NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|402282422|gb|EJU30975|]
View 

helicase, RecD/TraA family [Selenomonas sp. CM52]

Protein Classification

ATP-dependent RecD-like DNA helicase( domain architecture ID 1001067)

ATP-dependent RecD-like DNA helicase acts as a DNA-dependent ATPase (ssDNA better than dsDNA) and ATP-dependent 5'-3' DNA helicase

EC:  3.6.4.12
Gene Ontology:  GO:0004386|GO:0003677|GO:0008094|GO:0017116|GO:0016887|GO:0006310|GO:0043139

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
recD_rel super family cl36909
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 4-716 0e+00

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]


The actual alignment was detected with superfamily member TIGR01448:

Pssm-ID: 273632 [Multi-domain]  Cd Length: 720  Bit Score: 585.60  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422    4 LEGTAQSVVFAAPEGGFTVFRLR--PSGRRGLVTVTANAPAPLVGQEIALSGEWVQHPRFGEQFKAATLRVSAPTSLAGI 81
Cdd:TIGR01448   1 FSGTVEKILFENSTNFYVVLAVLrdETGEDTDATVVGVLPPLDEGDTYTFEGQWEEHAKYGYQFRAERMELEAPTSKEGI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422   82 ERFLASGAIAGIGEAMAHRLVQKFGKETLEIIEKKPSRLTEVAGVGKKTAAKIHASYMEKEELREIMLWLEMHGVSGAYA 161
Cdd:TIGR01448  81 VAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQWSQQGDERRLLAGLQGLGIGIKLA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  162 ARIFETYSSFAIEVMEKHPYRLARDVAGIGFLTADAIAKSAGIAEDSKERIEAGLGHAL-LTVSQQGHCCIPAPALTERA 240
Cdd:TIGR01448 161 QRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQALGIALNDPRRITAGLVYSLqQACTEEGHTYLPRNRFIKQV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  241 AKLLGTPTEEvREVLKEALAAERLAFEE----VGAETLIYPPWLYRAEKRTAQMLFFLQQKAAVLPAEKAAAIVADWERA 316
Cdd:TIGR01448 241 VHLLNVQPQE-RLLVPEAVELERLYLDEepklAAEDGRIYLPSLFRAEKQIASHIRRLLATSPAIGAINDQEHIWEVEKK 319

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  317 AGITLAAEQQQAVAAVLDHAVFVLTGGPGTGKTTVVRGMIAVLESQG--LSVLLGAPTGRAAKRLAEATGRKAETVHRLL 394
Cdd:TIGR01448 320 LRKGLSEEQKQALDTAIQHKVVILTGGPGTGKTTITRAIIELAEELGglLPVGLAAPTGRAAKRLGEVTGLTASTIHRLL 399

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  395 GAQGgieaDGSPvfEKDADDPLDADAIILDEVSMMDIVLMEHFLEAVPEGARVIFVGDVDQLPAVGPGSVLKDILRSGAV 474
Cdd:TIGR01448 400 GYGP----DTFR--HNHLEDPIDCDLLIVDESSMMDTWLALSLLAALPDHARLLLVGDTDQLPSVGPGQVLKDLILSQAI 473

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  475 PSVRLKEVFRQSGEGTIVLNAHAINRGRMPqftAGGDFEFL--EMPDEEAAARRIVALCREELP--REGFNALEDVQVLS 550
Cdd:TIGR01448 474 PVTRLTKVYRQAAGSPIITLAHGILHGEAP---AWGDFKFLnlTRSEPEGAARHIPLMVEKIVGmaRVGGIPGADIQVLA 550

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  551 PMHRTPCGVDNLNRLLQAALNPPAPEKAEFRNSTLTFRVGDKVMQTKNDYTKGVFNGDIGFIreVSADGVKVRYSEELTA 630
Cdd:TIGR01448 551 PMYKGPLGIDALNQHLQALLNPYQKGQGGIEIAEGEYRKGDRVMQTKNDYNNEIFNGDLGMI--VKIEGAKQGKKDQVVV 628

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  631 DYEPN-------ELMMLTLAYAMSVHKSQGSEYPVIVLPLVAAHHIMLQRNLLYTAVTRAKKKVVLLGSKAAVFTAVSND 703
Cdd:TIGR01448 629 DFDGNeveltraELFNLTLAYATSIHKSQGSEFPTVILPIHTAHMRMLYRNLLYTALTRAKKRVILVGSAEAFDIAAARQ 708

                         730
                  ....*....|...
gi 402282422  704 RTRRRyTLLAERL 716
Cdd:TIGR01448 709 GQARN-TGLLERI 720
 
Name Accession Description Interval E-value
recD_rel TIGR01448
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 4-716 0e+00

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: 585.60  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422    4 LEGTAQSVVFAAPEGGFTVFRLR--PSGRRGLVTVTANAPAPLVGQEIALSGEWVQHPRFGEQFKAATLRVSAPTSLAGI 81
Cdd:TIGR01448   1 FSGTVEKILFENSTNFYVVLAVLrdETGEDTDATVVGVLPPLDEGDTYTFEGQWEEHAKYGYQFRAERMELEAPTSKEGI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422   82 ERFLASGAIAGIGEAMAHRLVQKFGKETLEIIEKKPSRLTEVAGVGKKTAAKIHASYMEKEELREIMLWLEMHGVSGAYA 161
Cdd:TIGR01448  81 VAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQWSQQGDERRLLAGLQGLGIGIKLA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  162 ARIFETYSSFAIEVMEKHPYRLARDVAGIGFLTADAIAKSAGIAEDSKERIEAGLGHAL-LTVSQQGHCCIPAPALTERA 240
Cdd:TIGR01448 161 QRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQALGIALNDPRRITAGLVYSLqQACTEEGHTYLPRNRFIKQV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  241 AKLLGTPTEEvREVLKEALAAERLAFEE----VGAETLIYPPWLYRAEKRTAQMLFFLQQKAAVLPAEKAAAIVADWERA 316
Cdd:TIGR01448 241 VHLLNVQPQE-RLLVPEAVELERLYLDEepklAAEDGRIYLPSLFRAEKQIASHIRRLLATSPAIGAINDQEHIWEVEKK 319

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  317 AGITLAAEQQQAVAAVLDHAVFVLTGGPGTGKTTVVRGMIAVLESQG--LSVLLGAPTGRAAKRLAEATGRKAETVHRLL 394
Cdd:TIGR01448 320 LRKGLSEEQKQALDTAIQHKVVILTGGPGTGKTTITRAIIELAEELGglLPVGLAAPTGRAAKRLGEVTGLTASTIHRLL 399

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  395 GAQGgieaDGSPvfEKDADDPLDADAIILDEVSMMDIVLMEHFLEAVPEGARVIFVGDVDQLPAVGPGSVLKDILRSGAV 474
Cdd:TIGR01448 400 GYGP----DTFR--HNHLEDPIDCDLLIVDESSMMDTWLALSLLAALPDHARLLLVGDTDQLPSVGPGQVLKDLILSQAI 473

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  475 PSVRLKEVFRQSGEGTIVLNAHAINRGRMPqftAGGDFEFL--EMPDEEAAARRIVALCREELP--REGFNALEDVQVLS 550
Cdd:TIGR01448 474 PVTRLTKVYRQAAGSPIITLAHGILHGEAP---AWGDFKFLnlTRSEPEGAARHIPLMVEKIVGmaRVGGIPGADIQVLA 550

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  551 PMHRTPCGVDNLNRLLQAALNPPAPEKAEFRNSTLTFRVGDKVMQTKNDYTKGVFNGDIGFIreVSADGVKVRYSEELTA 630
Cdd:TIGR01448 551 PMYKGPLGIDALNQHLQALLNPYQKGQGGIEIAEGEYRKGDRVMQTKNDYNNEIFNGDLGMI--VKIEGAKQGKKDQVVV 628

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  631 DYEPN-------ELMMLTLAYAMSVHKSQGSEYPVIVLPLVAAHHIMLQRNLLYTAVTRAKKKVVLLGSKAAVFTAVSND 703
Cdd:TIGR01448 629 DFDGNeveltraELFNLTLAYATSIHKSQGSEFPTVILPIHTAHMRMLYRNLLYTALTRAKKRVILVGSAEAFDIAAARQ 708

                         730
                  ....*....|...
gi 402282422  704 RTRRRyTLLAERL 716
Cdd:TIGR01448 709 GQARN-TGLLERI 720
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 195-717 3.71e-139

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: 418.61  E-value: 3.71e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 195 ADAIAKSAGIAedskerieagLGHALLTVSQQGHCCiPAPALteRAAKLLGTPtEEVREVLKEALAAERLAFEEVgaetl 274
Cdd:COG0507   20 ADFIARDDPIR----------AAALLSRAAGEGHTF-PLEDL--AAARLLGVA-EDIEAALAALVESGPLVLDGR----- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 275 IYPPWLYRAEKRTAQmlFFLQQKAAVLPAEKAAAIVADWERAAGITLAAEQQQAVAAVL-DHAVFVLtggpgtgkttVVR 353
Cdd:COG0507   81 RYLTRLLEAEQRLAR--RLRRLARPALDEADVEAALAALEPRAGITLSDEQREAVALALtTRRVSVLtggagtgkttTLR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 354 GMIAVLESQGLSVLLGAPTGRAAKRLAEATGRKAETVHRLLGAQGGieadgSPVFEKDADDPLDADA-IILDEVSMMDIV 432
Cdd:COG0507  159 ALLAALEALGLRVALAAPTGKAAKRLSESTGIEARTIHRLLGLRPD-----SGRFRHNRDNPLTPADlLVVDEASMVDTR 233

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 433 LMEHFLEAVPE-GARVIFVGDVDQLPAVGPGSVLKDILRSGAVPSVRLKEVFRQSGEGTIVLNAHAINRGRMPQF--TAG 509
Cdd:COG0507  234 LMAALLEALPRaGARLILVGDPDQLPSVGAGAVLRDLIESGTVPVVELTEVYRQADDSRIIELAHAIREGDAPEAlnARY 313

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 510 GDFEFLEMPDEEAAARRIVALCREElPREGfnalEDVQVLSPMhrtPCGVDNLNRLLQAALNPPAPEKAEF-RNSTLTFR 588
Cdd:COG0507  314 ADVVFVEAEDAEEAAEAIVELYADR-PAGG----EDIQVLAPT---NAGVDALNQAIREALNPAGELERELaEDGELELY 385

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 589 VGDKVMQTKNDYTKGVFNGDIGFIREVSADG--VKVRYSEELTADYEPNELMMLTLAYAMSVHKSQGSEYPVIVLPLVAA 666
Cdd:COG0507  386 VGDRVMFTRNDYDLGVFNGDIGTVLSIDEDEgrLTVRFDGREIVTYDPSELDQLELAYAITVHKSQGSTFDRVILVLPSE 465

                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|.
gi 402282422 667 HHIMLQRNLLYTAVTRAKKKVVLLGSKAAVFTAVSNDrtRRRYTLLAERLA 717
Cdd:COG0507  466 HSPLLSRELLYTALTRARELLTLVGDRDALARAVRRD--TARATGLAERLR 514
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 333-483 1.65e-41

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: 148.47  E-value: 1.65e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 333 LDHAVFVLTGGPGTGKTTVVRGMIAVLESQGLSVLLGAPTGRAAKRLAEATGRKAETVHRLLGAQGgieadGSPVFEKDA 412
Cdd:cd17933   10 LRNRVSVLTGGAGTGKTTTLKALLAALEAEGKRVVLAAPTGKAAKRLSESTGIEASTIHRLLGINP-----GGGGFYYNE 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 402282422 413 DDPLDADAIILDEVSMMDIVLMEHFLEAVPEGARVIFVGDVDQLPAVGPGSVLKDILRSGAVPSVRLKEVF 483
Cdd:cd17933   85 ENPLDADLLIVDEASMVDTRLMAALLSAIPAGARLILVGDPDQLPSVGAGNVLRDLIASKGVPTVELTEVF 155
recD PRK10875
exodeoxyribonuclease V subunit alpha;
355-720 2.46e-36

exodeoxyribonuclease V subunit alpha;


Pssm-ID: 236783 [Multi-domain]  Cd Length: 615  Bit Score: 145.08  E-value: 2.46e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 355 MIAVLESQGLSVLLGAPTGRAAKRLAEATG-----------------RKAETVHRLLGAQGGIEA----DGSPVfekdad 413
Cdd:PRK10875 191 LIQLADGERCRIRLAAPTGKAAARLTESLGkalrqlpltdeqkkripEEASTLHRLLGAQPGSQRlryhAGNPL------ 264

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 414 dplDADAIILDEVSMMDIVLMEHFLEAVPEGARVIFVGDVDQLPAVGPGSVLKDILR----------------------- 470
Cdd:PRK10875 265 ---HLDVLVVDEASMVDLPMMARLIDALPPHARVIFLGDRDQLASVEAGAVLGDICRfaeagysaeraqqlsrltgchlp 341

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 471 ---SGAVPSVR-----LKEVFR---QSGEGTIvlnAHAINRG---RMPQFTAGG--DFEFLEMPDEE----------AAA 524
Cdd:PRK10875 342 agtGTEAASVRdslclLRKSYRfgsDSGIGQL---AAAVNRGdkrAAKAVFQQGfsDIEKRPLQSGEdyqamleealAGY 418

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 525 RRIVALCRE-ELPREGFNALEDVQVLSPMHRTPCGVDNLNRLLQAALN-------PPAPEKAEFrnstltfrVGDKVMQT 596
Cdd:PRK10875 419 GRYLDLLAArAEPEAILAAFNRYQLLCALREGPFGVAGLNERIEQALQqkrlirrPSGPHSRWY--------EGRPVMIA 490

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 597 KNDYTKGVFNGDIGFI--REVSADGVKVRYSEELTADYEPNELMMLTLAYAMSVHKSQGSEY--PVIVLPlvaaHHIM-- 670
Cdd:PRK10875 491 RNDSALGLFNGDIGIAldRGQGELRVWFQLPDGNIKSVQPSRLPEHETAWAMTVHKSQGSEFdhTALVLP----NQFTpv 566

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|
gi 402282422 671 LQRNLLYTAVTRAKKKVVLLGSKAAVFTAVSNdRTRRRyTLLAERLAGAG 720
Cdd:PRK10875 567 VTRELVYTAITRARRRLSLYADERVLSAAIAT-RTERR-SGLAARLSSRA 614
HHH_4 pfam14490
Helix-hairpin-helix containing domain; This presumed domain contains at least one ...
 140-230 5.40e-36

Helix-hairpin-helix containing domain; This presumed domain contains at least one helix-hairpin-helix motif. This domain is often found in RecD helicases.


Pssm-ID: 464187 [Multi-domain]  Cd Length: 91  Bit Score: 130.70  E-value: 5.40e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  140 EKEELREIMLWLEMHGVSGAYAARIFETYSSFAIEVMEKHPYRLARDVAGIGFLTADAIAKSAGIAEDSKERIEAGLGHA 219
Cdd:pfam14490   1 EQRGLREVMIFLQQYGISPALAVKIYKKYGEDALEILKENPYRLAEDIEGIGFKTADKIARKLGIAPDSPERIRAGILYV 80

                          90
                  ....*....|.
gi 402282422  220 LLTVSQQGHCC 230
Cdd:pfam14490  81 LKQAASNGHTY 91
 
Name Accession Description Interval E-value
recD_rel TIGR01448
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 4-716 0e+00

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: 585.60  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422    4 LEGTAQSVVFAAPEGGFTVFRLR--PSGRRGLVTVTANAPAPLVGQEIALSGEWVQHPRFGEQFKAATLRVSAPTSLAGI 81
Cdd:TIGR01448   1 FSGTVEKILFENSTNFYVVLAVLrdETGEDTDATVVGVLPPLDEGDTYTFEGQWEEHAKYGYQFRAERMELEAPTSKEGI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422   82 ERFLASGAIAGIGEAMAHRLVQKFGKETLEIIEKKPSRLTEVAGVGKKTAAKIHASYMEKEELREIMLWLEMHGVSGAYA 161
Cdd:TIGR01448  81 VAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQWSQQGDERRLLAGLQGLGIGIKLA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  162 ARIFETYSSFAIEVMEKHPYRLARDVAGIGFLTADAIAKSAGIAEDSKERIEAGLGHAL-LTVSQQGHCCIPAPALTERA 240
Cdd:TIGR01448 161 QRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQALGIALNDPRRITAGLVYSLqQACTEEGHTYLPRNRFIKQV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  241 AKLLGTPTEEvREVLKEALAAERLAFEE----VGAETLIYPPWLYRAEKRTAQMLFFLQQKAAVLPAEKAAAIVADWERA 316
Cdd:TIGR01448 241 VHLLNVQPQE-RLLVPEAVELERLYLDEepklAAEDGRIYLPSLFRAEKQIASHIRRLLATSPAIGAINDQEHIWEVEKK 319

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  317 AGITLAAEQQQAVAAVLDHAVFVLTGGPGTGKTTVVRGMIAVLESQG--LSVLLGAPTGRAAKRLAEATGRKAETVHRLL 394
Cdd:TIGR01448 320 LRKGLSEEQKQALDTAIQHKVVILTGGPGTGKTTITRAIIELAEELGglLPVGLAAPTGRAAKRLGEVTGLTASTIHRLL 399

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  395 GAQGgieaDGSPvfEKDADDPLDADAIILDEVSMMDIVLMEHFLEAVPEGARVIFVGDVDQLPAVGPGSVLKDILRSGAV 474
Cdd:TIGR01448 400 GYGP----DTFR--HNHLEDPIDCDLLIVDESSMMDTWLALSLLAALPDHARLLLVGDTDQLPSVGPGQVLKDLILSQAI 473

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  475 PSVRLKEVFRQSGEGTIVLNAHAINRGRMPqftAGGDFEFL--EMPDEEAAARRIVALCREELP--REGFNALEDVQVLS 550
Cdd:TIGR01448 474 PVTRLTKVYRQAAGSPIITLAHGILHGEAP---AWGDFKFLnlTRSEPEGAARHIPLMVEKIVGmaRVGGIPGADIQVLA 550

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  551 PMHRTPCGVDNLNRLLQAALNPPAPEKAEFRNSTLTFRVGDKVMQTKNDYTKGVFNGDIGFIreVSADGVKVRYSEELTA 630
Cdd:TIGR01448 551 PMYKGPLGIDALNQHLQALLNPYQKGQGGIEIAEGEYRKGDRVMQTKNDYNNEIFNGDLGMI--VKIEGAKQGKKDQVVV 628

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  631 DYEPN-------ELMMLTLAYAMSVHKSQGSEYPVIVLPLVAAHHIMLQRNLLYTAVTRAKKKVVLLGSKAAVFTAVSND 703
Cdd:TIGR01448 629 DFDGNeveltraELFNLTLAYATSIHKSQGSEFPTVILPIHTAHMRMLYRNLLYTALTRAKKRVILVGSAEAFDIAAARQ 708

                         730
                  ....*....|...
gi 402282422  704 RTRRRyTLLAERL 716
Cdd:TIGR01448 709 GQARN-TGLLERI 720
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 195-717 3.71e-139

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: 418.61  E-value: 3.71e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 195 ADAIAKSAGIAedskerieagLGHALLTVSQQGHCCiPAPALteRAAKLLGTPtEEVREVLKEALAAERLAFEEVgaetl 274
Cdd:COG0507   20 ADFIARDDPIR----------AAALLSRAAGEGHTF-PLEDL--AAARLLGVA-EDIEAALAALVESGPLVLDGR----- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 275 IYPPWLYRAEKRTAQmlFFLQQKAAVLPAEKAAAIVADWERAAGITLAAEQQQAVAAVL-DHAVFVLtggpgtgkttVVR 353
Cdd:COG0507   81 RYLTRLLEAEQRLAR--RLRRLARPALDEADVEAALAALEPRAGITLSDEQREAVALALtTRRVSVLtggagtgkttTLR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 354 GMIAVLESQGLSVLLGAPTGRAAKRLAEATGRKAETVHRLLGAQGGieadgSPVFEKDADDPLDADA-IILDEVSMMDIV 432
Cdd:COG0507  159 ALLAALEALGLRVALAAPTGKAAKRLSESTGIEARTIHRLLGLRPD-----SGRFRHNRDNPLTPADlLVVDEASMVDTR 233

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 433 LMEHFLEAVPE-GARVIFVGDVDQLPAVGPGSVLKDILRSGAVPSVRLKEVFRQSGEGTIVLNAHAINRGRMPQF--TAG 509
Cdd:COG0507  234 LMAALLEALPRaGARLILVGDPDQLPSVGAGAVLRDLIESGTVPVVELTEVYRQADDSRIIELAHAIREGDAPEAlnARY 313

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 510 GDFEFLEMPDEEAAARRIVALCREElPREGfnalEDVQVLSPMhrtPCGVDNLNRLLQAALNPPAPEKAEF-RNSTLTFR 588
Cdd:COG0507  314 ADVVFVEAEDAEEAAEAIVELYADR-PAGG----EDIQVLAPT---NAGVDALNQAIREALNPAGELERELaEDGELELY 385

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 589 VGDKVMQTKNDYTKGVFNGDIGFIREVSADG--VKVRYSEELTADYEPNELMMLTLAYAMSVHKSQGSEYPVIVLPLVAA 666
Cdd:COG0507  386 VGDRVMFTRNDYDLGVFNGDIGTVLSIDEDEgrLTVRFDGREIVTYDPSELDQLELAYAITVHKSQGSTFDRVILVLPSE 465

                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|.
gi 402282422 667 HHIMLQRNLLYTAVTRAKKKVVLLGSKAAVFTAVSNDrtRRRYTLLAERLA 717
Cdd:COG0507  466 HSPLLSRELLYTALTRARELLTLVGDRDALARAVRRD--TARATGLAERLR 514
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 204-707 5.21e-53

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: 193.05  E-value: 5.21e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  204 IAEDSKERIEAGLghALLTVS-QQGHCCIPApALTERAAKLLGTPTEEVREVLK----EALAAERLAFEEVGAETL---- 274
Cdd:TIGR01447  24 LAQKSNEEVALFA--AVASALlRRGHPCLDL-EKAAKSPGLTGISEPDLGEKLNfdwlAALPASVLVGLPGETAPPlvlc 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  275 ---IYPPWLYRAEKRTAQmlfFLQQKAAVLPAEKAAAIVADWERAAgiTLAAEQQQAVAAVLDHAVFVLTGGPGTGKTTV 351
Cdd:TIGR01447 101 dgrLYLRRYWREEEKLAA---KLRTLLEARKRTAPSAILENLFPLL--NEQNWRKTAVALALKSNFSLITGGPGTGKTTT 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  352 VRGMIAVLESQ-----GLSVLLGAPTGRAAKRLAEATGRK-----------------AETVHRLLGAQggieaDGSPVFE 409
Cdd:TIGR01447 176 VARLLLALVKQspkqgKLRIALAAPTGKAAARLAESLRKAvknlaaaealiaalpseAVTIHRLLGIK-----PDTKRFR 250

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  410 KDADDPLDADAIILDEVSMMDIVLMEHFLEAVPEGARVIFVGDVDQLPAVGPGSVLKDILR---SGAVPSV--------- 477
Cdd:TIGR01447 251 HHERNPLPLDVLVVDEASMVDLPLMAKLLKALPPNTKLILLGDKNQLPSVEAGAVLGDLCElasIGKSILYalckkinsk 330

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  478 ----------RLKEVFRQSGEGTIVLNAHAINRGRMPQFTA----GGDFEFLEMPDEEAAARRIVALCR----------- 532
Cdd:TIGR01447 331 trnplsdnvcFLKTSHRFGKDSGIGQLAKAINSGDIEAVLNnlrsGQLIEFEFLNSKEDAIERLKNLYVkyrtflqklaa 410

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  533 EELPREGFNALEDVQVLSPMHRTPCGVDNLNRLLQAALNppapEKAEFRNSTLTFrVGDKVMQTKNDYTKGVFNGDIGFI 612
Cdd:TIGR01447 411 LSDAKEILETFDRLRLLTALRDGPFGVLGLNRRIEQELQ----EKYFDPDEEGWY-IGRPIMVTENDYTLGLFNGDIGVL 485

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  613 REVSADGVKVRYS-EELTADYEPNELMMLTLAYAMSVHKSQGSEYPVIVLPLVAAHHIMLQRNLLYTAVTRAKKKVVLLG 691
Cdd:TIGR01447 486 LRDPDGILTVWFHfADGSKAVLPSRLPNYETAFAMTVHKSQGSEFDHVILILPNGNSPVLTRELLYTGITRAKDQLSVWS 565

                         570
                  ....*....|....*.
gi 402282422  692 SKAAVFTAVSNdRTRR 707
Cdd:TIGR01447 566 DKETLNAAIKR-KNKR 580
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 333-483 1.65e-41

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: 148.47  E-value: 1.65e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 333 LDHAVFVLTGGPGTGKTTVVRGMIAVLESQGLSVLLGAPTGRAAKRLAEATGRKAETVHRLLGAQGgieadGSPVFEKDA 412
Cdd:cd17933   10 LRNRVSVLTGGAGTGKTTTLKALLAALEAEGKRVVLAAPTGKAAKRLSESTGIEASTIHRLLGINP-----GGGGFYYNE 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 402282422 413 DDPLDADAIILDEVSMMDIVLMEHFLEAVPEGARVIFVGDVDQLPAVGPGSVLKDILRSGAVPSVRLKEVF 483
Cdd:cd17933   85 ENPLDADLLIVDEASMVDTRLMAALLSAIPAGARLILVGDPDQLPSVGAGNVLRDLIASKGVPTVELTEVF 155
recD PRK10875
exodeoxyribonuclease V subunit alpha;
355-720 2.46e-36

exodeoxyribonuclease V subunit alpha;


Pssm-ID: 236783 [Multi-domain]  Cd Length: 615  Bit Score: 145.08  E-value: 2.46e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 355 MIAVLESQGLSVLLGAPTGRAAKRLAEATG-----------------RKAETVHRLLGAQGGIEA----DGSPVfekdad 413
Cdd:PRK10875 191 LIQLADGERCRIRLAAPTGKAAARLTESLGkalrqlpltdeqkkripEEASTLHRLLGAQPGSQRlryhAGNPL------ 264

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 414 dplDADAIILDEVSMMDIVLMEHFLEAVPEGARVIFVGDVDQLPAVGPGSVLKDILR----------------------- 470
Cdd:PRK10875 265 ---HLDVLVVDEASMVDLPMMARLIDALPPHARVIFLGDRDQLASVEAGAVLGDICRfaeagysaeraqqlsrltgchlp 341

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 471 ---SGAVPSVR-----LKEVFR---QSGEGTIvlnAHAINRG---RMPQFTAGG--DFEFLEMPDEE----------AAA 524
Cdd:PRK10875 342 agtGTEAASVRdslclLRKSYRfgsDSGIGQL---AAAVNRGdkrAAKAVFQQGfsDIEKRPLQSGEdyqamleealAGY 418

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 525 RRIVALCRE-ELPREGFNALEDVQVLSPMHRTPCGVDNLNRLLQAALN-------PPAPEKAEFrnstltfrVGDKVMQT 596
Cdd:PRK10875 419 GRYLDLLAArAEPEAILAAFNRYQLLCALREGPFGVAGLNERIEQALQqkrlirrPSGPHSRWY--------EGRPVMIA 490

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 597 KNDYTKGVFNGDIGFI--REVSADGVKVRYSEELTADYEPNELMMLTLAYAMSVHKSQGSEY--PVIVLPlvaaHHIM-- 670
Cdd:PRK10875 491 RNDSALGLFNGDIGIAldRGQGELRVWFQLPDGNIKSVQPSRLPEHETAWAMTVHKSQGSEFdhTALVLP----NQFTpv 566

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|
gi 402282422 671 LQRNLLYTAVTRAKKKVVLLGSKAAVFTAVSNdRTRRRyTLLAERLAGAG 720
Cdd:PRK10875 567 VTRELVYTAITRARRRLSLYADERVLSAAIAT-RTERR-SGLAARLSSRA 614
HHH_4 pfam14490
Helix-hairpin-helix containing domain; This presumed domain contains at least one ...
 140-230 5.40e-36

Helix-hairpin-helix containing domain; This presumed domain contains at least one helix-hairpin-helix motif. This domain is often found in RecD helicases.


Pssm-ID: 464187 [Multi-domain]  Cd Length: 91  Bit Score: 130.70  E-value: 5.40e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  140 EKEELREIMLWLEMHGVSGAYAARIFETYSSFAIEVMEKHPYRLARDVAGIGFLTADAIAKSAGIAEDSKERIEAGLGHA 219
Cdd:pfam14490   1 EQRGLREVMIFLQQYGISPALAVKIYKKYGEDALEILKENPYRLAEDIEGIGFKTADKIARKLGIAPDSPERIRAGILYV 80

                          90
                  ....*....|.
gi 402282422  220 LLTVSQQGHCC 230
Cdd:pfam14490  81 LKQAASNGHTY 91
AAA_19 pfam13245
AAA domain;
351-461 5.86e-30

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 115.01  E-value: 5.86e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  351 VVRGMIAVLESQG---LSVLLGAPTGRAAKRLAEATGRKAETVHRLLGAQGGIEADgspvFEKDADDPLDADAIILDEVS 427
Cdd:pfam13245  27 TIRHIVALLVALGgvsFPILLAAPTGRAAKRLSERTGLPASTIHRLLGFDDLEAGG----FLRDEEEPLDGDLLIVDEFS 102

                          90       100       110
                  ....*....|....*....|....*....|....
gi 402282422  428 MMDIVLMEHFLEAVPEGARVIFVGDVDQLPAVGP 461
Cdd:pfam13245 103 MVDLPLAYRLLKALPDGAQLLLVGDPDQLPSVGP 136
SH3_13 pfam18335
ATP-dependent RecD-like DNA helicase SH3 domain; This is an SH3 (SRC homology domain 3) domain ...
 562-623 1.03e-27

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: 106.02  E-value: 1.03e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 402282422  562 LNRLLQAALNPPAPEKAEFRNSTLTFRVGDKVMQTKNDYTKGVFNGDIGFIREVSADGVKVR 623
Cdd:pfam18335   1 LNQRLQEALNPPSPGKKEIKFGGRIFRVGDKVMQTKNNYDLGVFNGDIGIIVAIDKEEKTLT 62
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 346-505 4.09e-27

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: 108.81  E-value: 4.09e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  346 TGKTTVVRGMIAVLESQGLSVLLGAPTGRAAKRLAEATGRKAETVHRLLGAQGGIEADGSPvfekdaddpldaDAIILDE 425
Cdd:pfam13604  29 TGKTTALKALREAWEAAGYRVIGLAPTGRAAKVLGEELGIPADTIAKLLHRLGGRAGLDPG------------TLLIVDE 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  426 VSMMDIVLMEHFLEAVPE-GARVIFVGDVDQLPAVGPGSVLKDILRSGAvPSVRLKEVFRQSGEGtIVLNAHAINRGRMP 504
Cdd:pfam13604  97 AGMVGTRQMARLLKLAEDaGARVILVGDPRQLPSVEAGGAFRDLLAAGI-GTAELTEIVRQRDPW-QRAASLALRDGDPA 174


                  .
gi 402282422  505 Q 505
Cdd:pfam13604 175 E 175
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
 635-691 3.00e-19

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: 82.61  E-value: 3.00e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 402282422 635 NELMmltLAYAMSVHKSQGSEYPVIVLPLVAAHHiMLQRNLLYTAVTRAKKKVVLLG 691
Cdd:cd18809   28 NERL---QAYAMTIHKSQGSEFDRVIVVLPTSHP-MLSRGLLYTALTRARKLLTLVG 80
TraA_Ti TIGR02768
Ti-type conjugative transfer relaxase TraA; This protein contains domains distinctive of a ...
 360-689 8.40e-17

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: 84.86  E-value: 8.40e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  360 ESQGLSVLLGAPTGRAAKRLAEATGRKAETVHRL--LGAQGGIEADGSPVFekdaddpldadaiILDEVSMMDIVLMEHF 437
Cdd:TIGR02768 393 EAAGYRVIGAALSGKAAEGLQAESGIESRTLASLeyAWANGRDLLSDKDVL-------------VIDEAGMVGSRQMARV 459

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  438 L-EAVPEGARVIFVGDVDQLPAVGPGSVLKDIL-RSGavpSVRLKEVFRQSGEG----TIVLNAHAINRGrMPQFTAGGD 511
Cdd:TIGR02768 460 LkEAEEAGAKVVLVGDPEQLQPIEAGAAFRAIAeRIG---YAELETIRRQREAWarqaSLELARGDVEKA-LAAYRDHGH 535

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  512 FEFLEMPDEeaAARRIVA----LCREELPREGFNAL----EDVQVLSPMHRTPCGVDNlnRLLQAALNPPApekaefrNS 583
Cdd:TIGR02768 536 ITIHDTREE--AIEQVVAdwkqDLREANPAGSQIMLahtrKDVRALNEAAREALIERG--ELGESILFQTA-------RG 604

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  584 TLTFRVGDKVMQTKNDYTKGVFNGDIGFIREVSADGVKVRYSEELTADYEPNELMMLTLAYAMSVHKSQGSEYP-VIVLP 662
Cdd:TIGR02768 605 ERKFAAGDRIVFLENNRDLGVKNGMLGTVEEIEDGRLVVQLDSGELVIIPQAEYDALDHGYATTIHKSQGVTVDrAFVLA 684

                         330       340
                  ....*....|....*....|....*..
gi 402282422  663 lvaahHIMLQRNLLYTAVTRAKKKVVL 689
Cdd:TIGR02768 685 -----SKSMDRHLAYVAMTRHRESVQL 706
UvrD_C_2 pfam13538
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ...
 642-690 2.81e-16

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: 72.99  E-value: 2.81e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 402282422  642 LAYAMSVHKSQGSEYPVIVL--PLVAAH-HIMLQRNLLYTAVTRAKKKVVLL 690
Cdd:pfam13538   1 LAYALTVHKAQGSEFPAVFLvdPDLTAHyHSMLRRRLLYTAVTRARKKLVLV 52
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 640-691 1.48e-12

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: 64.00  E-value: 1.48e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 402282422 640 LTLAYAMSVHKSQGSEYPVIVLPLVAAHhiMLQRNLLYTAVTRAKKKVVLLG 691
Cdd:cd18786   40 LQLVGAITIDSSQGLTFDVVTLYLPTAN--SLTPRRLYVALTRARKRLVIYD 89
RecB COG1074
3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, ...
 646-712 2.65e-06

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: 51.12  E-value: 2.65e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 402282422 646 MSVHKSQGSEYPVIVLPLVAAHHIMLQ----RNLLYTAVTRAKKKVVLLGSKAAVFTAVSNDRTRRRYTLL 712
Cdd:COG1074  648 MTIHKSKGLEFPVVFLPALRERARAEElaeeLRLLYVALTRARDRLVLSGAVKKKDAEKESSWLARRGTLV 718
TraI_TIGR TIGR02760
conjugative transfer relaxase protein TraI; This protein is a component of the relaxosome ...
 351-485 1.97e-05

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: 48.36  E-value: 1.97e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422   351 VVRGMIAVLESQGLSVLLGAPTGRAAKRLaEATGRKAETVHRLLgaqggieADGSpvFEKDADDPLDADAIILDEVSMMD 430
Cdd:TIGR02760 1056 RYKPVLQAFESEQLQVIGLAPTHEAVGEL-KSAGVQAQTLDSFL-------TDIS--LYRNSGGDFRNTLFILDESSMVS 1125

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 402282422   431 IVLMEHFLEAVPE-GARVIFVGDVDQLPAVGPGSVLKDILRSGAVPSVRLKEVFRQ 485
Cdd:TIGR02760 1126 NFQLTHATELVQKsGSRAVSLGDIAQLQSLAAGKPFELAITFDIIDTAIMKEIVRQ 1181
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 421-468 2.23e-05

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: 44.40  E-value: 2.23e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 402282422 421 IILDEVSMMDIVLMEHFLEAVPEGARVIFVGDVDQLPAVGPGSVLKDI 468
Cdd:cd17914   50 ILVDEAAQILEPETSRLIDLALDQGRVILVGDHDQLGPVWRGAVLAKI 97
PRK13766 PRK13766
Hef nuclease; Provisional
 74-134 2.83e-05

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 47.56  E-value: 2.83e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 402282422  74 APTSLAGIERFLASgAIAGIGEAMAHRLVQKFGkeTLE-IIEKKPSRLTEVAGVGKKTAAKI 134
Cdd:PRK13766 705 KAMTLKEQQEYIVE-SLPDVGPVLARNLLEHFG--SVEaVMTASEEELMEVEGIGEKTAKRI 763
HHH_5 pfam14520
Helix-hairpin-helix domain;
90-146 3.11e-05

Helix-hairpin-helix domain;


Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 42.09  E-value: 3.11e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 402282422   90 IAGIGEAMAHRLVQKFGKETLEIIEKKPSRLTEVAGVGKKTAAKIhasymeKEELRE 146
Cdd:pfam14520   7 ISGIGPKTALALLSAGIGTVEDLAEADVDELAEIPGIGEKTAQRI------ILELRD 57
PRK13889 PRK13889
conjugal transfer relaxase TraA; Provisional
 421-653 4.78e-05

conjugal transfer relaxase TraA; Provisional


Pssm-ID: 237546 [Multi-domain]  Cd Length: 988  Bit Score: 46.99  E-value: 4.78e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 421 IILDEVSMMDIVLMEHFL-EAVPEGARVIFVGDVDQLPAVGPGSVLKDIL-RSGavpSVRLKEVFRQSG----EGTIVL- 493
Cdd:PRK13889 437 LVIDEAGMVGTRQLERVLsHAADAGAKVVLVGDPQQLQAIEAGAAFRSIHeRHG---GAEIGEVRRQREdwqrDATRDLa 513

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 494 ---NAHAINRgrmpqFTAGGDFeflempdeEAAARRIVAlcREEL-----------PREGFNAL----EDVQVLSPMHRT 555
Cdd:PRK13889 514 tgrTGEALDA-----YEAHGMV--------HAAATREQA--RADLidrwdrdrqaaPDRSRIILthtnDEVRALNEAARE 578

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 556 pcgvdnlnRLLQA-ALNPPAPEKAEfrNSTLTFRVGDKVMQTKNDYTKGVFNGDIGFIREVSADGVKVRYSEELTADYEP 634
Cdd:PRK13889 579 --------RMRAAgDLGDDVRVTVE--RGERSFASGDRVMFLQNERGLGVKNGTLGTIEQVSAQSMSVRLDDGRSVAFDL 648

                        250
                 ....*....|....*....
gi 402282422 635 NELMMLTLAYAMSVHKSQG 653
Cdd:PRK13889 649 KDYDRIDHGYAATIHKAQG 667
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
648-715 8.52e-05

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 45.89  E-value: 8.52e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 402282422 648 VHKSQGSEYPVIVLPLVAAHH---------IMLQRNLLYTAVTRAKKKVVLLGSkAAVFTAVSNDRTRRRYTLLAER 715
Cdd:COG1112  743 VDRFQGDERDVIIFSLVYSNDedvprnfgfLNGGPRRLNVAVSRARRKLIVVGS-RELLDSDPSTPALKRLLEYLER 818
SF1_C_UvrD cd18807
C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase ...
 636-691 1.32e-04

C-terminal helicase domain of UvrD family helicases; 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. This family also includes ATP-dependent helicase/nuclease AddA and helicase/nuclease RecBCD subunit RecB, among others. UvrD 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: 350194 [Multi-domain]  Cd Length: 150  Bit Score: 42.60  E-value: 1.32e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 402282422 636 ELMMLTLayaMSVHKSQGSEYPVIVL--------PLVAAHHIML--------QRNLLYTAVTRAKKKVVLLG 691
Cdd:cd18807   82 EALRVTL---MTIHASKGLEFPVVFIvglgegfiPSDASYHAAKedeerleeERRLLYVALTRAKKELYLVG 150
MUS81 COG1948
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
88-135 1.87e-04

ERCC4-type crossover junction endonuclease [Replication, recombination and repair];


Pssm-ID: 441551 [Multi-domain]  Cd Length: 214  Bit Score: 43.24  E-value: 1.87e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 402282422  88 GAIAGIGEAMAHRLVQKFGkeTLE-IIEKKPSRLTEVAGVGKKTAAKIH 135
Cdd:COG1948  158 ESLPGIGPKLARRLLEHFG--SVEaVFNASEEELMKVEGIGEKTAERIR 204
COG3972 COG3972
Superfamily I DNA and RNA helicases [Replication, recombination and repair];
646-692 1.95e-04

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


Pssm-ID: 443172 [Multi-domain]  Cd Length: 565  Bit Score: 44.82  E-value: 1.95e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 402282422 646 MSVHKSQGSEYPVIVLP---LVAAHHIMLQ-RNLLYTAVTRAKKKVVLLGS 692
Cdd:COG3972  492 STIHRAKGLEAPVVIIVgldQLAKGESLERlRNLLYVAMTRARGWLVVSGS 542
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 647-692 4.28e-04

C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They 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: 350195 [Multi-domain]  Cd Length: 184  Bit Score: 41.84  E-value: 4.28e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 402282422 647 SVHKSQGSEYPVIVLPLVAAHHIMLQ------RNLLYTAVTRAKKKVVLLGS 692
Cdd:cd18808  115 TVDNFQGREKDVIILSLVRSNESGGSigflsdPRRLNVALTRAKRGLIIVGN 166
PRK13709 PRK13709
conjugal transfer nickase/helicase TraI; Provisional
 370-488 4.74e-04

conjugal transfer nickase/helicase TraI; Provisional


Pssm-ID: 237478 [Multi-domain]  Cd Length: 1747  Bit Score: 43.63  E-value: 4.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  370 APTGRAAKRLAEAtGRKAETV------HRLLGAQGGieadgSPVFEKDAddpldadaIILDEVSMMDIVLMEHFLEAVPE 443
Cdd:PRK13709 1023 GPTHRAVGEMRSA-GVDAQTLasflhdTQLQQRSGE-----TPDFSNTL--------FLLDESSMVGNTDMARAYALIAA 1088

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 402282422  444 -GARVIFVGDVDQLPAVGPGSVLKDILRSGAVPSVRLKEVFRQSGE 488
Cdd:PRK13709 1089 gGGRAVSSGDTDQLQAIAPGQPFRLMQTRSAADVAIMKEIVRQTPE 1134
DEXSc_Pif1_like cd18037
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like ...
 346-463 9.42e-04

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: 40.70  E-value: 9.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422 346 TGKTTVVRGMIAVLESQGLSVLLGAPTGRAAKRLAeatGRkaeTVHRLLGAqgGIEADGSPVFEKDADDPLDAD------ 419
Cdd:cd18037   23 TGKSYLLRRIIRALPSRPKRVAVTASTGIAACNIG---GT---TLHSFAGI--GLGSEPAEDLLERVKRSPYLVqrwrkc 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 402282422 420 -AIILDEVSMMDIVLMEHfLEAVPEGAR----------VIFVGDVDQLPAVGPGS 463
Cdd:cd18037   95 dVLIIDEISMLDADLFDK-LDRVAREVRgsdkpfggiqLILCGDFLQLPPVTKNS 148
PRK13826 PRK13826
Dtr system oriT relaxase; Provisional
 348-689 1.18e-03

Dtr system oriT relaxase; Provisional


Pssm-ID: 237524 [Multi-domain]  Cd Length: 1102  Bit Score: 42.46  E-value: 1.18e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  348 KTTVVRGMIAVLESQGLSVLLGAPTGRAAKRLAEATGRKAETVH--RLLGAQGGIEADGSPVFekdaddpldadaiILDE 425
Cdd:PRK13826  410 KTTMMKAAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLSswELRWNQGRDQLDNKTVF-------------VLDE 476

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  426 VSMMDIVLMEHFLEAVPE-GARVIFVGDVDQLPAVGPGSVLKDIL-RSGavpSVRLKEVFRQSgEGTIVLNAHAINRGRM 503
Cdd:PRK13826  477 AGMVASRQMALFVEAVTRaGAKLVLVGDPEQLQPIEAGAAFRAIAdRIG---YAELETIYRQR-EQWMRDASLDLARGNV 552

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  504 PQ----FTAGGDFEFLEMPDeEAAARRIVALCREELPREGFNAL----EDVQVLSPMHRTpcgvdnlnRLLQAALnppAP 575
Cdd:PRK13826  553 GKaldaYRANGRVIGSRLKA-EAVESLIADWNRDYDPTKTTLILahlrRDVRMLNEMARA--------KLVERGI---VG 620

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  576 EKAEFR--NSTLTFRVGDKVMQTKNDYTKGVFNGDIGFIREVSADgvkvRYSEELTADYEPNELMM-------LTLAYAM 646
Cdd:PRK13826  621 EGHAFRtaDGERRFAAGDQIVFLKNEGSLGVKNGMIGKVVEAAPN----RIVAEIGEGEHRRQVTVeqrfynnLDHGYAT 696

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....
gi 402282422  647 SVHKSQGSEYP-VIVLPLVAahhimLQRNLLYTAVTRAKKKVVL 689
Cdd:PRK13826  697 TIHKSQGATVDrVKVLASLS-----LDRHLTYVAMTRHREDLQL 735
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 618-691 1.52e-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: 40.83  E-value: 1.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  618 DGVKVRYSEELTADYEPNELMMLTL------------AYAMSVHKSQGSEYPVIVLPLVAA---HHIMLQRNLLYTAVTR 682
Cdd:pfam01443 139 FEVVVERSGEYKVDYDPNGVLVLVYltftqalkeslgVRVTTVHEVQGLTFDSVTLVLDTDtdlLIISDSPEHLYVALTR 218


                  ....*....
gi 402282422  683 AKKKVVLLG 691
Cdd:pfam01443 219 HRKSLHILT 227
Lig COG0272
NAD-dependent DNA ligase [Replication, recombination and repair];
54-172 1.95e-03

NAD-dependent DNA ligase [Replication, recombination and repair];


Pssm-ID: 440042 [Multi-domain]  Cd Length: 668  Bit Score: 41.55  E-value: 1.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  54 EWVQHPRFGEQfKAATLrvsaptsLAGIE--------RFLASGAIAGIGEAMAHRLVQKFGkeTLE-IIEKKPSRLTEVA 124
Cdd:COG0272  481 DLLGLERMGEK-SAQNL-------LAAIEkskktplaRFLFALGIRHVGETTAKLLARHFG--SLDaLMAASEEELAAVD 550

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 402282422 125 GVGKKTAAKIHASYMEKEELREIMLWLEmHGVSGAYAARIFETYSSFA 172
Cdd:COG0272  551 GIGPVVAESIVEFFAEPHNRELIERLRA-AGVNMEEEEAEAAADSPLA 597
ligA PRK07956
NAD-dependent DNA ligase LigA; Validated
 59-163 2.16e-03

NAD-dependent DNA ligase LigA; Validated


Pssm-ID: 236137 [Multi-domain]  Cd Length: 665  Bit Score: 41.26  E-value: 2.16e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402282422  59 PRFGEQfKAATLrvsaptsLAGIE--------RFLASGAIAGIGEAMAHRLVQKFGkeTLEIIEK-KPSRLTEVAGVGKK 129
Cdd:PRK07956 485 EGFGEK-SAQNL-------LDAIEksketslaRFLYALGIRHVGEKAAKALARHFG--SLEALRAaSEEELAAVEGVGEV 554

                         90       100       110
                 ....*....|....*....|....*....|....
gi 402282422 130 TAAKIHaSYMEKEELREIMLWLEMHGVSGAYAAR 163
Cdd:PRK07956 555 VAQSIV-EFFAVEENRELIDELLEAGVNMEYKGE 587
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH