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Conserved domains on  [gi|2216107309|gb|UOC05305|]
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helicase RecD/TraA (plasmid) [Bacillus thuringiensis serovar morrisoni str. 4AA1]

Protein Classification

ATP-dependent DNA helicase( domain architecture ID 11423480)

ATP-dependent DNA helicase belonging to the DEAD/DEAH box superfamily, utilizes the energy from ATP hydrolysis to unwind double-stranded DNA

CATH:  3.40.50.300
EC:  3.6.4.12
Gene Ontology:  GO:0032508|GO:0003677|GO:0005524|GO:0046872|GO:0003678|GO:0016887
PubMed:  2563148|20206133|20225155

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 424-763 4.01e-68

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


:

Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 234.10  E-value: 4.01e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 424 DNRITLLLGRAGTGKTYTLVNLLNRLKPDPNKTIVCTYTGKASSRIRELFREydlqdyKSLTIHKTCASNFNS-KFFRNE 502
Cdd:COG0507   139 TRRVSVLTGGAGTGKTTTLRALLAALEALGLRVALAAPTGKAAKRLSESTGI------EARTIHRLLGLRPDSgRFRHNR 212

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 503 YNII-DCAYLIIDEVSMIPREILSKLLQAVPS-HVKIIFAGDDAQLPPVNDTSIIPELEALEFVNTVRLTQVFR----SE 576
Cdd:COG0507   213 DNPLtPADLLVVDEASMVDTRLMAALLEALPRaGARLILVGDPDQLPSVGAGAVLRDLIESGTVPVVELTEVYRqaddSR 292

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 577 DAVL------GQAYNVLGRKSIDYNLF----GEDMKELVLKLISD------GYQILTNTRKLAKDINMIVQESKNDITKC 640
Cdd:COG0507   293 IIELahaireGDAPEALNARYADVVFVeaedAEEAAEAIVELYADrpaggeDIQVLAPTNAGVDALNQAIREALNPAGEL 372

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 641 FDDYKYNLN------DRVMIIANSSARNVSNGDTGKI--IDFDERGVCVRLDlEDREVFYKYEDTEEIVPAYAFTVHKSQ 712
Cdd:COG0507   373 ERELAEDGElelyvgDRVMFTRNDYDLGVFNGDIGTVlsIDEDEGRLTVRFD-GREIVTYDPSELDQLELAYAITVHKSQ 451

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2216107309 713 GSEYENVAVFVDSQP-KLNTNNLLYTGITRAKKDIKVYVPNEMVLTTMINTV 763
Cdd:COG0507   452 GSTFDRVILVLPSEHsPLLSRELLYTALTRARELLTLVGDRDALARAVRRDT 503
 
Name Accession Description Interval E-value
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 424-763 4.01e-68

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 234.10  E-value: 4.01e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 424 DNRITLLLGRAGTGKTYTLVNLLNRLKPDPNKTIVCTYTGKASSRIRELFREydlqdyKSLTIHKTCASNFNS-KFFRNE 502
Cdd:COG0507   139 TRRVSVLTGGAGTGKTTTLRALLAALEALGLRVALAAPTGKAAKRLSESTGI------EARTIHRLLGLRPDSgRFRHNR 212

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 503 YNII-DCAYLIIDEVSMIPREILSKLLQAVPS-HVKIIFAGDDAQLPPVNDTSIIPELEALEFVNTVRLTQVFR----SE 576
Cdd:COG0507   213 DNPLtPADLLVVDEASMVDTRLMAALLEALPRaGARLILVGDPDQLPSVGAGAVLRDLIESGTVPVVELTEVYRqaddSR 292

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 577 DAVL------GQAYNVLGRKSIDYNLF----GEDMKELVLKLISD------GYQILTNTRKLAKDINMIVQESKNDITKC 640
Cdd:COG0507   293 IIELahaireGDAPEALNARYADVVFVeaedAEEAAEAIVELYADrpaggeDIQVLAPTNAGVDALNQAIREALNPAGEL 372

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 641 FDDYKYNLN------DRVMIIANSSARNVSNGDTGKI--IDFDERGVCVRLDlEDREVFYKYEDTEEIVPAYAFTVHKSQ 712
Cdd:COG0507   373 ERELAEDGElelyvgDRVMFTRNDYDLGVFNGDIGTVlsIDEDEGRLTVRFD-GREIVTYDPSELDQLELAYAITVHKSQ 451

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2216107309 713 GSEYENVAVFVDSQP-KLNTNNLLYTGITRAKKDIKVYVPNEMVLTTMINTV 763
Cdd:COG0507   452 GSTFDRVILVLPSEHsPLLSRELLYTALTRARELLTLVGDRDALARAVRRDT 503
recD_rel TIGR01448
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 351-744 5.65e-45

helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273632 [Multi-domain]  Cd Length: 720  Bit Score: 173.05  E-value: 5.65e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 351 FVKEHSKMLRDEHAIRLHHLVRDlelsdEIKYSYMIhERLLQISSMD---------FLVERLGDYrteGLTFDQVRLMKS 421
Cdd:TIGR01448 264 YLDEEPKLAAEDGRIYLPSLFRA-----EKQIASHI-RRLLATSPAIgaindqehiWEVEKKLRK---GLSEEQKQALDT 334

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 422 FIDNRITLLLGRAGTGKTYT---LVNLLNRLKpDPNKTIVCTYTGKASSRIRELFREydlqdyKSLTIHKTCASNFNSKF 498
Cdd:TIGR01448 335 AIQHKVVILTGGPGTGKTTItraIIELAEELG-GLLPVGLAAPTGRAAKRLGEVTGL------TASTIHRLLGYGPDTFR 407

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 499 FRNEYNIIDCAYLIIDEVSMIPREILSKLLQAVPSHVKIIFAGDDAQLPPVNDTSIIPELEALEFVNTVRLTQVFRSED- 577
Cdd:TIGR01448 408 HNHLEDPIDCDLLIVDESSMMDTWLALSLLAALPDHARLLLVGDTDQLPSVGPGQVLKDLILSQAIPVTRLTKVYRQAAg 487

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 578 -AVLGQAYNVL-GRK--SIDYNLFGED--------------MKELVLKLISDGY-----QILTNTRKLA---KDINMIVQ 631
Cdd:TIGR01448 488 sPIITLAHGILhGEApaWGDFKFLNLTrsepegaarhiplmVEKIVGMARVGGIpgadiQVLAPMYKGPlgiDALNQHLQ 567

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 632 ESKNDITKC-----FDDYKYNLNDRVMIIANSSARNVSNGDTGKI--IDFDERGV--CVRLDLEDREVFYKYEDTEEIVP 702
Cdd:TIGR01448 568 ALLNPYQKGqggieIAEGEYRKGDRVMQTKNDYNNEIFNGDLGMIvkIEGAKQGKkdQVVVDFDGNEVELTRAELFNLTL 647

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|...
gi 2216107309 703 AYAFTVHKSQGSEYENV-AVFVDSQPKLNTNNLLYTGITRAKK 744
Cdd:TIGR01448 648 AYATSIHKSQGSEFPTViLPIHTAHMRMLYRNLLYTALTRAKK 690
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 414-573 5.65e-33

DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD 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: 350691 [Multi-domain]  Cd Length: 155  Bit Score: 124.59  E-value: 5.65e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 414 DQVRLMKSFIDNRITLLLGRAGTGKTYTLVNLLNRLKPDPNKTIVCTYTGKASSRIRELFreydlqDYKSLTIHKTCASN 493
Cdd:cd17933     1 EQKAAVRLVLRNRVSVLTGGAGTGKTTTLKALLAALEAEGKRVVLAAPTGKAAKRLSEST------GIEASTIHRLLGIN 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 494 FNSKFFR-NEYNIIDCAYLIIDEVSMIPREILSKLLQAVPSHVKIIFAGDDAQLPPVNDTSIIPELEALEFVNTVRLTQV 572
Cdd:cd17933    75 PGGGGFYyNEENPLDADLLIVDEASMVDTRLMAALLSAIPAGARLILVGDPDQLPSVGAGNVLRDLIASKGVPTVELTEV 154


                  .
gi 2216107309 573 F 573
Cdd:cd17933   155 F 155
AAA_19 pfam13245
AAA domain;
425-549 3.31e-25

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 101.53  E-value: 3.31e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 425 NRITLLLGRAGTGKTYTL---VNLLNRLKPDPNKTIVCTYTGKASSRIRE-LFREydlqdykSLTIHKtcASNFNSK--- 497
Cdd:pfam13245  11 SKVVLLTGGPGTGKTTTIrhiVALLVALGGVSFPILLAAPTGRAAKRLSErTGLP-------ASTIHR--LLGFDDLeag 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2216107309 498 -FFRNEYNIIDCAYLIIDEVSMIPREILSKLLQAVPSHVKIIFAGDDAQLPPV 549
Cdd:pfam13245  82 gFLRDEEEPLDGDLLIVDEFSMVDLPLAYRLLKALPDGAQLLLVGDPDQLPSV 134
recD PRK10875
exodeoxyribonuclease V subunit alpha;
426-762 1.61e-14

exodeoxyribonuclease V subunit alpha;


Pssm-ID: 236783 [Multi-domain]  Cd Length: 615  Bit Score: 77.29  E-value: 1.61e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 426 RITLLLGRAGTGKTYTLVNLLN---RLKPDPNKTI-VCTYTGKASSRIRE----LFREYDLQD-------YKSLTIHKTC 490
Cdd:PRK10875  168 RISVISGGPGTGKTTTVAKLLAaliQLADGERCRIrLAAPTGKAAARLTEslgkALRQLPLTDeqkkripEEASTLHRLL 247

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 491 ASNFNSKFFR-NEYNIIDCAYLIIDEVSMIPREILSKLLQAVPSHVKIIFAGDDAQLPPVNDTSII-------------- 555
Cdd:PRK10875  248 GAQPGSQRLRyHAGNPLHLDVLVVDEASMVDLPMMARLIDALPPHARVIFLGDRDQLASVEAGAVLgdicrfaeagysae 327

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 556 --PELEAL----------EFVNTVR-----LTQVFR-SEDAVLGQ---AYNVLGRKSIDyNLFGEDMKELVLKLISDG-- 612
Cdd:PRK10875  328 raQQLSRLtgchlpagtgTEAASVRdslclLRKSYRfGSDSGIGQlaaAVNRGDKRAAK-AVFQQGFSDIEKRPLQSGed 406

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 613 YQ-ILTNTRKLAKDINMIVQE--SKNDITKCFDDYKY------------NLNDR-------------------------- 651
Cdd:PRK10875  407 YQaMLEEALAGYGRYLDLLAAraEPEAILAAFNRYQLlcalregpfgvaGLNERieqalqqkrlirrpsgphsrwyegrp 486

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 652 VMIIANSSARNVSNGDTGKIIDFDERGVCVRLDLEDREVfykyedtEEIVP--------AYAFTVHKSQGSEYENVAVFV 723
Cdd:PRK10875  487 VMIARNDSALGLFNGDIGIALDRGQGELRVWFQLPDGNI-------KSVQPsrlpehetAWAMTVHKSQGSEFDHTALVL 559

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|.
gi 2216107309 724 DSQ--PKLnTNNLLYTGITRAKKDIKVYVpNEMVLTTMINT 762
Cdd:PRK10875  560 PNQftPVV-TRELVYTAITRARRRLSLYA-DERVLSAAIAT 598
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 425-555 7.43e-03

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 37.74  E-value: 7.43e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309  425 NRITLLLGRAGTGKTYTLVNLLNRLKPDPNKTIVCTytgkassriRELFREYDLQDYKSLTIHKTCASNFNSKFFRN--- 501
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYID---------GEDILEEVLDQLLLIIVGGKKASGSGELRLRLala 72

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2216107309  502 --EYNIIDCayLIIDEVSMIPREILSKLLQavpshvKIIFAGDDAQLPPVNDTSII 555
Cdd:smart00382  73 laRKLKPDV--LILDEITSLLDAEQEALLL------LLEELRLLLLLKSEKNLTVI 120
 
Name Accession Description Interval E-value
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 424-763 4.01e-68

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 234.10  E-value: 4.01e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 424 DNRITLLLGRAGTGKTYTLVNLLNRLKPDPNKTIVCTYTGKASSRIRELFREydlqdyKSLTIHKTCASNFNS-KFFRNE 502
Cdd:COG0507   139 TRRVSVLTGGAGTGKTTTLRALLAALEALGLRVALAAPTGKAAKRLSESTGI------EARTIHRLLGLRPDSgRFRHNR 212

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 503 YNII-DCAYLIIDEVSMIPREILSKLLQAVPS-HVKIIFAGDDAQLPPVNDTSIIPELEALEFVNTVRLTQVFR----SE 576
Cdd:COG0507   213 DNPLtPADLLVVDEASMVDTRLMAALLEALPRaGARLILVGDPDQLPSVGAGAVLRDLIESGTVPVVELTEVYRqaddSR 292

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 577 DAVL------GQAYNVLGRKSIDYNLF----GEDMKELVLKLISD------GYQILTNTRKLAKDINMIVQESKNDITKC 640
Cdd:COG0507   293 IIELahaireGDAPEALNARYADVVFVeaedAEEAAEAIVELYADrpaggeDIQVLAPTNAGVDALNQAIREALNPAGEL 372

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 641 FDDYKYNLN------DRVMIIANSSARNVSNGDTGKI--IDFDERGVCVRLDlEDREVFYKYEDTEEIVPAYAFTVHKSQ 712
Cdd:COG0507   373 ERELAEDGElelyvgDRVMFTRNDYDLGVFNGDIGTVlsIDEDEGRLTVRFD-GREIVTYDPSELDQLELAYAITVHKSQ 451

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2216107309 713 GSEYENVAVFVDSQP-KLNTNNLLYTGITRAKKDIKVYVPNEMVLTTMINTV 763
Cdd:COG0507   452 GSTFDRVILVLPSEHsPLLSRELLYTALTRARELLTLVGDRDALARAVRRDT 503
recD_rel TIGR01448
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 351-744 5.65e-45

helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273632 [Multi-domain]  Cd Length: 720  Bit Score: 173.05  E-value: 5.65e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 351 FVKEHSKMLRDEHAIRLHHLVRDlelsdEIKYSYMIhERLLQISSMD---------FLVERLGDYrteGLTFDQVRLMKS 421
Cdd:TIGR01448 264 YLDEEPKLAAEDGRIYLPSLFRA-----EKQIASHI-RRLLATSPAIgaindqehiWEVEKKLRK---GLSEEQKQALDT 334

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 422 FIDNRITLLLGRAGTGKTYT---LVNLLNRLKpDPNKTIVCTYTGKASSRIRELFREydlqdyKSLTIHKTCASNFNSKF 498
Cdd:TIGR01448 335 AIQHKVVILTGGPGTGKTTItraIIELAEELG-GLLPVGLAAPTGRAAKRLGEVTGL------TASTIHRLLGYGPDTFR 407

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 499 FRNEYNIIDCAYLIIDEVSMIPREILSKLLQAVPSHVKIIFAGDDAQLPPVNDTSIIPELEALEFVNTVRLTQVFRSED- 577
Cdd:TIGR01448 408 HNHLEDPIDCDLLIVDESSMMDTWLALSLLAALPDHARLLLVGDTDQLPSVGPGQVLKDLILSQAIPVTRLTKVYRQAAg 487

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 578 -AVLGQAYNVL-GRK--SIDYNLFGED--------------MKELVLKLISDGY-----QILTNTRKLA---KDINMIVQ 631
Cdd:TIGR01448 488 sPIITLAHGILhGEApaWGDFKFLNLTrsepegaarhiplmVEKIVGMARVGGIpgadiQVLAPMYKGPlgiDALNQHLQ 567

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 632 ESKNDITKC-----FDDYKYNLNDRVMIIANSSARNVSNGDTGKI--IDFDERGV--CVRLDLEDREVFYKYEDTEEIVP 702
Cdd:TIGR01448 568 ALLNPYQKGqggieIAEGEYRKGDRVMQTKNDYNNEIFNGDLGMIvkIEGAKQGKkdQVVVDFDGNEVELTRAELFNLTL 647

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|...
gi 2216107309 703 AYAFTVHKSQGSEYENV-AVFVDSQPKLNTNNLLYTGITRAKK 744
Cdd:TIGR01448 648 AYATSIHKSQGSEFPTViLPIHTAHMRMLYRNLLYTALTRAKK 690
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 425-763 2.21e-35

exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273631 [Multi-domain]  Cd Length: 582  Bit Score: 142.21  E-value: 2.21e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 425 NRITLLLGRAGTGKTYTLVNLLN-RLKPDPNKT---IVCTY-TGKASSRIRELFREYDLQDYKSL-----------TIHK 488
Cdd:TIGR01447 159 SNFSLITGGPGTGKTTTVARLLLaLVKQSPKQGklrIALAApTGKAAARLAESLRKAVKNLAAAEaliaalpseavTIHR 238

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 489 TCASNFNSKFFRNEY-NIIDCAYLIIDEVSMIPREILSKLLQAVPSHVKIIFAGDDAQLPPVNDTSIIPELeaLEFV--- 564
Cdd:TIGR01447 239 LLGIKPDTKRFRHHErNPLPLDVLVVDEASMVDLPLMAKLLKALPPNTKLILLGDKNQLPSVEAGAVLGDL--CELAsig 316

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 565 ---------------------NTVRLTQVFRS-EDAVLGQ----AYNVLGRKSIDYNLFGEDM-------KELVLKLISD 611
Cdd:TIGR01447 317 ksilyalckkinsktrnplsdNVCFLKTSHRFgKDSGIGQlakaINSGDIEAVLNNLRSGQLIefeflnsKEDAIERLKN 396

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 612 GY-QILTNTRKLAKD----------------------------INMIVQESKNDITKCFDDYKYNLNDRVMIIANSSARN 662
Cdd:TIGR01447 397 LYvKYRTFLQKLAALsdakeiletfdrlrlltalrdgpfgvlgLNRRIEQELQEKYFDPDEEGWYIGRPIMVTENDYTLG 476

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 663 VSNGDTgkiidfderGVCVRLDLEDREVFYKYEDTEEIVP---------AYAFTVHKSQGSEYENVAVFVDSQP-KLNTN 732
Cdd:TIGR01447 477 LFNGDI---------GVLLRDPDGILTVWFHFADGSKAVLpsrlpnyetAFAMTVHKSQGSEFDHVILILPNGNsPVLTR 547

                         410       420       430
                  ....*....|....*....|....*....|.
gi 2216107309 733 NLLYTGITRAKKDIKVYVPNEMVLTTMINTV 763
Cdd:TIGR01447 548 ELLYTGITRAKDQLSVWSDKETLNAAIKRKN 578
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 414-573 5.65e-33

DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD 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: 350691 [Multi-domain]  Cd Length: 155  Bit Score: 124.59  E-value: 5.65e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 414 DQVRLMKSFIDNRITLLLGRAGTGKTYTLVNLLNRLKPDPNKTIVCTYTGKASSRIRELFreydlqDYKSLTIHKTCASN 493
Cdd:cd17933     1 EQKAAVRLVLRNRVSVLTGGAGTGKTTTLKALLAALEAEGKRVVLAAPTGKAAKRLSEST------GIEASTIHRLLGIN 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 494 FNSKFFR-NEYNIIDCAYLIIDEVSMIPREILSKLLQAVPSHVKIIFAGDDAQLPPVNDTSIIPELEALEFVNTVRLTQV 572
Cdd:cd17933    75 PGGGGFYyNEENPLDADLLIVDEASMVDTRLMAALLSAIPAGARLILVGDPDQLPSVGAGNVLRDLIASKGVPTVELTEV 154


                  .
gi 2216107309 573 F 573
Cdd:cd17933   155 F 155
AAA_19 pfam13245
AAA domain;
425-549 3.31e-25

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 101.53  E-value: 3.31e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 425 NRITLLLGRAGTGKTYTL---VNLLNRLKPDPNKTIVCTYTGKASSRIRE-LFREydlqdykSLTIHKtcASNFNSK--- 497
Cdd:pfam13245  11 SKVVLLTGGPGTGKTTTIrhiVALLVALGGVSFPILLAAPTGRAAKRLSErTGLP-------ASTIHR--LLGFDDLeag 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2216107309 498 -FFRNEYNIIDCAYLIIDEVSMIPREILSKLLQAVPSHVKIIFAGDDAQLPPV 549
Cdd:pfam13245  82 gFLRDEEEPLDGDLLIVDEFSMVDLPLAYRLLKALPDGAQLLLVGDPDQLPSV 134
DEXSc_Pif1_like cd18037
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like ...
 414-574 3.97e-17

DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like helicases involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. The members of Pif1 helicase subfamily studied so far all appear to contribute to telomere maintenance. Pif1 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: 350795 [Multi-domain]  Cd Length: 183  Bit Score: 79.99  E-value: 3.97e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 414 DQVRLMKSFIDNRITLLLGRAGTGKTYTLVNLLNRLKPDPNKTIVCTYTGKASSRIRelfreydlqdykSLTIH------ 487
Cdd:cd18037     1 EQRRVLDLVLDGKNVFFTGSAGTGKSYLLRRIIRALPSRPKRVAVTASTGIAACNIG------------GTTLHsfagig 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 488 --KTCASNFNSKFFRNEYNI---IDCAYLIIDEVSMIPREILSKL---LQAV-PSH-----VKIIFAGDDAQLPPVNDTS 553
Cdd:cd18037    69 lgSEPAEDLLERVKRSPYLVqrwRKCDVLIIDEISMLDADLFDKLdrvAREVrGSDkpfggIQLILCGDFLQLPPVTKNS 148

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2216107309 554 IIPELEALEFVN--------------TVRLTQVFR 574
Cdd:cd18037   149 ERQAFFFRGDQQfcfeakswerciflTVELTKVFR 183
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
 703-750 9.10e-15

C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350196 [Multi-domain]  Cd Length: 80  Bit Score: 69.90  E-value: 9.10e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2216107309 703 AYAFTVHKSQGSEYENVAVFVDSQPKLNTNNLLYTGITRAKKDIKVYV 750
Cdd:cd18809    33 AYAMTIHKSQGSEFDRVIVVLPTSHPMLSRGLLYTALTRARKLLTLVG 80
recD PRK10875
exodeoxyribonuclease V subunit alpha;
426-762 1.61e-14

exodeoxyribonuclease V subunit alpha;


Pssm-ID: 236783 [Multi-domain]  Cd Length: 615  Bit Score: 77.29  E-value: 1.61e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 426 RITLLLGRAGTGKTYTLVNLLN---RLKPDPNKTI-VCTYTGKASSRIRE----LFREYDLQD-------YKSLTIHKTC 490
Cdd:PRK10875  168 RISVISGGPGTGKTTTVAKLLAaliQLADGERCRIrLAAPTGKAAARLTEslgkALRQLPLTDeqkkripEEASTLHRLL 247

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 491 ASNFNSKFFR-NEYNIIDCAYLIIDEVSMIPREILSKLLQAVPSHVKIIFAGDDAQLPPVNDTSII-------------- 555
Cdd:PRK10875  248 GAQPGSQRLRyHAGNPLHLDVLVVDEASMVDLPMMARLIDALPPHARVIFLGDRDQLASVEAGAVLgdicrfaeagysae 327

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 556 --PELEAL----------EFVNTVR-----LTQVFR-SEDAVLGQ---AYNVLGRKSIDyNLFGEDMKELVLKLISDG-- 612
Cdd:PRK10875  328 raQQLSRLtgchlpagtgTEAASVRdslclLRKSYRfGSDSGIGQlaaAVNRGDKRAAK-AVFQQGFSDIEKRPLQSGed 406

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 613 YQ-ILTNTRKLAKDINMIVQE--SKNDITKCFDDYKY------------NLNDR-------------------------- 651
Cdd:PRK10875  407 YQaMLEEALAGYGRYLDLLAAraEPEAILAAFNRYQLlcalregpfgvaGLNERieqalqqkrlirrpsgphsrwyegrp 486

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 652 VMIIANSSARNVSNGDTGKIIDFDERGVCVRLDLEDREVfykyedtEEIVP--------AYAFTVHKSQGSEYENVAVFV 723
Cdd:PRK10875  487 VMIARNDSALGLFNGDIGIALDRGQGELRVWFQLPDGNI-------KSVQPsrlpehetAWAMTVHKSQGSEFDHTALVL 559

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|.
gi 2216107309 724 DSQ--PKLnTNNLLYTGITRAKKDIKVYVpNEMVLTTMINT 762
Cdd:PRK10875  560 PNQftPVV-TRELVYTAITRARRRLSLYA-DERVLSAAIAT 598
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 410-583 6.75e-13

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.


Pssm-ID: 433343 [Multi-domain]  Cd Length: 191  Bit Score: 67.97  E-value: 6.75e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 410 GLTFDQVRLMKSFI--DNRITLLLGRAGTGKTYTLvNLLNRLKPDPNKT-IVCTYTGKASSRIRELFreydlqDYKSLTI 486
Cdd:pfam13604   1 TLNAEQAAAVRALLtsGDRVAVLVGPAGTGKTTAL-KALREAWEAAGYRvIGLAPTGRAAKVLGEEL------GIPADTI 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 487 HKTCASNfnskffRNEYNIIDCAYLIIDEVSMIPREILSKLLQAVPSH-VKIIFAGDDAQLPPVNDTSIIPELEAlEFVN 565
Cdd:pfam13604  74 AKLLHRL------GGRAGLDPGTLLIVDEAGMVGTRQMARLLKLAEDAgARVILVGDPRQLPSVEAGGAFRDLLA-AGIG 146

                         170
                  ....*....|....*...
gi 2216107309 566 TVRLTQVFRSEDAVLGQA 583
Cdd:pfam13604 147 TAELTEIVRQRDPWQRAA 164
TraA_Ti TIGR02768
Ti-type conjugative transfer relaxase TraA; This protein contains domains distinctive of a ...
 424-749 9.11e-13

Ti-type conjugative transfer relaxase TraA; This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.


Pssm-ID: 274289 [Multi-domain]  Cd Length: 744  Bit Score: 71.76  E-value: 9.11e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 424 DNRITLLLGRAGTGKTYTLVNLLNRLKPDPNKTIVCTYTGKASSrirelfreyDLQDYKSLTiHKTCASNfnSKFFRNEY 503
Cdd:TIGR02768 367 SGDIAVVVGRAGTGKSTMLKAAREAWEAAGYRVIGAALSGKAAE---------GLQAESGIE-SRTLASL--EYAWANGR 434

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 504 NII-DCAYLIIDEVSMIPREILSKLLQ-AVPSHVKIIFAGDDAQLPPVNDTSIIPELeaLEFVNTVRLTQVFRSEDAVLG 581
Cdd:TIGR02768 435 DLLsDKDVLVIDEAGMVGSRQMARVLKeAEEAGAKVVLVGDPEQLQPIEAGAAFRAI--AERIGYAELETIRRQREAWAR 512

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 582 QAYNVLGRKSIDYNL---------FGEDMK-ELVLKLISDGYQ------------ILTNTRKLAKDINMIVQESKNDITK 639
Cdd:TIGR02768 513 QASLELARGDVEKALaayrdhghiTIHDTReEAIEQVVADWKQdlreanpagsqiMLAHTRKDVRALNEAAREALIERGE 592

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 640 CFDDY---------KYNLNDRVMIIANSSARNVSNGDTGKIIDFDERGVCVRLDlEDREVFYKYEDTEEIVPAYAFTVHK 710
Cdd:TIGR02768 593 LGESIlfqtargerKFAAGDRIVFLENNRDLGVKNGMLGTVEEIEDGRLVVQLD-SGELVIIPQAEYDALDHGYATTIHK 671

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 2216107309 711 SQGSEYENvaVFVDSQPKLNtNNLLYTGITRAKKDIKVY 749
Cdd:TIGR02768 672 SQGVTVDR--AFVLASKSMD-RHLAYVAMTRHRESVQLY 707
UvrD_C_2 pfam13538
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ...
 702-750 3.00e-11

UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.


Pssm-ID: 463913 [Multi-domain]  Cd Length: 52  Bit Score: 59.12  E-value: 3.00e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2216107309 702 PAYAFTVHKSQGSEYENV----AVFVDSQPKLNTNNLLYTGITRAKKdiKVYV 750
Cdd:pfam13538   1 LAYALTVHKAQGSEFPAVflvdPDLTAHYHSMLRRRLLYTAVTRARK--KLVL 51
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 427-579 5.44e-09

DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438708 [Multi-domain]  Cd Length: 121  Bit Score: 54.93  E-value: 5.44e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 427 ITLLLGRAGTGKTYTLVNL-LNRLKPDPNKTI-VCTYTGKASSRIRelfreydlqdyksltihktcasnfnskffrneyn 504
Cdd:cd17934     1 ISLIQGPPGTGKTTTIAAIvLQLLKGLRGKRVlVTAQSNVAVDNVD---------------------------------- 46

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2216107309 505 iidcaYLIIDEVSMIPreiLSKLLQAVPSHVKIIFAGDDAQLPPVNDTSiipELEALEFVNTVRLTQVFRSEDAV 579
Cdd:cd17934    47 -----VVIIDEASQIT---EPELLIALIRAKKVVLVGDPKQLPPVVQED---HAALLGLSFILSLLLLFRLLLPG 110
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 687-750 2.49e-08

C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 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: 350173 [Multi-domain]  Cd Length: 89  Bit Score: 52.05  E-value: 2.49e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2216107309 687 DREVFYKY-----EDTEEIVPAYAFTVHKSQGSEYENVAVFVDSqPKLNTNNLLYTGITRAKKDIKVYV 750
Cdd:cd18786    22 DRAYLNQYlqglsLDEFDLQLVGAITIDSSQGLTFDVVTLYLPT-ANSLTPRRLYVALTRARKRLVIYD 89
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 427-549 4.59e-08

DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. 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. SF1 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: 438706 [Multi-domain]  Cd Length: 121  Bit Score: 52.10  E-value: 4.59e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 427 ITLLLGRAGTGKTYTLV----NLLNRLKPDPNKTIVCTYTGKASSRIRelfreydlqdyksltihktcasnfnskffrne 502
Cdd:cd17914     1 LSLIQGPPGTGKTRVLVkivaALMQNKNGEPGRILLVTPTNKAAAQLD-------------------------------- 48

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2216107309 503 yniidcaYLIIDEVSMIPREILSKLLQAVPSHVKIIFAGDDAQLPPV 549
Cdd:cd17914    49 -------NILVDEAAQILEPETSRLIDLALDQGRVILVGDHDQLGPV 88
AAA_22 pfam13401
AAA domain;
426-541 2.08e-07

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 50.42  E-value: 2.08e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 426 RITLLLGRAGTGKTYTLVNLLNRLK--PDPNKTIVCTYTGKASSRIRELFREYDLQDYKSLTIH---KTCASNFNSKFFR 500
Cdd:pfam13401   6 GILVLTGESGTGKTTLLRRLLEQLPevRDSVVFVDLPSGTSPKDLLRALLRALGLPLSGRLSKEellAALQQLLLALAVA 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2216107309 501 neyniidcAYLIIDEVSMIPREI---LSKLLQAVPSHVKIIFAG 541
Cdd:pfam13401  86 --------VVLIIDEAQHLSLEAleeLRDLLNLSSKLLQLILVG 121
COG3972 COG3972
Superfamily I DNA and RNA helicases [Replication, recombination and repair];
325-743 3.43e-07

Superfamily I DNA and RNA helicases [Replication, recombination and repair];


Pssm-ID: 443172 [Multi-domain]  Cd Length: 565  Bit Score: 53.68  E-value: 3.43e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 325 VFDYQLNSTNYEIPSNVGEVYESVEDFVKEHSKMLRDEHAIRLHHlvrdlelsdeikysymiHERLLQISSMDFLVERLG 404
Cdd:COG3972    89 ALFEVLLQVDRESVRNLTEDHLRSLRLLAASRRDFLFALLLPEIP-----------------PAPFVQALRLLNLVSLED 151

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 405 DYRTEGLTFD--QVRLMKSfIDNRITLLLGRAGTGKTytlVNLLNRLK----PDPNKTIVCTYTGKA-SSRIREL----- 472
Cdd:COG3972   152 FFLPLIAVLDlqQERIARS-IPDGPQRIRGVAGSGKT---VLLAAKAAylalKHPGWRILVTCFNRSlADHLRDLiprfl 227

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 473 --FREYDLQDYKSLTI-HKTCAS---NFNSKFFR----NEY---------NIID-------CAYLIIDEVSMIPREILSK 526
Cdd:COG3972   228 rrFSNGEPEDNVKLIVfHAWGGKllkQYGIPPLTfsqpNEAfdeackallEAIQgeiippiYDAILIDEAQDFEPEFLRL 307

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 527 LLQAV-PSHVKIIFAGDDAQlpPVNDTSIIPELEA-LEFVNTVRLTQVFRSEDAVLGQAYNV----------LGRKSIDY 594
Cdd:COG3972   308 LYQLLkPPKKRLIWAYDEAQ--NIYGRKIPSAGGIpAGIGRDTILKKNYRNTRPILTFAHAFgmgllrppglLQGDAEDY 385

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 595 NL--FGEDMKELVLKLISDGYQILTNTRKLAkDINMIVQESKNDITKCFDDYKYNLNDrVMIIANSSARNVSNGDtgKII 672
Cdd:COG3972   386 EVerPGDKVTLIRPPEPAGRKGPLPEFKKYD-DRAEELEAIAEEIKKNLRDEGLRPSD-IAVIYLGNNEAKELGD--RLA 461

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2216107309 673 DF-DERGV-CVRLDLEDREVFYKYEDTEEIVpayafTVHKSQGSEYENVAVF-VDSQPKLNTN----NLLYTGITRAK 743
Cdd:COG3972   462 AAlERQGIdSYIAGARSDPNFFWKDGGVTIS-----TIHRAKGLEAPVVIIVgLDQLAKGESLerlrNLLYVAMTRAR 534
UvrD-helicase pfam00580
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural ...
 425-507 7.27e-07

UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyze ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near to the carboxy-terminus relative to other members of the family.


Pssm-ID: 395462 [Multi-domain]  Cd Length: 267  Bit Score: 51.48  E-value: 7.27e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 425 NRITLLLGRAGTGKTYTLVN----LLNRLKPDPNKTIVCTYTGKASS----RIRELFREYDLQDYKSLTIHKTCA----S 492
Cdd:pfam00580  13 GGPLLVLAGAGSGKTRVLTEriayLILEGGIDPEEILAVTFTNKAARemkeRILKLLGKAELSELNISTFHSFCLrilrK 92

                          90
                  ....*....|....*
gi 2216107309 493 NFNSKFFRNEYNIID 507
Cdd:pfam00580  93 YANRIGLLPNFSILD 107
DEXQc_UvrD cd17932
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ...
 429-545 3.67e-06

DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. UvrD 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: 350690 [Multi-domain]  Cd Length: 189  Bit Score: 48.28  E-value: 3.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 429 LLLGRAGTGKTYTLV----NLLNRLKPDPNKTIVCTYTGKAS----SRIRELFREYDLQDYKSLTIHKTCAS------NF 494
Cdd:cd17932    16 LVLAGAGSGKTRVLThriaYLILEGGVPPERILAVTFTNKAAkemrERLRKLLGEQLASGVWIGTFHSFALRilrrygDF 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2216107309 495 NS------KFFRNEYNIID-----CAYLIIDE---VSMIPREILSKLLQavpSHVKIIFAGDDAQ 545
Cdd:cd17932    96 DDlllyalELLEENPDVREklqsrFRYILVDEyqdTNPLQYELLKLLAG---DGKNLFVVGDDDQ 157
PRK13889 PRK13889
conjugal transfer relaxase TraA; Provisional
 649-713 5.14e-05

conjugal transfer relaxase TraA; Provisional


Pssm-ID: 237546 [Multi-domain]  Cd Length: 988  Bit Score: 46.99  E-value: 5.14e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2216107309 649 NDRVMIIANSSARNVSNGDTGKIIDFDERGVCVRLDlEDREVFYKYEDTEEIVPAYAFTVHKSQG 713
Cdd:PRK13889  604 GDRVMFLQNERGLGVKNGTLGTIEQVSAQSMSVRLD-DGRSVAFDLKDYDRIDHGYAATIHKAQG 667
SH3_13 pfam18335
ATP-dependent RecD-like DNA helicase SH3 domain; This is an SH3 (SRC homology domain 3) domain ...
 641-682 2.73e-04

ATP-dependent RecD-like DNA helicase SH3 domain; This is an SH3 (SRC homology domain 3) domain found in RecD helicases (EC 3.6.4.12) that belong to the bacterial Superfamily 1B (SF1B). This superfamily of helicases translocate in a 5'-3' direction and are required for a range of cellular activities across all domains of life. Structural analysis indicate that the extension of the 5'-tail of the unwound DNA duplex induces a large conformational change in the RecD subunit, that is transferred through the RecC subunit to activate the nuclease domain of the RecB subunit. The process involves this SH3 domain that binds to a region of the RecB subunit. Studies of RecD in E. coli also revealed that the SH3 domain interacts with the ssDNA tail in a location different to that normally occupied by a peptide in canonical eukaryotic SH3 domains, thus retaining the potential to bind peptide at the same time as the ssDNA tail.


Pssm-ID: 465715 [Multi-domain]  Cd Length: 65  Bit Score: 39.77  E-value: 2.73e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2216107309 641 FDDYKYNLNDRVMIIANSSARNVSNGDTGKI--IDFDERGVCVR 682
Cdd:pfam18335  21 FGGRIFRVGDKVMQTKNNYDLGVFNGDIGIIvaIDKEEKTLTVD 64
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
 429-549 5.08e-04

DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and similar proteins. Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. All are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350796 [Multi-domain]  Cd Length: 229  Bit Score: 42.22  E-value: 5.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 429 LLLGRAGTGKTYTLVN-LLNRLKPDPNKTI-VCTYTGKAS----SRI-------RELFREYDLQ-DYKSLTIH-KTCASN 493
Cdd:cd18038    24 IIFGPPGTGKTVTLVEaILQVLRQPPEARIlVCAPSNSAAdllaERLlnalvtkREILRLNAPSrDRASVPPElLPYCNS 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 494 FNSKFFR-------NEYNIIDC------------------AYLIIDEV--SMIPrEILSKLLQAVPSHVKIIFAGDDAQL 546
Cdd:cd18038   104 KAEGTFRlpsleelKKYRIVVCtlmtagrlvqagvpnghfTHIFIDEAgqATEP-EALIPLSELASKNTQIVLAGDPKQL 182


                  ...
gi 2216107309 547 PPV 549
Cdd:cd18038   183 GPV 185
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
356-549 5.87e-04

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 43.58  E-value: 5.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 356 SKMLRDEHAIRLHHLVRDLELSDEIKYSYMIHERLLQISSMDFLVERLGDYRTEGLTFDQVRLMKSFIDNRITLLLGRAG 435
Cdd:COG1112   410 LLLALLLAAAAAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLLLAAAAALLALALLESLLEELI 489

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309 436 TGKTYTLVNLLNRLKPDPNKTIVCTYTGKASSRIRELFREyDLQDYKSLTIhKTCASNfnSKFFRNEYNIIDcaYLIIDE 515
Cdd:COG1112   490 EEHPEELEKLIAELREAARLRRALRRELKKRRELRKLLWD-ALLELAPVVG-MTPASV--ARLLPLGEGSFD--LVIIDE 563

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2216107309 516 VSMIPreiLSKLLQAVPSHVKIIFAGDDAQLPPV 549
Cdd:COG1112   564 ASQAT---LAEALGALARAKRVVLVGDPKQLPPV 594
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 705-749 1.26e-03

Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.


Pssm-ID: 366646 [Multi-domain]  Cd Length: 227  Bit Score: 41.21  E-value: 1.26e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2216107309 705 AFTVHKSQGSEYENVAVFVDSQPKLNTN----NLLYTGITRAKKDIKVY 749
Cdd:pfam01443 178 VTTVHEVQGLTFDSVTLVLDTDTDLLIIsdspEHLYVALTRHRKSLHIL 226
recB TIGR00609
exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with ...
 425-513 3.84e-03

exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with potent ATP-dependent exodeoxyribonuclease activity. Ejection of RecD, as occurs at chi recombinational hotspots, cripples exonuclease activity in favor of recombinagenic helicase activity. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273172 [Multi-domain]  Cd Length: 1087  Bit Score: 40.88  E-value: 3.84e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309  425 NRITLLLGRAGTGKTYTLVNLLNRL-----KPDPNKTIVCTYTGKASSRIRELFREyDLQDYKSLTIHKTcASNFNSKFF 499
Cdd:TIGR00609    9 NGTFLIEASAGTGKTFTIAQLYLRLlleggPLTVEEILVVTFTNAATEELKTRIRG-RIHQALRALKAAL-TSQELPEPL 86

                           90
                   ....*....|....
gi 2216107309  500 RNEYNIIDCAYLII 513
Cdd:TIGR00609   87 KEAIQDEKVKQAIT 100
TraI_TIGR TIGR02760
conjugative transfer relaxase protein TraI; This protein is a component of the relaxosome ...
 650-771 4.93e-03

conjugative transfer relaxase protein TraI; This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.


Pssm-ID: 274285 [Multi-domain]  Cd Length: 1960  Bit Score: 40.66  E-value: 4.93e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309  650 DRVMIIANSSAR--------NVSNGDTGKIIDFDERGVCVRLDLE-DREVFYKYedteeivpAYAFTVHKSQGSEYENVA 720
Cdd:TIGR02760 1393 DKIRLRATDKNRgikanevyTVTQVVNGLSVQLSKVKNSLSLKPIqAKDKHWDY--------AYTRTADSAQGATYTFVI 1464

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2216107309  721 VFVDSQPKLNTNNLLYTGITRAKKDIKVYVPN--EMVLTTMINTVPEPVSNVT 771
Cdd:TIGR02760 1465 ALIKGRLALTNYRSAYIDLTRASHHVELYTDNkeGTVKSWKQREANKTSAVET 1517
AAA_7 pfam12775
P-loop containing dynein motor region; This domain is found in human cytoplasmic dynein-2 ...
 412-462 6.84e-03

P-loop containing dynein motor region; This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities (AAA1-AAA6). This is the third nucleotide binding sites in the dynein motor. However, AAA3 has lost the catalytic residues necessary for ATP hydrolysis (the Walker B glutamate, the arginine finger, sensor-I and sensor-II motifs).


Pssm-ID: 463698 [Multi-domain]  Cd Length: 179  Bit Score: 38.14  E-value: 6.84e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2216107309 412 TFDQVR---LMKSFIDNRITLLL-GRAGTGKTYTLVNLLNRLKPDPNKTIVCTYT 462
Cdd:pfam12775  14 TVDTVRytyLLDLLLKNGKPVLLvGPTGTGKTVIIQNLLRKLDKEKYLPLFINFS 68
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 425-555 7.43e-03

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 37.74  E-value: 7.43e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2216107309  425 NRITLLLGRAGTGKTYTLVNLLNRLKPDPNKTIVCTytgkassriRELFREYDLQDYKSLTIHKTCASNFNSKFFRN--- 501
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYID---------GEDILEEVLDQLLLIIVGGKKASGSGELRLRLala 72

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2216107309  502 --EYNIIDCayLIIDEVSMIPREILSKLLQavpshvKIIFAGDDAQLPPVNDTSII 555
Cdd:smart00382  73 laRKLKPDV--LILDEITSLLDAEQEALLL------LLEELRLLLLLKSEKNLTVI 120
RecB COG1074
3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, ...
 434-475 8.78e-03

3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440692 [Multi-domain]  Cd Length: 866  Bit Score: 39.56  E-value: 8.78e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2216107309 434 AGTGKTYTLVNLLNRL---KPDPNKTIVC-TYTGKA----SSRIRELFRE 475
Cdd:COG1074    27 AGSGKTYTLVARYLRLlleRGLDPEEILVvTFTRAAaaemRERIRERLAE 76
 
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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