|
Name |
Accession |
Description |
Interval |
E-value |
| dinG_rel |
TIGR01407 |
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ... |
5-906 |
0e+00 |
|
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273602 [Multi-domain] Cd Length: 850 Bit Score: 759.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 5 YAVVDLETTGTDSTIDRIIQFGCVLVQDGKIINRFAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYNLLSNT 84
Cdd:TIGR01407 2 YAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLLEDG 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 85 IFVAHNIYFDYHFLSNEFVRCGLPPLSIPGIDTVELSQVFLPTESSFRLGDLADSIGFRHDNPHQADSDAEVTAALFLYI 164
Cdd:TIGR01407 82 IFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHENPHRADSDAQATAELLLLL 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 165 EAIMRQLPRTTLKQIALLSGQMGMQTSEYIHGIL-KEKGPELAEDFEVIDGVVLRKKTVPLFEATHFQE-TYPKVKTEKE 242
Cdd:TIGR01407 162 FEKMEKLPLDTLEQLLELSDQLLYESYDIIQETYrQYKIKPAPKSYEVVEQIAYRKQVASKKPETNYNTlSSLFSKNIDR 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 243 QRFGehliYRKQQARLMNAVYTHYTQPEKNLIiEAETGMGKTIGYLFPAAYLATPENPLIVSTSSILLQNQIISKDIPLV 322
Cdd:TIGR01407 242 LGLE----YRPEQLKLAELVLDQLTHSEKSLI-EAPTGTGKTLGYLLPALYYAITEKPVVISTNTKVLQSQLLEKDIPLL 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 323 NQVLQQPLQAVLVKSHRHYIDLQRFKATLEQPVEQKQYAQYQMGILVWLTKTETGDFDELNLVRLDHPLFTDIRHRGvdF 402
Cdd:TIGR01407 317 NEILNFKINAALIKGKSNYLSLGKFSQILKDNTDNYEFNIFKMQVLVWLTETETGDLDELNLKGGNKMFFAQVRHDG--N 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 403 LAKDQPFYEQDFVRHLYRRMAQSNVLIVNHAFLMQENRRAQPLLPTSDYLLIDEAQQLPQQAEGFSQHVFDSAHFKRQ-- 480
Cdd:TIGR01407 395 LSKKDLFYEVDFYNRAQKNAEQAQILITNHAYLITRLVDNPELFPSFRDLIIDEAHHLPDIAENQLQEELDYADIKYQid 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 481 -FLQLNEEGLFEEIAQIITEddflqrmfslyrnalsvlvETQEQYFRTLSIDApelqvvqhrdLYDGSLEQDKLHQKLSL 559
Cdd:TIGR01407 475 lIGKGENEQLLKRIQQLEKQ-------------------EILEKLFDFETKDI----------LKDLQAILDKLNKLLQI 525
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 560 YYQEINEIQQQLRqRFELTNdrwyarqRIVIARLFDFFSQMdaqeqtvtawltwwHPRYVHwLKKHPQSGNAVIELADLE 639
Cdd:TIGR01407 526 FSELSHKTVDQLR-KFDLAL-------KDDFKNIEQSLKEG--------------HTSWIS-IENLQQKSTIRLYIKDYE 582
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 640 GHSIVESTWYQRYQHIIYLGGTLKIPGNKEYFAHQIGLTDVPVKTI-PAFYDYSKQTRLYVIKKGLSIQQASAAEYADYL 718
Cdd:TIGR01407 583 VGDVLTKRLLPKFKSLIFTSATLKFSHSFESFPQLLGLTDVHFNTIePTPLNYAENQRVLIPTDAPAIQNKSLEEYAQEI 662
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 719 VEALVPILFDNPQPALVLFTAHETLKNVYDRLNKKALHYGREIVAQGTGGTREKILKKFLLAENGILLGTSSFWEGVDLP 798
Cdd:TIGR01407 663 ASYIIEITAITSPKILVLFTSYEMLHMVYDMLNELPEFEGYEVLAQGINGSRAKIKKRFNNGEKAILLGTSSFWEGVDFP 742
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 799 GQALKIAVVTRLPFENPKQPMVQARHAFLEAEGIDSFKEDALPKAILRLRQALGRLIRSEEDTGVMVVLDRRLLSTKYGK 878
Cdd:TIGR01407 743 GNGLVCLVIPRLPFANPKHPLTKKYWQKLEQEGKNPFYDYVLPMAIIRLRQALGRLIRRENDRGSIVILDRRLVGKRYGK 822
|
890 900
....*....|....*....|....*...
gi 505322933 879 RMVKGLPKNLPLIEASPTEIAEDIQHFF 906
Cdd:TIGR01407 823 RFEKSLPEYLQVKGDILGELLEAIKEFL 850
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
1-906 |
0e+00 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 631.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 1 MKPIYAVVDLETTGTD-STIDRIIQFGCVLVQDGKIINRFAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYN 79
Cdd:PRK08074 1 MSKRFVVVDLETTGNSpKKGDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 80 LLSNTIFVAHNIYFDYHFLSNEFVRCGLPPLSIPGIDTVELSQVFLPTESSFRLGDLADSIGFRHDNPHQADSDAEVTAA 159
Cdd:PRK08074 81 LLEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEELGLEHDQPHRADSDAEVTAE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 160 LFLYIEAIMRQLPRTTLKQIALLSGQMGMQTSEYIHGILKEK---GPELAEDFEVIDGVVLRKKTVPLFEATHFQETYPK 236
Cdd:PRK08074 161 LFLQLLNKLERLPLVTLQQLRRLSDHLKSDIAELLDENILKKmmhGKPLDEEFDEYRGIALRKREVEKNLEETCRSDFDA 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 237 VKTEKEQRFGEHLI---YRKQQARLMNAVYTHYTQpEKNLIIEAETGMGKTIGYLFPAAYLATPEN-PLIVSTSSILLQN 312
Cdd:PRK08074 241 FLEKTEEKLSLAMPkyeKREGQQEMMKEVYTALRD-SEHALIEAGTGTGKSLAYLLPAAYFAKKKEePVVISTYTIQLQQ 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 313 QIISKDIPLVNQVLQQPLQAVLVKSHRHYIDLQRFKATLEQpvEQKQY------AQyqmgILVWLTKTETGDFDELNLVR 386
Cdd:PRK08074 320 QLLEKDIPLLQKIFPFPVEAALLKGRSHYLCLRKFEQALQE--EDDNYdvaltkAQ----LLVWLTETETGDLDELNLPS 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 387 LDHPLFTDIRHRGVDFLAKDQPFYEQDFVRHLYRRMAQSNVLIVNHAFLMQENRRAQPLLPTSDYLLIDEAQQLPQQA-E 465
Cdd:PRK08074 394 GGKLLWNRIASDGESDGGKQSPWFSRCFYQRAKNRAKFADLVITNHALLLTDLTSEEPLLPSYEHIIIDEAHHFEEAAsR 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 466 GFSQHV-FDSAHFK-RQFLQLNEEGLFEEIAQIITEDDFLQRMfSLYR--NALSVLVETQEQYFRTL----SIDAPELQV 537
Cdd:PRK08074 474 HLGEQFsYMSFQLLlSRLGTLEEDGLLSKLAKLFKKSDQASRS-SFRDldESLKELKFEADELFQMLrsfvLKRKKQEQN 552
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 538 VQHRDLYDGSLEQDKLHQKLSLYYQEINEIQQQLRQRFE----LTNDRWYARQRIViARLFDFFSQMDAQEQTVTAWLTW 613
Cdd:PRK08074 553 GRLIYRYNTESEKGKLWDAITELANRLCYDLRDLLTLLEaqkkELQEKMESESAFL-TGEYAHLIDLLEKMAQLLQLLFE 631
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 614 WHPRYVHWL---KKHpqSGNAV------IELADLeghsiVESTWYQRYQHIIYLGGTLKIPGNKEYFAHQIGLTDVPVKT 684
Cdd:PRK08074 632 EDPDYVTWIeidAKG--AINATrlyaqpVEVAER-----LADEFFAKKKSVILTSATLTVNGSFDYIIERLGLEDFYPRT 704
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 685 --IPAFYDYSKQTRLYVIKKGLSIQQASAAEYADYLVEALVPILFDNPQPALVLFTAHETLKNVYDRLNKKALHYGREIV 762
Cdd:PRK08074 705 lqIPSPFSYEEQAKLMIPTDMPPIKDVPIEEYIEEVAAYIAKIAKATKGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLL 784
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 763 AQG-TGGTREKILKKFLLAENGILLGTSSFWEGVDLPGQALKIAVVTRLPFENPKQPMVQARHAFLEAEGIDSFKEDALP 841
Cdd:PRK08074 785 AQGvSSGSRARLTKQFQQFDKAILLGTSSFWEGIDIPGDELSCLVIVRLPFAPPDQPVMEAKSEWAKEQGENPFQELSLP 864
|
890 900 910 920 930 940
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 505322933 842 KAILRLRQALGRLIRSEEDTGVMVVLDRRLLSTKYGKRMVKGLPkNLPLIEASPTEIAEDIQHFF 906
Cdd:PRK08074 865 QAVLRFKQGFGRLIRTETDRGTVFVLDRRLTTTSYGKYFLESLP-TVPVYEGTLEELLEEVEEFL 928
|
|
| DinG |
COG1199 |
Rad3-related DNA helicase DinG [Replication, recombination and repair]; |
242-910 |
4.08e-139 |
|
Rad3-related DNA helicase DinG [Replication, recombination and repair];
Pssm-ID: 440812 [Multi-domain] Cd Length: 629 Bit Score: 428.57 E-value: 4.08e-139
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 242 EQRFGEHlIYRKQQARLMNAVYTHYTQpEKNLIIEAETGMGKTIGYLFPAAYLATPEN-PLIVSTSSILLQNQIISKDIP 320
Cdd:COG1199 7 ALAFPGF-EPRPGQREMAEAVARALAE-GRHLLIEAGTGTGKTLAYLVPALLAARETGkKVVISTATKALQEQLVEKDLP 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 321 LVNQVLQQPLQAVLVKSHRHYIDLQRFKATLEQPVEQKQYAQYQMGILVWLTKTETGDFDELNLVrLDHPLFTDIRHRGV 400
Cdd:COG1199 85 LLRKALGLPLRVALLKGRSNYLCLRRLEQALQEGDDLDDEELLLARILAWASETWTGDRDELPLP-EDDELWRQVTSDAD 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 401 DFLAKDQPFYEQDFVRHLYRRMAQSNVLIVNHAFLMQENRRAQPLLPTSDYLLIDEAQQLPQQAEGFSQHVFDSAHFKRQ 480
Cdd:COG1199 164 NCLGRRCPYYGVCPYELARRLAREADVVVVNHHLLFADLALGEELLPEDDVLIIDEAHNLPDRARDMFSAELSSRSLLRL 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 481 FLQLNEEGLFEEIAQIITEDDFLQRMFSLYRNALsvlvETQEQYFRTLsidapelqvvqhRDLYDgslEQDKLHQKLSLY 560
Cdd:COG1199 244 LRELRKLGLRPGLKKLLDLLERLREALDDLFLAL----EEEEELRLAL------------GELPD---EPEELLEALDAL 304
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 561 YQEINEIQQQLRQRFELTNDRWYARQRI--VIARLFDFFSQMDAqeqtvtawltwwhPRYVHWLKKHPqsGNAVIELADL 638
Cdd:COG1199 305 RDALEALAEALEEELERLAELDALLERLeeLLFALARFLRIAED-------------EGYVRWLEREG--GDVRLHAAPL 369
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 639 EGHSIVESTWYQRYQHIIYLGGTLKIPGNKEYFAHQIGLT-DVPVKTIPAFYDYSKQTRLYVIKKGLSIQQAsaAEYADY 717
Cdd:COG1199 370 DPADLLRELLFSRARSVVLTSATLSVGGPFDYFARRLGLDeDARTLSLPSPFDYENQALLYVPRDLPRPSDR--DGYLEA 447
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 718 LVEALVPILFDNPQPALVLFTAHETLKNVYDRLNKkalHYGREIVAQGTGgTREKILKKFLLAENGILLGTSSFWEGVDL 797
Cdd:COG1199 448 IAEAIAELLEASGGNTLVLFTSYRALEQVAELLRE---RLDIPVLVQGDG-SREALLERFREGGNSVLVGTGSFWEGVDL 523
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 798 PGQALKIAVVTRLPFENPKQPMVQARHAFLEAEGIDSFKEDALPKAILRLRQALGRLIRSEEDTGVMVVLDRRLLSTKYG 877
Cdd:COG1199 524 PGDALSLVIIVKLPFPPPDDPVLEARREALEARGGNGFMYAYLPPAVIKLKQGAGRLIRSEEDRGVVVLLDRRLLTKRYG 603
|
650 660 670
....*....|....*....|....*....|...
gi 505322933 878 KRMVKGLPknlplieASPTEIAEDIQHFFGQEE 910
Cdd:COG1199 604 KRFLDSLP-------PFRRTRPEELRAFLERLD 629
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
5-906 |
7.39e-131 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 413.31 E-value: 7.39e-131
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 5 YAVVDLETTGTDSTIdRIIQFGCVLVQDGKIINRFAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYNLLSNT 84
Cdd:PRK07246 9 YAVVDLEATGAGPNA-SIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDC 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 85 IFVAHNIYFDYHFLSNEFVRCGLPpLSIPGIDTVELSQVFLPTESSFRLGDLADSIGFRHDNPHQADSDAEVTAALFLYI 164
Cdd:PRK07246 88 IFVAHNVKFDANLLAEALFLEGYE-LRTPRVDTVELAQVFFPTLEKYSLSHLSRELNIDLADAHTAIADARATAELFLKL 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 165 EAIMRQLPRTTLKQIALLSGQMGMQTSEYIHGILKEKGPELAEDFEVIDGVVLrKKTVPLFEATHFQETYPKvkteKEQR 244
Cdd:PRK07246 167 LQKIESLPKECLERLLEYADSLLFESYLVIEEALANAKPYSSPDYIKVQGIVL-KKTAASLKPRKLSQDFSI----NIAL 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 245 FGehLIYRKQQARLMNAVYTHYTQPEKNLIiEAETGMGKTIGYLFPAAYLATpENPLIVSTSSILLQNQIISKDIPLVNQ 324
Cdd:PRK07246 242 LG--LEERPKQESFAKLVGEDFHDGPASFI-EAQTGIGKTYGYLLPLLAQSD-QRQIIVSVPTKILQDQIMAEEVKAIQE 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 325 VLQQPLQAVlvKSHRHYIDLQRFKATLEQPVEQKQYAQYQMGILVWLTKTETGDFDEL-NLVRLDHpLFTDIRHRGVdfL 403
Cdd:PRK07246 318 VFHIDCHSL--KGPQNYLKLDAFYDSLQQNDDNRLVNRYKMQLLVWLTETETGDLDEIkQKQRYAA-YFDQLKHDGN--L 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 404 AKDQPFYEQDFVRHLYRRMAQSNVLIVNHAFLMQenrRAQ--PLLPTSDYLLIDEAQQLPQQAEGFSQHvfdsahfkrqf 481
Cdd:PRK07246 393 SQSSLFYDYDFWKRSYEKAKTARLLITNHAYFLT---RVQddKDFARNKVLVFDEAQKLMLQLEQLSRH----------- 458
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 482 lQLNeeglfeeiaqiiteddflqrmfslyrnaLSVLVETQEQYfrtlsIDAPElQVVQHRDLYDGSLEqdkLHQKLSLYY 561
Cdd:PRK07246 459 -QLN----------------------------ITSFLQTIQKA-----LSGPL-PLLQKRLLESISFE---LLQLSEQFY 500
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 562 QEineiqqqlrQRFELTNDRWyarqriviARLFDFFSQMDAQE-QTVTAWLTwwHPRYVHWLKKHPQSGNAVIELADLEG 640
Cdd:PRK07246 501 QG---------KERQLIHDSL--------SRLHQYFSELEVAGfQELQAFFA--TAEGDYWLESEKQSEKRVTYLNSASK 561
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 641 HSIVESTWYQRYQHIIYLGGTLKIpGNKEYFAHQIGLTDVPVKTIPAfyDYSKQTRLYVIKKGLSIQQASAAEYAdYLVE 720
Cdd:PRK07246 562 AFTHFSQLLPETCKTYFVSATLQI-SPRVSLADLLGFEEYLFHKIEK--DKKQDQLVVVDQDMPLVTETSDEVYA-EEIA 637
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 721 ALVPILFDNPQPALVLFTAHETLKNVYDRLNKKALHYgreiVAQGTGGTREKILKKFLLAENGILLGTSSFWEGVDLPGQ 800
Cdd:PRK07246 638 KRLEELKQLQQPILVLFNSKKHLLAVSDLLDQWQVSH----LAQEKNGTAYNIKKRFDRGEQQILLGLGSFWEGVDFVQA 713
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 801 ALKIAVVTRLPFENPKQPMVQARHAFLEAEGIDSFKEDALPKAILRLRQALGRLIRSEEDTGVMVVLDRRLLSTKYGKRM 880
Cdd:PRK07246 714 DRMIEVITRLPFDNPEDPFVKKMNQYLLQEGKNPFYDYFLPMTILRLKQAIGRTMRREDQKSAVLILDRRILTKSYGKQI 793
|
890 900
....*....|....*....|....*.
gi 505322933 881 VKGLPKNLPLIEASPTEIAEDIQHFF 906
Cdd:PRK07246 794 LASLAEEFLISQQNFSDVLVEIDRFL 819
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
5-177 |
8.52e-65 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 215.39 E-value: 8.52e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 5 YAVVDLETTGTDSTIDRIIQFGCVLVQDGKIINRFAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYNLLSNT 84
Cdd:COG2176 10 YVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLEFLGDA 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 85 IFVAHNIYFDYHFLSNEFVRCGLpPLSIPGIDTVELSQVFLPTESSFRLGDLADSIGFRHDNPHQADSDAEVTAALFLYI 164
Cdd:COG2176 90 VLVAHNASFDLGFLNAALKRLGL-PFDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDRHRALGDAEATAELFLKL 168
|
170
....*....|...
gi 505322933 165 EAIMRQLPRTTLK 177
Cdd:COG2176 169 LEKLEEKGITTLR 181
|
|
| dinG |
PRK11747 |
ATP-dependent DNA helicase DinG; Provisional |
243-885 |
4.37e-55 |
|
ATP-dependent DNA helicase DinG; Provisional
Pssm-ID: 236966 [Multi-domain] Cd Length: 697 Bit Score: 203.52 E-value: 4.37e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 243 QRFGEHL---IYRKQQARLMNAVY----THYTQPEKNLIIEAETGMGKTIGYLFPAAYLATPEN-PLIVSTSSILLQNQI 314
Cdd:PRK11747 15 KALQEQLpgfIPRAGQRQMIAEVAktlaGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARAEKkKLVISTATVALQEQL 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 315 ISKDIPLVNQVLQQPLQAVLVKSHRHYI----------------DLQRFKATLEQPVEQKQYAQYQmGILVWL-TKTETG 377
Cdd:PRK11747 95 VSKDLPLLLKISGLDFKFTLAKGRGRYVcprklaalasdegtqqDLLLFLDDELTPPDEEEQKLLA-RLAKALaTGKWDG 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 378 DFDELNLVrLDHPLF----TDirHRGVdfLAKDQPFYEQ-DFvrHLYRR-MAQSNVLIVNHAFLMQ--ENRRAQPLLPTS 449
Cdd:PRK11747 174 DRDHWPEP-IDDSLWqritTD--KHSC--LGRNCPYFREcPF--FKARReIDEADVVVANHDLVLAdlELGGGVVLPDPE 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 450 DYLLI-DEAQQLPQQAEGFSQH---VFDSAHFKRQFLQLNEEgLFEEIAQI-ITEDDFLQRMFSLYRNALSVLVETQEQY 524
Cdd:PRK11747 247 NLLYVlDEGHHLPDVARDHFAAsaeLKGTADWLEKLLKLLTK-LVALIMEPpLALPERLNAHCEELRELLASLNQILNLF 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 525 FRTLSIDA---------PELQVVQHRDLYDGSleqDKLHQKLSLYYQEINE---IQQQLRQRFEltndRWYAR-----QR 587
Cdd:PRK11747 326 LPAGGEEAryrfemgelPEELLELAERLAKLT---EKLLGLLEKLLNDLSEamkTGKIDIVRLE----RLLLElgralGR 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 588 IV-IARLFDFFSQMDAQEQTVTAwltwwhpryvHWLKKHPQSGNAVIEL--ADLEGHSIVESTWYQRYQHIIYLGGTLKI 664
Cdd:PRK11747 399 LEaLSKLWRLAAKEDQESGAPMA----------RWITREERDGQGDYLFhaSPIRVGDQLERLLWSRAPGAVLTSATLRS 468
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 665 PGNKEYFAHQIGLTD---VPVKTIPAFYDYSKQTRLYVIKkgLSIQQASAAEYADYLVEALVPILfDNPQPALVLFTAHE 741
Cdd:PRK11747 469 LNSFDRFQEQSGLPEkdgDRFLALPSPFDYPNQGKLVIPK--MRAEPDNEEAHTAEMAEFLPELL-EKHKGSLVLFASRR 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 742 TLKNVYDRLNKKalhYGREIVAQGTGgTREKILKKFLLA-ENG---ILLGTSSFWEGVDLPGQALKIAVVTRLPFENPKQ 817
Cdd:PRK11747 546 QMQKVADLLPRD---LRLMLLVQGDQ-PRQRLLEKHKKRvDEGegsVLFGLQSFAEGLDLPGDYLTQVIITKIPFAVPDS 621
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 505322933 818 PMVQARHAFLEAEGIDSFKEDALPKAILRLRQALGRLIRSEEDTGVMVVLDRRLLSTKYGKRMVKGLP 885
Cdd:PRK11747 622 PVEATLAEWLKSRGGNPFMEISVPDASFKLIQAVGRLIRSEQDRGRVTILDRRLLTKRYGKRLLDALP 689
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
5-164 |
2.41e-51 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 177.29 E-value: 2.41e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 5 YAVVDLETTGTDSTIDRIIQFGCVLVQDGKIINRFAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYNLLSNT 84
Cdd:COG0847 2 FVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGA 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 85 IFVAHNIYFDYHFLSNEFVRCGLPPLSIPGIDTVELSQVFLPTESSFRLGDLADSIGFRHDNPHQADSDAEVTAALFLYI 164
Cdd:COG0847 82 VLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPSYSLDALCERLGIPFDERHRALADAEATAELFLAL 161
|
|
| Helicase_C_2 |
pfam13307 |
Helicase C-terminal domain; This domain is found at the C-terminus of DEAD-box helicases. |
730-887 |
3.84e-48 |
|
Helicase C-terminal domain; This domain is found at the C-terminus of DEAD-box helicases.
Pssm-ID: 463840 [Multi-domain] Cd Length: 168 Bit Score: 168.51 E-value: 3.84e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 730 PQPALVLFTAHETLKNVYDRLNKKALHYGREIVAQGTGGTREKILKKFLLAENG-ILLGTS--SFWEGVDLPGQALKIAV 806
Cdd:pfam13307 8 PGGVLVFFPSYSYLEKVAERLKESGLEKGIEIFVQPGEGSREKLLEEFKKKGKGaVLFGVCggSFSEGIDFPGDLLRAVI 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 807 VTRLPFENPKQPMVQARHAFLEAEGIDSFKEDALPKAILRLRQALGRLIRSEEDTGVMVVLDRRLLSTKYGKRMVKGLPK 886
Cdd:pfam13307 88 IVGLPFPNPDDPVVEAKREYLDSKGGNPFNEWYLPQAVRAVNQAIGRLIRHENDYGAIVLLDSRFLTKRYGKLLPKWLPP 167
|
.
gi 505322933 887 N 887
Cdd:pfam13307 168 G 168
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
6-162 |
2.59e-47 |
|
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Pssm-ID: 176648 [Multi-domain] Cd Length: 159 Bit Score: 165.94 E-value: 2.59e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 6 AVVDLETTGTDSTIDRIIQFGCVLVQDG-KIINRFAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYNLLSNT 84
Cdd:cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGiEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 505322933 85 IFVAHNIYFDYHFLSNEFVRCGLPPLSIPGIDTVELSQVFLPTESSFRLGDL-ADSIGFRHDNPHQADSDAEVTAALFL 162
Cdd:cd06127 81 VLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLlAERYGIPLEGAHRALADALATAELLL 159
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
5-179 |
6.93e-42 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 166.94 E-value: 6.93e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 5 YAVVDLETTGTDSTIDRIIQFGCVLVQDGKIINRFAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYNLLSNT 84
Cdd:PRK00448 421 YVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGDS 500
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 85 IFVAHNIYFDYHFLSNEFVRCGLPPLSIPGIDTVELSQVFLPTESSFRLGDLADSIGFRHDNPHQADSDAEVTAALFLYI 164
Cdd:PRK00448 501 ILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELEHHHRADYDAEATAYLLIKF 580
|
170
....*....|....*
gi 505322933 165 EAIMRQLPRTTLKQI 179
Cdd:PRK00448 581 LKDLKEKGITNLDEL 595
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
5-169 |
5.80e-34 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 128.19 E-value: 5.80e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 5 YAVVDLETTGTDSTIDRIIQFGCVLVQDGKIINRFAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYNLLSNT 84
Cdd:smart00479 2 LVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 85 IFVAHN-IYFDYHFLSNEFVRCGLP-PLSIPGIDTVELSQVFLPTESSFRLGDLADSIGFRHD-NPHQADSDAEVTAALF 161
Cdd:smart00479 82 ILVAGNsAHFDLRFLKLEHPRLGIKqPPKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIqRAHRALDDARATAKLF 161
|
....*...
gi 505322933 162 LYIEAIMR 169
Cdd:smart00479 162 KKLLERLE 169
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
5-158 |
5.19e-28 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 120.02 E-value: 5.19e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 5 YAVVDLETTGTDSTIDRIIQFGCVLVQDGKIINRFAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYNLLSNT 84
Cdd:PRK07883 17 FVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEFARGA 96
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 505322933 85 IFVAHNIYFDYHFLSNEFVRCGLPPLSIPGIDTVELSQVFLPTES--SFRLGDLADSIGFRHDNPHQADSDAEVTA 158
Cdd:PRK07883 97 VLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEapNVRLSTLARLFGATTTPTHRALDDARATV 172
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
5-162 |
1.68e-26 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 111.06 E-value: 1.68e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 5 YAVVDLETTGTDSTIDRIIQFGCVLVQDGKIINRFAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYNLLSNT 84
Cdd:PRK06807 10 YVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 505322933 85 IFVAHNIYFDYHFLSNEFVRCGLPPLSIPGIDTVELSQVFLPTESSFRLGDLADSIGFRHDNpHQADSDAEVTAALFL 162
Cdd:PRK06807 90 VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSS-HNAFDDCITCAAVYQ 166
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
7-161 |
5.54e-26 |
|
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;
Pssm-ID: 395743 [Multi-domain] Cd Length: 164 Bit Score: 105.13 E-value: 5.54e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 7 VVDLETTGTDSTIDRIIQFGCVLVQDG--KIINRFAADINPDR--RISKQIQRLTHITNQQVSKAPYFEDIADTIYNLL- 81
Cdd:pfam00929 2 VIDLETTGLDPEKDEIIEIAAVVIDGGenEIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFLr 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 82 SNTIFVAHNIYFDYHFLSNEFVRCG--LPPLSIPGIDTVELSQVFLPTESSFRLGDLADSIGFRHD-NPHQADSDAEVTA 158
Cdd:pfam00929 82 KGNLLVAHNASFDVGFLRYDDKRFLkkPMPKLNPVIDTLILDKATYKELPGRSLDALAEKLGLEHIgRAHRALDDARATA 161
|
...
gi 505322933 159 ALF 161
Cdd:pfam00929 162 KLF 164
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
4-161 |
2.66e-25 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 105.87 E-value: 2.66e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 4 IYAVVDLETTGTDSTIDRIIQFGCVLVQDGKIINRF-----AADINPDrriskqIQRLTHITNQQVSKAPYFEDIADTIY 78
Cdd:PRK08517 69 VFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFesfvkAKEVPEY------ITELTGITYEDLENAPSLKEVLEEFR 142
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 79 NLLSNTIFVAHNIYFDYHFLSNEFVRCGLPPLSIPGIDTVELSQVFLPTEsSFRLGDLADSIGFRHDNPHQADSDAEVTA 158
Cdd:PRK08517 143 LFLGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESP-RYGLSFLKELLGIEIEVHHRAYADALAAY 221
|
...
gi 505322933 159 ALF 161
Cdd:PRK08517 222 EIF 224
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
5-163 |
5.92e-25 |
|
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III; This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.
Pssm-ID: 99834 [Multi-domain] Cd Length: 156 Bit Score: 101.82 E-value: 5.92e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 5 YAVVDLETTGTDStiDRIIQFGCVLVQDGKIINRFAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYNLLSNT 84
Cdd:cd06130 1 FVAIDFETANADR--ASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGS 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 85 IFVAHNIYFDYHFLSNEFVRCGLPPLSIPGIDTVELSQVFLPTESSFRLGDLADSIG--FRHdnpHQADSDAEVTAALFL 162
Cdd:cd06130 79 LVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGieLNH---HDALEDARACAEILL 155
|
.
gi 505322933 163 Y 163
Cdd:cd06130 156 A 156
|
|
| HELICc2 |
smart00491 |
helicase superfamily c-terminal domain; |
740-872 |
4.89e-24 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 214694 [Multi-domain] Cd Length: 142 Bit Score: 98.89 E-value: 4.89e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 740 HETLKNVYDRLN-KKALHYGREIVAQG-TGGTREKILKKFLLAEN---GILLGTSS--FWEGVDLPGQALKIAVVTRLPF 812
Cdd:smart00491 1 YRYLEQVVEYWKeNGILEINKPVFIEGkDSGETEELLEKYSAACEargALLLAVARgkVSEGIDFPDDLGRAVIIVGIPF 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 505322933 813 ENPKQPMVQARHAFLEAEG-IDSFKEDALPKAILRLRQALGRLIRSEEDTGVMVVLDRRLL 872
Cdd:smart00491 81 PNPDSPILRARLEYLDEKGgIRPFDEVYLFDAMRALAQAIGRAIRHKNDYGVVVLLDKRYA 141
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
7-121 |
1.80e-22 |
|
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.
Pssm-ID: 99835 [Multi-domain] Cd Length: 167 Bit Score: 94.91 E-value: 1.80e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 7 VVDLETTGTDSTI-DRIIQFGCVLVQDGKII-NRFAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYNLLSNT 84
Cdd:cd06131 3 VLDTETTGLDPREgHRIIEIGCVELINRRLTgNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIRGA 82
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 505322933 85 IFVAHNIYFDYHFLSNEFVRCGLPPLSIPG---IDTVELS 121
Cdd:cd06131 83 ELVIHNASFDVGFLNAELSLLGLGKKIIDFcrvIDTLALA 122
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
7-183 |
1.18e-19 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 89.34 E-value: 1.18e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 7 VVDLETTG-TDSTIDRIIQFGCVLVQDGKIINR-FAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYNLLSNT 84
Cdd:PRK07740 63 VFDLETTGfSPQQGDEILSIGAVKTKGGEVETDtFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYAFIGAG 142
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 85 IFVAHNIYFDYHFLSNEFVRCGLPPLSIPGIDTVELSQVFLPTESSFRLGDLADSIGFRHDNPHQADSDAEVTAALFLYI 164
Cdd:PRK07740 143 VLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRRHHALGDALMTAKLWAIL 222
|
170 180
....*....|....*....|
gi 505322933 165 EAIMRQLPRTTLKQI-ALLS 183
Cdd:PRK07740 223 LVEAQQRGITTLHDLyAALS 242
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
5-161 |
1.64e-19 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 90.53 E-value: 1.64e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 5 YAVVDLETTGTDSTIDRIIQFGCVLVQ-DGKIINRFAADINPDRRISKqiqrlTHI---TNQQVSKAPYFEDIADTIYNL 80
Cdd:PRK06063 17 WAVVDVETSGFRPGQARIISLAVLGLDaDGNVEQSVVTLLNPGVDPGP-----THVhglTAEMLEGQPQFADIAGEVAEL 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 81 LSNTIFVAHNIYFDYHFLSNEFVRCGlppLSIPgID----TVELSQVF-LPTEsSFRLGDLADSIGFRHDNPHQADSDAE 155
Cdd:PRK06063 92 LRGRTLVAHNVAFDYSFLAAEAERAG---AELP-VDqvmcTVELARRLgLGLP-NLRLETLAAHWGVPQQRPHDALDDAR 166
|
....*.
gi 505322933 156 VTAALF 161
Cdd:PRK06063 167 VLAGIL 172
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
5-162 |
2.52e-19 |
|
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA]
Pssm-ID: 129663 [Multi-domain] Cd Length: 217 Bit Score: 87.51 E-value: 2.52e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 5 YAVVDLETTGTdSTIDRIIQFGCVLVQDGK-IINRFAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYNLLSN 83
Cdd:TIGR00573 9 ETTGDNETTGL-YAGHDIIEIGAVEIINRRiTGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRG 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 84 TIFVAHNIYFDYHFLSNEFVR-CGLPPLSIPGIDTVELSQVFLPT--ESSFRLGDLADSIGFR--HDNPHQADSDAEVTA 158
Cdd:TIGR00573 88 AELVIHNASFDVGFLNYEFSKlYKVEPKTNDVIDTTDTLQYARPEfpGKRNTLDALCKRYEITnsHRALHGALADAFILA 167
|
....
gi 505322933 159 ALFL 162
Cdd:TIGR00573 168 KLYL 171
|
|
| ExoI_N |
cd06138 |
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar ... |
9-160 |
8.04e-17 |
|
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Pssm-ID: 99841 [Multi-domain] Cd Length: 183 Bit Score: 79.23 E-value: 8.04e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 9 DLETTGTDSTIDRIIQFGCVLV-QDGKIINR--FAADINPDRRISKQIQRLTHITNQQVSK--APYFEDIADtIYNLL-- 81
Cdd:cd06138 4 DYETFGLNPSFDQILQFAAIRTdENFNEIEPfnIFCRLPPDVLPSPEALIVTGITPQQLLKegLSEYEFIAK-IHRLFnt 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 82 SNTIFVAHN-IYFDYHFLSNEFVRCGLPPLSIP---------GIDTVELSQVFLPT----------ESSFRLGDLADSIG 141
Cdd:cd06138 83 PGTCIVGYNnIRFDDEFLRFAFYRNLYDPYTWEwkngnsrwdLLDVVRAYYALRPDgivwpknddgKPSFKLEDLAQANG 162
|
170
....*....|....*....
gi 505322933 142 FRHDNPHQADSDAEVTAAL 160
Cdd:cd06138 163 IEHSNAHDALSDVEATIAL 181
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
2-161 |
3.98e-16 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 79.10 E-value: 3.98e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 2 KPIYAVVDLETTGTDSTIDRIIQFGCVLVQDGKIINRFAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYNLL 81
Cdd:PRK06310 6 DTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFF 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 82 SNT-IFVAHNIYFDYHFLSNEFVRCGLPPLS--IPGIDTVELSQVF--LPTESsfrLGDLADSIGFRHDNPHQADSDAEV 156
Cdd:PRK06310 86 KEGdYIVGHSVGFDLQVLSQESERIGETFLSkhYYIIDTLRLAKEYgdSPNNS---LEALAVHFNVPYDGNHRAMKDVEI 162
|
....*
gi 505322933 157 TAALF 161
Cdd:PRK06310 163 NIKVF 167
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
7-191 |
1.48e-13 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 70.90 E-value: 1.48e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 7 VVDLETTGTDSTIdriIQFGCVLVQDGKIINRFAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIadtIYNLLSNTIF 86
Cdd:PRK07983 4 VIDTETCGLQGGI---VEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDV---IPHYYGSEWY 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 87 VAHNIYFDyhflsnefvRCGLPPLSIPGIDTVELSQVFLPtessfrlgdladsiGFRHDN------------------PH 148
Cdd:PRK07983 78 VAHNASFD---------RRVLPEMPGEWICTMKLARRLWP--------------GIKYSNmalyksrklnvqtppglhHH 134
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 505322933 149 QADSDAEVTAALFLYieaIMRqLPRTTLKQIALLSGQMGMQTS 191
Cdd:PRK07983 135 RALYDCYITAALLID---IMN-TSGWTAEEMADITGRPSLLTT 173
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
9-153 |
2.07e-13 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 70.61 E-value: 2.07e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 9 DLETTGTDSTIDRIIQfgcVLVQDGKIINRFAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYNLLSN-TIFV 87
Cdd:PRK06309 8 DTETTGTQIDKDRIIE---IAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTdNILV 84
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 505322933 88 AHN-IYFDYHFLSNEFVRCGLPPLSIPGIDTVELSQVFLPTESSFRLGDLADSIGFRHDNPHQADSD 153
Cdd:PRK06309 85 AHNnDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEENQAHRALDD 151
|
|
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
7-111 |
5.87e-11 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 63.72 E-value: 5.87e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 7 VVDLETTGTDSTI-DRIIQFGCVlvqdgKIINR------FAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYN 79
Cdd:PRK05711 8 VLDTETTGLNQREgHRIIEIGAV-----ELINRrltgrnFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLD 82
|
90 100 110
....*....|....*....|....*....|....
gi 505322933 80 LLSNTIFVAHNIYFDYHFLSNEFVR--CGLPPLS 111
Cdd:PRK05711 83 FIRGAELIIHNAPFDIGFMDYEFALlgRDIPKTN 116
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
5-165 |
9.09e-11 |
|
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.
Pssm-ID: 99836 [Multi-domain] Cd Length: 176 Bit Score: 61.47 E-value: 9.09e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 5 YAVVDLETTGTDSTIDR-----IIQFGCVLV--QDGKIINRFAADINPDR--RISKQIQRLTHITNQQVSKAPYFEDIAD 75
Cdd:cd06133 1 YLVIDFEATCWEGNSKPdypneIIEIGAVLVdvKTKEIIDTFSSYVKPVInpKLSDFCTELTGITQEDVDNAPSFPEVLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 76 TIYNLL---SNTIFVAHNIYFDYHFLSNEFVRCGLPPLSIPG--IDtveLSQVF-----LPTESSfrLGDLADSIGFRHD 145
Cdd:cd06133 81 EFLEWLgknGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRqwID---LKKEFakfygLKKRTG--LSKALEYLGLEFE 155
|
170 180
....*....|....*....|.
gi 505322933 146 -NPHQADSDAEVTAALFLYIE 165
Cdd:cd06133 156 gRHHRGLDDARNIARILKRLL 176
|
|
| SF2_C_XPD |
cd18788 |
C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases; ... |
793-870 |
3.13e-09 |
|
C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases; The xeroderma pigmentosum group D (XPD)-like family members are DEAD-box helicases belonging to superfamily (SF)2. This family includes DDX11 (also called ChlR1), a protein involved in maintaining chromosome transmission fidelity and genome stability, the TFIIH basal transcription factor complex XPD subunit, and FANCJ (also known as BRIP1), a DNA helicase required for the maintenance of chromosomal stability. Similar to SF1 helicases, SF2 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: 350175 [Multi-domain] Cd Length: 159 Bit Score: 56.84 E-value: 3.13e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 793 EGVDLPGQALKIAVVTRLPFENPKQPMVQARHAFLEAE-------GIDSFKEDALpKAIlrlRQALGRLIRSEEDTGVMV 865
Cdd:cd18788 78 EGIDFSDDLGRAVIMVGIPYPNTKDPILKLKMDDLEYLrdkglltGEDWYTFQAM-RAV---NQAIGRAIRHKNDYGAIV 153
|
....*
gi 505322933 866 VLDRR 870
Cdd:cd18788 154 LLDKR 158
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
6-210 |
2.14e-08 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 55.75 E-value: 2.14e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 6 AVVDLETTGTDSTIDRIIQfGCVLVQD--GKIINRFAADINPDRRISKQIQRLTHITNQQVSK-----APYFEDIADTIY 78
Cdd:PRK07942 9 AAFDLETTGVDPETARIVT-AALVVVDadGEVVESREWLADPGVEIPEEASAVHGITTEYARAhgrpaAEVLAEIADALR 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 79 NLL-SNTIFVAHNIYFDYHFLSNEFVRCGLPPL-SIPGIDTVELSQVFLPtessFR-----LGDLADSIGFRHDNPHQAD 151
Cdd:PRK07942 88 EAWaRGVPVVVFNAPYDLTVLDRELRRHGLPSLvPGPVIDPYVIDKAVDR----YRkgkrtLTALCEHYGVRLDNAHEAT 163
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*....
gi 505322933 152 SDAEVTAALflyIEAIMRQLPRTTLKQIALLsgqMGMQTSEYIhgilkekgpELAEDFE 210
Cdd:PRK07942 164 ADALAAARV---AWALARRFPELAALSPAEL---HELQAVWYA---------EQAASFQ 207
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
6-182 |
4.14e-08 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 55.75 E-value: 4.14e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 6 AVVDLETTGTDSTIDRIIQFGCVLVQ---DGKI---INRFAADINPDRRISKQIQRLTHITN-----QQVSKAPYFEDIA 74
Cdd:PRK09182 40 VILDTETTGLDPRKDEIIEIGMVAFEyddDGRIgdvLDTFGGLQQPSRPIPPEITRLTGITDemvagQTIDPAAVDALIA 119
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 75 DTiynllsnTIFVAHNIYFDYHFL---SNEFVR----CglpplSIPGIDTVELSqvflpTESSfRLGDLADSIGFRHDNp 147
Cdd:PRK09182 120 PA-------DLIIAHNAGFDRPFLerfSPVFATkpwaC-----SVSEIDWSARG-----FEGT-KLGYLAGQAGFFHEG- 180
|
170 180 190
....*....|....*....|....*....|....*
gi 505322933 148 HQADSDAEVTaalflyIEAIMRQLPRTTLKQIALL 182
Cdd:PRK09182 181 HRAVDDCQAL------LELLARPLPETGQPPLAEL 209
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
5-184 |
3.47e-07 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 53.25 E-value: 3.47e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 5 YAVVDLETTGTDStiDRIIQFGCVLVQDGKIINRFAADINPDRRISKQIQRLTH-ITNQQVSKAPYFEDIADTIYNLLSN 83
Cdd:PRK06195 3 FVAIDFETANEKR--NSPCSIGIVVVKDGEIVEKVHYLIKPKEMRFMPINIGIHgIRPHMVEDELEFDKIWEKIKHYFNN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 84 TIFVAHNIYFDYHFLSNEFVRCGLPPLSIPGIDTVELSQVFLPTESSFRLGDLADSIG--FRHdnpHQADSDAEVTAALF 161
Cdd:PRK06195 81 NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFLGyeFKH---HDALADAMACSNIL 157
|
170 180
....*....|....*....|...
gi 505322933 162 LyieAIMRQLPRTTLKQIALLSG 184
Cdd:PRK06195 158 L---NISKELNSKDINEISKLLG 177
|
|
| Csf4_U |
cd09708 |
CRISPR/Cas system-associated DinG family helicase Csf4; CRISPR (Clustered Regularly ... |
254-857 |
7.62e-07 |
|
CRISPR/Cas system-associated DinG family helicase Csf4; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DinG family DNA helicase
Pssm-ID: 187839 [Multi-domain] Cd Length: 632 Bit Score: 53.05 E-value: 7.62e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 254 QQARLMNAVYTHYTQPeKNLIIEAETGMGKTIGYLFPAAYLAT--PENPLIVSTSSILLQNQIISKDIPLVNQVLQQPLQ 331
Cdd:cd09708 1 EQALFYRNCLTSLRQK-RIGMLEASTGVGKTLAMIMAALTMLKerPDQKIAIAVPTLALMGQLWSELERLTAEGLAGPVQ 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 332 AVLVKSHRHYIDLQRFKATLEQPveqKQYAQYQMGILVWLTKTEtgdfdelnlVRLDHPLFTdiRHRGVDFLAKDQPFYE 411
Cdd:cd09708 80 AGFFPGSQEFVSPGALQELLDQS---DGPGDKDAVVRLWMGQGG---------PRKVAPLFN--RMRDVTLLIHDTADIR 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 412 Q-DFVRHLYRRMAQSNVLIVNHAFL--MQENRRAQPLLPTSDYLLIDEAQQ---LPQQAEGFSQHVFDSAHFKRQflQLN 485
Cdd:cd09708 146 GyVSYREQWDSLPRCSAMSRAPTKMasMTHDLKALATLNPQDFVTEDEEDKrwvTSLVESREYYARKSRILACTH--TML 223
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 486 EEGLFEEIAQIITED--DFLQRMFSLYRNALSV------LVETQEQYFRTLSIDAPELQVVQHRDLYDGSLEQDklhQKL 557
Cdd:cd09708 224 KWGLLPQPDILIVDEahLFEQNISRVYSNALSLrmlrfhLEVSHRKTGAIGSAVVAAVSAVSHRLRQVSALGDG---QTL 300
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 558 SLyyQEINEIQQQLRQRFELTNDRWYARQRIVIARLFDFFSQMDAQEQTVTAWLTWWHPRYVHW--LKKHPQSGNAVIEL 635
Cdd:cd09708 301 CL--DAGNKELETLFADLDAALEIKSTPNKKALSVVKDVKKARIILDNAITAIQGKQSTVYLQFspDRRFPSLIVGREDL 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 636 ADLEGhsiveSTWYQRYQHIIYLGGTLKIP----GNKEYFAHQI-----GLTDVPV--------KTIPAFYDYSKQTRLY 698
Cdd:cd09708 379 GKVMG-----GLWKDVTHGAIIVSATLYLPdrfgQMSCDYLKRVlslplSRLDTPSpivapwvrNLIPHLHVPNAKARFL 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 699 VIKKGLSIQQASAAeYADYL---VEALVPILFDNPQPALVLFTAHETLKNVYDRLNKKALHygrEIVAQGTGGTREKILK 775
Cdd:cd09708 454 LSRPVGKTEQGDAN-LAGWLenvSLSTAAILRKAQGGTLVLTTAFSHISAIGQLVELGIPA---EIVIQSEKNRLASAEQ 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 776 KFLLAENG----ILLGTSSFWEGVDL--------PGQALKIAVVTRLPFENPKQPMVQARhafleAEgidsfKEDALPK- 842
Cdd:cd09708 530 QFLALYANgiqpVLIAAGGAWTGIDLhdpsvspdKDNLLTDLIITCAPFGLNRSLSMLKR-----IR-----KTSVRPEi 599
|
650
....*....|....*...
gi 505322933 843 ---AILRLRQALGRLIRS 857
Cdd:cd09708 600 ineSLMMLRQGLGRLVRH 617
|
|
| rad3 |
TIGR00604 |
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are ... |
714-886 |
3.41e-06 |
|
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. 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: 273169 [Multi-domain] Cd Length: 705 Bit Score: 50.87 E-value: 3.41e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 714 YADYLVEaLVPILfdnPQPALVLFTAHETLKNV---------YDRLNKKALHYGREIVAQGTGGTREKILKKFLLAENGI 784
Cdd:TIGR00604 510 LGELLVE-FSKII---PDGIVVFFPSYSYLENIvstwkemgiLENIEKKKLIFVETKDAQETSDALERYKQAVSEGRGAV 585
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 785 LL----GTSSfwEGVDLPGQALKIAVVTRLPFENPKQPMVQARHAFL-----EAEGIDSFKEDALPKAilrlRQALGRLI 855
Cdd:TIGR00604 586 LLsvagGKVS--EGIDFCDDLGRAVIMVGIPYEYTESRILLARLEFLrdqypIRENQDFYEFDAMRAV----NQAIGRVI 659
|
170 180 190
....*....|....*....|....*....|..
gi 505322933 856 RSEEDTGVMVVLDRRllstkYGKRMVKG-LPK 886
Cdd:TIGR00604 660 RHKDDYGSIVLLDKR-----YARSNKRKkLPK 686
|
|
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
8-161 |
7.12e-06 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 48.38 E-value: 7.12e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 8 VDLETTGTDSTIDRIIQFGCVLVQDGKIINRFAAD--INPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYNLLSNTI 85
Cdd:PRK09146 52 LDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHwvVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEALAGKV 131
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 86 FVAHniyfdYHFLSNEFVRCGL-----PPLSIPGIDTVELSQVFLPTES-------------SFRLGDLADSIGFRHDNP 147
Cdd:PRK09146 132 VVVH-----YRRIERDFLDQALrnrigEGIEFPVIDTMEIEARIQRKQAgglwnrlkgkkpeSIRLADSRLRYGLPAYSP 206
|
170
....*....|....
gi 505322933 148 HQADSDAEVTAALF 161
Cdd:PRK09146 207 HHALTDAIATAELL 220
|
|
| RNaseT |
cd06134 |
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ... |
7-164 |
3.99e-05 |
|
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Pssm-ID: 99837 [Multi-domain] Cd Length: 189 Bit Score: 45.36 E-value: 3.99e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 7 VVDLETTGTDSTIDRIIQFGCVLVQ---DG--KIINRFAADINP------DRRISKQIQ-RLTHITNQQVSKAPYFEDIA 74
Cdd:cd06134 9 VVDVETGGFNPQTDALLEIAAVTLEmdeQGnlYPDETFHFHILPfeganlDPAALEFNGiDPFHPFRFAVDEKEALKEIF 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 75 DTIYNLLSNT-----IFVAHNIYFDYHFLSNEFVRCGLP-----PLSIpgIDTVELSQVFLPTESSFRLGDLADsIGFRH 144
Cdd:cd06134 89 KPIRKALKAQgctraILVGHNAHFDLGFLNAAVARCKIKrnpfhPFST--FDTATLAGLAYGQTVLAKACQAAG-IEFDN 165
|
170 180
....*....|....*....|
gi 505322933 145 DNPHQADSDAEVTAALFLYI 164
Cdd:cd06134 166 KEAHSALYDTQKTAELFCKI 185
|
|
| PRK06722 |
PRK06722 |
exonuclease; Provisional |
22-162 |
2.03e-04 |
|
exonuclease; Provisional
Pssm-ID: 180670 [Multi-domain] Cd Length: 281 Bit Score: 44.27 E-value: 2.03e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505322933 22 IIQFGCVLVQDG--KIINRFAADINPDRRISKQIQRLTHITNQQVSKAPYFEDIADTIYNLL-SNTIFVAHNIYfDYHFL 98
Cdd:PRK06722 27 IVDIGAVKIEAStmKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQIIEKFIQFIgEDSIFVTWGKE-DYRFL 105
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 505322933 99 SNEfvrCGLPPLSIPGIDT---VELSQ-VFLPTESSFR----LGDLADSIGFRHDNP-HQADSDAEVTAALFL 162
Cdd:PRK06722 106 SHD---CTLHSVECPCMEKerrIDLQKfVFQAYEELFEhtpsLQSAVEQLGLIWEGKqHRALADAENTANILL 175
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
252-313 |
2.67e-03 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 40.17 E-value: 2.67e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 505322933 252 RKQQARLMNAVYTHYtqpeKNLIIEAETGMGKTIGYLFPAAYLATPENP---LIVSTSSILLQNQ 313
Cdd:smart00487 10 RPYQKEAIEALLSGL----RDVILAAPTGSGKTLAALLPALEALKRGKGgrvLVLVPTRELAEQW 70
|
|
| |
