|
Name |
Accession |
Description |
Interval |
E-value |
| dinG_rel |
TIGR01407 |
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ... |
5-896 |
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: 1146.46 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 5 TYAVVDLETTGNQLDFDDIIQIGITFVRNNQIIDTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKIKD 84
Cdd:TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLLED 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 85 CIFVAHNVDFDLNFIKKAFKDCNIQYRPKKVIDTLEIFKIAFPTDKSYQLSELAEAHGINLANAHRADEDAATTAKLMIL 164
Cdd:TIGR01407 81 GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHENPHRADSDAQATAELLLL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 165 AFEKFEKLPLDTLKQLYYLSKQLKYDLYDIFFEMVRQYDAKPLDKSYEKFEQIIYRKQVDFKKPTTNYNgSLKSLYSKAV 244
Cdd:TIGR01407 161 LFEKMEKLPLDTLEQLLELSDQLLYESYDIIQETYRQYKIKPAPKSYEVVEQIAYRKQVASKKPETNYN-TLSSLFSKNI 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 245 DQLGLTYRPQQLYLAETILDQLMHSEKAMIEASLGSGKSLAYLLAALMYNIeTGKHVMISTNTKLLQSQLLEKDIPAMNE 324
Cdd:TIGR01407 240 DRLGLEYRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI-TEKPVVISTNTKVLQSQLLEKDIPLLNE 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 325 ALNFKINALLIKSKSDYISLGLISQILKDDTSNYEVNILKMQLLIWITETPSGDIQELNLKGGQKMYFDQKIET---YVP 401
Cdd:TIGR01407 319 ILNFKINAALIKGKSNYLSLGKFSQILKDNTDNYEFNIFKMQVLVWLTETETGDLDELNLKGGNKMFFAQVRHDgnlSKK 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 402 AR-HDVHYYNFIKRNAQNIQIGITNHAHLIHSDVEN-SIYQLFDDCIVDEAHRLPDYALNQVTNELSYADIKYQLGLIGK 479
Cdd:TIGR01407 399 DLfYEVDFYNRAQKNAEQAQILITNHAYLITRLVDNpELFPSFRDLIIDEAHHLPDIAENQLQEELDYADIKYQIDLIGK 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 480 NENEKLLKAIDQLEKQRILEKLdiapidifglkasmneihelneqlfstiftiindsdvydddihrfhnvFTFETKDILK 559
Cdd:TIGR01407 479 GENEQLLKRIQQLEKQEILEKL------------------------------------------------FDFETKDILK 510
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 560 DLHAIIDKLNKTLEIFNGISHKTVKSLRKQLLYLKDKFKNIEQSLKAGHTSFISIKNLSQKSTIRLYVKDYAVKDVLTKQ 639
Cdd:TIGR01407 511 DLQAILDKLNKLLQIFSELSHKTVDQLRKFDLALKDDFKNIEQSLKEGHTSWISIENLQQKSTIRLYIKDYEVGDVLTKR 590
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 640 VLEKFKSLIFISGTLKFNHSFEAFKQLFN-KDVRFNTFEvNTSLQSAKNTSVFIPSDVASYQYKNIDEYVASIVSYIIEY 718
Cdd:TIGR01407 591 LLPKFKSLIFTSATLKFSHSFESFPQLLGlTDVHFNTIE-PTPLNYAENQRVLIPTDAPAIQNKSLEEYAQEIASYIIEI 669
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 719 TTITSSKCLVLFTSYKMMHMVQDMLNELPEFEDYVVLTQQQN-QNYKIVQQFNNFDKAILLGTSTFFEGFDFQANGIKCV 797
Cdd:TIGR01407 670 TAITSPKILVLFTSYEMLHMVYDMLNELPEFEGYEVLAQGINgSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCL 749
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 798 MIAKLPFMN-KHN--AKYWLMDS-EFTSTFKEYVLPDAVTRFRQGLGRLIRNENDRGIIVSFDDRLINSNYKNFFEQTLE 873
Cdd:TIGR01407 750 VIPRLPFANpKHPltKKYWQKLEqEGKNPFYDYVLPMAIIRLRQALGRLIRRENDRGSIVILDRRLVGKRYGKRFEKSLP 829
|
890 900
....*....|....*....|...
gi 1006182455 874 NYRQKKGDIqqFGKLLRQIQKKK 896
Cdd:TIGR01407 830 EYLQVKGDI--LGELLEAIKEFL 850
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
3-872 |
0e+00 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 576.13 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 3 MATYAVVDLETTGNQL-DFDDIIQIGITFVRNNQIIDTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDK 81
Cdd:PRK08074 2 SKRFVVVDLETTGNSPkKGDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVEL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 82 IKDCIFVAHNVDFDLNFIKKAFKDCNIQYRPKKVIDTLEIFKIAFPTDKSYQLSELAEAHGINLANAHRADEDAATTAKL 161
Cdd:PRK08074 82 LEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEELGLEHDQPHRADSDAEVTAEL 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 162 MILAFEKFEKLPLDTLKQLYYLSKQLKYDLYDIFFE--MVRQYDAKPLDKSYEKFEQIIYRKQVDFKKPTTNYNGSLKSL 239
Cdd:PRK08074 162 FLQLLNKLERLPLVTLQQLRRLSDHLKSDIAELLDEniLKKMMHGKPLDEEFDEYRGIALRKREVEKNLEETCRSDFDAF 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 240 YSKAVDQL-----GLTYRPQQLYLAETILDQLMHSEKAMIEASLGSGKSLAYLLAALMYNIETGKHVMISTNTKLLQSQL 314
Cdd:PRK08074 242 LEKTEEKLslampKYEKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKKEEPVVISTYTIQLQQQL 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 315 LEKDIPAMNEALNFKINALLIKSKSDYISLGLISQILKDDTSNYEVNILKMQLLIWITETPSGDIQELNLKGGQKMYFDQ 394
Cdd:PRK08074 322 LEKDIPLLQKIFPFPVEAALLKGRSHYLCLRKFEQALQEEDDNYDVALTKAQLLVWLTETETGDLDELNLPSGGKLLWNR 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 395 -KIETYVPA-RHDVHY----YNFIKRNAQNIQIGITNHAHLIHSDV-ENSIYQLFDDCIVDEAHRLPDYALNQVTNELSY 467
Cdd:PRK08074 402 iASDGESDGgKQSPWFsrcfYQRAKNRAKFADLVITNHALLLTDLTsEEPLLPSYEHIIIDEAHHFEEAASRHLGEQFSY 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 468 ADIKYQLGLIGKNENEKLLKAIDQLEKQRILEkldiAPIDIFGLKASMNEIHELNEQLFSTIFTIINDSDVYDDDIHRFH 547
Cdd:PRK08074 482 MSFQLLLSRLGTLEEDGLLSKLAKLFKKSDQA----SRSSFRDLDESLKELKFEADELFQMLRSFVLKRKKQEQNGRLIY 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 548 NVFTFETKD---------------ILKDLHAIIDKLNKTL-EIFNGISHkTVKSLRKQLLYLKDKFKNIEQSL---KAGH 608
Cdd:PRK08074 558 RYNTESEKGklwdaitelanrlcyDLRDLLTLLEAQKKELqEKMESESA-FLTGEYAHLIDLLEKMAQLLQLLfeeDPDY 636
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 609 TSFISIKNLSQKSTIRLYVKDYAVKDVLTKQVLEKFKSLIFISGTLKFNHSFE-AFKQLFNKDVRFNTFEVNTSLQSAKN 687
Cdd:PRK08074 637 VTWIEIDAKGAINATRLYAQPVEVAERLADEFFAKKKSVILTSATLTVNGSFDyIIERLGLEDFYPRTLQIPSPFSYEEQ 716
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 688 TSVFIPSDVASYQYKNIDEYVASIVSYIIEYTTITSSKCLVLFTSYKMMHMVQDMLNELPEFEDYVVLTQ--QQNQNYKI 765
Cdd:PRK08074 717 AKLMIPTDMPPIKDVPIEEYIEEVAAYIAKIAKATKGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLLAQgvSSGSRARL 796
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 766 VQQFNNFDKAILLGTSTFFEGFDFQANGIKCVMIAKLPFMNKHN----AKYWLMDSEFTSTFKEYVLPDAVTRFRQGLGR 841
Cdd:PRK08074 797 TKQFQQFDKAILLGTSSFWEGIDIPGDELSCLVIVRLPFAPPDQpvmeAKSEWAKEQGENPFQELSLPQAVLRFKQGFGR 876
|
890 900 910
....*....|....*....|....*....|.
gi 1006182455 842 LIRNENDRGIIVSFDDRLINSNYKNFFEQTL 872
Cdd:PRK08074 877 LIRTETDRGTVFVLDRRLTTTSYGKYFLESL 907
|
|
| DinG |
COG1199 |
Rad3-related DNA helicase DinG [Replication, recombination and repair]; |
248-885 |
7.32e-111 |
|
Rad3-related DNA helicase DinG [Replication, recombination and repair];
Pssm-ID: 440812 [Multi-domain] Cd Length: 629 Bit Score: 354.23 E-value: 7.32e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 248 GLTYRPQQLYLAETILDQLMHSEKAMIEASLGSGKSLAYLLAALMYNIETGKHVMISTNTKLLQSQLLEKDIPAMNEALN 327
Cdd:COG1199 12 GFEPRPGQREMAEAVARALAEGRHLLIEAGTGTGKTLAYLVPALLAARETGKKVVISTATKALQEQLVEKDLPLLRKALG 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 328 FKINALLIKSKSDYISLGLISQILKDDTSNYEVNILKMQLLIWITETPSGDIQELNLKGGQKMYF------DQKIETYVP 401
Cdd:COG1199 92 LPLRVALLKGRSNYLCLRRLEQALQEGDDLDDEELLLARILAWASETWTGDRDELPLPEDDELWRqvtsdaDNCLGRRCP 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 402 ARHDVHYYnFIKRNAQNIQIGITNHAHL-IHSDVENSIyqLFDDC--IVDEAHRLPDYALNQVTNELSYADIKYQLGLIG 478
Cdd:COG1199 172 YYGVCPYE-LARRLAREADVVVVNHHLLfADLALGEEL--LPEDDvlIIDEAHNLPDRARDMFSAELSSRSLLRLLRELR 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 479 KN-ENEKLLKAIDQLEKqrilekldiapidifgLKASMNEIHELNEQLFSTIFTiindsdvyDDDIHRFHNVFTFETKDI 557
Cdd:COG1199 249 KLgLRPGLKKLLDLLER----------------LREALDDLFLALEEEEELRLA--------LGELPDEPEELLEALDAL 304
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 558 LKDLHAIIDKLNKTLEIFNGIshktvKSLRKQLLYLKDKFKNIEQSLKAGHTSF-ISIKNlsqkSTIRLYVKDYAVKDVL 636
Cdd:COG1199 305 RDALEALAEALEEELERLAEL-----DALLERLEELLFALARFLRIAEDEGYVRwLEREG----GDVRLHAAPLDPADLL 375
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 637 TKQVLEKFKSLIFISGTLKFNHSFEAFKQL--FNKDVRfnTFEVNTSLQSAKNTSVFIPSDVAsyQYKNIDEYVASIVSY 714
Cdd:COG1199 376 RELLFSRARSVVLTSATLSVGGPFDYFARRlgLDEDAR--TLSLPSPFDYENQALLYVPRDLP--RPSDRDGYLEAIAEA 451
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 715 IIEYTTITSSKCLVLFTSYKMMHMVQDmlnELPEFEDYVVLTQQQNQNYKIVQQFNNFDKAILLGTSTFFEGFDFQANGI 794
Cdd:COG1199 452 IAELLEASGGNTLVLFTSYRALEQVAE---LLRERLDIPVLVQGDGSREALLERFREGGNSVLVGTGSFWEGVDLPGDAL 528
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 795 KCVMIAKLPFMN----KHNAKYWLMDSEFTSTFKEYVLPDAVTRFRQGLGRLIRNENDRGIIVSFDDRLINSNYKNFFEQ 870
Cdd:COG1199 529 SLVIIVKLPFPPpddpVLEARREALEARGGNGFMYAYLPPAVIKLKQGAGRLIRSEEDRGVVVLLDRRLLTKRYGKRFLD 608
|
650
....*....|....*.
gi 1006182455 871 TLENYRQKK-GDIQQF 885
Cdd:COG1199 609 SLPPFRRTRpEELRAF 624
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
6-885 |
1.01e-96 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 321.64 E-value: 1.01e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 6 YAVVDLETTGNQLDfDDIIQIGITFVRNNQIIDTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKIKDC 85
Cdd:PRK07246 9 YAVVDLEATGAGPN-ASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDC 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 86 IFVAHNVDFDLNFIKKA--FKDCNIQyRPKkvIDTLEIFKIAFPTDKSYQLSELAEAHGINLANAHRADEDAATTAKLMI 163
Cdd:PRK07246 88 IFVAHNVKFDANLLAEAlfLEGYELR-TPR--VDTVELAQVFFPTLEKYSLSHLSRELNIDLADAHTAIADARATAELFL 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 164 LAFEKFEKLPLDTLKQLYYLSKQLKYDLYDIFFEMVRQydAKPLD-KSYEKFEQIIYRKQVDFKKPTtnyngSLKSLYSK 242
Cdd:PRK07246 165 KLLQKIESLPKECLERLLEYADSLLFESYLVIEEALAN--AKPYSsPDYIKVQGIVLKKTAASLKPR-----KLSQDFSI 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 243 AVDQLGLTYRPQQLYLAETILDQLMHSEKAMIEASLGSGKSLAYLLAALmyNIETGKHVMISTNTKLLQSQLLEKDIPAM 322
Cdd:PRK07246 238 NIALLGLEERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLL--AQSDQRQIIVSVPTKILQDQIMAEEVKAI 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 323 NEAlnFKINALLIKSKSDYISLGLISQILKDDTSNYEVNILKMQLLIWITETPSGDIQELNLKGGQKMYFDQ-KIETYVP 401
Cdd:PRK07246 316 QEV--FHIDCHSLKGPQNYLKLDAFYDSLQQNDDNRLVNRYKMQLLVWLTETETGDLDEIKQKQRYAAYFDQlKHDGNLS 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 402 ARHDVHYYNFIKRN---AQNIQIGITNHAHLIHSDVENSIYQLFDDCIVDEAHRLPdYALNQVTNElsYADIKYQLGLIg 478
Cdd:PRK07246 394 QSSLFYDYDFWKRSyekAKTARLLITNHAYFLTRVQDDKDFARNKVLVFDEAQKLM-LQLEQLSRH--QLNITSFLQTI- 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 479 knenEKLLKAIDQLEKQRILEKLDiapidiFGLKASMNEIHELNEQLFSTiftiindsdvydDDIHRFHNVFTFETKDIL 558
Cdd:PRK07246 470 ----QKALSGPLPLLQKRLLESIS------FELLQLSEQFYQGKERQLIH------------DSLSRLHQYFSELEVAGF 527
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 559 KDLHAiidkLNKTLEIFNGIShkTVKSLRKQLLYLKdkfknieqSLKAGHTSFisiknlsqkstirlyvkdyavkdvltK 638
Cdd:PRK07246 528 QELQA----FFATAEGDYWLE--SEKQSEKRVTYLN--------SASKAFTHF--------------------------S 567
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 639 QVLEKFKSLIFISGTLKFNHSFEAFKQLFNKDVRFNTFEVNTSlqsaKNTSVFIPSDVASYQYKNIDEYVASIVSYIIEY 718
Cdd:PRK07246 568 QLLPETCKTYFVSATLQISPRVSLADLLGFEEYLFHKIEKDKK----QDQLVVVDQDMPLVTETSDEVYAEEIAKRLEEL 643
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 719 TTItSSKCLVLFTSYKMMHMVQDMLNELPEFEdyvvLTQQQNQN-YKIVQQFNNFDKAILLGTSTFFEGFDFQANGIKCV 797
Cdd:PRK07246 644 KQL-QQPILVLFNSKKHLLAVSDLLDQWQVSH----LAQEKNGTaYNIKKRFDRGEQQILLGLGSFWEGVDFVQADRMIE 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 798 MIAKLPFMNKHNAKYWLMDSEFT----STFKEYVLPDAVTRFRQGLGRLIRNENDRGIIVSFDDRLINSNYKNFFEQTL- 872
Cdd:PRK07246 719 VITRLPFDNPEDPFVKKMNQYLLqegkNPFYDYFLPMTILRLKQAIGRTMRREDQKSAVLILDRRILTKSYGKQILASLa 798
|
890 900
....*....|....*....|
gi 1006182455 873 -------ENYRQKKGDIQQF 885
Cdd:PRK07246 799 eeflisqQNFSDVLVEIDRF 818
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
3-178 |
1.68e-66 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 220.02 E-value: 1.68e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 3 MATYAVVDLETTGNQLDFDDIIQIGITFVRNNQIIDTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKI 82
Cdd:COG2176 7 DLTYVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLEFL 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 83 KDCIFVAHNVDFDLNFIKKAFKDCNIQYRPkKVIDTLEIFKIAFPTDKSYQLSELAEAHGINLANAHRADEDAATTAKLM 162
Cdd:COG2176 87 GDAVLVAHNASFDLGFLNAALKRLGLPFDN-PVLDTLELARRLLPELKSYKLDTLAERLGIPLEDRHRALGDAEATAELF 165
|
170
....*....|....*.
gi 1006182455 163 ILAFEKFEKLPLDTLK 178
Cdd:COG2176 166 LKLLEKLEEKGITTLR 181
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
6-163 |
2.46e-50 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 174.60 E-value: 2.46e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 6 YAVVDLETTGNQLDFDDIIQIGITFVRNNQIIDTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKIKDC 85
Cdd:COG0847 2 FVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGA 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1006182455 86 IFVAHNVDFDLNFIKKAFKDCNIQYRPKKVIDTLEIFKIAFPTDKSYQLSELAEAHGINLANAHRADEDAATTAKLMI 163
Cdd:COG0847 82 VLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPSYSLDALCERLGIPFDERHRALADAEATAELFL 159
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
7-163 |
1.08e-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: 166.71 E-value: 1.08e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 7 AVVDLETTGNQLDFDDIIQIGITFVRNN-QIIDTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKIKDC 85
Cdd:cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGiEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1006182455 86 IFVAHNVDFDLNFIKKAFKDCNIQYRPKKVIDTLEIFKIAFPTDKSYQLSELAEAH-GINLANAHRADEDAATTAKLMI 163
Cdd:cd06127 81 VLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERyGIPLEGAHRALADALATAELLL 159
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
4-186 |
3.82e-43 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 170.79 E-value: 3.82e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 4 ATYAVVDLETTGNQLDFDDIIQIGITFVRNNQIIDTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKIK 83
Cdd:PRK00448 419 ATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCG 498
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 84 DCIFVAHNVDFDLNFIKKAFKDCNIQYRPKKVIDTLEIFKIAFPTDKSYQLSELAEAHGINLANAHRADEDAATTAKLMI 163
Cdd:PRK00448 499 DSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELEHHHRADYDAEATAYLLI 578
|
170 180
....*....|....*....|...
gi 1006182455 164 LAFEKFEKLPLDTLKQLYYLSKQ 186
Cdd:PRK00448 579 KFLKDLKEKGITNLDELNKKLGS 601
|
|
| Helicase_C_2 |
pfam13307 |
Helicase C-terminal domain; This domain is found at the C-terminus of DEAD-box helicases. |
717-875 |
2.07e-42 |
|
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: 152.33 E-value: 2.07e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 717 EYTTITSSKCLVLFTSYKMMHMVQDMLNELPEFEDYVVLTQQ-QNQNYKIVQQFNNFDK-AILLGTS--TFFEGFDFQAN 792
Cdd:pfam13307 2 RLLKVIPGGVLVFFPSYSYLEKVAERLKESGLEKGIEIFVQPgEGSREKLLEEFKKKGKgAVLFGVCggSFSEGIDFPGD 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 793 GIKCVMIAKLPFMNKH----NAKYWLMDSEFTSTFKEYVLPDAVTRFRQGLGRLIRNENDRGIIVSFDDRLINSNYKNFF 868
Cdd:pfam13307 82 LLRAVIIVGLPFPNPDdpvvEAKREYLDSKGGNPFNEWYLPQAVRAVNQAIGRLIRHENDYGAIVLLDSRFLTKRYGKLL 161
|
....*..
gi 1006182455 869 EQTLENY 875
Cdd:pfam13307 162 PKWLPPG 168
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
5-163 |
8.81e-35 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 130.50 E-value: 8.81e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 5 TYAVVDLETTGNQLDFDDIIQIGITFVRNNQIIDTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKIKD 84
Cdd:smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 85 CIFVAHN-VDFDLNFIKKAFKDCNIQYRPK-KVIDTLEIFKIAFPTDKSYQLSELAEAHGI-NLANAHRADEDAATTAKL 161
Cdd:smart00479 81 RILVAGNsAHFDLRFLKLEHPRLGIKQPPKlPVIDTLKLARATNPGLPKYSLKKLAKRLLLeVIQRAHRALDDARATAKL 160
|
..
gi 1006182455 162 MI 163
Cdd:smart00479 161 FK 162
|
|
| dinG |
PRK11747 |
ATP-dependent DNA helicase DinG; Provisional |
240-864 |
6.59e-29 |
|
ATP-dependent DNA helicase DinG; Provisional
Pssm-ID: 236966 [Multi-domain] Cd Length: 697 Bit Score: 123.78 E-value: 6.59e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 240 YSKAVDQL-GLTYRPQQLYLAETI---LDQLMHSEKAM--IEASLGSGKSLAYLLAALMYNIETGKHVMISTNTKLLQSQ 313
Cdd:PRK11747 14 YKALQEQLpGFIPRAGQRQMIAEVaktLAGEYLKDGRIlvIEAGTGVGKTLSYLLAGIPIARAEKKKLVISTATVALQEQ 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 314 LLEKDIPAMNEA--LNFKinALLIKSKSDYISLGLISQILKDDTSNYEvnilkmQLLIWITETPSGDIQELNLKggQKMY 391
Cdd:PRK11747 94 LVSKDLPLLLKIsgLDFK--FTLAKGRGRYVCPRKLAALASDEGTQQD------LLLFLDDELTPPDEEEQKLL--ARLA 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 392 FD----------------------QKIET---YVPARHdVHYYN----FIKRNA-QNIQIGITNHAHL----------IH 431
Cdd:PRK11747 164 KAlatgkwdgdrdhwpepiddslwQRITTdkhSCLGRN-CPYFRecpfFKARREiDEADVVVANHDLVladlelgggvVL 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 432 SDVENSIYqlfddcIVDEAHRLPDYALNQVTnelSYADIKYQLGLIgknenEKLLKAIDQLEKQrILEKLDIAPIDIFGL 511
Cdd:PRK11747 243 PDPENLLY------VLDEGHHLPDVARDHFA---ASAELKGTADWL-----EKLLKLLTKLVAL-IMEPPLALPERLNAH 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 512 KASMNE-IHELNEQLfstiftIINDSDVYDDDIHRFhnvftfETKDILKDLHAIIDKLNKTLEIFNGISHKTVKSLRKql 590
Cdd:PRK11747 308 CEELRElLASLNQIL------NLFLPAGGEEARYRF------EMGELPEELLELAERLAKLTEKLLGLLEKLLNDLSE-- 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 591 lYLKDKFKNIEQSLKA-GHTSFI--SIKNLSQksTIRLYVKDYAVKDV-----LTKQVLEKFKSLIF------------- 649
Cdd:PRK11747 374 -AMKTGKIDIVRLERLlLELGRAlgRLEALSK--LWRLAAKEDQESGApmarwITREERDGQGDYLFhaspirvgdqler 450
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 650 -----------ISGTLKFNHSFEAFKQ---LFNKD-VRFntfevnTSLQS----AKNTSVFIPSDVASYqyKNIDEYVAS 710
Cdd:PRK11747 451 llwsrapgavlTSATLRSLNSFDRFQEqsgLPEKDgDRF------LALPSpfdyPNQGKLVIPKMRAEP--DNEEAHTAE 522
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 711 IVSYIIEYttITSSK-CLVLFTSYKMMhmvQDMLNELPEFEDYVVLTQQQNQNYKIVQQ----FNNFDKAILLGTSTFFE 785
Cdd:PRK11747 523 MAEFLPEL--LEKHKgSLVLFASRRQM---QKVADLLPRDLRLMLLVQGDQPRQRLLEKhkkrVDEGEGSVLFGLQSFAE 597
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 786 GFDFQANGIKCVMIAKLPFMnkhnakywLMDSEFTSTFKEYV------------LPDAVTRFRQGLGRLIRNENDRGIIV 853
Cdd:PRK11747 598 GLDLPGDYLTQVIITKIPFA--------VPDSPVEATLAEWLksrggnpfmeisVPDASFKLIQAVGRLIRSEQDRGRVT 669
|
730
....*....|.
gi 1006182455 854 SFDDRLINSNY 864
Cdd:PRK11747 670 ILDRRLLTKRY 680
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
8-186 |
4.76e-28 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 113.61 E-value: 4.76e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 8 VVDLETTGnqldF-----DDIIQIGITFVRNNQII-DTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDK 81
Cdd:PRK07740 63 VFDLETTG----FspqqgDEILSIGAVKTKGGEVEtDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYAF 138
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 82 IKDCIFVAHNVDFDLNFIKKAFKDcniQYRPK---KVIDTLEIFKIAFPTDKSYQLSELAEAHGINLANAHRADEDAATT 158
Cdd:PRK07740 139 IGAGVLVAHHAGHDKAFLRHALWR---TYRQPfthRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRRHHALGDALMT 215
|
170 180
....*....|....*....|....*....
gi 1006182455 159 AKLMILAFEKFEKLPLDTLKQLY-YLSKQ 186
Cdd:PRK07740 216 AKLWAILLVEAQQRGITTLHDLYaALSRC 244
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
5-169 |
8.03e-27 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 110.50 E-value: 8.03e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 5 TYAVVDLETTGNQLDFDDIIQIGITFVRNNQIIDTYHSMIRTNlEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKIKD 84
Cdd:PRK08517 69 VFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAK-EVPEYITELTGITYEDLENAPSLKEVLEEFRLFLGD 147
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 85 CIFVAHNVDFDLNFIKKAFKDCNIQYRPKKVIDTLEIFKIAFPTDKsYQLSELAEAHGINLANAHRADEDAATTAKLMIL 164
Cdd:PRK08517 148 SVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPR-YGLSFLKELLGIEIEVHHRAYADALAAYEIFKI 226
|
....*
gi 1006182455 165 AFEKF 169
Cdd:PRK08517 227 CLLNL 231
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
6-163 |
2.85e-26 |
|
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: 105.67 E-value: 2.85e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 6 YAVVDLETTGNqlDFDDIIQIGITFVRNNQIIDTYHSMIRtnleiPP------FIQaLTSIEENMLQQAPYFNQVAQEIY 79
Cdd:cd06130 1 FVAIDFETANA--DRASACSIGLVKVRDGQIVDTFYTLIR-----PPtrfdpfNIA-IHGITPEDVADAPTFPEVWPEIK 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 80 DKIKDCIFVAHNVDFDLNFIKKAFKDCNIQYRPKKVIDTLEIFKIAFPTDKSYQLSELAEAHGINLaNAHRADEDAATTA 159
Cdd:cd06130 73 PFLGGSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIEL-NHHDALEDARACA 151
|
....
gi 1006182455 160 KLMI 163
Cdd:cd06130 152 EILL 155
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
4-162 |
1.36e-24 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 109.24 E-value: 1.36e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 4 ATYAVVDLETTGNQLDFDDIIQIGITFVRNNQIIDTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKIK 83
Cdd:PRK07883 15 VTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEFAR 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 84 DCIFVAHNVDFDLNFIKKAFKDCNIQYRPKKVIDTLEIFKIAFPTD--KSYQLSELAEAHGINLANAHRADEDAATTAKL 161
Cdd:PRK07883 95 GAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDeaPNVRLSTLARLFGATTTPTHRALDDARATVDV 174
|
.
gi 1006182455 162 M 162
Cdd:PRK07883 175 L 175
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
8-162 |
7.73e-23 |
|
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: 95.88 E-value: 7.73e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 8 VVDLETTGNQLDFDDIIQIG-ITFVRN-NQIIDTYHSMIRT--NLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKI- 82
Cdd:pfam00929 2 VIDLETTGLDPEKDEIIEIAaVVIDGGeNEIGETFHTYVKPtrLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFLr 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 83 KDCIFVAHNVDFDLNFIKKAFKDCNIQYRPK--KVIDTLEIFKIAFPTDKSYQLSELAEAHGI-NLANAHRADEDAATTA 159
Cdd:pfam00929 82 KGNLLVAHNASFDVGFLRYDDKRFLKKPMPKlnPVIDTLILDKATYKELPGRSLDALAEKLGLeHIGRAHRALDDARATA 161
|
...
gi 1006182455 160 KLM 162
Cdd:pfam00929 162 KLF 164
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
6-161 |
1.06e-19 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 91.03 E-value: 1.06e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 6 YAVVDLETTGNQLDFDDIIQIGITFVRNNQIIDTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKIKDC 85
Cdd:PRK06807 10 YVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1006182455 86 IFVAHNVDFDLNFIKKAFKDCNIQYRPKKVIDTLEIFKIAFPTDKSYQLSELAEAHGINLaNAHRADEDAATTAKL 161
Cdd:PRK06807 90 VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRL-SSHNAFDDCITCAAV 164
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
5-172 |
6.93e-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: 86.35 E-value: 6.93e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 5 TYAVVDLETTGNQLDFDDIIQIGITFVRNNQIIDTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKIKD 84
Cdd:TIGR00573 8 TETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRG 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 85 CIFVAHNVDFDLNFIKKAFKD-CNIQYRPKKVIDTLEIFKIAFPTDKSYQLSELAEAHGINLAN----AHRADEDAATTA 159
Cdd:TIGR00573 88 AELVIHNASFDVGFLNYEFSKlYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNshraLHGALADAFILA 167
|
170
....*....|...
gi 1006182455 160 KLMILAFEKFEKL 172
Cdd:TIGR00573 168 KLYLVMTGKQTKY 180
|
|
| KapD |
COG5018 |
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
3-171 |
1.91e-17 |
|
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];
Pssm-ID: 444042 [Multi-domain] Cd Length: 181 Bit Score: 81.06 E-value: 1.91e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 3 MATYAVVDLETT-----GNQLDFDDIIQIGITFV-RNNQIIDTYHSMIRTNL--EIPPFIQALTSIEENMLQQAPYFNQV 74
Cdd:COG5018 1 MMKYLVIDLEATcwdgkPPPGFPMEIIEIGAVKVdENGEIIDEFSSFVKPVRrpKLSPFCTELTGITQEDVDSAPSFAEA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 75 AQEIYDKI--KDCIFVAhNVDFDLNFIKKAFKDCNIQYR-PKKVIDTLEIFKIAFPTDKSYQLSELAEAHGINLA-NAHR 150
Cdd:COG5018 81 IEDFKKWIgsEDYILCS-WGDYDRKQLERNCRFHGVPYPfGDRHINLKKLFALYFGLKKRIGLKKALELLGLEFEgTHHR 159
|
170 180
....*....|....*....|.
gi 1006182455 151 ADEDAATTAKLMILAFEKFEK 171
Cdd:COG5018 160 ALDDARNTAKLFKKILGDKRL 180
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
6-164 |
6.83e-17 |
|
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: 79.19 E-value: 6.83e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 6 YAVVDLETT-----GNQLDFDDIIQIGITFV--RNNQIIDTYHSMIR--TNLEIPPFIQALTSIEENMLQQAPYFNQVAQ 76
Cdd:cd06133 1 YLVIDFEATcwegnSKPDYPNEIIEIGAVLVdvKTKEIIDTFSSYVKpvINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 77 EIYDKIKD---CIFVAhNVDFDLNFIKKAFKDCNIQYRP---KKVIDTLEIFKIAFPTDKSYQLSELAEAHGINLA-NAH 149
Cdd:cd06133 81 EFLEWLGKngkYAFVT-WGDWDLKDLLQNQCKYKIINLPpffRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEgRHH 159
|
170
....*....|....*
gi 1006182455 150 RADEDAATTAKLMIL 164
Cdd:cd06133 160 RGLDDARNIARILKR 174
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
8-127 |
4.76e-16 |
|
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: 76.42 E-value: 4.76e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 8 VVDLETTG-NQLDFDDIIQIGITFVRNNQIID-TYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKIKDC 85
Cdd:cd06131 3 VLDTETTGlDPREGHRIIEIGCVELINRRLTGnTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIRGA 82
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 1006182455 86 IFVAHNVDFDLNFIKKAFKDCNIQYRPKK---VIDTLEIFKIAFP 127
Cdd:cd06131 83 ELVIHNASFDVGFLNAELSLLGLGKKIIDfcrVIDTLALARKKFP 127
|
|
| HELICc2 |
smart00491 |
helicase superfamily c-terminal domain; |
733-859 |
7.71e-13 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 214694 [Multi-domain] Cd Length: 142 Bit Score: 66.53 E-value: 7.71e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 733 YKMMHMVQDMLNELPEFEDYVVL---TQQQNQNYKIVQQFN---NFDKAILLGTS--TFFEGFDFQANGIKCVMIAKLPF 804
Cdd:smart00491 1 YRYLEQVVEYWKENGILEINKPVfieGKDSGETEELLEKYSaacEARGALLLAVArgKVSEGIDFPDDLGRAVIIVGIPF 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 805 MNK----HNAKYWLMDSEFTS-TFKEYVLPDAVTRFRQGLGRLIRNENDRGIIVSFDDRL 859
Cdd:smart00491 81 PNPdspiLRARLEYLDEKGGIrPFDEVYLFDAMRALAQAIGRAIRHKNDYGVVVLLDKRY 140
|
|
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
8-150 |
1.04e-12 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 68.73 E-value: 1.04e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 8 VVDLETTG-NQLDFDDIIQIGITFVRNNQII-DTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKIKDC 85
Cdd:PRK05711 8 VLDTETTGlNQREGHRIIEIGAVELINRRLTgRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDFIRGA 87
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 86 IFVAHNVDFDLNFIKKAFKDCNiQYRPK-----KVIDTLEIFKIAFPTdKSYQLSELAEAHGINlaNAHR 150
Cdd:PRK05711 88 ELIIHNAPFDIGFMDYEFALLG-RDIPKtntfcKVTDTLAMARRMFPG-KRNSLDALCKRYGID--NSHR 153
|
|
| rad3 |
TIGR00604 |
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are ... |
427-879 |
5.16e-11 |
|
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: 66.66 E-value: 5.16e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 427 AHLIHSDVENSIyqlfddCIVDEAHRLPDYALNQVTNELSYADIK--------YQLgLIGKNENEKLLKAIDQLEKQ-RI 497
Cdd:TIGR00604 212 RSAVSIELKDSI------VIFDEAHNLDNVCISSLSSNLSVRSLKrcskeiaeYFE-KIEERKEVDARKLLDELQKLvEG 284
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 498 LEKLDIA-PIDIFGLKASMNeihelNEQLFSTIFTIINDSDVYDDDIHRFHNVftfeTKDILKDLHaIIDKLNKtlEIFN 576
Cdd:TIGR00604 285 LKQEDLLtDEDIFLANPVLP-----KEVLPEAVPGNIRIAEIFLHKLSRYLEY----LKDALKVLG-VVSELPD--AFLE 352
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 577 GISHKTvkSLRKQLLYLKDKFKNIEQSLKAGHT-SFISIKNLSQKST-----------IRLYVKDYAVKD---------- 634
Cdd:TIGR00604 353 HLKEKT--FIDRPLRFCSERLSNLLRELEITHPeDFSALVLLFTFATlvltytngfleGIEPYENKTVPNpilkfmcldp 430
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 635 -VLTKQVLEKFKSLIFISGTLKfnhSFEAFKQLFNkdVRFNTFEVNTSLQSAKNTSVFIPSDVA-------SYQYKNIDE 706
Cdd:TIGR00604 431 sIALKPLFERVRSVILASGTLS---PLDAFPRNLG--FNPVSQDSPTHILKRENLLTLIVTRGSdqvplssTFEIRNDPS 505
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 707 YVASIVSYIIEYTTITSSKCLVLFTSYKMMHMVQ------DMLNELPEFEDYVVLTQQQNQNYKIVQQF----NNFDKAI 776
Cdd:TIGR00604 506 LVRNLGELLVEFSKIIPDGIVVFFPSYSYLENIVstwkemGILENIEKKKLIFVETKDAQETSDALERYkqavSEGRGAV 585
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 777 LLGT--STFFEGFDFQANGIKCVMIAKLPFMNKHNAKYwLMDSEFTSTFK------EYVLPDAVTRFRQGLGRLIRNEND 848
Cdd:TIGR00604 586 LLSVagGKVSEGIDFCDDLGRAVIMVGIPYEYTESRIL-LARLEFLRDQYpirenqDFYEFDAMRAVNQAIGRVIRHKDD 664
|
490 500 510
....*....|....*....|....*....|.
gi 1006182455 849 RGIIVSFDDRLINSNYKNFFEQTLENYRQKK 879
Cdd:TIGR00604 665 YGSIVLLDKRYARSNKRKKLPKWIQDTIQSS 695
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
3-249 |
5.67e-11 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 63.29 E-value: 5.67e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 3 MATYAVVDLETTGNQLDFDDIIQIGitfVRNNQIIDTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKI 82
Cdd:PRK06309 1 MPALIFYDTETTGTQIDKDRIIEIA---AYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFC 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 83 -KDCIFVAHNVD-FDLNFIKKAFKDCNIQYRPKKVIDTLEIFKIAFPTDKSYQLSELAEAHGINLANAHRADEDAATTAK 160
Cdd:PRK06309 78 gTDNILVAHNNDaFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEENQAHRALDDVITLHR 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 161 LmilafekFEKLPLDtlkqlyyLSKQLKYDLYD------IFFEMVRQYDAKPLD---KSYEKFEQiiyrKQVDFKKPTtn 231
Cdd:PRK06309 158 V-------FSALVGD-------LSPQQVYDLLNeschprIFKMPFGKYKGKPLSevpKSYIAWLE----KQGALDKPE-- 217
|
250
....*....|....*...
gi 1006182455 232 yNGSLKSlyskAVDQLGL 249
Cdd:PRK06309 218 -NKEIKA----AIELLQQ 230
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
6-165 |
1.04e-10 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 63.95 E-value: 1.04e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 6 YAVVDLETTGNQLDFDDIIQIGITFVR-NNQIIDTYHSMIrtNLEIPP---FIQALTSieeNMLQQAPYFNQVAQEIYDK 81
Cdd:PRK06063 17 WAVVDVETSGFRPGQARIISLAVLGLDaDGNVEQSVVTLL--NPGVDPgptHVHGLTA---EMLEGQPQFADIAGEVAEL 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 82 IKDCIFVAHNVDFDLNFIKKAFKDCNIQYRPKKVIDTLEIFK-IAFPTDkSYQLSELAEAHGINLANAHRADEDAattak 160
Cdd:PRK06063 92 LRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARrLGLGLP-NLRLETLAAHWGVPQQRPHDALDDA----- 165
|
....*
gi 1006182455 161 lMILA 165
Cdd:PRK06063 166 -RVLA 169
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
6-188 |
1.96e-10 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 62.15 E-value: 1.96e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 6 YAVVDLETTGNQLDFDDIIQIGITFVRNNQIIDTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKIKDC 85
Cdd:PRK06310 9 FVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFKEG 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 86 -IFVAHNVDFDLNFIKKAFKDCNIQYRPKK--VIDTLEIFKIaFPTDKSYQLSELAEAHGINLANAHRADEDAATTAKLm 162
Cdd:PRK06310 89 dYIVGHSVGFDLQVLSQESERIGETFLSKHyyIIDTLRLAKE-YGDSPNNSLEALAVHFNVPYDGNHRAMKDVEINIKV- 166
|
170 180
....*....|....*....|....*..
gi 1006182455 163 ilaFEKFEKlPLDTLKQLYY-LSKQLK 188
Cdd:PRK06310 167 ---FKHLCK-RFRTLEQLKQiLSKPIK 189
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
6-180 |
1.98e-10 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 62.88 E-value: 1.98e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 6 YAVVDLETTGNQLDfdDIIQIGITFVRNNQIIDTYHSMIR-TNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKIKD 84
Cdd:PRK06195 3 FVAIDFETANEKRN--SPCSIGIVVVKDGEIVEKVHYLIKpKEMRFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 85 CIFVAHNVDFDLNFIKKAFKDCNIQYRPKKVIDTLEIFKIAFPTDKSYQLSELAEAHGINLANaHRADEDAATTAKLMIL 164
Cdd:PRK06195 81 NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFLGYEFKH-HDALADAMACSNILLN 159
|
170
....*....|....*.
gi 1006182455 165 AFEKFEKLPLDTLKQL 180
Cdd:PRK06195 160 ISKELNSKDINEISKL 175
|
|
| RNaseT |
cd06134 |
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ... |
8-161 |
1.11e-08 |
|
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: 55.76 E-value: 1.11e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 8 VVDLETTGNQLDFDDIIQIGITFVRNN-----QIIDTYHSMI---------RTNLEIP------PFIQALTsiEENMLQQ 67
Cdd:cd06134 9 VVDVETGGFNPQTDALLEIAAVTLEMDeqgnlYPDETFHFHIlpfeganldPAALEFNgidpfhPFRFAVD--EKEALKE 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 68 ApyFNQVAQEIydKIKDC---IFVAHNVDFDLNFIKKAFKDCNIQYRP---KKVIDTLEIFKIAFPtdksyQ--LSELAE 139
Cdd:cd06134 87 I--FKPIRKAL--KAQGCtraILVGHNAHFDLGFLNAAVARCKIKRNPfhpFSTFDTATLAGLAYG-----QtvLAKACQ 157
|
170 180
....*....|....*....|....
gi 1006182455 140 AHGI--NLANAHRADEDAATTAKL 161
Cdd:cd06134 158 AAGIefDNKEAHSALYDTQKTAEL 181
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
7-167 |
2.25e-07 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 53.44 E-value: 2.25e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 7 AVVDLETTGNQLDFDDIIQIGITFVRNN------QIIDTYHSMIRTNLEIPPFIQALTSIEENML--QQAPYfnqvaQEI 78
Cdd:PRK09182 40 VILDTETTGLDPRKDEIIEIGMVAFEYDddgrigDVLDTFGGLQQPSRPIPPEITRLTGITDEMVagQTIDP-----AAV 114
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 79 YDKIKDC-IFVAHNVDFDLNFIkKAFKDCniqYRPK------KVID-TLEIFkiafptdKSYQLSELAEAHGInLANAHR 150
Cdd:PRK09182 115 DALIAPAdLIIAHNAGFDRPFL-ERFSPV---FATKpwacsvSEIDwSARGF-------EGTKLGYLAGQAGF-FHEGHR 182
|
170
....*....|....*..
gi 1006182455 151 ADEDAAttAKLMILAFE 167
Cdd:PRK09182 183 AVDDCQ--ALLELLARP 197
|
|
| SF2_C_XPD |
cd18788 |
C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases; ... |
704-858 |
2.29e-06 |
|
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: 48.37 E-value: 2.29e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 704 IDEYVASIVSYIieytTITSSKCLVLFTSYKMMHMVQDmlnelpefedyvvltqqqnqnykivqqfnnfDKAILLGTS-- 781
Cdd:cd18788 30 MDELGNLLLELC----AVVPDGVLVFFPSYSYMERVVS-------------------------------RGALLLAVCrg 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 782 TFFEGFDFQANGIKCVMIAKLPFMN--------KHNAKYWLMDsEFTSTFKEYVLPDAVTRFRQGLGRLIRNENDRGIIV 853
Cdd:cd18788 75 KVSEGIDFSDDLGRAVIMVGIPYPNtkdpilklKMDDLEYLRD-KGLLTGEDWYTFQAMRAVNQAIGRAIRHKNDYGAIV 153
|
....*
gi 1006182455 854 SFDDR 858
Cdd:cd18788 154 LLDKR 158
|
|
| Csf4_U |
cd09708 |
CRISPR/Cas system-associated DinG family helicase Csf4; CRISPR (Clustered Regularly ... |
262-851 |
4.10e-05 |
|
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: 47.28 E-value: 4.10e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 262 ILDQLMHSEKAMIEASLGSGKSLAYLLAAL-MYNIETGKHVMISTNTKLLQSQLLEKDIPAMNEALNFKINALLIKSKSD 340
Cdd:cd09708 9 CLTSLRQKRIGMLEASTGVGKTLAMIMAALtMLKERPDQKIAIAVPTLALMGQLWSELERLTAEGLAGPVQAGFFPGSQE 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 341 YISLGLISQILKDdtSNYEVNILKMQLLIWITETPSGDIQELNlkggqKMYFDQKIETYVPARHDVHYYNFIKRNAQNIQ 420
Cdd:cd09708 89 FVSPGALQELLDQ--SDGPGDKDAVVRLWMGQGGPRKVAPLFN-----RMRDVTLLIHDTADIRGYVSYREQWDSLPRCS 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 421 IGITNHAHLIHsdvensiyqLFDDCIVDEAHRLPDYALNQvtnelsYADIKYQLGLIGKNENEKLLKAI----DQLEKQR 496
Cdd:cd09708 162 AMSRAPTKMAS---------MTHDLKALATLNPQDFVTED------EEDKRWVTSLVESREYYARKSRIlactHTMLKWG 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 497 ILEKLDIAPID-IFGLKASMNEIHELNEQLFSTIFTI---------INDSDV--YDDDIHRFHNVFTF---------ETK 555
Cdd:cd09708 227 LLPQPDILIVDeAHLFEQNISRVYSNALSLRMLRFHLevshrktgaIGSAVVaaVSAVSHRLRQVSALgdgqtlcldAGN 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 556 DILKDLHAIIDKLNKTLEIFNGISHKTVKSLRKQLLYLKDKFknieqSLKAGHTSFISIKNLSQKSTIRLYVKDYAVKDV 635
Cdd:cd09708 307 KELETLFADLDAALEIKSTPNKKALSVVKDVKKARIILDNAI-----TAIQGKQSTVYLQFSPDRRFPSLIVGREDLGKV 381
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 636 LTKQVLEKFKSLIFISGTLKFNHSFEAFKQLFNKDV------RFNTFE-VNTSLQSAKNTSVFIPSDVASY-------QY 701
Cdd:cd09708 382 MGGLWKDVTHGAIIVSATLYLPDRFGQMSCDYLKRVlslplsRLDTPSpIVAPWVRNLIPHLHVPNAKARFllsrpvgKT 461
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 702 KNIDEYVASIVSYIIEYTT-ITSSK---CLVLFTSYkmmHMVQDmLNELPEFE--DYVVLTQQQNQNYKIVQQF----NN 771
Cdd:cd09708 462 EQGDANLAGWLENVSLSTAaILRKAqggTLVLTTAF---SHISA-IGQLVELGipAEIVIQSEKNRLASAEQQFlalyAN 537
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 772 FDKAILLGTSTFFEGFDF--------QANGIKCVMIAKLPF-MNKHNAKywLMDSEFTSTFKEyVLPDAVTRFRQGLGRL 842
Cdd:cd09708 538 GIQPVLIAAGGAWTGIDLhdpsvspdKDNLLTDLIITCAPFgLNRSLSM--LKRIRKTSVRPE-IINESLMMLRQGLGRL 614
|
650
....*....|..
gi 1006182455 843 IRN---ENDRGI 851
Cdd:cd09708 615 VRHpdmPINRRI 626
|
|
| PRK07748 |
PRK07748 |
3'-5' exonuclease KapD; |
1-168 |
1.85e-04 |
|
3'-5' exonuclease KapD;
Pssm-ID: 236087 Cd Length: 207 Bit Score: 43.52 E-value: 1.85e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 1 MGMATYAVVDLETTGNQLD------FDDIIQIGITFVRNNQIIDTYHSMIRtnleiPPFIQALT-------SIEENMLQQ 67
Cdd:PRK07748 1 MDEQQFLFLDFEFTMPQHKkkpkgfFPEIIEVGLVSVVGCEVEDTFSSYVK-----PKTFPSLTercksflGITQEDVDK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 68 APYFNQVAQEI--YDKIKDCIFVAHNvDFDLNFIKKAFKDCNIQYRPK-KVIDTLEIFKIAFPTDKSYQLSELAEAHGI- 143
Cdd:PRK07748 76 GISFEELVEKLaeYDKRCKPTIVTWG-NMDMKVLKHNCEKAGVPFPFKgQCRDLSLEYKKFFGERNQTGLWKAIEEYGKe 154
|
170 180
....*....|....*....|....*
gi 1006182455 144 NLANAHRADEDAATTAKLMILaFEK 168
Cdd:PRK07748 155 GTGKHHCALDDAMTTYNIFKL-VEK 178
|
|
| PRK07247 |
PRK07247 |
3'-5' exonuclease; |
3-186 |
2.21e-04 |
|
3'-5' exonuclease;
Pssm-ID: 180906 [Multi-domain] Cd Length: 195 Bit Score: 43.23 E-value: 2.21e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 3 MATYAVVDLETtgNQL-DFDDIIQIGITFVRNNQIIDTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDK 81
Cdd:PRK07247 4 LETYIAFDLEF--NTVnGVSHIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFKEF 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 82 IKDCIFVAHNV-DFDLNFIKKAFKDCNIQYRpkkvidtLEIFKIAFPTDKS-------YQLSELAEAHGINlANAHRADE 153
Cdd:PRK07247 82 VGELPLIGYNAqKSDLPILAENGLDLSDQYQ-------VDLYDEAFERRSSdlngianLKLQTVADFLGIK-GRGHNSLE 153
|
170 180 190
....*....|....*....|....*....|...
gi 1006182455 154 DAATTAKLmilaFEKFekLPLDTLKQlyYLSKQ 186
Cdd:PRK07247 154 DARMTARV----YESF--LESDQNKE--YLEQQ 178
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
8-163 |
5.57e-04 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 42.40 E-value: 5.57e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 8 VVDLETTGNQldfDDIIQIGITFVRNNQIIDTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKIkdcIF 87
Cdd:PRK07983 4 VIDTETCGLQ---GGIVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYYGSE---WY 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 88 VAHNVDFDLNFIKKAfkdcniqyrPKKVIDTLEIFKIAFPTDKsYQLSELAEAHGINLA-----NAHRADEDAATTAKLM 162
Cdd:PRK07983 78 VAHNASFDRRVLPEM---------PGEWICTMKLARRLWPGIK-YSNMALYKSRKLNVQtppglHHHRALYDCYITAALL 147
|
.
gi 1006182455 163 I 163
Cdd:PRK07983 148 I 148
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
274-316 |
9.45e-04 |
|
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.
Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 40.46 E-value: 9.45e-04
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 1006182455 274 IEASLGSGKSLAYLLAALMYNIETGKHVMISTNTKLLQSQLLE 316
Cdd:cd00046 6 ITAPTGSGKTLAALLAALLLLLKKGKKVLVLVPTKALALQTAE 48
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
267-316 |
2.45e-03 |
|
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350676 [Multi-domain] Cd Length: 180 Bit Score: 39.71 E-value: 2.45e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 1006182455 267 MHSEKAM---IEASLGSGKSLAYLLAALMYnIETGKHVMISTNTKLLQSQLLE 316
Cdd:cd17918 31 LHSPEPMdrlLSGDVGSGKTLVALGAALLA-YKNGKQVAILVPTEILAHQHYE 82
|
|
| PAN2_exo |
cd06143 |
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ... |
85-161 |
7.36e-03 |
|
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with 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.
Pssm-ID: 99846 Cd Length: 174 Bit Score: 38.37 E-value: 7.36e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1006182455 85 CIFVAHNvdfdlnfIKKAFKDCNIQYRPKKVIDTLEIFKIafPTDKSYQLSELAeAHGINL---ANAHRADEDAATTAKL 161
Cdd:cd06143 103 CIFVGHG-------LAKDFRVINIQVPKEQVIDTVELFHL--PGQRKLSLRFLA-WYLLGEkiqSETHDSIEDARTALKL 172
|
|
| |
