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Conserved domains on  [gi|1442252631|gb|RDS22134|]
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ATP-dependent DNA helicase RecG [Escherichia marmotae]

Protein Classification

ATP-dependent DNA helicase RecG( domain architecture ID 11485085)

ATP-dependent DNA helicase RecG protein acts in the processing of stalled replication forks via the creation of a four-way junction

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
1-693 0e+00

ATP-dependent DNA helicase RecG; Provisional


:

Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 1095.97  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631   1 MKGRLLDAVPLSSLTGVGAAQSNKLAKINLHTVQDLLLHLPLRYEDRTHLYPIGELLPGIYATVEGEVLNCNISFGGRRM 80
Cdd:PRK10917    1 PSLLLLLDAPLTSLKGVGPKTAEKLAKLGIHTVQDLLLHLPRRYEDRTRLKPIAELRPGEKVTVEGEVLSAEVVFGKRRR 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  81 MTCQISDGSGILTMRFFNFNAAM-KNSLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDLStPELQETLTPVYPTTEGVK 159
Cdd:PRK10917   81 LTVTVSDGTGNLTLRFFNFNQPYlKKQLKVGKRVAVYGKVKRGKYGLEMVHPEYEVLEEES-PELEGRLTPVYPLTEGLK 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 160 QATLRKLTDQALDLLDtcAIEELLPPELSQ--GMMTLPEALRTLHRPPPTLQLsdletgqHPAQRRLILEELLAHNLSML 237
Cdd:PRK10917  160 QKTLRKLIKQALELLD--ALPELLPEELLEkyGLLSLAEALRAIHFPPSDEDL-------HPARRRLKFEELFALQLSLL 230
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 238 ALRAGAQRFHAQPLSASDALKDKLLVALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHG 317
Cdd:PRK10917  231 LLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAG 310
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 318 KQVALMAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARLAQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIID 397
Cdd:PRK10917  311 YQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIID 390
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 398 EQHRFGVHQRLALWEKGQqqgfHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRNDIIDRVRH 477
Cdd:PRK10917  391 EQHRFGVEQRLALREKGE----NPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIRE 466
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 478 AcITEGRQAYWVCTLIEESELLEAQAAEATWEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGV 557
Cdd:PRK10917  467 E-IAKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGV 545
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 558 DVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTPLSKTAQVRLQVLRDSNDGFVIAQKDLEIRGPGELLG 637
Cdd:PRK10917  546 DVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFVIAEKDLELRGPGELLG 625
                         650       660       670       680       690
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1442252631 638 TRQTGNAEFKVADLLRDQAMIPEVQRLARHIHERYPQQAKALIERWMPETERYSNA 693
Cdd:PRK10917  626 TRQSGLPEFKVADLVRDEELLEEARKDARELLERDPELAEALLERWLGERERYDKA 681
 
Name Accession Description Interval E-value
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
1-693 0e+00

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 1095.97  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631   1 MKGRLLDAVPLSSLTGVGAAQSNKLAKINLHTVQDLLLHLPLRYEDRTHLYPIGELLPGIYATVEGEVLNCNISFGGRRM 80
Cdd:PRK10917    1 PSLLLLLDAPLTSLKGVGPKTAEKLAKLGIHTVQDLLLHLPRRYEDRTRLKPIAELRPGEKVTVEGEVLSAEVVFGKRRR 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  81 MTCQISDGSGILTMRFFNFNAAM-KNSLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDLStPELQETLTPVYPTTEGVK 159
Cdd:PRK10917   81 LTVTVSDGTGNLTLRFFNFNQPYlKKQLKVGKRVAVYGKVKRGKYGLEMVHPEYEVLEEES-PELEGRLTPVYPLTEGLK 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 160 QATLRKLTDQALDLLDtcAIEELLPPELSQ--GMMTLPEALRTLHRPPPTLQLsdletgqHPAQRRLILEELLAHNLSML 237
Cdd:PRK10917  160 QKTLRKLIKQALELLD--ALPELLPEELLEkyGLLSLAEALRAIHFPPSDEDL-------HPARRRLKFEELFALQLSLL 230
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 238 ALRAGAQRFHAQPLSASDALKDKLLVALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHG 317
Cdd:PRK10917  231 LLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAG 310
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 318 KQVALMAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARLAQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIID 397
Cdd:PRK10917  311 YQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIID 390
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 398 EQHRFGVHQRLALWEKGQqqgfHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRNDIIDRVRH 477
Cdd:PRK10917  391 EQHRFGVEQRLALREKGE----NPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIRE 466
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 478 AcITEGRQAYWVCTLIEESELLEAQAAEATWEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGV 557
Cdd:PRK10917  467 E-IAKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGV 545
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 558 DVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTPLSKTAQVRLQVLRDSNDGFVIAQKDLEIRGPGELLG 637
Cdd:PRK10917  546 DVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFVIAEKDLELRGPGELLG 625
                         650       660       670       680       690
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1442252631 638 TRQTGNAEFKVADLLRDQAMIPEVQRLARHIHERYPQQAKALIERWMPETERYSNA 693
Cdd:PRK10917  626 TRQSGLPEFKVADLVRDEELLEEARKDARELLERDPELAEALLERWLGERERYDKA 681
RecG COG1200
RecG-like helicase [Replication, recombination and repair];
10-689 0e+00

RecG-like helicase [Replication, recombination and repair];


Pssm-ID: 440813 [Multi-domain]  Cd Length: 684  Bit Score: 1060.04  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  10 PLSSLTGVGAAQSNKLAKINLHTVQDLLLHLPLRYEDRTHLYPIGELLPGIYATVEGEVLNCNISF--GGRRMMTCQISD 87
Cdd:COG1200     7 PLTYLKGVGPKRAKLLAKLGIRTVGDLLFHLPRRYEDRTRLTPIAELRPGETVTVEGTVVSVEVVRrrRRRRILEVTLSD 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  88 GSGILTMRFFNFnAAMKNSLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDlSTPELQETLTPVYPTTEGVKQATLRKLT 167
Cdd:COG1200    87 GTGSLTLVFFNQ-PYLKKQLKPGTRVLVSGKVERFRGGLQMVHPEYELLDE-EEAELAGRLTPVYPLTEGLSQKTLRKLI 164
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 168 DQALDLLDTcAIEELLPPEL--SQGMMTLPEALRTLHRPPPTLQLsdletgqHPAQRRLILEELLAHNLSMLALRAGAQR 245
Cdd:COG1200   165 RQALDLLAP-DLPEPLPEELraRYGLPSLAEALRNIHFPPSDEDL-------HPARRRLAFEELLALQLALLLRRARRRK 236
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 246 FHAQPLSASDALKDKLLVALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQVALMAP 325
Cdd:COG1200   237 RKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVEAGYQAALMAP 316
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 326 TELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARLAQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVH 405
Cdd:COG1200   317 TEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVVIDEQHRFGVE 396
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 406 QRLALWEKGQqqgfHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRNDIIDRVRHACiTEGRQ 485
Cdd:COG1200   397 QRLALREKGE----APHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVVPEERRDEVYERIREEI-AKGRQ 471
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 486 AYWVCTLIEESELLEAQAAEATWEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLM 565
Cdd:COG1200   472 AYVVCPLIEESEKLDLQAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDVPNATVM 551
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 566 IIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTPLSKTAQVRLQVLRDSNDGFVIAQKDLEIRGPGELLGTRQTGNAE 645
Cdd:COG1200   552 VIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAPLSETARERLEVMRETNDGFEIAEEDLELRGPGEFLGTRQSGLPD 631
                         650       660       670       680
                  ....*....|....*....|....*....|....*....|....*
gi 1442252631 646 FKVADLLRDQAMIPEVQRLARHIHERYPQQAK-ALIERWMPETER 689
Cdd:COG1200   632 LRIADLVRDADLLEAAREDAEELLEEDPELAShPALRRWLGLRFR 676
recG TIGR00643
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
28-665 0e+00

ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273192 [Multi-domain]  Cd Length: 630  Bit Score: 942.54  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  28 INLHTVQDLLLHLPLRYEDRTHLYPIGELLPGIYATVEGEVLN-CNISFGGRRMMTCQISD-GSGILTMRFFNfNAAMKN 105
Cdd:TIGR00643   1 LGIHTVQDLLFYFPRRYEDRTLLQTIGELLPGERATIVGEVLShCIFGFKRRKVLKLRLKDgGYKKLELRFFN-RAFLKK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 106 SLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDLSTPELqeTLTPVYPTTEGVKQATLRKLTDQALDLLDTCaIEELLPP 185
Cdd:TIGR00643  80 KFKVGSKVVVYGKVKSSKFKAYLIHPEFISEKDGVEFEL--KILPVYPLTEGLTQKKLRKLIQQALDQLDKS-LEDPLPE 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 186 ELSQ--GMMTLPEALRTLHrPPPTLQLsdletgQHPAQRRLILEELLAHNLSMLALRAG-AQRFHAQPLSASDALKDKLL 262
Cdd:TIGR00643 157 ELREkyGLLSLEDALRAIH-FPKTLSL------LELARRRLIFDEFFYLQLAMLARRLGeKQQFSAPPANPSEELLTKFL 229
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 263 VALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFE 342
Cdd:TIGR00643 230 ASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLA 309
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 343 PLGIEVGWLAGKQKGKARLAQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEKGQQqGFHPH 422
Cdd:TIGR00643 310 PLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQG-GFTPH 388
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 423 QLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRnDIIDRVRHACITEGRQAYWVCTLIEESELLEAQ 502
Cdd:TIGR00643 389 VLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEK-DIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLK 467
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 503 AAEATWEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLR 582
Cdd:TIGR00643 468 AAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLR 547
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 583 GRVGRGAVASHCVLLYKTPLSKTAQVRLQVLRDSNDGFVIAQKDLEIRGPGELLGTRQTGNAEFKVADLLRDQAMIPEVQ 662
Cdd:TIGR00643 548 GRVGRGDHQSYCLLVYKNPKSESAKKRLRVMADTLDGFVIAEEDLELRGPGDLLGTKQSGYPEFRVADLVRDREILVEAR 627

                  ...
gi 1442252631 663 RLA 665
Cdd:TIGR00643 628 EDA 630
DEXHc_RecG cd17992
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ...
224-452 1.68e-116

DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. It is a member 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: 350750 [Multi-domain]  Cd Length: 225  Bit Score: 348.37  E-value: 1.68e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 224 LILEELLAHNLSMLALRAGAQRFHAQPLSASDALKDKLLVALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKT 303
Cdd:cd17992     1 LAFEELFALQLALLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 304 LVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARLAQQEAIASGQVQMIVGTHAIFQ 383
Cdd:cd17992    81 VVAALAMLAAVENGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQ 160
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1442252631 384 EQVQFNGLALVIIDEQHRFGVHQRLALWEKGQqqgfHPHQLIMTATPIPRTLAMTAYADLDTSVIDELP 452
Cdd:cd17992   161 EDVEFHNLGLVIIDEQHRFGVEQRLKLREKGE----TPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
270-438 2.58e-22

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: 94.23  E-value: 2.58e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 270 TGAQARVVAEI--ERDMaldvpmmrLVQGDVGSGKT---LVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFEPL 344
Cdd:pfam00270   1 TPIQAEAIPAIleGRDV--------LVQAPTGSGKTlafLLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLGKGL 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 345 GIEVGWLAGkqkGKARLAQQEAIASgqVQMIVGTH----AIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEKGQQQGFH 420
Cdd:pfam00270  73 GLKVASLLG---GDSRKEQLEKLKG--PDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPK 147
                         170
                  ....*....|....*....
gi 1442252631 421 PHQLI-MTATPiPRTLAMT 438
Cdd:pfam00270 148 KRQILlLSATL-PRNLEDL 165
DEXDc smart00487
DEAD-like helicases superfamily;
264-456 6.86e-22

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 94.10  E-value: 6.86e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  264 ALPFKPTGAQARVVAEIERDMaldvpMMRLVQGDVGSGKTLVAAL--AALRAIAHGKQVALMAPTELLAEQHANNFRNWF 341
Cdd:smart00487   4 FGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLpaLEALKRGKGGRVLVLVPTRELAEQWAEELKKLG 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  342 EPLGIEVgwlAGKQKGKARLAQQEAIASGQVQMIVGT-----HAIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEK-GQ 415
Cdd:smart00487  79 PSLGLKV---VGLYGGDSKREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKlLK 155
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 1442252631  416 QQGFHPHQLIMTATP---IPRTLAMTAYADLDTSVIDELPPGRT 456
Cdd:smart00487 156 LLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPIE 199
 
Name Accession Description Interval E-value
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
1-693 0e+00

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 1095.97  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631   1 MKGRLLDAVPLSSLTGVGAAQSNKLAKINLHTVQDLLLHLPLRYEDRTHLYPIGELLPGIYATVEGEVLNCNISFGGRRM 80
Cdd:PRK10917    1 PSLLLLLDAPLTSLKGVGPKTAEKLAKLGIHTVQDLLLHLPRRYEDRTRLKPIAELRPGEKVTVEGEVLSAEVVFGKRRR 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  81 MTCQISDGSGILTMRFFNFNAAM-KNSLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDLStPELQETLTPVYPTTEGVK 159
Cdd:PRK10917   81 LTVTVSDGTGNLTLRFFNFNQPYlKKQLKVGKRVAVYGKVKRGKYGLEMVHPEYEVLEEES-PELEGRLTPVYPLTEGLK 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 160 QATLRKLTDQALDLLDtcAIEELLPPELSQ--GMMTLPEALRTLHRPPPTLQLsdletgqHPAQRRLILEELLAHNLSML 237
Cdd:PRK10917  160 QKTLRKLIKQALELLD--ALPELLPEELLEkyGLLSLAEALRAIHFPPSDEDL-------HPARRRLKFEELFALQLSLL 230
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 238 ALRAGAQRFHAQPLSASDALKDKLLVALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHG 317
Cdd:PRK10917  231 LLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAG 310
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 318 KQVALMAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARLAQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIID 397
Cdd:PRK10917  311 YQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIID 390
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 398 EQHRFGVHQRLALWEKGQqqgfHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRNDIIDRVRH 477
Cdd:PRK10917  391 EQHRFGVEQRLALREKGE----NPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIRE 466
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 478 AcITEGRQAYWVCTLIEESELLEAQAAEATWEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGV 557
Cdd:PRK10917  467 E-IAKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGV 545
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 558 DVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTPLSKTAQVRLQVLRDSNDGFVIAQKDLEIRGPGELLG 637
Cdd:PRK10917  546 DVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFVIAEKDLELRGPGELLG 625
                         650       660       670       680       690
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1442252631 638 TRQTGNAEFKVADLLRDQAMIPEVQRLARHIHERYPQQAKALIERWMPETERYSNA 693
Cdd:PRK10917  626 TRQSGLPEFKVADLVRDEELLEEARKDARELLERDPELAEALLERWLGERERYDKA 681
RecG COG1200
RecG-like helicase [Replication, recombination and repair];
10-689 0e+00

RecG-like helicase [Replication, recombination and repair];


Pssm-ID: 440813 [Multi-domain]  Cd Length: 684  Bit Score: 1060.04  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  10 PLSSLTGVGAAQSNKLAKINLHTVQDLLLHLPLRYEDRTHLYPIGELLPGIYATVEGEVLNCNISF--GGRRMMTCQISD 87
Cdd:COG1200     7 PLTYLKGVGPKRAKLLAKLGIRTVGDLLFHLPRRYEDRTRLTPIAELRPGETVTVEGTVVSVEVVRrrRRRRILEVTLSD 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  88 GSGILTMRFFNFnAAMKNSLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDlSTPELQETLTPVYPTTEGVKQATLRKLT 167
Cdd:COG1200    87 GTGSLTLVFFNQ-PYLKKQLKPGTRVLVSGKVERFRGGLQMVHPEYELLDE-EEAELAGRLTPVYPLTEGLSQKTLRKLI 164
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 168 DQALDLLDTcAIEELLPPEL--SQGMMTLPEALRTLHRPPPTLQLsdletgqHPAQRRLILEELLAHNLSMLALRAGAQR 245
Cdd:COG1200   165 RQALDLLAP-DLPEPLPEELraRYGLPSLAEALRNIHFPPSDEDL-------HPARRRLAFEELLALQLALLLRRARRRK 236
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 246 FHAQPLSASDALKDKLLVALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQVALMAP 325
Cdd:COG1200   237 RKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVEAGYQAALMAP 316
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 326 TELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARLAQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVH 405
Cdd:COG1200   317 TEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVVIDEQHRFGVE 396
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 406 QRLALWEKGQqqgfHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRNDIIDRVRHACiTEGRQ 485
Cdd:COG1200   397 QRLALREKGE----APHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVVPEERRDEVYERIREEI-AKGRQ 471
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 486 AYWVCTLIEESELLEAQAAEATWEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLM 565
Cdd:COG1200   472 AYVVCPLIEESEKLDLQAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDVPNATVM 551
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 566 IIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTPLSKTAQVRLQVLRDSNDGFVIAQKDLEIRGPGELLGTRQTGNAE 645
Cdd:COG1200   552 VIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAPLSETARERLEVMRETNDGFEIAEEDLELRGPGEFLGTRQSGLPD 631
                         650       660       670       680
                  ....*....|....*....|....*....|....*....|....*
gi 1442252631 646 FKVADLLRDQAMIPEVQRLARHIHERYPQQAK-ALIERWMPETER 689
Cdd:COG1200   632 LRIADLVRDADLLEAAREDAEELLEEDPELAShPALRRWLGLRFR 676
recG TIGR00643
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
28-665 0e+00

ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273192 [Multi-domain]  Cd Length: 630  Bit Score: 942.54  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  28 INLHTVQDLLLHLPLRYEDRTHLYPIGELLPGIYATVEGEVLN-CNISFGGRRMMTCQISD-GSGILTMRFFNfNAAMKN 105
Cdd:TIGR00643   1 LGIHTVQDLLFYFPRRYEDRTLLQTIGELLPGERATIVGEVLShCIFGFKRRKVLKLRLKDgGYKKLELRFFN-RAFLKK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 106 SLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDLSTPELqeTLTPVYPTTEGVKQATLRKLTDQALDLLDTCaIEELLPP 185
Cdd:TIGR00643  80 KFKVGSKVVVYGKVKSSKFKAYLIHPEFISEKDGVEFEL--KILPVYPLTEGLTQKKLRKLIQQALDQLDKS-LEDPLPE 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 186 ELSQ--GMMTLPEALRTLHrPPPTLQLsdletgQHPAQRRLILEELLAHNLSMLALRAG-AQRFHAQPLSASDALKDKLL 262
Cdd:TIGR00643 157 ELREkyGLLSLEDALRAIH-FPKTLSL------LELARRRLIFDEFFYLQLAMLARRLGeKQQFSAPPANPSEELLTKFL 229
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 263 VALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFE 342
Cdd:TIGR00643 230 ASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLA 309
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 343 PLGIEVGWLAGKQKGKARLAQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEKGQQqGFHPH 422
Cdd:TIGR00643 310 PLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQG-GFTPH 388
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 423 QLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRnDIIDRVRHACITEGRQAYWVCTLIEESELLEAQ 502
Cdd:TIGR00643 389 VLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEK-DIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLK 467
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 503 AAEATWEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLR 582
Cdd:TIGR00643 468 AAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLR 547
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 583 GRVGRGAVASHCVLLYKTPLSKTAQVRLQVLRDSNDGFVIAQKDLEIRGPGELLGTRQTGNAEFKVADLLRDQAMIPEVQ 662
Cdd:TIGR00643 548 GRVGRGDHQSYCLLVYKNPKSESAKKRLRVMADTLDGFVIAEEDLELRGPGDLLGTKQSGYPEFRVADLVRDREILVEAR 627

                  ...
gi 1442252631 663 RLA 665
Cdd:TIGR00643 628 EDA 630
DEXHc_RecG cd17992
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ...
224-452 1.68e-116

DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. It is a member 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: 350750 [Multi-domain]  Cd Length: 225  Bit Score: 348.37  E-value: 1.68e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 224 LILEELLAHNLSMLALRAGAQRFHAQPLSASDALKDKLLVALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKT 303
Cdd:cd17992     1 LAFEELFALQLALLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 304 LVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARLAQQEAIASGQVQMIVGTHAIFQ 383
Cdd:cd17992    81 VVAALAMLAAVENGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQ 160
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1442252631 384 EQVQFNGLALVIIDEQHRFGVHQRLALWEKGQqqgfHPHQLIMTATPIPRTLAMTAYADLDTSVIDELP 452
Cdd:cd17992   161 EDVEFHNLGLVIIDEQHRFGVEQRLKLREKGE----TPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
mfd TIGR00580
transcription-repair coupling factor (mfd); All proteins in this family for which functions ...
226-642 1.87e-103

transcription-repair coupling factor (mfd); All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273152 [Multi-domain]  Cd Length: 926  Bit Score: 336.64  E-value: 1.87e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 226 LEELLAHNLSMLALRAgAQRFHAQPlsASDALKDKLLVALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLV 305
Cdd:TIGR00580 412 VREIAAKLIELYAKRK-AIKGHAFP--PDLEWQQEFEDSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEV 488
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 306 AALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARLAQQEAIASGQVQMIVGTHAIFQEQ 385
Cdd:TIGR00580 489 AMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKD 568
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 386 VQFNGLALVIIDEQHRFGVHQRlalwEKGQQQGFHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPd 465
Cdd:TIGR00580 569 VKFKDLGLLIIDEEQRFGVKQK----EKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRTFVME- 643
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 466 trRNDIIdrVRHACITE---GRQAYWVCTLIEESELLEAQaaeatweeLKLALPELNVGLVHGRMKPAEKQAVMASFKQG 542
Cdd:TIGR00580 644 --YDPEL--VREAIRREllrGGQVFYVHNRIESIEKLATQ--------LRELVPEARIAIAHGQMTENELEEVMLEFYKG 711
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 543 ELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLY--KTPLSKTAQVRLQVLRDSND-- 618
Cdd:TIGR00580 712 EFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYphQKALTEDAQKRLEAIQEFSElg 791
                         410       420
                  ....*....|....*....|....*
gi 1442252631 619 -GFVIAQKDLEIRGPGELLGTRQTG 642
Cdd:TIGR00580 792 aGFKIALHDLEIRGAGNLLGEEQSG 816
Mfd COG1197
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ...
266-643 1.13e-93

Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];


Pssm-ID: 440810 [Multi-domain]  Cd Length: 1130  Bit Score: 313.93  E-value: 1.13e-93
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  266 PFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTlvaalaalraiahGKQVALMAPTELLAEQHANNFRNWFEPLG 345
Cdd:COG1197    584 PYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTevalraafkavmdGKQVAVLVPTTLLAQQHYETFKERFAGFP 663
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  346 IEVGWL-----AGKQKgKARlaqqEAIASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQ--RL-ALWEkgqqq 417
Cdd:COG1197    664 VRVEVLsrfrtAKEQK-ETL----EGLADGKVDIVIGTHRLLSKDVKFKDLGLLIIDEEQRFGVRHkeKLkALRA----- 733
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  418 gfHPHQLIMTATPIPRTLAMtAYADL-DTSVIDELPPGRTPVTTVAIPdtrRNDIIdrVRHACITE---GRQAYWVCTLI 493
Cdd:COG1197    734 --NVDVLTLTATPIPRTLQM-SLSGIrDLSIIATPPEDRLPVKTFVGE---YDDAL--IREAILREllrGGQVFYVHNRV 805
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  494 EEselLEAQAaeatwEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERL 573
Cdd:COG1197    806 ED---IEKVA-----ARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDIPNANTIIIERADRF 877
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1442252631  574 GLAQLHQLRGRVGRGAVASHCVLLYK--TPLSKTAQVRLQVLRDSND---GFVIAQKDLEIRGPGELLGTRQTGN 643
Cdd:COG1197    878 GLAQLYQLRGRVGRSHRRAYAYLLYPpdKVLTEDAEKRLEAIQEFTElgaGFKLAMHDLEIRGAGNLLGEEQSGH 952
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
457-615 9.56e-84

C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase 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: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 261.12  E-value: 9.56e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 457 PVTTVAIPDTRRnDIIDRVRHACITEGRQAYWVCTLIEESELLEAQAAEATWEELKLAL-PELNVGLVHGRMKPAEKQAV 535
Cdd:cd18811     1 PITTYLIFHTRL-DKVYEFVREEIAKGRQAYVIYPLIEESEKLDLKAAVAMYEYLKERFrPELNVGLLHGRLKSDEKDAV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 536 MASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTPLSKTAQVRLQVLRD 615
Cdd:cd18811    80 MAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKDPLTETAKQRLRVMTE 159
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
457-615 6.83e-72

C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. 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: 350179 [Multi-domain]  Cd Length: 160  Bit Score: 230.23  E-value: 6.83e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 457 PVTTVAIPDTRRnDIIDRVRHACITEGRQAYWVCTLIEESELLEAQAAEATWEELKLALPELNVGLVHGRMKPAEKQAVM 536
Cdd:cd18792     1 PIRTYVIPHDDL-DLVYEAIERELARGGQVYYVYPRIEESEKLDLKSIEALAEELKELVPEARVALLHGKMTEDEKEAVM 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 537 ASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTP--LSKTAQVRLQVLR 614
Cdd:cd18792    80 LEFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPkkLTETAKKRLRAIA 159

                  .
gi 1442252631 615 D 615
Cdd:cd18792   160 E 160
PRK10689 PRK10689
transcription-repair coupling factor; Provisional
264-645 3.89e-66

transcription-repair coupling factor; Provisional


Pssm-ID: 182649 [Multi-domain]  Cd Length: 1147  Bit Score: 236.56  E-value: 3.89e-66
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  264 ALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQVALMAPTELLAEQHANNFR----N 339
Cdd:PRK10689   596 SFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRdrfaN 675
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  340 WfePLGIEVgwLAGKQKGKARLAQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRlalwEKGQQQGF 419
Cdd:PRK10689   676 W--PVRIEM--LSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHK----ERIKAMRA 747
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  420 HPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVaipdTRRNDIIdRVRHACITE---GRQAYWVCTLIEES 496
Cdd:PRK10689   748 DVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTF----VREYDSL-VVREAILREilrGGQVYYLYNDVENI 822
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  497 ElleaqAAEATWEELklaLPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERLGLA 576
Cdd:PRK10689   823 Q-----KAAERLAEL---VPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLA 894
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1442252631  577 QLHQLRGRVGRGAVASHCVLLYKTP--LSKTAQVRLQV---LRDSNDGFVIAQKDLEIRGPGELLGTRQTGNAE 645
Cdd:PRK10689   895 QLHQLRGRVGRSHHQAYAWLLTPHPkaMTTDAQKRLEAiasLEDLGAGFALATHDLEIRGAGELLGEEQSGQME 968
DEXHc_TRCF cd17991
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ...
266-449 1.06e-55

DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF 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: 350749 [Multi-domain]  Cd Length: 193  Bit Score: 188.16  E-value: 1.06e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 266 PFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFEPLG 345
Cdd:cd17991    13 PYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFKERFANFP 92
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 346 IEVGWLAGKQKGKARLAQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRlalwEKGQQQGFHPHQLI 425
Cdd:cd17991    93 VNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQK----EKLKELRPNVDVLT 168
                         170       180
                  ....*....|....*....|....*.
gi 1442252631 426 MTATPIPRTL--AMTAYADLdtSVID 449
Cdd:cd17991   169 LSATPIPRTLhmALSGIRDL--SVIA 192
DEXHc_RecG cd17918
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ...
261-449 5.55e-52

DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part 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: 350676 [Multi-domain]  Cd Length: 180  Bit Score: 177.99  E-value: 5.55e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 261 LLVALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNW 340
Cdd:cd17918     8 LCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARKF 87
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 341 FEPLGIEVGWLAGKQKgkarlaqqeaiASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEKGQqqgfh 420
Cdd:cd17918    88 LPFINVELVTGGTKAQ-----------ILSGISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLGA----- 151
                         170       180
                  ....*....|....*....|....*....
gi 1442252631 421 PHQLIMTATPIPRTLAMTAYADLDTSVID 449
Cdd:cd17918   152 THFLEATATPIPRTLALALSGLLDLSVID 180
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
475-613 7.54e-32

C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a DEAD-like helicase 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: 350197 [Multi-domain]  Cd Length: 151  Bit Score: 120.91  E-value: 7.54e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 475 VRHACITE---GRQAYWVCTLIEESELLEAQaaeatweeLKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATT 551
Cdd:cd18810    14 IREAIEREllrGGQVFYVHNRIESIEKLATQ--------LRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDILVCTT 85
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1442252631 552 VIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKT--PLSKTAQVRLQVL 613
Cdd:cd18810    86 IIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYPDqkKLTEDALKRLEAI 149
RecG_wedge_OBF cd04488
RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal ...
63-135 9.39e-23

RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched chain substrates.


Pssm-ID: 239934 [Multi-domain]  Cd Length: 75  Bit Score: 92.26  E-value: 9.39e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1442252631  63 TVEGEVLNCNI-SFGGRRMMTCQISDGSGILTMRFFNFNAAMKNSLATGRRVLAYGEAKRGKYGAEMIHPEYRV 135
Cdd:cd04488     1 TVEGTVVSVEVvPRRGRRRLKVTLSDGTGTLTLVFFNFQPYLKKQLPPGTRVRVSGKVKRFRGGLQIVHPEYEL 74
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
270-438 2.58e-22

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: 94.23  E-value: 2.58e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 270 TGAQARVVAEI--ERDMaldvpmmrLVQGDVGSGKT---LVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFEPL 344
Cdd:pfam00270   1 TPIQAEAIPAIleGRDV--------LVQAPTGSGKTlafLLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLGKGL 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 345 GIEVGWLAGkqkGKARLAQQEAIASgqVQMIVGTH----AIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEKGQQQGFH 420
Cdd:pfam00270  73 GLKVASLLG---GDSRKEQLEKLKG--PDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPK 147
                         170
                  ....*....|....*....
gi 1442252631 421 PHQLI-MTATPiPRTLAMT 438
Cdd:pfam00270 148 KRQILlLSATL-PRNLEDL 165
DEXDc smart00487
DEAD-like helicases superfamily;
264-456 6.86e-22

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 94.10  E-value: 6.86e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  264 ALPFKPTGAQARVVAEIERDMaldvpMMRLVQGDVGSGKTLVAAL--AALRAIAHGKQVALMAPTELLAEQHANNFRNWF 341
Cdd:smart00487   4 FGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLpaLEALKRGKGGRVLVLVPTRELAEQWAEELKKLG 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  342 EPLGIEVgwlAGKQKGKARLAQQEAIASGQVQMIVGT-----HAIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEK-GQ 415
Cdd:smart00487  79 PSLGLKV---VGLYGGDSKREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKlLK 155
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 1442252631  416 QQGFHPHQLIMTATP---IPRTLAMTAYADLDTSVIDELPPGRT 456
Cdd:smart00487 156 LLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPIE 199
RecG_wedge pfam17191
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations.
16-166 1.36e-21

RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations.


Pssm-ID: 407316 [Multi-domain]  Cd Length: 162  Bit Score: 92.12  E-value: 1.36e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  16 GVGAAQSNKLAKINLHTVQDLLLHLPLRYEDRTHLYPIGELLPGIYATVEGEVLNCN-ISFGGRRMMTCQISDGSGILTM 94
Cdd:pfam17191   7 GVGPKREKILKKLGIETIGDLIWYFPRDYEDRRKIIPISDIRHDEKVTTKGKIVNFEtKKIGSLVIISAVLSDGIGQVLL 86
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1442252631  95 RFFNfNAAMKNSLATGRRVLAYGEAKRGKYGA-EMIHPEYRVQGDlsTPELQetLTPVYPTTEGVKQATLRKL 166
Cdd:pfam17191  87 KWFN-QEYIKKFLQKGKEVYITGTVKEGPFGPiEMNNPEIEEITG--EQERE--ILPVYPLTEGISQKNMRKI 154
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
517-587 3.70e-19

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: 83.03  E-value: 3.70e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1442252631 517 ELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERlGLAQLHQLRGRVGR 587
Cdd:pfam00271  38 GIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPW-NPASYIQRIGRAGR 107
HELICc smart00490
helicase superfamily c-terminal domain;
509-587 7.53e-18

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 78.41  E-value: 7.53e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631  509 EELKLALPELN--VGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPeRLGLAQLHQLRGRVG 586
Cdd:smart00490   1 EELAELLKELGikVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL-PWSPASYIQRIGRAG 79

                   .
gi 1442252631  587 R 587
Cdd:smart00490  80 R 80
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
293-598 5.20e-12

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 68.90  E-value: 5.20e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 293 LVQGDVGSGKTLVAALAALRAIaHGKQVALMAPTELLAEQHANNFRNWFeplgievgwlagkqkGKARLAQQEAIASGQV 372
Cdd:COG1061   104 LVVAPTGTGKTVLALALAAELL-RGKRVLVLVPRRELLEQWAEELRRFL---------------GDPLAGGGKKDSDAPI 167
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 373 qmIVGTHAIFQEQVQFNGLA----LVIIDEQHRFG--VHQRLAlwekgqqQGFHPHQLI-MTATPIpRTLAMTAYADLDT 445
Cdd:COG1061   168 --TVATYQSLARRAHLDELGdrfgLVIIDEAHHAGapSYRRIL-------EAFPAAYRLgLTATPF-RSDGREILLFLFD 237
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 446 SVIDELPPGR-------TPVTTVAIPD------------------------TRRNDIIDRVRHACiTEGRQAYWVCTLIE 494
Cdd:COG1061   238 GIVYEYSLKEaiedgylAPPEYYGIRVdltderaeydalserlrealaadaERKDKILRELLREH-PDDRKTLVFCSSVD 316
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 495 EselleaqaAEATWEELKLAlpELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMII----ENP 570
Cdd:COG1061   317 H--------AEALAELLNEA--GIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILlrptGSP 386
                         330       340
                  ....*....|....*....|....*...
gi 1442252631 571 erlglAQLHQLRGRVGRGAVASHCVLLY 598
Cdd:COG1061   387 -----REFIQRLGRGLRPAPGKEDALVY 409
RecG_dom3_C pfam19833
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent ...
616-674 2.86e-10

ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent DNA helicase RecG from bacteria the homolog from Arabidopsis, which has a critical role in recombination and DNA repair. This protein comprises three structural domains, the largest N-terminal Domain 1 which interacts with DNA junctions, and Domains 2 and 3 at the C-terminal which contain the characteriztic motifs that identify RecG as an SF2 helicase. This domain represents the C-terminal of Domain 3. Around 50 residues that extend from its end cross back to Domain 1 forming a hook that wraps around the extended alpha-helix. This interaction provides a link between Domain 1 and 3 and it is likely that these residues are involved in conformational changes associated with domain movements arising from ATP binding and hydrolysis.


Pssm-ID: 437665 [Multi-domain]  Cd Length: 87  Bit Score: 57.10  E-value: 2.86e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 616 SNDGFVIAQKDLEIRGPGELLGTRQTGNA-EFKVADLLRDQAMIPEVQRLARHIHERYPQ 674
Cdd:pfam19833   1 TNDGFEIAEADLKLRGPGDLEGTQQSGIAfDLKIADIARDGQLLQLARTEAEEIIDNDPE 60
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
293-429 5.07e-09

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


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 55.49  E-value: 5.07e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 293 LVQGDVGSGKTLVAALA-ALRAIAHGKQVALMAPTELLAEQHANNFRNWFEPlGIEVGWLAgkqkGKARLAQQEAIASGQ 371
Cdd:cd00046     5 LITAPTGSGKTLAALLAaLLLLLKKGKKVLVLVPTKALALQTAERLRELFGP-GIRVAVLV----GGSSAEEREKNKLGD 79
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1442252631 372 VQMIVGTHAIFQEQVQFNGLA------LVIIDEQHRFGV--HQRLALWEKGQQQGFHPHQLI-MTAT 429
Cdd:cd00046    80 ADIIIATPDMLLNLLLREDRLflkdlkLIIVDEAHALLIdsRGALILDLAVRKAGLKNAQVIlLSAT 146
tRNA_anti-codon pfam01336
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ...
63-135 1.35e-08

OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.


Pssm-ID: 460164 [Multi-domain]  Cd Length: 75  Bit Score: 51.85  E-value: 1.35e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1442252631  63 TVEGEVLNcnISFGGRRMMTCQISDGSGILTMRFFN-FNAAMKNSLATGRRVLAYGEAKRGKYGA-EMIHPEYRV 135
Cdd:pfam01336   2 TVAGRVTS--IRRSGGKLLFLTLRDGTGSIQVVVFKeEAEKLAKKLKEGDVVRVTGKVKKRKGGElELVVEEIEL 74
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
317-439 1.79e-08

DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family 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: 350685 [Multi-domain]  Cd Length: 201  Bit Score: 55.13  E-value: 1.79e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 317 GKQVALMAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARLaqQEAIASGQVqmIVGTHAIFQ------EQVQFNG 390
Cdd:cd17927    50 KGKVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSENVSV--EQIVESSDV--IIVTPQILVndlksgTIVSLSD 125
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1442252631 391 LALVIIDEQHRfgvhqrlalwekgqQQGFHPHQLIMT---------ATPIPRTLAMTA 439
Cdd:cd17927   126 FSLLVFDECHN--------------TTKNHPYNEIMFryldqklgsSGPLPQILGLTA 169
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
543-589 2.34e-08

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: 51.55  E-value: 2.34e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1442252631 543 ELHLLVATTVIEVGVDVPNASLMIIENPERlGLAQLHQLRGRVGRGA 589
Cdd:cd18785    22 SLEILVATNVLGEGIDVPSLDTVIFFDPPS-SAASYIQRVGRAGRGG 67
Cas3_I cd09639
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ...
390-587 4.46e-08

CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I


Pssm-ID: 187770 [Multi-domain]  Cd Length: 353  Bit Score: 55.51  E-value: 4.46e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 390 GLALVIIDEQHRFGVHQR---LALWEKGQQQGFhPHqLIMTATpIPRTLaMTAYADLDTsVIDELPPGRTPVTTVAIPdT 466
Cdd:cd09639   123 ANSLLIFDEVHFYDEYTLaliLAVLEVLKDNDV-PI-LLMSAT-LPKFL-KEYAEKIGY-VEENEPLDLKPNERAPFI-K 196
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 467 RRND------IIDRVRHACITEGRQAYwVCTLIEEselleaqaAEATWEELKLALPELNVGLVHGRMKP---AEKQA-VM 536
Cdd:cd09639   197 IESDkvgeisSLERLLEFIKKGGSVAI-IVNTVDR--------AQEFYQQLKEKGPEEEIMLIHSRFTEkdrAKKEAeLL 267
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1442252631 537 ASFKQGELHLLVATTVIEVGVDVpNASLMIIEnperlgLAQLHQLRGRVGR 587
Cdd:cd09639   268 LEFKKSEKFVIVATQVIEASLDI-SVDVMITE------LAPIDSLIQRLGR 311
DEXHc_priA cd17929
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ...
293-400 1.03e-07

DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA 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: 350687 [Multi-domain]  Cd Length: 178  Bit Score: 52.21  E-value: 1.03e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 293 LVQGDVGSGKTLVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFeplGIEVGWLAGKQKGKARLAQQEAIASGQV 372
Cdd:cd17929    19 LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRF---GDKVAVLHSKLSDKERADEWRKIKRGEA 95
                          90       100
                  ....*....|....*....|....*....
gi 1442252631 373 QMIVGTH-AIFqeqVQFNGLALVIIDEQH 400
Cdd:cd17929    96 KVVIGARsALF---APFKNLGLIIVDEEH 121
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
424-559 3.92e-07

CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 440816 [Multi-domain]  Cd Length: 535  Bit Score: 53.16  E-value: 3.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 424 LIMTAT-PIPRTLAMTAYADL-------DTSVIDELPPGRTPVTTVAIPDtrrNDIIDRVRhACITEGRQAYWVCTLIee 495
Cdd:COG1203   303 ILMTATlPPLLREELLEAYELipdepeeLPEYFRAFVRKRVELKEGPLSD---EELAELIL-EALHKGKSVLVIVNTV-- 376
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1442252631 496 selleaQAAEATWEELKLALPELNVGLVHGRMKPAEKQA----VMASFKQGELHLLVATTVIEVGVDV 559
Cdd:COG1203   377 ------KDAQELYEALKEKLPDEEVYLLHSRFCPADRSEiekeIKERLERGKPCILVSTQVVEAGVDI 438
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
509-597 1.20e-06

C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains 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: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 48.36  E-value: 1.20e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 509 EELKLALPELNVGLVHGR----------MKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERlGLAQL 578
Cdd:cd18802    46 KEHPSTLAFIRCGFLIGRgnssqrkrslMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPK-TLRSY 124
                          90
                  ....*....|....*....
gi 1442252631 579 HQLRGRvGRgAVASHCVLL 597
Cdd:cd18802   125 IQSRGR-AR-APNSKYILM 141
cas3_core TIGR01587
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ...
390-587 1.42e-06

CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.


Pssm-ID: 273707 [Multi-domain]  Cd Length: 359  Bit Score: 50.92  E-value: 1.42e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 390 GLALVIIDEQHRFGVHQR---LALWEKGQQQGFhPHqLIMTATpIPRTLaMTAYADLDTSVIDELPPGRTPVTTVAIPDT 466
Cdd:TIGR01587 124 ANSLLIFDEVHFYDEYTLaliLAVLEVLKDNDV-PI-LLMSAT-LPKFL-KEYAEKIGYVEFNEPLDLKEERRFENHRFI 199
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 467 RRND-------IIDRVRHACITEGRQAYwVCTLIEEselleaqaAEATWEELKLALPELNVGLVHGRMKP---AEKQA-V 535
Cdd:TIGR01587 200 LIESdkvgeisSLERLLEFIKKGGSIAI-IVNTVDR--------AQEFYQQLKEKAPEEEIILYHSRFTEkdrAKKEAeL 270
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1442252631 536 MASF-KQGELHLLVATTVIEVGVDVpNASLMIIEnperlgLAQLHQLRGRVGR 587
Cdd:TIGR01587 271 LREMkKSNEKFVIVATQVIEASLDI-SADVMITE------LAPIDSLIQRLGR 316
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
509-566 4.36e-06

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: 46.35  E-value: 4.36e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 509 EELKLALPELN--VGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMI 566
Cdd:cd18787    41 DRLAELLEELGikVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHVI 100
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
316-430 4.65e-06

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 50.11  E-value: 4.65e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 316 HGKQVALMAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARlaqQEAIASGQVqmIVGThaifqEQVQFNGL---- 391
Cdd:COG1111    45 KGGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGEVSPEKR---KELWEKARI--IVAT-----PQVIENDLiagr 114
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1442252631 392 ------ALVIIDEQHR-FGVHQRLALWEKGQQQGFHPHQLIMTATP 430
Cdd:COG1111   115 idlddvSLLIFDEAHRaVGNYAYVYIAERYHEDAKDPLILGMTASP 160
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
317-430 1.28e-05

DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef 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: 350793 [Multi-domain]  Cd Length: 181  Bit Score: 46.35  E-value: 1.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 317 GKQVALMAPTELLAEQHANNFRNWFEpLGIEVGWLAGKQKGKARlaqQEAIASGQVqmIVGT-----HAIFQEQVQFNGL 391
Cdd:cd18035    45 GGKVLILAPSRPLVEQHAENLKRVLN-IPDKITSLTGEVKPEER---AERWDASKI--IVATpqvieNDLLAGRITLDDV 118
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1442252631 392 ALVIIDEQHR-FGVHQRLALWEKGQQQGFHPHQLIMTATP 430
Cdd:cd18035   119 SLLIFDEAHHaVGNYAYVYIAHRYKREANNPLILGLTASP 158
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
299-412 2.60e-05

DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350679 [Multi-domain]  Cd Length: 181  Bit Score: 45.33  E-value: 2.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 299 GSGKTLVAALAALRAIAHGKQVAL-MAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARLAQQEAIasgqvqmIVG 377
Cdd:cd17921    27 SSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNVGLLTGDPSVNKLLLAEADI-------LVA 99
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1442252631 378 THAIFQ------EQVQFNGLALVIIDEQHRFGVHQRLALWE 412
Cdd:cd17921   100 TPEKLDlllrngGERLIQDVRLVVVDEAHLIGDGERGVVLE 140
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
502-587 6.69e-05

C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family helicases 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: 350183 [Multi-domain]  Cd Length: 150  Bit Score: 43.41  E-value: 6.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 502 QAAEATWEELKLALPE----LNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMI-IENPerLGLA 576
Cdd:cd18796    49 SQAERLAQRLRELCPDrvppDFIALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDVDLVIqIGSP--KSVA 126
                          90
                  ....*....|.
gi 1442252631 577 QLHQLRGRVGR 587
Cdd:cd18796   127 RLLQRLGRSGH 137
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
520-587 2.13e-04

C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. This family includes spliceosomal Brr2 RNA helicase, ASCC3 (involved in the repair of N-alkylated nucleotides), Mtr4 (involved in processing of structured RNAs), DDX60 (involved in viral RNA degradation), and other proteins. Ski2-like RNA helicases 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: 350182 [Multi-domain]  Cd Length: 154  Bit Score: 42.15  E-value: 2.13e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1442252631 520 VGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPnASLMIIENPER--------LGLAQLHQLRGRVGR 587
Cdd:cd18795    66 IAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLP-ARTVIIKGTQRydgkgyreLSPLEYLQMIGRAGR 140
PRK05580 PRK05580
primosome assembly protein PriA; Validated
223-430 2.39e-04

primosome assembly protein PriA; Validated


Pssm-ID: 235514 [Multi-domain]  Cd Length: 679  Bit Score: 44.38  E-value: 2.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 223 RLILEELLAHNLSMLALRA----GAQRFHAQPLSASDALKDKLLVALPFkpTGAQARVVAEIERDMALDVPmmrLVQGDV 298
Cdd:PRK05580   97 RLALLAELALAASSAVLKGlvkkGLIELEEVEVLRLRPPPDPAFEPPTL--NPEQAAAVEAIRAAAGFSPF---LLDGVT 171
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 299 GSGKTLVAALAALRAIAHGKQVALMAPtEL-LAEQHANNFRNWFeplGIEVG-W---LAGKQKGKARLAqqeaIASGQVQ 373
Cdd:PRK05580  172 GSGKTEVYLQAIAEVLAQGKQALVLVP-EIaLTPQMLARFRARF---GAPVAvLhsgLSDGERLDEWRK----AKRGEAK 243
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 374 MIVGTH-AIFqeqVQFNGLALVIIDEQH----------RFgvHQR-LALWeKGQQQGFhphQLIM-TATP 430
Cdd:PRK05580  244 VVIGARsALF---LPFKNLGLIIVDEEHdssykqqegpRY--HARdLAVV-RAKLENI---PVVLgSATP 304
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
527-588 2.47e-04

C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef 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: 350188 [Multi-domain]  Cd Length: 143  Bit Score: 41.96  E-value: 2.47e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1442252631 527 MKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLhQLRGRVGRG 588
Cdd:cd18801    74 MSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMI-QRMGRTGRK 134
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
297-439 3.38e-04

DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer 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: 350792 [Multi-domain]  Cd Length: 200  Bit Score: 42.25  E-value: 3.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 297 DVGSGKTL-------VAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWfepLGIEVGWLAGKQ--KGKARLAQQEAI 367
Cdd:cd18034    24 PTGSGKTLiavmlikEMGELNRKEKNPKKRAVFLVPTVPLVAQQAEAIRSH---TDLKVGEYSGEMgvDKWTKERWKEEL 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 368 ASGQVqmIVGTHAIF-----QEQVQFNGLALVIIDEQHrfgvHQRlalwekgqqqGFHPHQLIM-------TATPIPRTL 435
Cdd:cd18034   101 EKYDV--LVMTAQILldalrHGFLSLSDINLLIFDECH----HAT----------GDHPYARIMkefyhleGRTSRPRIL 164

                  ....
gi 1442252631 436 AMTA 439
Cdd:cd18034   165 GLTA 168
PriA COG1198
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ...
183-400 4.26e-04

Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];


Pssm-ID: 440811 [Multi-domain]  Cd Length: 728  Bit Score: 43.57  E-value: 4.26e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 183 LPPELSQGMMTLPEALRTLhrpppTLQLSDLETGQHPAQRRLiLEELLAHN----LSMLALRAGAQRfhaqplSASDALK 258
Cdd:COG1198   100 LPAGLRQGYPARIKTERYV-----RLTLGEELPKRAPKQRRV-LEALREHGgpltLSELAKEAGVSR------SVLKALV 167
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 259 DKLLVAL------------------PFKPTGAQARVVAEIERDMALDVPMmrLVQGDVGSGKTLVAALAALRAIAHGKQV 320
Cdd:COG1198   168 KKGLLEIeerevdrdpfapdvpaepPPTLNEEQQAAVEAIRAAAGGFSVF--LLHGVTGSGKTEVYLQAIAEVLAQGKQA 245
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 321 ALMAPtEL-LAEQHANNFRNWFeplGIEVGWLAGKQKGKARLAQQEAIASGQVQMIVGTH-AIFqeqVQFNGLALVIIDE 398
Cdd:COG1198   246 LVLVP-EIaLTPQTVERFRARF---GARVAVLHSGLSDGERLDEWRRARRGEARIVIGTRsALF---APFPNLGLIIVDE 318

                  ..
gi 1442252631 399 QH 400
Cdd:COG1198   319 EH 320
PLN03137 PLN03137
ATP-dependent DNA helicase; Q4-like; Provisional
524-598 1.58e-03

ATP-dependent DNA helicase; Q4-like; Provisional


Pssm-ID: 215597 [Multi-domain]  Cd Length: 1195  Bit Score: 41.81  E-value: 1.58e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1442252631  524 HGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERlGLAQLHQLRGRVGRGAVASHCVLLY 598
Cdd:PLN03137   711 HGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPK-SIEGYHQECGRAGRDGQRSSCVLYY 784
ResIII pfam04851
Type III restriction enzyme, res subunit;
299-431 3.03e-03

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 38.81  E-value: 3.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 299 GSGKTL--VAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKgkarlaqqeAIASGQVQMIV 376
Cdd:pfam04851  33 GSGKTLtaAKLIARLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPNYVEIGEIISGDKK---------DESVDDNKIVV 103
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1442252631 377 GT-HAIF------QEQVQFNGLALVIIDEQHRFG--VHQRLALWEKgqqqgfHPHQLIMTATPI 431
Cdd:pfam04851 104 TTiQSLYkalelaSLELLPDFFDVIIIDEAHRSGasSYRNILEYFK------PAFLLGLTATPE 161
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
518-566 5.40e-03

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 39.75  E-value: 5.40e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1442252631 518 LNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMI 566
Cdd:COG0513   266 ISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHVI 314
PRK00254 PRK00254
ski2-like helicase; Provisional
317-587 6.85e-03

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 39.80  E-value: 6.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 317 GKQVALMaPTELLAEQHANNFRNWfEPLGIEVGWLAGKQKGKARLAqqeaiasGQVQMIVGTHAIFQEQVQ-----FNGL 391
Cdd:PRK00254   69 GKAVYLV-PLKALAEEKYREFKDW-EKLGLRVAMTTGDYDSTDEWL-------GKYDIIIATAEKFDSLLRhgsswIKDV 139
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 392 ALVIIDEQHRFGVHQRLALWEKGQQQGFHPHQLIMTATPI--PRTLAMTAYADL-------------------------- 443
Cdd:PRK00254  140 KLVVADEIHLIGSYDRGATLEMILTHMLGRAQILGLSATVgnAEELAEWLNAELvvsdwrpvklrkgvfyqgflfwedgk 219
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 444 --------DTSVIDELPPGRTPVTTVaipDTRRndiidRVRHACITEGRQAYWVCTLIEESELLE-AQAAEA--TWEELK 512
Cdd:PRK00254  220 ierfpnswESLVYDAVKKGKGALVFV---NTRR-----SAEKEALELAKKIKRFLTKPELRALKElADSLEEnpTNEKLK 291
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 513 LALPElNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPnASLMIIENP--------ERLGLAQLHQLRGR 584
Cdd:PRK00254  292 KALRG-GVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLP-AFRVIIRDTkrysnfgwEDIPVLEIQQMMGR 369

                  ...
gi 1442252631 585 VGR 587
Cdd:PRK00254  370 AGR 372
PRK13766 PRK13766
Hef nuclease; Provisional
527-599 7.50e-03

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 39.47  E-value: 7.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 527 MKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENP--------ERlglaqlhqlRGRVGRGAVASHCVLLY 598
Cdd:PRK13766  407 MSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPvpseirsiQR---------KGRTGRQEEGRVVVLIA 477

                  .
gi 1442252631 599 K 599
Cdd:PRK13766  478 K 478
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
517-567 8.29e-03

C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase 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: 350176 [Multi-domain]  Cd Length: 153  Bit Score: 37.61  E-value: 8.29e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1442252631 517 ELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMII 567
Cdd:cd18789    68 RLLKPFITGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANVAIQ 118
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
529-597 8.62e-03

C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases 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: 350184 [Multi-domain]  Cd Length: 146  Bit Score: 37.24  E-value: 8.62e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1442252631 529 PAEKQAVMASFKQGELHLLVATTVIEVGVDVpnASL---MIIENPErlGLAQLHQLRGRVGRGAVASHCVLL 597
Cdd:cd18797    78 AEDRREIEAELFNGELLGVVATNALELGIDI--GGLdavVLAGYPG--SLASLWQQAGRAGRRGKDSLVILV 145
PRK13766 PRK13766
Hef nuclease; Provisional
316-430 9.69e-03

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 39.09  E-value: 9.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442252631 316 HGKQVALMAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARlaqQEAIASGQVqmIVGThaifqEQVQFNGL---- 391
Cdd:PRK13766   57 KGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTGEVSPEKR---AELWEKAKV--IVAT-----PQVIENDLiagr 126
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1442252631 392 ------ALVIIDEQHR-FGVHQRLALWEKGQQQGFHPHQLIMTATP 430
Cdd:PRK13766  127 isledvSLLIFDEAHRaVGNYAYVYIAERYHEDAKNPLVLGLTASP 172
 
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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