|
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: 2388.52 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 1 MNDVAETLDPLRLPLTGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATEELRGRIRSNI 80
Cdd:PRK10876 2 MSDVAETLDPLRLPLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEEILVVTFTEAATEELRGRIRSNI 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 81 HELRIACLRESTDNPLYARLLEEISDKKQAAQWLLLAERQMDEAAVFTIHGFCQRMLSLNAFESGMLFEQQLIEDESLLR 160
Cdd:PRK10876 82 HELRIACLREETDNPLYQRLLAEIDDKAQAAQWLLLAERQMDEAAIFTIHGFCQRMLNLNAFESGMLFEQQLIEDESLLR 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 161 YQACADFWRRHCYPLPRDIAQVVFDVWKGPKALLKDIDRYLQGEAPVIKAPPSQEETLASRHEQILARINQVKQQWCEAV 240
Cdd:PRK10876 162 YQACADFWRRHCYPLPREIARVVFQEWKGPEALLKDISRYLQGEAPVIKAPPPDDETLASRHEQIVARIDAVKQQWREAV 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 241 SELDALIESSGIDRRKFNRGNQAKWIEKITAWAQEETKNYQLPEALGKFSQRFLAERTKAsGVTPQHPLFVAIDNLLGEP 320
Cdd:PRK10876 242 GELDALIESSGVDRRSYNSKNLPKWLEKISAWAEEETNSYQLPKELEKFSQRFLLEKTKK-GETPQHPLFEAIDQLLAEP 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 321 LSIKDLVLTRALSEIRETVAQEKRRRGELGFDDMLSRLDTALRSESGEALATAIRTRFPVAMIDEFQDTDPQQYRIFRRI 400
Cdd:PRK10876 321 LSLRDLVITRALAEIRETVAQEKRRRGELGFDDLLSRLDSALQSEGGEALAAAIRTRYPVAMIDEFQDTDPQQYRIFRRI 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 401 WRHQPDTALLLIGDPKQAIYAFRGADIFTYMKARSEVSAHYTLDTNWRSAPGMVNSVNKLFSQMNDAFMFRDIPFSPVKF 480
Cdd:PRK10876 401 YRHQPETALLLIGDPKQAIYAFRGADIFTYMKARSEVSAHYTLDTNWRSAPGMVNSVNKLFSQTDDPFLFREIPFIPVKA 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 481 APRNQSLQFKVNDAPQPAMTLWLMEGESCGSGDYQSYMAQVCATQIRDWLRAGQTGDALLTNGDSSRPVRASDISVLVRS 560
Cdd:PRK10876 481 AGKNQALRFVVKGETQPAMKFWLMEGEGVGVGDYQQTMAQQCAAQIRDWLQAGQRGEALLMNGDDSRPVRASDITVLVRS 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 561 RREAALIRDALTLLAIPSVYLSNRDSVFETLEAQEMLWVLQAVMAPERENTLRSALATSMMGLTALDIETLNNDENAWDA 640
Cdd:PRK10876 561 RQEAALIRDALTLLAIPSVYLSNRDSVFETLEAQEMLWLLQAVLAPERERTLRSALATSMMGLDALDIDALNNDERAWDA 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 641 VVEEFDGYRQIWHKRGVMPMLRALMSARNIAENLLATAGGERRLTDILHISELLQEAGSQLESEHALVRWLAQHILEPDS 720
Cdd:PRK10876 641 LVEEFDGYRQIWRKRGVLPMLRALMSARNIAENLLATAGGERRLTDILHIGELLQEASSQLDSEHALVRWLAQQILEPDS 720
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 721 NASSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFITHFRVQDQAFYHDRHSYEAVLDLSHAEESIALAEAERLAEDLR 800
Cdd:PRK10876 721 QASSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFITNFRVQDQAFYHDRHSFEAVLDLNAAEESVALAEEERLAEDLR 800
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 801 LLYVALTRAVWHCSLGVAPLVRRRSDKKGETDVHQSALGRLLQKGEPMDAAGLRACIEALCDEDIVCRTPGSTDNDRWQI 880
Cdd:PRK10876 801 LLYVALTRSVWHCSLGVAPLVRRRRKKKGETDLHQSALGYLLQKGEPGDAAGLRACLEALCDDDIALQTAQETDNQPWQP 880
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 881 AAASHAELSARTLQRLLYDSWRVTSYSGLQQRGHSVAQDLIPRLDIDAAGVGEAAEAPAMTPHHFPRGASPGTFLHSLFE 960
Cdd:PRK10876 881 QDASLAELSARTLQRLLQDNWRVTSYSGLQQHGHSIAQDLLPRLDVDAAGEGSVVEEPQLTPHTFPRGASPGTFLHSLFE 960
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 961 ELDFTQPIDPQWVQEKLELSGFETRWEPVLTRWLDTVLHVPLNETGVSLSVLTEREKQVEMEFYLPIAQPLTAGELDALI 1040
Cdd:PRK10876 961 DLDFTQPVDPEWLQEQLELQGFEEQWEPVLTQWITAVLQTPLNETGVSLSQLSARDKQVEMQFYLPIDQPLTASQLDALI 1040
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 1041 RRYDPLSAGCPALDFMQVRGMLKGFIDLVFRYEGRYYLLDYKSNWLGEDSAAYTQTAMAAAMQAHRYDLQYQLYTLALHR 1120
Cdd:PRK10876 1041 RQYDPLSAGCPPLDFMQVRGMLKGFIDLVFRWQGRYYLLDYKSNWLGEDSSAYTQEAMAQAMQAHRYDLQYQLYTLALHR 1120
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 340763223 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: 1308.57 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 8 LDPLRLPLTGERLIEASAGTGKTFTIAALYLRLLLGLGgsaafprPLTVEELLVVTFTEAATEELRGRIRSNIHELRIAC 87
Cdd:TIGR00609 1 LDPLTIPLNGTFLIEASAGTGKTFTIAQLYLRLLLEGG-------PLTVEEILVVTFTNAATEELKTRIRGRIHQALRAL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 88 LRESTDNPLYARLLEEISDKK--QAAQWLLLAERQMDEAAVFTIHGFCQRMLSLNAFESGMLFEQQLIEDESLLRYQACA 165
Cdd:TIGR00609 74 KAALTSQELPEPLKEAIQDEKvkQAITRLRNALATMDEAAIYTIHGFCQRMLEQHAFESDEIFDVELIEDESLLLAEITK 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 166 DFWRRHCYPLPRDIAQVVFDVWKGPKALLKDIDRYLQGEA-PVIKAPPSQEETLASRHEQILARINQVKqqwceavseld 244
Cdd:TIGR00609 154 DFWRRNFYNLPFDIAQIVLKTKKSPQAVLTQILADLLLQSyLAFPSPPLDLEQLIKWHEQIYKDLDKLD----------- 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 245 aliessgidrrkfnrgnqakwiekitawaqeetknyqlpealgkfsqrflaertkasgvtpqHPLFVAIDNLL---GEPL 321
Cdd:TIGR00609 223 --------------------------------------------------------------HAVFEEIDKLNaerNNLF 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 322 SIKDLVLTRALSEIRETVAQEKRRRGELGFDDMLSRLDTALRSESGEALATAIRTRFPVAMIDEFQDTDPQQYRIFRRIW 401
Cdd:TIGR00609 241 CLKDRVFLTLLKEVQEELKKEKKRRREIGFDDLLSRLETALKSAEGEKLAQAIREQYPIALIDEFQDTDPQQYRIFSKLF 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 402 RHQPDTALLLIGDPKQAIYAFRGADIFTYMKARSEVSAHYTLDTNWRSAPGMVNSVNKLFSQMNDAFMFRDIpFSPVKFA 481
Cdd:TIGR00609 321 IAQKETSLFLIGDPKQAIYSFRGADIFTYLQAKSKADARYTLGTNWRSTPALVGSLNKLFSLISNPFLEKPI-FIPVLAH 399
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 482 PRNQSLQFKVNDAPQPAMTLWLMEGESCGSGDYQSYMAQVCATQIRDWLRAGQTGDALLTNGDSSRPVRASDISVLVRSR 561
Cdd:TIGR00609 400 QKNSKGSFVINGQEQPPIHFFTTEVESEGVDDYRQTIAQKCAREIALWLASAALGLANFIATFGGRPLRAGDIAVLVRGR 479
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 562 REAALIRDALTLLAIPSVYLSNRDSVFETLEAQEMLWVLQAVMAPERENTLRSALATSMMGLTALDIETLNNDENAWDAV 641
Cdd:TIGR00609 480 KEANQIRKALKKAQIPSVYLSDKSSVFATEEAQELLALLEALLEPENEGTLRAALASSIFGLSALELETLNQDEITWERV 559
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 642 VEEFDGYRQIWHKRGVMPMLRALMSARNIAENLLATAGGERRLTDILHISELLQEAGSQLESEHALVRWLAQHILEPDSN 721
Cdd:TIGR00609 560 VEKFREYHDIWRKIGVLAMFQRLMLEKGIGERLLSQPGGERILTNLLHLAELLQEAAHQERNKLSLLRWLEDQISNEEEE 639
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 722 aSSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFITHFRVQDQAFYHDRHSYEAVL-DLSHAEESIALAEAERLAEDLR 800
Cdd:TIGR00609 640 -EEEIIRLESDAELVKIVTIHKSKGLEYPIVFLPFITDAKKSNFASLHDQHSHEYQLyDFNQSEENQKLARVERLAEDLR 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 801 LLYVALTRAVWHCSLGVAPLVRRRSDKKGETDVHQSALGRLLQKGEPMDAAGLRACIEALCDED-IVCRTPGSTDNDRWQ 879
Cdd:TIGR00609 719 LLYVALTRAKKQLFIGIAPLITSKLSNLAYSALHNSALGYQKQDGETDNITGLKQCLAALADPAgISSIPAKPIGANSSK 798
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 880 IAAASHAELSARTLQRLLYDSWRVTSYSGLQQRGHSVAQDLIPRLDIDAAGVgeaaeapAMTPHHFPRGASPGTFLHSLF 959
Cdd:TIGR00609 799 KEPASTALLEARTFHRRIRENWRITSFSSLKELEEAVTEEPAPGLDYEVSSL-------EISAQDFPKGKKTGTLLHAIL 871
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 960 EELDFTQPIDPQ----WVQEKLELSGFETRWEPVLTRWLDTVLHVPLN-ETGVSLSVLTEREKQVEMEFYLPIAQPLTAG 1034
Cdd:TIGR00609 872 ESLIFSQAADLEkqnnLIAEKLKKTGLEGLWEPELQEWLEKMLNTPLTfSRAITLSQIDPEDRQREMEFLLPINPEFQKQ 951
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 1035 ELDALIRRYdPLSAGCPALDFMQVRGMLKGFIDLVFRYEGRYYLLDYKSNWLGEDSAAYTQTAMAAAMQAHRYDLQYQLY 1114
Cdd:TIGR00609 952 KLNFVIRAY-PDRAGSPDLHFQLLRGLLKGFIDLVFEHNGRYYILDYKSNWLGKDASDYSPEALTEAILKERYDLQYLIY 1030
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*...
gi 340763223 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: 685.54 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 1 MNDVAETLDPLR--LPLTGERLIEASAGTGKTFTIAALYLRLLLGlggsaafpRPLTVEELLVVTFTEAATEELRGRIRS 78
Cdd:COG1074 1 MSEPPWTDAQRRalDPLGGSVLVEASAGSGKTYTLVARYLRLLLE--------RGLDPEEILVVTFTRAAAAEMRERIRE 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 79 NIHELRiaclreSTDNPLYARLleeisdkKQAAQWLLLAERQMDEAAVFTIHGFCQRMLSLNAFESGMLFEQQLIED-ES 157
Cdd:COG1074 73 RLAEAA------DLEDPDLEEL-------ARARRRLARALENLDRAAISTIHSFCQRLLREFAFEAGLDPNFELLDDaEA 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 158 LLRYQACADFWRRHCYPLPRDIAQVVFDVW-KGPKALLKDIDRYLQgeapvikappsqeetLASRheqilarinqvkQQW 236
Cdd:COG1074 140 LLLEEAVDDLLREAYAPLDALALARLLDAFgRDDDSLEELLLALYK---------------LRSR------------PDW 192
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 237 CEAVSELDaliessgidrrkfnrgnqakwiekitawaqeetknyqlpEALGKFSQRFLAERTkasgvtpqhpLFVAIDNL 316
Cdd:COG1074 193 LEELAELD---------------------------------------EALEALREALLKAKE----------ALAALREA 223
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 317 LGEPLSIKDLVLTRALSEIRETVAQEKRRRGELGFDDMLSRLDTALRSESGEALATAIRTRFPVAMIDEFQDTDPQQYRI 396
Cdd:COG1074 224 LAAAAAPLLAALLRLLAAVLARYERRKRERGLLDFDDLLHRALRLLRDEDAPWVAERLRERYRHILVDEFQDTSPLQWEI 303
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 397 FRRIWRHQP--DTALLLIGDPKQAIYAFRGADIFTYMKARSEVSAH-----YTLDTNWRSAPGMVNSVNKLFSQMNDAFm 469
Cdd:COG1074 304 LRRLAGEALadGRTLFLVGDPKQSIYRFRGADPELFLEARRALEGRvdgerLTLTTNFRSTPEVVDAVNALFAQLMGAG- 382
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 470 FRDIPFSPVKfaprnqslqfKVNDAPQPAMTLWLMEGESCGSGDYQSYMAQVCATQIRDWLRAGQTGDalltngDSSRPV 549
Cdd:COG1074 383 FGEIPYEPVE----------ALRPGAYPAVELWPLEPDDVSEEDAREREARAVAARIRRLLAEGTTVE------GGGRPV 446
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 550 RASDISVLVRSRREAALIRDALTLLAIPsVYLSNRDSVFETLEAQEMLWVLQAVMAPERENTLRSALATSMMGLTALDIE 629
Cdd:COG1074 447 RPGDIAVLVRTRSEAAAIARALKAAGIP-VAASDRLSLFESPEVRDLLALLRALLNPEDDLALAAVLRSPLFGLSDEDLA 525
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 630 TLNND---ENAWDAV---------VEEFDGYRQIWHKRGVMPMLRALMSARNIAENLLATAGGERRLTDILHISELLQEA 697
Cdd:COG1074 526 ALAADrkgESLWEALrayerlaraLERLRALRELARRLGLAELLERLLEETGLLERLLALPGGERRLANLLHLDELLQLA 605
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 698 ----GSQLESEHALVRWLAQHIlepDSNASSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFIthfrvqdqafyhdrhs 773
Cdd:COG1074 606 leyeQTGGPGLAGFLRWLERLI---EDGGDEEKRRLESDADAVRIMTIHKSKGLEFPVVFLPAL---------------- 666
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 774 yeavldlshaeesIALAEAERLAEDLRLLYVALTRAVWHCslgvaplvrrrsdkkgetdvhqsalgrllqkgepmdaagl 853
Cdd:COG1074 667 -------------RERARAEELAEELRLLYVALTRARDRL---------------------------------------- 693
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 854 raciealcdedIVCRTPGSTDNDRWqiaaashaelsartlqrllyDSWrvtsysglqqrghsvaqdliprldidaagvge 933
Cdd:COG1074 694 -----------VLSGAVKKKDAEKE--------------------SSW-------------------------------- 710
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 934 aaeapamtphhfprGASPGTFLHSLFEELDFTQPID-PQWVQEKLELSGFETRWEPVLTRWLDTVLHVPLnetgvsLS-V 1011
Cdd:COG1074 711 --------------LARRGTLVHRLLEHLDFSAPAElRAALARLLARGGLDEEEAEALAEALLAFLATPL------LAeL 770
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 1012 LTEREKQVEMEFYLPIAQPltageldalirrydplsagcpaldfmQVRGMLKGFIDLVFRYEGRYYLLDYKSNWLGEDSA 1091
Cdd:COG1074 771 FAAAEVLREVPFLLPDLYR--------------------------GLGGLLKGRIDLVFEDDGRVYIVDYKTNRLGPDDE 824
|
1130 1140 1150
....*....|....*....|....*....|....
gi 340763223 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 |
2.52e-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: 2.52e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 901 WRVTSYSGLQQRGHSVAQDLIPRLDIDAAGVGEAAEAPAMTPHHFPRGASPGTFLHSLFEELDFtqpidpqwvqeklels 980
Cdd:cd22352 1 WRITSFSSLTRGLGGKAAEASHDEEPDEDEEAAPEEADEEGIDALPRGAKTGTFLHEILENIDR---------------- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 981 gfetrwepvltrwldtvlhvplnetgvslsvlterekQVEMEFYLPIAQPLTAGELDALIRRYDPLSAGCPaLDFMQVRG 1060
Cdd:cd22352 65 -------------------------------------LSEMEFYLPLSDKLDAEALNELLRQHGPPGALPP-LSFETLRG 106
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 1061 MLKGFIDLVFRYEGRYYLLDYKSNWLGEDSAAYTQTAMAAAMQAHRYDLQYQLYTLALHRYLRHRMANYDYERHFGGVIY 1140
Cdd:cd22352 107 FLKGFIDLVFEHEGRYYILDYKSNYLGDYLEDYSPEALEAAMLEHHYDLQYLLYTLALHRYLKQRLPDYDYERHFGGVYY 186
|
250 260
....*....|....*....|....*....
gi 340763223 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 |
6.75e-41 |
|
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: 152.01 E-value: 6.75e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 13 LPLTGERLIEASAGTGKTFTIAALYLRLLLGlggsaafpRPLTVEELLVVTFTEAATEELRGRIRSnihelriaclrest 92
Cdd:pfam00580 10 THLGGPLLVLAGAGSGKTRVLTERIAYLILE--------GGIDPEEILAVTFTNKAAREMKERILK-------------- 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 93 dnplyarlleeisdkkqaaqwlLLAERQMDEAAVFTIHGFCQRMLSLNAFESGmlfeqqliedesllryqacadfwRRHC 172
Cdd:pfam00580 68 ----------------------LLGKAELSELNISTFHSFCLRILRKYANRIG-----------------------LLPN 102
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 173 YPLPRDIAQVvfdvwkgpkALLKDIdrylqgeapvikappsqeetlasrheqilarinqvkqqwceavseldALIESSGI 252
Cdd:pfam00580 103 FSILDELDQL---------ALLKEL-----------------------------------------------LEKDRLNL 126
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 253 DRRKFNRGNQAKWIEKItawaqeetKNYQLpealgkfsqrfLAERTKASGVTPQHPLFVAIDnllgeplsikdlvltral 332
Cdd:pfam00580 127 DPKLLRKLELKELISKA--------KNRLL-----------SPEELQQGAADPRDKLAAEFY------------------ 169
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 333 seirETVAQEKRRRGELGFDDMLSRLDTALRSesGEALATAIRTRFPVAMIDEFQDTDPQQYRIFRRIWRHQPdtALLLI 412
Cdd:pfam00580 170 ----QEYQERLKENNALDFDDLLLLTLELLRS--DPELLEAYRERFKYILVDEFQDTNPIQYRLLKLLAGGHE--NLFLV 241
|
410 420
....*....|....*....|....
gi 340763223 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: 2388.52 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 1 MNDVAETLDPLRLPLTGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATEELRGRIRSNI 80
Cdd:PRK10876 2 MSDVAETLDPLRLPLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEEILVVTFTEAATEELRGRIRSNI 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 81 HELRIACLRESTDNPLYARLLEEISDKKQAAQWLLLAERQMDEAAVFTIHGFCQRMLSLNAFESGMLFEQQLIEDESLLR 160
Cdd:PRK10876 82 HELRIACLREETDNPLYQRLLAEIDDKAQAAQWLLLAERQMDEAAIFTIHGFCQRMLNLNAFESGMLFEQQLIEDESLLR 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 161 YQACADFWRRHCYPLPRDIAQVVFDVWKGPKALLKDIDRYLQGEAPVIKAPPSQEETLASRHEQILARINQVKQQWCEAV 240
Cdd:PRK10876 162 YQACADFWRRHCYPLPREIARVVFQEWKGPEALLKDISRYLQGEAPVIKAPPPDDETLASRHEQIVARIDAVKQQWREAV 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 241 SELDALIESSGIDRRKFNRGNQAKWIEKITAWAQEETKNYQLPEALGKFSQRFLAERTKAsGVTPQHPLFVAIDNLLGEP 320
Cdd:PRK10876 242 GELDALIESSGVDRRSYNSKNLPKWLEKISAWAEEETNSYQLPKELEKFSQRFLLEKTKK-GETPQHPLFEAIDQLLAEP 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 321 LSIKDLVLTRALSEIRETVAQEKRRRGELGFDDMLSRLDTALRSESGEALATAIRTRFPVAMIDEFQDTDPQQYRIFRRI 400
Cdd:PRK10876 321 LSLRDLVITRALAEIRETVAQEKRRRGELGFDDLLSRLDSALQSEGGEALAAAIRTRYPVAMIDEFQDTDPQQYRIFRRI 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 401 WRHQPDTALLLIGDPKQAIYAFRGADIFTYMKARSEVSAHYTLDTNWRSAPGMVNSVNKLFSQMNDAFMFRDIPFSPVKF 480
Cdd:PRK10876 401 YRHQPETALLLIGDPKQAIYAFRGADIFTYMKARSEVSAHYTLDTNWRSAPGMVNSVNKLFSQTDDPFLFREIPFIPVKA 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 481 APRNQSLQFKVNDAPQPAMTLWLMEGESCGSGDYQSYMAQVCATQIRDWLRAGQTGDALLTNGDSSRPVRASDISVLVRS 560
Cdd:PRK10876 481 AGKNQALRFVVKGETQPAMKFWLMEGEGVGVGDYQQTMAQQCAAQIRDWLQAGQRGEALLMNGDDSRPVRASDITVLVRS 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 561 RREAALIRDALTLLAIPSVYLSNRDSVFETLEAQEMLWVLQAVMAPERENTLRSALATSMMGLTALDIETLNNDENAWDA 640
Cdd:PRK10876 561 RQEAALIRDALTLLAIPSVYLSNRDSVFETLEAQEMLWLLQAVLAPERERTLRSALATSMMGLDALDIDALNNDERAWDA 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 641 VVEEFDGYRQIWHKRGVMPMLRALMSARNIAENLLATAGGERRLTDILHISELLQEAGSQLESEHALVRWLAQHILEPDS 720
Cdd:PRK10876 641 LVEEFDGYRQIWRKRGVLPMLRALMSARNIAENLLATAGGERRLTDILHIGELLQEASSQLDSEHALVRWLAQQILEPDS 720
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 721 NASSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFITHFRVQDQAFYHDRHSYEAVLDLSHAEESIALAEAERLAEDLR 800
Cdd:PRK10876 721 QASSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFITNFRVQDQAFYHDRHSFEAVLDLNAAEESVALAEEERLAEDLR 800
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 801 LLYVALTRAVWHCSLGVAPLVRRRSDKKGETDVHQSALGRLLQKGEPMDAAGLRACIEALCDEDIVCRTPGSTDNDRWQI 880
Cdd:PRK10876 801 LLYVALTRSVWHCSLGVAPLVRRRRKKKGETDLHQSALGYLLQKGEPGDAAGLRACLEALCDDDIALQTAQETDNQPWQP 880
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 881 AAASHAELSARTLQRLLYDSWRVTSYSGLQQRGHSVAQDLIPRLDIDAAGVGEAAEAPAMTPHHFPRGASPGTFLHSLFE 960
Cdd:PRK10876 881 QDASLAELSARTLQRLLQDNWRVTSYSGLQQHGHSIAQDLLPRLDVDAAGEGSVVEEPQLTPHTFPRGASPGTFLHSLFE 960
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 961 ELDFTQPIDPQWVQEKLELSGFETRWEPVLTRWLDTVLHVPLNETGVSLSVLTEREKQVEMEFYLPIAQPLTAGELDALI 1040
Cdd:PRK10876 961 DLDFTQPVDPEWLQEQLELQGFEEQWEPVLTQWITAVLQTPLNETGVSLSQLSARDKQVEMQFYLPIDQPLTASQLDALI 1040
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 1041 RRYDPLSAGCPALDFMQVRGMLKGFIDLVFRYEGRYYLLDYKSNWLGEDSAAYTQTAMAAAMQAHRYDLQYQLYTLALHR 1120
Cdd:PRK10876 1041 RQYDPLSAGCPPLDFMQVRGMLKGFIDLVFRWQGRYYLLDYKSNWLGEDSSAYTQEAMAQAMQAHRYDLQYQLYTLALHR 1120
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 340763223 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: 1308.57 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 8 LDPLRLPLTGERLIEASAGTGKTFTIAALYLRLLLGLGgsaafprPLTVEELLVVTFTEAATEELRGRIRSNIHELRIAC 87
Cdd:TIGR00609 1 LDPLTIPLNGTFLIEASAGTGKTFTIAQLYLRLLLEGG-------PLTVEEILVVTFTNAATEELKTRIRGRIHQALRAL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 88 LRESTDNPLYARLLEEISDKK--QAAQWLLLAERQMDEAAVFTIHGFCQRMLSLNAFESGMLFEQQLIEDESLLRYQACA 165
Cdd:TIGR00609 74 KAALTSQELPEPLKEAIQDEKvkQAITRLRNALATMDEAAIYTIHGFCQRMLEQHAFESDEIFDVELIEDESLLLAEITK 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 166 DFWRRHCYPLPRDIAQVVFDVWKGPKALLKDIDRYLQGEA-PVIKAPPSQEETLASRHEQILARINQVKqqwceavseld 244
Cdd:TIGR00609 154 DFWRRNFYNLPFDIAQIVLKTKKSPQAVLTQILADLLLQSyLAFPSPPLDLEQLIKWHEQIYKDLDKLD----------- 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 245 aliessgidrrkfnrgnqakwiekitawaqeetknyqlpealgkfsqrflaertkasgvtpqHPLFVAIDNLL---GEPL 321
Cdd:TIGR00609 223 --------------------------------------------------------------HAVFEEIDKLNaerNNLF 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 322 SIKDLVLTRALSEIRETVAQEKRRRGELGFDDMLSRLDTALRSESGEALATAIRTRFPVAMIDEFQDTDPQQYRIFRRIW 401
Cdd:TIGR00609 241 CLKDRVFLTLLKEVQEELKKEKKRRREIGFDDLLSRLETALKSAEGEKLAQAIREQYPIALIDEFQDTDPQQYRIFSKLF 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 402 RHQPDTALLLIGDPKQAIYAFRGADIFTYMKARSEVSAHYTLDTNWRSAPGMVNSVNKLFSQMNDAFMFRDIpFSPVKFA 481
Cdd:TIGR00609 321 IAQKETSLFLIGDPKQAIYSFRGADIFTYLQAKSKADARYTLGTNWRSTPALVGSLNKLFSLISNPFLEKPI-FIPVLAH 399
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 482 PRNQSLQFKVNDAPQPAMTLWLMEGESCGSGDYQSYMAQVCATQIRDWLRAGQTGDALLTNGDSSRPVRASDISVLVRSR 561
Cdd:TIGR00609 400 QKNSKGSFVINGQEQPPIHFFTTEVESEGVDDYRQTIAQKCAREIALWLASAALGLANFIATFGGRPLRAGDIAVLVRGR 479
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 562 REAALIRDALTLLAIPSVYLSNRDSVFETLEAQEMLWVLQAVMAPERENTLRSALATSMMGLTALDIETLNNDENAWDAV 641
Cdd:TIGR00609 480 KEANQIRKALKKAQIPSVYLSDKSSVFATEEAQELLALLEALLEPENEGTLRAALASSIFGLSALELETLNQDEITWERV 559
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 642 VEEFDGYRQIWHKRGVMPMLRALMSARNIAENLLATAGGERRLTDILHISELLQEAGSQLESEHALVRWLAQHILEPDSN 721
Cdd:TIGR00609 560 VEKFREYHDIWRKIGVLAMFQRLMLEKGIGERLLSQPGGERILTNLLHLAELLQEAAHQERNKLSLLRWLEDQISNEEEE 639
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 722 aSSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFITHFRVQDQAFYHDRHSYEAVL-DLSHAEESIALAEAERLAEDLR 800
Cdd:TIGR00609 640 -EEEIIRLESDAELVKIVTIHKSKGLEYPIVFLPFITDAKKSNFASLHDQHSHEYQLyDFNQSEENQKLARVERLAEDLR 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 801 LLYVALTRAVWHCSLGVAPLVRRRSDKKGETDVHQSALGRLLQKGEPMDAAGLRACIEALCDED-IVCRTPGSTDNDRWQ 879
Cdd:TIGR00609 719 LLYVALTRAKKQLFIGIAPLITSKLSNLAYSALHNSALGYQKQDGETDNITGLKQCLAALADPAgISSIPAKPIGANSSK 798
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 880 IAAASHAELSARTLQRLLYDSWRVTSYSGLQQRGHSVAQDLIPRLDIDAAGVgeaaeapAMTPHHFPRGASPGTFLHSLF 959
Cdd:TIGR00609 799 KEPASTALLEARTFHRRIRENWRITSFSSLKELEEAVTEEPAPGLDYEVSSL-------EISAQDFPKGKKTGTLLHAIL 871
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 960 EELDFTQPIDPQ----WVQEKLELSGFETRWEPVLTRWLDTVLHVPLN-ETGVSLSVLTEREKQVEMEFYLPIAQPLTAG 1034
Cdd:TIGR00609 872 ESLIFSQAADLEkqnnLIAEKLKKTGLEGLWEPELQEWLEKMLNTPLTfSRAITLSQIDPEDRQREMEFLLPINPEFQKQ 951
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 1035 ELDALIRRYdPLSAGCPALDFMQVRGMLKGFIDLVFRYEGRYYLLDYKSNWLGEDSAAYTQTAMAAAMQAHRYDLQYQLY 1114
Cdd:TIGR00609 952 KLNFVIRAY-PDRAGSPDLHFQLLRGLLKGFIDLVFEHNGRYYILDYKSNWLGKDASDYSPEALTEAILKERYDLQYLIY 1030
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*...
gi 340763223 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: 685.54 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 1 MNDVAETLDPLR--LPLTGERLIEASAGTGKTFTIAALYLRLLLGlggsaafpRPLTVEELLVVTFTEAATEELRGRIRS 78
Cdd:COG1074 1 MSEPPWTDAQRRalDPLGGSVLVEASAGSGKTYTLVARYLRLLLE--------RGLDPEEILVVTFTRAAAAEMRERIRE 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 79 NIHELRiaclreSTDNPLYARLleeisdkKQAAQWLLLAERQMDEAAVFTIHGFCQRMLSLNAFESGMLFEQQLIED-ES 157
Cdd:COG1074 73 RLAEAA------DLEDPDLEEL-------ARARRRLARALENLDRAAISTIHSFCQRLLREFAFEAGLDPNFELLDDaEA 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 158 LLRYQACADFWRRHCYPLPRDIAQVVFDVW-KGPKALLKDIDRYLQgeapvikappsqeetLASRheqilarinqvkQQW 236
Cdd:COG1074 140 LLLEEAVDDLLREAYAPLDALALARLLDAFgRDDDSLEELLLALYK---------------LRSR------------PDW 192
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 237 CEAVSELDaliessgidrrkfnrgnqakwiekitawaqeetknyqlpEALGKFSQRFLAERTkasgvtpqhpLFVAIDNL 316
Cdd:COG1074 193 LEELAELD---------------------------------------EALEALREALLKAKE----------ALAALREA 223
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 317 LGEPLSIKDLVLTRALSEIRETVAQEKRRRGELGFDDMLSRLDTALRSESGEALATAIRTRFPVAMIDEFQDTDPQQYRI 396
Cdd:COG1074 224 LAAAAAPLLAALLRLLAAVLARYERRKRERGLLDFDDLLHRALRLLRDEDAPWVAERLRERYRHILVDEFQDTSPLQWEI 303
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 397 FRRIWRHQP--DTALLLIGDPKQAIYAFRGADIFTYMKARSEVSAH-----YTLDTNWRSAPGMVNSVNKLFSQMNDAFm 469
Cdd:COG1074 304 LRRLAGEALadGRTLFLVGDPKQSIYRFRGADPELFLEARRALEGRvdgerLTLTTNFRSTPEVVDAVNALFAQLMGAG- 382
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 470 FRDIPFSPVKfaprnqslqfKVNDAPQPAMTLWLMEGESCGSGDYQSYMAQVCATQIRDWLRAGQTGDalltngDSSRPV 549
Cdd:COG1074 383 FGEIPYEPVE----------ALRPGAYPAVELWPLEPDDVSEEDAREREARAVAARIRRLLAEGTTVE------GGGRPV 446
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 550 RASDISVLVRSRREAALIRDALTLLAIPsVYLSNRDSVFETLEAQEMLWVLQAVMAPERENTLRSALATSMMGLTALDIE 629
Cdd:COG1074 447 RPGDIAVLVRTRSEAAAIARALKAAGIP-VAASDRLSLFESPEVRDLLALLRALLNPEDDLALAAVLRSPLFGLSDEDLA 525
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 630 TLNND---ENAWDAV---------VEEFDGYRQIWHKRGVMPMLRALMSARNIAENLLATAGGERRLTDILHISELLQEA 697
Cdd:COG1074 526 ALAADrkgESLWEALrayerlaraLERLRALRELARRLGLAELLERLLEETGLLERLLALPGGERRLANLLHLDELLQLA 605
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 698 ----GSQLESEHALVRWLAQHIlepDSNASSQQLRLESDKHLVQIVTIHKSKGLEYPLVWLPFIthfrvqdqafyhdrhs 773
Cdd:COG1074 606 leyeQTGGPGLAGFLRWLERLI---EDGGDEEKRRLESDADAVRIMTIHKSKGLEFPVVFLPAL---------------- 666
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 774 yeavldlshaeesIALAEAERLAEDLRLLYVALTRAVWHCslgvaplvrrrsdkkgetdvhqsalgrllqkgepmdaagl 853
Cdd:COG1074 667 -------------RERARAEELAEELRLLYVALTRARDRL---------------------------------------- 693
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 854 raciealcdedIVCRTPGSTDNDRWqiaaashaelsartlqrllyDSWrvtsysglqqrghsvaqdliprldidaagvge 933
Cdd:COG1074 694 -----------VLSGAVKKKDAEKE--------------------SSW-------------------------------- 710
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 934 aaeapamtphhfprGASPGTFLHSLFEELDFTQPID-PQWVQEKLELSGFETRWEPVLTRWLDTVLHVPLnetgvsLS-V 1011
Cdd:COG1074 711 --------------LARRGTLVHRLLEHLDFSAPAElRAALARLLARGGLDEEEAEALAEALLAFLATPL------LAeL 770
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 1012 LTEREKQVEMEFYLPIAQPltageldalirrydplsagcpaldfmQVRGMLKGFIDLVFRYEGRYYLLDYKSNWLGEDSA 1091
Cdd:COG1074 771 FAAAEVLREVPFLLPDLYR--------------------------GLGGLLKGRIDLVFEDDGRVYIVDYKTNRLGPDDE 824
|
1130 1140 1150
....*....|....*....|....*....|....
gi 340763223 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 |
2.52e-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: 2.52e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 901 WRVTSYSGLQQRGHSVAQDLIPRLDIDAAGVGEAAEAPAMTPHHFPRGASPGTFLHSLFEELDFtqpidpqwvqeklels 980
Cdd:cd22352 1 WRITSFSSLTRGLGGKAAEASHDEEPDEDEEAAPEEADEEGIDALPRGAKTGTFLHEILENIDR---------------- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 981 gfetrwepvltrwldtvlhvplnetgvslsvlterekQVEMEFYLPIAQPLTAGELDALIRRYDPLSAGCPaLDFMQVRG 1060
Cdd:cd22352 65 -------------------------------------LSEMEFYLPLSDKLDAEALNELLRQHGPPGALPP-LSFETLRG 106
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 1061 MLKGFIDLVFRYEGRYYLLDYKSNWLGEDSAAYTQTAMAAAMQAHRYDLQYQLYTLALHRYLRHRMANYDYERHFGGVIY 1140
Cdd:cd22352 107 FLKGFIDLVFEHEGRYYILDYKSNYLGDYLEDYSPEALEAAMLEHHYDLQYLLYTLALHRYLKQRLPDYDYERHFGGVYY 186
|
250 260
....*....|....*....|....*....
gi 340763223 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 |
6.75e-41 |
|
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: 152.01 E-value: 6.75e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 13 LPLTGERLIEASAGTGKTFTIAALYLRLLLGlggsaafpRPLTVEELLVVTFTEAATEELRGRIRSnihelriaclrest 92
Cdd:pfam00580 10 THLGGPLLVLAGAGSGKTRVLTERIAYLILE--------GGIDPEEILAVTFTNKAAREMKERILK-------------- 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 93 dnplyarlleeisdkkqaaqwlLLAERQMDEAAVFTIHGFCQRMLSLNAFESGmlfeqqliedesllryqacadfwRRHC 172
Cdd:pfam00580 68 ----------------------LLGKAELSELNISTFHSFCLRILRKYANRIG-----------------------LLPN 102
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 173 YPLPRDIAQVvfdvwkgpkALLKDIdrylqgeapvikappsqeetlasrheqilarinqvkqqwceavseldALIESSGI 252
Cdd:pfam00580 103 FSILDELDQL---------ALLKEL-----------------------------------------------LEKDRLNL 126
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 253 DRRKFNRGNQAKWIEKItawaqeetKNYQLpealgkfsqrfLAERTKASGVTPQHPLFVAIDnllgeplsikdlvltral 332
Cdd:pfam00580 127 DPKLLRKLELKELISKA--------KNRLL-----------SPEELQQGAADPRDKLAAEFY------------------ 169
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 333 seirETVAQEKRRRGELGFDDMLSRLDTALRSesGEALATAIRTRFPVAMIDEFQDTDPQQYRIFRRIWRHQPdtALLLI 412
Cdd:pfam00580 170 ----QEYQERLKENNALDFDDLLLLTLELLRS--DPELLEAYRERFKYILVDEFQDTNPIQYRLLKLLAGGHE--NLFLV 241
|
410 420
....*....|....*....|....
gi 340763223 413 GDPKQAIYAFRGADIFTYMKARSE 436
Cdd:pfam00580 242 GDPDQSIYGFRGADIENILKFEKD 265
|
|
| UvrD |
COG0210 |
Superfamily I DNA or RNA helicase [Replication, recombination and repair]; |
276-809 |
2.12e-38 |
|
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
Pssm-ID: 439980 [Multi-domain] Cd Length: 721 Bit Score: 154.32 E-value: 2.12e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 276 ETKNYQLPEALGKFSqrflaeRTKASGVTPQHplfvAIDNLLGEPLsikdlvlTRALSEIRETVAQEKRRRGELGFDDML 355
Cdd:COG0210 130 DEKRFPPRELLSLIS------RAKNEGLTPEE----LAELLAADPE-------WRAAAELYEAYQERLRANNALDFDDLL 192
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 356 SRLDTALRSEsgEALATAIRTRFPVAMIDEFQDTDPQQYRIFRRIwrHQPDTALLLIGDPKQAIYAFRGADI-----FT- 429
Cdd:COG0210 193 LLAVRLLEEN--PEVLEKYQNRFRYILVDEYQDTNPAQYELLRLL--AGDGRNLCVVGDDDQSIYGFRGADPenilrFEk 268
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 430 -YMKARSevsahYTLDTNWRSAPGMVNSVNKLfsqmndafmfrdIPFSPVKFAPRNQSlqfkVNDAPQPamtlwlMEGES 508
Cdd:COG0210 269 dFPDAKV-----IKLEQNYRSTQNILDAANAV------------IANNPGRLGKNLWT----DNGEGEK------VRLYV 321
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 509 CGSGDYQsymAQVCATQIRDWLRAGqtgdalltngdssrpVRASDISVLVRSRREAALIRDALTLLAIPsVYLSNRDSVF 588
Cdd:COG0210 322 APDEEEE---ARFVADEIRELHEEG---------------VPLSDIAVLYRTNAQSRALEEALRRAGIP-YRVVGGLRFY 382
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 589 ETLEAQEMLWVLQAVMAPERENTLRSALATSMMGLTALDIETL-----NNDENAWDAV--------------------VE 643
Cdd:COG0210 383 ERAEIKDLLAYLRLLANPDDDVALLRILNVPRRGIGAATLERLreaarEEGISLLEALrdlgelaglsgraakalrrfAE 462
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 644 EFDGYRQIWHKRGVMPMLRALMSARNIAENLLATAG--GERRLTdilHISELLQEAG--SQLESEHALVRWLAQHILEPD 719
Cdd:COG0210 463 LLEALRAAAERLPLEELLEALLDESGYEEELREEAGeeAERRLE---NLEELVDAAArfEERNPGASLEAFLEELALLSD 539
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 720 SNassqQLRLESDKhlVQIVTIHKSKGLEYPLVwlpFITHfrVQDQAFYHDRhsyeavldlshaeesiALAEAERLAEDL 799
Cdd:COG0210 540 LD----AADEDEDA--VTLMTLHAAKGLEFPVV---FLVG--LEEGLFPHQR----------------SLDDEEELEEER 592
|
570
....*....|
gi 340763223 800 RLLYVALTRA 809
Cdd:COG0210 593 RLFYVAITRA 602
|
|
| addA_alphas |
TIGR02784 |
double-strand break repair helicase AddA, alphaproteobacterial type; AddAB, also called RexAB, ... |
57-809 |
7.74e-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: 109.01 E-value: 7.74e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 57 EELLVVTFTEAATEELRGRIRSnihelRIACLRESTDNPLYARLlEEISDKKQAAQWLLLAERQMDEA-------AVFTI 129
Cdd:TIGR02784 42 SKILCLTYTKAAAAEMQNRVFK-----RLGEWAVLDDADLRARL-EALEGKRPDAAKLAEARRLFARAletpgglKIQTI 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 130 HGFCQRMLSLNAFESGMLFEQQLIED--ESLLRYQA---CADFWRRHCYPLPRDIAQV--VFDvWKGPKALLKDIDR--- 199
Cdd:TIGR02784 116 HAFCEALLHQFPLEANVAGHFSVIDDraAATLLEEArraLLAGPAAPDDALADALATVleAAG-ETGLEALLAEIVArrd 194
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 200 ----YLQ------GEAPVIKA----PPSQEETLASR-------HEQILARINQVKQQWCEAVSELDALIEssgiDRRKFN 258
Cdd:TIGR02784 195 almaFLDeaggegAEARLRRAlglaPGDTAEDLLEAvwplpglPRLALALIAALLKSGGGSKDAAAALSQ----LREAAA 270
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 259 RGNQAKWIEKITAW---AQEETKNYQLP------EALGKFSQRFLAERTKASGVTPQHPLFVAIDnllgepLSIKDLVLT 329
Cdd:TIGR02784 271 EPDPVARLDLLLGAfltSKGEPKSASFVikkaiqKSLPDLAEALEDAASRVEALRERLRALRMAQ------RTLAALRLA 344
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 330 RALSEIREtvaQEKRRRGELGFDDMLSRlDTALRSESGEA------LATAIRTrfpvAMIDEFQDTDPQQYRIFRRI--- 400
Cdd:TIGR02784 345 ARLLQRYA---RLKKARGLLDFNDLIER-TVALLARPGAGawvhykLDRGIDH----ILVDEAQDTSPEQWDIIQALaee 416
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 401 ------WRHQPDTALLLIGDPKQAIYAFRGADIFTYMKARSEVSAHY----------TLDTNWRSAPGMVNSVNKlfsqm 464
Cdd:TIGR02784 417 ffsgegARSGVERTIFAVGDEKQSIYSFQGADPERFAEERREFSRKVravgrkfedlSLNYSFRSTPDVLAAVDL----- 491
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 465 ndafMFRDIP----FSPVKFAPRNQSLQfkvNDAPQpAMTLWLM----EGES----------CGSGDYQSYMAQVCATQI 526
Cdd:TIGR02784 492 ----VFADPEnargLSADSDAPVHEAFR---DDLPG-RVDLWDLiskeEGEEpedwtdpvdeLGERAPEVRLAERIAAEI 563
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 527 RDWLRAGQTGDALltngdsSRPVRASDISVLVRSRRE--AALIRdALTLLAIPsVYLSNRDSVFETLEAQEMLWVLQAVM 604
Cdd:TIGR02784 564 RAWLDRGTPIPGR------GRAVRPGDILVLVRKRDAffSALIR-ALKRRGIP-VAGADRLKLTSHIAVKDLMALGRFVL 635
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 605 APERENTLRSALATSMMGLTALDIETL---NNDENAWDAVVEEFDGYRQIWHKrgvmpmLRALMS-ARNIA-----ENLL 675
Cdd:TIGR02784 636 QPEDDLSLAALLKSPLFGLDEDDLFRLaagRSGGSLWAALRRREAEFAATLAV------LRDWLSlADFLTpfefyARLL 709
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 676 ATAGGERRL--------TDILH--ISELLQEAGSQLESEHALVRWLaqhilepDSNASSQQLRLESDKHLVQIVTIHKSK 745
Cdd:TIGR02784 710 GRDGGRRKLlarlgaeaEDILDefLSQALAYERTGLPGLQAFLSWL-------EADDPEIKREMDQARDEVRVMTVHGAK 782
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 340763223 746 GLEYPLVWLPFITHFRVQDQAFYH---DRHSYEAVL------DLSHAEESIALAEAERLAED--LRLLYVALTRA 809
Cdd:TIGR02784 783 GLEAPVVFLVDTGSKPFASQRAPLllaTGGSGGKAPlwrpasAFDPSLSAAARERLKERAEDeyRRLLYVAMTRA 857
|
|
| DEXQc_UvrD |
cd17932 |
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ... |
351-447 |
4.16e-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: 95.28 E-value: 4.16e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 351 FDDMLSRLDTALrsESGEALATAIRTRFPVAMIDEFQDTDPQQYRIFRRIWRhqPDTALLLIGDPKQAIYAFRGADIFTY 430
Cdd:cd17932 95 FDDLLLYALELL--EENPDVREKLQSRFRYILVDEYQDTNPLQYELLKLLAG--DGKNLFVVGDDDQSIYGFRGADPENI 170
|
90
....*....|....*....
gi 340763223 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 340763223 690 ISELLQEAGSQLESEHALVRwlaqhilepdSNASSQQLRlesDKHLVQIVTIHKSKGLEYPLVWLPFITHFRVQDQAFYH 769
Cdd:cd18807 53 IKRLIESGPVQYSDIAILVR----------TNRQARVIE---EALRVTLMTIHASKGLEFPVVFIVGLGEGFIPSDASYH 119
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 340763223 770 drhsyeavldlshaeesIALAEAERLAEDLRLLYVALTRAVWHCSLG 816
Cdd:cd18807 120 -----------------AAKEDEERLEEERRLLYVALTRAKKELYLV 149
|
|
| PRK13909 |
PRK13909 |
RecB-like helicase; |
22-810 |
9.17e-17 |
|
RecB-like helicase;
Pssm-ID: 237554 [Multi-domain] Cd Length: 910 Bit Score: 85.79 E-value: 9.17e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 22 EASAGTGKTFTiaalylrlllglggsaafprpLTVE------------ELLVVTFTEAATEELRGRIrsnihelrIACLR 89
Cdd:PRK13909 4 KASAGSGKTFA---------------------LSVRflallfkganpsEILALTFTKKAANEMKERI--------IDTLL 54
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 90 ESTDNPLYARLL----------EEISDKKQAAQWLLLAErqmdEAAVFTIHGFCQRML---SLNA-----FESGMLFEQQ 151
Cdd:PRK13909 55 NLEKEKEESELNeleeklglskEELLNKRDKVYQEFLNS----ELKISTIDAFFQKILrkfCLNLglspdFSIKEDTKEE 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 152 LIED-----------ESLLRYQACADfwrrhcyplprdiaqvvfdvwKGPKALLKDIDRYLQGEAPVIKAPPSQEETlAS 220
Cdd:PRK13909 131 LNEKflsalskeellELLAFIKQCES---------------------KKNNSFFELLEKLYEKNNELKLFEKAKNPI-EF 188
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 221 RHEQILARINQVKQQWCEAVSELDALIESsgIDRRKFNRG--NQAKWIEKitawaqEETKNYQLPEALGKFSQrflaert 298
Cdd:PRK13909 189 DEEKFLEELRSLKQQIQSIETASKNAKKA--FKKEDFEELlnSSKTWLEK------ESEYRYFKKLYNEELDA------- 253
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 299 kasgvtpqhpLFVAIDNLLGEPLSIKDLVLTRALSEI----RETVAQEKRRRGELGFDDMLSRLDTALRSESGEALATAI 374
Cdd:PRK13909 254 ----------EFEELKNALKRYYDAKENYKLSKLFKLlqlyKEAKNELNKKKNALDFDDISKKVYELLGEEEIDKDFLYF 323
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 375 R--TRFPVAMIDEFQDTDPQQYRIFRriwrhqP-------------DTALLLIGDPKQAIYAFRG--ADIFTYMKARSEV 437
Cdd:PRK13909 324 RldSKISHILIDEFQDTSVLQYKILL------PlideiksgegqkkFRSFFYVGDVKQSIYRFRGgkKELFDKVSKDFKQ 397
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 438 sAHYTLDTNWRSAPGMVNSVNKLFsqmNDAFmfrdiPFSPVKFAPRNQSLQF-KVndapqpamtlwlmegeSCGSGDYQS 516
Cdd:PRK13909 398 -KVDNLDTNYRSAPLIVDFVNEVF---KKKY-----KNYKTQYAEQHKSGGYvEV----------------VEVADESEE 452
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 517 YMAQVCATQIRdwlragqtgdaLLTNGdssrpVRASDISVLVRSRREAALIRDALT-LLAIP-----SVYLSNRDSVFET 590
Cdd:PRK13909 453 LLEQLLQEIQF-----------LLEKG-----IDPDDIAILCWTNDDALEIKEFLQeQFGIKavtesSAKLINQPEVKAL 516
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 591 LEAqemlwvLQAVMAPER---ENTLrsALAtsmmgltaldietlnndENAWDAVVEEFDgyrqiwHKRGVMPMLRALMSA 667
Cdd:PRK13909 517 IEA------LKYCLFGEEiykHNVL--KLL-----------------GKEPDKIPSFLP------KEESVAEFVKKLIEE 565
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 668 RNIA-ENLL----ATAGGERrltdilhISELLQEagsqlesehalvrwlaqhiLEPDSNASSQQlrlESDKhlVQIVTIH 742
Cdd:PRK13909 566 LKLYdENLLkfleLASGYED-------IEEFLFK-------------------LEPCDKEIASE---ESKG--VQIMTVH 614
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 743 KSKGLEYPLVWL------------PFITHFRVQ--DQAFYhdRHSYEAVLDLSHAEesiALAEAERLA--EDLRLLYVAL 806
Cdd:PRK13909 615 KSKGLEFEHVIVcdrlgkpnsdssNLLFEYDGIelWQIYY--RIKGRENFDKDYAR---ALEKEKALKyeEEINVLYVAF 689
|
....
gi 340763223 807 TRAV 810
Cdd:PRK13909 690 TRAK 693
|
|
| SF1_C |
cd18786 |
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
728-817 |
4.07e-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: 4.07e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 728 RLESDKHLVQIVTIHKSKGLEYPLVWLPFITHFrvqdqafyhdrhsyeavldlshaeesialaeaerlAEDLRLLYVALT 807
Cdd:cd18786 35 LDEFDLQLVGAITIDSSQGLTFDVVTLYLPTAN-----------------------------------SLTPRRLYVALT 79
|
90
....*....|
gi 340763223 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 |
3.87e-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: 63.19 E-value: 3.87e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 552 SDISVLVRSRREAALIRDALTLLAIPsVYLSNRDSVFETLEAQEMLWVLQAVMAPERENTLRSALATSMMGLTALDIETL 631
Cdd:pfam13361 76 NDIAVLTRSNSDADLIEEALKKLGIP-YFVVGQTKFFRREEIKDILAYLRLIANKHDSISLKRILNGPKRGIGNATLERI 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 632 NNDENAWDAVVEEFDGYRQIWhkrgVMPMLRALMSARN-------------------IAENLLATAG--GER-------- 682
Cdd:pfam13361 155 REYKKRGLRLSDFINPDTLTY----GDPFVIALEQDNIvvfdvettgldttedeiiqIAAIKLNKKGvvIESferflrlk 230
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 683 -----RLTDILHISELLQEAG-----------SQLESEHALVRWLAQ---------------HILEpDSNASSQQLRLES 731
Cdd:pfam13361 231 kpvgdSLQVHGFSDEFLQENGetpaealrdflEKLENLRELYSILREyddieetpepedalrNFLE-IATLSNSELEGSD 309
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 340763223 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 340763223 16 TGERLIEASAGTGKTFTIAALYLRLLLGlggsaafpRPLTVEELLVVTFTEAATEELRGRIRSnihelriaclrestdnp 95
Cdd:cd17932 12 DGPLLVLAGAGSGKTRVLTHRIAYLILE--------GGVPPERILAVTFTNKAAKEMRERLRK----------------- 66
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 340763223 96 lyarlleeisdkkqaaqwlLLAERQMDEAAVFTIHGFCQRMLSLNA-FESGMLFEQQLIEDESLLRYQACADF 167
Cdd:cd17932 67 -------------------LLGEQLASGVWIGTFHSFALRILRRYGdFDDLLLYALELLEENPDVREKLQSRF 120
|
|
| uvrD |
PRK11773 |
DNA-dependent helicase II; Provisional |
375-809 |
2.80e-08 |
|
DNA-dependent helicase II; Provisional
Pssm-ID: 236976 [Multi-domain] Cd Length: 721 Bit Score: 57.96 E-value: 2.80e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 375 RTRFPVAMIDEFQDTDPQQYRIFRRIWRHQpdTALLLIGDPKQAIYAFRGADIFTYMKARSEVSAHYT--LDTNWRSAPG 452
Cdd:PRK11773 211 QERFTHILVDEFQDTNAIQYAWIRLLAGDT--GKVMIVGDDDQSIYGWRGAQVENIQRFLNDFPGAETirLEQNYRSTAN 288
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 453 MVNSVNKLFSQmNDAFMFRDipfspvkfaprnqslqfkvndapqpamtLWLMEGESCGSGDYQSY----MAQVCATQIRD 528
Cdd:PRK11773 289 ILKAANALIAN-NNGRLGKE----------------------------LWTDGGDGEPISLYCAFneldEARFVVERIKT 339
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 529 WLRAGQtgdalltngdssrpvRASDISVLVRSRR-----EAALIR--------------------DALTLLAIpsvyLSN 583
Cdd:PRK11773 340 WQDNGG---------------ALSDCAILYRSNAqsrvlEEALLQagipyriyggmrfferqeikDALAYLRL----IAN 400
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 584 R--DSVFE-------------TLEA--------QEMLWvlQAVMAPERENTLRSALATSMMGLTALdIETLNNDenawda 640
Cdd:PRK11773 401 RndDAAFErvvntptrgigdrTLDVvrqtardrQLTLW--QACRALLQEKVLAGRAASALQRFIEL-IDALAQE------ 471
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 641 vVEEFDGYRQIWH---KRGVMPMLRALMSARNIA--ENL--LATAGGERRLTDilhisellqeagsQLESEHALVRWLAQ 713
Cdd:PRK11773 472 -TADMPLHEQTDRvikDSGLRAMYEQEKGEKGQAriENLeeLVTATRQFSYPD-------------EDEDLTPLQAFLSH 537
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 714 HILEpdsnASSQQLRLESDKhlVQIVTIHKSKGLEYPLVwlpFITHfrVQDQAFYHDRhsyeavldlshaeesiALAEAE 793
Cdd:PRK11773 538 AALE----AGEGQADAHEDA--VQLMTLHSAKGLEFPLV---FIVG--MEEGLFPSQM----------------SLEEGG 590
|
490
....*....|....*.
gi 340763223 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 340763223 382 MIDEFQDTDPQQYRIFRRIWRHQPDTALLLIGDPKQAIYAFRGADI--FTYMKARSEVSAHYTLDTNWR 448
Cdd:PRK11054 435 LVDEFQDISPQRAALLAALRKQNSQTTLFAVGDDWQAIYRFSGADLslTTAFHERFGEGDRCHLDTTYR 503
|
|
| AAA_19 |
pfam13245 |
AAA domain; |
316-423 |
1.91e-06 |
|
AAA domain;
Pssm-ID: 433059 [Multi-domain] Cd Length: 136 Bit Score: 48.37 E-value: 1.91e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340763223 316 LLGEPLSIKDLVLT-RALSEIRETVAQEKRR-RGELGFDDMLSrlDTALRSESGEALATAIrtrfpvaMIDEFQDTD-PQ 392
Cdd:pfam13245 38 LGGVSFPILLAAPTgRAAKRLSERTGLPASTiHRLLGFDDLEA--GGFLRDEEEPLDGDLL-------IVDEFSMVDlPL 108
|
90 100 110
....*....|....*....|....*....|.
gi 340763223 393 QYRIFRRIwrhQPDTALLLIGDPKQAIYAFR 423
Cdd:pfam13245 109 AYRLLKAL---PDGAQLLLVGDPDQLPSVGP 136
|
|
| |
