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Conserved domains on  [gi|1447699881|ref|NP_313288|]
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ATP-dependent helicase [Escherichia coli O157:H7 str. Sakai]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 13029331)

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
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
 108-311 2.02e-69

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: 229.48  E-value: 2.02e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 108 MPFQLDPTRMALAQPRQRILIADAVGLGKTLEAGILVSELIRRGRGKRILVLAVKSMLTQFQKEFWSRFAIPLTRLDSAG 187
Cdd:cd18011     2 LPHQIDAVLRALRKPPVRLLLADEVGLGKTIEAGLIIKELLLRGDAKRVLILCPASLVEQWQDELQDKFGLPFLILDRET 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 188 LQKVRNRIptnHNPFHYFDKTIISIDTLKQDIEYRHHLENAWWDIIVIDEAHNVAERG--TSSLRSKLAKLLAGRSDTLI 265
Cdd:cd18011    82 AAQLRRLI---GNPFEEFPIVIVSLDLLKRSEERRGLLLSEEWDLVVVDEAHKLRNSGggKETKRYKLGRLLAKRARHVL 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1447699881 266 MLSATPHDGKAESFASLMNMLDPTAIANPKEY---EYADFADKNLVVRR 311
Cdd:cd18011   159 LLTATPHNGKEEDFRALLSLLDPGRFAVLGRFlrlDGLREVLAKVLLRR 207
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 109-589 3.98e-59

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


:

Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 215.47  E-value: 3.98e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 109 PFQLDPTRMA--LAQPRQRILIADAVGLGKTLEAGILVSELIRRGRGKRILVLAVKSMLTQFQKEFwSRFA--IPLTRLD 184
Cdd:COG0553   244 PYQLEGAAWLlfLRRLGLGGLLADDMGLGKTIQALALLLELKERGLARPVLIVAPTSLVGNWQREL-AKFApgLRVLVLD 322

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 185 SAglqKVRNRIPtnhNPFHYFDKTIISIDTLKQDIEyrhHLENAWWDIIVIDEAHNVAERGTssLRSKLAKLLAGRSdtL 264
Cdd:COG0553   323 GT---RERAKGA---NPFEDADLVITSYGLLRRDIE---LLAAVDWDLVILDEAQHIKNPAT--KRAKAVRALKARH--R 389

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 265 IMLSATPHDGKAESFASLMNMLDP----------TAIANPKEYEYADFAD------KNLVVRRFKKDVKDqmsgEFPERN 328
Cdd:COG0553   390 LALTGTPVENRLEELWSLLDFLNPgllgslkafrERFARPIEKGDEEALErlrrllRPFLLRRTKEDVLK----DLPEKT 465

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 329 IVKLTRLASGAEEEAYRRLVESQFRDDDDEQAQSNKGRLFKITLekalfsspmacasvvanRLKRLESrkdhnsqsqine 408
Cdd:COG0553   466 EETLYVELTPEQRALYEAVLEYLRRELEGAEGIRRRGLILAALT-----------------RLRQICS------------ 516

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 409 leSLLLALNNIDASQF--SKYQLLLDTIRKDLAWKannteDRLVIFTESIKTLEFLEQQLRAdlklKDDQIATLRGDQGD 486
Cdd:COG0553   517 --HPALLLEEGAELSGrsAKLEALLELLEELLAEG-----EKVLVFSQFTDTLDLLEERLEE----RGIEYAYLHGGTSA 585

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 487 TVLMETVEAFGKTQSPLRLLVCSDVASEGINLHHLSHkMIHFDIPWSLMVFQQRNGRIDRYGQKHQPQIRYLLTEASepq 566
Cdd:COG0553   586 EERDELVDRFQEGPEAPVFLISLKAGGEGLNLTAADH-VIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGT--- 661

                         490       500
                  ....*....|....*....|...
gi 1447699881 567 IngDMRVLEVLINKDEQAQKNIG 589
Cdd:COG0553   662 I--EEKILELLEEKRALAESVLG 682
 
Name Accession Description Interval E-value
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
 108-311 2.02e-69

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: 229.48  E-value: 2.02e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 108 MPFQLDPTRMALAQPRQRILIADAVGLGKTLEAGILVSELIRRGRGKRILVLAVKSMLTQFQKEFWSRFAIPLTRLDSAG 187
Cdd:cd18011     2 LPHQIDAVLRALRKPPVRLLLADEVGLGKTIEAGLIIKELLLRGDAKRVLILCPASLVEQWQDELQDKFGLPFLILDRET 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 188 LQKVRNRIptnHNPFHYFDKTIISIDTLKQDIEYRHHLENAWWDIIVIDEAHNVAERG--TSSLRSKLAKLLAGRSDTLI 265
Cdd:cd18011    82 AAQLRRLI---GNPFEEFPIVIVSLDLLKRSEERRGLLLSEEWDLVVVDEAHKLRNSGggKETKRYKLGRLLAKRARHVL 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1447699881 266 MLSATPHDGKAESFASLMNMLDPTAIANPKEY---EYADFADKNLVVRR 311
Cdd:cd18011   159 LLTATPHNGKEEDFRALLSLLDPGRFAVLGRFlrlDGLREVLAKVLLRR 207
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 109-589 3.98e-59

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 215.47  E-value: 3.98e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 109 PFQLDPTRMA--LAQPRQRILIADAVGLGKTLEAGILVSELIRRGRGKRILVLAVKSMLTQFQKEFwSRFA--IPLTRLD 184
Cdd:COG0553   244 PYQLEGAAWLlfLRRLGLGGLLADDMGLGKTIQALALLLELKERGLARPVLIVAPTSLVGNWQREL-AKFApgLRVLVLD 322

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 185 SAglqKVRNRIPtnhNPFHYFDKTIISIDTLKQDIEyrhHLENAWWDIIVIDEAHNVAERGTssLRSKLAKLLAGRSdtL 264
Cdd:COG0553   323 GT---RERAKGA---NPFEDADLVITSYGLLRRDIE---LLAAVDWDLVILDEAQHIKNPAT--KRAKAVRALKARH--R 389

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 265 IMLSATPHDGKAESFASLMNMLDP----------TAIANPKEYEYADFAD------KNLVVRRFKKDVKDqmsgEFPERN 328
Cdd:COG0553   390 LALTGTPVENRLEELWSLLDFLNPgllgslkafrERFARPIEKGDEEALErlrrllRPFLLRRTKEDVLK----DLPEKT 465

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 329 IVKLTRLASGAEEEAYRRLVESQFRDDDDEQAQSNKGRLFKITLekalfsspmacasvvanRLKRLESrkdhnsqsqine 408
Cdd:COG0553   466 EETLYVELTPEQRALYEAVLEYLRRELEGAEGIRRRGLILAALT-----------------RLRQICS------------ 516

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 409 leSLLLALNNIDASQF--SKYQLLLDTIRKDLAWKannteDRLVIFTESIKTLEFLEQQLRAdlklKDDQIATLRGDQGD 486
Cdd:COG0553   517 --HPALLLEEGAELSGrsAKLEALLELLEELLAEG-----EKVLVFSQFTDTLDLLEERLEE----RGIEYAYLHGGTSA 585

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 487 TVLMETVEAFGKTQSPLRLLVCSDVASEGINLHHLSHkMIHFDIPWSLMVFQQRNGRIDRYGQKHQPQIRYLLTEASepq 566
Cdd:COG0553   586 EERDELVDRFQEGPEAPVFLISLKAGGEGLNLTAADH-VIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGT--- 661

                         490       500
                  ....*....|....*....|...
gi 1447699881 567 IngDMRVLEVLINKDEQAQKNIG 589
Cdd:COG0553   662 I--EEKILELLEEKRALAESVLG 682
DpdE NF041062
protein DpdE;
109-554 4.34e-30

protein DpdE;


Pssm-ID: 468989 [Multi-domain]  Cd Length: 1048  Bit Score: 128.55  E-value: 4.34e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  109 PFQLDPTRMALAQPRQRILIADAVGLGKTLEAGILVSELIRRGRGKRILVLAVKSMLTQFQKEFWSRFaipltRLDSAGL 188
Cdd:NF041062   156 PHQVAVVRRVLQDPVQRYLLADEVGLGKTIEAGLVIRQHLLDNPDARVLVLVPDALVRQWRRELRDKF-----FLDDFPG 230

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  189 QKVRnriptnhnpfhyfdktIISIDTLkqdIEYRHHLENAwwDIIVIDEAHNVAERGTSS---LRSKLAKL--LAGRSDT 263
Cdd:NF041062   231 ARVR----------------VLSHEEP---ERWEPLLDAP--DLLVVDEAHQLARLAWSGdppERARYRELaaLAHAAPR 289

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  264 LIMLSATPHDGKAESFASLMNMLDP--------------------------------------TAIAN-----PKEYE-- 298
Cdd:NF041062   290 LLLLSATPVLGNEETFLALLHLLDPdlyplddleafrerleereelgrlvlgldpdnpnfllrQALDElralfPEDEElq 369

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  299 ---------YADFADKNLVVR----------------------RFKKDVKDQMSGEFPERNIVKLTRLASGAEE------ 341
Cdd:NF041062   370 elaeellplLDEFDDEEPEERaravsalrahisetyrlhrrmiRNRRSSVLGADYLVPGRAGPRVLVWESPAREaadeal 449

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  342 EAYRRLVeSQFRDDDDEQAQSNKGRLFKITLekALFSSPMACASvvanrlkRLESRKDHNSQSQINELE-SLLLALNNId 420
Cdd:NF041062   450 EDWREEA-ALLDAESDPAARAAYARALAWLV--ARLGGPDDLAA-------LLRWRLRGDAASADLAGErELLEALIAA- 518

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  421 ASQFSKYQLLLDTIRKDLaWKANNTEDRLVIFTESIKTLEFLEQQLRADLKlkdDQIATLRGDQGDTVLMETVEAFgKTQ 500
Cdd:NF041062   519 LEDEAKDADLLAALADWL-LPLLRGSGKAVVFCGDGSLADHLAAALARLGA---GSVERHLSGQGADQAERAVRAF-RQD 593

                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1447699881  501 SPLRLLVCSDVASEGINLHhLSHKMIHFDIPWSLMVFQQRNGRIDRYGQKHQPQ 554
Cdd:NF041062   594 PSARVLVCDRSGEEGLNLQ-GADRLVHLDLPWSPNRLEQRIGRLDRYASLRGGR 646
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 425-559 6.17e-26

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: 104.10  E-value: 6.17e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 425 SKYQLLLDTIRKdlaWKANNteDRLVIFTESIKTLEFLEQQLRAdlklKDDQIATLRGDQGDTVLMETVEAFGKTQSPLR 504
Cdd:cd18793    11 GKLEALLELLEE---LREPG--EKVLIFSQFTDTLDILEEALRE----RGIKYLRLDGSTSSKERQKLVDRFNEDPDIRV 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1447699881 505 LLVCSDVASEGINLHHLSHkMIHFDIPWSLMVFQQRNGRIDRYGQKHQPQIRYLL 559
Cdd:cd18793    82 FLLSTKAGGVGLNLTAANR-VILYDPWWNPAVEEQAIDRAHRIGQKKPVVVYRLI 135
DEXDc smart00487
DEAD-like helicases superfamily;
123-286 8.80e-18

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 82.54  E-value: 8.80e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  123 RQRILIADAVGLGKTLEAGILVSELIRRGRGKRILVLA-----VKSMLTQFQKEFWSRFAIPLTRLDSAGLQKVRNRIPT 197
Cdd:smart00487  24 LRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVptrelAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLES 103

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  198 NHNPFhyfdkTIISIDTLKQDIEyRHHLENAWWDIIVIDEAHNVAERGTSSLRSKLAKLLAgRSDTLIMLSATPHDGKAE 277
Cdd:smart00487 104 GKTDI-----LVTTPGRLLDLLE-NDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLP-KNVQLLLLSATPPEEIEN 176


                   ....*....
gi 1447699881  278 SFASLMNML 286
Cdd:smart00487 177 LLELFLNDP 185
PRK04914 PRK04914
RNA polymerase-associated protein RapA;
125-555 6.59e-16

RNA polymerase-associated protein RapA;


Pssm-ID: 235319 [Multi-domain]  Cd Length: 956  Bit Score: 82.58  E-value: 6.59e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 125 RILIADAVGLGKTLEAGILVSELIRRGRGKRILVLAVKSMLTQFQKEFWSRFAIPLTRLDSAGLQKVRNripTNHNPFHY 204
Cdd:PRK04914  171 RVLLADEVGLGKTIEAGMIIHQQLLTGRAERVLILVPETLQHQWLVEMLRRFNLRFSLFDEERYAEAQH---DADNPFET 247

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 205 FDKTIISIDTLKQDIEYRHHLENAWWDIIVIDEAHNVA-ERGTSSLRSKLAKLLAGRSDTLIMLSATPHDGKAES-FASL 282
Cdd:PRK04914  248 EQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVwSEEAPSREYQVVEQLAEVIPGVLLLTATPEQLGQEShFARL 327

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 283 mNMLDPTaianpKEYEYADFADKNLVVRRFKKDVKDQMSGE-FPERNIVKLTRLASGAEEEAYRRLVESqfrDDDDEQAQ 361
Cdd:PRK04914  328 -RLLDPD-----RFHDYEAFVEEQQQYRPVADAVQALLAGEkLSDDALNALGELLGEQDIEPLLQAANS---DSEEAQAA 398

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 362 SNK-----------GR-LFKITL-------EKALFSSPMACASVVANRLKRLESRKDHNSQSQinelESLLLALNNiDAS 422
Cdd:PRK04914  399 RQEliselldrhgtGRvLFRNTRaavkgfpKRELHPIPLPLPEQYQTAIKVSLEARARDMLYP----EQIYQEFED-NAT 473

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 423 --QF-SKYQLLLDTIrkdlawKANNTEDRLVIfTESIKTLEFLEQQLRadlklkddqiaTLRGDQGdTVL---METVE-- 494
Cdd:PRK04914  474 wwNFdPRVEWLIDFL------KSHRSEKVLVI-CAKAATALQLEQALR-----------EREGIRA-AVFhegMSIIErd 534

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1447699881 495 ----AFGKTQSPLRLLVCSDVASEGINL---HHLshkmIHFDIPWSLMVFQQRNGRIDRYGQKHQPQI 555
Cdd:PRK04914  535 raaaYFADEEDGAQVLLCSEIGSEGRNFqfaSHL----VLFDLPFNPDLLEQRIGRLDRIGQKHDIQI 598
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 425-548 3.15e-13

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


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 66.85  E-value: 3.15e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 425 SKYQLLLDTIRKdlawkanNTEDRLVIFTESIKTLEflEQQLRADLKLKddqIATLRGDQGDTVLMETVEAFGKtqSPLR 504
Cdd:pfam00271   1 EKLEALLELLKK-------ERGGKVLIFSQTKKTLE--AELLLEKEGIK---VARLHGDLSQEEREEILEDFRK--GKID 66

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1447699881 505 LLVCSDVASEGINLHHLSHkMIHFDIPWSLMVFQQRNGRIDRYG 548
Cdd:pfam00271  67 VLVATDVAERGLDLPDVDL-VINYDLPWNPASYIQRIGRAGRAG 109
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 127-356 2.04e-12

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: 68.86  E-value: 2.04e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 127 LIADAVGLGKTLEAGILVSEL--IRRGRGKRILVLAVKSMLTQFQKEFwSRFAIP--LTRLDSAGLQKVRNRIPTNHNPF 202
Cdd:pfam00176  21 ILADEMGLGKTLQTISLLLYLkhVDKNWGGPTLIVVPLSLLHNWMNEF-ERWVSPpaLRVVVLHGNKRPQERWKNDPNFL 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 203 HYFDKTIISIDTLkqdIEYRHHLENAWWDIIVIDEAHNVaeRGTSSLRSKLAKLLagRSDTLIMLSATPHDGKAESFASL 282
Cdd:pfam00176 100 ADFDVVITTYETL---RKHKELLKKVHWHRIVLDEGHRL--KNSKSKLSKALKSL--KTRNRWILTGTPLQNNLEELWAL 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 283 MNMLDP--------------TAIANPKEYE-YADFAD--KNLVVRRFKKDVkdqmSGEFPeRNIVKLTRLA-SGAEEEAY 344
Cdd:pfam00176 173 LNFLRPgpfgslstfrnwfdRPIERGGGKKgVSRLHKllKPFLLRRTKKDV----EKSLP-PKVEYILFCRlSKLQRKLY 247

                         250
                  ....*....|..
gi 1447699881 345 RRLVesQFRDDD 356
Cdd:pfam00176 248 QTFL--LKKDLN 257
HELICc smart00490
helicase superfamily c-terminal domain;
464-548 9.67e-11

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 58.76  E-value: 9.67e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  464 QQLRADLKLKDDQIATLRGDQGDTVLMETVEAFgkTQSPLRLLVCSDVASEGINLHHLSHkMIHFDIPWSLMVFQQRNGR 543
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKF--NNGKIKVLVATDVAERGLDLPGVDL-VIIYDLPWSPASYIQRIGR 77


                   ....*
gi 1447699881  544 IDRYG 548
Cdd:smart00490  78 AGRAG 82
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
 127-298 3.73e-05

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 47.87  E-value: 3.73e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  127 LIADAVGLGKTLEAGILVSELIR-RGRGKRILVLAVKSMLTQFQKEFwSRFAIPLTRLDSAGLQKVRNRIPTNHNPFHYF 205
Cdd:PLN03142   192 ILADEMGLGKTLQTISLLGYLHEyRGITGPHMVVAPKSTLGNWMNEI-RRFCPVLRAVKFHGNPEERAHQREELLVAGKF 270

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  206 DKTIISIDTLkqdIEYRHHLENAWWDIIVIDEAHNVaeRGTSSLRSKLAKLLAGRSDTLImlSATPHDGKAESFASLMNM 285
Cdd:PLN03142   271 DVCVTSFEMA---IKEKTALKRFSWRYIIIDEAHRI--KNENSLLSKTMRLFSTNYRLLI--TGTPLQNNLHELWALLNF 343

                          170
                   ....*....|...
gi 1447699881  286 LDPTAIANPKEYE 298
Cdd:PLN03142   344 LLPEIFSSAETFD 356
 
Name Accession Description Interval E-value
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
 108-311 2.02e-69

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: 229.48  E-value: 2.02e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 108 MPFQLDPTRMALAQPRQRILIADAVGLGKTLEAGILVSELIRRGRGKRILVLAVKSMLTQFQKEFWSRFAIPLTRLDSAG 187
Cdd:cd18011     2 LPHQIDAVLRALRKPPVRLLLADEVGLGKTIEAGLIIKELLLRGDAKRVLILCPASLVEQWQDELQDKFGLPFLILDRET 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 188 LQKVRNRIptnHNPFHYFDKTIISIDTLKQDIEYRHHLENAWWDIIVIDEAHNVAERG--TSSLRSKLAKLLAGRSDTLI 265
Cdd:cd18011    82 AAQLRRLI---GNPFEEFPIVIVSLDLLKRSEERRGLLLSEEWDLVVVDEAHKLRNSGggKETKRYKLGRLLAKRARHVL 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1447699881 266 MLSATPHDGKAESFASLMNMLDPTAIANPKEY---EYADFADKNLVVRR 311
Cdd:cd18011   159 LLTATPHNGKEEDFRALLSLLDPGRFAVLGRFlrlDGLREVLAKVLLRR 207
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 109-589 3.98e-59

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 215.47  E-value: 3.98e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 109 PFQLDPTRMA--LAQPRQRILIADAVGLGKTLEAGILVSELIRRGRGKRILVLAVKSMLTQFQKEFwSRFA--IPLTRLD 184
Cdd:COG0553   244 PYQLEGAAWLlfLRRLGLGGLLADDMGLGKTIQALALLLELKERGLARPVLIVAPTSLVGNWQREL-AKFApgLRVLVLD 322

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 185 SAglqKVRNRIPtnhNPFHYFDKTIISIDTLKQDIEyrhHLENAWWDIIVIDEAHNVAERGTssLRSKLAKLLAGRSdtL 264
Cdd:COG0553   323 GT---RERAKGA---NPFEDADLVITSYGLLRRDIE---LLAAVDWDLVILDEAQHIKNPAT--KRAKAVRALKARH--R 389

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 265 IMLSATPHDGKAESFASLMNMLDP----------TAIANPKEYEYADFAD------KNLVVRRFKKDVKDqmsgEFPERN 328
Cdd:COG0553   390 LALTGTPVENRLEELWSLLDFLNPgllgslkafrERFARPIEKGDEEALErlrrllRPFLLRRTKEDVLK----DLPEKT 465

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 329 IVKLTRLASGAEEEAYRRLVESQFRDDDDEQAQSNKGRLFKITLekalfsspmacasvvanRLKRLESrkdhnsqsqine 408
Cdd:COG0553   466 EETLYVELTPEQRALYEAVLEYLRRELEGAEGIRRRGLILAALT-----------------RLRQICS------------ 516

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 409 leSLLLALNNIDASQF--SKYQLLLDTIRKDLAWKannteDRLVIFTESIKTLEFLEQQLRAdlklKDDQIATLRGDQGD 486
Cdd:COG0553   517 --HPALLLEEGAELSGrsAKLEALLELLEELLAEG-----EKVLVFSQFTDTLDLLEERLEE----RGIEYAYLHGGTSA 585

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 487 TVLMETVEAFGKTQSPLRLLVCSDVASEGINLHHLSHkMIHFDIPWSLMVFQQRNGRIDRYGQKHQPQIRYLLTEASepq 566
Cdd:COG0553   586 EERDELVDRFQEGPEAPVFLISLKAGGEGLNLTAADH-VIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGT--- 661

                         490       500
                  ....*....|....*....|...
gi 1447699881 567 IngDMRVLEVLINKDEQAQKNIG 589
Cdd:COG0553   662 I--EEKILELLEEKRALAESVLG 682
DpdE NF041062
protein DpdE;
109-554 4.34e-30

protein DpdE;


Pssm-ID: 468989 [Multi-domain]  Cd Length: 1048  Bit Score: 128.55  E-value: 4.34e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  109 PFQLDPTRMALAQPRQRILIADAVGLGKTLEAGILVSELIRRGRGKRILVLAVKSMLTQFQKEFWSRFaipltRLDSAGL 188
Cdd:NF041062   156 PHQVAVVRRVLQDPVQRYLLADEVGLGKTIEAGLVIRQHLLDNPDARVLVLVPDALVRQWRRELRDKF-----FLDDFPG 230

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  189 QKVRnriptnhnpfhyfdktIISIDTLkqdIEYRHHLENAwwDIIVIDEAHNVAERGTSS---LRSKLAKL--LAGRSDT 263
Cdd:NF041062   231 ARVR----------------VLSHEEP---ERWEPLLDAP--DLLVVDEAHQLARLAWSGdppERARYRELaaLAHAAPR 289

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  264 LIMLSATPHDGKAESFASLMNMLDP--------------------------------------TAIAN-----PKEYE-- 298
Cdd:NF041062   290 LLLLSATPVLGNEETFLALLHLLDPdlyplddleafrerleereelgrlvlgldpdnpnfllrQALDElralfPEDEElq 369

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  299 ---------YADFADKNLVVR----------------------RFKKDVKDQMSGEFPERNIVKLTRLASGAEE------ 341
Cdd:NF041062   370 elaeellplLDEFDDEEPEERaravsalrahisetyrlhrrmiRNRRSSVLGADYLVPGRAGPRVLVWESPAREaadeal 449

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  342 EAYRRLVeSQFRDDDDEQAQSNKGRLFKITLekALFSSPMACASvvanrlkRLESRKDHNSQSQINELE-SLLLALNNId 420
Cdd:NF041062   450 EDWREEA-ALLDAESDPAARAAYARALAWLV--ARLGGPDDLAA-------LLRWRLRGDAASADLAGErELLEALIAA- 518

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  421 ASQFSKYQLLLDTIRKDLaWKANNTEDRLVIFTESIKTLEFLEQQLRADLKlkdDQIATLRGDQGDTVLMETVEAFgKTQ 500
Cdd:NF041062   519 LEDEAKDADLLAALADWL-LPLLRGSGKAVVFCGDGSLADHLAAALARLGA---GSVERHLSGQGADQAERAVRAF-RQD 593

                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1447699881  501 SPLRLLVCSDVASEGINLHhLSHKMIHFDIPWSLMVFQQRNGRIDRYGQKHQPQ 554
Cdd:NF041062   594 PSARVLVCDRSGEEGLNLQ-GADRLVHLDLPWSPNRLEQRIGRLDRYASLRGGR 646
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 425-559 6.17e-26

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: 104.10  E-value: 6.17e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 425 SKYQLLLDTIRKdlaWKANNteDRLVIFTESIKTLEFLEQQLRAdlklKDDQIATLRGDQGDTVLMETVEAFGKTQSPLR 504
Cdd:cd18793    11 GKLEALLELLEE---LREPG--EKVLIFSQFTDTLDILEEALRE----RGIKYLRLDGSTSSKERQKLVDRFNEDPDIRV 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1447699881 505 LLVCSDVASEGINLHHLSHkMIHFDIPWSLMVFQQRNGRIDRYGQKHQPQIRYLL 559
Cdd:cd18793    82 FLLSTKAGGVGLNLTAANR-VILYDPWWNPAVEEQAIDRAHRIGQKKPVVVYRLI 135
DEXDc smart00487
DEAD-like helicases superfamily;
123-286 8.80e-18

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 82.54  E-value: 8.80e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  123 RQRILIADAVGLGKTLEAGILVSELIRRGRGKRILVLA-----VKSMLTQFQKEFWSRFAIPLTRLDSAGLQKVRNRIPT 197
Cdd:smart00487  24 LRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVptrelAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLES 103

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  198 NHNPFhyfdkTIISIDTLKQDIEyRHHLENAWWDIIVIDEAHNVAERGTSSLRSKLAKLLAgRSDTLIMLSATPHDGKAE 277
Cdd:smart00487 104 GKTDI-----LVTTPGRLLDLLE-NDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLP-KNVQLLLLSATPPEEIEN 176


                   ....*....
gi 1447699881  278 SFASLMNML 286
Cdd:smart00487 177 LLELFLNDP 185
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
 108-288 2.15e-17

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: 81.07  E-value: 2.15e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 108 MPFQLDPTR--MALAQPRQRILIADAVGLGKTLEAGILVSELI-RRGRGKRILVLAVKSMLTQFQKEFwSRFAIPLT--R 182
Cdd:cd17919     2 RPYQLEGLNflLELYENGPGGILADEMGLGKTLQAIAFLAYLLkEGKERGPVLVVCPLSVLENWEREF-EKWTPDLRvvV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 183 LDSAGLQKVRNRIPTNHNPFHYFdktIISIDTLKQDIEyrhHLENAWWDIIVIDEAHNVaeRGTSSLRSKLAKLLagRSD 262
Cdd:cd17919    81 YHGSQRERAQIRAKEKLDKFDVV---LTTYETLRRDKA---SLRKFRWDLVVVDEAHRL--KNPKSQLSKALKAL--RAK 150

                         170       180
                  ....*....|....*....|....*.
gi 1447699881 263 TLIMLSATPHDGKAESFASLMNMLDP 288
Cdd:cd17919   151 RRLLLTGTPLQNNLEELWALLDFLDP 176
PRK04914 PRK04914
RNA polymerase-associated protein RapA;
125-555 6.59e-16

RNA polymerase-associated protein RapA;


Pssm-ID: 235319 [Multi-domain]  Cd Length: 956  Bit Score: 82.58  E-value: 6.59e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 125 RILIADAVGLGKTLEAGILVSELIRRGRGKRILVLAVKSMLTQFQKEFWSRFAIPLTRLDSAGLQKVRNripTNHNPFHY 204
Cdd:PRK04914  171 RVLLADEVGLGKTIEAGMIIHQQLLTGRAERVLILVPETLQHQWLVEMLRRFNLRFSLFDEERYAEAQH---DADNPFET 247

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 205 FDKTIISIDTLKQDIEYRHHLENAWWDIIVIDEAHNVA-ERGTSSLRSKLAKLLAGRSDTLIMLSATPHDGKAES-FASL 282
Cdd:PRK04914  248 EQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVwSEEAPSREYQVVEQLAEVIPGVLLLTATPEQLGQEShFARL 327

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 283 mNMLDPTaianpKEYEYADFADKNLVVRRFKKDVKDQMSGE-FPERNIVKLTRLASGAEEEAYRRLVESqfrDDDDEQAQ 361
Cdd:PRK04914  328 -RLLDPD-----RFHDYEAFVEEQQQYRPVADAVQALLAGEkLSDDALNALGELLGEQDIEPLLQAANS---DSEEAQAA 398

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 362 SNK-----------GR-LFKITL-------EKALFSSPMACASVVANRLKRLESRKDHNSQSQinelESLLLALNNiDAS 422
Cdd:PRK04914  399 RQEliselldrhgtGRvLFRNTRaavkgfpKRELHPIPLPLPEQYQTAIKVSLEARARDMLYP----EQIYQEFED-NAT 473

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 423 --QF-SKYQLLLDTIrkdlawKANNTEDRLVIfTESIKTLEFLEQQLRadlklkddqiaTLRGDQGdTVL---METVE-- 494
Cdd:PRK04914  474 wwNFdPRVEWLIDFL------KSHRSEKVLVI-CAKAATALQLEQALR-----------EREGIRA-AVFhegMSIIErd 534

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1447699881 495 ----AFGKTQSPLRLLVCSDVASEGINL---HHLshkmIHFDIPWSLMVFQQRNGRIDRYGQKHQPQI 555
Cdd:PRK04914  535 raaaYFADEEDGAQVLLCSEIGSEGRNFqfaSHL----VLFDLPFNPDLLEQRIGRLDRIGQKHDIQI 598
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 425-548 3.15e-13

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


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 66.85  E-value: 3.15e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 425 SKYQLLLDTIRKdlawkanNTEDRLVIFTESIKTLEflEQQLRADLKLKddqIATLRGDQGDTVLMETVEAFGKtqSPLR 504
Cdd:pfam00271   1 EKLEALLELLKK-------ERGGKVLIFSQTKKTLE--AELLLEKEGIK---VARLHGDLSQEEREEILEDFRK--GKID 66

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1447699881 505 LLVCSDVASEGINLHHLSHkMIHFDIPWSLMVFQQRNGRIDRYG 548
Cdd:pfam00271  67 VLVATDVAERGLDLPDVDL-VINYDLPWNPASYIQRIGRAGRAG 109
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 127-356 2.04e-12

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: 68.86  E-value: 2.04e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 127 LIADAVGLGKTLEAGILVSEL--IRRGRGKRILVLAVKSMLTQFQKEFwSRFAIP--LTRLDSAGLQKVRNRIPTNHNPF 202
Cdd:pfam00176  21 ILADEMGLGKTLQTISLLLYLkhVDKNWGGPTLIVVPLSLLHNWMNEF-ERWVSPpaLRVVVLHGNKRPQERWKNDPNFL 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 203 HYFDKTIISIDTLkqdIEYRHHLENAWWDIIVIDEAHNVaeRGTSSLRSKLAKLLagRSDTLIMLSATPHDGKAESFASL 282
Cdd:pfam00176 100 ADFDVVITTYETL---RKHKELLKKVHWHRIVLDEGHRL--KNSKSKLSKALKSL--KTRNRWILTGTPLQNNLEELWAL 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 283 MNMLDP--------------TAIANPKEYE-YADFAD--KNLVVRRFKKDVkdqmSGEFPeRNIVKLTRLA-SGAEEEAY 344
Cdd:pfam00176 173 LNFLRPgpfgslstfrnwfdRPIERGGGKKgVSRLHKllKPFLLRRTKKDV----EKSLP-PKVEYILFCRlSKLQRKLY 247

                         250
                  ....*....|..
gi 1447699881 345 RRLVesQFRDDD 356
Cdd:pfam00176 248 QTFL--LKKDLN 257
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
109-544 3.25e-11

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 66.97  E-value: 3.25e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 109 PFQ---LDPTRMALAQPRQRILIADAVGLGKTleagILVSELIRR-GRGKRILVLA-VKSMLTQFQKEFWSRFAIPLtrl 183
Cdd:COG1061    83 PYQqeaLEALLAALERGGGRGLVVAPTGTGKT----VLALALAAElLRGKRVLVLVpRRELLEQWAEELRRFLGDPL--- 155

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 184 DSAGLQKVRNRIptnhnpfhyfdkTIISIDTLKQDIEYRHHLENawWDIIVIDEAHNVaerGTSSLRSKLAKLLAGRsdt 263
Cdd:COG1061   156 AGGGKKDSDAPI------------TVATYQSLARRAHLDELGDR--FGLVIIDEAHHA---GAPSYRRILEAFPAAY--- 215

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 264 LIMLSATPH--DGKAESFASLMNMLdptaianpKEYEYADFADKNLVVRRFKKDVKDQMSGEfpernivkltrlasgaee 341
Cdd:COG1061   216 RLGLTATPFrsDGREILLFLFDGIV--------YEYSLKEAIEDGYLAPPEYYGIRVDLTDE------------------ 269

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 342 eayrrlvesqfRDDDDEQAQSnkgrlfkitlekalfsspmacasvVANRLKRLESRKDHnsqsqineleslllalnnida 421
Cdd:COG1061   270 -----------RAEYDALSER------------------------LREALAADAERKDK--------------------- 293

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 422 sqfskyqlLLDTIRKDLAwkannTEDRLVIFTESIKTLEFLEQQLRAdlklKDDQIATLRGDQGDTVLMETVEAFGktQS 501
Cdd:COG1061   294 --------ILRELLREHP-----DDRKTLVFCSSVDHAEALAELLNE----AGIRAAVVTGDTPKKEREEILEAFR--DG 354

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1447699881 502 PLRLLVCSDVASEGinlhhlshkmihFDIPW-----------SLMVFQQRNGRI 544
Cdd:COG1061   355 ELRILVTVDVLNEG------------VDVPRldvaillrptgSPREFIQRLGRG 396
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 118-275 7.37e-11

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: 61.42  E-value: 7.37e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 118 ALAQPRQRILIADAVGLGKTLEAGILVSELIRRGRGKRILVLA-VKSMLTQFQKEFWsrfaiPLTRLDSAGLQKVRNRIP 196
Cdd:cd18032    15 AREKGQRRALLVMATGTGKTYTAAFLIKRLLEANRKKRILFLAhREELLEQAERSFK-----EVLPDGSFGNLKGGKKKP 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 197 TNHNpfHYFdktiISIDTLKQDIEYRHHLENAwWDIIVIDEAHnvaeRGTSslrSKLAKLLAGRSD-TLIMLSATP--HD 273
Cdd:cd18032    90 DDAR--VVF----ATVQTLNKRKRLEKFPPDY-FDLIIIDEAH----HAIA---SSYRKILEYFEPaFLLGLTATPerTD 155


                  ..
gi 1447699881 274 GK 275
Cdd:cd18032   156 GL 157
DEXQc_arch_SWI2_SNF2 cd18012
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ...
 126-288 8.31e-11

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: 62.58  E-value: 8.31e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 126 ILiADAVGLGKTLEAGILVSELIRRGRGKRILVLAVKSMLTQFQKEFwSRFAIPLTRLDSAGlqKVRNRIPTNHNPFHyf 205
Cdd:cd18012    27 IL-ADDMGLGKTLQTLALLLSRKEEGRKGPSLVVAPTSLIYNWEEEA-AKFAPELKVLVIHG--TKRKREKLRALEDY-- 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 206 DKTIISIDTLKQDIEYRHHLEnawWDIIVIDEAHNVaeRGTSSLRSKLAKLLagRSDTLIMLSATPHDGKAESFASLMNM 285
Cdd:cd18012   101 DLVITSYGLLRRDIELLKEVK---FHYLVLDEAQNI--KNPQTKTAKAVKAL--KADHRLALTGTPIENHLGELWSIFDF 173


                  ...
gi 1447699881 286 LDP 288
Cdd:cd18012   174 LNP 176
HELICc smart00490
helicase superfamily c-terminal domain;
464-548 9.67e-11

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 58.76  E-value: 9.67e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  464 QQLRADLKLKDDQIATLRGDQGDTVLMETVEAFgkTQSPLRLLVCSDVASEGINLHHLSHkMIHFDIPWSLMVFQQRNGR 543
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKF--NNGKIKVLVATDVAERGLDLPGVDL-VIIYDLPWSPASYIQRIGR 77


                   ....*
gi 1447699881  544 IDRYG 548
Cdd:smart00490  78 AGRAG 82
DEXHc_CHD8 cd18060
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; ...
 123-304 5.14e-10

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: 60.45  E-value: 5.14e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 123 RQRILIADAVGLGKTLEAGILVSELIRRGRGKRILVLAVKSMLTQFQKEF--WSRFAIPLTRLDSAGLQKVRNR------ 194
Cdd:cd18060    19 RQNCILADEMGLGKTIQSIAFLQEVYNVGIHGPFLVIAPLSTITNWEREFntWTEMNTIVYHGSLASRQMIQQYemyckd 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 195 -----IPTNHNpfhyFDKTIISIDTLKQDIEYRHHLEnawWDIIVIDEAHNVAERGTSSLRS-KLAKLlagrsDTLIMLS 268
Cdd:cd18060    99 srgrlIPGAYK----FDALITTFEMILSDCPELREIE---WRCVIIDEAHRLKNRNCKLLDSlKHMDL-----EHKVLLT 166

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1447699881 269 ATPHDGKAESFASLMNMLDPTAIANPKEYeYADFAD 304
Cdd:cd18060   167 GTPLQNTVEELFSLLHFLEPSQFPSESEF-LKDFGD 201
DEXHc_ATRX-like cd18007
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ...
 127-271 1.08e-09

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: 60.00  E-value: 1.08e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 127 LIADAVGLGKTLEA-GILVSELIRRGRGKRILVLAVKSMLTQFQKEF--WS-RFAIPLTRLDSAGLQKVRNRIPTNHNPF 202
Cdd:cd18007    30 ILAHTMGLGKTLQViTFLHTYLAAAPRRSRPLVLCPASTLYNWEDEFkkWLpPDLRPLLVLVSLSASKRADARLRKINKW 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 203 H-----------YFDKTIISIDT---LKQDIEYRHHLENAwwDIIVIDEAHNVaeRGTSSLRSKLAKLLagRSDTLIMLS 268
Cdd:cd18007   110 HkeggvlligyeLFRNLASNATTdprLKQEFIAALLDPGP--DLLVLDEGHRL--KNEKSQLSKALSKV--KTKRRILLT 183


                  ...
gi 1447699881 269 ATP 271
Cdd:cd18007   184 GTP 186
DEXHc_HARP_SMARCAL1 cd18010
DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin ...
 108-297 1.60e-09

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: 58.76  E-value: 1.60e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 108 MPFQLDPTRMALAQpRQRILIADAVGLGKTLEAgilvselIRRGRGKR----ILVLAVKSMLTQFQKEFwsrfaipLTRL 183
Cdd:cd18010     2 LPFQREGVCFALRR-GGRVLIADEMGLGKTVQA-------IAIAAYYReewpLLIVCPSSLRLTWADEI-------ERWL 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 184 DSAGLQKVrNRIPTNHNPFHYFDK--TIISIDTLKQDIEyrhHLENAWWDIIVIDEAHNVAERgtSSLRSKLAKLLAGRS 261
Cdd:cd18010    67 PSLPPDDI-QVIVKSKDGLRDGDAkvVIVSYDLLRRLEK---QLLARKFKVVICDESHYLKNS--KAKRTKAALPLLKRA 140

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1447699881 262 DTLIMLSATPHDGKAESFASLMNMLDPTAIANPKEY 297
Cdd:cd18010   141 KRVILLSGTPALSRPIELFTQLDALDPKLFGRFHDF 176
DEXHc_CHD6 cd18058
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; ...
 123-308 2.32e-09

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; Chromodomain-helicase-DNA-binding protein 6 (CHD6) is a DNA-dependent ATPase that plays a role in chromatin remodeling. It regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin. It activates transcription of specific genes in response to oxidative stress through interaction with NFE2L2.2 and acts as a transcriptional repressor of different viruses including influenza virus or papillomavirus. During influenza virus infection, the viral polymerase complex localizes CHD6 to inactive chromatin where it gets degraded in a proteasome independent-manner. CHD6 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350816 [Multi-domain]  Cd Length: 222  Bit Score: 58.51  E-value: 2.32e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 123 RQRILIADAVGLGKTLEAGILVSELIRRGRGKRILVLAVKSMLTQFQKEFwsRFAIPLTRLDSAGLQKVRNRI------- 195
Cdd:cd18058    19 RKNCILADEMGLGKTIQSITFLSEIFLMGIRGPFLIIAPLSTITNWEREF--RTWTEMNAIVYHGSQISRQMIqqyemyy 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 196 -PTNHNPFHYFDKTIISIDTLKQDIEYRHHLENAWWDIIVIDEAHNVAERGTSSLRSklAKLLAgrSDTLIMLSATPHDG 274
Cdd:cd18058    97 rDEQGNPLSGIFKFQVVITTFEMILADCPELKKINWSCVIIDEAHRLKNRNCKLLEG--LKLMA--LEHKVLLTGTPLQN 172

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1447699881 275 KAESFASLMNMLDPTAIANPKEY--EYADFADKNLV 308
Cdd:cd18058   173 SVEELFSLLNFLEPSQFPSETTFleEFGDLKTEEQV 208
DEXHc_RAD54 cd18004
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ...
 127-323 9.40e-09

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: 56.91  E-value: 9.40e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 127 LIADAVGLGKTLEAGILVSELIRRGRG-----KRILVLAVKSMLTQFQKEF--W--SRFAIPLTRLDSAglqKVRNRIPT 197
Cdd:cd18004    28 ILADEMGLGKTLQAIALVWTLLKQGPYgkptaKKALIVCPSSLVGNWKAEFdkWlgLRRIKVVTADGNA---KDVKASLD 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 198 NHNPFHYFDKTIISIDTLkqdieyRHHLENAW----WDIIVIDEAHNVAERGTSSLRSkLAKLLAGRSdtlIMLSATPHD 273
Cdd:cd18004   105 FFSSASTYPVLIISYETL------RRHAEKLSkkisIDLLICDEGHRLKNSESKTTKA-LNSLPCRRR---LLLTGTPIQ 174

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1447699881 274 GKAESFASLMNMLDPTAIANPKEYEyADFADKNLVVRRFKKDVKDQMSGE 323
Cdd:cd18004   175 NDLDEFFALVDFVNPGILGSLASFR-KVFEEPILRSRDPDASEEDKELGA 223
ResIII pfam04851
Type III restriction enzyme, res subunit;
118-271 1.48e-08

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 54.99  E-value: 1.48e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 118 ALAQPRQRILIADAVGLGKTLEAGILVSELIRRGRGKRILVLA-VKSMLTQFQKEFWSRFAIPLtrlDSAGLQKVRNRIP 196
Cdd:pfam04851  18 SIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVpRKDLLEQALEEFKKFLPNYV---EIGEIISGDKKDE 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1447699881 197 TNHNPFHYFdktiISIDTL-KQDIEYRHHLENAWWDIIVIDEAHnvaeRGTSSLRSKLAKLLagRSDTLIMLSATP 271
Cdd:pfam04851  95 SVDDNKIVV----TTIQSLyKALELASLELLPDFFDVIIIDEAH----RSGASSYRNILEYF--KPAFLLGLTATP 160
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 127-270 1.72e-08

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


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 54.33  E-value: 1.72e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 127 LIADAVGLGKTLEAG-ILVSELIRRGrgKRILVLAVKSMLT-QFQKEFWSRFAIP-----LTRLDSAgLQKVRNRIPTNh 199
Cdd:cd00046     5 LITAPTGSGKTLAALlAALLLLLKKG--KKVLVLVPTKALAlQTAERLRELFGPGirvavLVGGSSA-EEREKNKLGDA- 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1447699881 200 npfhyfDKTIISIDTLKQDIEYRHHLENAWWDIIVIDEAHNVAERGTSSLRSKLAKLLAGRSDTLIM-LSAT 270
Cdd:cd00046    81 ------DIIIATPDMLLNLLLREDRLFLKDLKLIIVDEAHALLIDSRGALILDLAVRKAGLKNAQVIlLSAT 146
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 419-550 2.72e-08

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 53.28  E-value: 2.72e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 419 IDASQFSKYQLLLDTIrkdlawKANNTEDRLVIFTESIKTLEFLEQQLRaDLKLKddqIATLRGDQGDTVLMETVEAFGK 498
Cdd:cd18787     6 VVVEEEEKKLLLLLLL------LEKLKPGKAIIFVNTKKRVDRLAELLE-ELGIK---VAALHGDLSQEERERALKKFRS 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1447699881 499 TQSplRLLVCSDVASEGINLHHLSHkMIHFDIPWSLMVFQQRNGRIDRYGQK 550
Cdd:cd18787    76 GKV--RVLVATDVAARGLDIPGVDH-VINYDLPRDAEDYVHRIGRTGRAGRK 124
DEXHc_HELLS_SMARCA6 cd18009
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ...
 127-307 7.02e-08

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: 54.31  E-value: 7.02e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 127 LIADAVGLGKTLEAGILVSELIRRGRGKRILVLAVKSMLTQFQKEFwSRFAIPLTRLDSAGLQKVRNRIPTNHNPFHY-- 204
Cdd:cd18009    26 ILADEMGLGKTIQTIALLAHLRERGVWGPFLVIAPLSTLPNWVNEF-ARFTPSVPVLLYHGTKEERERLRKKIMKREGtl 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 205 --FDKTIISIDTLKQDIEYRHHLEnawWDIIVIDEAHNVaergtSSLRSKLAKLLAG-RSDTLIMLSATPHDGKAESFAS 281
Cdd:cd18009   105 qdFPVVVTSYEIAMRDRKALQHYA---WKYLIVDEGHRL-----KNLNCRLIQELKTfNSDNRLLLTGTPLQNNLSELWS 176

                         170       180
                  ....*....|....*....|....*..
gi 1447699881 282 LMNMLDPTAIANPKEYE-YADFADKNL 307
Cdd:cd18009   177 LLNFLLPDVFDDLSSFEsWFDFSSLSD 203
DEXHc_CHD6_7_8_9 cd17995
DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; ...
 123-304 1.10e-06

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: 50.71  E-value: 1.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 123 RQRILiADAVGLGKTLEAGILVSELIRRG--RGKrILVLAVKSMLTQFQKEF--WSrfaiPLTRLDSAGLQKVRNRI--- 195
Cdd:cd17995    20 RNCIL-ADEMGLGKTIQSIAFLEHLYQVEgiRGP-FLVIAPLSTIPNWQREFetWT----DMNVVVYHGSGESRQIIqqy 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 196 ---------PTNHNPFHyFDKTIISIDTLKQDIEyrhHLENAWWDIIVIDEAHNvaergtssLRSKLAKLLAG----RSD 262
Cdd:cd17995    94 emyfkdaqgRKKKGVYK-FDVLITTYEMVIADAE---ELRKIPWRVVVVDEAHR--------LKNRNSKLLQGlkklTLE 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1447699881 263 TLIMLSATPHDGKAESFASLMNMLDPTAIANPKEYEyADFAD 304
Cdd:cd17995   162 HKLLLTGTPLQNNTEELWSLLNFLEPEKFPSSEEFL-EEFGD 202
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 503-550 1.29e-06

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


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 46.93  E-value: 1.29e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1447699881 503 LRLLVCSDVASEGINLHHLSHkMIHFDIPWSLMVFQQRNGRIDRYGQK 550
Cdd:cd18785    23 LEILVATNVLGEGIDVPSLDT-VIFFDPPSSAASYIQRVGRAGRGGKD 69
DEXHc_CHD7 cd18059
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; ...
 127-288 2.23e-06

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: 49.64  E-value: 2.23e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 127 LIADAVGLGKTLEAGILVSELIRRGRGKRILVLAVKSMLTQFQKEF--WSRFAIPLTRLDSAGLQKV----------RNR 194
Cdd:cd18059    23 ILADEMGLGKTIQSITFLYEIYLKGIHGPFLVIAPLSTIPNWEREFrtWTELNVVVYHGSQASRRTIqlyemyfkdpQGR 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 195 IPTNHNPFHyfdKTIISIDTLKQDIEyrhHLENAWWDIIVIDEAHNvaergtssLRSKLAKLLAGRS----DTLIMLSAT 270
Cdd:cd18059   103 VIKGSYKFH---AIITTFEMILTDCP---ELRNIPWRCVVIDEAHR--------LKNRNCKLLEGLKmmdlEHKVLLTGT 168

                         170
                  ....*....|....*...
gi 1447699881 271 PHDGKAESFASLMNMLDP 288
Cdd:cd18059   169 PLQNTVEELFSLLHFLEP 186
DEXHc_CHD5 cd18057
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; ...
 109-308 3.11e-06

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


Pssm-ID: 350815 [Multi-domain]  Cd Length: 232  Bit Score: 49.29  E-value: 3.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 109 PFQLDPT---RMALAQPRQRILiADAVGLGKTLEAGILVSELIRRGRGK-RILVLAVKSMLTQFQKEFwSRFAIPLTRLD 184
Cdd:cd18057     3 PYQLEGLnwlRFSWAQGTDTIL-ADEMGLGKTVQTIVFLYSLYKEGHSKgPYLVSAPLSTIINWEREF-EMWAPDFYVVT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 185 SAGLQKVRNRIptNHNPFHYFDKTIIS---IDTLKQDIEYRHH---------------LENAWWDIIVIDEAHNVAERgt 246
Cdd:cd18057    81 YTGDKESRSVI--RENEFSFEDNAIRSgkkVFRMKKEAQIKFHvlltsyelitidqaiLGSIEWACLVVDEAHRLKNN-- 156

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1447699881 247 sslRSKLAKLLAG-RSDTLIMLSATPHDGKAESFASLMNMLDPTAIANPKEY--EYADFADKNLV 308
Cdd:cd18057   157 ---QSKFFRVLNSyKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFleEFADISKEDQI 218
DEXHc_ERCC6L cd18001
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ...
 127-271 3.47e-06

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: 49.29  E-value: 3.47e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 127 LIADAVGLGKTLEAGILVSELIRRGRGKRILVLAVKSMLTQFQKEFwsRFAIPLTRL------DSAGLQKVRNRIPTNHN 200
Cdd:cd18001    23 ILADDMGLGKTVQICAFLSGMFDSGLIKSVLVVMPTSLIPHWVKEF--AKWTPGLRVkvfhgtSKKERERNLERIQRGGG 100

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1447699881 201 PFHYFDKTIISidTLKQDIEYRHhlENAWWDIIVIDEAHNVaeRGTSSLRSKlaKLLAGRSDTLIMLSATP 271
Cdd:cd18001   101 VLLTTYGMVLS--NTEQLSADDH--DEFKWDYVILDEGHKI--KNSKTKSAK--SLREIPAKNRIILTGTP 163
DEXHc_RAD54B cd18066
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ...
 123-297 5.19e-06

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: 48.69  E-value: 5.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 123 RQRILIADAVGLGKTLEAGILVSELIRRGR------GKRILVLAVKSMLTQFQKEF--W---SRFAIPLTRLDsaglQKV 191
Cdd:cd18066    24 RFGAILADEMGLGKTLQCISLIWTLLRQGPyggkpvIKRALIVTPGSLVKNWKKEFqkWlgsERIKVFTVDQD----HKV 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 192 RNRIPTNhnpfhYFDKTIISIDTLKQDIEyrhHLENAWWDIIVIDEAHNVAergTSSLRSKLAkLLAGRSDTLIMLSATP 271
Cdd:cd18066   100 EEFIASP-----LYSVLIISYEMLLRSLD---QISKLNFDLVICDEGHRLK---NTSIKTTTA-LTSLSCERRIILTGTP 167

                         170       180
                  ....*....|....*....|....*.
gi 1447699881 272 HDGKAESFASLMNMLDPTAIANPKEY 297
Cdd:cd18066   168 IQNDLQEFFALIDFVNPGILGSLSTY 193
DEXHc_Mot1 cd17999
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ...
 126-271 2.25e-05

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: 46.96  E-value: 2.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 126 ILiADAVGLGKTLEA-GILVSELIRR-----GRGKRILVLAVKSMLTQFQKEfWSRFA--IPLTRLDSAGLQKVRNRIPt 197
Cdd:cd17999    23 IL-CDDMGLGKTLQTlCILASDHHKRansfnSENLPSLVVCPPTLVGHWVAE-IKKYFpnAFLKPLAYVGPPQERRRLR- 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1447699881 198 nhNPFHYFDKTIISIDTLKQDIEYrhhLENAWWDIIVIDEAHNVaeRGTSSLRSKLAKLLAGRSDtlIMLSATP 271
Cdd:cd17999   100 --EQGEKHNVIVASYDVLRNDIEV---LTKIEWNYCVLDEGHII--KNSKTKLSKAVKQLKANHR--LILSGTP 164
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
 127-298 3.73e-05

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 47.87  E-value: 3.73e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  127 LIADAVGLGKTLEAGILVSELIR-RGRGKRILVLAVKSMLTQFQKEFwSRFAIPLTRLDSAGLQKVRNRIPTNHNPFHYF 205
Cdd:PLN03142   192 ILADEMGLGKTLQTISLLGYLHEyRGITGPHMVVAPKSTLGNWMNEI-RRFCPVLRAVKFHGNPEERAHQREELLVAGKF 270

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881  206 DKTIISIDTLkqdIEYRHHLENAWWDIIVIDEAHNVaeRGTSSLRSKLAKLLAGRSDTLImlSATPHDGKAESFASLMNM 285
Cdd:PLN03142   271 DVCVTSFEMA---IKEKTALKRFSWRYIIIDEAHRI--KNENSLLSKTMRLFSTNYRLLI--TGTPLQNNLHELWALLNF 343

                          170
                   ....*....|...
gi 1447699881  286 LDPTAIANPKEYE 298
Cdd:PLN03142   344 LLPEIFSSAETFD 356
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
426-550 4.28e-05

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 47.06  E-value: 4.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 426 KYQLLLDTIRkdlawkaNNTEDRLVIFTESIKTLEFLEQQLRADlKLKddqIATLRGDQGDTVLMETVEAF--GKtqspL 503
Cdd:COG0513   228 KLELLRRLLR-------DEDPERAIVFCNTKRGADRLAEKLQKR-GIS---AAALHGDLSQGQRERALDAFrnGK----I 292

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1447699881 504 RLLVCSDVASEGINLHHLSHkMIHFDIPWSLMVFQQRNGRIDRYGQK 550
Cdd:COG0513   293 RVLVATDVAARGIDIDDVSH-VINYDLPEDPEDYVHRIGRTGRAGAE 338
DEXHc_SMARCA2 cd18063
DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent ...
 127-298 1.59e-04

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: 44.28  E-value: 1.59e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 127 LIADAVGLGKTLEAGILVSELIRRGR-GKRILVLAVKSMLTQFQKEFwSRFAIPLTRLDSAGLQKVRNRIPtnhnPFHYF 205
Cdd:cd18063    46 ILADEMGLGKTIQTIALITYLMEHKRlNGPYLIIVPLSTLSNWTYEF-DKWAPSVVKISYKGTPAMRRSLV----PQLRS 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 206 DKTIISIDTLKQDIEYRHHLENAWWDIIVIDEAHNVAERGTSSLRSKLAKLLAGRSdtlIMLSATPHDGKAESFASLMNM 285
Cdd:cd18063   121 GKFNVLLTTYEYIIKDKHILAKIRWKYMIVDEGHRMKNHHCKLTQVLNTHYVAPRR---ILLTGTPLQNKLPELWALLNF 197

                         170
                  ....*....|...
gi 1447699881 286 LDPTAIANPKEYE 298
Cdd:cd18063   198 LLPTIFKSCSTFE 210
DEXHc_SMARCA2_SMARCA4 cd17996
DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin ...
 127-298 1.73e-04

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: 44.28  E-value: 1.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 127 LIADAVGLGKTLEAGILVSELI--RRGRGKrILVLAVKSMLTQFQKEFwSRFAIPLTRLDSAGLQKVRNRIptnhnpfhy 204
Cdd:cd17996    26 ILADEMGLGKTIQTISLITYLMekKKNNGP-YLVIVPLSTLSNWVSEF-EKWAPSVSKIVYKGTPDVRKKL--------- 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 205 fDKTIIS--IDTLKQDIEY----RHHLENAWWDIIVIDEAHNVAERgtsslRSKLAKLLAG--RSDTLIMLSATPHDGKA 276
Cdd:cd17996    95 -QSQIRAgkFNVLLTTYEYiikdKPLLSKIKWKYMIIDEGHRMKNA-----QSKLTQTLNTyyHARYRLLLTGTPLQNNL 168

                         170       180
                  ....*....|....*....|..
gi 1447699881 277 ESFASLMNMLDPTAIANPKEYE 298
Cdd:cd17996   169 PELWALLNFLLPKIFKSCKTFE 190
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
 406-548 1.74e-04

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 45.29  E-value: 1.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 406 INELESLLLALNNIDASQFS-----KYQLLLDTIRKdlawkanNTEDRLVIFTESIKTLEFLEQQLRADlklkDDQIATL 480
Cdd:PRK01297  297 IVEIEPENVASDTVEQHVYAvagsdKYKLLYNLVTQ-------NPWERVMVFANRKDEVRRIEERLVKD----GINAAQL 365

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1447699881 481 RGDQGDTVLMETVEAFgkTQSPLRLLVCSDVASEGINLHHLSHkMIHFDIPWSLMVFQQRNGRIDRYG 548
Cdd:PRK01297  366 SGDVPQHKRIKTLEGF--REGKIRVLVATDVAGRGIHIDGISH-VINFTLPEDPDDYVHRIGRTGRAG 430
DEXHc_CHD1L cd18006
DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, ...
 127-288 4.18e-04

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: 42.81  E-value: 4.18e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 127 LIADAVGLGKTLEAGILVSELIRRGRGKR-ILVLAVKSMLTQFQKEFwSRFAIPLTRLDSAGLQKVRNRIPTNHNPFHYF 205
Cdd:cd18006    23 ILGDEMGLGKTCQTISLLWYLAGRLKLLGpFLVLCPLSVLDNWKEEL-NRFAPDLSVITYMGDKEKRLDLQQDIKSTNRF 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 206 DKTIISIDTLKQDIEYrhhLENAWWDIIVIDEAHNVAERgTSSLRSKLAKLLAGRSdtlIMLSATPHDGKAESFASLMNM 285
Cdd:cd18006   102 HVLLTTYEICLKDASF---LKSFPWASLVVDEAHRLKNQ-NSLLHKTLSEFSVDFR---LLLTGTPIQNSLQELYALLSF 174


                  ...
gi 1447699881 286 LDP 288
Cdd:cd18006   175 IEP 177
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 126-271 6.31e-04

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: 41.46  E-value: 6.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 126 ILIADAVGLGKTLEAGI-LVSELIRRGRGKRILVLA-----VKSMLTQFQKEFWSRFAIPLTRLDSAGLQKVRNRIPTNH 199
Cdd:pfam00270  17 VLVQAPTGSGKTLAFLLpALEALDKLDNGPQALVLAptrelAEQIYEELKKLGKGLGLKVASLLGGDSRKEQLEKLKGPD 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1447699881 200 NpfhyfdkTIISIDTLKQDIEYRHHLENAwwDIIVIDEAHNVAERG-TSSLRSKLAKLLAGRsdTLIMLSATP 271
Cdd:pfam00270  97 I-------LVGTPGRLLDLLQERKLLKNL--KLLVLDEAHRLLDMGfGPDLEEILRRLPKKR--QILLLSATL 158
DEXHc_ATRX cd18068
DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha ...
 127-297 9.73e-04

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: 41.80  E-value: 9.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 127 LIADAVGLGKTLEAGILVSELI---RRGRGKRILVLAVKSMLTQFQKEF--WSRFAIPLTRLDSAGLQKVRnRIPTNHNP 201
Cdd:cd18068    32 ILAHCMGLGKTLQVVTFLHTVLlceKLENFSRVLVVCPLNTVLNWLNEFekWQEGLKDEEKIEVNELATYK-RPQERSYK 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 202 FHYFDKT----IISIDTL-------------KQDIEYRHHLENAWWDIIVIDEAHnVAERGTSSLRSKLAKLLAGRSdtl 264
Cdd:cd18068   111 LQRWQEEggvmIIGYDMYrilaqernvksreKLKEIFNKALVDPGPDFVVCDEGH-ILKNEASAVSKAMNSIRTKRR--- 186

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1447699881 265 IMLSATPHDGKAESFASLMNMLDPTAIANPKEY 297
Cdd:cd18068   187 IVLTGTPLQNNLIEYHCMVNFVKPNLLGTIKEF 219
DEXQc_bact_SNF2 cd18013
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ...
 109-271 1.43e-03

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: 41.18  E-value: 1.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 109 PFQLDPTRMALAQPRQRILIAdaVGLGKTLEAGILVSELIRRGRGKRILVLAVKSMLTQFQKEFWSRFAIPLTRLDSAGL 188
Cdd:cd18013     3 PYQKVAINFIIEHPYCGLFLD--MGLGKTVTTLTALSDLQLDDFTRRVLVIAPLRVARSTWPDEVEKWNHLRNLTVSVAV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 189 QKVRNRIPTNHNPFHYFdktIISIDTLKQDIEYrhhLENAW-WDIIVIDEAHNVaeRGTSSLRSKLAKLLAGRSDTLIML 267
Cdd:cd18013    81 GTERQRSKAANTPADLY---VINRENLKWLVNK---SGDPWpFDMVVIDELSSF--KSPRSKRFKALRKVRPVIKRLIGL 152


                  ....
gi 1447699881 268 SATP 271
Cdd:cd18013   153 TGTP 156
DEXHc_SMARCA4 cd18062
DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent ...
 127-298 2.22e-03

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: 40.80  E-value: 2.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 127 LIADAVGLGKTLEAGILVSELIRRGR-GKRILVLAVKSMLTQFQKEFwSRFAIPLTRLDSAGLQKVRNRIPtnhnPFHYF 205
Cdd:cd18062    46 ILADEMGLGKTIQTIALITYLMEHKRiNGPFLIIVPLSTLSNWVYEF-DKWAPSVVKVSYKGSPAARRAFV----PQLRS 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 206 DKTIISIDTLKQDIEYRHHLENAWWDIIVIDEAHNVAERGTSSLRSKLAKLLAGRSdtlIMLSATPHDGKAESFASLMNM 285
Cdd:cd18062   121 GKFNVLLTTYEYIIKDKQILAKIRWKYMIVDEGHRMKNHHCKLTQVLNTHYVAPRR---LLLTGTPLQNKLPELWALLNF 197

                         170
                  ....*....|...
gi 1447699881 286 LDPTAIANPKEYE 298
Cdd:cd18062   198 LLPTIFKSCSTFE 210
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 109-271 2.42e-03

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


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 39.21  E-value: 2.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 109 PFQLDPTRMALA--QPRQRILIAdAVGLGKTLEAgILVSELIRRgrgKRILVLA-VKSMLTQFQKEFWSRFAIPLTRLDS 185
Cdd:cd17926     3 PYQEEALEAWLAhkNNRRGILVL-PTGSGKTLTA-LALIAYLKE---LRTLIVVpTDALLDQWKERFEDFLGDSSIGLIG 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 186 AGLQKVRNRIPTnhnpfhyfdkTIISIDTLKQDIEYRHHLENAWWDIIViDEAHNVaerGTSSLRSKLAKLLAGRsdtLI 265
Cdd:cd17926    78 GGKKKDFDDANV----------VVATYQSLSNLAEEEKDLFDQFGLLIV-DEAHHL---PAKTFSEILKELNAKY---RL 140


                  ....*.
gi 1447699881 266 MLSATP 271
Cdd:cd17926   141 GLTATP 146
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
425-597 3.33e-03

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 41.25  E-value: 3.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 425 SKYQLLLDTIRKDLAwkaNNTEDRLVIFTESIKTLEFLEQqlradlKLKDDQIATLR--------GDQG--DTVLMETVE 494
Cdd:COG1111   335 PKLSKLREILKEQLG---TNPDSRIIVFTQYRDTAEMIVE------FLSEPGIKAGRfvgqaskeGDKGltQKEQIEILE 405

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 495 AF--GKtqspLRLLVCSDVASEGInlhhlshkmihfDIP-----------WSLMVFQQRNGRIDRYGQKHqpqIRYLLTE 561
Cdd:COG1111   406 RFraGE----FNVLVATSVAEEGL------------DIPevdlvifyepvPSEIRSIQRKGRTGRKREGR---VVVLIAK 466

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1447699881 562 ASEpqingDMRVLEVLINKDEQAQKNIGDSSEFTGK 597
Cdd:COG1111   467 GTR-----DEAYYWSSRRKEKKMKSILKKLKKLLDK 497
DEXQc_SRCAP cd18003
DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or ...
 127-299 6.69e-03

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: 39.26  E-value: 6.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 127 LIADAVGLGKTLEAGILVSELirrGRGKRI----LVLAVKSMLTQFQKEFwSRFAIPLTRLDSAGLQKVRNRIP---TNH 199
Cdd:cd18003    23 ILADEMGLGKTIQTIALLAHL---ACEKGNwgphLIVVPTSVMLNWEMEF-KRWCPGFKILTYYGSAKERKLKRqgwMKP 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 200 NPFHyfdktiISIDTLKQDIEYRHHLENAWWDIIVIDEAHNVaeRGTSSLRSKLakLLAGRSDTLIMLSATPHDGKAESF 279
Cdd:cd18003    99 NSFH------VCITSYQLVVQDHQVFKRKKWKYLILDEAHNI--KNFKSQRWQT--LLNFNTQRRLLLTGTPLQNSLMEL 168

                         170       180
                  ....*....|....*....|
gi 1447699881 280 ASLMNMLDPTAIANPKEYEY 299
Cdd:cd18003   169 WSLMHFLMPHIFQSHQEFKE 188
DEXHc_SMARCA1_SMARCA5 cd17997
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ...
 127-288 9.84e-03

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: 38.46  E-value: 9.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 127 LIADAVGLGKTLEAGILVSEL--IRRGRGKRiLVLAVKSMLTQFQKEFwSRFAIPLTRLDSAGLQKVRNRIPTNHNPFHY 204
Cdd:cd17997    26 ILADEMGLGKTLQTISLLGYLkhYKNINGPH-LIIVPKSTLDNWMREF-KRWCPSLRVVVLIGDKEERADIIRDVLLPGK 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1447699881 205 FDKTIISIDTLkqdIEYRHHLENAWWDIIVIDEAHNVaeRGTSSLRSKLAKLLagRSDTLIMLSATPHDGKAESFASLMN 284
Cdd:cd17997   104 FDVCITSYEMV---IKEKTVLKKFNWRYIIIDEAHRI--KNEKSKLSQIVRLF--NSRNRLLLTGTPLQNNLHELWALLN 176


                  ....
gi 1447699881 285 MLDP 288
Cdd:cd17997   177 FLLP 180
 
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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