|
Name |
Accession |
Description |
Interval |
E-value |
| recB |
PRK10876 |
exonuclease V subunit beta; Provisional |
1-1181 |
0e+00 |
|
exonuclease V subunit beta; Provisional
Pssm-ID: 236784 [Multi-domain] Cd Length: 1181 Bit Score: 2385.82 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 1 MNDVAETLDPLRLPLTGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATEELRGRIRSNI 80
Cdd:PRK10876 2 MSDVAETLDPLRLPLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEEILVVTFTEAATEELRGRIRSNI 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 81 HELRIACLRESTDNPLYARLLEEISDKKQAAQWLLLAERQMDEAAVFTIHGFCQRMLSLNAFESGMLFEQQLIEDESLLR 160
Cdd:PRK10876 82 HELRIACLREETDNPLYQRLLAEIDDKAQAAQWLLLAERQMDEAAIFTIHGFCQRMLNLNAFESGMLFEQQLIEDESLLR 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 161 YQACADFWRRHCYPLPRDIAQVVFDVWKGPKALLKDIDRYLQGEAPVIKAPPSQEETLASRHEQILARINQVKQQWCEAV 240
Cdd:PRK10876 162 YQACADFWRRHCYPLPREIARVVFQEWKGPEALLKDISRYLQGEAPVIKAPPPDDETLASRHEQIVARIDAVKQQWREAV 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 241 SELDALIESSGIDRRKFNRGNQAKWIEKITAWAQEETKNYQLPEALGKFSQRFLAERTKAGgVTPQHPLFVAIDNLLGEP 320
Cdd:PRK10876 242 GELDALIESSGVDRRSYNSKNLPKWLEKISAWAEEETNSYQLPKELEKFSQRFLLEKTKKG-ETPQHPLFEAIDQLLAEP 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 321 LSIKDLVLTRALSEIRETVAQEKRRRGELGFDDMLSRLDTALRSESGEALAAAIRTRFPVAMIDEFQDTDPQQYRIFRRI 400
Cdd:PRK10876 321 LSLRDLVITRALAEIRETVAQEKRRRGELGFDDLLSRLDSALQSEGGEALAAAIRTRYPVAMIDEFQDTDPQQYRIFRRI 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 401 WRHQPDTALLLIGDPKQAIYAFRGADIFTYMKARSEVSAHYTLDTNWRSAPGMVNSVNKLFSQMNDAFMFRDIPFSPVKF 480
Cdd:PRK10876 401 YRHQPETALLLIGDPKQAIYAFRGADIFTYMKARSEVSAHYTLDTNWRSAPGMVNSVNKLFSQTDDPFLFREIPFIPVKA 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 481 APRNQSLQFKVNDAPQPAMTLWLMEGESCGSGDYQSYMAQVCATQIRDWLRAGQTGDALLTNGDSSRPVRASDISVLVRS 560
Cdd:PRK10876 481 AGKNQALRFVVKGETQPAMKFWLMEGEGVGVGDYQQTMAQQCAAQIRDWLQAGQRGEALLMNGDDSRPVRASDITVLVRS 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 561 RREAALIRDALTLLAIPSVYLSNRDSVFETLEAQEMLWVLQAVMAPERENTLRSALATSMMGLTALDIETLNNDESAWDA 640
Cdd:PRK10876 561 RQEAALIRDALTLLAIPSVYLSNRDSVFETLEAQEMLWLLQAVLAPERERTLRSALATSMMGLDALDIDALNNDERAWDA 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 641 VVEEFDGYRQIWHKRGVMPMLRALMSARNIAENLLATAGGERRLTDILHISELLQEAGSQLESEHALVRWLAQHILEPDS 720
Cdd:PRK10876 641 LVEEFDGYRQIWRKRGVLPMLRALMSARNIAENLLATAGGERRLTDILHIGELLQEASSQLDSEHALVRWLAQQILEPDS 720
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 721 NASSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFITHFRVQDQAFYHDRHSYEAVLDLSHAEESIALAEAERLAEDLR 800
Cdd:PRK10876 721 QASSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFITNFRVQDQAFYHDRHSFEAVLDLNAAEESVALAEEERLAEDLR 800
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 801 LLYVALTRAVWHCSLGVAPLVRRRSDKKGETDVHQSALGRLLQKGEPMDAAGLRACIEALCDEDIVCRTPGNTDNDRWQI 880
Cdd:PRK10876 801 LLYVALTRSVWHCSLGVAPLVRRRRKKKGETDLHQSALGYLLQKGEPGDAAGLRACLEALCDDDIALQTAQETDNQPWQP 880
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 881 AAASHAELSARTLQRLLYDSWRVTSYSGLQQRGHSVAQDLIPRLDIDAAGVGEAAEAPAMTPHHFPRGASPGTFLHSLFE 960
Cdd:PRK10876 881 QDASLAELSARTLQRLLQDNWRVTSYSGLQQHGHSIAQDLLPRLDVDAAGEGSVVEEPQLTPHTFPRGASPGTFLHSLFE 960
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 961 ELDFTQPINPQWVQEKLELSGFETRWEPVLTRWLDTVLHVPLNETGVSLGVLTEREKQVEMEFYLPIAQPLTAGELDALI 1040
Cdd:PRK10876 961 DLDFTQPVDPEWLQEQLELQGFEEQWEPVLTQWITAVLQTPLNETGVSLSQLSARDKQVEMQFYLPIDQPLTASQLDALI 1040
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 1041 RRYDPLSAGCPALDFMQVRGMLKGFIDLVFRYEGRYYLLDYKSNWLGEDSAAYTQTAMAAAMQAHRYDLQYQLYTLALHR 1120
Cdd:PRK10876 1041 RQYDPLSAGCPPLDFMQVRGMLKGFIDLVFRWQGRYYLLDYKSNWLGEDSSAYTQEAMAQAMQAHRYDLQYQLYTLALHR 1120
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2747077403 1121 YLRHRMANYDYERHFGGVIYLFLRGVDSERPQQGIFTTRPAAALINQLDDMFAGEMSEEAQ 1181
Cdd:PRK10876 1121 YLRHRLADYDYQRHFGGVIYLFLRGVDKEHPGQGIFTTRPNAALIDGLDELFAGETLEEAQ 1181
|
|
| recB |
TIGR00609 |
exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with ... |
8-1172 |
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: 1309.34 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 8 LDPLRLPLTGERLIEASAGTGKTFTIAALYLRLLLGLGgsaafprPLTVEELLVVTFTEAATEELRGRIRSNIHELRIAC 87
Cdd:TIGR00609 1 LDPLTIPLNGTFLIEASAGTGKTFTIAQLYLRLLLEGG-------PLTVEEILVVTFTNAATEELKTRIRGRIHQALRAL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 88 LRESTDNPLYARLLEEISDKK--QAAQWLLLAERQMDEAAVFTIHGFCQRMLSLNAFESGMLFEQQLIEDESLLRYQACA 165
Cdd:TIGR00609 74 KAALTSQELPEPLKEAIQDEKvkQAITRLRNALATMDEAAIYTIHGFCQRMLEQHAFESDEIFDVELIEDESLLLAEITK 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 166 DFWRRHCYPLPRDIAQVVFDVWKGPKALLKDIDRYLQGEA-PVIKAPPSQEETLASRHEQILARINQVKqqwceavseld 244
Cdd:TIGR00609 154 DFWRRNFYNLPFDIAQIVLKTKKSPQAVLTQILADLLLQSyLAFPSPPLDLEQLIKWHEQIYKDLDKLD----------- 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 245 aliessgidrrkfnrgnqakwiekitawaqeetknyqlpealgkfsqrflaertkaggvtpqHPLFVAIDNLL---GEPL 321
Cdd:TIGR00609 223 --------------------------------------------------------------HAVFEEIDKLNaerNNLF 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 322 SIKDLVLTRALSEIRETVAQEKRRRGELGFDDMLSRLDTALRSESGEALAAAIRTRFPVAMIDEFQDTDPQQYRIFRRIW 401
Cdd:TIGR00609 241 CLKDRVFLTLLKEVQEELKKEKKRRREIGFDDLLSRLETALKSAEGEKLAQAIREQYPIALIDEFQDTDPQQYRIFSKLF 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 402 RHQPDTALLLIGDPKQAIYAFRGADIFTYMKARSEVSAHYTLDTNWRSAPGMVNSVNKLFSQMNDAFMFRDIpFSPVKFA 481
Cdd:TIGR00609 321 IAQKETSLFLIGDPKQAIYSFRGADIFTYLQAKSKADARYTLGTNWRSTPALVGSLNKLFSLISNPFLEKPI-FIPVLAH 399
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 482 PRNQSLQFKVNDAPQPAMTLWLMEGESCGSGDYQSYMAQVCATQIRDWLRAGQTGDALLTNGDSSRPVRASDISVLVRSR 561
Cdd:TIGR00609 400 QKNSKGSFVINGQEQPPIHFFTTEVESEGVDDYRQTIAQKCAREIALWLASAALGLANFIATFGGRPLRAGDIAVLVRGR 479
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 562 REAALIRDALTLLAIPSVYLSNRDSVFETLEAQEMLWVLQAVMAPERENTLRSALATSMMGLTALDIETLNNDESAWDAV 641
Cdd:TIGR00609 480 KEANQIRKALKKAQIPSVYLSDKSSVFATEEAQELLALLEALLEPENEGTLRAALASSIFGLSALELETLNQDEITWERV 559
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 642 VEEFDGYRQIWHKRGVMPMLRALMSARNIAENLLATAGGERRLTDILHISELLQEAGSQLESEHALVRWLAQHILEPDSN 721
Cdd:TIGR00609 560 VEKFREYHDIWRKIGVLAMFQRLMLEKGIGERLLSQPGGERILTNLLHLAELLQEAAHQERNKLSLLRWLEDQISNEEEE 639
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 722 aSSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFITHFRVQDQAFYHDRHSYEAVL-DLSHAEESIALAEAERLAEDLR 800
Cdd:TIGR00609 640 -EEEIIRLESDAELVKIVTIHKSKGLEYPIVFLPFITDAKKSNFASLHDQHSHEYQLyDFNQSEENQKLARVERLAEDLR 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 801 LLYVALTRAVWHCSLGVAPLVRRRSDKKGETDVHQSALGRLLQKGEPMDAAGLRACIEALCDED-IVCRTPGNTDNDRWQ 879
Cdd:TIGR00609 719 LLYVALTRAKKQLFIGIAPLITSKLSNLAYSALHNSALGYQKQDGETDNITGLKQCLAALADPAgISSIPAKPIGANSSK 798
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 880 IAAASHAELSARTLQRLLYDSWRVTSYSGLQQRGHSVAQDLIPRLDIDAAGVgeaaeapAMTPHHFPRGASPGTFLHSLF 959
Cdd:TIGR00609 799 KEPASTALLEARTFHRRIRENWRITSFSSLKELEEAVTEEPAPGLDYEVSSL-------EISAQDFPKGKKTGTLLHAIL 871
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 960 EELDFTQPINPQ----WVQEKLELSGFETRWEPVLTRWLDTVLHVPLN-ETGVSLGVLTEREKQVEMEFYLPIAQPLTAG 1034
Cdd:TIGR00609 872 ESLIFSQAADLEkqnnLIAEKLKKTGLEGLWEPELQEWLEKMLNTPLTfSRAITLSQIDPEDRQREMEFLLPINPEFQKQ 951
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 1035 ELDALIRRYdPLSAGCPALDFMQVRGMLKGFIDLVFRYEGRYYLLDYKSNWLGEDSAAYTQTAMAAAMQAHRYDLQYQLY 1114
Cdd:TIGR00609 952 KLNFVIRAY-PDRAGSPDLHFQLLRGLLKGFIDLVFEHNGRYYILDYKSNWLGKDASDYSPEALTEAILKERYDLQYLIY 1030
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*...
gi 2747077403 1115 TLALHRYLRHRMANYDYERHFGGVIYLFLRGVDSERpQQGIFTTRPAAALINQLDDMF 1172
Cdd:TIGR00609 1031 TLALHRYLRKRLKDYDYERHFGGVIYLFLRGIDGNK-GNGIFFWNPPANLIDLLKELF 1087
|
|
| RecB |
COG1074 |
3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, ... |
1-1125 |
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: 686.31 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 1 MNDVAETLDPLR--LPLTGERLIEASAGTGKTFTIAALYLRLLLGlggsaafpRPLTVEELLVVTFTEAATEELRGRIRS 78
Cdd:COG1074 1 MSEPPWTDAQRRalDPLGGSVLVEASAGSGKTYTLVARYLRLLLE--------RGLDPEEILVVTFTRAAAAEMRERIRE 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 79 NIHELRiaclreSTDNPLYARLleeisdkKQAAQWLLLAERQMDEAAVFTIHGFCQRMLSLNAFESGMLFEQQLIED-ES 157
Cdd:COG1074 73 RLAEAA------DLEDPDLEEL-------ARARRRLARALENLDRAAISTIHSFCQRLLREFAFEAGLDPNFELLDDaEA 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 158 LLRYQACADFWRRHCYPLPRDIAQVVFDVW-KGPKALLKDIDRYLQgeapvikappsqeetLASRheqilarinqvkQQW 236
Cdd:COG1074 140 LLLEEAVDDLLREAYAPLDALALARLLDAFgRDDDSLEELLLALYK---------------LRSR------------PDW 192
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 237 CEAVSELDaliessgidrrkfnrgnqakwiekitawaqeetknyqlpEALGKFSQRFLAERTkaggvtpqhpLFVAIDNL 316
Cdd:COG1074 193 LEELAELD---------------------------------------EALEALREALLKAKE----------ALAALREA 223
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 317 LGEPLSIKDLVLTRALSEIRETVAQEKRRRGELGFDDMLSRLDTALRSESGEALAAAIRTRFPVAMIDEFQDTDPQQYRI 396
Cdd:COG1074 224 LAAAAAPLLAALLRLLAAVLARYERRKRERGLLDFDDLLHRALRLLRDEDAPWVAERLRERYRHILVDEFQDTSPLQWEI 303
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 397 FRRIWRHQP--DTALLLIGDPKQAIYAFRGADIFTYMKARSEVSAH-----YTLDTNWRSAPGMVNSVNKLFSQMNDAFm 469
Cdd:COG1074 304 LRRLAGEALadGRTLFLVGDPKQSIYRFRGADPELFLEARRALEGRvdgerLTLTTNFRSTPEVVDAVNALFAQLMGAG- 382
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 470 FRDIPFSPVKfaprnqslqfKVNDAPQPAMTLWLMEGESCGSGDYQSYMAQVCATQIRDWLRAGQTGDalltngDSSRPV 549
Cdd:COG1074 383 FGEIPYEPVE----------ALRPGAYPAVELWPLEPDDVSEEDAREREARAVAARIRRLLAEGTTVE------GGGRPV 446
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 550 RASDISVLVRSRREAALIRDALTLLAIPsVYLSNRDSVFETLEAQEMLWVLQAVMAPERENTLRSALATSMMGLTALDIE 629
Cdd:COG1074 447 RPGDIAVLVRTRSEAAAIARALKAAGIP-VAASDRLSLFESPEVRDLLALLRALLNPEDDLALAAVLRSPLFGLSDEDLA 525
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 630 TLNND---ESAWDAV---------VEEFDGYRQIWHKRGVMPMLRALMSARNIAENLLATAGGERRLTDILHISELLQEA 697
Cdd:COG1074 526 ALAADrkgESLWEALrayerlaraLERLRALRELARRLGLAELLERLLEETGLLERLLALPGGERRLANLLHLDELLQLA 605
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 698 ----GSQLESEHALVRWLAQHIlepDSNASSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFIthfrvqdqafyhdrhs 773
Cdd:COG1074 606 leyeQTGGPGLAGFLRWLERLI---EDGGDEEKRRLESDADAVRIMTIHKSKGLEFPVVFLPAL---------------- 666
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 774 yeavldlshaeesIALAEAERLAEDLRLLYVALTRAVWHCslgvaplvrrrsdkkgetdvhqsalgrllqkgepmdaagl 853
Cdd:COG1074 667 -------------RERARAEELAEELRLLYVALTRARDRL---------------------------------------- 693
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 854 raciealcdedIVCRTPGNTDNDRWqiaaashaelsartlqrllyDSWrvtsysglqqrghsvaqdliprldidaagvge 933
Cdd:COG1074 694 -----------VLSGAVKKKDAEKE--------------------SSW-------------------------------- 710
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 934 aaeapamtphhfprGASPGTFLHSLFEELDFTQPIN-PQWVQEKLELSGFETRWEPVLTRWLDTVLHVPLnetgvsLG-V 1011
Cdd:COG1074 711 --------------LARRGTLVHRLLEHLDFSAPAElRAALARLLARGGLDEEEAEALAEALLAFLATPL------LAeL 770
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 1012 LTEREKQVEMEFYLPIAQPltageldalirrydplsagcpaldfmQVRGMLKGFIDLVFRYEGRYYLLDYKSNWLGEDSA 1091
Cdd:COG1074 771 FAAAEVLREVPFLLPDLYR--------------------------GLGGLLKGRIDLVFEDDGRVYIVDYKTNRLGPDDE 824
|
1130 1140 1150
....*....|....*....|....*....|....
gi 2747077403 1092 AYTQTamaaamqahRYDLQYQLYTLALHRYLRHR 1125
Cdd:COG1074 825 EYLPE---------RYRLQLALYALALERLLPGR 849
|
|
| RecB_C-like |
cd22352 |
C-terminal nuclease domain of exodeoxyribonuclease V subunit RecB and similar proteins; ... |
901-1169 |
2.57e-84 |
|
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: 273.00 E-value: 2.57e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 901 WRVTSYSGLQQRGHSVAQDLIPRLDIDAAGVGEAAEAPAMTPHHFPRGASPGTFLHSLFEELDFtqpinpqwvqeklels 980
Cdd:cd22352 1 WRITSFSSLTRGLGGKAAEASHDEEPDEDEEAAPEEADEEGIDALPRGAKTGTFLHEILENIDR---------------- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 981 gfetrwepvltrwldtvlhvplnetgvslgvlterekQVEMEFYLPIAQPLTAGELDALIRRYDPLSAGCPaLDFMQVRG 1060
Cdd:cd22352 65 -------------------------------------LSEMEFYLPLSDKLDAEALNELLRQHGPPGALPP-LSFETLRG 106
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 1061 MLKGFIDLVFRYEGRYYLLDYKSNWLGEDSAAYTQTAMAAAMQAHRYDLQYQLYTLALHRYLRHRMANYDYERHFGGVIY 1140
Cdd:cd22352 107 FLKGFIDLVFEHEGRYYILDYKSNYLGDYLEDYSPEALEAAMLEHHYDLQYLLYTLALHRYLKQRLPDYDYERHFGGVYY 186
|
250 260
....*....|....*....|....*....
gi 2747077403 1141 LFLRGVDSERPQQGIFTTRPAAALINQLD 1169
Cdd:cd22352 187 LFLRGMDPEGPGNGVFFDRPSAELIEALD 215
|
|
| UvrD-helicase |
pfam00580 |
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural ... |
13-436 |
7.85e-42 |
|
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: 154.71 E-value: 7.85e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 13 LPLTGERLIEASAGTGKTFTIAALYLRLLLGlggsaafpRPLTVEELLVVTFTEAATEELRGRIRSnihelriaclrest 92
Cdd:pfam00580 10 THLGGPLLVLAGAGSGKTRVLTERIAYLILE--------GGIDPEEILAVTFTNKAAREMKERILK-------------- 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 93 dnplyarlleeisdkkqaaqwlLLAERQMDEAAVFTIHGFCQRMLSLNAFESGmlfeqqliedesllryqacadfwRRHC 172
Cdd:pfam00580 68 ----------------------LLGKAELSELNISTFHSFCLRILRKYANRIG-----------------------LLPN 102
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 173 YPLPRDIAQVvfdvwkgpkALLKDIdrylqgeapvikappsqeetlasrheqilarinqvkqqwceavseldALIESSGI 252
Cdd:pfam00580 103 FSILDELDQL---------ALLKEL-----------------------------------------------LEKDRLNL 126
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 253 DRRKFNRGNQAKWIEKItawaqeetKNYQLpealgkfsqrfLAERTKAGGVTPQHPLFVAIDnllgeplsikdlvltral 332
Cdd:pfam00580 127 DPKLLRKLELKELISKA--------KNRLL-----------SPEELQQGAADPRDKLAAEFY------------------ 169
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 333 seirETVAQEKRRRGELGFDDMLSRLDTALRSesGEALAAAIRTRFPVAMIDEFQDTDPQQYRIFRRIWRHQPdtALLLI 412
Cdd:pfam00580 170 ----QEYQERLKENNALDFDDLLLLTLELLRS--DPELLEAYRERFKYILVDEFQDTNPIQYRLLKLLAGGHE--NLFLV 241
|
410 420
....*....|....*....|....
gi 2747077403 413 GDPKQAIYAFRGADIFTYMKARSE 436
Cdd:pfam00580 242 GDPDQSIYGFRGADIENILKFEKD 265
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| recB |
PRK10876 |
exonuclease V subunit beta; Provisional |
1-1181 |
0e+00 |
|
exonuclease V subunit beta; Provisional
Pssm-ID: 236784 [Multi-domain] Cd Length: 1181 Bit Score: 2385.82 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 1 MNDVAETLDPLRLPLTGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATEELRGRIRSNI 80
Cdd:PRK10876 2 MSDVAETLDPLRLPLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEEILVVTFTEAATEELRGRIRSNI 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 81 HELRIACLRESTDNPLYARLLEEISDKKQAAQWLLLAERQMDEAAVFTIHGFCQRMLSLNAFESGMLFEQQLIEDESLLR 160
Cdd:PRK10876 82 HELRIACLREETDNPLYQRLLAEIDDKAQAAQWLLLAERQMDEAAIFTIHGFCQRMLNLNAFESGMLFEQQLIEDESLLR 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 161 YQACADFWRRHCYPLPRDIAQVVFDVWKGPKALLKDIDRYLQGEAPVIKAPPSQEETLASRHEQILARINQVKQQWCEAV 240
Cdd:PRK10876 162 YQACADFWRRHCYPLPREIARVVFQEWKGPEALLKDISRYLQGEAPVIKAPPPDDETLASRHEQIVARIDAVKQQWREAV 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 241 SELDALIESSGIDRRKFNRGNQAKWIEKITAWAQEETKNYQLPEALGKFSQRFLAERTKAGgVTPQHPLFVAIDNLLGEP 320
Cdd:PRK10876 242 GELDALIESSGVDRRSYNSKNLPKWLEKISAWAEEETNSYQLPKELEKFSQRFLLEKTKKG-ETPQHPLFEAIDQLLAEP 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 321 LSIKDLVLTRALSEIRETVAQEKRRRGELGFDDMLSRLDTALRSESGEALAAAIRTRFPVAMIDEFQDTDPQQYRIFRRI 400
Cdd:PRK10876 321 LSLRDLVITRALAEIRETVAQEKRRRGELGFDDLLSRLDSALQSEGGEALAAAIRTRYPVAMIDEFQDTDPQQYRIFRRI 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 401 WRHQPDTALLLIGDPKQAIYAFRGADIFTYMKARSEVSAHYTLDTNWRSAPGMVNSVNKLFSQMNDAFMFRDIPFSPVKF 480
Cdd:PRK10876 401 YRHQPETALLLIGDPKQAIYAFRGADIFTYMKARSEVSAHYTLDTNWRSAPGMVNSVNKLFSQTDDPFLFREIPFIPVKA 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 481 APRNQSLQFKVNDAPQPAMTLWLMEGESCGSGDYQSYMAQVCATQIRDWLRAGQTGDALLTNGDSSRPVRASDISVLVRS 560
Cdd:PRK10876 481 AGKNQALRFVVKGETQPAMKFWLMEGEGVGVGDYQQTMAQQCAAQIRDWLQAGQRGEALLMNGDDSRPVRASDITVLVRS 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 561 RREAALIRDALTLLAIPSVYLSNRDSVFETLEAQEMLWVLQAVMAPERENTLRSALATSMMGLTALDIETLNNDESAWDA 640
Cdd:PRK10876 561 RQEAALIRDALTLLAIPSVYLSNRDSVFETLEAQEMLWLLQAVLAPERERTLRSALATSMMGLDALDIDALNNDERAWDA 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 641 VVEEFDGYRQIWHKRGVMPMLRALMSARNIAENLLATAGGERRLTDILHISELLQEAGSQLESEHALVRWLAQHILEPDS 720
Cdd:PRK10876 641 LVEEFDGYRQIWRKRGVLPMLRALMSARNIAENLLATAGGERRLTDILHIGELLQEASSQLDSEHALVRWLAQQILEPDS 720
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 721 NASSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFITHFRVQDQAFYHDRHSYEAVLDLSHAEESIALAEAERLAEDLR 800
Cdd:PRK10876 721 QASSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFITNFRVQDQAFYHDRHSFEAVLDLNAAEESVALAEEERLAEDLR 800
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 801 LLYVALTRAVWHCSLGVAPLVRRRSDKKGETDVHQSALGRLLQKGEPMDAAGLRACIEALCDEDIVCRTPGNTDNDRWQI 880
Cdd:PRK10876 801 LLYVALTRSVWHCSLGVAPLVRRRRKKKGETDLHQSALGYLLQKGEPGDAAGLRACLEALCDDDIALQTAQETDNQPWQP 880
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 881 AAASHAELSARTLQRLLYDSWRVTSYSGLQQRGHSVAQDLIPRLDIDAAGVGEAAEAPAMTPHHFPRGASPGTFLHSLFE 960
Cdd:PRK10876 881 QDASLAELSARTLQRLLQDNWRVTSYSGLQQHGHSIAQDLLPRLDVDAAGEGSVVEEPQLTPHTFPRGASPGTFLHSLFE 960
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 961 ELDFTQPINPQWVQEKLELSGFETRWEPVLTRWLDTVLHVPLNETGVSLGVLTEREKQVEMEFYLPIAQPLTAGELDALI 1040
Cdd:PRK10876 961 DLDFTQPVDPEWLQEQLELQGFEEQWEPVLTQWITAVLQTPLNETGVSLSQLSARDKQVEMQFYLPIDQPLTASQLDALI 1040
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 1041 RRYDPLSAGCPALDFMQVRGMLKGFIDLVFRYEGRYYLLDYKSNWLGEDSAAYTQTAMAAAMQAHRYDLQYQLYTLALHR 1120
Cdd:PRK10876 1041 RQYDPLSAGCPPLDFMQVRGMLKGFIDLVFRWQGRYYLLDYKSNWLGEDSSAYTQEAMAQAMQAHRYDLQYQLYTLALHR 1120
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2747077403 1121 YLRHRMANYDYERHFGGVIYLFLRGVDSERPQQGIFTTRPAAALINQLDDMFAGEMSEEAQ 1181
Cdd:PRK10876 1121 YLRHRLADYDYQRHFGGVIYLFLRGVDKEHPGQGIFTTRPNAALIDGLDELFAGETLEEAQ 1181
|
|
| recB |
TIGR00609 |
exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with ... |
8-1172 |
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: 1309.34 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 8 LDPLRLPLTGERLIEASAGTGKTFTIAALYLRLLLGLGgsaafprPLTVEELLVVTFTEAATEELRGRIRSNIHELRIAC 87
Cdd:TIGR00609 1 LDPLTIPLNGTFLIEASAGTGKTFTIAQLYLRLLLEGG-------PLTVEEILVVTFTNAATEELKTRIRGRIHQALRAL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 88 LRESTDNPLYARLLEEISDKK--QAAQWLLLAERQMDEAAVFTIHGFCQRMLSLNAFESGMLFEQQLIEDESLLRYQACA 165
Cdd:TIGR00609 74 KAALTSQELPEPLKEAIQDEKvkQAITRLRNALATMDEAAIYTIHGFCQRMLEQHAFESDEIFDVELIEDESLLLAEITK 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 166 DFWRRHCYPLPRDIAQVVFDVWKGPKALLKDIDRYLQGEA-PVIKAPPSQEETLASRHEQILARINQVKqqwceavseld 244
Cdd:TIGR00609 154 DFWRRNFYNLPFDIAQIVLKTKKSPQAVLTQILADLLLQSyLAFPSPPLDLEQLIKWHEQIYKDLDKLD----------- 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 245 aliessgidrrkfnrgnqakwiekitawaqeetknyqlpealgkfsqrflaertkaggvtpqHPLFVAIDNLL---GEPL 321
Cdd:TIGR00609 223 --------------------------------------------------------------HAVFEEIDKLNaerNNLF 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 322 SIKDLVLTRALSEIRETVAQEKRRRGELGFDDMLSRLDTALRSESGEALAAAIRTRFPVAMIDEFQDTDPQQYRIFRRIW 401
Cdd:TIGR00609 241 CLKDRVFLTLLKEVQEELKKEKKRRREIGFDDLLSRLETALKSAEGEKLAQAIREQYPIALIDEFQDTDPQQYRIFSKLF 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 402 RHQPDTALLLIGDPKQAIYAFRGADIFTYMKARSEVSAHYTLDTNWRSAPGMVNSVNKLFSQMNDAFMFRDIpFSPVKFA 481
Cdd:TIGR00609 321 IAQKETSLFLIGDPKQAIYSFRGADIFTYLQAKSKADARYTLGTNWRSTPALVGSLNKLFSLISNPFLEKPI-FIPVLAH 399
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 482 PRNQSLQFKVNDAPQPAMTLWLMEGESCGSGDYQSYMAQVCATQIRDWLRAGQTGDALLTNGDSSRPVRASDISVLVRSR 561
Cdd:TIGR00609 400 QKNSKGSFVINGQEQPPIHFFTTEVESEGVDDYRQTIAQKCAREIALWLASAALGLANFIATFGGRPLRAGDIAVLVRGR 479
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 562 REAALIRDALTLLAIPSVYLSNRDSVFETLEAQEMLWVLQAVMAPERENTLRSALATSMMGLTALDIETLNNDESAWDAV 641
Cdd:TIGR00609 480 KEANQIRKALKKAQIPSVYLSDKSSVFATEEAQELLALLEALLEPENEGTLRAALASSIFGLSALELETLNQDEITWERV 559
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 642 VEEFDGYRQIWHKRGVMPMLRALMSARNIAENLLATAGGERRLTDILHISELLQEAGSQLESEHALVRWLAQHILEPDSN 721
Cdd:TIGR00609 560 VEKFREYHDIWRKIGVLAMFQRLMLEKGIGERLLSQPGGERILTNLLHLAELLQEAAHQERNKLSLLRWLEDQISNEEEE 639
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 722 aSSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFITHFRVQDQAFYHDRHSYEAVL-DLSHAEESIALAEAERLAEDLR 800
Cdd:TIGR00609 640 -EEEIIRLESDAELVKIVTIHKSKGLEYPIVFLPFITDAKKSNFASLHDQHSHEYQLyDFNQSEENQKLARVERLAEDLR 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 801 LLYVALTRAVWHCSLGVAPLVRRRSDKKGETDVHQSALGRLLQKGEPMDAAGLRACIEALCDED-IVCRTPGNTDNDRWQ 879
Cdd:TIGR00609 719 LLYVALTRAKKQLFIGIAPLITSKLSNLAYSALHNSALGYQKQDGETDNITGLKQCLAALADPAgISSIPAKPIGANSSK 798
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 880 IAAASHAELSARTLQRLLYDSWRVTSYSGLQQRGHSVAQDLIPRLDIDAAGVgeaaeapAMTPHHFPRGASPGTFLHSLF 959
Cdd:TIGR00609 799 KEPASTALLEARTFHRRIRENWRITSFSSLKELEEAVTEEPAPGLDYEVSSL-------EISAQDFPKGKKTGTLLHAIL 871
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 960 EELDFTQPINPQ----WVQEKLELSGFETRWEPVLTRWLDTVLHVPLN-ETGVSLGVLTEREKQVEMEFYLPIAQPLTAG 1034
Cdd:TIGR00609 872 ESLIFSQAADLEkqnnLIAEKLKKTGLEGLWEPELQEWLEKMLNTPLTfSRAITLSQIDPEDRQREMEFLLPINPEFQKQ 951
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 1035 ELDALIRRYdPLSAGCPALDFMQVRGMLKGFIDLVFRYEGRYYLLDYKSNWLGEDSAAYTQTAMAAAMQAHRYDLQYQLY 1114
Cdd:TIGR00609 952 KLNFVIRAY-PDRAGSPDLHFQLLRGLLKGFIDLVFEHNGRYYILDYKSNWLGKDASDYSPEALTEAILKERYDLQYLIY 1030
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*...
gi 2747077403 1115 TLALHRYLRHRMANYDYERHFGGVIYLFLRGVDSERpQQGIFTTRPAAALINQLDDMF 1172
Cdd:TIGR00609 1031 TLALHRYLRKRLKDYDYERHFGGVIYLFLRGIDGNK-GNGIFFWNPPANLIDLLKELF 1087
|
|
| RecB |
COG1074 |
3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, ... |
1-1125 |
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: 686.31 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 1 MNDVAETLDPLR--LPLTGERLIEASAGTGKTFTIAALYLRLLLGlggsaafpRPLTVEELLVVTFTEAATEELRGRIRS 78
Cdd:COG1074 1 MSEPPWTDAQRRalDPLGGSVLVEASAGSGKTYTLVARYLRLLLE--------RGLDPEEILVVTFTRAAAAEMRERIRE 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 79 NIHELRiaclreSTDNPLYARLleeisdkKQAAQWLLLAERQMDEAAVFTIHGFCQRMLSLNAFESGMLFEQQLIED-ES 157
Cdd:COG1074 73 RLAEAA------DLEDPDLEEL-------ARARRRLARALENLDRAAISTIHSFCQRLLREFAFEAGLDPNFELLDDaEA 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 158 LLRYQACADFWRRHCYPLPRDIAQVVFDVW-KGPKALLKDIDRYLQgeapvikappsqeetLASRheqilarinqvkQQW 236
Cdd:COG1074 140 LLLEEAVDDLLREAYAPLDALALARLLDAFgRDDDSLEELLLALYK---------------LRSR------------PDW 192
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 237 CEAVSELDaliessgidrrkfnrgnqakwiekitawaqeetknyqlpEALGKFSQRFLAERTkaggvtpqhpLFVAIDNL 316
Cdd:COG1074 193 LEELAELD---------------------------------------EALEALREALLKAKE----------ALAALREA 223
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 317 LGEPLSIKDLVLTRALSEIRETVAQEKRRRGELGFDDMLSRLDTALRSESGEALAAAIRTRFPVAMIDEFQDTDPQQYRI 396
Cdd:COG1074 224 LAAAAAPLLAALLRLLAAVLARYERRKRERGLLDFDDLLHRALRLLRDEDAPWVAERLRERYRHILVDEFQDTSPLQWEI 303
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 397 FRRIWRHQP--DTALLLIGDPKQAIYAFRGADIFTYMKARSEVSAH-----YTLDTNWRSAPGMVNSVNKLFSQMNDAFm 469
Cdd:COG1074 304 LRRLAGEALadGRTLFLVGDPKQSIYRFRGADPELFLEARRALEGRvdgerLTLTTNFRSTPEVVDAVNALFAQLMGAG- 382
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 470 FRDIPFSPVKfaprnqslqfKVNDAPQPAMTLWLMEGESCGSGDYQSYMAQVCATQIRDWLRAGQTGDalltngDSSRPV 549
Cdd:COG1074 383 FGEIPYEPVE----------ALRPGAYPAVELWPLEPDDVSEEDAREREARAVAARIRRLLAEGTTVE------GGGRPV 446
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 550 RASDISVLVRSRREAALIRDALTLLAIPsVYLSNRDSVFETLEAQEMLWVLQAVMAPERENTLRSALATSMMGLTALDIE 629
Cdd:COG1074 447 RPGDIAVLVRTRSEAAAIARALKAAGIP-VAASDRLSLFESPEVRDLLALLRALLNPEDDLALAAVLRSPLFGLSDEDLA 525
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 630 TLNND---ESAWDAV---------VEEFDGYRQIWHKRGVMPMLRALMSARNIAENLLATAGGERRLTDILHISELLQEA 697
Cdd:COG1074 526 ALAADrkgESLWEALrayerlaraLERLRALRELARRLGLAELLERLLEETGLLERLLALPGGERRLANLLHLDELLQLA 605
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 698 ----GSQLESEHALVRWLAQHIlepDSNASSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFIthfrvqdqafyhdrhs 773
Cdd:COG1074 606 leyeQTGGPGLAGFLRWLERLI---EDGGDEEKRRLESDADAVRIMTIHKSKGLEFPVVFLPAL---------------- 666
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 774 yeavldlshaeesIALAEAERLAEDLRLLYVALTRAVWHCslgvaplvrrrsdkkgetdvhqsalgrllqkgepmdaagl 853
Cdd:COG1074 667 -------------RERARAEELAEELRLLYVALTRARDRL---------------------------------------- 693
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 854 raciealcdedIVCRTPGNTDNDRWqiaaashaelsartlqrllyDSWrvtsysglqqrghsvaqdliprldidaagvge 933
Cdd:COG1074 694 -----------VLSGAVKKKDAEKE--------------------SSW-------------------------------- 710
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 934 aaeapamtphhfprGASPGTFLHSLFEELDFTQPIN-PQWVQEKLELSGFETRWEPVLTRWLDTVLHVPLnetgvsLG-V 1011
Cdd:COG1074 711 --------------LARRGTLVHRLLEHLDFSAPAElRAALARLLARGGLDEEEAEALAEALLAFLATPL------LAeL 770
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 1012 LTEREKQVEMEFYLPIAQPltageldalirrydplsagcpaldfmQVRGMLKGFIDLVFRYEGRYYLLDYKSNWLGEDSA 1091
Cdd:COG1074 771 FAAAEVLREVPFLLPDLYR--------------------------GLGGLLKGRIDLVFEDDGRVYIVDYKTNRLGPDDE 824
|
1130 1140 1150
....*....|....*....|....*....|....
gi 2747077403 1092 AYTQTamaaamqahRYDLQYQLYTLALHRYLRHR 1125
Cdd:COG1074 825 EYLPE---------RYRLQLALYALALERLLPGR 849
|
|
| RecB_C-like |
cd22352 |
C-terminal nuclease domain of exodeoxyribonuclease V subunit RecB and similar proteins; ... |
901-1169 |
2.57e-84 |
|
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: 273.00 E-value: 2.57e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 901 WRVTSYSGLQQRGHSVAQDLIPRLDIDAAGVGEAAEAPAMTPHHFPRGASPGTFLHSLFEELDFtqpinpqwvqeklels 980
Cdd:cd22352 1 WRITSFSSLTRGLGGKAAEASHDEEPDEDEEAAPEEADEEGIDALPRGAKTGTFLHEILENIDR---------------- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 981 gfetrwepvltrwldtvlhvplnetgvslgvlterekQVEMEFYLPIAQPLTAGELDALIRRYDPLSAGCPaLDFMQVRG 1060
Cdd:cd22352 65 -------------------------------------LSEMEFYLPLSDKLDAEALNELLRQHGPPGALPP-LSFETLRG 106
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 1061 MLKGFIDLVFRYEGRYYLLDYKSNWLGEDSAAYTQTAMAAAMQAHRYDLQYQLYTLALHRYLRHRMANYDYERHFGGVIY 1140
Cdd:cd22352 107 FLKGFIDLVFEHEGRYYILDYKSNYLGDYLEDYSPEALEAAMLEHHYDLQYLLYTLALHRYLKQRLPDYDYERHFGGVYY 186
|
250 260
....*....|....*....|....*....
gi 2747077403 1141 LFLRGVDSERPQQGIFTTRPAAALINQLD 1169
Cdd:cd22352 187 LFLRGMDPEGPGNGVFFDRPSAELIEALD 215
|
|
| UvrD-helicase |
pfam00580 |
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural ... |
13-436 |
7.85e-42 |
|
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: 154.71 E-value: 7.85e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 13 LPLTGERLIEASAGTGKTFTIAALYLRLLLGlggsaafpRPLTVEELLVVTFTEAATEELRGRIRSnihelriaclrest 92
Cdd:pfam00580 10 THLGGPLLVLAGAGSGKTRVLTERIAYLILE--------GGIDPEEILAVTFTNKAAREMKERILK-------------- 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 93 dnplyarlleeisdkkqaaqwlLLAERQMDEAAVFTIHGFCQRMLSLNAFESGmlfeqqliedesllryqacadfwRRHC 172
Cdd:pfam00580 68 ----------------------LLGKAELSELNISTFHSFCLRILRKYANRIG-----------------------LLPN 102
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 173 YPLPRDIAQVvfdvwkgpkALLKDIdrylqgeapvikappsqeetlasrheqilarinqvkqqwceavseldALIESSGI 252
Cdd:pfam00580 103 FSILDELDQL---------ALLKEL-----------------------------------------------LEKDRLNL 126
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 253 DRRKFNRGNQAKWIEKItawaqeetKNYQLpealgkfsqrfLAERTKAGGVTPQHPLFVAIDnllgeplsikdlvltral 332
Cdd:pfam00580 127 DPKLLRKLELKELISKA--------KNRLL-----------SPEELQQGAADPRDKLAAEFY------------------ 169
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 333 seirETVAQEKRRRGELGFDDMLSRLDTALRSesGEALAAAIRTRFPVAMIDEFQDTDPQQYRIFRRIWRHQPdtALLLI 412
Cdd:pfam00580 170 ----QEYQERLKENNALDFDDLLLLTLELLRS--DPELLEAYRERFKYILVDEFQDTNPIQYRLLKLLAGGHE--NLFLV 241
|
410 420
....*....|....*....|....
gi 2747077403 413 GDPKQAIYAFRGADIFTYMKARSE 436
Cdd:pfam00580 242 GDPDQSIYGFRGADIENILKFEKD 265
|
|
| UvrD |
COG0210 |
Superfamily I DNA or RNA helicase [Replication, recombination and repair]; |
321-809 |
3.82e-39 |
|
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
Pssm-ID: 439980 [Multi-domain] Cd Length: 721 Bit Score: 156.63 E-value: 3.82e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 321 LSIKDLVLTRALSEIRETVA-------QEKRRRGELGFDDMLSRLDTALRSEsgEALAAAIRTRFPVAMIDEFQDTDPQQ 393
Cdd:COG0210 151 LTPEELAELLAADPEWRAAAelyeayqERLRANNALDFDDLLLLAVRLLEEN--PEVLEKYQNRFRYILVDEYQDTNPAQ 228
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 394 YRIFRRIwrHQPDTALLLIGDPKQAIYAFRGADI-----FT--YMKARSevsahYTLDTNWRSAPGMVNSVNKLfsqmnd 466
Cdd:COG0210 229 YELLRLL--AGDGRNLCVVGDDDQSIYGFRGADPenilrFEkdFPDAKV-----IKLEQNYRSTQNILDAANAV------ 295
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 467 afmfrdIPFSPVKFAPRNQSlqfkVNDAPQPamtlwlMEGESCGSGDYQsymAQVCATQIRDWLRAGqtgdalltngdss 546
Cdd:COG0210 296 ------IANNPGRLGKNLWT----DNGEGEK------VRLYVAPDEEEE---ARFVADEIRELHEEG------------- 343
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 547 rpVRASDISVLVRSRREAALIRDALTLLAIPsVYLSNRDSVFETLEAQEMLWVLQAVMAPERENTLRSALATSMMGLTAL 626
Cdd:COG0210 344 --VPLSDIAVLYRTNAQSRALEEALRRAGIP-YRVVGGLRFYERAEIKDLLAYLRLLANPDDDVALLRILNVPRRGIGAA 420
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 627 DIETL-----NNDESAWDAV--------------------VEEFDGYRQIWHKRGVMPMLRALMSARNIAENLLATAG-- 679
Cdd:COG0210 421 TLERLreaarEEGISLLEALrdlgelaglsgraakalrrfAELLEALRAAAERLPLEELLEALLDESGYEEELREEAGee 500
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 680 GERRLTdilHISELLQEAG--SQLESEHALVRWLAQHILEPDSNassqQLRLESDKhlVQIVTIHKSKGLEYPLVwlpFI 757
Cdd:COG0210 501 AERRLE---NLEELVDAAArfEERNPGASLEAFLEELALLSDLD----AADEDEDA--VTLMTLHAAKGLEFPVV---FL 568
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|..
gi 2747077403 758 THfrVQDQAFYHDRhsyeavldlshaeesiALAEAERLAEDLRLLYVALTRA 809
Cdd:COG0210 569 VG--LEEGLFPHQR----------------SLDDEEELEEERRLFYVAITRA 602
|
|
| addA_alphas |
TIGR02784 |
double-strand break repair helicase AddA, alphaproteobacterial type; AddAB, also called RexAB, ... |
57-809 |
2.41e-24 |
|
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: 110.93 E-value: 2.41e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 57 EELLVVTFTEAATEELRGRIRSnihelRIACLRESTDNPLYARLlEEISDKKQAAQWLLLAERQMDEA-------AVFTI 129
Cdd:TIGR02784 42 SKILCLTYTKAAAAEMQNRVFK-----RLGEWAVLDDADLRARL-EALEGKRPDAAKLAEARRLFARAletpgglKIQTI 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 130 HGFCQRMLSLNAFESGMLFEQQLIED--ESLLRYQA---CADFWRRHCYPLPRDIAQV--VFDvWKGPKALLKDIDR--- 199
Cdd:TIGR02784 116 HAFCEALLHQFPLEANVAGHFSVIDDraAATLLEEArraLLAGPAAPDDALADALATVleAAG-ETGLEALLAEIVArrd 194
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 200 ----YLQ------GEAPVIKA----PPSQEETLASR-------HEQILARINQVKQQWCEAVSELDALIEssgiDRRKFN 258
Cdd:TIGR02784 195 almaFLDeaggegAEARLRRAlglaPGDTAEDLLEAvwplpglPRLALALIAALLKSGGGSKDAAAALSQ----LREAAA 270
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 259 RGNQAKWIEKITAW---AQEETKNYQLP------EALGKFSQRFLAERTKAGGVTPQHPLFVAIDnllgepLSIKDLVLT 329
Cdd:TIGR02784 271 EPDPVARLDLLLGAfltSKGEPKSASFVikkaiqKSLPDLAEALEDAASRVEALRERLRALRMAQ------RTLAALRLA 344
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 330 RALSEIREtvaQEKRRRGELGFDDMLSRlDTALRSESGEalAAAIRTRFPVA----MIDEFQDTDPQQYRIFRRI----- 400
Cdd:TIGR02784 345 ARLLQRYA---RLKKARGLLDFNDLIER-TVALLARPGA--GAWVHYKLDRGidhiLVDEAQDTSPEQWDIIQALaeeff 418
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 401 ----WRHQPDTALLLIGDPKQAIYAFRGADIFTYMKARSEVSAHY----------TLDTNWRSAPGMVNSVNKlfsqmnd 466
Cdd:TIGR02784 419 sgegARSGVERTIFAVGDEKQSIYSFQGADPERFAEERREFSRKVravgrkfedlSLNYSFRSTPDVLAAVDL------- 491
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 467 afMFRDIP----FSPVKFAPRNQSLQfkvNDAPQpAMTLWLM----EGES----------CGSGDYQSYMAQVCATQIRD 528
Cdd:TIGR02784 492 --VFADPEnargLSADSDAPVHEAFR---DDLPG-RVDLWDLiskeEGEEpedwtdpvdeLGERAPEVRLAERIAAEIRA 565
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 529 WLRAGQTGDALltngdsSRPVRASDISVLVRSRRE--AALIRdALTLLAIPsVYLSNRDSVFETLEAQEMLWVLQAVMAP 606
Cdd:TIGR02784 566 WLDRGTPIPGR------GRAVRPGDILVLVRKRDAffSALIR-ALKRRGIP-VAGADRLKLTSHIAVKDLMALGRFVLQP 637
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 607 ERENTLRSALATSMMGLTALDIETL---NNDESAWDAVVEEFDGYRQIWHKrgvmpmLRALMS-ARNIA-----ENLLAT 677
Cdd:TIGR02784 638 EDDLSLAALLKSPLFGLDEDDLFRLaagRSGGSLWAALRRREAEFAATLAV------LRDWLSlADFLTpfefyARLLGR 711
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 678 AGGERRL--------TDILH--ISELLQEAGSQLESEHALVRWLaqhilepDSNASSQQLRLESDKHLVQIVTIHKSKGL 747
Cdd:TIGR02784 712 DGGRRKLlarlgaeaEDILDefLSQALAYERTGLPGLQAFLSWL-------EADDPEIKREMDQARDEVRVMTVHGAKGL 784
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2747077403 748 EYPLVWLPFITHFRVQDQAFYH---DRHSYEAVL------DLSHAEESIALAEAERLAED--LRLLYVALTRA 809
Cdd:TIGR02784 785 EAPVVFLVDTGSKPFASQRAPLllaTGGSGGKAPlwrpasAFDPSLSAAARERLKERAEDeyRRLLYVAMTRA 857
|
|
| DEXQc_UvrD |
cd17932 |
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ... |
351-447 |
1.22e-22 |
|
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: 96.43 E-value: 1.22e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 351 FDDMLSRLDTALrsESGEALAAAIRTRFPVAMIDEFQDTDPQQYRIFRRIWRhqPDTALLLIGDPKQAIYAFRGADIFTY 430
Cdd:cd17932 95 FDDLLLYALELL--EENPDVREKLQSRFRYILVDEYQDTNPLQYELLKLLAG--DGKNLFVVGDDDQSIYGFRGADPENI 170
|
90
....*....|....*....
gi 2747077403 431 MKARSE--VSAHYTLDTNW 447
Cdd:cd17932 171 LDFEKDfpDAKVIKLEENY 189
|
|
| SF1_C_UvrD |
cd18807 |
C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase ... |
690-816 |
5.51e-21 |
|
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: 90.75 E-value: 5.51e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 690 ISELLQEAGSQLESEHALVRwlaqhilepdSNASSQQLRlesDKHLVQIVTIHKSKGLEYPLVWLPFITHFRVQDQAFYH 769
Cdd:cd18807 53 IKRLIESGPVQYSDIAILVR----------TNRQARVIE---EALRVTLMTIHASKGLEFPVVFIVGLGEGFIPSDASYH 119
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 2747077403 770 drhsyeavldlshaeesIALAEAERLAEDLRLLYVALTRAVWHCSLG 816
Cdd:cd18807 120 -----------------AAKEDEERLEEERRLLYVALTRAKKELYLV 149
|
|
| PRK13909 |
PRK13909 |
RecB-like helicase; |
22-810 |
7.41e-17 |
|
RecB-like helicase;
Pssm-ID: 237554 [Multi-domain] Cd Length: 910 Bit Score: 86.18 E-value: 7.41e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 22 EASAGTGKTFTiaalylrlllglggsaafprpLTVE------------ELLVVTFTEAATEELRGRIrsnihelrIACLR 89
Cdd:PRK13909 4 KASAGSGKTFA---------------------LSVRflallfkganpsEILALTFTKKAANEMKERI--------IDTLL 54
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 90 ESTDNPLYARLL----------EEISDKKQAAQWLLLAErqmdEAAVFTIHGFCQRML---SLNA-----FESGMLFEQQ 151
Cdd:PRK13909 55 NLEKEKEESELNeleeklglskEELLNKRDKVYQEFLNS----ELKISTIDAFFQKILrkfCLNLglspdFSIKEDTKEE 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 152 LIED-----------ESLLRYQACADfwrrhcyplprdiaqvvfdvwKGPKALLKDIDRYLQGEAPVIKAPPSQEETlAS 220
Cdd:PRK13909 131 LNEKflsalskeellELLAFIKQCES---------------------KKNNSFFELLEKLYEKNNELKLFEKAKNPI-EF 188
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 221 RHEQILARINQVKQQWCEAVSELDALIESsgIDRRKFNRG--NQAKWIEKitawaqEETKNYQLPEALGKFSQrflaert 298
Cdd:PRK13909 189 DEEKFLEELRSLKQQIQSIETASKNAKKA--FKKEDFEELlnSSKTWLEK------ESEYRYFKKLYNEELDA------- 253
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 299 kaggvtpqhpLFVAIDNLLGEPLSIKDLVLTRALSEI----RETVAQEKRRRGELGFDDMLSRLDTALRSESGEA----- 369
Cdd:PRK13909 254 ----------EFEELKNALKRYYDAKENYKLSKLFKLlqlyKEAKNELNKKKNALDFDDISKKVYELLGEEEIDKdflyf 323
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 370 -LAAAIRTrfpvAMIDEFQDTDPQQYRIFRriwrhqP-------------DTALLLIGDPKQAIYAFRG--ADIFTYMKA 433
Cdd:PRK13909 324 rLDSKISH----ILIDEFQDTSVLQYKILL------PlideiksgegqkkFRSFFYVGDVKQSIYRFRGgkKELFDKVSK 393
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 434 RSEVsAHYTLDTNWRSAPGMVNSVNKLFsqmNDAFmfrdiPFSPVKFAPRNQSLQF-KVndapqpamtlwlmegeSCGSG 512
Cdd:PRK13909 394 DFKQ-KVDNLDTNYRSAPLIVDFVNEVF---KKKY-----KNYKTQYAEQHKSGGYvEV----------------VEVAD 448
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 513 DYQSYMAQVCATQIRdwlragqtgdaLLTNGdssrpVRASDISVLVRSRREAALIRDALT-LLAIP-----SVYLSNRDS 586
Cdd:PRK13909 449 ESEELLEQLLQEIQF-----------LLEKG-----IDPDDIAILCWTNDDALEIKEFLQeQFGIKavtesSAKLINQPE 512
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 587 VFETLEAqemlwvLQAVMAPER---ENTLrsalatSMMGLTALD-IETLNNDESawdavveefdgyrqiwhkrgVMPMLR 662
Cdd:PRK13909 513 VKALIEA------LKYCLFGEEiykHNVL------KLLGKEPDKiPSFLPKEES--------------------VAEFVK 560
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 663 ALMSARNIA-ENLL----ATAGGERrltdilhISELLQEagsqlesehalvrwlaqhiLEPDSNASSQQlrlESDKhlVQ 737
Cdd:PRK13909 561 KLIEELKLYdENLLkfleLASGYED-------IEEFLFK-------------------LEPCDKEIASE---ESKG--VQ 609
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 738 IVTIHKSKGLEYPLVWL------------PFITHFRVQ--DQAFYhdRHSYEAVLDLSHAEesiALAEAERLA--EDLRL 801
Cdd:PRK13909 610 IMTVHKSKGLEFEHVIVcdrlgkpnsdssNLLFEYDGIelWQIYY--RIKGRENFDKDYAR---ALEKEKALKyeEEINV 684
|
....*....
gi 2747077403 802 LYVALTRAV 810
Cdd:PRK13909 685 LYVAFTRAK 693
|
|
| SF1_C |
cd18786 |
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
728-817 |
3.88e-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: 63.23 E-value: 3.88e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 728 RLESDKHLVQIVTIHKSKGLEYPLVWLPFITHFrvqdqafyhdrhsyeavldlshaeesialaeaerlAEDLRLLYVALT 807
Cdd:cd18786 35 LDEFDLQLVGAITIDSSQGLTFDVVTLYLPTAN-----------------------------------SLTPRRLYVALT 79
|
90
....*....|
gi 2747077403 808 RAVWHCSLGV 817
Cdd:cd18786 80 RARKRLVIYD 89
|
|
| UvrD_C |
pfam13361 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
552-809 |
5.22e-10 |
|
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: 62.81 E-value: 5.22e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 552 SDISVLVRSRREAALIRDALTLLAIPsVYLSNRDSVFETLEAQEMLWVLQAVMAPERENTLRSALATSMMGLTALDIETL 631
Cdd:pfam13361 76 NDIAVLTRSNSDADLIEEALKKLGIP-YFVVGQTKFFRREEIKDILAYLRLIANKHDSISLKRILNGPKRGIGNATLERI 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 632 NNDESAWDAVVEEFDGYRQIWhkrgVMPMLRALMSARN-------------------IAENLLATAG--GER-------- 682
Cdd:pfam13361 155 REYKKRGLRLSDFINPDTLTY----GDPFVIALEQDNIvvfdvettgldttedeiiqIAAIKLNKKGvvIESferflrlk 230
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 683 -----RLTDILHISELLQEAG-----------SQLESEHALVRWLAQ---------------HILEpDSNASSQQLRLES 731
Cdd:pfam13361 231 kpvgdSLQVHGFSDEFLQENGetpaealrdflEKLENLRELYSILREyddieetpepedalrNFLE-IATLSNSELEGSD 309
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2747077403 732 DKHLVQIVTIHKSKGLEYPLVWLPfithfRVQDQAFYHdrhsYEAVLDLshaeesialaeaERLAEDLRLLYVALTRA 809
Cdd:pfam13361 310 IKERIPIMTIHQAKGLEFDTVFLA-----GLEEGIFPS----YRSIKDE------------GNLEEERRLFYVAITRA 366
|
|
| DEXQc_UvrD |
cd17932 |
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ... |
16-167 |
3.66e-09 |
|
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: 57.53 E-value: 3.66e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 16 TGERLIEASAGTGKTFTIAALYLRLLLGlggsaafpRPLTVEELLVVTFTEAATEELRGRIRSnihelriaclrestdnp 95
Cdd:cd17932 12 DGPLLVLAGAGSGKTRVLTHRIAYLILE--------GGVPPERILAVTFTNKAAKEMRERLRK----------------- 66
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2747077403 96 lyarlleeisdkkqaaqwlLLAERQMDEAAVFTIHGFCQRMLSLNA-FESGMLFEQQLIEDESLLRYQACADF 167
Cdd:cd17932 67 -------------------LLGEQLASGVWIGTFHSFALRILRRYGdFDDLLLYALELLEENPDVREKLQSRF 120
|
|
| uvrD |
PRK11773 |
DNA-dependent helicase II; Provisional |
375-809 |
2.73e-08 |
|
DNA-dependent helicase II; Provisional
Pssm-ID: 236976 [Multi-domain] Cd Length: 721 Bit Score: 58.34 E-value: 2.73e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 375 RTRFPVAMIDEFQDTDPQQYRIFRRIWRHQpdTALLLIGDPKQAIYAFRGADIFTYMKARSEVSAHYT--LDTNWRSAPG 452
Cdd:PRK11773 211 QERFTHILVDEFQDTNAIQYAWIRLLAGDT--GKVMIVGDDDQSIYGWRGAQVENIQRFLNDFPGAETirLEQNYRSTAN 288
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 453 MVNSVNKLFSQmNDAFMFRDipfspvkfaprnqslqfkvndapqpamtLWLMEGESCGSGDYQSY----MAQVCATQIRD 528
Cdd:PRK11773 289 ILKAANALIAN-NNGRLGKE----------------------------LWTDGGDGEPISLYCAFneldEARFVVERIKT 339
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 529 WLRAGQtgdalltngdssrpvRASDISVLVRSRR-----EAALIR--------------------DALTLLAIpsvyLSN 583
Cdd:PRK11773 340 WQDNGG---------------ALSDCAILYRSNAqsrvlEEALLQagipyriyggmrfferqeikDALAYLRL----IAN 400
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 584 R--DSVFE-------------TLEA--------QEMLWvlQAVMAPERENTLRSALATSMMGLTALdIETLNNDesawda 640
Cdd:PRK11773 401 RndDAAFErvvntptrgigdrTLDVvrqtardrQLTLW--QACRALLQEKVLAGRAASALQRFIEL-IDALAQE------ 471
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 641 vVEEFDGYRQIWH---KRGVMPMLRALMSARNIA--ENL--LATAGGERRLTDilhisellqeagsQLESEHALVRWLAQ 713
Cdd:PRK11773 472 -TADMPLHEQTDRvikDSGLRAMYEQEKGEKGQAriENLeeLVTATRQFSYPD-------------EDEDLTPLQAFLSH 537
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 714 HILEpdsnASSQQLRLESDKhlVQIVTIHKSKGLEYPLVwlpFITHfrVQDQAFYHDRhsyeavldlshaeesiALAEAE 793
Cdd:PRK11773 538 AALE----AGEGQADAHEDA--VQLMTLHSAKGLEFPLV---FIVG--MEEGLFPSQM----------------SLEEGG 590
|
490
....*....|....*.
gi 2747077403 794 RLAEDLRLLYVALTRA 809
Cdd:PRK11773 591 RLEEERRLAYVGITRA 606
|
|
| helD |
PRK11054 |
DNA helicase IV; Provisional |
382-448 |
7.70e-08 |
|
DNA helicase IV; Provisional
Pssm-ID: 182930 [Multi-domain] Cd Length: 684 Bit Score: 56.50 E-value: 7.70e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2747077403 382 MIDEFQDTDPQQYRIFRRIWRHQPDTALLLIGDPKQAIYAFRGADI--FTYMKARSEVSAHYTLDTNWR 448
Cdd:PRK11054 435 LVDEFQDISPQRAALLAALRKQNSQTTLFAVGDDWQAIYRFSGADLslTTAFHERFGEGDRCHLDTTYR 503
|
|
| AAA_19 |
pfam13245 |
AAA domain; |
316-423 |
1.47e-06 |
|
AAA domain;
Pssm-ID: 433059 [Multi-domain] Cd Length: 136 Bit Score: 48.75 E-value: 1.47e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2747077403 316 LLGEPLSIKDLVLT-RALSEIRETVAQEKRR-RGELGFDDMLSrlDTALRSESGEALAAAIrtrfpvaMIDEFQDTD-PQ 392
Cdd:pfam13245 38 LGGVSFPILLAAPTgRAAKRLSERTGLPASTiHRLLGFDDLEA--GGFLRDEEEPLDGDLL-------IVDEFSMVDlPL 108
|
90 100 110
....*....|....*....|....*....|.
gi 2747077403 393 QYRIFRRIwrhQPDTALLLIGDPKQAIYAFR 423
Cdd:pfam13245 109 AYRLLKAL---PDGAQLLLVGDPDQLPSVGP 136
|
|
| |
