1502-1592 6.74e-28

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: 464035  Cd Length: 93  Bit Score: 108.88  E-value: 6.74e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983 1502 ELDQKTFS-ICKERMRPVKAALKQLDRPEKGLSEREQLEHTRQCLIKIGDHITECLKEYtNPEQIKQWRKNLWIFVSKFT 1580
Cdd:pfam13907    1 DEYESMDEeECKELMRPVKKSLKRLKKGTKGLSRKERAKILKKELLKIGDFIDSLLEET-KKEKKEKLRKHLWSFVSKFW 79
                           90
                   ....*....|....
gi 1622945983 1581 E--FDARKLHKLYK 1592
Cdd:pfam13907   80 PnkVSGKKLKEMYK 93
HisXaaSer_A3 super family cl45756
His-Xaa-Ser repeat protein HxsA3; This model represents an alternate form of the His-Xaa-Ser ...
1725-1756 2.02e-04

His-Xaa-Ser repeat protein HxsA3; This model represents an alternate form of the His-Xaa-Ser repeat protein HxsA, while TIGR03979 represents a more common form. The model covers a conserved N-terminal region, followed by the His-Xaa-Ser repeat region, but does not cover the C-terminal region, which is highly variable in this branch of His-Xaa-Ser repeat family protein.


The actual alignment was detected with superfamily member NF038309:

Pssm-ID: 439608  Cd Length: 81  Bit Score: 41.53  E-value: 2.02e-04
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1622945983 1725 HRSHSDHRLHSDHRSSSEYTH--HKSSRDYRYHS 1756
Cdd:NF038309    47 HRSHSSHSSHSSHSSGSSGGHssHSSHSSHSSHS 80
U2AF_lg super family cl36941
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
1694-1803 6.36e-04

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


The actual alignment was detected with superfamily member TIGR01642:

Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 44.50  E-value: 6.36e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983 1694 DREKHRKLDDHRSRDhRSNLEGSLKDRSHSDHRSHSDHRLHSDHRSSSEYTHH-KSSRDYRYHSDWQMDHRASSsgpRSP 1772
Cdd:TIGR01642    2 DEEPDREREKSRGRD-RDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRdRRRYDSRSPRSLRYSSVRRS---RDR 77
                           90       100       110
                   ....*....|....*....|....*....|.
gi 1622945983 1773 LDQRSPYGSRSPFEHSVEHKSTPEHTWSSRK 1803
Cdd:TIGR01642   78 PRRRSRSVRSIEQHRRRLRDRSPSNQWRKDD 108
 
Name Accession Description Interval E-value
DEXHc_CHD2 cd18054
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; ...
466-703 2.79e-162

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: 493.75  E-value: 2.79e-162
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  466 RPRFVALKKQPSYIGGhEGLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPL 545
Cdd:cd18054      1 RPRFVALKKQPSYIGG-ENLELRDYQLEGLNWLAHSWCKNNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLLVVPL 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  546 STLTSWQREIQTWASQMNAVVYLGDINSRNMIRTHEWTHHQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRL 625
Cdd:cd18054     80 STLTSWQREFEIWAPEINVVVYIGDLMSRNTIREYEWIHSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRL 159
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622945983  626 KNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYGYASLHKELEPFLLRR 703
Cdd:cd18054    160 KNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGRENGYQSLHKVLEPFLLRR 237
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
470-1006 9.29e-160

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 516.66  E-value: 9.29e-160
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  470 VALKKQPSYIGGheglELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLT 549
Cdd:PLN03142   157 TRLLVQPSCIKG----KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPKSTLG 232
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  550 SWQREIQTWASQMNAVVYLGDINSRNMIRthewtHHQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDD 629
Cdd:PLN03142   233 NWMNEIRRFCPVLRAVKFHGNPEERAHQR-----EELLVAGKFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNEN 307
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  630 SLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYGYAS----LHKELEPFLLRRVK 705
Cdd:PLN03142   308 SLLSKTMRLFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDQQEvvqqLHKVLRPFLLRRLK 387
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  706 KDVEKSLPAKVEQILRMEMSALQKQYYKWILTRNYKALSKGskGSTSGFLNIMMELKKCCNHCYLIKPPDNNEFYNKQEa 785
Cdd:PLN03142   388 SDVEKGLPPKKETILKVGMSQMQKQYYKALLQKDLDVVNAG--GERKRLLNIAMQLRKCCNHPYLFQGAEPGPPYTTGE- 464
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  786 lqHLIRSSGKLILLDKLLIRLRERGNRVLIFSQMVRMLDILAEYLKYRQFPFQRLDGSIKGELRKQALDHFNAEGSEDFC 865
Cdd:PLN03142   465 --HLVENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFV 542
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  866 FLLSTRAGGLGINLASADTVVIFDSDWNPQNDLQAQARAHRIGQKKQVNIYRLVTKGSVEEDILERAKKKMVLDHLVIQ- 944
Cdd:PLN03142   543 FLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVIQq 622
                          490       500       510       520       530       540
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1622945983  945 -RMdTTGKTVlhtgsapssstpfNKEELSAILKFGAEELFKEPEGEEQEPqemDIDEILKRAE 1006
Cdd:PLN03142   623 gRL-AEQKTV-------------NKDELLQMVRYGAEMVFSSKDSTITDE---DIDRIIAKGE 668
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
484-942 3.20e-119

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 393.05  E-value: 3.20e-119
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  484 GLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLyGPFLLVVPLSTLTSWQREIQTWASQMN 563
Cdd:COG0553    239 KATLRPYQLEGAAWLLFLRRLGLGGLLADDMGLGKTIQALALLLELKERGLA-RPVLIVAPTSLVGNWQRELAKFAPGLR 317
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  564 AVVYLGDINSRNMIRthEWTHHQtkrlkfnILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNH 643
Cdd:COG0553    318 VLVLDGTRERAKGAN--PFEDAD-------LVITSYGLLRRDIELLAAVDWDLVILDEAQHIKNPATKRAKAVRALKARH 388
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  644 RLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYG----YASLHKELEPFLLRRVKKDVEKSLPAKVEQI 719
Cdd:COG0553    389 RLALTGTPVENRLEELWSLLDFLNPGLLGSLKAFRERFARPIEKGdeeaLERLRRLLRPFLLRRTKEDVLKDLPEKTEET 468
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  720 LRMEMSALQKQYYKwILTRNYKALSKGSKGSTSGF--LNIMMELKKCCNHCYLIKppDNNEFYN----KQEALQHLIRSs 793
Cdd:COG0553    469 LYVELTPEQRALYE-AVLEYLRRELEGAEGIRRRGliLAALTRLRQICSHPALLL--EEGAELSgrsaKLEALLELLEE- 544
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  794 gklilldkllirLRERGNRVLIFSQMVRMLDILAEYLKYRQFPFQRLDGSIKGELRKQALDHFNAEGSEDFcFLLSTRAG 873
Cdd:COG0553    545 ------------LLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQEGPEAPV-FLISLKAG 611
                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  874 GLGINLASADTVVIFDSDWNPQNDLQAQARAHRIGQKKQVNIYRLVTKGSVEEDILER-AKKKMVLDHLV 942
Cdd:COG0553    612 GEGLNLTAADHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEEKILELlEEKRALAESVL 681
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
490-771 7.37e-113

SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.


Pssm-ID: 425504 [Multi-domain]  Cd Length: 289  Bit Score: 359.69  E-value: 7.37e-113
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  490 YQLNGLNWLAHSWCK-GNSCILADEMGLGKTIQTISFLNYLFHEHQLYG-PFLLVVPLSTLTSWQREIQTWA--SQMNAV 565
Cdd:pfam00176    1 YQIEGVNWMLSLENNlGRGGILADEMGLGKTLQTISLLLYLKHVDKNWGgPTLIVVPLSLLHNWMNEFERWVspPALRVV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  566 VYLGDINSRnmirtHEWTHHQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRL 645
Cdd:pfam00176   81 VLHGNKRPQ-----ERWKNDPNFLADFDVVITTYETLRKHKELLKKVHWHRIVLDEGHRLKNSKSKLSKALKSLKTRNRW 155
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  646 LITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGK-----GREYGYASLHKELEPFLLRRVKKDVEKSLPAKVEQIL 720
Cdd:pfam00176  156 ILTGTPLQNNLEELWALLNFLRPGPFGSLSTFRNWFDRpiergGGKKGVSRLHKLLKPFLLRRTKKDVEKSLPPKVEYIL 235
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1622945983  721 RMEMSALQKQYYK-WILTRNYKALSKGSKGST--SGFLNIMMELKKCCNHCYLI 771
Cdd:pfam00176  236 FCRLSKLQRKLYQtFLLKKDLNAIKTGEGGREikASLLNILMRLRKICNHPGLI 289
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
808-919 2.14e-51

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: 177.67  E-value: 2.14e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  808 ERGNRVLIFSQMVRMLDILAEYLKYRQFPFQRLDGSIKGELRKQALDHFNaEGSEDFCFLLSTRAGGLGINLASADTVVI 887
Cdd:cd18793     25 EPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFN-EDPDIRVFLLSTKAGGVGLNLTAANRVIL 103
                           90       100       110
                   ....*....|....*....|....*....|..
gi 1622945983  888 FDSDWNPQNDLQAQARAHRIGQKKQVNIYRLV 919
Cdd:cd18793    104 YDPWWNPAVEEQAIDRAHRIGQKKPVVVYRLI 135
CD1_tandem_CHD1-2_like cd18666
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ...
282-360 1.63e-45

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: 158.61  E-value: 1.63e-45
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1622945983  282 RFMDCRIGRKGATGATTTIYAVEADGDPNAGFEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKK 360
Cdd:cd18666      7 RVLDHRIGRKGATGASTTIYAVEADGDPNAGFDPEDEETEIQYLIKWKGWSHIHNTWESEESLKDQNVKGMKKLENYKK 85
CD2_tandem_CHD1-2_like cd18661
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ...
393-449 2.28e-34

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: 125.88  E-value: 2.28e-34
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622945983  393 QYQIVERIIAHSNQKSA-AGYPDYYCKWQGLPYSECSWEDGALISKKFQACIDEYFSR 449
Cdd:cd18661      1 QYQIVERIIAHSPQKSAaSGYPDYLCKWQGLPYSECTWEDGALISKKFQACIDEYHSR 58
CDH1_2_SANT_HL1 pfam18375
CDH1/2 SANT-Helical linker 1; CDH1 is an ATP-dependent chromatin-remodelling factor and plays ...
1130-1216 2.69e-33

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: 465731  Cd Length: 90  Bit Score: 124.00  E-value: 2.69e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983 1130 KGFSDAEIRRFIKSYKKFGGPLERLDAIARDAELVDKSETDLRRLGELVHNGCIKALKD----SSSGTERTGGRlGKVKG 1205
Cdd:pfam18375    1 KGFTDAEIRRFVKSYKKFSAPLKRLDAIACDAELQEKPLSDLRRLGELLKERCDEAMEEytekEDENPGADGGK-KRIRG 79
                           90
                   ....*....|.
gi 1622945983 1206 PTFRISGVQVN 1216
Cdd:pfam18375   80 PSFKLGGVSVN 90
DEXDc smart00487
DEAD-like helicases superfamily;
479-680 5.75e-28

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 112.97  E-value: 5.75e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983   479 IGGHEGLELRDYQLNGLNWLAHSWckgNSCILADEMGLGKTIQTISFLNYLFHEHQlYGPFLLVVPLSTLT-SWQREIQT 557
Cdd:smart00487    1 IEKFGFEPLRPYQKEAIEALLSGL---RDVILAAPTGSGKTLAALLPALEALKRGK-GGRVLVLVPTRELAeQWAEELKK 76
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983   558 WASQMN--AVVYLGDINSRNMIRthewthhQTKRLKFNILLTTYEILLKD--KAFLGGLNWAFIGVDEAHRLKND---DS 630
Cdd:smart00487   77 LGPSLGlkVVGLYGGDSKREQLR-------KLESGKTDILVTTPGRLLDLleNDKLSLSNVDLVILDEAHRLLDGgfgDQ 149
                           170       180       190       200       210
                    ....*....|....*....|....*....|....*....|....*....|...
gi 1622945983   631 LLYKTLIDFKSNHRLLITGTP---LQNSLKELWSLLHFIMPEkFSSWEDFEEE 680
Cdd:smart00487  150 LEKLLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVG-FTPLEPIEQF 201
DUF4208 pfam13907
Domain of unknown function (DUF4208); This domain is found at the C-terminus of ...
1502-1592 6.74e-28

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: 464035  Cd Length: 93  Bit Score: 108.88  E-value: 6.74e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983 1502 ELDQKTFS-ICKERMRPVKAALKQLDRPEKGLSEREQLEHTRQCLIKIGDHITECLKEYtNPEQIKQWRKNLWIFVSKFT 1580
Cdd:pfam13907    1 DEYESMDEeECKELMRPVKKSLKRLKKGTKGLSRKERAKILKKELLKIGDFIDSLLEET-KKEKKEKLRKHLWSFVSKFW 79
                           90
                   ....*....|....
gi 1622945983 1581 E--FDARKLHKLYK 1592
Cdd:pfam13907   80 PnkVSGKKLKEMYK 93
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
808-908 8.10e-26

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 103.44  E-value: 8.10e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  808 ERGNRVLIFSQMVRMLDilAEYLKYRQ-FPFQRLDGSIKGELRKQALDHFNaegSEDFCFLLSTRAGGLGINLASADTVV 886
Cdd:pfam00271   13 ERGGKVLIFSQTKKTLE--AELLLEKEgIKVARLHGDLSQEEREEILEDFR---KGKIDVLVATDVAERGLDLPDVDLVI 87
                           90       100
                   ....*....|....*....|..
gi 1622945983  887 IFDSDWNPQNDLQAQARAHRIG 908
Cdd:pfam00271   88 NYDLPWNPASYIQRIGRAGRAG 109
HELICc smart00490
helicase superfamily c-terminal domain;
824-908 1.89e-22

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 93.05  E-value: 1.89e-22
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983   824 DILAEYLKYRQFPFQRLDGSIKGELRKQALDHFNaegSEDFCFLLSTRAGGLGINLASADTVVIFDSDWNPQNDLQAQAR 903
Cdd:smart00490    1 EELAELLKELGIKVARLHGGLSQEEREEILDKFN---NGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGR 77

                    ....*
gi 1622945983   904 AHRIG 908
Cdd:smart00490   78 AGRAG 82
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
396-449 1.10e-10

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 58.36  E-value: 1.10e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1622945983  396 IVERIIAHSNQKSaaGYPDYYCKWQGLPYSECSWEDGALISKKfQACIDEYFSR 449
Cdd:pfam00385    2 EVERILDHRKDKG--GKEEYLVKWKGYPYDENTWEPEENLSKC-PELIEEFKDR 52
CHROMO smart00298
Chromatin organization modifier domain;
315-361 3.08e-09

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 54.53  E-value: 3.08e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1622945983   315 KNKEPGEIQYLIKWKGWSHIHNTWETEETLKQqnvrGMKKLDNYKKK 361
Cdd:smart00298   11 RWKKKGELEYLVKWKGYSYSEDTWEPEENLLN----CSKKLDNYKKK 53
CHROMO smart00298
Chromatin organization modifier domain;
397-451 1.04e-07

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 49.90  E-value: 1.04e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 1622945983   397 VERIIAHSNQKSaaGYPDYYCKWQGLPYSECSWEDGALISkKFQACIDEYFSRNQ 451
Cdd:smart00298    4 VEKILDHRWKKK--GELEYLVKWKGYSYSEDTWEPEENLL-NCSKKLDNYKKKER 55
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
314-361 5.32e-06

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 45.26  E-value: 5.32e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1622945983  314 EKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNvrgmKKLDNYKKK 361
Cdd:pfam00385    9 HRKDKGGKEEYLVKWKGYPYDENTWEPEENLSKCP----ELIEEFKDR 52
HisXaaSer_A3 NF038309
His-Xaa-Ser repeat protein HxsA3; This model represents an alternate form of the His-Xaa-Ser ...
1725-1756 2.02e-04

His-Xaa-Ser repeat protein HxsA3; This model represents an alternate form of the His-Xaa-Ser repeat protein HxsA, while TIGR03979 represents a more common form. The model covers a conserved N-terminal region, followed by the His-Xaa-Ser repeat region, but does not cover the C-terminal region, which is highly variable in this branch of His-Xaa-Ser repeat family protein.


Pssm-ID: 439608  Cd Length: 81  Bit Score: 41.53  E-value: 2.02e-04
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1622945983 1725 HRSHSDHRLHSDHRSSSEYTH--HKSSRDYRYHS 1756
Cdd:NF038309    47 HRSHSSHSSHSSHSSGSSGGHssHSSHSSHSSHS 80
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
1694-1803 6.36e-04

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 44.50  E-value: 6.36e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983 1694 DREKHRKLDDHRSRDhRSNLEGSLKDRSHSDHRSHSDHRLHSDHRSSSEYTHH-KSSRDYRYHSDWQMDHRASSsgpRSP 1772
Cdd:TIGR01642    2 DEEPDREREKSRGRD-RDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRdRRRYDSRSPRSLRYSSVRRS---RDR 77
                           90       100       110
                   ....*....|....*....|....*....|.
gi 1622945983 1773 LDQRSPYGSRSPFEHSVEHKSTPEHTWSSRK 1803
Cdd:TIGR01642   78 PRRRSRSVRSIEQHRRRLRDRSPSNQWRKDD 108
HisXaaSer_A2 NF038296
His-Xaa-Ser repeat protein HxsA2; This model represents a short form of the His-Xaa-Ser repeat ...
1721-1741 1.14e-03

His-Xaa-Ser repeat protein HxsA2; This model represents a short form of the His-Xaa-Ser repeat protein HxsA, while TIGR03979 represents a long form. In the short form, sequences average about 97 amino acids in length and end with the HXS repeat region.


Pssm-ID: 468458  Cd Length: 96  Bit Score: 40.09  E-value: 1.14e-03
                           10        20
                   ....*....|....*....|.
gi 1622945983 1721 SHSDHRSHSDHRLHSDHRSSS 1741
Cdd:NF038296    76 YHSSHSSHSSHSSHSSHYSSS 96
 
Name Accession Description Interval E-value
DEXHc_CHD2 cd18054
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; ...
466-703 2.79e-162

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: 493.75  E-value: 2.79e-162
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  466 RPRFVALKKQPSYIGGhEGLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPL 545
Cdd:cd18054      1 RPRFVALKKQPSYIGG-ENLELRDYQLEGLNWLAHSWCKNNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLLVVPL 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  546 STLTSWQREIQTWASQMNAVVYLGDINSRNMIRTHEWTHHQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRL 625
Cdd:cd18054     80 STLTSWQREFEIWAPEINVVVYIGDLMSRNTIREYEWIHSQTKRLKFNALITTYEILLKDKTVLGSINWAFLGVDEAHRL 159
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622945983  626 KNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYGYASLHKELEPFLLRR 703
Cdd:cd18054    160 KNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGKGRENGYQSLHKVLEPFLLRR 237
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
470-1006 9.29e-160

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 516.66  E-value: 9.29e-160
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  470 VALKKQPSYIGGheglELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLT 549
Cdd:PLN03142   157 TRLLVQPSCIKG----KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPKSTLG 232
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  550 SWQREIQTWASQMNAVVYLGDINSRNMIRthewtHHQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDD 629
Cdd:PLN03142   233 NWMNEIRRFCPVLRAVKFHGNPEERAHQR-----EELLVAGKFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNEN 307
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  630 SLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYGYAS----LHKELEPFLLRRVK 705
Cdd:PLN03142   308 SLLSKTMRLFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDQQEvvqqLHKVLRPFLLRRLK 387
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  706 KDVEKSLPAKVEQILRMEMSALQKQYYKWILTRNYKALSKGskGSTSGFLNIMMELKKCCNHCYLIKPPDNNEFYNKQEa 785
Cdd:PLN03142   388 SDVEKGLPPKKETILKVGMSQMQKQYYKALLQKDLDVVNAG--GERKRLLNIAMQLRKCCNHPYLFQGAEPGPPYTTGE- 464
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  786 lqHLIRSSGKLILLDKLLIRLRERGNRVLIFSQMVRMLDILAEYLKYRQFPFQRLDGSIKGELRKQALDHFNAEGSEDFC 865
Cdd:PLN03142   465 --HLVENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFV 542
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  866 FLLSTRAGGLGINLASADTVVIFDSDWNPQNDLQAQARAHRIGQKKQVNIYRLVTKGSVEEDILERAKKKMVLDHLVIQ- 944
Cdd:PLN03142   543 FLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVIQq 622
                          490       500       510       520       530       540
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1622945983  945 -RMdTTGKTVlhtgsapssstpfNKEELSAILKFGAEELFKEPEGEEQEPqemDIDEILKRAE 1006
Cdd:PLN03142   623 gRL-AEQKTV-------------NKDELLQMVRYGAEMVFSSKDSTITDE---DIDRIIAKGE 668
DEXHc_CHD1 cd18053
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; ...
467-703 8.16e-158

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: 481.47  E-value: 8.16e-158
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  467 PRFVALKKQPSYIGGHEGLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLS 546
Cdd:cd18053      1 PRFVALKKQPSYIGGHEGLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  547 TLTSWQREIQTWASQMNAVVYLGDINSRNMIRTHEWTHHQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLK 626
Cdd:cd18053     81 TLTSWQREIQTWAPQMNAVVYLGDINSRNMIRTHEWMHPQTKRLKFNILLTTYEILLKDKSFLGGLNWAFIGVDEAHRLK 160
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1622945983  627 NDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYGYASLHKELEPFLLRR 703
Cdd:cd18053    161 NDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYGYASLHKELEPFLLRR 237
DEXHc_CHD1_2 cd17993
DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and ...
486-703 3.06e-145

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: 446.42  E-value: 3.06e-145
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  486 ELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAV 565
Cdd:cd17993      1 ELRDYQLTGLNWLAHSWCKGNNGILADEMGLGKTVQTISFLSYLFHSQQQYGPFLVVVPLSTMPAWQREFAKWAPDMNVI 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  566 VYLGDINSRNMIRTHEWTHHQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRL 645
Cdd:cd17993     81 VYLGDIKSRDTIREYEFYFSQTKKLKFNVLLTTYEIILKDKAFLGSIKWQYLAVDEAHRLKNDESLLYEALKEFKTNNRL 160
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622945983  646 LITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYGYASLHKELEPFLLRR 703
Cdd:cd17993    161 LITGTPLQNSLKELWALLHFLMPGKFDIWEEFEEEHDEEQEKGIADLHKELEPFILRR 218
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
484-942 3.20e-119

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 393.05  E-value: 3.20e-119
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  484 GLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLyGPFLLVVPLSTLTSWQREIQTWASQMN 563
Cdd:COG0553    239 KATLRPYQLEGAAWLLFLRRLGLGGLLADDMGLGKTIQALALLLELKERGLA-RPVLIVAPTSLVGNWQRELAKFAPGLR 317
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  564 AVVYLGDINSRNMIRthEWTHHQtkrlkfnILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNH 643
Cdd:COG0553    318 VLVLDGTRERAKGAN--PFEDAD-------LVITSYGLLRRDIELLAAVDWDLVILDEAQHIKNPATKRAKAVRALKARH 388
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  644 RLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYG----YASLHKELEPFLLRRVKKDVEKSLPAKVEQI 719
Cdd:COG0553    389 RLALTGTPVENRLEELWSLLDFLNPGLLGSLKAFRERFARPIEKGdeeaLERLRRLLRPFLLRRTKEDVLKDLPEKTEET 468
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  720 LRMEMSALQKQYYKwILTRNYKALSKGSKGSTSGF--LNIMMELKKCCNHCYLIKppDNNEFYN----KQEALQHLIRSs 793
Cdd:COG0553    469 LYVELTPEQRALYE-AVLEYLRRELEGAEGIRRRGliLAALTRLRQICSHPALLL--EEGAELSgrsaKLEALLELLEE- 544
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  794 gklilldkllirLRERGNRVLIFSQMVRMLDILAEYLKYRQFPFQRLDGSIKGELRKQALDHFNAEGSEDFcFLLSTRAG 873
Cdd:COG0553    545 ------------LLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQEGPEAPV-FLISLKAG 611
                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  874 GLGINLASADTVVIFDSDWNPQNDLQAQARAHRIGQKKQVNIYRLVTKGSVEEDILER-AKKKMVLDHLV 942
Cdd:COG0553    612 GEGLNLTAADHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEEKILELlEEKRALAESVL 681
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
490-771 7.37e-113

SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.


Pssm-ID: 425504 [Multi-domain]  Cd Length: 289  Bit Score: 359.69  E-value: 7.37e-113
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  490 YQLNGLNWLAHSWCK-GNSCILADEMGLGKTIQTISFLNYLFHEHQLYG-PFLLVVPLSTLTSWQREIQTWA--SQMNAV 565
Cdd:pfam00176    1 YQIEGVNWMLSLENNlGRGGILADEMGLGKTLQTISLLLYLKHVDKNWGgPTLIVVPLSLLHNWMNEFERWVspPALRVV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  566 VYLGDINSRnmirtHEWTHHQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRL 645
Cdd:pfam00176   81 VLHGNKRPQ-----ERWKNDPNFLADFDVVITTYETLRKHKELLKKVHWHRIVLDEGHRLKNSKSKLSKALKSLKTRNRW 155
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  646 LITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGK-----GREYGYASLHKELEPFLLRRVKKDVEKSLPAKVEQIL 720
Cdd:pfam00176  156 ILTGTPLQNNLEELWALLNFLRPGPFGSLSTFRNWFDRpiergGGKKGVSRLHKLLKPFLLRRTKKDVEKSLPPKVEYIL 235
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1622945983  721 RMEMSALQKQYYK-WILTRNYKALSKGSKGST--SGFLNIMMELKKCCNHCYLI 771
Cdd:pfam00176  236 FCRLSKLQRKLYQtFLLKKDLNAIKTGEGGREikASLLNILMRLRKICNHPGLI 289
DEXHc_CHD6_7_8_9 cd17995
DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; ...
487-703 5.33e-91

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: 294.54  E-value: 5.33e-91
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWaSQMNAVV 566
Cdd:cd17995      1 LRDYQLEGVNWLLFNWYNRRNCILADEMGLGKTIQSIAFLEHLYQVEGIRGPFLVIAPLSTIPNWQREFETW-TDMNVVV 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 YLGDINSRNMIRTHEWTHHQTKRL------KFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFK 640
Cdd:cd17995     80 YHGSGESRQIIQQYEMYFKDAQGRkkkgvyKFDVLITTYEMVIADAEELRKIPWRVVVVDEAHRLKNRNSKLLQGLKKLT 159
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622945983  641 SNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGR-EYGYASLHKELEPFLLRR 703
Cdd:cd17995    160 LEHKLLLTGTPLQNNTEELWSLLNFLEPEKFPSSEEFLEEFGDLKtAEQVEKLQALLKPYMLRR 223
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
487-668 1.63e-81

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: 265.58  E-value: 1.63e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAVV 566
Cdd:cd17919      1 LRPYQLEGLNFLLELYENGPGGILADEMGLGKTLQAIAFLAYLLKEGKERGPVLVVCPLSVLENWEREFEKWTPDLRVVV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 YLGDINSRNMIRTHEWTHhqtkrlKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRLL 646
Cdd:cd17919     81 YHGSQRERAQIRAKEKLD------KFDVVLTTYETLRRDKASLRKFRWDLVVVDEAHRLKNPKSQLSKALKALRAKRRLL 154
                          170       180
                   ....*....|....*....|..
gi 1622945983  647 ITGTPLQNSLKELWSLLHFIMP 668
Cdd:cd17919    155 LTGTPLQNNLEELWALLDFLDP 176
DEXHc_SMARCA1_SMARCA5 cd17997
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ...
486-705 5.26e-74

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: 246.08  E-value: 5.26e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  486 ELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAV 565
Cdd:cd17997      3 TMRDYQIRGLNWLISLFENGINGILADEMGLGKTLQTISLLGYLKHYKNINGPHLIIVPKSTLDNWMREFKRWCPSLRVV 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  566 VYLGDINSRnmirtHEWTHHQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRL 645
Cdd:cd17997     83 VLIGDKEER-----ADIIRDVLLPGKFDVCITSYEMVIKEKTVLKKFNWRYIIIDEAHRIKNEKSKLSQIVRLFNSRNRL 157
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622945983  646 LITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEE----EHGKGREYGYAS-LHKELEPFLLRRVK 705
Cdd:cd17997    158 LLTGTPLQNNLHELWALLNFLLPDVFTSSEDFDEwfnvNNCDDDNQEVVQrLHKVLRPFLLRRIK 222
DEXHc_SMARCA2_SMARCA4 cd17996
DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin ...
484-705 2.77e-71

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: 238.42  E-value: 2.77e-71
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  484 GLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMN 563
Cdd:cd17996      1 GGTLKEYQLKGLQWMVSLYNNNLNGILADEMGLGKTIQTISLITYLMEKKKNNGPYLVIVPLSTLSNWVSEFEKWAPSVS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  564 AVVYLGDINSRNMIrthewtHHQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLID-FKSN 642
Cdd:cd17996     81 KIVYKGTPDVRKKL------QSQIRAGKFNVLLTTYEYIIKDKPLLSKIKWKYMIIDEGHRMKNAQSKLTQTLNTyYHAR 154
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1622945983  643 HRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEE--------EHGKGREYGYAS--------LHKELEPFLLRRVK 705
Cdd:cd17996    155 YRLLLTGTPLQNNLPELWALLNFLLPKIFKSCKTFEQwfntpfanTGEQVKIELNEEetlliirrLHKVLRPFLLRRLK 233
DEXHc_HELLS_SMARCA6 cd18009
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ...
484-705 3.48e-70

DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or SMARCA6) is a major epigenetic regulator crucial for normal heterochromatin structure and function. HELLS is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350767 [Multi-domain]  Cd Length: 236  Bit Score: 235.74  E-value: 3.48e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  484 GLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFhEHQLYGPFLLVVPLSTLTSWQREIQTWASQMN 563
Cdd:cd18009      1 GGVMRPYQLEGMEWLRMLWENGINGILADEMGLGKTIQTIALLAHLR-ERGVWGPFLVIAPLSTLPNWVNEFARFTPSVP 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  564 AVVYLGDINSRNMIRTHEWTHHQTKRlKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNH 643
Cdd:cd18009     80 VLLYHGTKEERERLRKKIMKREGTLQ-DFPVVVTSYEIAMRDRKALQHYAWKYLIVDEGHRLKNLNCRLIQELKTFNSDN 158
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622945983  644 RLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFE----------------EEHGKGREYGYASLHKELEPFLLRRVK 705
Cdd:cd18009    159 RLLLTGTPLQNNLSELWSLLNFLLPDVFDDLSSFEswfdfsslsdnaadisNLSEEREQNIVHMLHAILKPFLLRRLK 236
DEXHc_CHD3_4_5 cd17994
DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; ...
487-703 9.22e-68

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: 226.94  E-value: 9.22e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAVV 566
Cdd:cd17994      1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTIQTIVFLYSLYKEGHSKGPFLVSAPLSTIINWEREFEMWAPDFYVVT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 YLGDinsrnmirthewthhqtkrlkfNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRLL 646
Cdd:cd17994     81 YVGD----------------------HVLLTSYELISIDQAILGSIDWAVLVVDEAHRLKNNQSKFFRILNSYKIGYKLL 138
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622945983  647 ITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGK-GREYGYASLHKELEPFLLRR 703
Cdd:cd17994    139 LTGTPLQNNLEELFHLLNFLTPERFNNLQGFLEEFADiSKEDQIKKLHDLLGPHMLRR 196
DEXHc_CHD1L cd18006
DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, ...
487-703 1.88e-67

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: 226.94  E-value: 1.88e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAVV 566
Cdd:cd18006      1 LRPYQLEGVNWLLQCRAEQHGCILGDEMGLGKTCQTISLLWYLAGRLKLLGPFLVLCPLSVLDNWKEELNRFAPDLSVIT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 YLGDINSRNMIRTHEWTHhqtkrLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRLL 646
Cdd:cd18006     81 YMGDKEKRLDLQQDIKST-----NRFHVLLTTYEICLKDASFLKSFPWASLVVDEAHRLKNQNSLLHKTLSEFSVDFRLL 155
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622945983  647 ITGTPLQNSLKELWSLLHFIMPEKFS--SWEDF---EEEHGKGREYgYASLHKELEPFLLRR 703
Cdd:cd18006    156 LTGTPIQNSLQELYALLSFIEPNVFPkdKLDDFikaYSETDDESET-VEELHLLLQPFLLRR 216
DEXHc_CHD3 cd18055
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; ...
487-703 8.90e-63

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: 214.10  E-value: 8.90e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAVV 566
Cdd:cd18055      1 LHMYQLEGLNWLRFSWAQGTDTILADEMGLGKTIQTIVFLYSLYKEGHTKGPFLVSAPLSTIINWEREFQMWAPDFYVVT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 YLGDINSRNMIRTHEWTHHQT--------------KRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLL 632
Cdd:cd18055     81 YTGDKDSRAIIRENEFSFDDNavkggkkafkmkreAQVKFHVLLTSYELVTIDQAALGSIRWACLVVDEAHRLKNNQSKF 160
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622945983  633 YKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGK-GREYGYASLHKELEPFLLRR 703
Cdd:cd18055    161 FRVLNGYKIDHKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADiSKEDQIKKLHDLLGPHMLRR 232
DEXQc_SRCAP cd18003
DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or ...
487-703 5.37e-62

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: 211.44  E-value: 5.37e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAVV 566
Cdd:cd18003      1 LREYQHIGLDWLATLYEKNLNGILADEMGLGKTIQTIALLAHLACEKGNWGPHLIVVPTSVMLNWEMEFKRWCPGFKILT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 YLGDINSRNMIRThEWTHHQTkrlkFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRLL 646
Cdd:cd18003     81 YYGSAKERKLKRQ-GWMKPNS----FHVCITSYQLVVQDHQVFKRKKWKYLILDEAHNIKNFKSQRWQTLLNFNTQRRLL 155
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622945983  647 ITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHG--------KGREYGYA---SLHKELEPFLLRR 703
Cdd:cd18003    156 LTGTPLQNSLMELWSLMHFLMPHIFQSHQEFKEWFSnpltamseGSQEENEElvrRLHKVLRPFLLRR 223
DEXQc_INO80 cd18002
DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 ...
487-703 1.35e-60

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: 207.74  E-value: 1.35e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAVV 566
Cdd:cd18002      1 LKEYQLKGLNWLANLYEQGINGILADEMGLGKTVQSIAVLAHLAEEHNIWGPFLVIAPASTLHNWQQEISRFVPQFKVLP 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 YLGDINSRNMIRTHeWT--HHQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHR 644
Cdd:cd18002     81 YWGNPKDRKVLRKF-WDrkNLYTRDAPFHVVITSYQLVVQDEKYFQRVKWQYMVLDEAQAIKSSSSSRWKTLLSFHCRNR 159
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  645 LLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYGYAS-----------LHKELEPFLLRR 703
Cdd:cd18002    160 LLLTGTPIQNSMAELWALLHFIMPTLFDSHDEFNEWFSKDIESHAENktglnehqlkrLHMILKPFMLRR 229
DEXHc_CHD5 cd18057
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; ...
487-703 1.73e-59

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: 204.91  E-value: 1.73e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAVV 566
Cdd:cd18057      1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 YLGDINSRNMIRTHEWTHH--------------QTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLL 632
Cdd:cd18057     81 YTGDKESRSVIRENEFSFEdnairsgkkvfrmkKEAQIKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 160
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622945983  633 YKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGK-GREYGYASLHKELEPFLLRR 703
Cdd:cd18057    161 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADiSKEDQIKKLHDLLGPHMLRR 232
DEXHc_CHD6 cd18058
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; ...
487-703 3.07e-59

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: 203.74  E-value: 3.07e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHeHQLYGPFLLVVPLSTLTSWQREIQTWaSQMNAVV 566
Cdd:cd18058      1 LREYQLEGMNWLLFNWYNRKNCILADEMGLGKTIQSITFLSEIFL-MGIRGPFLIIAPLSTITNWEREFRTW-TEMNAIV 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 YLGDINSRNMIRTHEWTHHQTK------RLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFK 640
Cdd:cd18058     79 YHGSQISRQMIQQYEMYYRDEQgnplsgIFKFQVVITTFEMILADCPELKKINWSCVIIDEAHRLKNRNCKLLEGLKLMA 158
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622945983  641 SNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGR-EYGYASLHKELEPFLLRR 703
Cdd:cd18058    159 LEHKVLLTGTPLQNSVEELFSLLNFLEPSQFPSETTFLEEFGDLKtEEQVKKLQSILKPMMLRR 222
DEXHc_CHD4 cd18056
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; ...
487-703 3.12e-59

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: 204.14  E-value: 3.12e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAVV 566
Cdd:cd18056      1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTAVFLYSLYKEGHSKGPFLVSAPLSTIINWEREFEMWAPDMYVVT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 YLGDINSRNMIRTHEWTHH--------------QTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLL 632
Cdd:cd18056     81 YVGDKDSRAIIRENEFSFEdnairggkkasrmkKEASVKFHVLLTSYELITIDMAILGSIDWACLIVDEAHRLKNNQSKF 160
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622945983  633 YKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGK-GREYGYASLHKELEPFLLRR 703
Cdd:cd18056    161 FRVLNGYSLQHKLLLTGTPLQNNLEELFHLLNFLTPERFHNLEGFLEEFADiAKEDQIKKLHDMLGPHMLRR 232
DEXHc_SMARCA5 cd18064
DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent ...
472-715 4.20e-58

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: 201.43  E-value: 4.20e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  472 LKKQPSYIgghEGLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSW 551
Cdd:cd18064      4 FEDSPSYV---KWGKLRDYQVRGLNWLISLYENGINGILADEMGLGKTLQTISLLGYMKHYRNIPGPHMVLVPKSTLHNW 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  552 QREIQTWASQMNAVVYLGDINSR-----NMIRTHEWthhqtkrlkfNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLK 626
Cdd:cd18064     81 MAEFKRWVPTLRAVCLIGDKDQRaafvrDVLLPGEW----------DVCVTSYEMLIKEKSVFKKFNWRYLVIDEAHRIK 150
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  627 NDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEE----EHGKGREYGYASLHKELEPFLLR 702
Cdd:cd18064    151 NEKSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALLNFLLPDVFNSAEDFDSwfdtNNCLGDQKLVERLHMVLRPFLLR 230
                          250
                   ....*....|...
gi 1622945983  703 RVKKDVEKSLPAK 715
Cdd:cd18064    231 RIKADVEKSLPPK 243
DEXHc_CHD8 cd18060
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; ...
487-703 1.01e-57

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: 199.12  E-value: 1.01e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEhQLYGPFLLVVPLSTLTSWQREIQTWaSQMNAVV 566
Cdd:cd18060      1 LREYQLEGVNWLLFNWYNRQNCILADEMGLGKTIQSIAFLQEVYNV-GIHGPFLVIAPLSTITNWEREFNTW-TEMNTIV 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 YLGDINSRNMIRTHEWTHHQTK-RL-----KFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFK 640
Cdd:cd18060     79 YHGSLASRQMIQQYEMYCKDSRgRLipgayKFDALITTFEMILSDCPELREIEWRCVIIDEAHRLKNRNCKLLDSLKHMD 158
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622945983  641 SNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGR-EYGYASLHKELEPFLLRR 703
Cdd:cd18060    159 LEHKVLLTGTPLQNTVEELFSLLHFLEPSQFPSESEFLKDFGDLKtEEQVQKLQAILKPMMLRR 222
DEXHc_SMARCAD1 cd17998
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ...
487-671 1.60e-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: 197.22  E-value: 1.60e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFhEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAVV 566
Cdd:cd17998      1 LKDYQLIGLNWLNLLYQKKLSGILADEMGLGKTIQVIAFLAYLK-EIGIPGPHLVVVPSSTLDNWLREFKRWCPSLKVEP 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 YLGDINSRNMIRTHEwthhQTKRLKFNILLTTYEILL---KDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNH 643
Cdd:cd17998     80 YYGSQEERKHLRYDI----LKGLEDFDVIVTTYNLATsnpDDRSFFKRLKLNYVVYDEGHMLKNMTSERYRHLMTINANF 155
                          170       180
                   ....*....|....*....|....*...
gi 1622945983  644 RLLITGTPLQNSLKELWSLLHFIMPEKF 671
Cdd:cd17998    156 RLLLTGTPLQNNLLELMSLLNFIMPKPF 183
DEXHc_SMARCA1 cd18065
DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent ...
470-705 1.12e-54

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: 191.00  E-value: 1.12e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  470 VALKKQPSYIgghEGLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLT 549
Cdd:cd18065      2 VRFEESPSYV---KGGTLRDYQVRGLNWMISLYENGVNGILADEMGLGKTLQTIALLGYLKHYRNIPGPHMVLVPKSTLH 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  550 SWQREIQTWASQMNAVVYLGDINSR-----NMIRTHEWthhqtkrlkfNILLTTYEILLKDKAFLGGLNWAFIGVDEAHR 624
Cdd:cd18065     79 NWMNEFKRWVPSLRAVCLIGDKDARaafirDVMMPGEW----------DVCVTSYEMVIKEKSVFKKFNWRYLVIDEAHR 148
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  625 LKNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEE----EHGKGREYGYASLHKELEPFL 700
Cdd:cd18065    149 IKNEKSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALLNFLLPDVFNSADDFDSwfdtKNCLGDQKLVERLHAVLKPFL 228

                   ....*
gi 1622945983  701 LRRVK 705
Cdd:cd18065    229 LRRIK 233
DEXQc_arch_SWI2_SNF2 cd18012
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ...
486-705 2.98e-54

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: 188.93  E-value: 2.98e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  486 ELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLyGPFLLVVPLSTLTSWQREIQTWASQMNAV 565
Cdd:cd18012      4 TLRPYQKEGFNWLSFLRHYGLGGILADDMGLGKTLQTLALLLSRKEEGRK-GPSLVVAPTSLIYNWEEEAAKFAPELKVL 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  566 VYLGDINSRNMIRTHEwthhqtkrlKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRL 645
Cdd:cd18012     83 VIHGTKRKREKLRALE---------DYDLVITSYGLLRRDIELLKEVKFHYLVLDEAQNIKNPQTKTAKAVKALKADHRL 153
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622945983  646 LITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGK-----GREYGYASLHKELEPFLLRRVK 705
Cdd:cd18012    154 ALTGTPIENHLGELWSIFDFLNPGLLGSYKRFKKRFAKpiekdGDEEALEELKKLISPFILRRLK 218
DEXHc_CHD7 cd18059
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; ...
487-703 1.12e-52

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: 184.85  E-value: 1.12e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLnYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWaSQMNAVV 566
Cdd:cd18059      1 LREYQLEGVNWLLFNWYNTRNCILADEMGLGKTIQSITFL-YEIYLKGIHGPFLVIAPLSTIPNWEREFRTW-TELNVVV 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 YLGDINSRNMIRTHEWTHHQTK------RLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFK 640
Cdd:cd18059     79 YHGSQASRRTIQLYEMYFKDPQgrvikgSYKFHAIITTFEMILTDCPELRNIPWRCVVIDEAHRLKNRNCKLLEGLKMMD 158
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622945983  641 SNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGR-EYGYASLHKELEPFLLRR 703
Cdd:cd18059    159 LEHKVLLTGTPLQNTVEELFSLLHFLEPSRFPSETTFMQEFGDLKtEEQVQKLQAILKPMMLRR 222
DEXHc_CHD9 cd18061
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; ...
487-703 1.24e-51

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: 181.74  E-value: 1.24e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLnYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWaSQMNAVV 566
Cdd:cd18061      1 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFL-YEILLTGIRGPFLIIAPLSTIANWEREFRTW-TDLNVVV 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 YLGDINSRNMIRTHEWTHHQTK------RLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFK 640
Cdd:cd18061     79 YHGSLISRQMIQQYEMYFRDSQgriirgAYRFQAIITTFEMILGGCPELNAIDWRCVIIDEAHRLKNKNCKLLEGLKLMN 158
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622945983  641 SNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGR-EYGYASLHKELEPFLLRR 703
Cdd:cd18061    159 LEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKtEEQVQKLQAILKPMMLRR 222
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
808-919 2.14e-51

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: 177.67  E-value: 2.14e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  808 ERGNRVLIFSQMVRMLDILAEYLKYRQFPFQRLDGSIKGELRKQALDHFNaEGSEDFCFLLSTRAGGLGINLASADTVVI 887
Cdd:cd18793     25 EPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFN-EDPDIRVFLLSTKAGGVGLNLTAANRVIL 103
                           90       100       110
                   ....*....|....*....|....*....|..
gi 1622945983  888 FDSDWNPQNDLQAQARAHRIGQKKQVNIYRLV 919
Cdd:cd18793    104 YDPWWNPAVEEQAIDRAHRIGQKKPVVVYRLI 135
DEXHc_SMARCA4 cd18062
DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent ...
486-705 1.29e-48

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: 174.08  E-value: 1.29e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  486 ELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAV 565
Cdd:cd18062     23 VLKQYQIKGLEWLVSLYNNNLNGILADEMGLGKTIQTIALITYLMEHKRINGPFLIIVPLSTLSNWVYEFDKWAPSVVKV 102
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  566 VYLGDINSRNMIRThewthhQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTL-IDFKSNHR 644
Cdd:cd18062    103 SYKGSPAARRAFVP------QLRSGKFNVLLTTYEYIIKDKQILAKIRWKYMIVDEGHRMKNHHCKLTQVLnTHYVAPRR 176
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622945983  645 LLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHG-----KGREYGYAS---------LHKELEPFLLRRVK 705
Cdd:cd18062    177 LLLTGTPLQNKLPELWALLNFLLPTIFKSCSTFEQWFNapfamTGEKVDLNEeetiliirrLHKVLRPFLLRRLK 251
DEXHc_SMARCA2 cd18063
DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent ...
487-705 7.65e-48

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: 172.17  E-value: 7.65e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAVV 566
Cdd:cd18063     24 LKHYQLQGLEWMVSLYNNNLNGILADEMGLGKTIQTIALITYLMEHKRLNGPYLIIVPLSTLSNWTYEFDKWAPSVVKIS 103
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 YLGDINSRNMIRThewthhQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTL-IDFKSNHRL 645
Cdd:cd18063    104 YKGTPAMRRSLVP------QLRSGKFNVLLTTYEYIIKDKHILAKIRWKYMIVDEGHRMKNHHCKLTQVLnTHYVAPRRI 177
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622945983  646 LITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHG-----KGREYGYAS---------LHKELEPFLLRRVK 705
Cdd:cd18063    178 LLTGTPLQNKLPELWALLNFLLPTIFKSCSTFEQWFNapfamTGERVDLNEeetiliirrLHKVLRPFLLRRLK 251
CD1_tandem_CHD1-2_like cd18666
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ...
282-360 1.63e-45

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: 158.61  E-value: 1.63e-45
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1622945983  282 RFMDCRIGRKGATGATTTIYAVEADGDPNAGFEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKK 360
Cdd:cd18666      7 RVLDHRIGRKGATGASTTIYAVEADGDPNAGFDPEDEETEIQYLIKWKGWSHIHNTWESEESLKDQNVKGMKKLENYKK 85
DEXHc_ERCC6 cd18000
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ...
487-668 4.62e-45

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: 161.72  E-value: 4.62e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAVV 566
Cdd:cd18000      1 LFKYQQTGVQWLWELHCQRVGGILGDEMGLGKTIQIIAFLAALHHSKLGLGPSLIVCPATVLKQWVKEFHRWWPPFRVVV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 -------------YLGDINSRNMIRTHEWTHHqtkrlkfnILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLY 633
Cdd:cd18000     81 lhssgsgtgseekLGSIERKSQLIRKVVGDGG--------ILITTYEGFRKHKDLLLNHNWQYVILDEGHKIRNPDAEIT 152
                          170       180       190
                   ....*....|....*....|....*....|....*
gi 1622945983  634 KTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMP 668
Cdd:cd18000    153 LACKQLRTPHRLILSGTPIQNNLKELWSLFDFVFP 187
DEXHc_ERCC6L2 cd18005
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
487-703 9.30e-44

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: 159.85  E-value: 9.30e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHE--------------------HQLYGPFLLVVPLS 546
Cdd:cd18005      1 LRDYQREGVEFMYDLYKNGRGGILGDDMGLGKTVQVIAFLAAVLGKtgtrrdrennrprfkkkppaSSAKKPVLIVAPLS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  547 TLTSWQREIQTWASqMNAVVYLGDINSRNMIRThewthhqTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLK 626
Cdd:cd18005     81 VLYNWKDELDTWGH-FEVGVYHGSRKDDELEGR-------LKAGRLEVVVTTYDTLRRCIDSLNSINWSAVIADEAHRIK 152
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  627 NDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEE------EHG-----------KGREYGy 689
Cdd:cd18005    153 NPKSKLTQAMKELKCKVRIGLTGTLLQNNMKELWCLLDWAVPGALGSRSQFKKhfsepiKRGqrhtatarelrLGRKRK- 231
                          250
                   ....*....|....
gi 1622945983  690 ASLHKELEPFLLRR 703
Cdd:cd18005    232 QELAVKLSKFFLRR 245
DEXHc_ERCC6L cd18001
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ...
487-703 7.30e-42

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: 154.07  E-value: 7.30e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEhQLYGPFLLVVPLSTLTSWQREIQTWASQMNAVV 566
Cdd:cd18001      1 LYPHQREGVAWLWSLHDGGKGGILADDMGLGKTVQICAFLSGMFDS-GLIKSVLVVMPTSLIPHWVKEFAKWTPGLRVKV 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 YLGdINSRNMIRTHEWTHHqtkrlKFNILLTTYEILLKDKAFLG-----GLNWAFIGVDEAHRLKNDDSLLYKTLIDFKS 641
Cdd:cd18001     80 FHG-TSKKERERNLERIQR-----GGGVLLTTYGMVLSNTEQLSaddhdEFKWDYVILDEGHKIKNSKTKSAKSLREIPA 153
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1622945983  642 NHRLLITGTPLQNSLKELWSLLHFIMPEKF---SSWEDFEEEH--GKGRE---------YGY---ASLHKELEPFLLRR 703
Cdd:cd18001    154 KNRIILTGTPIQNNLKELWALFDFACNGSLlgtRKTFKMEFENpiTRGRDkdatqgekaLGSevaENLRQIIKPYFLRR 232
DEXHc_Mot1 cd17999
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ...
487-703 1.22e-41

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: 153.28  E-value: 1.22e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYG-----PFLLVVPlSTLTS-WQREIQTWAS 560
Cdd:cd17999      1 LRPYQQEGINWLAFLNKYNLHGILCDDMGLGKTLQTLCILASDHHKRANSFnsenlPSLVVCP-PTLVGhWVAEIKKYFP 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  561 Q--MNAVVYLGDINSRNMIRthewthHQTKrlKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLID 638
Cdd:cd17999     80 NafLKPLAYVGPPQERRRLR------EQGE--KHNVIVASYDVLRNDIEVLTKIEWNYCVLDEGHIIKNSKTKLSKAVKQ 151
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  639 FKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKG-------------REYGYAS---LHKELEPFLLR 702
Cdd:cd17999    152 LKANHRLILSGTPIQNNVLELWSLFDFLMPGYLGTEKQFQRRFLKPilasrdskasakeQEAGALAleaLHKQVLPFLLR 231

                   .
gi 1622945983  703 R 703
Cdd:cd17999    232 R 232
DEXDc_SHPRH-like cd18008
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ...
487-703 3.75e-37

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: 140.89  E-value: 3.75e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAhswCKGNscILADEMGLGKTIQTIS---------------FLNYLFHEHQLY--GPFLLVVPLSTLT 549
Cdd:cd18008      1 LLPYQKQGLAWML---PRGG--ILADEMGLGKTIQALAlilatrpqdpkipeeLEENSSDPKKLYlsKTTLIVVPLSLLS 75
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  550 SWQREIQ--TWASQMNAVVYLGdinSRNMIRTHEWthhqtkrLKFNILLTTYEILLKD----------------KAFLGG 611
Cdd:cd18008     76 QWKDEIEkhTKPGSLKVYVYHG---SKRIKSIEEL-------SDYDIVITTYGTLASEfpknkkgggrdskekeASPLHR 145
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  612 LNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEE----HGKGREY 687
Cdd:cd18008    146 IRWYRVILDEAHNIKNRSTKTSRAVCALKAERRWCLTGTPIQNSLDDLYSLLRFLRVEPFGDYPWFNSDiskpFSKNDRK 225
                          250
                   ....*....|....*.
gi 1622945983  688 GYASLHKELEPFLLRR 703
Cdd:cd18008    226 ALERLQALLKPILLRR 241
CD2_tandem_CHD1-2_like cd18661
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ...
393-449 2.28e-34

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: 125.88  E-value: 2.28e-34
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622945983  393 QYQIVERIIAHSNQKSA-AGYPDYYCKWQGLPYSECSWEDGALISKKFQACIDEYFSR 449
Cdd:cd18661      1 QYQIVERIIAHSPQKSAaSGYPDYLCKWQGLPYSECTWEDGALISKKFQACIDEYHSR 58
DEXHc_ATRX-like cd18007
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ...
504-677 9.20e-34

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: 130.87  E-value: 9.20e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  504 KGNSCILADEMGLGKTIQTISFLnylfHEHQLYGP----FLLVVPLSTLTSWQREIQTWASQMNAVVYLGDINSRnmirt 579
Cdd:cd18007     25 EGGGCILAHTMGLGKTLQVITFL----HTYLAAAPrrsrPLVLCPASTLYNWEDEFKKWLPPDLRPLLVLVSLSA----- 95
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  580 hewTHHQTKRL-KFN-------ILLTTYEI---LLKDKAFLGGLNWAFIG-----------VDEAHRLKNDDSLLYKTLI 637
Cdd:cd18007     96 ---SKRADARLrKINkwhkeggVLLIGYELfrnLASNATTDPRLKQEFIAalldpgpdllvLDEGHRLKNEKSQLSKALS 172
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1622945983  638 DFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDF 677
Cdd:cd18007    173 KVKTKRRILLTGTPLQNNLKEYWTMVDFARPKYLGTLKEF 212
CDH1_2_SANT_HL1 pfam18375
CDH1/2 SANT-Helical linker 1; CDH1 is an ATP-dependent chromatin-remodelling factor and plays ...
1130-1216 2.69e-33

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: 465731  Cd Length: 90  Bit Score: 124.00  E-value: 2.69e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983 1130 KGFSDAEIRRFIKSYKKFGGPLERLDAIARDAELVDKSETDLRRLGELVHNGCIKALKD----SSSGTERTGGRlGKVKG 1205
Cdd:pfam18375    1 KGFTDAEIRRFVKSYKKFSAPLKRLDAIACDAELQEKPLSDLRRLGELLKERCDEAMEEytekEDENPGADGGK-KRIRG 79
                           90
                   ....*....|.
gi 1622945983 1206 PTFRISGVQVN 1216
Cdd:pfam18375   80 PSFKLGGVSVN 90
DEXHc_RAD54 cd18004
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ...
487-703 2.76e-31

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: 123.94  E-value: 2.76e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWL-----AHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGP----FLLVVPLSTLTSWQREIQT 557
Cdd:cd18004      1 LRPHQREGVQFLydcltGRRGYGGGGAILADEMGLGKTLQAIALVWTLLKQGPYGKPtakkALIVCPSSLVGNWKAEFDK 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  558 WASQMNAVVYLGDINSRNMIRThewTHHQTKRLKFNILLTTYEILLKDKAFLGGLnwAFIGV---DEAHRLKNDDSLLYK 634
Cdd:cd18004     81 WLGLRRIKVVTADGNAKDVKAS---LDFFSSASTYPVLIISYETLRRHAEKLSKK--ISIDLlicDEGHRLKNSESKTTK 155
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  635 TLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDF----EEEHGKGREYGYASLHKEL------------EP 698
Cdd:cd18004    156 ALNSLPCRRRLLLTGTPIQNDLDEFFALVDFVNPGILGSLASFrkvfEEPILRSRDPDASEEDKELgaersqelseltSR 235

                   ....*
gi 1622945983  699 FLLRR 703
Cdd:cd18004    236 FILRR 240
DEXDc smart00487
DEAD-like helicases superfamily;
479-680 5.75e-28

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 112.97  E-value: 5.75e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983   479 IGGHEGLELRDYQLNGLNWLAHSWckgNSCILADEMGLGKTIQTISFLNYLFHEHQlYGPFLLVVPLSTLT-SWQREIQT 557
Cdd:smart00487    1 IEKFGFEPLRPYQKEAIEALLSGL---RDVILAAPTGSGKTLAALLPALEALKRGK-GGRVLVLVPTRELAeQWAEELKK 76
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983   558 WASQMN--AVVYLGDINSRNMIRthewthhQTKRLKFNILLTTYEILLKD--KAFLGGLNWAFIGVDEAHRLKND---DS 630
Cdd:smart00487   77 LGPSLGlkVVGLYGGDSKREQLR-------KLESGKTDILVTTPGRLLDLleNDKLSLSNVDLVILDEAHRLLDGgfgDQ 149
                           170       180       190       200       210
                    ....*....|....*....|....*....|....*....|....*....|...
gi 1622945983   631 LLYKTLIDFKSNHRLLITGTP---LQNSLKELWSLLHFIMPEkFSSWEDFEEE 680
Cdd:smart00487  150 LEKLLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVG-FTPLEPIEQF 201
DUF4208 pfam13907
Domain of unknown function (DUF4208); This domain is found at the C-terminus of ...
1502-1592 6.74e-28

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: 464035  Cd Length: 93  Bit Score: 108.88  E-value: 6.74e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983 1502 ELDQKTFS-ICKERMRPVKAALKQLDRPEKGLSEREQLEHTRQCLIKIGDHITECLKEYtNPEQIKQWRKNLWIFVSKFT 1580
Cdd:pfam13907    1 DEYESMDEeECKELMRPVKKSLKRLKKGTKGLSRKERAKILKKELLKIGDFIDSLLEET-KKEKKEKLRKHLWSFVSKFW 79
                           90
                   ....*....|....
gi 1622945983 1581 E--FDARKLHKLYK 1592
Cdd:pfam13907   80 PnkVSGKKLKEMYK 93
DEXHc_HARP_SMARCAL1 cd18010
DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin ...
487-704 8.32e-28

DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1, also known as HARP) is recruited to stalled replication forks to promote repair and helps restart replication. It plays a role in DNA repair, telomere maintenance and replication fork stability in response to DNA replication stress. Mutations cause Schimke Immunoosseous Dysplasia. SMARCAL1 is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350768 [Multi-domain]  Cd Length: 213  Bit Score: 113.07  E-value: 8.32e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNW-LAHswckGNSCILADEMGLGKTIQTISFLNYLFHEhqlyGPFLLVVPLSTLTSWQREIQTWASqmnaV 565
Cdd:cd18010      1 LLPFQREGVCFaLRR----GGRVLIADEMGLGKTVQAIAIAAYYREE----WPLLIVCPSSLRLTWADEIERWLP----S 68
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  566 VYLGDINSRNMIRThEWTHHQTKrlkfnILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDF--KSNH 643
Cdd:cd18010     69 LPPDDIQVIVKSKD-GLRDGDAK-----VVIVSYDLLRRLEKQLLARKFKVVICDESHYLKNSKAKRTKAALPLlkRAKR 142
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1622945983  644 RLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDF------EEEHGKGREYGYASLHKELEPFLLRRV 704
Cdd:cd18010    143 VILLSGTPALSRPIELFTQLDALDPKLFGRFHDFgrrycaAKQGGFGWDYSGSSNLEELHLLLLATI 209
DEXHc_HLTF1_SMARC3 cd18071
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ...
509-703 6.81e-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: 111.02  E-value: 6.81e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  509 ILADEMGLGKTIQTISFLnylfhehqLYGPFLLVVPLSTLTSW--QREIQTWASQMNAVVYLGDINSRNMirthewthhq 586
Cdd:cd18071     52 ILADDMGLGKTLTTISLI--------LANFTLIVCPLSVLSNWetQFEEHVKPGQLKVYTYHGGERNRDP---------- 113
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  587 TKRLKFNILLTTYEILL-----KDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWS 661
Cdd:cd18071    114 KLLSKYDIVLTTYNTLAsdfgaKGDSPLHTINWLRVVLDEGHQIRNPNAQQTKAVLNLSSERRWVLTGTPIQNSPKDLGS 193
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1622945983  662 LLHFIMPEKFSSWEDFEEEHGK----GREYGYASLHKELEPFLLRR 703
Cdd:cd18071    194 LLSFLHLKPFSNPEYWRRLIQRpltmGDPTGLKRLQVLMKQITLRR 239
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
808-908 8.10e-26

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 103.44  E-value: 8.10e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  808 ERGNRVLIFSQMVRMLDilAEYLKYRQ-FPFQRLDGSIKGELRKQALDHFNaegSEDFCFLLSTRAGGLGINLASADTVV 886
Cdd:pfam00271   13 ERGGKVLIFSQTKKTLE--AELLLEKEgIKVARLHGDLSQEEREEILEDFR---KGKIDVLVATDVAERGLDLPDVDLVI 87
                           90       100
                   ....*....|....*....|..
gi 1622945983  887 IFDSDWNPQNDLQAQARAHRIG 908
Cdd:pfam00271   88 NYDLPWNPASYIQRIGRAGRAG 109
DEXHc_RAD54A cd18067
DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as ...
506-677 8.96e-25

DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as RAD54L or RAD54, plays a role in homologous recombination related repair of DNA double-strand breaks. RAD54A is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350825 [Multi-domain]  Cd Length: 243  Bit Score: 105.24  E-value: 8.96e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  506 NSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFL----LVVPLSTLTSWQREIQTW-ASQMNAVVYLGDINSRNMIRTH 580
Cdd:cd18067     25 HGCIMADEMGLGKTLQCITLMWTLLRQSPQCKPEIdkaiVVSPSSLVKNWANELGKWlGGRLQPLAIDGGSKKEIDRKLV 104
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  581 EWTHHQTKRLKFNILLTTYEILlkdKAFLGGLNWAFIGV---DEAHRLKNDDSLLYKTLIDFKSNHRLLITGTPLQNSLK 657
Cdd:cd18067    105 QWASQQGRRVSTPVLIISYETF---RLHVEVLQKGEVGLvicDEGHRLKNSDNQTYQALDSLNTQRRVLLSGTPIQNDLS 181
                          170       180
                   ....*....|....*....|
gi 1622945983  658 ELWSLLHFIMPEKFSSWEDF 677
Cdd:cd18067    182 EYFSLVNFVNPGILGTAAEF 201
HELICc smart00490
helicase superfamily c-terminal domain;
824-908 1.89e-22

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 93.05  E-value: 1.89e-22
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983   824 DILAEYLKYRQFPFQRLDGSIKGELRKQALDHFNaegSEDFCFLLSTRAGGLGINLASADTVVIFDSDWNPQNDLQAQAR 903
Cdd:smart00490    1 EELAELLKELGIKVARLHGGLSQEEREEILDKFN---NGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGR 77

                    ....*
gi 1622945983   904 AHRIG 908
Cdd:smart00490   78 AGRAG 82
DEXHc_RAD54B cd18066
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ...
487-668 3.79e-22

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: 97.22  E-value: 3.79e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHS-----WCKGNSCILADEMGLGKTIQTISFLNYLFHEHQlYGP------FLLVVPLSTLTSWQREI 555
Cdd:cd18066      1 LRPHQREGIEFLYECvmgmrVNERFGAILADEMGLGKTLQCISLIWTLLRQGP-YGGkpvikrALIVTPGSLVKNWKKEF 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  556 QTWASQMNAVVYLGDINSRnmirthewTHHQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKT 635
Cdd:cd18066     80 QKWLGSERIKVFTVDQDHK--------VEEFIASPLYSVLIISYEMLLRSLDQISKLNFDLVICDEGHRLKNTSIKTTTA 151
                          170       180       190
                   ....*....|....*....|....*....|...
gi 1622945983  636 LIDFKSNHRLLITGTPLQNSLKELWSLLHFIMP 668
Cdd:cd18066    152 LTSLSCERRIILTGTPIQNDLQEFFALIDFVNP 184
DEXHc_ATRX cd18068
DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha ...
487-677 3.76e-21

DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) is involved in transcriptional regulation and chromatin remodeling. Mutations in humans cause mental retardation, X-linked, syndromic, with hypotonic facies 1 (MRXSHF1) and alpha-thalassemia myelodysplasia syndrome (ATMDS). ATRX is part of the a DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350826 [Multi-domain]  Cd Length: 246  Bit Score: 94.57  E-value: 3.76e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAHSWCK---------GNSCILADEMGLGKTIQTISFLNYLFHEHQLYG--PFLLVVPLSTLTSWQREI 555
Cdd:cd18068      1 LKPHQVDGVQFMWDCCCEslkktkkspGSGCILAHCMGLGKTLQVVTFLHTVLLCEKLENfsRVLVVCPLNTVLNWLNEF 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  556 QTWasqmnaVVYLGDINSRNMIRTHEWTHHQTKRLKFN-------ILLTTYEIL----------LKDKA------FLGGL 612
Cdd:cd18068     81 EKW------QEGLKDEEKIEVNELATYKRPQERSYKLQrwqeeggVMIIGYDMYrilaqernvkSREKLkeifnkALVDP 154
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622945983  613 NWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDF 677
Cdd:cd18068    155 GPDFVVCDEGHILKNEASAVSKAMNSIRTKRRIVLTGTPLQNNLIEYHCMVNFVKPNLLGTIKEF 219
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
508-703 4.47e-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: 93.12  E-value: 4.47e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  508 CILADEMGLGKTIQTISFLNYLFHEHqLYGPFLLVVPLSTLTSWQREIQTWASQmNAVVYLGDINSRNMIRTHEWTHHqt 587
Cdd:cd18011     20 LLLADEVGLGKTIEAGLIIKELLLRG-DAKRVLILCPASLVEQWQDELQDKFGL-PFLILDRETAAQLRRLIGNPFEE-- 95
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  588 krlkFNILLTTYEiLLKDKAFLGGL----NWAFIGVDEAHRLKN----DDSLLYKT---LIDfKSNHRLLITGTPLQNSL 656
Cdd:cd18011     96 ----FPIVIVSLD-LLKRSEERRGLllseEWDLVVVDEAHKLRNsgggKETKRYKLgrlLAK-RARHVLLLTATPHNGKE 169
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 1622945983  657 KELWSLLHFIMPEKFSSWEDFEEEHGkgreygyasLHKELEPFLLRR 703
Cdd:cd18011    170 EDFRALLSLLDPGRFAVLGRFLRLDG---------LREVLAKVLLRR 207
CD2_tandem cd18659
repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier ...
393-446 5.53e-20

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: 84.93  E-value: 5.53e-20
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1622945983  393 QYQIVERIIAHsnQKSAAGYPDYYCKWQGLPYSECSWEDGALISKKFQACIDEY 446
Cdd:cd18659      1 EYTIVERIIAH--REDDEGVTEYLVKWKGLPYDECTWESEEDISDIFQEAIDEY 52
DEXHc_ARIP4 cd18069
DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called ...
504-677 7.19e-20

DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called RAD54 like 2 or RAD54L2 ) modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. ARIP4 is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350827 [Multi-domain]  Cd Length: 227  Bit Score: 90.26  E-value: 7.19e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  504 KGNSCILADEMGLGKTIQTISFLnYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWasqMNAVVYLGDINSRNMiRTHEWT 583
Cdd:cd18069     27 SGFGCILAHSMGLGKTLQVISFL-DVLLRHTGAKTVLAIVPVNTLQNWLSEFNKW---LPPPEALPNVRPRPF-KVFILN 101
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  584 -HHQTKRLKFN----------ILLTTYEIL-LKDKAFLgglnwafIGVDEAHRLKNDDSLLYKTLIDFKSNHRLLITGTP 651
Cdd:cd18069    102 dEHKTTAARAKviedwvkdggVLLMGYEMFrLRPGPDV-------VICDEGHRIKNCHASTSQALKNIRSRRRIVLTGYP 174
                          170       180
                   ....*....|....*....|....*.
gi 1622945983  652 LQNSLKELWSLLHFIMPEKFSSWEDF 677
Cdd:cd18069    175 LQNNLIEYWCMVDFVRPDFLGTRQEF 200
CD1_tandem cd18660
repeat 1 of paired tandem chromodomains; Repeat 1 of tandem CHRomatin Organization Modifier ...
304-360 2.16e-17

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: 78.17  E-value: 2.16e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1622945983  304 EADGDPNAGFEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQnvRGMKKLDNYKK 360
Cdd:cd18660     16 PVEEASLDLTDPDEPWDEREFLVKWKGKSYLHCTWVTEETLEQL--RGKKKLKNYIK 70
DEXHc_TTF2 cd18072
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ...
509-703 6.37e-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: 79.45  E-value: 6.37e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  509 ILADEMGLGKTIQTISFL-----------------NYLFHEHQLYGPF-----LLVVPLSTLTSWQREIQTWASQMNAVV 566
Cdd:cd18072     24 ILADDMGLGKTLTMIALIlaqkntqnrkeeekekaLTEWESKKDSTLVpsagtLVVCPASLVHQWKNEVESRVASNKLRV 103
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  567 YLGDINSRnmirthewtHHQTKRLK-FNILLTTYEILLKD---------KAFLGGLNWAFIGVDEAHRLKNDDSLLYKTL 636
Cdd:cd18072    104 CLYHGPNR---------ERIGEVLRdYDIVITTYSLVAKEiptykeesrSSPLFRIAWARIILDEAHNIKNPKVQASIAV 174
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1622945983  637 IDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFS------SWEDFEEEHGKGReygyasLHKELEPFLLRR 703
Cdd:cd18072    175 CKLRAHARWALTGTPIQNNLLDMYSLLKFLRCSPFDdlkvwkKQVDNKSRKGGER------LNILTKSLLLRR 241
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
487-702 6.85e-13

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


Pssm-ID: 350828 [Multi-domain]  Cd Length: 257  Bit Score: 70.84  E-value: 6.85e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNWLAhsWCKGnscILADEMGLGKTIQTISFLnyLFH--------------------EHQLY-------GPF 539
Cdd:cd18070      1 LLPYQRRAVNWML--VPGG---ILADEMGLGKTVEVLALI--LLHprpdndldaadddsdemvccPDCLVaetpvssKAT 73
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  540 LLVVPLSTLTSWQREIQTWASQMNAV-VYlgdinsrNMIRTHEWTH-HQTKRL-KFNILLTTYEILLKDKAF-------- 608
Cdd:cd18070     74 LIVCPSAILAQWLDEINRHVPSSLKVlTY-------QGVKKDGALAsPAPEILaEYDIVVTTYDVLRTELHYaeanrsnr 146
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  609 --------------LGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKF--S 672
Cdd:cd18070    147 rrrrqkryeappspLVLVEWWRVCLDEAQMVESSTSKAAEMARRLPRVNRWCVSGTPIQRGLDDLFGLLSFLGVEPFcdS 226
                          250       260       270
                   ....*....|....*....|....*....|
gi 1622945983  673 SWEDFEEEHGKGREYGYASLHKELEPFLLR 702
Cdd:cd18070    227 DWWARVLIRPQGRNKAREPLAALLKELLWR 256
CD1_tandem_CHD1_yeast_like cd18665
repeat 1 of the paired tandem chromodomains of yeast chromodomain helicase DNA-binding protein ...
314-360 6.89e-13

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: 65.10  E-value: 6.89e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1622945983  314 EKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQqnVRGMKKLDNYKK 360
Cdd:cd18665     21 ELDDPKENYEFLIKWTDESHLHNTWETYESLKQ--VRGLKKVDNYIK 65
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
396-449 1.10e-10

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 58.36  E-value: 1.10e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1622945983  396 IVERIIAHSNQKSaaGYPDYYCKWQGLPYSECSWEDGALISKKfQACIDEYFSR 449
Cdd:pfam00385    2 EVERILDHRKDKG--GKEEYLVKWKGYPYDENTWEPEENLSKC-PELIEEFKDR 52
DEXQc_bact_SNF2 cd18013
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ...
487-666 1.83e-10

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


Pssm-ID: 350771 [Multi-domain]  Cd Length: 218  Bit Score: 62.75  E-value: 1.83e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGLNW-LAHSWCkgnsCILADeMGLGKTIQTISFLNYLFHEhQLYGPFLLVVPLSTLTS-WQREIQTWASQMNA 564
Cdd:cd18013      1 PHPYQKVAINFiIEHPYC----GLFLD-MGLGKTVTTLTALSDLQLD-DFTRRVLVIAPLRVARStWPDEVEKWNHLRNL 74
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  565 VVYLGDINSRNMIRT--HEWThhqtkrlkfnILLTTYEILLK-DKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTL--IDF 639
Cdd:cd18013     75 TVSVAVGTERQRSKAanTPAD----------LYVINRENLKWlVNKSGDPWPFDMVVIDELSSFKSPRSKRFKALrkVRP 144
                          170       180
                   ....*....|....*....|....*..
gi 1622945983  640 KSNHRLLITGTPLQNSLKELWSLLHFI 666
Cdd:cd18013    145 VIKRLIGLTGTPSPNGLMDLWAQIALL 171
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
485-1045 3.29e-10

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 65.05  E-value: 3.29e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  485 LELRDYQLNGLN-WLAHSWCKGNSCILADEMGLGKTIqTISFLnylFHEHQLYGPFLLVVPLSTL-TSWQREIQTWasqm 562
Cdd:COG1061     79 FELRPYQQEALEaLLAALERGGGRGLVVAPTGTGKTV-LALAL---AAELLRGKRVLVLVPRRELlEQWAEELRRF---- 150
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  563 navvyLGDINSrnmirthewtHHQTKRLKFNILLTTYEILLKDKAF--LGGlNWAFIGVDEAHRLKnddSLLYKTLID-F 639
Cdd:COG1061    151 -----LGDPLA----------GGGKKDSDAPITVATYQSLARRAHLdeLGD-RFGLVIIDEAHHAG---APSYRRILEaF 211
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  640 KSNHRLLITGTPlqnslkelwsllhFIMPEKfssWEDFEEEHGKGREYGYASLHKE--LEPFLLRRVKKDVEKSlpakve 717
Cdd:COG1061    212 PAAYRLGLTATP-------------FRSDGR---EILLFLFDGIVYEYSLKEAIEDgyLAPPEYYGIRVDLTDE------ 269
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  718 qilRMEMSALQKQYykwiltrnYKALSKGSKgstsgflnimmelkkccnhcylikppdnnefyNKQEALQHLIRSSGkli 797
Cdd:COG1061    270 ---RAEYDALSERL--------REALAADAE--------------------------------RKDKILRELLREHP--- 303
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  798 lldkllirlreRGNRVLIFSQMVRMLDILAEYLKYRQFPFQRLDGSIKGELRKQALDHFnAEGSEDfcFLLSTRAGGLGI 877
Cdd:COG1061    304 -----------DDRKTLVFCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAF-RDGELR--ILVTVDVLNEGV 369
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  878 NLASADTVVIFDSDWNPQNDLQAQARAHRIGQ-KKQVNIYRLVTkgsVEEDILERAKKKmvLDHLVIQRMDTTGKTVLHT 956
Cdd:COG1061    370 DVPRLDVAILLRPTGSPREFIQRLGRGLRPAPgKEDALVYDFVG---NDVPVLEELAKD--LRDLAGYRVEFLDEEESEE 444
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  957 GSAPSSSTPFNKEELSAILKFGAEELFKEPEGEEQEPQEMDIDEILKRAETHENEPGPLTVGDELLSQFKVANFSHMDED 1036
Cdd:COG1061    445 LALLIAVKPALEVKGELEEELLEELELLEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLLLALAKLL 524

                   ....*....
gi 1622945983 1037 DIELEPERN 1045
Cdd:COG1061    525 KLLLLLLLL 533
CHROMO smart00298
Chromatin organization modifier domain;
315-361 3.08e-09

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 54.53  E-value: 3.08e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1622945983   315 KNKEPGEIQYLIKWKGWSHIHNTWETEETLKQqnvrGMKKLDNYKKK 361
Cdd:smart00298   11 RWKKKGELEYLVKWKGYSYSEDTWEPEENLLN----CSKKLDNYKKK 53
CHROMO smart00298
Chromatin organization modifier domain;
397-451 1.04e-07

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 49.90  E-value: 1.04e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 1622945983   397 VERIIAHSNQKSaaGYPDYYCKWQGLPYSECSWEDGALISkKFQACIDEYFSRNQ 451
Cdd:smart00298    4 VEKILDHRWKKK--GELEYLVKWKGYSYSEDTWEPEENLL-NCSKKLDNYKKKER 55
ResIII pfam04851
Type III restriction enzyme, res subunit;
485-651 2.61e-07

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 52.29  E-value: 2.61e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  485 LELRDYQLNGLNWLAHSWCKGNSCILAdEM--GLGKTIqTISFLNYLFHEHQLYGPFLLVVP-LSTLTSWQREIQTWASq 561
Cdd:pfam04851    2 LELRPYQIEAIENLLESIKNGQKRGLI-VMatGSGKTL-TAAKLIARLFKKGPIKKVLFLVPrKDLLEQALEEFKKFLP- 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  562 mNAVVYLGDINSRNMIRthewthhqtKRLKFNILLTTY-----EILLKDKAFLGGLNWAFIgVDEAHRLkNDDSllYKTL 636
Cdd:pfam04851   79 -NYVEIGEIISGDKKDE---------SVDDNKIVVTTIqslykALELASLELLPDFFDVII-IDEAHRS-GASS--YRNI 144
                          170
                   ....*....|....*.
gi 1622945983  637 ID-FKSNHRLLITGTP 651
Cdd:pfam04851  145 LEyFKPAFLLGLTATP 160
CD_CSD cd00024
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
317-346 3.28e-07

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: 48.63  E-value: 3.28e-07
                           10        20        30
                   ....*....|....*....|....*....|
gi 1622945983  317 KEPGEIQYLIKWKGWSHIHNTWETEETLKQ 346
Cdd:cd00024     11 VRKGKLEYLVKWKGYPPEENTWEPEENLTN 40
CD2_tandem_ScCHD1_like cd18664
repeat 2 of the paired tandem chromodomains of yeast chromodomain helicase DNA-binding protein ...
393-449 4.10e-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: 48.42  E-value: 4.10e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1622945983  393 QYQIVERIIAHSNQKSAAGYP--DYYCKWQGLPYSECSWEDGALISKKFQACIDEYFSR 449
Cdd:cd18664      1 EFHVVERIIASQRASLEDGTSqlQYLVKWRRLNYDECTWEDATLIAKLAPEQVDHFQNR 59
CD_polycomb cd18644
chromodomain of polycomb; CHRomatin Organization Modifier (chromo) domain of the PcG ...
300-360 1.03e-06

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: 47.07  E-value: 1.03e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1622945983  300 IYAVEADgdpnagFEKNKEPGEIQYLIKWKGWSHIHNTWETEEtlkqqNVRGMKKLDNYKK 360
Cdd:cd18644      3 VYAAEKI------LKKRVRKGKVEYLVKWKGWSNKHNTWEPEE-----NILDRRLIEIFER 52
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
487-651 2.24e-06

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: 49.23  E-value: 2.24e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  487 LRDYQLNGL-NWLAHSWCKGNSCILAdeMGLGKTIQTISFLNYLFHEhqlygPFLLVVP-LSTLTSWQREIQTWAsqMNA 564
Cdd:cd17926      1 LRPYQEEALeAWLAHKNNRRGILVLP--TGSGKTLTALALIAYLKEL-----RTLIVVPtDALLDQWKERFEDFL--GDS 71
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  565 VVYLGDINSRNMIRThewthhqtkrlkFNILLTTYEIL---LKDKAFLGGLNWAFIgVDEAHRLkndDSLLYKTLID-FK 640
Cdd:cd17926     72 SIGLIGGGKKKDFDD------------ANVVVATYQSLsnlAEEEKDLFDQFGLLI-VDEAHHL---PAKTFSEILKeLN 135
                          170
                   ....*....|.
gi 1622945983  641 SNHRLLITGTP 651
Cdd:cd17926    136 AKYRLGLTATP 146
CD_polycomb_like cd18627
chromodomain of polycomb and chromobox family proteins; CHRomatin Organization Modifier ...
320-342 2.29e-06

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: 46.23  E-value: 2.29e-06
                           10        20
                   ....*....|....*....|...
gi 1622945983  320 GEIQYLIKWKGWSHIHNTWETEE 342
Cdd:cd18627     14 GKVEYLVKWKGWSQKYNTWEPEE 36
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
314-361 5.32e-06

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 45.26  E-value: 5.32e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1622945983  314 EKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNvrgmKKLDNYKKK 361
Cdd:pfam00385    9 HRKDKGGKEEYLVKWKGYPYDENTWEPEENLSKCP----ELIEEFKDR 52
chromodomain cd18968
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
323-346 1.22e-05

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: 44.26  E-value: 1.22e-05
                           10        20
                   ....*....|....*....|....
gi 1622945983  323 QYLIKWKGWSHIHNTWETEETLKQ 346
Cdd:cd18968     24 KYLVKWAGYPDEENTWEPEESFDG 47
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
812-911 1.58e-05

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: 44.62  E-value: 1.58e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  812 RVLIFSQMVRMLDILAEYLKyrqfpfqrldgsikgelrkqaldhfnaegsedfcFLLSTRAGGLGINLASADTVVIFDSD 891
Cdd:cd18785      5 KIIVFTNSIEHAEEIASSLE----------------------------------ILVATNVLGEGIDVPSLDTVIFFDPP 50
                           90       100
                   ....*....|....*....|
gi 1622945983  892 WNPQNDLQAQARAHRIGQKK 911
Cdd:cd18785     51 SSAASYIQRVGRAGRGGKDE 70
CD_Cbx2 cd18647
chromodomain of chromobox homolog 2; CHRomatin Organization Modifier (chromo) domain of ...
313-344 2.20e-05

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: 43.51  E-value: 2.20e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1622945983  313 FEKNKEPGEIQYLIKWKGWSHIHNTWETEETL 344
Cdd:cd18647     10 LSKRLRKGKLEYLVKWRGWSSKHNSWEPEENI 41
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
505-640 1.07e-04

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: 1.07e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  505 GNSCILADEMGLGKTIQtisFLNYLFHEHQLYGP-FLLVVPLSTLT-SWQREIQTWASQMNAVVYLGDINSRNmirthew 582
Cdd:cd00046      1 GENVLITAPTGSGKTLA---ALLAALLLLLKKGKkVLVLVPTKALAlQTAERLRELFGPGIRVAVLVGGSSAE------- 70
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622945983  583 THHQTKRLKFNILLTTYEILLKDKAFLGGL---NWAFIGVDEAHR-LKNDDSLLYKTLIDFK 640
Cdd:cd00046     71 EREKNKLGDADIIIATPDMLLNLLLREDRLflkDLKLIIVDEAHAlLIDSRGALILDLAVRK 132
CD2_tandem_CHD3-4_like cd18662
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and ...
397-447 1.19e-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: 41.48  E-value: 1.19e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1622945983  397 VERIIAHSnqKSAAGYPDYYCKWQGLPYSECSWE-DGALISkKFQACIDEYF 447
Cdd:cd18662      6 IHRIINHR--VDKDGNTWYLVKWRDLPYDQSTWEsEDDDIP-DYEKHIQEYW 54
HDA2-3 pfam11496
Class II histone deacetylase complex subunits 2 and 3; This family of class II histone ...
724-942 1.44e-04

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


Pssm-ID: 402894  Cd Length: 281  Bit Score: 45.78  E-value: 1.44e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  724 MSALQKQYYKWILTRNYKALSKG-----SKGSTSGFLNIMMELKKCC---NHCYLI----KPPDnneFYNKQEAlQHLIR 791
Cdd:pfam11496   12 MTSYQKELTEQIVSLHYSDILKYcetsdSKEDISLIKSMTLCLENLSlvaTHPYLLvdhyMPKS---LLLKDEP-EKLAY 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  792 SSGKLILLDKLLIRLRERGNR----VLIFSQMVRMLDILAEYLKYRQFPFQRLDG-SIKGELRKQALDHFNAEGSEDFCF 866
Cdd:pfam11496   88 TSGKFLVLNDLVNLLIERDRKepinVAIVARSGKTLDLVEALLLGKGLSYKRYSGeMLYGENKKVSDSGNKKIHSTTCHL 167
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983  867 LLSTR-----AGGLGINlaSADTVVIFDSDWNPQNDLQAQARAHRIGQKKQVNIYRLVTKGSVEEDILERAKKKMVLDHL 941
Cdd:pfam11496  168 LSSTGqltndDSLLENY--KFDLIIAFDSSVDTSSPSVEHLRTQNRRKGNLAPIIRLVVINSIEHVELCFPKPPDSPDYL 245

                   .
gi 1622945983  942 V 942
Cdd:pfam11496  246 Y 246
CD1_tandem_CHD5-9_like cd18668
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ...
314-360 1.67e-04

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: 41.55  E-value: 1.67e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1622945983  314 EKNKEPGEI---QYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKK 360
Cdd:cd18668     19 EKEEGAEEIeveEYLVKYKNFSYLHCEWKTEEELEKGDKRIKQKIKRFKQ 68
HisXaaSer_A3 NF038309
His-Xaa-Ser repeat protein HxsA3; This model represents an alternate form of the His-Xaa-Ser ...
1725-1756 2.02e-04

His-Xaa-Ser repeat protein HxsA3; This model represents an alternate form of the His-Xaa-Ser repeat protein HxsA, while TIGR03979 represents a more common form. The model covers a conserved N-terminal region, followed by the His-Xaa-Ser repeat region, but does not cover the C-terminal region, which is highly variable in this branch of His-Xaa-Ser repeat family protein.


Pssm-ID: 439608  Cd Length: 81  Bit Score: 41.53  E-value: 2.02e-04
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1622945983 1725 HRSHSDHRLHSDHRSSSEYTH--HKSSRDYRYHS 1756
Cdd:NF038309    47 HRSHSSHSSHSSHSSGSSGGHssHSSHSSHSSHS 80
CD_HP1beta_Cbx1 cd18650
chromodomain of heterochromatin protein 1 homolog beta; CHRomatin Organization Modifier ...
320-344 2.03e-04

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: 40.70  E-value: 2.03e-04
                           10        20
                   ....*....|....*....|....*
gi 1622945983  320 GEIQYLIKWKGWSHIHNTWETEETL 344
Cdd:cd18650     15 GKVEYLLKWKGFSDEDNTWEPEENL 39
CD_HP1alpha_Cbx5 cd18651
chromodomain of heterochromatin protein 1 homolog alpha; CHRomatin Organization Modifier ...
320-344 2.19e-04

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: 40.74  E-value: 2.19e-04
                           10        20
                   ....*....|....*....|....*
gi 1622945983  320 GEIQYLIKWKGWSHIHNTWETEETL 344
Cdd:cd18651     15 GQVEYLLKWKGFSEEHNTWEPEKNL 39
CD_Cbx4 cd18645
chromodomain of chromobox homolog 4; CHRomatin Organization Modifier (chromo) domain of ...
300-344 3.22e-04

chromodomain of chromobox homolog 4; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 4 (CBX4), 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. In addition to a chromodomain with H3K27me3-binding activity, Cbx4 contains two SUMO-interacting motifs responsible for its small ubiquitin-related modifier (SUMO) E3 ligase activity. CBX proteins may act as an oncogene or tumor suppressor in a cell-type-dependent manner, for example CBX8 promotes proliferation while suppressing metastasis, in colorectal carcinoma progression. CBX4 may serve as a tumor suppressor in colorectal carcinoma, and has been shown to be an oncogene in osteosarcoma and breast cancer.


Pssm-ID: 349292  Cd Length: 55  Bit Score: 40.43  E-value: 3.22e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1622945983  300 IYAVEadgdpnaGFEKNK-EPGEIQYLIKWKGWSHIHNTWETEETL 344
Cdd:cd18645      3 VFAVE-------SIEKKRiRKGRVEYLVKWRGWSPKYNTWEPEENI 41
CD_HP1_like cd18631
chromodomain of heterochromatin protein 1 proteins, including HP1alpha, HP1beta, and HP1gamma; ...
320-344 3.81e-04

chromodomain of heterochromatin protein 1 proteins, including HP1alpha, HP1beta, and HP1gamma; CHRomatin Organization Modifier (chromo) domain of mammalian HP1alpha (Cbx5), HP1beta (Cbx1), HP1gamma (Cbx5), and similar proteins. HP1 has diverse functions in heterochromatin formation and impacts both gene expression and gene silencing. 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 (also known as Cbx1), and HP1gamma (also known as Cbx3).


Pssm-ID: 349281  Cd Length: 50  Bit Score: 39.73  E-value: 3.81e-04
                           10        20
                   ....*....|....*....|....*
gi 1622945983  320 GEIQYLIKWKGWSHIHNTWETEETL 344
Cdd:cd18631     15 GKVEYLLKWKGYPDEDNTWEPEENL 39
CD_HP1a_insect cd18653
chromodomain of insect HP1a; CHRomatin Organization Modifier (chromo) domain of insect HP1a. ...
320-349 5.01e-04

chromodomain of insect HP1a; CHRomatin Organization Modifier (chromo) domain of insect HP1a. HP1a is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1 has diverse functions in heterochromatin formation and impacts both gene expression and gene silencing. 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. In Drosophila, there are at least five HP1 family proteins, this subgroup includes the CD of Drosophila melanogaster HP1a.


Pssm-ID: 349300  Cd Length: 50  Bit Score: 39.63  E-value: 5.01e-04
                           10        20        30
                   ....*....|....*....|....*....|
gi 1622945983  320 GEIQYLIKWKGWSHIHNTWETEETLKQQNV 349
Cdd:cd18653     15 GKVEYYLKWKGYPETENTWEPEENLDCQDL 44
CD_Cbx8 cd18649
chromodomain of chromobox homolog 8; CHRomatin Organization Modifier (chromo) domain of ...
320-344 5.91e-04

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: 39.70  E-value: 5.91e-04
                           10        20
                   ....*....|....*....|....*
gi 1622945983  320 GEIQYLIKWKGWSHIHNTWETEETL 344
Cdd:cd18649     18 GRMEYLVKWKGWSQKYSTWEPEENI 42
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
1694-1803 6.36e-04

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 44.50  E-value: 6.36e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622945983 1694 DREKHRKLDDHRSRDhRSNLEGSLKDRSHSDHRSHSDHRLHSDHRSSSEYTHH-KSSRDYRYHSDWQMDHRASSsgpRSP 1772
Cdd:TIGR01642    2 DEEPDREREKSRGRD-RDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRdRRRYDSRSPRSLRYSSVRRS---RDR 77
                           90       100       110
                   ....*....|....*....|....*....|.
gi 1622945983 1773 LDQRSPYGSRSPFEHSVEHKSTPEHTWSSRK 1803
Cdd:TIGR01642   78 PRRRSRSVRSIEQHRRRLRDRSPSNQWRKDD 108
CD_POL_like cd18972
chromodomain of a Moniliophthora perniciosa FA553 putative retrotransposon polyprotein, and ...
323-360 7.55e-04

chromodomain of a Moniliophthora perniciosa FA553 putative retrotransposon polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Moniliophthora perniciosa FA553 putative retrotelement polyprotein, which includes domains in the following order: 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: 349328  Cd Length: 50  Bit Score: 39.03  E-value: 7.55e-04
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1622945983  323 QYLIKWKGWSHIHNTWETEETLKQqnvrGMKKLDNYKK 360
Cdd:cd18972     17 QFLVSWLGYDSSHNEWKQKEELEN----ARELLQDYLK 50
CD_CSD cd00024
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
397-448 1.03e-03

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: 38.61  E-value: 1.03e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1622945983  397 VERIIAHSNQKsaaGYPDYYCKWQGLPYSECSWEDGALISKKFQAcIDEYFS 448
Cdd:cd00024      3 VEKILDHRVRK---GKLEYLVKWKGYPPEENTWEPEENLTNAPEL-IKEYEK 50
HisXaaSer_A2 NF038296
His-Xaa-Ser repeat protein HxsA2; This model represents a short form of the His-Xaa-Ser repeat ...
1721-1741 1.14e-03

His-Xaa-Ser repeat protein HxsA2; This model represents a short form of the His-Xaa-Ser repeat protein HxsA, while TIGR03979 represents a long form. In the short form, sequences average about 97 amino acids in length and end with the HXS repeat region.


Pssm-ID: 468458  Cd Length: 96  Bit Score: 40.09  E-value: 1.14e-03
                           10        20
                   ....*....|....*....|.
gi 1622945983 1721 SHSDHRSHSDHRLHSDHRSSS 1741
Cdd:NF038296    76 YHSSHSSHSSHSSHSSHYSSS 96
CD_MarY1_POL_like cd18975
chromodomain of Tricholoma matsutake polyprotein, and similar proteins; This subgroup includes ...
320-345 1.56e-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: 38.29  E-value: 1.56e-03
                           10        20
                   ....*....|....*....|....*.
gi 1622945983  320 GEIQYLIKWKGWSHIHNTWETEETLK 345
Cdd:cd18975     14 GKLQYLIQWKGYPLEEASWELEDNIK 39
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
1683-1751 2.04e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 42.96  E-value: 2.04e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1622945983 1683 DHYKQDSRYYgDREKHRKLDDHRSRDHRSNLEGSLKDRSHSDHRSHsdhrlHSDHRSSSEYTHHKSSRD 1751
Cdd:TIGR01642   14 GRDRDRSSER-PRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRY-----DSRSPRSLRYSSVRRSRD 76
CD_HP1gamma_Cbx3 cd18652
chromodomain of heterochromatin protein 1 homolog gamma; CHRomatin Organization Modifier ...
320-344 2.34e-03

chromodomain of heterochromatin protein 1 homolog gamma; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog gamma (also known as HP1gamma, Cbx3, and Chromobox 3), and related proteins. HP1gamma 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. In addition to being involved in transcriptional silencing in heterochromatin-like complexes, HP1gamma also binds lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the protein may explain the association of heterochromatin with the inner nuclear membrane. HP1gamma is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. 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 (also known as Cbx1), and HP1gamma.


Pssm-ID: 349299  Cd Length: 50  Bit Score: 37.68  E-value: 2.34e-03
                           10        20
                   ....*....|....*....|....*
gi 1622945983  320 GEIQYLIKWKGWSHIHNTWETEETL 344
Cdd:cd18652     15 GKVEYFLKWKGFTDADNTWEPEENL 39
CD_Cbx6 cd18648
chromodomain of chromobox homolog 6; CHRomatin Organization Modifier (chromo) domain of ...
320-344 3.10e-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: 37.73  E-value: 3.10e-03
                           10        20
                   ....*....|....*....|....*
gi 1622945983  320 GEIQYLIKWKGWSHIHNTWETEETL 344
Cdd:cd18648     17 GRIEYLVKWKGWAIKYSTWEPEENI 41
CD2_tandem_CHD5-9_like cd18663
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ...
394-430 3.77e-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: 37.27  E-value: 3.77e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1622945983  394 YQIVERII---AHSNQKSAAGYPDYYCKWQGLPYSECSWE 430
Cdd:cd18663      3 YVEVDRILdvsVSTDPNTGEPVTHYLVKWCSLPYEDSTWE 42
CD_POL_like cd18974
chromodomain of Penicillium solitum protein PENSOL_c198G03123; This subgroup includes the ...
320-344 4.13e-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: 37.07  E-value: 4.13e-03
                           10        20
                   ....*....|....*....|....*
gi 1622945983  320 GEIQYLIKWKGWSHIHNTWETEETL 344
Cdd:cd18974     14 DELHYLVKWKGWPAEYNQWEPEDDM 38
CD2_tandem cd18659
repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier ...
314-347 4.54e-03

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


Pssm-ID: 349306 [Multi-domain]  Cd Length: 54  Bit Score: 36.78  E-value: 4.54e-03
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1622945983  314 EKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQ 347
Cdd:cd18659     11 HREDDEGVTEYLVKWKGLPYDECTWESEEDISDI 44
CD_HP1_like cd18960
chromodomain of heterochromatin protein 1 proteins, including HP1alpha, HP1beta, and HP1gamma; ...
396-430 5.72e-03

chromodomain of heterochromatin protein 1 proteins, including HP1alpha, HP1beta, and HP1gamma; uncharacterized subgroup; CHRomatin Organization Modifier (chromo) domain of mammalian HP1alpha (Cbx5), HP1beta (Cbx1), HP1gamma (Cbx5), and similar proteins. HP1 has diverse functions in heterochromatin formation and impacts both gene expression and gene silencing. 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 (also known as Cbx1), and HP1gamma (also known as Cbx3).


Pssm-ID: 349316  Cd Length: 51  Bit Score: 36.77  E-value: 5.72e-03
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1622945983  396 IVERIIahSNQKSAAGYPDYYCKWQGLPYSECSWE 430
Cdd:cd18960      3 VVERIL--DKRLGRNGGEEFLIKWQGFPESDSSWE 35
CD_Cbx7 cd18646
chromodomain of chromobox homolog 7; CHRomatin Organization Modifier (chromo) domain of ...
314-342 7.26e-03

chromodomain of chromobox homolog 7; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 7 (CBX7), 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, for example CBX8 promotes proliferation while suppressing metastasis, in colorectal carcinoma progression. CBX7 has been shown to function as a tumor suppressor in lung carcinoma and an oncogene in gastric cancer and lymphoma.


Pssm-ID: 349293  Cd Length: 56  Bit Score: 36.61  E-value: 7.26e-03
                           10        20
                   ....*....|....*....|....*....
gi 1622945983  314 EKNKEPGEIQYLIKWKGWSHIHNTWETEE 342
Cdd:cd18646     12 KKRVRKGKVEYLVKWKGWPPKYSTWEPEE 40
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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