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Conserved domains on  [gi|488291551|ref|WP_002362759|]
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MULTISPECIES: DEAD/DEAH box helicase [Lactobacillales]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 13029788)

DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA; such as human DNA excision repair protein ERCC-6-like and DNA repair and recombination protein RAD54-like

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEXQc_bact_SNF2 cd18013
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ...
 5-223 4.96e-116

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: 338.94  E-value: 4.96e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   5 PHEYQQYSIDFIKNNKIAALLLEMGLGKTVTTLTAIKDLMHDDFsIKKVLIVAPLRVAQSTWPNEIEKWDHLKDLTYSVV 84
Cdd:cd18013    1 PHPYQKVAINFIIEHPYCGLFLDMGLGKTVTTLTALSDLQLDDF-TRRVLVIAPLRVARSTWPDEVEKWNHLRNLTVSVA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  85 LGTPKQRKEALWKKADLYLINRENLDWLITKSGFDFDFDMVVIDELSSFKNYKAKRFTSLMQVRHKVDRIVGLTGTPSSN 164
Cdd:cd18013   80 VGTERQRSKAANTPADLYVINRENLKWLVNKSGDPWPFDMVVIDELSSFKSPRSKRFKALRKVRPVIKRLIGLTGTPSPN 159

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488291551 165 GLMDLFAEFKVLDMGERLEYYISRYRDKYFLPDKRNGLQIYSWKPRENAEQEIYDKISD 223
Cdd:cd18013  160 GLMDLWAQIALLDQGERLGRSITAYRERWFDPDKRNGQQVFKYKPKPGAEEEIYRAISD 218
HepA super family cl33945
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 1-442 6.75e-44

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


The actual alignment was detected with superfamily member COG0553:

Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 163.47  E-value: 6.75e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   1 MKFIPHEYQQYSIDFIKNNKIAAL--LL--EMGLGKTVTTLTAIKDLMHDDfSIKKVLIVAPLRVaQSTWPNEIEKWDHl 76
Cdd:COG0553  238 LKATLRPYQLEGAAWLLFLRRLGLggLLadDMGLGKTIQALALLLELKERG-LARPVLIVAPTSL-VGNWQRELAKFAP- 314

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  77 kDLTYSVVLGTPK-QRKEALWKKADLYLIN----RENLDWLItksgfDFDFDMVVIDELSSFKNYKAKRFTSLMQVrhKV 151
Cdd:COG0553  315 -GLRVLVLDGTRErAKGANPFEDADLVITSygllRRDIELLA-----AVDWDLVILDEAQHIKNPATKRAKAVRAL--KA 386

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 152 DRIVGLTGTPSSNGLMDLFAEFKVLDMGeRLEYYiSRYRDKYFLPDKRNglqiyswkpRENAEQEIYDKISDITIS-MKS 230
Cdd:COG0553  387 RHRLALTGTPVENRLEELWSLLDFLNPG-LLGSL-KAFRERFARPIEKG---------DEEALERLRRLLRPFLLRrTKE 455

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 231 VDFLDMPELVINEVPVSLGETEKHKYDKFKADLVLQLKDADIDAANAAVLS--NKLLQMANG-AIYDEFNVSHHIHDQKL 307
Cdd:COG0553  456 DVLKDLPEKTEETLYVELTPEQRALYEAVLEYLRRELEGAEGIRRRGLILAalTRLRQICSHpALLLEEGAELSGRSAKL 535

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 308 DALEDLIEG--ANGKSILIAYWFQHDLERIKERFKVRQIK-------TAKD-----IEEWNKG-NIPIGVIHPASAGHGL 372
Cdd:COG0553  536 EALLELLEEllAEGEKVLVFSQFTDTLDLLEERLEERGIEyaylhggTSAEerdelVDRFQEGpEAPVFLISLKAGGEGL 615

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 373 NLQAGgSTLVWFGLTWSLELYQQTNARLWRQGQNETVVIHHIIAKDTIDEdVMLALkLKDKtqASLIDAV 442
Cdd:COG0553  616 NLTAA-DHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEE-KILEL-LEEK--RALAESV 680
 
Name Accession Description Interval E-value
DEXQc_bact_SNF2 cd18013
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ...
 5-223 4.96e-116

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: 338.94  E-value: 4.96e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   5 PHEYQQYSIDFIKNNKIAALLLEMGLGKTVTTLTAIKDLMHDDFsIKKVLIVAPLRVAQSTWPNEIEKWDHLKDLTYSVV 84
Cdd:cd18013    1 PHPYQKVAINFIIEHPYCGLFLDMGLGKTVTTLTALSDLQLDDF-TRRVLVIAPLRVARSTWPDEVEKWNHLRNLTVSVA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  85 LGTPKQRKEALWKKADLYLINRENLDWLITKSGFDFDFDMVVIDELSSFKNYKAKRFTSLMQVRHKVDRIVGLTGTPSSN 164
Cdd:cd18013   80 VGTERQRSKAANTPADLYVINRENLKWLVNKSGDPWPFDMVVIDELSSFKSPRSKRFKALRKVRPVIKRLIGLTGTPSPN 159

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488291551 165 GLMDLFAEFKVLDMGERLEYYISRYRDKYFLPDKRNGLQIYSWKPRENAEQEIYDKISD 223
Cdd:cd18013  160 GLMDLWAQIALLDQGERLGRSITAYRERWFDPDKRNGQQVFKYKPKPGAEEEIYRAISD 218
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 1-442 6.75e-44

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 163.47  E-value: 6.75e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   1 MKFIPHEYQQYSIDFIKNNKIAAL--LL--EMGLGKTVTTLTAIKDLMHDDfSIKKVLIVAPLRVaQSTWPNEIEKWDHl 76
Cdd:COG0553  238 LKATLRPYQLEGAAWLLFLRRLGLggLLadDMGLGKTIQALALLLELKERG-LARPVLIVAPTSL-VGNWQRELAKFAP- 314

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  77 kDLTYSVVLGTPK-QRKEALWKKADLYLIN----RENLDWLItksgfDFDFDMVVIDELSSFKNYKAKRFTSLMQVrhKV 151
Cdd:COG0553  315 -GLRVLVLDGTRErAKGANPFEDADLVITSygllRRDIELLA-----AVDWDLVILDEAQHIKNPATKRAKAVRAL--KA 386

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 152 DRIVGLTGTPSSNGLMDLFAEFKVLDMGeRLEYYiSRYRDKYFLPDKRNglqiyswkpRENAEQEIYDKISDITIS-MKS 230
Cdd:COG0553  387 RHRLALTGTPVENRLEELWSLLDFLNPG-LLGSL-KAFRERFARPIEKG---------DEEALERLRRLLRPFLLRrTKE 455

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 231 VDFLDMPELVINEVPVSLGETEKHKYDKFKADLVLQLKDADIDAANAAVLS--NKLLQMANG-AIYDEFNVSHHIHDQKL 307
Cdd:COG0553  456 DVLKDLPEKTEETLYVELTPEQRALYEAVLEYLRRELEGAEGIRRRGLILAalTRLRQICSHpALLLEEGAELSGRSAKL 535

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 308 DALEDLIEG--ANGKSILIAYWFQHDLERIKERFKVRQIK-------TAKD-----IEEWNKG-NIPIGVIHPASAGHGL 372
Cdd:COG0553  536 EALLELLEEllAEGEKVLVFSQFTDTLDLLEERLEERGIEyaylhggTSAEerdelVDRFQEGpEAPVFLISLKAGGEGL 615

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 373 NLQAGgSTLVWFGLTWSLELYQQTNARLWRQGQNETVVIHHIIAKDTIDEdVMLALkLKDKtqASLIDAV 442
Cdd:COG0553  616 NLTAA-DHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEE-KILEL-LEEK--RALAESV 680
DEXDc smart00487
DEAD-like helicases superfamily;
3-164 1.04e-16

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 78.30  E-value: 1.04e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551     3 FIPHEYQQYSIDFI-KNNKIAALLLEMGLGKTVTTLTAIKDLMHDDFSiKKVLIVAPLRVAQSTWPNEIEKWDHLKDLTY 81
Cdd:smart00487   7 EPLRPYQKEAIEALlSGLRDVILAAPTGSGKTLAALLPALEALKRGKG-GRVLVLVPTRELAEQWAEELKKLGPSLGLKV 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551    82 SVVLG---TPKQRKEALWKKADLYLINRENLDWLITKSGFDF-DFDMVVIDELSSFKNYKAKR-FTSLMQVRHKVDRIVG 156
Cdd:smart00487  86 VGLYGgdsKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLsNVDLVILDEAHRLLDGGFGDqLEKLLKLLPKNVQLLL 165


                   ....*...
gi 488291551   157 LTGTPSSN 164
Cdd:smart00487 166 LSATPPEE 173
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 18-176 1.48e-16

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: 79.65  E-value: 1.48e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   18 NNKIAALLL--EMGLGKTVTTLTAIKDLMH-DDFSIKKVLIVAPLRVAQStWPNEIEKWDHLKDLTYSVVLGTPKQRkeA 94
Cdd:pfam00176  14 NNLGRGGILadEMGLGKTLQTISLLLYLKHvDKNWGGPTLIVVPLSLLHN-WMNEFERWVSPPALRVVVLHGNKRPQ--E 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   95 LWKKADLYlinRENLDWLIT--------KSGFD-FDFDMVVIDELSSFKNYKAKrfTSLMQVRHKVDRIVGLTGTPSSNG 165
Cdd:pfam00176  91 RWKNDPNF---LADFDVVITtyetlrkhKELLKkVHWHRIVLDEGHRLKNSKSK--LSKALKSLKTRNRWILTGTPLQNN 165

                         170
                  ....*....|.
gi 488291551  166 LMDLFAEFKVL 176
Cdd:pfam00176 166 LEELWALLNFL 176
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
1-173 1.07e-09

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 60.42  E-value: 1.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   1 MKFIPHEYQQ-----YSIDFIKNNKIAALLLEMGLGKTVTTLTAIKDLMHddfsIKKVLIVAPLRVAQSTWPNEIEKWDH 75
Cdd:COG1061   77 TSFELRPYQQealeaLLAALERGGGRGLVVAPTGTGKTVLALALAAELLR----GKRVLVLVPRRELLEQWAEELRRFLG 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  76 L-------KDLTYSVVLGTPKQrkealwkkadlyLINRENLDWlitksgFDFDFDMVVIDElssFKNYKAKRFTSLMQvR 148
Cdd:COG1061  153 DplagggkKDSDAPITVATYQS------------LARRAHLDE------LGDRFGLVIIDE---AHHAGAPSYRRILE-A 210

                        170       180
                 ....*....|....*....|....*.
gi 488291551 149 HKVDRIVGLTGTP-SSNGLMDLFAEF 173
Cdd:COG1061  211 FPAAYRLGLTATPfRSDGREILLFLF 236
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 301-415 2.41e-06

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: 46.70  E-value: 2.41e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 301 HIHDQKLDALEDLIEG---ANGKSILIAYWFQHdLERIKERFKVRQIKTA------------KDIEEWNKG-NIPIGVIH 364
Cdd:cd18793    7 EVVSGKLEALLELLEElrePGEKVLIFSQFTDT-LDILEEALRERGIKYLrldgstsskerqKLVDRFNEDpDIRVFLLS 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 488291551 365 PASAGHGLNLQAGgSTLVWFGLTWSLELYQQTNARLWRQGQNETVVIHHII 415
Cdd:cd18793   86 TKAGGVGLNLTAA-NRVILYDPWWNPAVEEQAIDRAHRIGQKKPVVVYRLI 135
 
Name Accession Description Interval E-value
DEXQc_bact_SNF2 cd18013
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ...
 5-223 4.96e-116

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: 338.94  E-value: 4.96e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   5 PHEYQQYSIDFIKNNKIAALLLEMGLGKTVTTLTAIKDLMHDDFsIKKVLIVAPLRVAQSTWPNEIEKWDHLKDLTYSVV 84
Cdd:cd18013    1 PHPYQKVAINFIIEHPYCGLFLDMGLGKTVTTLTALSDLQLDDF-TRRVLVIAPLRVARSTWPDEVEKWNHLRNLTVSVA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  85 LGTPKQRKEALWKKADLYLINRENLDWLITKSGFDFDFDMVVIDELSSFKNYKAKRFTSLMQVRHKVDRIVGLTGTPSSN 164
Cdd:cd18013   80 VGTERQRSKAANTPADLYVINRENLKWLVNKSGDPWPFDMVVIDELSSFKSPRSKRFKALRKVRPVIKRLIGLTGTPSPN 159

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488291551 165 GLMDLFAEFKVLDMGERLEYYISRYRDKYFLPDKRNGLQIYSWKPRENAEQEIYDKISD 223
Cdd:cd18013  160 GLMDLWAQIALLDQGERLGRSITAYRERWFDPDKRNGQQVFKYKPKPGAEEEIYRAISD 218
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 1-442 6.75e-44

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 163.47  E-value: 6.75e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   1 MKFIPHEYQQYSIDFIKNNKIAAL--LL--EMGLGKTVTTLTAIKDLMHDDfSIKKVLIVAPLRVaQSTWPNEIEKWDHl 76
Cdd:COG0553  238 LKATLRPYQLEGAAWLLFLRRLGLggLLadDMGLGKTIQALALLLELKERG-LARPVLIVAPTSL-VGNWQRELAKFAP- 314

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  77 kDLTYSVVLGTPK-QRKEALWKKADLYLIN----RENLDWLItksgfDFDFDMVVIDELSSFKNYKAKRFTSLMQVrhKV 151
Cdd:COG0553  315 -GLRVLVLDGTRErAKGANPFEDADLVITSygllRRDIELLA-----AVDWDLVILDEAQHIKNPATKRAKAVRAL--KA 386

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 152 DRIVGLTGTPSSNGLMDLFAEFKVLDMGeRLEYYiSRYRDKYFLPDKRNglqiyswkpRENAEQEIYDKISDITIS-MKS 230
Cdd:COG0553  387 RHRLALTGTPVENRLEELWSLLDFLNPG-LLGSL-KAFRERFARPIEKG---------DEEALERLRRLLRPFLLRrTKE 455

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 231 VDFLDMPELVINEVPVSLGETEKHKYDKFKADLVLQLKDADIDAANAAVLS--NKLLQMANG-AIYDEFNVSHHIHDQKL 307
Cdd:COG0553  456 DVLKDLPEKTEETLYVELTPEQRALYEAVLEYLRRELEGAEGIRRRGLILAalTRLRQICSHpALLLEEGAELSGRSAKL 535

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 308 DALEDLIEG--ANGKSILIAYWFQHDLERIKERFKVRQIK-------TAKD-----IEEWNKG-NIPIGVIHPASAGHGL 372
Cdd:COG0553  536 EALLELLEEllAEGEKVLVFSQFTDTLDLLEERLEERGIEyaylhggTSAEerdelVDRFQEGpEAPVFLISLKAGGEGL 615

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 373 NLQAGgSTLVWFGLTWSLELYQQTNARLWRQGQNETVVIHHIIAKDTIDEdVMLALkLKDKtqASLIDAV 442
Cdd:COG0553  616 NLTAA-DHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEE-KILEL-LEEK--RALAESV 680
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
 5-178 1.42e-38

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: 137.70  E-value: 1.42e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   5 PHEYQQYSIDFI----KNNKIAALLLEMGLGKTVTTLTAIKDLMHDDFSIKKVLIVAPLrVAQSTWPNEIEKWDHlkDLT 80
Cdd:cd17919    1 LRPYQLEGLNFLlelyENGPGGILADEMGLGKTLQAIAFLAYLLKEGKERGPVLVVCPL-SVLENWEREFEKWTP--DLR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  81 YSVVLGTPKQRKEAL----WKKADLYLINRENLDWLITKSGfDFDFDMVVIDELSSFKNYKAKRFTSLMQVRHKvdRIVG 156
Cdd:cd17919   78 VVVYHGSQRERAQIRakekLDKFDVVLTTYETLRRDKASLR-KFRWDLVVVDEAHRLKNPKSQLSKALKALRAK--RRLL 154

                        170       180
                 ....*....|....*....|..
gi 488291551 157 LTGTPSSNGLMDLFAEFKVLDM 178
Cdd:cd17919  155 LTGTPLQNNLEELWALLDFLDP 176
DEXQc_arch_SWI2_SNF2 cd18012
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ...
 7-201 4.67e-19

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: 85.31  E-value: 4.67e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   7 EYQQYSID---FIKNNKIAALLL-EMGLGKTVTTLTAIKDLMHDDFSiKKVLIVAPLRVAqSTWPNEIEKW-DHLKDLTY 81
Cdd:cd18012    7 PYQKEGFNwlsFLRHYGLGGILAdDMGLGKTLQTLALLLSRKEEGRK-GPSLVVAPTSLI-YNWEEEAAKFaPELKVLVI 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  82 SvvlGTPKQRKEALW-KKADLYLIN----RENLDWLITKSgfdfdFDMVVIDELSSFKNYKAKRFTSLMQVrhKVDRIVG 156
Cdd:cd18012   85 H---GTKRKREKLRAlEDYDLVITSygllRRDIELLKEVK-----FHYLVLDEAQNIKNPQTKTAKAVKAL--KADHRLA 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 488291551 157 LTGTPSSNGLMDLFAEFKVLDMGerLEYYISRYRDKYFLPDKRNG 201
Cdd:cd18012  155 LTGTPIENHLGELWSIFDFLNPG--LLGSYKRFKKRFAKPIEKDG 197
DEXDc smart00487
DEAD-like helicases superfamily;
3-164 1.04e-16

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 78.30  E-value: 1.04e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551     3 FIPHEYQQYSIDFI-KNNKIAALLLEMGLGKTVTTLTAIKDLMHDDFSiKKVLIVAPLRVAQSTWPNEIEKWDHLKDLTY 81
Cdd:smart00487   7 EPLRPYQKEAIEALlSGLRDVILAAPTGSGKTLAALLPALEALKRGKG-GRVLVLVPTRELAEQWAEELKKLGPSLGLKV 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551    82 SVVLG---TPKQRKEALWKKADLYLINRENLDWLITKSGFDF-DFDMVVIDELSSFKNYKAKR-FTSLMQVRHKVDRIVG 156
Cdd:smart00487  86 VGLYGgdsKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLsNVDLVILDEAHRLLDGGFGDqLEKLLKLLPKNVQLLL 165


                   ....*...
gi 488291551   157 LTGTPSSN 164
Cdd:smart00487 166 LSATPPEE 173
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 18-176 1.48e-16

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: 79.65  E-value: 1.48e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   18 NNKIAALLL--EMGLGKTVTTLTAIKDLMH-DDFSIKKVLIVAPLRVAQStWPNEIEKWDHLKDLTYSVVLGTPKQRkeA 94
Cdd:pfam00176  14 NNLGRGGILadEMGLGKTLQTISLLLYLKHvDKNWGGPTLIVVPLSLLHN-WMNEFERWVSPPALRVVVLHGNKRPQ--E 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   95 LWKKADLYlinRENLDWLIT--------KSGFD-FDFDMVVIDELSSFKNYKAKrfTSLMQVRHKVDRIVGLTGTPSSNG 165
Cdd:pfam00176  91 RWKNDPNF---LADFDVVITtyetlrkhKELLKkVHWHRIVLDEGHRLKNSKSK--LSKALKSLKTRNRWILTGTPLQNN 165

                         170
                  ....*....|.
gi 488291551  166 LMDLFAEFKVL 176
Cdd:pfam00176 166 LEELWALLNFL 176
DEXHc_ATRX-like cd18007
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ...
 28-171 4.27e-16

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: 77.33  E-value: 4.27e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  28 MGLGKTVTTLTAIKDLMHDDFSIKKVLIVAPlRVAQSTWPNEIEKW-----DHLKDLTYSVVLGTPKQRKEAL---WKKA 99
Cdd:cd18007   35 MGLGKTLQVITFLHTYLAAAPRRSRPLVLCP-ASTLYNWEDEFKKWlppdlRPLLVLVSLSASKRADARLRKInkwHKEG 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 100 DLYLINRENLDWLITKSGFDFDF-------------DMVVIDELSSFKNYKAKRFTSLMQVRHKvDRIVgLTGTPSSNGL 166
Cdd:cd18007  114 GVLLIGYELFRNLASNATTDPRLkqefiaalldpgpDLLVLDEGHRLKNEKSQLSKALSKVKTK-RRIL-LTGTPLQNNL 191


                 ....*
gi 488291551 167 MDLFA 171
Cdd:cd18007  192 KEYWT 196
DEXHc_HARP_SMARCAL1 cd18010
DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin ...
 6-194 4.97e-15

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: 73.78  E-value: 4.97e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   6 HEYQQYSIDF-IKNNKIAALLLEMGLGKTVTTLtAIKDLMHDDFSikkVLIVAP--LRVaqsTWPNEIEKWDHLKDLTYS 82
Cdd:cd18010    2 LPFQREGVCFaLRRGGRVLIADEMGLGKTVQAI-AIAAYYREEWP---LLIVCPssLRL---TWADEIERWLPSLPPDDI 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  83 VVLGTPKQRKEALWKKA-----DLYLINRENLDwlitksgfDFDFDMVVIDELSSFKNYKAKRFTSLMQVRHKVDRIVGL 157
Cdd:cd18010   75 QVIVKSKDGLRDGDAKVvivsyDLLRRLEKQLL--------ARKFKVVICDESHYLKNSKAKRTKAALPLLKRAKRVILL 146

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 488291551 158 TGTPSSNGLMDLFAEFKVLD---MGeRLEYYISRYRDKYF 194
Cdd:cd18010  147 SGTPALSRPIELFTQLDALDpklFG-RFHDFGRRYCAAKQ 185
DEXHc_ERCC6L2 cd18005
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
 7-199 1.48e-11

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: 64.32  E-value: 1.48e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   7 EYQQYSIDFI----KNNKIAALLLEMGLGKTVTTLTAIKDLMH------DDFSIKK--------------VLIVAPLRVA 62
Cdd:cd18005    3 DYQREGVEFMydlyKNGRGGILGDDMGLGKTVQVIAFLAAVLGktgtrrDRENNRPrfkkkppassakkpVLIVAPLSVL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  63 QsTWPNEIEKWDHlkdltYSVVLGTPKQRKEALWKKADL---------YLINRENLDWLItksgfDFDFDMVVIDELSSF 133
Cdd:cd18005   83 Y-NWKDELDTWGH-----FEVGVYHGSRKDDELEGRLKAgrlevvvttYDTLRRCIDSLN-----SINWSAVIADEAHRI 151

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488291551 134 KNYKAKRFTSLMQVRHKVdRIvGLTGTPSSNGLMDLFAefkVLD------MGERleyyiSRYRDKYFLPDKR 199
Cdd:cd18005  152 KNPKSKLTQAMKELKCKV-RI-GLTGTLLQNNMKELWC---LLDwavpgaLGSR-----SQFKKHFSEPIKR 213
DEXHc_ERCC6L cd18001
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ...
 7-199 2.34e-11

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: 63.54  E-value: 2.34e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   7 EYQQYSIDFI----KNNKIAALLLEMGLGKTVTTLTAIKDLMHDDFsIKKVLIVAPLRVAqSTWPNEIEKWDhlKDLTYS 82
Cdd:cd18001    3 PHQREGVAWLwslhDGGKGGILADDMGLGKTVQICAFLSGMFDSGL-IKSVLVVMPTSLI-PHWVKEFAKWT--PGLRVK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  83 VVLGT-PKQRKEALWKKAD-------LYLINRENLDWLITKSGFDFDFDMVVIDELSSFKNYKAKRFTSLMQVRHKvDRI 154
Cdd:cd18001   79 VFHGTsKKERERNLERIQRgggvlltTYGMVLSNTEQLSADDHDEFKWDYVILDEGHKIKNSKTKSAKSLREIPAK-NRI 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 488291551 155 VgLTGTPSSNGLMDLFAEFKVLDMGERL----------EYYISRYRDKYFLPDKR 199
Cdd:cd18001  158 I-LTGTPIQNNLKELWALFDFACNGSLLgtrktfkmefENPITRGRDKDATQGEK 211
DEXHc_Mot1 cd17999
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ...
 7-176 1.08e-10

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: 61.60  E-value: 1.08e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   7 EYQQYSI---DFIKNNKIAALLL-EMGLGKTVTTLTAI-----KDLMHDDFSIKKVLIVAPLRVAQStWPNEIEKW---D 74
Cdd:cd17999    3 PYQQEGInwlAFLNKYNLHGILCdDMGLGKTLQTLCILasdhhKRANSFNSENLPSLVVCPPTLVGH-WVAEIKKYfpnA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  75 HLKDLTYSvvlGTPKQRK--EALWKKADL----YLINRENLDWLitksgFDFDFDMVVIDELSSFKNYKAKRFTSLMQVR 148
Cdd:cd17999   82 FLKPLAYV---GPPQERRrlREQGEKHNVivasYDVLRNDIEVL-----TKIEWNYCVLDEGHIIKNSKTKLSKAVKQLK 153

                        170       180
                 ....*....|....*....|....*...
gi 488291551 149 HKvDRIVgLTGTPSSNGLMDLFAEFKVL 176
Cdd:cd17999  154 AN-HRLI-LSGTPIQNNVLELWSLFDFL 179
DEXHc_RAD54 cd18004
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ...
 27-171 1.51e-10

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: 61.15  E-value: 1.51e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  27 EMGLGKTVTTL----TAIKDLMHDDFSIKKVLIVAPlrvaqST----WPNEIEKWDHLKDLTYSVVLGTPKQRKEALWKK 98
Cdd:cd18004   32 EMGLGKTLQAIalvwTLLKQGPYGKPTAKKALIVCP-----SSlvgnWKAEFDKWLGLRRIKVVTADGNAKDVKASLDFF 106

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488291551  99 --ADLY---LINRENLDWLITKSGFDFDFDMVVIDELSSFKNYKAKRFTSLMQVRhkVDRIVGLTGTPSSNGLMDLFA 171
Cdd:cd18004  107 ssASTYpvlIISYETLRRHAEKLSKKISIDLLICDEGHRLKNSESKTTKALNSLP--CRRRLLLTGTPIQNDLDEFFA 182
DEXHc_SMARCA2_SMARCA4 cd17996
DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin ...
 18-171 2.34e-10

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: 60.46  E-value: 2.34e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  18 NNKIAALLL-EMGLGKTVTTLTAIKDLMHDDFSIKKVLIVAPLRVAqSTWPNEIEKWdhLKDLTYSVVLGTPKQRKEaLW 96
Cdd:cd17996   20 NNNLNGILAdEMGLGKTIQTISLITYLMEKKKNNGPYLVIVPLSTL-SNWVSEFEKW--APSVSKIVYKGTPDVRKK-LQ 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  97 KKadlylINRENLDWLITKSGF---------DFDFDMVVIDELSSFKNYKAKRFTSLMQVRHKVDRIVgLTGTPSSNGLM 167
Cdd:cd17996   96 SQ-----IRAGKFNVLLTTYEYiikdkpllsKIKWKYMIIDEGHRMKNAQSKLTQTLNTYYHARYRLL-LTGTPLQNNLP 169


                 ....
gi 488291551 168 DLFA 171
Cdd:cd17996  170 ELWA 173
DEXDc_SHPRH-like cd18008
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ...
 27-194 4.98e-10

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: 59.61  E-value: 4.98e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  27 EMGLGKTVTTLTAIKDLMHDDFSIKKV-----------------LIVAPLRVAqSTWPNEIEKWDHLKDLTYSVVLGTPK 89
Cdd:cd18008   22 EMGLGKTIQALALILATRPQDPKIPEEleenssdpkklylskttLIVVPLSLL-SQWKDEIEKHTKPGSLKVYVYHGSKR 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  90 QRKEALWKKADLYL-----INRENLDWLITKSG----------FDFDFDMVVIDELSSFKNYKAKRFTSLMQVrHKVDRI 154
Cdd:cd18008  101 IKSIEELSDYDIVIttygtLASEFPKNKKGGGRdskekeasplHRIRWYRVILDEAHNIKNRSTKTSRAVCAL-KAERRW 179

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 488291551 155 VgLTGTPSSNGLMDLFAEFKVLdmgeRLEYYISRYRDKYF 194
Cdd:cd18008  180 C-LTGTPIQNSLDDLYSLLRFL----RVEPFGDYPWFNSD 214
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
1-173 1.07e-09

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 60.42  E-value: 1.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   1 MKFIPHEYQQ-----YSIDFIKNNKIAALLLEMGLGKTVTTLTAIKDLMHddfsIKKVLIVAPLRVAQSTWPNEIEKWDH 75
Cdd:COG1061   77 TSFELRPYQQealeaLLAALERGGGRGLVVAPTGTGKTVLALALAAELLR----GKRVLVLVPRRELLEQWAEELRRFLG 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  76 L-------KDLTYSVVLGTPKQrkealwkkadlyLINRENLDWlitksgFDFDFDMVVIDElssFKNYKAKRFTSLMQvR 148
Cdd:COG1061  153 DplagggkKDSDAPITVATYQS------------LARRAHLDE------LGDRFGLVIIDE---AHHAGAPSYRRILE-A 210

                        170       180
                 ....*....|....*....|....*.
gi 488291551 149 HKVDRIVGLTGTP-SSNGLMDLFAEF 173
Cdd:COG1061  211 FPAAYRLGLTATPfRSDGREILLFLF 236
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
 24-179 1.70e-09

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: 57.30  E-value: 1.70e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  24 LLL--EMGLGKTVTTLTAIKDLMHDDfSIKKVLIVAPLRVAQStWpnEIEKWDHLKDLTYSVVlgtpKQRKEALWKKADL 101
Cdd:cd18011   20 LLLadEVGLGKTIEAGLIIKELLLRG-DAKRVLILCPASLVEQ-W--QDELQDKFGLPFLILD----RETAAQLRRLIGN 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 102 ------YLINRenLDWL-----ITKSGFDFDFDMVVIDEL----SSFKNYKAKRFTSLMQVRHKVDRIVGLTGTPSSNGL 166
Cdd:cd18011   92 pfeefpIVIVS--LDLLkrseeRRGLLLSEEWDLVVVDEAhklrNSGGGKETKRYKLGRLLAKRARHVLLLTATPHNGKE 169

                        170
                 ....*....|...
gi 488291551 167 MDLFAEFKVLDMG 179
Cdd:cd18011  170 EDFRALLSLLDPG 182
DEXHc_CHD6_7_8_9 cd17995
DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; ...
 27-170 1.89e-09

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: 57.64  E-value: 1.89e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  27 EMGLGKTVTTLTAIKDLMHDDFSIKKVLIVAPLrvaqST---WPNEIEKWDHLKDLTYSvvlGTPKQRK-----EALWKK 98
Cdd:cd17995   27 EMGLGKTIQSIAFLEHLYQVEGIRGPFLVIAPL----STipnWQREFETWTDMNVVVYH---GSGESRQiiqqyEMYFKD 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  99 ADLYLINRE-NLDWLITK-----SGFDF----DFDMVVIDELSSFKNYKAKRFTSLMQVRHkvDRIVGLTGTPSSNGLMD 168
Cdd:cd17995  100 AQGRKKKGVyKFDVLITTyemviADAEElrkiPWRVVVVDEAHRLKNRNSKLLQGLKKLTL--EHKLLLTGTPLQNNTEE 177


                 ..
gi 488291551 169 LF 170
Cdd:cd17995  178 LW 179
DEXHc_ATRX cd18068
DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha ...
 28-168 7.30e-09

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: 56.43  E-value: 7.30e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  28 MGLGKTVTTLTAIKD-LMHDDFS-IKKVLIVAPLRVAQStWPNEIEKW------DHLKDLTYSVVLGTPKQRKEALWKKA 99
Cdd:cd18068   37 MGLGKTLQVVTFLHTvLLCEKLEnFSRVLVVCPLNTVLN-WLNEFEKWqeglkdEEKIEVNELATYKRPQERSYKLQRWQ 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 100 ----------DLYLI--------NRENLDWLITKSGFDFDFDMVVIDELSSFKNYKAKRFTSLMQVRHKvDRIVgLTGTP 161
Cdd:cd18068  116 eeggvmiigyDMYRIlaqernvkSREKLKEIFNKALVDPGPDFVVCDEGHILKNEASAVSKAMNSIRTK-RRIV-LTGTP 193


                 ....*..
gi 488291551 162 SSNGLMD 168
Cdd:cd18068  194 LQNNLIE 200
DEXHc_RAD54B cd18066
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ...
 22-171 7.53e-09

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: 56.01  E-value: 7.53e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  22 AALLLEMGLGKTVTTLTAIKDLM---HDDFS--IKKVLIVAPLRVAQStWPNEIEKWDHLKDLTYSVVLGTPKQRKEAlw 96
Cdd:cd18066   27 AILADEMGLGKTLQCISLIWTLLrqgPYGGKpvIKRALIVTPGSLVKN-WKKEFQKWLGSERIKVFTVDQDHKVEEFI-- 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488291551  97 kKADLY---LINRENLDWLITKSGfDFDFDMVVIDELSSFKNYKAKRFTSLMQVRhkVDRIVGLTGTPSSNGLMDLFA 171
Cdd:cd18066  104 -ASPLYsvlIISYEMLLRSLDQIS-KLNFDLVICDEGHRLKNTSIKTTTALTSLS--CERRIILTGTPIQNDLQEFFA 177
DEXQc_SRCAP cd18003
DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or ...
 7-171 1.71e-08

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: 54.67  E-value: 1.71e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   7 EYQQYSIDFIKN---NKIAALLL-EMGLGKTVTTLTAIKDLMHDDFSIKKVLIVAPLRVAQStWPNEIEKW-DHLKDLTY 81
Cdd:cd18003    3 EYQHIGLDWLATlyeKNLNGILAdEMGLGKTIQTIALLAHLACEKGNWGPHLIVVPTSVMLN-WEMEFKRWcPGFKILTY 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  82 svvLGTPKQRKEAL--WKKADLY--LINRENldwLITKSGFDF---DFDMVVIDELSSFKNYKAKRFTSLMQVrhKVDRI 154
Cdd:cd18003   82 ---YGSAKERKLKRqgWMKPNSFhvCITSYQ---LVVQDHQVFkrkKWKYLILDEAHNIKNFKSQRWQTLLNF--NTQRR 153

                        170
                 ....*....|....*..
gi 488291551 155 VGLTGTPSSNGLMDLFA 171
Cdd:cd18003  154 LLLTGTPLQNSLMELWS 170
DEXHc_SMARCAD1 cd17998
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ...
 6-169 5.55e-08

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: 52.77  E-value: 5.55e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   6 HEYQQYSIDFIK---NNKIAALLL-EMGLGKTVTTLTAIKDLM-------HddfsikkvLIVAPlrvaQST---WPNEIE 71
Cdd:cd17998    2 KDYQLIGLNWLNllyQKKLSGILAdEMGLGKTIQVIAFLAYLKeigipgpH--------LVVVP----SSTldnWLREFK 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  72 KW-DHLKDLTYsvvLGTPKQRKEAlwkkADLYLINRENLDWLIT-----------KSGFD-FDFDMVVIDELSSFKNYKA 138
Cdd:cd17998   70 RWcPSLKVEPY---YGSQEERKHL----RYDILKGLEDFDVIVTtynlatsnpddRSFFKrLKLNYVVYDEGHMLKNMTS 142

                        170       180       190
                 ....*....|....*....|....*....|.
gi 488291551 139 KRFTSLMQVRHKVdRIVgLTGTPSSNGLMDL 169
Cdd:cd17998  143 ERYRHLMTINANF-RLL-LTGTPLQNNLLEL 171
DEXHc_CHD8 cd18060
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; ...
 7-177 6.93e-08

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; Chromodomain-helicase-DNA-binding protein 8 (CHD8) is a DNA helicase that acts as a chromatin remodeling factor and regulates transcription. It also acts as a transcription repressor by remodeling chromatin structure and recruiting histone H1 to target genes. It suppresses p53/TP53-mediated apoptosis by recruiting histone H1 and preventing p53/TP53 transactivation activity and of STAT3 activity by suppressing the LIF-induced STAT3 transcriptional activity. It also acts as a negative regulator of Wnt signaling pathway and CTNNB1-targeted gene expression. CHD8 is also involved in both enhancer blocking and epigenetic remodeling at chromatin boundary via its interaction with CTCF. It also acts as a transcription activator via its interaction with ZNF143 by participating in efficient U6 RNA polymerase III transcription. CHD8 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350818 [Multi-domain]  Cd Length: 222  Bit Score: 53.13  E-value: 6.93e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   7 EYQQYSIDFI----KNNKIAALLLEMGLGKTVTTLTAIKDLMHDDFSiKKVLIVAPLRVAqSTWPNEIEKWDHLKDLTYS 82
Cdd:cd18060    3 EYQLEGVNWLlfnwYNRQNCILADEMGLGKTIQSIAFLQEVYNVGIH-GPFLVIAPLSTI-TNWEREFNTWTEMNTIVYH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  83 VVLGTPK--QRKEALWKKADLYLI-NRENLDWLITKSGF---------DFDFDMVVIDELSSFKNYKAKRFTSL--MQVR 148
Cdd:cd18060   81 GSLASRQmiQQYEMYCKDSRGRLIpGAYKFDALITTFEMilsdcpelrEIEWRCVIIDEAHRLKNRNCKLLDSLkhMDLE 160

                        170       180
                 ....*....|....*....|....*....
gi 488291551 149 HKVDrivgLTGTPSSNGLMDLFAEFKVLD 177
Cdd:cd18060  161 HKVL----LTGTPLQNTVEELFSLLHFLE 185
DEXHc_SMARCA1_SMARCA5 cd17997
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ...
 19-171 1.20e-07

DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 and 5 (SMARCA1 and SMARCA5) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350755 [Multi-domain]  Cd Length: 222  Bit Score: 52.32  E-value: 1.20e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  19 NKIAALLL-EMGLGKTVTTLTAIKDLMHddfsIKKV----LIVAPLrvaqST---WPNEIEKWdhLKDLTYSVVLGTPKQ 90
Cdd:cd17997   21 NGINGILAdEMGLGKTLQTISLLGYLKH----YKNIngphLIIVPK----STldnWMREFKRW--CPSLRVVVLIGDKEE 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  91 RKEALWKkadlyLINRENLDWLIT--------KSGFD-FDFDMVVIDELSSFKNYKAKRFTSLMQVRHKvDRIVgLTGTP 161
Cdd:cd17997   91 RADIIRD-----VLLPGKFDVCITsyemvikeKTVLKkFNWRYIIIDEAHRIKNEKSKLSQIVRLFNSR-NRLL-LTGTP 163

                        170
                 ....*....|
gi 488291551 162 SSNGLMDLFA 171
Cdd:cd17997  164 LQNNLHELWA 173
DEXHc_CHD3_4_5 cd17994
DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; ...
 6-170 2.70e-07

DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; Chromodomain-helicase-DNA-binding protein 3 (CHD3) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. It is required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity. Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. It is thought to specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3 and plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. As a tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. CHD3, CHD4, and CHD5 are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350752 [Multi-domain]  Cd Length: 196  Bit Score: 50.90  E-value: 2.70e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   6 HEYQQYSIDFIK---NNKIAALLL-EMGLGKTVTTLTAIKDLMHDDFSIKKVLIVAPLrvaqST---WPNEIEKW----- 73
Cdd:cd17994    2 HPYQLEGLNWLRfswAQGTDTILAdEMGLGKTIQTIVFLYSLYKEGHSKGPFLVSAPL----STiinWEREFEMWapdfy 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  74 ------DHLKDLTYSVVlgtpkqrkealwkkadlylinreNLDWLITKSgfdFDFDMVVIDELSSFKNYKAKRFTSLMQv 147
Cdd:cd17994   78 vvtyvgDHVLLTSYELI-----------------------SIDQAILGS---IDWAVLVVDEAHRLKNNQSKFFRILNS- 130

                        170       180
                 ....*....|....*....|...
gi 488291551 148 rHKVDRIVGLTGTPSSNGLMDLF 170
Cdd:cd17994  131 -YKIGYKLLLTGTPLQNNLEELF 152
DEXHc_ARIP4 cd18069
DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called ...
 28-170 3.82e-07

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: 50.97  E-value: 3.82e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  28 MGLGKTVTTLTAIKDLMHDDfSIKKVLIVAPLRVAQStWPNEIEKWdhlkdltysvvLGTPKQRKEALWKKADLYLINRE 107
Cdd:cd18069   37 MGLGKTLQVISFLDVLLRHT-GAKTVLAIVPVNTLQN-WLSEFNKW-----------LPPPEALPNVRPRPFKVFILNDE 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 108 N----------LDWLITKSGFDFDFDM---------VVIDELSSFKNYKAKRFTSLMQVRHKvdRIVGLTGTPSSNGLMD 168
Cdd:cd18069  104 HkttaarakviEDWVKDGGVLLMGYEMfrlrpgpdvVICDEGHRIKNCHASTSQALKNIRSR--RRIVLTGYPLQNNLIE 181


                 ..
gi 488291551 169 LF 170
Cdd:cd18069  182 YW 183
DEXHc_HLTF1_SMARC3 cd18071
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ...
 27-176 4.88e-07

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: 50.55  E-value: 4.88e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  27 EMGLGKTVTTLTAIkdlmhddfSIKKVLIVAPLRVAqSTWPNEIEkwDHLKD--LTYSVVLGTPKQRKEALWKKADLYLI 104
Cdd:cd18071   56 DMGLGKTLTTISLI--------LANFTLIVCPLSVL-SNWETQFE--EHVKPgqLKVYTYHGGERNRDPKLLSKYDIVLT 124

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 105 NRE---------------NLDWLitksgfdfdfdMVVIDELSSFKNYKAKRFTSLMQVrhKVDRIVGLTGTPSSNGLMDL 169
Cdd:cd18071  125 TYNtlasdfgakgdsplhTINWL-----------RVVLDEGHQIRNPNAQQTKAVLNL--SSERRWVLTGTPIQNSPKDL 191


                 ....*..
gi 488291551 170 FAEFKVL 176
Cdd:cd18071  192 GSLLSFL 198
DEXHc_SMARCA2 cd18063
DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent ...
 10-176 6.82e-07

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: 50.45  E-value: 6.82e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  10 QYSIDFIKNNKIAALLLEMGLGKTVTTLTAIKDLMHDDFSIKKVLIVAPLRVAqSTWPNEIEKW-DHLKDLTYSvvlGTP 88
Cdd:cd18063   33 EWMVSLYNNNLNGILADEMGLGKTIQTIALITYLMEHKRLNGPYLIIVPLSTL-SNWTYEFDKWaPSVVKISYK---GTP 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  89 KQRKEALWK-KADLYLINRENLDWLITKSGF--DFDFDMVVIDELSSFKNYKAKrFTSLMQVRHKVDRIVGLTGTPSSNG 165
Cdd:cd18063  109 AMRRSLVPQlRSGKFNVLLTTYEYIIKDKHIlaKIRWKYMIVDEGHRMKNHHCK-LTQVLNTHYVAPRRILLTGTPLQNK 187

                        170
                 ....*....|.
gi 488291551 166 LMDLFAEFKVL 176
Cdd:cd18063  188 LPELWALLNFL 198
DEXHc_CHD2 cd18054
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; ...
 17-185 1.58e-06

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: 49.23  E-value: 1.58e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  17 KNNKIAaLLLEMGLGKTVTTLTAIKDLMHDDFSIKKVLIVAPLRVAQStWPNEIEKWDhlKDLTYSVVLGTPKQRK---E 93
Cdd:cd18054   38 KNNSVI-LADEMGLGKTIQTISFLSYLFHQHQLYGPFLLVVPLSTLTS-WQREFEIWA--PEINVVVYIGDLMSRNtirE 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  94 ALWKKADlylINRENLDWLITKSGF---------DFDFDMVVIDELSSFKNYKAKRFTSLMQVRHKvDRIVgLTGTPSSN 164
Cdd:cd18054  114 YEWIHSQ---TKRLKFNALITTYEIllkdktvlgSINWAFLGVDEAHRLKNDDSLLYKTLIDFKSN-HRLL-ITGTPLQN 188

                        170       180
                 ....*....|....*....|.
gi 488291551 165 GLMDLFAEFKVLdMGERLEYY 185
Cdd:cd18054  189 SLKELWSLLHFI-MPEKFEFW 208
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 301-415 2.41e-06

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: 46.70  E-value: 2.41e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 301 HIHDQKLDALEDLIEG---ANGKSILIAYWFQHdLERIKERFKVRQIKTA------------KDIEEWNKG-NIPIGVIH 364
Cdd:cd18793    7 EVVSGKLEALLELLEElrePGEKVLIFSQFTDT-LDILEEALRERGIKYLrldgstsskerqKLVDRFNEDpDIRVFLLS 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 488291551 365 PASAGHGLNLQAGgSTLVWFGLTWSLELYQQTNARLWRQGQNETVVIHHII 415
Cdd:cd18793   86 TKAGGVGLNLTAA-NRVILYDPWWNPAVEEQAIDRAHRIGQKKPVVVYRLI 135
ResIII pfam04851
Type III restriction enzyme, res subunit;
2-161 5.71e-06

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 46.13  E-value: 5.71e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551    2 KFIPHEYQQYSID----FIKNNKIAALL-LEMGLGKTVTTLTAIKDLMHDdFSIKKVLIVAPLR--VAQstWPNEIEKWD 74
Cdd:pfam04851   1 KLELRPYQIEAIEnlleSIKNGQKRGLIvMATGSGKTLTAAKLIARLFKK-GPIKKVLFLVPRKdlLEQ--ALEEFKKFL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   75 HLKDLTYSVVLGtpkQRKEALWKKADLYLINRENLDWLITKSGFDFD---FDMVVIDEL--SSFKNYK--AKRFTSLMQV 147
Cdd:pfam04851  78 PNYVEIGEIISG---DKKDESVDDNKIVVTTIQSLYKALELASLELLpdfFDVIIIDEAhrSGASSYRniLEYFKPAFLL 154

                         170
                  ....*....|....
gi 488291551  148 rhkvdrivGLTGTP 161
Cdd:pfam04851 155 --------GLTATP 160
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 5-161 6.39e-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: 45.76  E-value: 6.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   5 PHEYQQYSID-FIKNNKIAALLLEM--GLGKTVTTLTAIKDLmhddfSIKKVLIVAPlRVAQstwpneIEKW-DHLKDLT 80
Cdd:cd17926    1 LRPYQEEALEaWLAHKNNRRGILVLptGSGKTLTALALIAYL-----KELRTLIVVP-TDAL------LDQWkERFEDFL 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  81 YSVVLGTPKQRKEALWKKADLYLINRENLDWLITKSGFDFD-FDMVVIDELssfKNYKAKRFTSlMQVRHKVDRIVGLTG 159
Cdd:cd17926   69 GDSSIGLIGGGKKKDFDDANVVVATYQSLSNLAEEEKDLFDqFGLLIVDEA---HHLPAKTFSE-ILKELNAKYRLGLTA 144


                 ..
gi 488291551 160 TP 161
Cdd:cd17926  145 TP 146
DEXHc_CHD1L cd18006
DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, ...
 24-191 9.69e-06

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: 46.66  E-value: 9.69e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  24 LLLEMGLGKTVTTLTAIKDLMHDDFSIKKVLIVAPLRVAqSTWPNEIEKWDhlKDLTYSVVLGTpkqrKEalwKKADLYL 103
Cdd:cd18006   24 LGDEMGLGKTCQTISLLWYLAGRLKLLGPFLVLCPLSVL-DNWKEELNRFA--PDLSVITYMGD----KE---KRLDLQQ 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 104 INRENLDWLITKSGFD-----------FDFDMVVIDELSSFKNYKAKRFTSLMQVrhKVDRIVGLTGTPSSNGLMDLFAE 172
Cdd:cd18006   94 DIKSTNRFHVLLTTYEiclkdasflksFPWASLVVDEAHRLKNQNSLLHKTLSEF--SVDFRLLLTGTPIQNSLQELYAL 171

                        170       180
                 ....*....|....*....|...
gi 488291551 173 FKVLD----MGERLEYYISRYRD 191
Cdd:cd18006  172 LSFIEpnvfPKDKLDDFIKAYSE 194
DEXHc_ERCC6 cd18000
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ...
 27-173 1.05e-05

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: 46.16  E-value: 1.05e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  27 EMGLGKTVTTLTAIKDLMHDDFSIKKVLIVAPLRVAqSTWPNEIEKWdhlKDLTYSVVL----GTPKQRKEALWKKADLY 102
Cdd:cd18000   27 EMGLGKTIQIIAFLAALHHSKLGLGPSLIVCPATVL-KQWVKEFHRW---WPPFRVVVLhssgSGTGSEEKLGSIERKSQ 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551 103 LINRENLDWLI---TKSGF----DF----DFDMVVIDELSSFKNYKAKRFTSLMQVRhKVDRIVgLTGTPSSNGLMDLFA 171
Cdd:cd18000  103 LIRKVVGDGGIlitTYEGFrkhkDLllnhNWQYVILDEGHKIRNPDAEITLACKQLR-TPHRLI-LSGTPIQNNLKELWS 180


                 ..
gi 488291551 172 EF 173
Cdd:cd18000  181 LF 182
DEXHc_CHD9 cd18061
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; ...
 7-177 1.08e-05

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: 46.54  E-value: 1.08e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   7 EYQQYSIDFI----KNNKIAALLLEMGLGKTVTTLTAIKDLMHDDFSiKKVLIVAPLRVAqSTWPNEIEKWDHLKDLTY- 81
Cdd:cd18061    3 EYQLEGLNWLlfnwYNRRNCILADEMGLGKTIQSITFLYEILLTGIR-GPFLIIAPLSTI-ANWEREFRTWTDLNVVVYh 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  82 -SVVLGTPKQRKEALWKKADLYLInRENLDWLITKSGFDF-----------DFDMVVIDELSSFKNYKAKRFT--SLMQV 147
Cdd:cd18061   81 gSLISRQMIQQYEMYFRDSQGRII-RGAYRFQAIITTFEMilggcpelnaiDWRCVIIDEAHRLKNKNCKLLEglKLMNL 159

                        170       180       190
                 ....*....|....*....|....*....|
gi 488291551 148 RHKVDrivgLTGTPSSNGLMDLFAEFKVLD 177
Cdd:cd18061  160 EHKVL----LTGTPLQNTVEELFSLLHFLE 185
DEXHc_SMARCA4 cd18062
DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent ...
 10-176 1.43e-05

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: 46.19  E-value: 1.43e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  10 QYSIDFIKNNKIAALLLEMGLGKTVTTLTAIKDLMHDDFSIKKVLIVAPLRVAqSTWPNEIEKW-DHLKDLTYSvvlGTP 88
Cdd:cd18062   33 EWLVSLYNNNLNGILADEMGLGKTIQTIALITYLMEHKRINGPFLIIVPLSTL-SNWVYEFDKWaPSVVKVSYK---GSP 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  89 KQRKEALWK-KADLYLINRENLDWLITKSGF--DFDFDMVVIDELSSFKNYKAKrFTSLMQVRHKVDRIVGLTGTPSSNG 165
Cdd:cd18062  109 AARRAFVPQlRSGKFNVLLTTYEYIIKDKQIlaKIRWKYMIVDEGHRMKNHHCK-LTQVLNTHYVAPRRLLLTGTPLQNK 187

                        170
                 ....*....|.
gi 488291551 166 LMDLFAEFKVL 176
Cdd:cd18062  188 LPELWALLNFL 198
DEXQc_INO80 cd18002
DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 ...
 7-171 2.71e-05

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: 45.19  E-value: 2.71e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   7 EYQQYSIDFIKN------NKIAALllEMGLGKTVTTLTAIKDLMHDDFSIKKVLIVAPLRVAQStWPNEIEKW-DHLKDL 79
Cdd:cd18002    3 EYQLKGLNWLANlyeqgiNGILAD--EMGLGKTVQSIAVLAHLAEEHNIWGPFLVIAPASTLHN-WQQEISRFvPQFKVL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  80 TYsvvLGTPKQRK--EALWKKADLY--------LINRENLDWLITKSGFDFDFDMVVIDELSSFKNYKAKRFTSLMQVrH 149
Cdd:cd18002   80 PY---WGNPKDRKvlRKFWDRKNLYtrdapfhvVITSYQLVVQDEKYFQRVKWQYMVLDEAQAIKSSSSSRWKTLLSF-H 155

                        170       180
                 ....*....|....*....|..
gi 488291551 150 KVDRIVgLTGTPSSNGLMDLFA 171
Cdd:cd18002  156 CRNRLL-LTGTPIQNSMAELWA 176
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 7-164 2.76e-05

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


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 44.16  E-value: 2.76e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551    7 EYQQYSIDFIKNNKIAALLLEMGLGKTVTTLTAIKDLMHDDFSIKKVLIVAPLR--VAQSTwpNEIEKW-DHLKDLTYSV 83
Cdd:pfam00270   2 PIQAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALEALDKLDNGPQALVLAPTRelAEQIY--EELKKLgKGLGLKVASL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   84 VLGTPKQRKEALWKKADLYLINRENLDWLITKSGFDFDFDMVVIDE--LSSFKNYKAKRFTSLMQVRHKVdRIVGLTGTP 161
Cdd:pfam00270  80 LGGDSRKEQLEKLKGPDILVGTPGRLLDLLQERKLLKNLKLLVLDEahRLLDMGFGPDLEEILRRLPKKR-QILLLSATL 158


                  ...
gi 488291551  162 SSN 164
Cdd:pfam00270 159 PRN 161
DEXHc_CHD7 cd18059
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; ...
 7-179 2.86e-05

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: 45.02  E-value: 2.86e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   7 EYQQYSIDFI----KNNKIAALLLEMGLGKTVTTLTAIKDL----MHDDFsikkvLIVAPLRVAQStWPNEIEKWDHLKD 78
Cdd:cd18059    3 EYQLEGVNWLlfnwYNTRNCILADEMGLGKTIQSITFLYEIylkgIHGPF-----LVIAPLSTIPN-WEREFRTWTELNV 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  79 LTYSvvlGTPKQRkealwKKADLYLINRENLDWLITKSGFDF-----DFDM---------------VVIDELSSFKNYKA 138
Cdd:cd18059   77 VVYH---GSQASR-----RTIQLYEMYFKDPQGRVIKGSYKFhaiitTFEMiltdcpelrnipwrcVVIDEAHRLKNRNC 148

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 488291551 139 KRFTSL--MQVRHKVDrivgLTGTPSSNGLMDLFAEFKVLDMG 179
Cdd:cd18059  149 KLLEGLkmMDLEHKVL----LTGTPLQNTVEELFSLLHFLEPS 187
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 5-173 4.64e-05

DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350790 [Multi-domain]  Cd Length: 163  Bit Score: 43.70  E-value: 4.64e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551   5 PHEYQQYSID-----FIKNNKIAALLLEMGLGKTVTTLTAIKDLMhDDFSIKKVLIVAPlRVA---QStwpnEIEKWDHL 76
Cdd:cd18032    1 PRYYQQEAIEaleeaREKGQRRALLVMATGTGKTYTAAFLIKRLL-EANRKKRILFLAH-REElleQA----ERSFKEVL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  77 KDLTYSVVLGTPKQRKEAlwkkaDLY------LINRENLDWlitksgFDFD-FDMVVIDEL--SSFKNYKA--KRFTSlm 145
Cdd:cd18032   75 PDGSFGNLKGGKKKPDDA-----RVVfatvqtLNKRKRLEK------FPPDyFDLIIIDEAhhAIASSYRKilEYFEP-- 141

                        170       180
                 ....*....|....*....|....*...
gi 488291551 146 qvrhkvDRIVGLTGTPSSNGLMDLFAEF 173
Cdd:cd18032  142 ------AFLLGLTATPERTDGLDTYELF 163
DEXHc_CHD1_2 cd17993
DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and ...
 18-171 6.03e-05

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: 44.27  E-value: 6.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  18 NNKIAALllEMGLGKTVTTLTAIKDLMHDDFSIKKVLIVAPLrvaqST---WPNEIEKWdhLKDLTYSVVLGTPKQRKea 94
Cdd:cd17993   21 NNGILAD--EMGLGKTVQTISFLSYLFHSQQQYGPFLVVVPL----STmpaWQREFAKW--APDMNVIVYLGDIKSRD-- 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  95 LWKKADLYLINRENLDW--LITK-----------SGFDFDFDMVviDELSSFKNYKAKRFTSLMQVRHKvDRIVgLTGTP 161
Cdd:cd17993   91 TIREYEFYFSQTKKLKFnvLLTTyeiilkdkaflGSIKWQYLAV--DEAHRLKNDESLLYEALKEFKTN-NRLL-ITGTP 166

                        170
                 ....*....|
gi 488291551 162 SSNGLMDLFA 171
Cdd:cd17993  167 LQNSLKELWA 176
DEXHc_HELLS_SMARCA6 cd18009
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ...
 27-171 1.14e-04

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: 43.53  E-value: 1.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  27 EMGLGKTVTTLTAIKdLMHDDFSIKKVLIVAPLRVAqSTWPNEIEKWDHlkdlTYSVVL--GTPKQRKEaLWKKADLYLI 104
Cdd:cd18009   30 EMGLGKTIQTIALLA-HLRERGVWGPFLVIAPLSTL-PNWVNEFARFTP----SVPVLLyhGTKEERER-LRKKIMKREG 102

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488291551 105 NRENLDWLITK---SGFDFDFDM------VVIDELSSFKNYKAKRFTSLMQVRHkvDRIVGLTGTPSSNGLMDLFA 171
Cdd:cd18009  103 TLQDFPVVVTSyeiAMRDRKALQhyawkyLIVDEGHRLKNLNCRLIQELKTFNS--DNRLLLTGTPLQNNLSELWS 176
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 24-160 1.25e-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: 42.01  E-value: 1.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  24 LLLEMGLGKTVTTLTAIKDLMhdDFSIKKVLIVAPLR-VAQSTWPNEIEKWDHLKDLTYSVVLGTPKQRKEALWKKADL- 101
Cdd:cd00046    6 ITAPTGSGKTLAALLAALLLL--LKKGKKVLVLVPTKaLALQTAERLRELFGPGIRVAVLVGGSSAEEREKNKLGDADIi 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488291551 102 -----YLINRENLDWLITKSgfdfDFDMVVIDELSSFKNYKAKRFTSLMQVRHKVD---RIVGLTGT 160
Cdd:cd00046   84 iatpdMLLNLLLREDRLFLK----DLKLIIVDEAHALLIDSRGALILDLAVRKAGLknaQVILLSAT 146
DEXHc_SMARCA5 cd18064
DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent ...
 13-176 2.05e-03

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: 39.65  E-value: 2.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  13 IDFIKNNKIAALLLEMGLGKTVTTLTAIKDLMHDDFSIKKVLIVAPlRVAQSTWPNEIEKWdhLKDLTYSVVLGTPKQRK 92
Cdd:cd18064   28 ISLYENGINGILADEMGLGKTLQTISLLGYMKHYRNIPGPHMVLVP-KSTLHNWMAEFKRW--VPTLRAVCLIGDKDQRA 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  93 E-----ALWKKADLYLINRENLdwLITKSGF-DFDFDMVVIDELSSFKNYKAKrFTSLMQVRHKVDRIVgLTGTPSSNGL 166
Cdd:cd18064  105 AfvrdvLLPGEWDVCVTSYEML--IKEKSVFkKFNWRYLVIDEAHRIKNEKSK-LSEIVREFKTTNRLL-LTGTPLQNNL 180

                        170
                 ....*....|
gi 488291551 167 MDLFAEFKVL 176
Cdd:cd18064  181 HELWALLNFL 190
DEXHc_SMARCA1 cd18065
DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent ...
 11-176 5.69e-03

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: 38.46  E-value: 5.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  11 YSIDFIKNNKIAALLLEMGLGKTVTTLTAIKDLMHDDFSIKKVLIVAPlRVAQSTWPNEIEKWdhLKDLTYSVVLGTPKQ 90
Cdd:cd18065   26 WMISLYENGVNGILADEMGLGKTLQTIALLGYLKHYRNIPGPHMVLVP-KSTLHNWMNEFKRW--VPSLRAVCLIGDKDA 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  91 -----RKEALWKKADLYLINRENLdwLITKSGF-DFDFDMVVIDELSSFKNYKAKrFTSLMQVRHKVDRIVgLTGTPSSN 164
Cdd:cd18065  103 raafiRDVMMPGEWDVCVTSYEMV--IKEKSVFkKFNWRYLVIDEAHRIKNEKSK-LSEIVREFKTTNRLL-LTGTPLQN 178

                        170
                 ....*....|..
gi 488291551 165 GLMDLFAEFKVL 176
Cdd:cd18065  179 NLHELWALLNFL 190
DEXHc_CHD1 cd18053
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; ...
 27-171 6.57e-03

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: 38.11  E-value: 6.57e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488291551  27 EMGLGKTVTTLTAIKDLMHDDFSIKKVLIVAPLRVAQStWPNEIEKWD-------HLKDLTYSVVLGT-----PKQRKea 94
Cdd:cd18053   47 EMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTS-WQREIQTWApqmnavvYLGDINSRNMIRThewmhPQTKR-- 123

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488291551  95 lwKKADLYLINRENLdwLITKSGF-DFDFDMVVIDELSSFKNYKAKRFTSLMQVrhKVDRIVGLTGTPSSNGLMDLFA 171
Cdd:cd18053  124 --LKFNILLTTYEIL--LKDKSFLgGLNWAFIGVDEAHRLKNDDSLLYKTLIDF--KSNHRLLITGTPLQNSLKELWS 195
 
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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