|
Name |
Accession |
Description |
Interval |
E-value |
| recB |
PRK10876 |
exonuclease V subunit beta; Provisional |
2-1187 |
0e+00 |
|
exonuclease V subunit beta; Provisional
Pssm-ID: 236784 [Multi-domain] Cd Length: 1181 Bit Score: 941.32 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 2 QALNPLTMPLIGQSLIEASAGTGKTYTITGLYLRYLLGMQIEGELNTPLSVEQILVVTFTDAATQEIKDRVRSRIIAARD 81
Cdd:PRK10876 7 ETLDPLRLPLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEEILVVTFTEAATEELRGRIRSNIHELRI 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 82 ALLGQDPNDELIEGVIAKIDDKHRAFDLLDAAAKSMDEAAIFTIHGFCQRMLKQHAFESGVAFNLEFILDERDILLETIK 161
Cdd:PRK10876 87 ACLREETDNPLYQRLLAEIDDKAQAAQWLLLAERQMDEAAIFTIHGFCQRMLNLNAFESGMLFEQQLIEDESLLRYQACA 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 162 DFWRAFVYPLNKERTDAILDVFAAPEALFAQVASILNKANAHITPQINLDDVWRARDEYIT-RVPAFKKAVLEQ--EFIG 238
Cdd:PRK10876 167 DFWRRHCYPLPREIARVVFQEWKGPEALLKDISRYLQGEAPVIKAPPPDDETLASRHEQIVaRIDAVKQQWREAvgELDA 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 239 AIKSSGLSgsktpARKGSLGALEAFCLGGDLFFEFGTNKYSF----EVWSTENLSDVSnyKKNQPLfVHPLLSQFDELAA 314
Cdd:PRK10876 247 LIESSGVD-----RRSYNSKNLPKWLEKISAWAEEETNSYQLpkelEKFSQRFLLEKT--KKGETP-QHPLFEAIDQLLA 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 315 LNNTinqgLKIAVVQHAARWVKAAIVKRKQEQSVITPDDLLTNLHSALNNEQGDVLAQKIAQLFPVAMIDEFQDTDPIQY 394
Cdd:PRK10876 319 EPLS----LRDLVITRALAEIRETVAQEKRRRGELGFDDLLSRLDSALQSEGGEALAAAIRTRYPVAMIDEFQDTDPQQY 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 395 GIFSKIYGQQ-NTTLAMIGDPKQAIYGFRGADVFTYIGAKEAVqtDQQFTLGTNFRSSTDIVNSVNSLFGKHANSFIYND 473
Cdd:PRK10876 395 RIFRRIYRHQpETALLLIGDPKQAIYAFRGADIFTYMKARSEV--SAHYTLDTNWRSAPGMVNSVNKLFSQTDDPFLFRE 472
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 474 aIPFNAVAAKGKKAEDSFLIDGKPATAFEFNVFVDEAAdeknkptnkGVG--QAHLATHFANKIVTLLEKAKQGDACI-- 549
Cdd:PRK10876 473 -IPFIPVKAAGKNQALRFVVKGETQPAMKFWLMEGEGV---------GVGdyQQTMAQQCAAQIRDWLQAGQRGEALLmn 542
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 550 --GSTPVSAADICILVRDRVEAQIMKKALSEAKIASVYLS-RESVFSQELSHHLLNFLTALHGQYDESLLRGVLAGPLFC 626
Cdd:PRK10876 543 gdDSRPVRASDITVLVRSRQEAALIRDALTLLAIPSVYLSnRDSVFETLEAQEMLWLLQAVLAPERERTLRSALATSMMG 622
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 627 LSYNEIHALADDENKWQDYLNFFAQLSHIWNKQGAMAMLERLMSHNQLSakwQGL--GYNVERWLTDFRHLGEILQQKQI 704
Cdd:PRK10876 623 LDALDIDALNNDERAWDALVEEFDGYRQIWRKRGVLPMLRALMSARNIA---ENLlaTAGGERRLTDILHIGELLQEASS 699
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 705 ELEGTLRLLRWFAQKVSQQDG--ETVQVRLESDANLVKIVTMHASKGLEYPLVFMPFASGYRETKEALYH--NNGKLVYD 780
Cdd:PRK10876 700 QLDSEHALVRWLAQQILEPDSqaSSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFITNFRVQDQAFYHdrHSFEAVLD 779
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 781 LSKDEDALQKAEQERLAEDLRLLYVALTRAVHFCALGVYNIGQGQSSRLA---MQSSALGHVLFAGlELASSQTWRTHLS 857
Cdd:PRK10876 780 LNAAEESVALAEEERLAEDLRLLYVALTRSVWHCSLGVAPLVRRRRKKKGetdLHQSALGYLLQKG-EPGDAAGLRACLE 858
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 858 EFCDANSAMSYQQFTSQTLLEQgklcfsnSKIAQQTLSVNRVTANIERNWRATSFSALSFKKHS--DQLAPgRSDEDHEK 935
Cdd:PRK10876 859 ALCDDDIALQTAQETDNQPWQP-------QDASLAELSARTLQRLLQDNWRVTSYSGLQQHGHSiaQDLLP-RLDVDAAG 930
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 936 DEFAVQEDELpSPYSFPKGPKPGSCLHEIFEQIDFISPIvhstnTEQNLSEvvkrSLEKYHISEQWREVAEKWVLDVLAC 1015
Cdd:PRK10876 931 EGSVVEEPQL-TPHTFPRGASPGTFLHSLFEDLDFTQPV-----DPEWLQE----QLELQGFEEQWEPVLTQWITAVLQT 1000
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 1016 PLDKSslensllslGV----LTPSDCLVEMEFNLPLES-LSAPKLNEMLVKHFGFTQ--SKLEFSQVKGLLKGFVDLIFC 1088
Cdd:PRK10876 1001 PLNET---------GVslsqLSARDKQVEMQFYLPIDQpLTASQLDALIRQYDPLSAgcPPLDFMQVRGMLKGFIDLVFR 1071
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 1089 YQGKYYILDYKSNYLGSTPADYEGDMLEQAMSSHQYHLQYLIYTVALHRLLKQRIADYSIETHLGGVYYTFLRGM---PA 1165
Cdd:PRK10876 1072 WQGRYYLLDYKSNWLGEDSSAYTQEAMAQAMQAHRYDLQYQLYTLALHRYLRHRLADYDYQRHFGGVIYLFLRGVdkeHP 1151
|
1210 1220
....*....|....*....|..
gi 498239896 1166 GQGVYFKKLTVEQVTILDGLFS 1187
Cdd:PRK10876 1152 GQGIFTTRPNAALIDGLDELFA 1173
|
|
| recB |
TIGR00609 |
exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with ... |
4-1186 |
0e+00 |
|
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: 803.19 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 4 LNPLTMPLIGQSLIEASAGTGKTYTITGLYLRYLLGMqiegelnTPLSVEQILVVTFTDAATQEIKDRVRSRIIAARDAL 83
Cdd:TIGR00609 1 LDPLTIPLNGTFLIEASAGTGKTFTIAQLYLRLLLEG-------GPLTVEEILVVTFTNAATEELKTRIRGRIHQALRAL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 84 LGQDPNDELIEGVIAKIDD--KHRAFDLLDAAAKSMDEAAIFTIHGFCQRMLKQHAFESGVAFNLEFILDERDILLETIK 161
Cdd:TIGR00609 74 KAALTSQELPEPLKEAIQDekVKQAITRLRNALATMDEAAIYTIHGFCQRMLEQHAFESDEIFDVELIEDESLLLAEITK 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 162 DFWRAFVYPLNKERTDAILDVFAAPEALFAQVAsilnkanahitpqinlddvwraRDEYITRVPAFKKAVLEQEFIgaik 241
Cdd:TIGR00609 154 DFWRRNFYNLPFDIAQIVLKTKKSPQAVLTQIL----------------------ADLLLQSYLAFPSPPLDLEQL---- 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 242 ssglsgsktparkgslgaleafclggdlffefgtnkysfevwstenLSDVSNYKKNQPLFVHPLLSQFDELAAlNNTINQ 321
Cdd:TIGR00609 208 ----------------------------------------------IKWHEQIYKDLDKLDHAVFEEIDKLNA-ERNNLF 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 322 GLKIAVVQHAARWVKAAIVKRKQEQSVITPDDLLTNLHSALNNEQGDVLAQKIAQLFPVAMIDEFQDTDPIQYGIFSKIY 401
Cdd:TIGR00609 241 CLKDRVFLTLLKEVQEELKKEKKRRREIGFDDLLSRLETALKSAEGEKLAQAIREQYPIALIDEFQDTDPQQYRIFSKLF 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 402 GQQNTT-LAMIGDPKQAIYGFRGADVFTYIGAKEavQTDQQFTLGTNFRSSTDIVNSVNSLFGKHANSFIYndAIPFNAV 480
Cdd:TIGR00609 321 IAQKETsLFLIGDPKQAIYSFRGADIFTYLQAKS--KADARYTLGTNWRSTPALVGSLNKLFSLISNPFLE--KPIFIPV 396
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 481 AAKGKKAEDSFLIDGKPATAFEFNVFVDEAADeknkptnKGVGQAHLATHFANKIVTLLEKAKQGDACIGST----PVSA 556
Cdd:TIGR00609 397 LAHQKNSKGSFVINGQEQPPIHFFTTEVESEG-------VDDYRQTIAQKCAREIALWLASAALGLANFIATfggrPLRA 469
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 557 ADICILVRDRVEAQIMKKALSEAKIASVYLSRESVFSQELSHH-LLNFLTALHGQYDESLLRGVLAGPLFCLSYNEIHAL 635
Cdd:TIGR00609 470 GDIAVLVRGRKEANQIRKALKKAQIPSVYLSDKSSVFATEEAQeLLALLEALLEPENEGTLRAALASSIFGLSALELETL 549
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 636 ADDENKWQDYLNFFAQLSHIWNKQGAMAMLERLMShnqlsakWQGLGYNV------ERWLTDFRHLGEILQQKQIELEGT 709
Cdd:TIGR00609 550 NQDEITWERVVEKFREYHDIWRKIGVLAMFQRLML-------EKGIGERLlsqpggERILTNLLHLAELLQEAAHQERNK 622
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 710 LRLLRWFAQKVSQQD-GETVQVRLESDANLVKIVTMHASKGLEYPLVFMPFASGYRETKEALYHN---NGKLVYDLSKDE 785
Cdd:TIGR00609 623 LSLLRWLEDQISNEEeEEEEIIRLESDAELVKIVTIHKSKGLEYPIVFLPFITDAKKSNFASLHDqhsHEYQLYDFNQSE 702
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 786 DALQKAEQERLAEDLRLLYVALTRAVHFCALGVYNIG---QGQSSRLAMQSSALGHVLFAGlELASSQTWRTHLSEFCDA 862
Cdd:TIGR00609 703 ENQKLARVERLAEDLRLLYVALTRAKKQLFIGIAPLItskLSNLAYSALHNSALGYQKQDG-ETDNITGLKQCLAALADP 781
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 863 NsamsyqQFTSQTLLEQGKLCFSNSKIAQQTLSVNRVTANIERNWRATSFSALSFKKHsdqlapGRSDEDHEKDEFAVQE 942
Cdd:TIGR00609 782 A------GISSIPAKPIGANSSKKEPASTALLEARTFHRRIRENWRITSFSSLKELEE------AVTEEPAPGLDYEVSS 849
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 943 DELpSPYSFPKGPKPGSCLHEIFEQIDFISPivhsTNTEQNLSEVVKRsLEKYHISEQWREVAEKWVLDVLACPLDKSSL 1022
Cdd:TIGR00609 850 LEI-SAQDFPKGKKTGTLLHAILESLIFSQA----ADLEKQNNLIAEK-LKKTGLEGLWEPELQEWLEKMLNTPLTFSRA 923
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 1023 ENSLLslgvLTPSDCLVEMEFNLPLESLSAPKLNEMLVKHF--GFTQSKLEFSQVKGLLKGFVDLIFCYQGKYYILDYKS 1100
Cdd:TIGR00609 924 ITLSQ----IDPEDRQREMEFLLPINPEFQKQKLNFVIRAYpdRAGSPDLHFQLLRGLLKGFIDLVFEHNGRYYILDYKS 999
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 1101 NYLGSTPADYEGDMLEQAMSSHQYHLQYLIYTVALHRLLKQRIADYSIETHLGGVYYTFLRGM--PAGQGVYFKKLTVEQ 1178
Cdd:TIGR00609 1000 NWLGKDASDYSPEALTEAILKERYDLQYLIYTLALHRYLRKRLKDYDYERHFGGVIYLFLRGIdgNKGNGIFFWNPPANL 1079
|
....*...
gi 498239896 1179 VTILDGLF 1186
Cdd:TIGR00609 1080 IDLLKELF 1087
|
|
| RecB |
COG1074 |
3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, ... |
2-1158 |
0e+00 |
|
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: 601.57 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 2 QALNPLTmpliGQSLIEASAGTGKTYTITGLYLRYLLgmqiegelNTPLSVEQILVVTFTDAATQEIKDRVRSRIiaaRD 81
Cdd:COG1074 12 RALDPLG----GSVLVEASAGSGKTYTLVARYLRLLL--------ERGLDPEEILVVTFTRAAAAEMRERIRERL---AE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 82 ALLGQDPNDELIEgviakiddkhRAFDLLDAAAKSMDEAAIFTIHGFCQRMLKQHAFESGVAFNLEFILDERDILL-ETI 160
Cdd:COG1074 77 AADLEDPDLEELA----------RARRRLARALENLDRAAISTIHSFCQRLLREFAFEAGLDPNFELLDDAEALLLeEAV 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 161 KDFWRAFVYPLNKERTDAILDVFAA-PEALFAQVASILNKANAhitpQINLDDVWRARDEYITrvpafkkavLEQEFIGA 239
Cdd:COG1074 147 DDLLREAYAPLDALALARLLDAFGRdDDSLEELLLALYKLRSR----PDWLEELAELDEALEA---------LREALLKA 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 240 IKSsglsgsktparkgslgaleafclggdlffefgtnkysfevwstenlsdvsnykknqplfVHPLLSQFDELAALnnti 319
Cdd:COG1074 214 KEA-----------------------------------------------------------LAALREALAAAAAP---- 230
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 320 nqglKIAVVQHAARWVKAAIVKRKQEQSVITPDDLLTNLHSALNNEQGDVLAQKIAQLFPVAMIDEFQDTDPIQYGIFSK 399
Cdd:COG1074 231 ----LLAALLRLLAAVLARYERRKRERGLLDFDDLLHRALRLLRDEDAPWVAERLRERYRHILVDEFQDTSPLQWEILRR 306
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 400 IYG---QQNTTLAMIGDPKQAIYGFRGADVFTYIGAKEAVQTDQQF---TLGTNFRSSTDIVNSVNSLFGKH-ANSFIyn 472
Cdd:COG1074 307 LAGealADGRTLFLVGDPKQSIYRFRGADPELFLEARRALEGRVDGerlTLTTNFRSTPEVVDAVNALFAQLmGAGFG-- 384
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 473 dAIPFNAVAAkgkkaedsfLIDGKPAtAFEFNVFVDEAADEKNKptnkgvgQAHLATHFANKIVTLLEKAKQGDAciGST 552
Cdd:COG1074 385 -EIPYEPVEA---------LRPGAYP-AVELWPLEPDDVSEEDA-------REREARAVAARIRRLLAEGTTVEG--GGR 444
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 553 PVSAADICILVRDRVEAQIMKKALSEAKIAsVYLS-RESVFSQELSHHLLNFLTALHGQYDESLLRGVLAGPLFCLSYNE 631
Cdd:COG1074 445 PVRPGDIAVLVRTRSEAAAIARALKAAGIP-VAASdRLSLFESPEVRDLLALLRALLNPEDDLALAAVLRSPLFGLSDED 523
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 632 IHALADDEN------------KWQDYLNFFAQLSHIWNKQGAMAMLERLMSHNQLSAKWQGLGyNVERWLTDFRHLGEIL 699
Cdd:COG1074 524 LAALAADRKgeslwealrayeRLARALERLRALRELARRLGLAELLERLLEETGLLERLLALP-GGERRLANLLHLDELL 602
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 700 QQ-KQIELEGTL---RLLRWFAQKVSQQDGEtVQVRLESDANLVKIVTMHASKGLEYPLVFMPfasgyretkealyhnng 775
Cdd:COG1074 603 QLaLEYEQTGGPglaGFLRWLERLIEDGGDE-EKRRLESDADAVRIMTIHKSKGLEFPVVFLP----------------- 664
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 776 klvydlskdeDALQKAEQERLAEDLRLLYVALTRAVHFCalgvynigqgqssrlamqssalghVLFAGLELASSQTWRTH 855
Cdd:COG1074 665 ----------ALRERARAEELAEELRLLYVALTRARDRL------------------------VLSGAVKKKDAEKESSW 710
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 856 LSEFcdansamsyqqftsqtlleqgklcfsnskiaqqtlsvnrvtaniernwratsfsalsfkkhsdqlapgrsdedhek 935
Cdd:COG1074 711 LARR---------------------------------------------------------------------------- 714
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 936 defavqedelpspysfpkgpkpGSCLHEIFEQIDFispivhstNTEQNLSEVVKRSLEKYHISEQWREVAEKWVLDVLAC 1015
Cdd:COG1074 715 ----------------------GTLVHRLLEHLDF--------SAPAELRAALARLLARGGLDEEEAEALAEALLAFLAT 764
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 1016 PLdksslensllSLGVLTPSDCLVEMEFNLPleslsapklnemlvkhfgftqskLEFSQVKGLLKGFVDLIFCYQGKYYI 1095
Cdd:COG1074 765 PL----------LAELFAAAEVLREVPFLLP-----------------------DLYRGLGGLLKGRIDLVFEDDGRVYI 811
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 498239896 1096 LDYKSNYLGSTPADYegdmleqamSSHQYHLQYLIYTVALHRLLKQRIADysiethlGGVYYT 1158
Cdd:COG1074 812 VDYKTNRLGPDDEEY---------LPERYRLQLALYALALERLLPGRPVR-------AGLYFT 858
|
|
| RecB_C-like |
cd22352 |
C-terminal nuclease domain of exodeoxyribonuclease V subunit RecB and similar proteins; ... |
907-1183 |
3.42e-73 |
|
C-terminal nuclease domain of exodeoxyribonuclease V subunit RecB and similar proteins; Exodeoxyribonuclease V subunit beta (RecB) is a helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair; it binds to DSBs and unwinds DNA via a rapid and highly processive ATP-dependent bidirectional helicase. The C-terminal PDDEXK nuclease domain belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.
Pssm-ID: 411756 [Multi-domain] Cd Length: 215 Bit Score: 242.19 E-value: 3.42e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 907 WRATSFSALSFKKHSDQLAPGRSDE-DHEKDEFAVQEDELPsPYSFPKGPKPGSCLHEIFEQIDFISpivhstnteqnls 985
Cdd:cd22352 1 WRITSFSSLTRGLGGKAAEASHDEEpDEDEEAAPEEADEEG-IDALPRGAKTGTFLHEILENIDRLS------------- 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 986 evvkrslekyhiseqwrevaekwvldvlacpldksslensllslgvltpsdclvEMEFNLPLES-LSAPKLNEMLVKHFG 1064
Cdd:cd22352 67 ------------------------------------------------------EMEFYLPLSDkLDAEALNELLRQHGP 92
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 1065 FTQ-SKLEFSQVKGLLKGFVDLIFCYQGKYYILDYKSNYLGSTPADYEGDMLEQAMSSHQYHLQYLIYTVALHRLLKQRI 1143
Cdd:cd22352 93 PGAlPPLSFETLRGFLKGFIDLVFEHEGRYYILDYKSNYLGDYLEDYSPEALEAAMLEHHYDLQYLLYTLALHRYLKQRL 172
|
250 260 270 280
....*....|....*....|....*....|....*....|...
gi 498239896 1144 ADYSIETHLGGVYYTFLRGMPA---GQGVYFKKLTVEQVTILD 1183
Cdd:cd22352 173 PDYDYERHFGGVYYLFLRGMDPegpGNGVFFDRPSAELIEALD 215
|
|
| UvrD-helicase |
pfam00580 |
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural ... |
2-434 |
1.15e-38 |
|
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: 145.47 E-value: 1.15e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 2 QALNPLTMPLigqsLIEASAGTGKTYTITGLYLRYLLGMQIEgelntplsVEQILVVTFTDAATQEIKDRVRSriiaard 81
Cdd:pfam00580 7 KAVTHLGGPL----LVLAGAGSGKTRVLTERIAYLILEGGID--------PEEILAVTFTNKAAREMKERILK------- 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 82 aLLGQDPndeliegviakiddkhrafdlldaaaksMDEAAIFTIHGFCQRMLKQHAFESGVAFNLEfILDERDILletik 161
Cdd:pfam00580 68 -LLGKAE----------------------------LSELNISTFHSFCLRILRKYANRIGLLPNFS-ILDELDQL----- 112
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 162 dfwrafvyplnkertdaildvfaapealfAQVASILNKANAHITPQInlddvwrardeyitrvpafKKAVLEQEFIGAIK 241
Cdd:pfam00580 113 -----------------------------ALLKELLEKDRLNLDPKL-------------------LRKLELKELISKAK 144
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 242 SSGLSgsktParkgslgaleafclggdlffefgtnkysfevwstenlsdvsnyKKNQPLFVHPLLSQFDELAALnntinq 321
Cdd:pfam00580 145 NRLLS----P-------------------------------------------EELQQGAADPRDKLAAEFYQE------ 171
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 322 glkiavvqhaarwvkaaIVKRKQEQSVITPDDLLTNLHSALnnEQGDVLAQKIAQLFPVAMIDEFQDTDPIQYGIFSKIY 401
Cdd:pfam00580 172 -----------------YQERLKENNALDFDDLLLLTLELL--RSDPELLEAYRERFKYILVDEFQDTNPIQYRLLKLLA 232
|
410 420 430
....*....|....*....|....*....|...
gi 498239896 402 GqQNTTLAMIGDPKQAIYGFRGADVFTYIGAKE 434
Cdd:pfam00580 233 G-GHENLFLVGDPDQSIYGFRGADIENILKFEK 264
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| recB |
PRK10876 |
exonuclease V subunit beta; Provisional |
2-1187 |
0e+00 |
|
exonuclease V subunit beta; Provisional
Pssm-ID: 236784 [Multi-domain] Cd Length: 1181 Bit Score: 941.32 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 2 QALNPLTMPLIGQSLIEASAGTGKTYTITGLYLRYLLGMQIEGELNTPLSVEQILVVTFTDAATQEIKDRVRSRIIAARD 81
Cdd:PRK10876 7 ETLDPLRLPLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEEILVVTFTEAATEELRGRIRSNIHELRI 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 82 ALLGQDPNDELIEGVIAKIDDKHRAFDLLDAAAKSMDEAAIFTIHGFCQRMLKQHAFESGVAFNLEFILDERDILLETIK 161
Cdd:PRK10876 87 ACLREETDNPLYQRLLAEIDDKAQAAQWLLLAERQMDEAAIFTIHGFCQRMLNLNAFESGMLFEQQLIEDESLLRYQACA 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 162 DFWRAFVYPLNKERTDAILDVFAAPEALFAQVASILNKANAHITPQINLDDVWRARDEYIT-RVPAFKKAVLEQ--EFIG 238
Cdd:PRK10876 167 DFWRRHCYPLPREIARVVFQEWKGPEALLKDISRYLQGEAPVIKAPPPDDETLASRHEQIVaRIDAVKQQWREAvgELDA 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 239 AIKSSGLSgsktpARKGSLGALEAFCLGGDLFFEFGTNKYSF----EVWSTENLSDVSnyKKNQPLfVHPLLSQFDELAA 314
Cdd:PRK10876 247 LIESSGVD-----RRSYNSKNLPKWLEKISAWAEEETNSYQLpkelEKFSQRFLLEKT--KKGETP-QHPLFEAIDQLLA 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 315 LNNTinqgLKIAVVQHAARWVKAAIVKRKQEQSVITPDDLLTNLHSALNNEQGDVLAQKIAQLFPVAMIDEFQDTDPIQY 394
Cdd:PRK10876 319 EPLS----LRDLVITRALAEIRETVAQEKRRRGELGFDDLLSRLDSALQSEGGEALAAAIRTRYPVAMIDEFQDTDPQQY 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 395 GIFSKIYGQQ-NTTLAMIGDPKQAIYGFRGADVFTYIGAKEAVqtDQQFTLGTNFRSSTDIVNSVNSLFGKHANSFIYND 473
Cdd:PRK10876 395 RIFRRIYRHQpETALLLIGDPKQAIYAFRGADIFTYMKARSEV--SAHYTLDTNWRSAPGMVNSVNKLFSQTDDPFLFRE 472
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 474 aIPFNAVAAKGKKAEDSFLIDGKPATAFEFNVFVDEAAdeknkptnkGVG--QAHLATHFANKIVTLLEKAKQGDACI-- 549
Cdd:PRK10876 473 -IPFIPVKAAGKNQALRFVVKGETQPAMKFWLMEGEGV---------GVGdyQQTMAQQCAAQIRDWLQAGQRGEALLmn 542
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 550 --GSTPVSAADICILVRDRVEAQIMKKALSEAKIASVYLS-RESVFSQELSHHLLNFLTALHGQYDESLLRGVLAGPLFC 626
Cdd:PRK10876 543 gdDSRPVRASDITVLVRSRQEAALIRDALTLLAIPSVYLSnRDSVFETLEAQEMLWLLQAVLAPERERTLRSALATSMMG 622
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 627 LSYNEIHALADDENKWQDYLNFFAQLSHIWNKQGAMAMLERLMSHNQLSakwQGL--GYNVERWLTDFRHLGEILQQKQI 704
Cdd:PRK10876 623 LDALDIDALNNDERAWDALVEEFDGYRQIWRKRGVLPMLRALMSARNIA---ENLlaTAGGERRLTDILHIGELLQEASS 699
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 705 ELEGTLRLLRWFAQKVSQQDG--ETVQVRLESDANLVKIVTMHASKGLEYPLVFMPFASGYRETKEALYH--NNGKLVYD 780
Cdd:PRK10876 700 QLDSEHALVRWLAQQILEPDSqaSSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFITNFRVQDQAFYHdrHSFEAVLD 779
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 781 LSKDEDALQKAEQERLAEDLRLLYVALTRAVHFCALGVYNIGQGQSSRLA---MQSSALGHVLFAGlELASSQTWRTHLS 857
Cdd:PRK10876 780 LNAAEESVALAEEERLAEDLRLLYVALTRSVWHCSLGVAPLVRRRRKKKGetdLHQSALGYLLQKG-EPGDAAGLRACLE 858
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 858 EFCDANSAMSYQQFTSQTLLEQgklcfsnSKIAQQTLSVNRVTANIERNWRATSFSALSFKKHS--DQLAPgRSDEDHEK 935
Cdd:PRK10876 859 ALCDDDIALQTAQETDNQPWQP-------QDASLAELSARTLQRLLQDNWRVTSYSGLQQHGHSiaQDLLP-RLDVDAAG 930
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 936 DEFAVQEDELpSPYSFPKGPKPGSCLHEIFEQIDFISPIvhstnTEQNLSEvvkrSLEKYHISEQWREVAEKWVLDVLAC 1015
Cdd:PRK10876 931 EGSVVEEPQL-TPHTFPRGASPGTFLHSLFEDLDFTQPV-----DPEWLQE----QLELQGFEEQWEPVLTQWITAVLQT 1000
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 1016 PLDKSslensllslGV----LTPSDCLVEMEFNLPLES-LSAPKLNEMLVKHFGFTQ--SKLEFSQVKGLLKGFVDLIFC 1088
Cdd:PRK10876 1001 PLNET---------GVslsqLSARDKQVEMQFYLPIDQpLTASQLDALIRQYDPLSAgcPPLDFMQVRGMLKGFIDLVFR 1071
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 1089 YQGKYYILDYKSNYLGSTPADYEGDMLEQAMSSHQYHLQYLIYTVALHRLLKQRIADYSIETHLGGVYYTFLRGM---PA 1165
Cdd:PRK10876 1072 WQGRYYLLDYKSNWLGEDSSAYTQEAMAQAMQAHRYDLQYQLYTLALHRYLRHRLADYDYQRHFGGVIYLFLRGVdkeHP 1151
|
1210 1220
....*....|....*....|..
gi 498239896 1166 GQGVYFKKLTVEQVTILDGLFS 1187
Cdd:PRK10876 1152 GQGIFTTRPNAALIDGLDELFA 1173
|
|
| recB |
TIGR00609 |
exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with ... |
4-1186 |
0e+00 |
|
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: 803.19 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 4 LNPLTMPLIGQSLIEASAGTGKTYTITGLYLRYLLGMqiegelnTPLSVEQILVVTFTDAATQEIKDRVRSRIIAARDAL 83
Cdd:TIGR00609 1 LDPLTIPLNGTFLIEASAGTGKTFTIAQLYLRLLLEG-------GPLTVEEILVVTFTNAATEELKTRIRGRIHQALRAL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 84 LGQDPNDELIEGVIAKIDD--KHRAFDLLDAAAKSMDEAAIFTIHGFCQRMLKQHAFESGVAFNLEFILDERDILLETIK 161
Cdd:TIGR00609 74 KAALTSQELPEPLKEAIQDekVKQAITRLRNALATMDEAAIYTIHGFCQRMLEQHAFESDEIFDVELIEDESLLLAEITK 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 162 DFWRAFVYPLNKERTDAILDVFAAPEALFAQVAsilnkanahitpqinlddvwraRDEYITRVPAFKKAVLEQEFIgaik 241
Cdd:TIGR00609 154 DFWRRNFYNLPFDIAQIVLKTKKSPQAVLTQIL----------------------ADLLLQSYLAFPSPPLDLEQL---- 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 242 ssglsgsktparkgslgaleafclggdlffefgtnkysfevwstenLSDVSNYKKNQPLFVHPLLSQFDELAAlNNTINQ 321
Cdd:TIGR00609 208 ----------------------------------------------IKWHEQIYKDLDKLDHAVFEEIDKLNA-ERNNLF 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 322 GLKIAVVQHAARWVKAAIVKRKQEQSVITPDDLLTNLHSALNNEQGDVLAQKIAQLFPVAMIDEFQDTDPIQYGIFSKIY 401
Cdd:TIGR00609 241 CLKDRVFLTLLKEVQEELKKEKKRRREIGFDDLLSRLETALKSAEGEKLAQAIREQYPIALIDEFQDTDPQQYRIFSKLF 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 402 GQQNTT-LAMIGDPKQAIYGFRGADVFTYIGAKEavQTDQQFTLGTNFRSSTDIVNSVNSLFGKHANSFIYndAIPFNAV 480
Cdd:TIGR00609 321 IAQKETsLFLIGDPKQAIYSFRGADIFTYLQAKS--KADARYTLGTNWRSTPALVGSLNKLFSLISNPFLE--KPIFIPV 396
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 481 AAKGKKAEDSFLIDGKPATAFEFNVFVDEAADeknkptnKGVGQAHLATHFANKIVTLLEKAKQGDACIGST----PVSA 556
Cdd:TIGR00609 397 LAHQKNSKGSFVINGQEQPPIHFFTTEVESEG-------VDDYRQTIAQKCAREIALWLASAALGLANFIATfggrPLRA 469
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 557 ADICILVRDRVEAQIMKKALSEAKIASVYLSRESVFSQELSHH-LLNFLTALHGQYDESLLRGVLAGPLFCLSYNEIHAL 635
Cdd:TIGR00609 470 GDIAVLVRGRKEANQIRKALKKAQIPSVYLSDKSSVFATEEAQeLLALLEALLEPENEGTLRAALASSIFGLSALELETL 549
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 636 ADDENKWQDYLNFFAQLSHIWNKQGAMAMLERLMShnqlsakWQGLGYNV------ERWLTDFRHLGEILQQKQIELEGT 709
Cdd:TIGR00609 550 NQDEITWERVVEKFREYHDIWRKIGVLAMFQRLML-------EKGIGERLlsqpggERILTNLLHLAELLQEAAHQERNK 622
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 710 LRLLRWFAQKVSQQD-GETVQVRLESDANLVKIVTMHASKGLEYPLVFMPFASGYRETKEALYHN---NGKLVYDLSKDE 785
Cdd:TIGR00609 623 LSLLRWLEDQISNEEeEEEEIIRLESDAELVKIVTIHKSKGLEYPIVFLPFITDAKKSNFASLHDqhsHEYQLYDFNQSE 702
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 786 DALQKAEQERLAEDLRLLYVALTRAVHFCALGVYNIG---QGQSSRLAMQSSALGHVLFAGlELASSQTWRTHLSEFCDA 862
Cdd:TIGR00609 703 ENQKLARVERLAEDLRLLYVALTRAKKQLFIGIAPLItskLSNLAYSALHNSALGYQKQDG-ETDNITGLKQCLAALADP 781
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 863 NsamsyqQFTSQTLLEQGKLCFSNSKIAQQTLSVNRVTANIERNWRATSFSALSFKKHsdqlapGRSDEDHEKDEFAVQE 942
Cdd:TIGR00609 782 A------GISSIPAKPIGANSSKKEPASTALLEARTFHRRIRENWRITSFSSLKELEE------AVTEEPAPGLDYEVSS 849
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 943 DELpSPYSFPKGPKPGSCLHEIFEQIDFISPivhsTNTEQNLSEVVKRsLEKYHISEQWREVAEKWVLDVLACPLDKSSL 1022
Cdd:TIGR00609 850 LEI-SAQDFPKGKKTGTLLHAILESLIFSQA----ADLEKQNNLIAEK-LKKTGLEGLWEPELQEWLEKMLNTPLTFSRA 923
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 1023 ENSLLslgvLTPSDCLVEMEFNLPLESLSAPKLNEMLVKHF--GFTQSKLEFSQVKGLLKGFVDLIFCYQGKYYILDYKS 1100
Cdd:TIGR00609 924 ITLSQ----IDPEDRQREMEFLLPINPEFQKQKLNFVIRAYpdRAGSPDLHFQLLRGLLKGFIDLVFEHNGRYYILDYKS 999
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 1101 NYLGSTPADYEGDMLEQAMSSHQYHLQYLIYTVALHRLLKQRIADYSIETHLGGVYYTFLRGM--PAGQGVYFKKLTVEQ 1178
Cdd:TIGR00609 1000 NWLGKDASDYSPEALTEAILKERYDLQYLIYTLALHRYLRKRLKDYDYERHFGGVIYLFLRGIdgNKGNGIFFWNPPANL 1079
|
....*...
gi 498239896 1179 VTILDGLF 1186
Cdd:TIGR00609 1080 IDLLKELF 1087
|
|
| RecB |
COG1074 |
3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, ... |
2-1158 |
0e+00 |
|
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: 601.57 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 2 QALNPLTmpliGQSLIEASAGTGKTYTITGLYLRYLLgmqiegelNTPLSVEQILVVTFTDAATQEIKDRVRSRIiaaRD 81
Cdd:COG1074 12 RALDPLG----GSVLVEASAGSGKTYTLVARYLRLLL--------ERGLDPEEILVVTFTRAAAAEMRERIRERL---AE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 82 ALLGQDPNDELIEgviakiddkhRAFDLLDAAAKSMDEAAIFTIHGFCQRMLKQHAFESGVAFNLEFILDERDILL-ETI 160
Cdd:COG1074 77 AADLEDPDLEELA----------RARRRLARALENLDRAAISTIHSFCQRLLREFAFEAGLDPNFELLDDAEALLLeEAV 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 161 KDFWRAFVYPLNKERTDAILDVFAA-PEALFAQVASILNKANAhitpQINLDDVWRARDEYITrvpafkkavLEQEFIGA 239
Cdd:COG1074 147 DDLLREAYAPLDALALARLLDAFGRdDDSLEELLLALYKLRSR----PDWLEELAELDEALEA---------LREALLKA 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 240 IKSsglsgsktparkgslgaleafclggdlffefgtnkysfevwstenlsdvsnykknqplfVHPLLSQFDELAALnnti 319
Cdd:COG1074 214 KEA-----------------------------------------------------------LAALREALAAAAAP---- 230
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 320 nqglKIAVVQHAARWVKAAIVKRKQEQSVITPDDLLTNLHSALNNEQGDVLAQKIAQLFPVAMIDEFQDTDPIQYGIFSK 399
Cdd:COG1074 231 ----LLAALLRLLAAVLARYERRKRERGLLDFDDLLHRALRLLRDEDAPWVAERLRERYRHILVDEFQDTSPLQWEILRR 306
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 400 IYG---QQNTTLAMIGDPKQAIYGFRGADVFTYIGAKEAVQTDQQF---TLGTNFRSSTDIVNSVNSLFGKH-ANSFIyn 472
Cdd:COG1074 307 LAGealADGRTLFLVGDPKQSIYRFRGADPELFLEARRALEGRVDGerlTLTTNFRSTPEVVDAVNALFAQLmGAGFG-- 384
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 473 dAIPFNAVAAkgkkaedsfLIDGKPAtAFEFNVFVDEAADEKNKptnkgvgQAHLATHFANKIVTLLEKAKQGDAciGST 552
Cdd:COG1074 385 -EIPYEPVEA---------LRPGAYP-AVELWPLEPDDVSEEDA-------REREARAVAARIRRLLAEGTTVEG--GGR 444
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 553 PVSAADICILVRDRVEAQIMKKALSEAKIAsVYLS-RESVFSQELSHHLLNFLTALHGQYDESLLRGVLAGPLFCLSYNE 631
Cdd:COG1074 445 PVRPGDIAVLVRTRSEAAAIARALKAAGIP-VAASdRLSLFESPEVRDLLALLRALLNPEDDLALAAVLRSPLFGLSDED 523
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 632 IHALADDEN------------KWQDYLNFFAQLSHIWNKQGAMAMLERLMSHNQLSAKWQGLGyNVERWLTDFRHLGEIL 699
Cdd:COG1074 524 LAALAADRKgeslwealrayeRLARALERLRALRELARRLGLAELLERLLEETGLLERLLALP-GGERRLANLLHLDELL 602
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 700 QQ-KQIELEGTL---RLLRWFAQKVSQQDGEtVQVRLESDANLVKIVTMHASKGLEYPLVFMPfasgyretkealyhnng 775
Cdd:COG1074 603 QLaLEYEQTGGPglaGFLRWLERLIEDGGDE-EKRRLESDADAVRIMTIHKSKGLEFPVVFLP----------------- 664
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 776 klvydlskdeDALQKAEQERLAEDLRLLYVALTRAVHFCalgvynigqgqssrlamqssalghVLFAGLELASSQTWRTH 855
Cdd:COG1074 665 ----------ALRERARAEELAEELRLLYVALTRARDRL------------------------VLSGAVKKKDAEKESSW 710
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 856 LSEFcdansamsyqqftsqtlleqgklcfsnskiaqqtlsvnrvtaniernwratsfsalsfkkhsdqlapgrsdedhek 935
Cdd:COG1074 711 LARR---------------------------------------------------------------------------- 714
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 936 defavqedelpspysfpkgpkpGSCLHEIFEQIDFispivhstNTEQNLSEVVKRSLEKYHISEQWREVAEKWVLDVLAC 1015
Cdd:COG1074 715 ----------------------GTLVHRLLEHLDF--------SAPAELRAALARLLARGGLDEEEAEALAEALLAFLAT 764
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 1016 PLdksslensllSLGVLTPSDCLVEMEFNLPleslsapklnemlvkhfgftqskLEFSQVKGLLKGFVDLIFCYQGKYYI 1095
Cdd:COG1074 765 PL----------LAELFAAAEVLREVPFLLP-----------------------DLYRGLGGLLKGRIDLVFEDDGRVYI 811
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 498239896 1096 LDYKSNYLGSTPADYegdmleqamSSHQYHLQYLIYTVALHRLLKQRIADysiethlGGVYYT 1158
Cdd:COG1074 812 VDYKTNRLGPDDEEY---------LPERYRLQLALYALALERLLPGRPVR-------AGLYFT 858
|
|
| RecB_C-like |
cd22352 |
C-terminal nuclease domain of exodeoxyribonuclease V subunit RecB and similar proteins; ... |
907-1183 |
3.42e-73 |
|
C-terminal nuclease domain of exodeoxyribonuclease V subunit RecB and similar proteins; Exodeoxyribonuclease V subunit beta (RecB) is a helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair; it binds to DSBs and unwinds DNA via a rapid and highly processive ATP-dependent bidirectional helicase. The C-terminal PDDEXK nuclease domain belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.
Pssm-ID: 411756 [Multi-domain] Cd Length: 215 Bit Score: 242.19 E-value: 3.42e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 907 WRATSFSALSFKKHSDQLAPGRSDE-DHEKDEFAVQEDELPsPYSFPKGPKPGSCLHEIFEQIDFISpivhstnteqnls 985
Cdd:cd22352 1 WRITSFSSLTRGLGGKAAEASHDEEpDEDEEAAPEEADEEG-IDALPRGAKTGTFLHEILENIDRLS------------- 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 986 evvkrslekyhiseqwrevaekwvldvlacpldksslensllslgvltpsdclvEMEFNLPLES-LSAPKLNEMLVKHFG 1064
Cdd:cd22352 67 ------------------------------------------------------EMEFYLPLSDkLDAEALNELLRQHGP 92
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 1065 FTQ-SKLEFSQVKGLLKGFVDLIFCYQGKYYILDYKSNYLGSTPADYEGDMLEQAMSSHQYHLQYLIYTVALHRLLKQRI 1143
Cdd:cd22352 93 PGAlPPLSFETLRGFLKGFIDLVFEHEGRYYILDYKSNYLGDYLEDYSPEALEAAMLEHHYDLQYLLYTLALHRYLKQRL 172
|
250 260 270 280
....*....|....*....|....*....|....*....|...
gi 498239896 1144 ADYSIETHLGGVYYTFLRGMPA---GQGVYFKKLTVEQVTILD 1183
Cdd:cd22352 173 PDYDYERHFGGVYYLFLRGMDPegpGNGVFFDRPSAELIEALD 215
|
|
| UvrD |
COG0210 |
Superfamily I DNA or RNA helicase [Replication, recombination and repair]; |
16-810 |
1.71e-39 |
|
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
Pssm-ID: 439980 [Multi-domain] Cd Length: 721 Bit Score: 157.79 E-value: 1.71e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 16 LIEASAGTGKTYTITGLyLRYLLgmqiegeLNTPLSVEQILVVTFTDAATQEIKDRVRSriiaardallgqdpndelieg 95
Cdd:COG0210 23 LVLAGAGSGKTRVLTHR-IAYLI-------AEGGVDPEQILAVTFTNKAAREMRERIEA--------------------- 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 96 viakiddkhrafdLLDAAAKSMDeaaIFTIHGFCQRMLKQHAFESGVAFNLEfILDERDilletikdfwrafvyplnker 175
Cdd:COG0210 74 -------------LLGRLARGLW---VGTFHSLALRILRRHAELLGLPPNFT-ILDGDD--------------------- 115
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 176 TDAILdvfaapealfaqvasilnkanAHITPQINLDDvwrardeyiTRVPAfkKAVleQEFIGAIKSSGLsgskTParkg 255
Cdd:COG0210 116 QLRLI---------------------KELLKELGLDE---------KRFPP--REL--LSLISRAKNEGL----TP---- 153
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 256 slgaleafclggdlffefgtnkysfevwstenlsdvsnykknqplfvhpllsqfDELAALnntinqglkiavVQHAARWV 335
Cdd:COG0210 154 ------------------------------------------------------EELAEL------------LAADPEWR 167
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 336 KAAIV-----KRKQEQSVITPDDLLTNLHSALNnEQGDVLAqKIAQLFPVAMIDEFQDTDPIQYGIFSKIYGQQNTtLAM 410
Cdd:COG0210 168 AAAELyeayqERLRANNALDFDDLLLLAVRLLE-ENPEVLE-KYQNRFRYILVDEYQDTNPAQYELLRLLAGDGRN-LCV 244
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 411 IGDPKQAIYGFRGADV-----FT--YIGAKeavqtdqQFTLGTNFRSSTDIVNSvnslfgkhANSFIYN--DAIPFNAVA 481
Cdd:COG0210 245 VGDDDQSIYGFRGADPenilrFEkdFPDAK-------VIKLEQNYRSTQNILDA--------ANAVIANnpGRLGKNLWT 309
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 482 AKGkkaedsfliDGKPatafefnVFVDEAADEknkptnkgvgqAHLATHFANKIVTLLEKAkqgdacigstpVSAADICI 561
Cdd:COG0210 310 DNG---------EGEK-------VRLYVAPDE-----------EEEARFVADEIRELHEEG-----------VPLSDIAV 351
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 562 LVRDRVEAQIMKKALSEAKIASVYLSRESVFSQELSHHLLNFLTALHGQYDESLLRGVLAGPLFCL---SYNEIHALADD 638
Cdd:COG0210 352 LYRTNAQSRALEEALRRAGIPYRVVGGLRFYERAEIKDLLAYLRLLANPDDDVALLRILNVPRRGIgaaTLERLREAARE 431
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 639 ENK-WQDYLNFFAQLSHIWNKQGA-----MAMLERLMS-------HNQLSAKWQGLGYnverwltdfrhLGEILQQKQIE 705
Cdd:COG0210 432 EGIsLLEALRDLGELAGLSGRAAKalrrfAELLEALRAaaerlplEELLEALLDESGY-----------EEELREEAGEE 500
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 706 ----LEGTLRLLRWFAQKVSQQDGETVQ-----VRLESDANL-------VKIVTMHASKGLEYPLVFMPFASgyretkEA 769
Cdd:COG0210 501 aerrLENLEELVDAAARFEERNPGASLEafleeLALLSDLDAadededaVTLMTLHAAKGLEFPVVFLVGLE------EG 574
|
810 820 830 840
....*....|....*....|....*....|....*....|..
gi 498239896 770 LY-HNNgklvydlskdedALQkaEQERLAEDLRLLYVALTRA 810
Cdd:COG0210 575 LFpHQR------------SLD--DEEELEEERRLFYVAITRA 602
|
|
| UvrD-helicase |
pfam00580 |
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural ... |
2-434 |
1.15e-38 |
|
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: 145.47 E-value: 1.15e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 2 QALNPLTMPLigqsLIEASAGTGKTYTITGLYLRYLLGMQIEgelntplsVEQILVVTFTDAATQEIKDRVRSriiaard 81
Cdd:pfam00580 7 KAVTHLGGPL----LVLAGAGSGKTRVLTERIAYLILEGGID--------PEEILAVTFTNKAAREMKERILK------- 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 82 aLLGQDPndeliegviakiddkhrafdlldaaaksMDEAAIFTIHGFCQRMLKQHAFESGVAFNLEfILDERDILletik 161
Cdd:pfam00580 68 -LLGKAE----------------------------LSELNISTFHSFCLRILRKYANRIGLLPNFS-ILDELDQL----- 112
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 162 dfwrafvyplnkertdaildvfaapealfAQVASILNKANAHITPQInlddvwrardeyitrvpafKKAVLEQEFIGAIK 241
Cdd:pfam00580 113 -----------------------------ALLKELLEKDRLNLDPKL-------------------LRKLELKELISKAK 144
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 242 SSGLSgsktParkgslgaleafclggdlffefgtnkysfevwstenlsdvsnyKKNQPLFVHPLLSQFDELAALnntinq 321
Cdd:pfam00580 145 NRLLS----P-------------------------------------------EELQQGAADPRDKLAAEFYQE------ 171
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 322 glkiavvqhaarwvkaaIVKRKQEQSVITPDDLLTNLHSALnnEQGDVLAQKIAQLFPVAMIDEFQDTDPIQYGIFSKIY 401
Cdd:pfam00580 172 -----------------YQERLKENNALDFDDLLLLTLELL--RSDPELLEAYRERFKYILVDEFQDTNPIQYRLLKLLA 232
|
410 420 430
....*....|....*....|....*....|...
gi 498239896 402 GqQNTTLAMIGDPKQAIYGFRGADVFTYIGAKE 434
Cdd:pfam00580 233 G-GHENLFLVGDPDQSIYGFRGADIENILKFEK 264
|
|
| addA_alphas |
TIGR02784 |
double-strand break repair helicase AddA, alphaproteobacterial type; AddAB, also called RexAB, ... |
19-810 |
1.03e-32 |
|
double-strand break repair helicase AddA, alphaproteobacterial type; AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 274298 [Multi-domain] Cd Length: 1135 Bit Score: 137.90 E-value: 1.03e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 19 ASAGTGKTYTITGLYLRYLL-GMQiegelntPlsvEQILVVTFTDAATQEIKDRVRSRIiaARDALLGQDPNDELIEGV- 96
Cdd:TIGR02784 17 ANAGSGKTHVLTQRVIRLLLaGTE-------P---SKILCLTYTKAAAAEMQNRVFKRL--GEWAVLDDADLRARLEALe 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 97 IAKIDDKHRAfdllDAA---AKSMDEAA---IFTIHGFCQRMLKQHAFESGVAFNLEfILDERD--ILLETIKDFWRAFV 168
Cdd:TIGR02784 85 GKRPDAAKLA----EARrlfARALETPGglkIQTIHAFCEALLHQFPLEANVAGHFS-VIDDRAaaTLLEEARRALLAGP 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 169 YPLNKERTDAILDVFAAP-----EALFAQVASILNKANAHITPQINLDDVWRARDEYITRVPAFKKAVLEQEFIG----- 238
Cdd:TIGR02784 160 AAPDDALADALATVLEAAgetglEALLAEIVARRDALMAFLDEAGGEGAEARLRRALGLAPGDTAEDLLEAVWPLpglpr 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 239 ----AIKSSGLSGSKTPARKGSLGALEAFCLGGD----------LFFEFGTNKYSFevwstenlSDVSNyKKNQPL--FV 302
Cdd:TIGR02784 240 lalaLIAALLKSGGGSKDAAAALSQLREAAAEPDpvarldlllgAFLTSKGEPKSA--------SFVIK-KAIQKSlpDL 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 303 HPLLSqfDELAALNNTINQGLKIAVVQ------HAARWVKAAIVKRKQEQSVITPDDLLTNLhSALNNEQGdvLAQ---- 372
Cdd:TIGR02784 311 AEALE--DAASRVEALRERLRALRMAQrtlaalRLAARLLQRYARLKKARGLLDFNDLIERT-VALLARPG--AGAwvhy 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 373 KIAQLFPVAMIDEFQDTDPIQYGIFSKI-------YGQQNT---TLAMIGDPKQAIYGFRGAD--VF----TYIGAK--- 433
Cdd:TIGR02784 386 KLDRGIDHILVDEAQDTSPEQWDIIQALaeeffsgEGARSGverTIFAVGDEKQSIYSFQGADpeRFaeerREFSRKvra 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 434 -EAVQTDQQFTLgtNFRSSTDIVNSVNSLFGKHANS---FIYNDAIPFNAVAAKGKKAEDSFLIDGKPATAF--EFNVFV 507
Cdd:TIGR02784 466 vGRKFEDLSLNY--SFRSTPDVLAAVDLVFADPENArglSADSDAPVHEAFRDDLPGRVDLWDLISKEEGEEpeDWTDPV 543
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 508 DEAADEknKPTNKgvgqahLATHFANKIVTLLEKakqGDACIG-STPVSAADICILVRDR---VEAQImkKALSEAKIAS 583
Cdd:TIGR02784 544 DELGER--APEVR------LAERIAAEIRAWLDR---GTPIPGrGRAVRPGDILVLVRKRdafFSALI--RALKRRGIPV 610
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 584 VYLSRESVFSQELSHHLLNFLTALHGQYDESLLRGVLAGPLFCLSYNEIHALADDENK---WQ-------DYLNFFAQLS 653
Cdd:TIGR02784 611 AGADRLKLTSHIAVKDLMALGRFVLQPEDDLSLAALLKSPLFGLDEDDLFRLAAGRSGgslWAalrrreaEFAATLAVLR 690
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 654 HiWNKQGA----MAMLERLMSHNQLSAKWQG-LGYNVERWLTDFrhLGEILQQKQIELEGTLRLLRWFaqkvsQQDGETV 728
Cdd:TIGR02784 691 D-WLSLADfltpFEFYARLLGRDGGRRKLLArLGAEAEDILDEF--LSQALAYERTGLPGLQAFLSWL-----EADDPEI 762
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 729 QVRLESDANLVKIVTMHASKGLEYPLVFM------PFASGY--RETKEALYHNNGKLVYDLSKDEDALQKAEQERL---A 797
Cdd:TIGR02784 763 KREMDQARDEVRVMTVHGAKGLEAPVVFLvdtgskPFASQRapLLLATGGSGGKAPLWRPASAFDPSLSAAARERLkerA 842
|
890
....*....|....*
gi 498239896 798 ED--LRLLYVALTRA 810
Cdd:TIGR02784 843 EDeyRRLLYVAMTRA 857
|
|
| PRK13909 |
PRK13909 |
RecB-like helicase; |
18-811 |
2.82e-24 |
|
RecB-like helicase;
Pssm-ID: 237554 [Multi-domain] Cd Length: 910 Bit Score: 110.44 E-value: 2.82e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 18 EASAGTGKTYTITGLYLRYLLgmqiEGElntplSVEQILVVTFTDAATQEIKdrvrSRIIaarDAL--LGQDPNDELIEG 95
Cdd:PRK13909 4 KASAGSGKTFALSVRFLALLF----KGA-----NPSEILALTFTKKAANEMK----ERII---DTLlnLEKEKEESELNE 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 96 VIAKID-DKHrafDLLDAAAKSMD-----EAAIFTIHGFCQRMLKQHAFESGVAFNleFILDErdillETIKDFWRAFVY 169
Cdd:PRK13909 68 LEEKLGlSKE---ELLNKRDKVYQeflnsELKISTIDAFFQKILRKFCLNLGLSPD--FSIKE-----DTKEELNEKFLS 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 170 PLNKERTdaildvfaapEALFAQVASILNKANAHITPqiNLDDVW-RARDEYITRVPAFKKAVLEQEFIGAIKSSGLSGS 248
Cdd:PRK13909 138 ALSKEEL----------LELLAFIKQCESKKNNSFFE--LLEKLYeKNNELKLFEKAKNPIEFDEEKFLEELRSLKQQIQ 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 249 KTParKGSLGALEAFclGGDLFFEFgtnKYSFEVWSTENlSDVSNYKKnqpLFVHPLLSQFDEL-AALNNTINQgLKIAV 327
Cdd:PRK13909 206 SIE--TASKNAKKAF--KKEDFEEL---LNSSKTWLEKE-SEYRYFKK---LYNEELDAEFEELkNALKRYYDA-KENYK 273
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 328 VQHAARWV---KAAIVKRKQEQSVITPDDLLTNLHSALNNEQGDV------LAQKIAQLfpvaMIDEFQDTDPIQYGIFS 398
Cdd:PRK13909 274 LSKLFKLLqlyKEAKNELNKKKNALDFDDISKKVYELLGEEEIDKdflyfrLDSKISHI----LIDEFQDTSVLQYKILL 349
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 399 KI-------YGQQ-NTTLAMIGDPKQAIYGFRG--ADVFTYIGAKEAVQTDQqftLGTNFRSSTDIVNSVNSLFGKHANS 468
Cdd:PRK13909 350 PLideiksgEGQKkFRSFFYVGDVKQSIYRFRGgkKELFDKVSKDFKQKVDN---LDTNYRSAPLIVDFVNEVFKKKYKN 426
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 469 fiYNDAIPFnavaakgKKAEDSFlidgkpatafefnVFVDEAADEKNKptnkgvgqahLATHFANKIVTLLEKAkqgdac 548
Cdd:PRK13909 427 --YKTQYAE-------QHKSGGY-------------VEVVEVADESEE----------LLEQLLQEIQFLLEKG------ 468
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 549 igstpVSAADICILVRDRVEAQIMKKALSEA-KIASVYLSRESVFSQELSHHLLNFLTALHGQ---YDESLLRgvLAGpl 624
Cdd:PRK13909 469 -----IDPDDIAILCWTNDDALEIKEFLQEQfGIKAVTESSAKLINQPEVKALIEALKYCLFGeeiYKHNVLK--LLG-- 539
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 625 fclsyneihALADDENKWQDylnffaqlshiwNKQGAMAMLERLMSHnqlsakwqgLGYNVERWLtdfrhlgeilqqKQI 704
Cdd:PRK13909 540 ---------KEPDKIPSFLP------------KEESVAEFVKKLIEE---------LKLYDENLL------------KFL 577
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 705 ELEGTLRLLRWFAQKVSQQDGETVQvrleSDANLVKIVTMHASKGLEYPLV-FMPFASGYRETKEA-LYHNNGK----LV 778
Cdd:PRK13909 578 ELASGYEDIEEFLFKLEPCDKEIAS----EESKGVQIMTVHKSKGLEFEHViVCDRLGKPNSDSSNlLFEYDGIelwqIY 653
|
810 820 830 840
....*....|....*....|....*....|....*....|
gi 498239896 779 YDLSK----DED---ALQKAEQERLAEDLRLLYVALTRAV 811
Cdd:PRK13909 654 YRIKGrenfDKDyarALEKEKALKYEEEINVLYVAFTRAK 693
|
|
| DEXQc_UvrD |
cd17932 |
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ... |
352-448 |
2.11e-21 |
|
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: 92.96 E-value: 2.11e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 352 DDLLTNLHSALNNEQGdvLAQKIAQLFPVAMIDEFQDTDPIQYGIFSKIYGQqNTTLAMIGDPKQAIYGFRGADVFTYIG 431
Cdd:cd17932 96 DDLLLYALELLEENPD--VREKLQSRFRYILVDEYQDTNPLQYELLKLLAGD-GKNLFVVGDDDQSIYGFRGADPENILD 172
|
90
....*....|....*..
gi 498239896 432 AKEAVQTDQQFTLGTNF 448
Cdd:cd17932 173 FEKDFPDAKVIKLEENY 189
|
|
| SF1_C_UvrD |
cd18807 |
C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase ... |
734-817 |
5.40e-19 |
|
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: 84.98 E-value: 5.40e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 734 SDANLVKIVTMHASKGLEYPLVFMPFAsgyretkealyhNNGKLVYDLSKDedaLQKAEQERLAEDLRLLYVALTRAVHF 813
Cdd:cd18807 81 EEALRVTLMTIHASKGLEFPVVFIVGL------------GEGFIPSDASYH---AAKEDEERLEEERRLLYVALTRAKKE 145
|
....
gi 498239896 814 CALG 817
Cdd:cd18807 146 LYLV 149
|
|
| DEXQc_UvrD |
cd17932 |
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ... |
16-165 |
1.37e-15 |
|
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: 76.40 E-value: 1.37e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 16 LIEASAGTGKTYTITGLYLrYLLgmqiegeLNTPLSVEQILVVTFTDAATQEIKDRVRSRIiaardallgqdpndelieg 95
Cdd:cd17932 16 LVLAGAGSGKTRVLTHRIA-YLI-------LEGGVPPERILAVTFTNKAAKEMRERLRKLL------------------- 68
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 498239896 96 viakiddkhrafdlldaAAKSMDEAAIFTIHGFCQRMLKQHA-FESGVAFNLEfILDERDILLETIKDFWR 165
Cdd:cd17932 69 -----------------GEQLASGVWIGTFHSFALRILRRYGdFDDLLLYALE-LLEENPDVREKLQSRFR 121
|
|
| PRK10919 |
PRK10919 |
ATP-dependent DNA helicase Rep; Provisional |
382-810 |
9.56e-13 |
|
ATP-dependent DNA helicase Rep; Provisional
Pssm-ID: 182838 [Multi-domain] Cd Length: 672 Bit Score: 72.57 E-value: 9.56e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 382 MIDEFQDTDPIQYGIFSKIYGQQnTTLAMIGDPKQAIYGFRGADVFTYIGAKEAVQTDQQFTLGTNFRSSTDIVNSVNSL 461
Cdd:PRK10919 212 LVDEYQDTNTSQYELVKLLVGSR-ARFTVVGDDDQSIYSWRGARPQNLVLLSQDFPALQVIKLEQNYRSSGRILKAANIL 290
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 462 FGKHANSFiyndaipfnavaakgKKAEDSFLIDGKPATAFEFNVFVDEAadeknkptNKGVGQAhLATHFANKivtllek 541
Cdd:PRK10919 291 IANNPHVF---------------EKRLFSELGYGDELKVLSANNEEHEA--------ERVTGEL-IAHHFVNK------- 339
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 542 akqgdacigstpVSAADICILVRDRVEAQIMKKALSEAKIASVYLSRESVFSQELSHHLLNFLTALHGQYDESLLRGVLA 621
Cdd:PRK10919 340 ------------TQYKDYAILYRGNHQSRVFEKFLMQNRIPYKISGGTSFFSRPEIKDLLAYLRVLTNPDDDSAFLRIVN 407
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 622 GPLFCLSYNEIHAL---ADDENKWQDYLNFFAQLSHIWNKQGA---------MAMLERLMSHNQLSAKWQGL-GYNVERW 688
Cdd:PRK10919 408 TPKREIGPATLQKLgewAMTRNKSLFTASFDMGLSQTLSGRGYesltrfthwLAEIQRLAEREPVAAVRDLIhGIDYESW 487
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 689 LTD------------------FRHLGEILQQKQIELEGTLrllrwfAQKVSQQDGETVQVRLESDANL--VKIVTMHASK 748
Cdd:PRK10919 488 LYEtspspkaaemrmknvnqlFSWMTEMLEGSELDEPMTL------TQVVTRFTLRDMMERGESEEELdqVQLMTLHASK 561
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 498239896 749 GLEYPLVFMpfaSGYREtkealyhnnGKLVYDLSKDEDALqkaEQERlaedlRLLYVALTRA 810
Cdd:PRK10919 562 GLEFPYVYL---VGMEE---------GLLPHQSSIDEDNI---DEER-----RLAYVGITRA 603
|
|
| UvrD_C |
pfam13361 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
731-810 |
1.12e-07 |
|
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: 433145 [Multi-domain] Cd Length: 377 Bit Score: 55.49 E-value: 1.12e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 731 RLESDANLVKIVTMHASKGLEYPLVFMPFAsgyretkealyhNNGKLVYDLSKDEDalqkaeqERLAEDLRLLYVALTRA 810
Cdd:pfam13361 306 EGSDIKERIPIMTIHQAKGLEFDTVFLAGL------------EEGIFPSYRSIKDE-------GNLEEERRLFYVAITRA 366
|
|
| uvrD |
PRK11773 |
DNA-dependent helicase II; Provisional |
382-461 |
3.41e-07 |
|
DNA-dependent helicase II; Provisional
Pssm-ID: 236976 [Multi-domain] Cd Length: 721 Bit Score: 54.49 E-value: 3.41e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 382 MIDEFQDTDPIQYGiFSKIYGQQNTTLAMIGDPKQAIYGFRGADVftyigakEAVqtdQQFT----------LGTNFRSS 451
Cdd:PRK11773 218 LVDEFQDTNAIQYA-WIRLLAGDTGKVMIVGDDDQSIYGWRGAQV-------ENI---QRFLndfpgaetirLEQNYRST 286
|
90
....*....|
gi 498239896 452 TDIVNSVNSL 461
Cdd:PRK11773 287 ANILKAANAL 296
|
|
| SF1_C |
cd18786 |
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
731-812 |
1.19e-05 |
|
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: 44.74 E-value: 1.19e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 731 RLESDANLVKIVTMHASKGLEYPLVFMPFAsgyretkealyhnngklvydlskdedalqkaeqERLAEDLRLLYVALTRA 810
Cdd:cd18786 35 LDEFDLQLVGAITIDSSQGLTFDVVTLYLP---------------------------------TANSLTPRRLYVALTRA 81
|
..
gi 498239896 811 VH 812
Cdd:cd18786 82 RK 83
|
|
| helD |
PRK11054 |
DNA helicase IV; Provisional |
382-487 |
3.96e-05 |
|
DNA helicase IV; Provisional
Pssm-ID: 182930 [Multi-domain] Cd Length: 684 Bit Score: 48.02 E-value: 3.96e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 382 MIDEFQDTDPIQYGIFSKIYGQQ-NTTLAMIGDPKQAIYGFRGADVFTYIGAKEAVQTDQQFTLGTNFRsstdivnsVNS 460
Cdd:PRK11054 435 LVDEFQDISPQRAALLAALRKQNsQTTLFAVGDDWQAIYRFSGADLSLTTAFHERFGEGDRCHLDTTYR--------FNS 506
|
90 100 110
....*....|....*....|....*....|.
gi 498239896 461 LFGKHANSFIYNDAI----PFNAVAAKGKKA 487
Cdd:PRK11054 507 RIGEVANRFIQQNPHqlkkPLNSLTKGDKKA 537
|
|
| HelD |
COG3973 |
DNA helicase IV [Replication, recombination and repair]; |
342-456 |
1.95e-04 |
|
DNA helicase IV [Replication, recombination and repair];
Pssm-ID: 443173 [Multi-domain] Cd Length: 699 Bit Score: 45.63 E-value: 1.95e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 342 RKQEQSVITPDD--LLTNLHSALnneQGDVLAQKIAQLFpvamIDEFQDTDPIQYGIFSKIYGQQNTTlaMIGDPKQAIY 419
Cdd:COG3973 439 RELKKGRWTVADvaLLDELAELL---GGPDRTWTYGHVV----VDEAQDLSPMQWRVLKRRFPSASFT--IVGDLAQAIH 509
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 498239896 420 GFRGA----DVFTYIGAKEAvqtdQQFTLGTNFRSSTDIVN 456
Cdd:COG3973 510 PYRGAesweEVLEPLGGDRA----RLVELTKSYRSTAEIME 546
|
|
| HelD |
COG3973 |
DNA helicase IV [Replication, recombination and repair]; |
717-822 |
6.57e-04 |
|
DNA helicase IV [Replication, recombination and repair];
Pssm-ID: 443173 [Multi-domain] Cd Length: 699 Bit Score: 44.09 E-value: 6.57e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 717 AQKVSQQDGETVQVRL-----ESDANLVKIVTMHASKGLEYPLVFMPFASgyretkEALYHNngklvydlskdedalqka 791
Cdd:COG3973 612 AEALYAALKAGLPVTLiddesEELEAGVVVLPAYLAKGLEFDAVVVVDPD------EIVYES------------------ 667
|
90 100 110
....*....|....*....|....*....|.
gi 498239896 792 eqerlAEDLRLLYVALTRAVHfcALGVYNIG 822
Cdd:COG3973 668 -----PRGRRLLYVALTRATH--RLTVLHTG 691
|
|
| AAA_19 |
pfam13245 |
AAA domain; |
15-118 |
1.08e-03 |
|
AAA domain;
Pssm-ID: 433059 [Multi-domain] Cd Length: 136 Bit Score: 40.66 E-value: 1.08e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 15 SLIEASAGTGKTYTITGLyLRYLLgmQIEGELNtplsveQILVVTFTDAATQEIKDR--VRSRIIAardALLGQDP---- 88
Cdd:pfam13245 14 VLLTGGPGTGKTTTIRHI-VALLV--ALGGVSF------PILLAAPTGRAAKRLSERtgLPASTIH---RLLGFDDleag 81
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 498239896 89 -----NDELIEGVIAKID-----DKHRAFDLLDAAAKSMD 118
Cdd:pfam13245 82 gflrdEEEPLDGDLLIVDefsmvDLPLAYRLLKALPDGAQ 121
|
|
| UvrD_C_2 |
pfam13538 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
741-810 |
8.84e-03 |
|
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: 35.63 E-value: 8.84e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498239896 741 IVTMHASKGLEYPLVFMPFASGyretkealyhnngklvydlskdedalqkAEQERLAEDLRLLYVALTRA 810
Cdd:pfam13538 4 ALTVHKAQGSEFPAVFLVDPDL----------------------------TAHYHSMLRRRLLYTAVTRA 45
|
|
| |
