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Conserved domains on  [gi|446601133|ref|WP_000678479|]
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ATP-dependent DNA helicase RecG [Escherichia coli]

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: 1093.65  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133   1 MKGRLLDTVPLSSLTGVGAALSNKLAKINLHTVQDLLLHLPLRYEDRTHLYPIGELLPGVYATVEGEVLNCNISFGGRRM 80
Cdd:PRK10917   1 PSLLLLLDAPLTSLKGVGPKTAEKLAKLGIHTVQDLLLHLPRRYEDRTRLKPIAELRPGEKVTVEGEVLSAEVVFGKRRR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  81 MTCQISDGSGILTMRFFNFSAAM-KNSLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDLStPELQETLTPVYPTTEGVK 159
Cdd:PRK10917  81 LTVTVSDGTGNLTLRFFNFNQPYlKKQLKVGKRVAVYGKVKRGKYGLEMVHPEYEVLEEES-PELEGRLTPVYPLTEGLK 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 160 QATLRKLTDQALDLLDtcAIEELLPPELSQ--GMMTLPEALRTLHRPPPTLQLsdletgqHPAQRRLILEELLAHNLSML 237
Cdd:PRK10917 160 QKTLRKLIKQALELLD--ALPELLPEELLEkyGLLSLAEALRAIHFPPSDEDL-------HPARRRLKFEELFALQLSLL 230
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 238 ALRAGAQRFHAQPLSANDTLKNKLLAALPFKPTGAQARVVAEIEHDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHG 317
Cdd:PRK10917 231 LLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAG 310
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 318 KQVALMAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIID 397
Cdd:PRK10917 311 YQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIID 390
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 398 EQHRFGVHQRLALWEKGQqqgfHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRTDIIDRVRH 477
Cdd:PRK10917 391 EQHRFGVEQRLALREKGE----NPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIRE 466
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 478 AcITEGRQAYWVCTLIEESELLEAQAAEATWEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGV 557
Cdd:PRK10917 467 E-IAKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGV 545
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 558 DVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTPLSKTAQIRLQVLRDSNDGFVIAQKDLEIRGPGELLG 637
Cdd:PRK10917 546 DVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFVIAEKDLELRGPGELLG 625
                        650       660       670       680       690
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446601133 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: 1093.65  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133   1 MKGRLLDTVPLSSLTGVGAALSNKLAKINLHTVQDLLLHLPLRYEDRTHLYPIGELLPGVYATVEGEVLNCNISFGGRRM 80
Cdd:PRK10917   1 PSLLLLLDAPLTSLKGVGPKTAEKLAKLGIHTVQDLLLHLPRRYEDRTRLKPIAELRPGEKVTVEGEVLSAEVVFGKRRR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  81 MTCQISDGSGILTMRFFNFSAAM-KNSLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDLStPELQETLTPVYPTTEGVK 159
Cdd:PRK10917  81 LTVTVSDGTGNLTLRFFNFNQPYlKKQLKVGKRVAVYGKVKRGKYGLEMVHPEYEVLEEES-PELEGRLTPVYPLTEGLK 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 160 QATLRKLTDQALDLLDtcAIEELLPPELSQ--GMMTLPEALRTLHRPPPTLQLsdletgqHPAQRRLILEELLAHNLSML 237
Cdd:PRK10917 160 QKTLRKLIKQALELLD--ALPELLPEELLEkyGLLSLAEALRAIHFPPSDEDL-------HPARRRLKFEELFALQLSLL 230
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 238 ALRAGAQRFHAQPLSANDTLKNKLLAALPFKPTGAQARVVAEIEHDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHG 317
Cdd:PRK10917 231 LLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAG 310
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 318 KQVALMAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIID 397
Cdd:PRK10917 311 YQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIID 390
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 398 EQHRFGVHQRLALWEKGQqqgfHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRTDIIDRVRH 477
Cdd:PRK10917 391 EQHRFGVEQRLALREKGE----NPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIRE 466
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 478 AcITEGRQAYWVCTLIEESELLEAQAAEATWEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGV 557
Cdd:PRK10917 467 E-IAKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGV 545
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 558 DVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTPLSKTAQIRLQVLRDSNDGFVIAQKDLEIRGPGELLG 637
Cdd:PRK10917 546 DVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFVIAEKDLELRGPGELLG 625
                        650       660       670       680       690
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446601133 638 TRQTGNAEFKVADLLRDQAMIPEVQRLARHIHERYPQQAKALIERWMPETERYSNA 693
Cdd:PRK10917 626 TRQSGLPEFKVADLVRDEELLEEARKDARELLERDPELAEALLERWLGERERYDKA 681
RecG COG1200
RecG-like helicase [Replication, recombination and repair];
5-689 0e+00

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


Pssm-ID: 440813 [Multi-domain]  Cd Length: 684  Bit Score: 1063.51  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133   5 LLDTvPLSSLTGVGAALSNKLAKINLHTVQDLLLHLPLRYEDRTHLYPIGELLPGVYATVEGEVLNCNISF--GGRRMMT 82
Cdd:COG1200    3 PLDT-PLTYLKGVGPKRAKLLAKLGIRTVGDLLFHLPRRYEDRTRLTPIAELRPGETVTVEGTVVSVEVVRrrRRRRILE 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  83 CQISDGSGILTMRFFNFsAAMKNSLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDlSTPELQETLTPVYPTTEGVKQAT 162
Cdd:COG1200   82 VTLSDGTGSLTLVFFNQ-PYLKKQLKPGTRVLVSGKVERFRGGLQMVHPEYELLDE-EEAELAGRLTPVYPLTEGLSQKT 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 163 LRKLTDQALDLLDTcAIEELLPPEL--SQGMMTLPEALRTLHRPPPTLQLsdletgqHPAQRRLILEELLAHNLSMLALR 240
Cdd:COG1200  160 LRKLIRQALDLLAP-DLPEPLPEELraRYGLPSLAEALRNIHFPPSDEDL-------HPARRRLAFEELLALQLALLLRR 231
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 241 AGAQRFHAQPLSANDTLKNKLLAALPFKPTGAQARVVAEIEHDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQV 320
Cdd:COG1200  232 ARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVEAGYQA 311
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 321 ALMAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQH 400
Cdd:COG1200  312 ALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVVIDEQH 391
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 401 RFGVHQRLALWEKGQqqgfHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRTDIIDRVRHACi 480
Cdd:COG1200  392 RFGVEQRLALREKGE----APHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVVPEERRDEVYERIREEI- 466
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 481 TEGRQAYWVCTLIEESELLEAQAAEATWEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVP 560
Cdd:COG1200  467 AKGRQAYVVCPLIEESEKLDLQAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDVP 546
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 561 NASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTPLSKTAQIRLQVLRDSNDGFVIAQKDLEIRGPGELLGTRQ 640
Cdd:COG1200  547 NATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAPLSETARERLEVMRETNDGFEIAEEDLELRGPGEFLGTRQ 626
                        650       660       670       680       690
                 ....*....|....*....|....*....|....*....|....*....|
gi 446601133 641 TGNAEFKVADLLRDQAMIPEVQRLARHIHERYPQQAK-ALIERWMPETER 689
Cdd:COG1200  627 SGLPDLRIADLVRDADLLEAAREDAEELLEEDPELAShPALRRWLGLRFR 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: 949.86  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133   28 INLHTVQDLLLHLPLRYEDRTHLYPIGELLPGVYATVEGEVLN-CNISFGGRRMMTCQISD-GSGILTMRFFNfSAAMKN 105
Cdd:TIGR00643   1 LGIHTVQDLLFYFPRRYEDRTLLQTIGELLPGERATIVGEVLShCIFGFKRRKVLKLRLKDgGYKKLELRFFN-RAFLKK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  106 SLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDLSTPELqeTLTPVYPTTEGVKQATLRKLTDQALDLLDTCaIEELLPP 185
Cdd:TIGR00643  80 KFKVGSKVVVYGKVKSSKFKAYLIHPEFISEKDGVEFEL--KILPVYPLTEGLTQKKLRKLIQQALDQLDKS-LEDPLPE 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  186 ELSQ--GMMTLPEALRTLHrPPPTLQLsdletgQHPAQRRLILEELLAHNLSMLALRAG-AQRFHAQPLSANDTLKNKLL 262
Cdd:TIGR00643 157 ELREkyGLLSLEDALRAIH-FPKTLSL------LELARRRLIFDEFFYLQLAMLARRLGeKQQFSAPPANPSEELLTKFL 229
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  263 AALPFKPTGAQARVVAEIEHDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFA 342
Cdd:TIGR00643 230 ASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLA 309
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  343 PLGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEKGQQqGFHPH 422
Cdd:TIGR00643 310 PLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQG-GFTPH 388
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  423 QLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRtDIIDRVRHACITEGRQAYWVCTLIEESELLEAQ 502
Cdd:TIGR00643 389 VLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEK-DIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLK 467
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  503 AAEATWEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLR 582
Cdd:TIGR00643 468 AAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLR 547
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  583 GRVGRGAVASHCVLLYKTPLSKTAQIRLQVLRDSNDGFVIAQKDLEIRGPGELLGTRQTGNAEFKVADLLRDQAMIPEVQ 662
Cdd:TIGR00643 548 GRVGRGDHQSYCLLVYKNPKSESAKKRLRVMADTLDGFVIAEEDLELRGPGDLLGTKQSGYPEFRVADLVRDREILVEAR 627

                  ...
gi 446601133  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 4.58e-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: 347.21  E-value: 4.58e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 224 LILEELLAHNLSMLALRAGAQRFHAQPLSANDTLKNKLLAALPFKPTGAQARVVAEIEHDMALDVPMMRLVQGDVGSGKT 303
Cdd:cd17992    1 LAFEELFALQLALLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKT 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 304 LVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQ 383
Cdd:cd17992   81 VVAALAMLAAVENGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQ 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446601133 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 4.61e-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: 93.46  E-value: 4.61e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  270 TGAQARVVAEIEHDMalDVpmmrLVQGDVGSGKT---LVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFAPLGI 346
Cdd:pfam00270   1 TPIQAEAIPAILEGR--DV----LVQAPTGSGKTlafLLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLGKGLGL 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  347 EVGWLAGkqkGKARLSQQEAIASgqVQMIVGTH----AIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEKGQQQGFHPH 422
Cdd:pfam00270  75 KVASLLG---GDSRKEQLEKLKG--PDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPKKR 149
                         170
                  ....*....|....*..
gi 446601133  423 QLI-MTATPiPRTLAMT 438
Cdd:pfam00270 150 QILlLSATL-PRNLEDL 165
DEXDc smart00487
DEAD-like helicases superfamily;
261-456 1.24e-21

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 93.33  E-value: 1.24e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133   261 LLAALPFKPTGAQARVVAEIEHDMaldvpMMRLVQGDVGSGKTLVAAL--AALRAIAHGKQVALMAPTELLAEQHANNFR 338
Cdd:smart00487   1 IEKFGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLpaLEALKRGKGGRVLVLVPTRELAEQWAEELK 75
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133   339 NWFAPLGIEVgwlAGKQKGKARLSQQEAIASGQVQMIVGT-----HAIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEK 413
Cdd:smart00487  76 KLGPSLGLKV---VGLYGGDSKREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEK 152
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 446601133   414 -GQQQGFHPHQLIMTATP---IPRTLAMTAYADLDTSVIDELPPGRT 456
Cdd:smart00487 153 lLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPIE 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: 1093.65  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133   1 MKGRLLDTVPLSSLTGVGAALSNKLAKINLHTVQDLLLHLPLRYEDRTHLYPIGELLPGVYATVEGEVLNCNISFGGRRM 80
Cdd:PRK10917   1 PSLLLLLDAPLTSLKGVGPKTAEKLAKLGIHTVQDLLLHLPRRYEDRTRLKPIAELRPGEKVTVEGEVLSAEVVFGKRRR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  81 MTCQISDGSGILTMRFFNFSAAM-KNSLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDLStPELQETLTPVYPTTEGVK 159
Cdd:PRK10917  81 LTVTVSDGTGNLTLRFFNFNQPYlKKQLKVGKRVAVYGKVKRGKYGLEMVHPEYEVLEEES-PELEGRLTPVYPLTEGLK 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 160 QATLRKLTDQALDLLDtcAIEELLPPELSQ--GMMTLPEALRTLHRPPPTLQLsdletgqHPAQRRLILEELLAHNLSML 237
Cdd:PRK10917 160 QKTLRKLIKQALELLD--ALPELLPEELLEkyGLLSLAEALRAIHFPPSDEDL-------HPARRRLKFEELFALQLSLL 230
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 238 ALRAGAQRFHAQPLSANDTLKNKLLAALPFKPTGAQARVVAEIEHDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHG 317
Cdd:PRK10917 231 LLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAG 310
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 318 KQVALMAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIID 397
Cdd:PRK10917 311 YQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIID 390
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 398 EQHRFGVHQRLALWEKGQqqgfHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRTDIIDRVRH 477
Cdd:PRK10917 391 EQHRFGVEQRLALREKGE----NPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIRE 466
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 478 AcITEGRQAYWVCTLIEESELLEAQAAEATWEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGV 557
Cdd:PRK10917 467 E-IAKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGV 545
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 558 DVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTPLSKTAQIRLQVLRDSNDGFVIAQKDLEIRGPGELLG 637
Cdd:PRK10917 546 DVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFVIAEKDLELRGPGELLG 625
                        650       660       670       680       690
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446601133 638 TRQTGNAEFKVADLLRDQAMIPEVQRLARHIHERYPQQAKALIERWMPETERYSNA 693
Cdd:PRK10917 626 TRQSGLPEFKVADLVRDEELLEEARKDARELLERDPELAEALLERWLGERERYDKA 681
RecG COG1200
RecG-like helicase [Replication, recombination and repair];
5-689 0e+00

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


Pssm-ID: 440813 [Multi-domain]  Cd Length: 684  Bit Score: 1063.51  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133   5 LLDTvPLSSLTGVGAALSNKLAKINLHTVQDLLLHLPLRYEDRTHLYPIGELLPGVYATVEGEVLNCNISF--GGRRMMT 82
Cdd:COG1200    3 PLDT-PLTYLKGVGPKRAKLLAKLGIRTVGDLLFHLPRRYEDRTRLTPIAELRPGETVTVEGTVVSVEVVRrrRRRRILE 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  83 CQISDGSGILTMRFFNFsAAMKNSLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDlSTPELQETLTPVYPTTEGVKQAT 162
Cdd:COG1200   82 VTLSDGTGSLTLVFFNQ-PYLKKQLKPGTRVLVSGKVERFRGGLQMVHPEYELLDE-EEAELAGRLTPVYPLTEGLSQKT 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 163 LRKLTDQALDLLDTcAIEELLPPEL--SQGMMTLPEALRTLHRPPPTLQLsdletgqHPAQRRLILEELLAHNLSMLALR 240
Cdd:COG1200  160 LRKLIRQALDLLAP-DLPEPLPEELraRYGLPSLAEALRNIHFPPSDEDL-------HPARRRLAFEELLALQLALLLRR 231
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 241 AGAQRFHAQPLSANDTLKNKLLAALPFKPTGAQARVVAEIEHDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQV 320
Cdd:COG1200  232 ARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVEAGYQA 311
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 321 ALMAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQH 400
Cdd:COG1200  312 ALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVVIDEQH 391
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 401 RFGVHQRLALWEKGQqqgfHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRTDIIDRVRHACi 480
Cdd:COG1200  392 RFGVEQRLALREKGE----APHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVVPEERRDEVYERIREEI- 466
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 481 TEGRQAYWVCTLIEESELLEAQAAEATWEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVP 560
Cdd:COG1200  467 AKGRQAYVVCPLIEESEKLDLQAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDVP 546
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 561 NASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTPLSKTAQIRLQVLRDSNDGFVIAQKDLEIRGPGELLGTRQ 640
Cdd:COG1200  547 NATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAPLSETARERLEVMRETNDGFEIAEEDLELRGPGEFLGTRQ 626
                        650       660       670       680       690
                 ....*....|....*....|....*....|....*....|....*....|
gi 446601133 641 TGNAEFKVADLLRDQAMIPEVQRLARHIHERYPQQAK-ALIERWMPETER 689
Cdd:COG1200  627 SGLPDLRIADLVRDADLLEAAREDAEELLEEDPELAShPALRRWLGLRFR 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: 949.86  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133   28 INLHTVQDLLLHLPLRYEDRTHLYPIGELLPGVYATVEGEVLN-CNISFGGRRMMTCQISD-GSGILTMRFFNfSAAMKN 105
Cdd:TIGR00643   1 LGIHTVQDLLFYFPRRYEDRTLLQTIGELLPGERATIVGEVLShCIFGFKRRKVLKLRLKDgGYKKLELRFFN-RAFLKK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  106 SLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDLSTPELqeTLTPVYPTTEGVKQATLRKLTDQALDLLDTCaIEELLPP 185
Cdd:TIGR00643  80 KFKVGSKVVVYGKVKSSKFKAYLIHPEFISEKDGVEFEL--KILPVYPLTEGLTQKKLRKLIQQALDQLDKS-LEDPLPE 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  186 ELSQ--GMMTLPEALRTLHrPPPTLQLsdletgQHPAQRRLILEELLAHNLSMLALRAG-AQRFHAQPLSANDTLKNKLL 262
Cdd:TIGR00643 157 ELREkyGLLSLEDALRAIH-FPKTLSL------LELARRRLIFDEFFYLQLAMLARRLGeKQQFSAPPANPSEELLTKFL 229
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  263 AALPFKPTGAQARVVAEIEHDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFA 342
Cdd:TIGR00643 230 ASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLA 309
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  343 PLGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEKGQQqGFHPH 422
Cdd:TIGR00643 310 PLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQG-GFTPH 388
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  423 QLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRtDIIDRVRHACITEGRQAYWVCTLIEESELLEAQ 502
Cdd:TIGR00643 389 VLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEK-DIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLK 467
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  503 AAEATWEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLR 582
Cdd:TIGR00643 468 AAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLR 547
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  583 GRVGRGAVASHCVLLYKTPLSKTAQIRLQVLRDSNDGFVIAQKDLEIRGPGELLGTRQTGNAEFKVADLLRDQAMIPEVQ 662
Cdd:TIGR00643 548 GRVGRGDHQSYCLLVYKNPKSESAKKRLRVMADTLDGFVIAEEDLELRGPGDLLGTKQSGYPEFRVADLVRDREILVEAR 627

                  ...
gi 446601133  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 4.58e-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: 347.21  E-value: 4.58e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 224 LILEELLAHNLSMLALRAGAQRFHAQPLSANDTLKNKLLAALPFKPTGAQARVVAEIEHDMALDVPMMRLVQGDVGSGKT 303
Cdd:cd17992    1 LAFEELFALQLALLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKT 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 304 LVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQ 383
Cdd:cd17992   81 VVAALAMLAAVENGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQ 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446601133 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 2.76e-102

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: 333.55  E-value: 2.76e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  226 LEELLAHNLSMLALRAgAQRFHAQPlsANDTLKNKLLAALPFKPTGAQARVVAEIEHDMALDVPMMRLVQGDVGSGKTLV 305
Cdd:TIGR00580 412 VREIAAKLIELYAKRK-AIKGHAFP--PDLEWQQEFEDSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEV 488
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  306 AALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQEQ 385
Cdd:TIGR00580 489 AMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKD 568
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  386 VQFNGLALVIIDEQHRFGVHQRlalwEKGQQQGFHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPD 465
Cdd:TIGR00580 569 VKFKDLGLLIIDEEQRFGVKQK----EKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRTFVMEY 644
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  466 TRRTdiidrVRHACITE---GRQAYWVCTLIEESELLEAQaaeatweeLKLALPELNVGLVHGRMKPAEKQAVMASFKQG 542
Cdd:TIGR00580 645 DPEL-----VREAIRREllrGGQVFYVHNRIESIEKLATQ--------LRELVPEARIAIAHGQMTENELEEVMLEFYKG 711
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  543 ELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLY--KTPLSKTAQIRLQVLRDSND-- 618
Cdd:TIGR00580 712 EFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYphQKALTEDAQKRLEAIQEFSElg 791
                         410       420
                  ....*....|....*....|....*
gi 446601133  619 -GFVIAQKDLEIRGPGELLGTRQTG 642
Cdd:TIGR00580 792 aGFKIALHDLEIRGAGNLLGEEQSG 816
Mfd COG1197
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ...
238-643 9.92e-94

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


Pssm-ID: 440810 [Multi-domain]  Cd Length: 1130  Bit Score: 314.31  E-value: 9.92e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  238 ALRAGAQRFhaqPLSANDTLKNKLLAALPFKPTGAQARVVAEIEHDMALDVPMMRLVQGDVGSGKTlvaalaalraiahG 317
Cdd:COG1197   559 AERAARKGF---AFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTevalraafkavmdG 635
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  318 KQVALMAPTELLAEQHANNFRNWFAPLGIEVGWL-----AGKQKgKARlsqqEAIASGQVQMIVGTHAIFQEQVQFNGLA 392
Cdd:COG1197   636 KQVAVLVPTTLLAQQHYETFKERFAGFPVRVEVLsrfrtAKEQK-ETL----EGLADGKVDIVIGTHRLLSKDVKFKDLG 710
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  393 LVIIDEQHRFGVHQ--RL-ALWEkgqqqgfHPHQLIMTATPIPRTLAMtAYADL-DTSVIDELPPGRTPVTTVAIPdtrR 468
Cdd:COG1197   711 LLIIDEEQRFGVRHkeKLkALRA-------NVDVLTLTATPIPRTLQM-SLSGIrDLSIIATPPEDRLPVKTFVGE---Y 779
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  469 TDIIdrVRHACITE---GRQAYWVCTLIEEselLEAQAaeatwEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELH 545
Cdd:COG1197   780 DDAL--IREAILREllrGGQVFYVHNRVED---IEKVA-----ARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFD 849
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  546 LLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYK--TPLSKTAQIRLQVLRDSND---GF 620
Cdd:COG1197   850 VLVCTTIIETGIDIPNANTIIIERADRFGLAQLYQLRGRVGRSHRRAYAYLLYPpdKVLTEDAEKRLEAIQEFTElgaGF 929
                         410       420
                  ....*....|....*....|...
gi 446601133  621 VIAQKDLEIRGPGELLGTRQTGN 643
Cdd:COG1197   930 KLAMHDLEIRGAGNLLGEEQSGH 952
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
457-615 1.80e-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: 263.05  E-value: 1.80e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 457 PVTTVAIPDTRRtDIIDRVRHACITEGRQAYWVCTLIEESELLEAQAAEATWEELKLAL-PELNVGLVHGRMKPAEKQAV 535
Cdd:cd18811    1 PITTYLIFHTRL-DKVYEFVREEIAKGRQAYVIYPLIEESEKLDLKAAVAMYEYLKERFrPELNVGLLHGRLKSDEKDAV 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 536 MASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTPLSKTAQIRLQVLRD 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 1.44e-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: 231.77  E-value: 1.44e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 457 PVTTVAIPDTRrTDIIDRVRHACITEGRQAYWVCTLIEESELLEAQAAEATWEELKLALPELNVGLVHGRMKPAEKQAVM 536
Cdd:cd18792    1 PIRTYVIPHDD-LDLVYEAIERELARGGQVYYVYPRIEESEKLDLKSIEALAEELKELVPEARVALLHGKMTEDEKEAVM 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 537 ASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTP--LSKTAQIRLQVLR 614
Cdd:cd18792   80 LEFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPkkLTETAKKRLRAIA 159

                 .
gi 446601133 615 D 615
Cdd:cd18792  160 E 160
PRK10689 PRK10689
transcription-repair coupling factor; Provisional
264-645 4.17e-67

transcription-repair coupling factor; Provisional


Pssm-ID: 182649 [Multi-domain]  Cd Length: 1147  Bit Score: 239.65  E-value: 4.17e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  264 ALPFKPTGAQARVVAEIEHDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFA- 342
Cdd:PRK10689  596 SFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFAn 675
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  343 -PLGIEVgwLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRlalwEKGQQQGFHP 421
Cdd:PRK10689  676 wPVRIEM--LSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHK----ERIKAMRADV 749
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  422 HQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVaipdTRRTDIIdRVRHACITE---GRQAYWVCTLIEESEl 498
Cdd:PRK10689  750 DILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTF----VREYDSL-VVREAILREilrGGQVYYLYNDVENIQ- 823
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  499 leaqAAEATWEELklaLPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQL 578
Cdd:PRK10689  824 ----KAAERLAEL---VPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQL 896
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446601133  579 HQLRGRVGRGAVASHCVLLYKTP--LSKTAQIRLQV---LRDSNDGFVIAQKDLEIRGPGELLGTRQTGNAE 645
Cdd:PRK10689  897 HQLRGRVGRSHHQAYAWLLTPHPkaMTTDAQKRLEAiasLEDLGAGFALATHDLEIRGAGELLGEEQSGQME 968
DEXHc_TRCF cd17991
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ...
263-449 6.28e-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: 186.24  E-value: 6.28e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 263 AALPFKPTGAQARVVAEIEHDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFA 342
Cdd:cd17991   10 ASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFKERFA 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 343 PLGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRlalwEKGQQQGFHPH 422
Cdd:cd17991   90 NFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQK----EKLKELRPNVD 165
                        170       180
                 ....*....|....*....|....*....
gi 446601133 423 QLIMTATPIPRTL--AMTAYADLdtSVID 449
Cdd:cd17991  166 VLTLSATPIPRTLhmALSGIRDL--SVIA 192
DEXHc_RecG cd17918
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ...
261-449 4.43e-53

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: 180.69  E-value: 4.43e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 261 LLAALPFKPTGAQARVVAEIEHDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNW 340
Cdd:cd17918    8 LCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARKF 87
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 341 FAPLGIEVGWLAGKQKgkarlsqqeaiASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEKGQqqgfh 420
Cdd:cd17918   88 LPFINVELVTGGTKAQ-----------ILSGISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLGA----- 151
                        170       180
                 ....*....|....*....|....*....
gi 446601133 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 5.63e-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: 121.30  E-value: 5.63e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 475 VRHACITE---GRQAYWVCTLIEESELLEAQaaeatweeLKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATT 551
Cdd:cd18810   14 IREAIEREllrGGQVFYVHNRIESIEKLATQ--------LRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDILVCTT 85
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446601133 552 VIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKT--PLSKTAQIRLQVL 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 9.30e-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: 9.30e-23
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446601133  63 TVEGEVLNCNI-SFGGRRMMTCQISDGSGILTMRFFNFSAAMKNSLATGRRVLAYGEAKRGKYGAEMIHPEYRV 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 4.61e-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: 93.46  E-value: 4.61e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  270 TGAQARVVAEIEHDMalDVpmmrLVQGDVGSGKT---LVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFAPLGI 346
Cdd:pfam00270   1 TPIQAEAIPAILEGR--DV----LVQAPTGSGKTlafLLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLGKGLGL 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  347 EVGWLAGkqkGKARLSQQEAIASgqVQMIVGTH----AIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEKGQQQGFHPH 422
Cdd:pfam00270  75 KVASLLG---GDSRKEQLEKLKG--PDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPKKR 149
                         170
                  ....*....|....*..
gi 446601133  423 QLI-MTATPiPRTLAMT 438
Cdd:pfam00270 150 QILlLSATL-PRNLEDL 165
DEXDc smart00487
DEAD-like helicases superfamily;
261-456 1.24e-21

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 93.33  E-value: 1.24e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133   261 LLAALPFKPTGAQARVVAEIEHDMaldvpMMRLVQGDVGSGKTLVAAL--AALRAIAHGKQVALMAPTELLAEQHANNFR 338
Cdd:smart00487   1 IEKFGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLpaLEALKRGKGGRVLVLVPTRELAEQWAEELK 75
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133   339 NWFAPLGIEVgwlAGKQKGKARLSQQEAIASGQVQMIVGT-----HAIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEK 413
Cdd:smart00487  76 KLGPSLGLKV---VGLYGGDSKREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEK 152
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 446601133   414 -GQQQGFHPHQLIMTATP---IPRTLAMTAYADLDTSVIDELPPGRT 456
Cdd:smart00487 153 lLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPIE 199
RecG_wedge pfam17191
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations.
16-166 3.46e-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: 90.96  E-value: 3.46e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133   16 GVGAALSNKLAKINLHTVQDLLLHLPLRYEDRTHLYPIGELLPGVYATVEGEVLNCN-ISFGGRRMMTCQISDGSGILTM 94
Cdd:pfam17191   7 GVGPKREKILKKLGIETIGDLIWYFPRDYEDRRKIIPISDIRHDEKVTTKGKIVNFEtKKIGSLVIISAVLSDGIGQVLL 86
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446601133   95 RFFNfSAAMKNSLATGRRVLAYGEAKRGKYGA-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 3.45e-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: 83.41  E-value: 3.45e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446601133  517 ELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERlGLAQLHQLRGRVGR 587
Cdd:pfam00271  38 GIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPW-NPASYIQRIGRAGR 107
HELICc smart00490
helicase superfamily c-terminal domain;
509-587 6.51e-18

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 78.79  E-value: 6.51e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133   509 EELKLALPELN--VGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPeRLGLAQLHQLRGRVG 586
Cdd:smart00490   1 EELAELLKELGikVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL-PWSPASYIQRIGRAG 79

                   .
gi 446601133   587 R 587
Cdd:smart00490  80 R 80
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
293-598 4.30e-12

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 69.28  E-value: 4.30e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 293 LVQGDVGSGKTLVAALAALRAIaHGKQVALMAPTELLAEQHANNFRNWFaplgievgwlagkqkGKARLSQQEAIASGQV 372
Cdd:COG1061  104 LVVAPTGTGKTVLALALAAELL-RGKRVLVLVPRRELLEQWAEELRRFL---------------GDPLAGGGKKDSDAPI 167
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 373 qmIVGTHAIFQEQVQFNGLA----LVIIDEQHRFG--VHQRLAlwekgqqQGFHPHQLI-MTATPIpRTLAMTAYADLDT 445
Cdd:COG1061  168 --TVATYQSLARRAHLDELGdrfgLVIIDEAHHAGapSYRRIL-------EAFPAAYRLgLTATPF-RSDGREILLFLFD 237
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 446 SVIDELPPGR-------TPVTTVAIPD------------------------TRRTDIIDRVRHACiTEGRQAYWVCTLIE 494
Cdd:COG1061  238 GIVYEYSLKEaiedgylAPPEYYGIRVdltderaeydalserlrealaadaERKDKILRELLREH-PDDRKTLVFCSSVD 316
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 495 EselleaqaAEATWEELKLAlpELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMII----ENP 570
Cdd:COG1061  317 H--------AEALAELLNEA--GIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILlrptGSP 386
                        330       340
                 ....*....|....*....|....*...
gi 446601133 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 2.38e-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: 57.48  E-value: 2.38e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  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 3.48e-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: 55.87  E-value: 3.48e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 293 LVQGDVGSGKTLVAALA-ALRAIAHGKQVALMAPTELLAEQHANNFRNWFAPlGIEVGWLAgkqkGKARLSQQEAIASGQ 371
Cdd:cd00046    5 LITAPTGSGKTLAALLAaLLLLLKKGKKVLVLVPTKALALQTAERLRELFGP-GIRVAVLV----GGSSAEEREKNKLGD 79
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446601133 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 1.90e-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: 51.47  E-value: 1.90e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446601133   63 TVEGEVLNcnISFGGRRMMTCQISDGSGILTMRFFN-FSAAMKNSLATGRRVLAYGEAKRGKYGA-EMIHPEYRV 135
Cdd:pfam01336   2 TVAGRVTS--IRRSGGKLLFLTLRDGTGSIQVVVFKeEAEKLAKKLKEGDVVRVTGKVKKRKGGElELVVEEIEL 74
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
543-589 2.10e-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: 2.10e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 446601133 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 6.36e-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: 55.13  E-value: 6.36e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 390 GLALVIIDEQHRFGVHQR---LALWEKGQQQGFhPHqLIMTATpIPRTLaMTAYADLDTsVIDELPPGRTPVTTVAIP-- 464
Cdd:cd09639  123 ANSLLIFDEVHFYDEYTLaliLAVLEVLKDNDV-PI-LLMSAT-LPKFL-KEYAEKIGY-VEENEPLDLKPNERAPFIki 197
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 465 ---DTRRTDIIDRVRHACITEGRQAYwVCTLIEEselleaqaAEATWEELKLALPELNVGLVHGRMKP---AEKQA-VMA 537
Cdd:cd09639  198 esdKVGEISSLERLLEFIKKGGSVAI-IVNTVDR--------AQEFYQQLKEKGPEEEIMLIHSRFTEkdrAKKEAeLLL 268
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 446601133 538 SFKQGELHLLVATTVIEVGVDVpNASLMIIEnperlgLAQLHQLRGRVGR 587
Cdd:cd09639  269 EFKKSEKFVIVATQVIEASLDI-SVDVMITE------LAPIDSLIQRLGR 311
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
317-439 1.10e-07

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: 52.82  E-value: 1.10e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 317 GKQVALMAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARLsqQEAIASGQVqmIVGTHAIFQ------EQVQFNG 390
Cdd:cd17927   50 KGKVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSENVSV--EQIVESSDV--IIVTPQILVndlksgTIVSLSD 125
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446601133 391 LALVIIDEQHRfgvhqrlalwekgqQQGFHPHQLIMT---------ATPIPRTLAMTA 439
Cdd:cd17927  126 FSLLVFDECHN--------------TTKNHPYNEIMFryldqklgsSGPLPQILGLTA 169
DEXHc_priA cd17929
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ...
293-400 1.40e-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: 51.83  E-value: 1.40e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 293 LVQGDVGSGKTLVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFaplGIEVGWLAGKQKGKARLSQQEAIASGQV 372
Cdd:cd17929   19 LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRF---GDKVAVLHSKLSDKERADEWRKIKRGEA 95
                         90       100
                 ....*....|....*....|....*....
gi 446601133 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 4.42e-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: 4.42e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 424 LIMTAT-PIPRTLAMTAYADL-------DTSVIDELPPGRTPVTTVAIPDTrrtDIIDRVRhACITEGRQAYWVCTLIee 495
Cdd:COG1203  303 ILMTATlPPLLREELLEAYELipdepeeLPEYFRAFVRKRVELKEGPLSDE---ELAELIL-EALHKGKSVLVIVNTV-- 376
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446601133 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 1.14e-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: 1.14e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 509 EELKLALPELNVGLVHGR----------MKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERlGLAQL 578
Cdd:cd18802   46 KEHPSTLAFIRCGFLIGRgnssqrkrslMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPK-TLRSY 124
                         90
                 ....*....|....*....
gi 446601133 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 1.30e-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: 1.30e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  390 GLALVIIDEQHRFGVHQR---LALWEKGQQQGFhPHqLIMTATpIPRTLaMTAYADLDTSVIDELPPGRTPVTTVAIPDT 466
Cdd:TIGR01587 124 ANSLLIFDEVHFYDEYTLaliLAVLEVLKDNDV-PI-LLMSAT-LPKFL-KEYAEKIGYVEFNEPLDLKEERRFENHRFI 199
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  467 RRTD-------IIDRVRHACITEGRQAYwVCTLIEEselleaqaAEATWEELKLALPELNVGLVHGRMKP---AEKQA-V 535
Cdd:TIGR01587 200 LIESdkvgeisSLERLLEFIKKGGSIAI-IVNTVDR--------AQEFYQQLKEKAPEEEIILYHSRFTEkdrAKKEAeL 270
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 446601133  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 4.32e-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: 4.32e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 509 EELKLALPELN--VGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMI 566
Cdd:cd18787   41 DRLAELLEELGikVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHVI 100
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
316-430 5.07e-06

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 49.73  E-value: 5.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 316 HGKQVALMAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARlsqQEAIASGQVqmIVGThaifqEQVQFNGL---- 391
Cdd:COG1111   45 KGGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGEVSPEKR---KELWEKARI--IVAT-----PQVIENDLiagr 114
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 446601133 392 ------ALVIIDEQHR-FGVHQRLALWEKGQQQGFHPHQLIMTATP 430
Cdd:COG1111  115 idlddvSLLIFDEAHRaVGNYAYVYIAERYHEDAKDPLILGMTASP 160
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
299-412 1.04e-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: 46.49  E-value: 1.04e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 299 GSGKTLVAALAALRAIAHGKQVAL-MAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKgkarlSQQEAIASGQVqmIVG 377
Cdd:cd17921   27 SSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNVGLLTGDPS-----VNKLLLAEADI--LVA 99
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 446601133 378 THAIFQ------EQVQFNGLALVIIDEQHRFGVHQRLALWE 412
Cdd:cd17921  100 TPEKLDlllrngGERLIQDVRLVVVDEAHLIGDGERGVVLE 140
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
317-430 1.53e-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: 45.97  E-value: 1.53e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 317 GKQVALMAPTELLAEQHANNFRNWFApLGIEVGWLAGKQKGKARlsqQEAIASGQVqmIVGT-----HAIFQEQVQFNGL 391
Cdd:cd18035   45 GGKVLILAPSRPLVEQHAENLKRVLN-IPDKITSLTGEVKPEER---AERWDASKI--IVATpqvieNDLLAGRITLDDV 118
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446601133 392 ALVIIDEQHR-FGVHQRLALWEKGQQQGFHPHQLIMTATP 430
Cdd:cd18035  119 SLLIFDEAHHaVGNYAYVYIAHRYKREANNPLILGLTASP 158
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 446601133 502 QAAEATWEELKLALPE----LNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMI-IENPerLGLA 576
Cdd:cd18796   49 SQAERLAQRLRELCPDrvppDFIALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDVDLVIqIGSP--KSVA 126
                         90
                 ....*....|.
gi 446601133 577 QLHQLRGRVGR 587
Cdd:cd18796  127 RLLQRLGRSGH 137
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
297-439 2.07e-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: 43.02  E-value: 2.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 297 DVGSGKTL-------VAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWfapLGIEVGWLAGKQ--KGKARLSQQEAI 367
Cdd:cd18034   24 PTGSGKTLiavmlikEMGELNRKEKNPKKRAVFLVPTVPLVAQQAEAIRSH---TDLKVGEYSGEMgvDKWTKERWKEEL 100
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 368 ASGQVqmIVGTHAIF-----QEQVQFNGLALVIIDEQHrfgvHQRlalwekgqqqGFHPHQLIM-------TATPIPRTL 435
Cdd:cd18034  101 EKYDV--LVMTAQILldalrHGFLSLSDINLLIFDECH----HAT----------GDHPYARIMkefyhleGRTSRPRIL 164

                 ....
gi 446601133 436 AMTA 439
Cdd:cd18034  165 GLTA 168
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
520-587 2.07e-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: 2.07e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446601133 520 VGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPnASLMIIENPER--------LGLAQLHQLRGRVGR 587
Cdd:cd18795   66 IAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLP-ARTVIIKGTQRydgkgyreLSPLEYLQMIGRAGR 140
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 446601133 527 MKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLhQLRGRVGRG 588
Cdd:cd18801   74 MSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMI-QRMGRTGRK 134
PRK05580 PRK05580
primosome assembly protein PriA; Validated
223-430 4.03e-04

primosome assembly protein PriA; Validated


Pssm-ID: 235514 [Multi-domain]  Cd Length: 679  Bit Score: 43.61  E-value: 4.03e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 223 RLILEELLAHNLSMLALRA----GAQRFHAQPLSANDTLKNKLLAALPFkpTGAQARVVAEIEHDMALDVPmmrLVQGDV 298
Cdd:PRK05580  97 RLALLAELALAASSAVLKGlvkkGLIELEEVEVLRLRPPPDPAFEPPTL--NPEQAAAVEAIRAAAGFSPF---LLDGVT 171
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 299 GSGKTLVAALAALRAIAHGKQVALMAPtEL-LAEQHANNFRNWFaplGIEVG-W---LAGKQKGKARLsqqeAIASGQVQ 373
Cdd:PRK05580 172 GSGKTEVYLQAIAEVLAQGKQALVLVP-EIaLTPQMLARFRARF---GAPVAvLhsgLSDGERLDEWR----KAKRGEAK 243
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 374 MIVGTH-AIFqeqVQFNGLALVIIDEQH----------RFgvHQR-LALWeKGQQQGFhphQLIM-TATP 430
Cdd:PRK05580 244 VVIGARsALF---LPFKNLGLIIVDEEHdssykqqegpRY--HARdLAVV-RAKLENI---PVVLgSATP 304
PriA COG1198
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ...
183-400 1.30e-03

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


Pssm-ID: 440811 [Multi-domain]  Cd Length: 728  Bit Score: 42.03  E-value: 1.30e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 183 LPPELSQGMMTLPEALRTLhrpppTLQLSDLETGQHPAQRRLiLEELLAHN----LSMLALRAGAQRFHAQPL------- 251
Cdd:COG1198  100 LPAGLRQGYPARIKTERYV-----RLTLGEELPKRAPKQRRV-LEALREHGgpltLSELAKEAGVSRSVLKALvkkglle 173
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 252 -----SANDTLKNKLLAALPFKPTGAQARVVAEIEHDMALDVPMmrLVQGDVGSGKTLVAALAALRAIAHGKQVALMAPt 326
Cdd:COG1198  174 ieereVDRDPFAPDVPAEPPPTLNEEQQAAVEAIRAAAGGFSVF--LLHGVTGSGKTEVYLQAIAEVLAQGKQALVLVP- 250
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446601133 327 EL-LAEQHANNFRNWFaplGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTH-AIFqeqVQFNGLALVIIDEQH 400
Cdd:COG1198  251 EIaLTPQTVERFRARF---GARVAVLHSGLSDGERLDEWRRARRGEARIVIGTRsALF---APFPNLGLIIVDEEH 320
PLN03137 PLN03137
ATP-dependent DNA helicase; Q4-like; Provisional
524-611 1.54e-03

ATP-dependent DNA helicase; Q4-like; Provisional


Pssm-ID: 215597 [Multi-domain]  Cd Length: 1195  Bit Score: 41.81  E-value: 1.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133  524 HGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERlGLAQLHQLRGRVGRGAVASHCVLLYktplS 603
Cdd:PLN03137  711 HGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPK-SIEGYHQECGRAGRDGQRSSCVLYY----S 785

                  ....*...
gi 446601133  604 KTAQIRLQ 611
Cdd:PLN03137  786 YSDYIRVK 793
PRK13766 PRK13766
Hef nuclease; Provisional
316-430 4.85e-03

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 40.24  E-value: 4.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 316 HGKQVALMAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARlsqQEAIASGQVqmIVGThaifqEQVQFNGL---- 391
Cdd:PRK13766  57 KGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTGEVSPEKR---AELWEKAKV--IVAT-----PQVIENDLiagr 126
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 446601133 392 ------ALVIIDEQHR-FGVHQRLALWEKGQQQGFHPHQLIMTATP 430
Cdd:PRK13766 127 isledvSLLIFDEAHRaVGNYAYVYIAERYHEDAKNPLVLGLTASP 172
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
518-566 5.08e-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: 5.08e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 446601133 518 LNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMI 566
Cdd:COG0513  266 ISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHVI 314
PRK13766 PRK13766
Hef nuclease; Provisional
527-599 6.77e-03

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 39.86  E-value: 6.77e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446601133 527 MKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENP--------ERlglaqlhqlRGRVGRGAVASHCVLLY 598
Cdd:PRK13766 407 MSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPvpseirsiQR---------KGRTGRQEEGRVVVLIA 477

                 .
gi 446601133 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 7.69e-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: 7.69e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446601133 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 7.84e-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: 37.62  E-value: 7.84e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446601133 529 PAEKQAVMASFKQGELHLLVATTVIEVGVDVpnASL---MIIENPErlGLAQLHQLRGRVGRGAVASHCVLL 597
Cdd:cd18797   78 AEDRREIEAELFNGELLGVVATNALELGIDI--GGLdavVLAGYPG--SLASLWQQAGRAGRRGKDSLVILV 145
 
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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