|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
2-785 |
0e+00 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 1413.85 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 2 TQPQAGFLLTRHWRDTPLGTELAFWLATDNGPLQVTLPPQESVAFIPEAQRPQAERLLQGENGYRLAQLALKDFHRQPVF 81
Cdd:PRK05762 1 MMLQQGFILTRHYRDTPGGPEVELWLATDEGPRVVLLDPQFRPYFIPAEQDERAESLLAGEIGVRLSPLALKDFHRRPVL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 82 GLYCRGHRQLMRLEKKLRENGVTVYEGDIRPPERYLMERFITAPVWVEGETRGSQ----LVNARMKPHPDYRPPLKWVSL 157
Cdd:PRK05762 81 GLYCRQHRQLTRLPKRLREGGVDVYEADIRFPERYLMERFITPCVWFSGEVEQYTtdgvLRNARLKPAPDYRPPLKVVSL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 158 DIETSRHGELYCIGLEGCGQRVVYMLGPEPATPPDvgfSLVYVASRPLLLEKLNAWFAEHDPDVLIGWNVVQFDLRVLQK 237
Cdd:PRK05762 161 DIETSNKGELYSIGLEGCGQRPVIMLGPPNGEALD---FLEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQE 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 238 HAERYRIPLLLGRGNSELEWREHGFKNGVFFAQANGRLIIDGIEALKSAFWNFSSFSLEAVARELLGEGKAIDNPWDRMD 317
Cdd:PRK05762 238 RAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATWVFDSFSLEYVSQRLLGEGKAIDDPYDRMD 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 318 EIDRRFHEDKPALATYNLQDCELVTRIFHKTEIMPFLLERATVNGLPADRHGGSVAAFSHLYFPRMHRLGYVAPNLGEIP 397
Cdd:PRK05762 318 EIDRRFAEDKPALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLPLDRVGGSVAAFEHLYLPRAHRAGYVAPNLGERP 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 398 PQASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGLAQPDDrHSTEGFLGARFSREKHCLPGIVGQIWH 477
Cdd:PRK05762 398 GEASPGGYVMDSKPGLYDSVLVLDFKSLYPSIIRTFNIDPDGLVEGLAQPPE-ESVAGFLGARFSREKHFLPEIVERLWE 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 478 GRDEAKRQHNKPLSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHAIMRQTKALIEAQGYDVIYGDTDSTFVWLKR 557
Cdd:PRK05762 477 GRDEAKREMNKPLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQGYQVIYGDTDSTFVWLGG 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 558 PHSEAQAAEIGRKLVAYVNDWWAQELGKS-QLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGMIQEGD-AQRMVFKG 635
Cdd:PRK05762 557 AHDEEDAAKIGRALVQEINQWWQEHLQQEfGLESALELEFEKHYRRFFMPTIRGAEEGSKKRYAGLIQEGDgDGRIVFKG 636
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 636 LETVRTDWTPLAQQFQQELYLRIFRHQPYQDYVRETIARLMNGELDEQLVYRKRLRRPLAEYQRNVPPHVRAARLADEHN 715
Cdd:PRK05762 637 LETVRTDWTPLAKEFQQELYERIFRGEPYVDYVREVIDKLRAGELDEKLVYRKRLRRPLDEYQRNVPPHVRAARLADEMG 716
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 716 VKLGRAQQYQQRGTIKYVWTTGGPEPVDYQQSPLDYDHYLSKQLQPVAEGILPFVNDDFATIVTGQLGLF 785
Cdd:PRK05762 717 YKVGRPLQYQNGGKIGYVITVNGPEPLEYRKSPIDYDYYIEKQLQPVADRILPFFGDDFATLKTGQLGLF 786
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
4-785 |
0e+00 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 1056.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 4 PQAGFLLTRHWRDTPLGTELAFWLATDNGP-LQVTLPPQESVAFIPEAQRPQAERLLQGENG-YRLAQLALKDFHRQ--P 79
Cdd:COG0417 2 KIPGFLLDRSYRDEDGKPVIELWGRTEDGPsVLLDVTGFRPYFYVPLPDEEKLEELLRDIKEiTEVEPVKLKSFFGEpvP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 80 VFGLYCRGHRQLMRLEKKLRENGVTVYEGDIRPPERYLMERFITAPVWVEGETRGSQLV-------NARMKPHpDYRPPL 152
Cdd:COG0417 82 VLKIYTRDPRDVRELRDRLKEGGIDVYEADIRFHDRYLIDRFLTPGVWYEGEVEEDGGKldyevkeNPRLKPE-DYRPKL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 153 KWVSLDIETS---------RHGELYCIGLEGC-GQRVVYMLGPepatpPDVGFSLVYVASRPLLLEKLNAWFAEHDPDVL 222
Cdd:COG0417 161 KVLSFDIEVStprgfpdpeRDGPIISIGLAGSdGEKKVLMLGR-----EGVDFEVEYFDDEKALLEAFFEIIREYDPDII 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 223 IGWNVVQFDLRVLQKHAERYRIPLLLGRGNSELEWREHGfknGVFFAQANGRLIIDGIEALKSAFWNFSSFSLEAVAREL 302
Cdd:COG0417 236 IGWNVDNFDLPYLQKRAERLGIPLDLGRDGSEPSWREHG---GQGFASIPGRVVIDLYDALKSATYKFKSYSLDAVAEEL 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 303 LGEGKAIDNpwdrMDEIDRRFHEDKPALATYNLQDCELVTRIFHKTEIMPFLLERATVNGLPADRHG--GSVAAFSHLYF 380
Cdd:COG0417 313 LGEGKLIVD----GGEIERLWDDDKPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGraGSSAAFENLLL 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 381 PRMHRLGYVAPNLGEIPPQASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGLAQP-DDRHSTEGFlGA 459
Cdd:COG0417 389 PEAHRRGYLAPNKGEIKGEAYPGGYVLDPKPGLYENVLVLDFKSLYPSIIRTFNISPETLVEGGEEPcGDEDVAPGF-GH 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 460 RFSRE-KHCLPGIVGQIWHGRDEAKRQHNK------------PLSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGH 526
Cdd:COG0417 468 RFCREpKGILPSILEELWDERDEAKKKMKKakpdseeyrlydALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGR 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 527 AIMRQTKALIEAQGYDVIYGDTDSTFVWLKrPHSEAQAAEIGRKLVAYVNDWWaqelgksqlTSALELEYETHFCRFLMP 606
Cdd:COG0417 548 EIIKQTIEKAEELGYKVIYGDTDSLFVWLP-KASLEEAIEIGKELAEEINAWW---------PSGLELEFEKHYRRFFFP 617
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 607 TirgadtgSKKRYAGMIQEGdaqRMVFKGLETVRTDWTPLAQQFQQELYLRIFRHQPYQ---DYVRETIARLMNGELD-E 682
Cdd:COG0417 618 G-------SKKRYAGLTEDG---KIDIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEkavEYVRDVIEKLRAGEVDlD 687
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 683 QLVYRKRLRRPLAEYQRNVPPHVRAARLADEHNVKlgraqqYQQRGTIKYVWTTGG--PEPVDY---QQSPLDYDHYLSK 757
Cdd:COG0417 688 DLVIRKRLRKPLSEYEKNVPPHVRAARKLDERGRP------YQRGDKISYVITKGGgrVEPVELakeRESEIDYDYYIEK 761
|
810 820 830
....*....|....*....|....*....|
gi 1994014905 758 QLQPVAEGILPFVNDDFATIVTG--QLGLF 785
Cdd:COG0417 762 QLKPTADRILEAFGVSFDELKGGskQLGLF 791
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
399-771 |
0e+00 |
|
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Pssm-ID: 99920 Cd Length: 371 Bit Score: 687.46 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 399 QASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGLAQPDDRHSTEGFLGARFSREKHCLPGIVGQIWHG 478
Cdd:cd05537 1 ISSPGGYVMDSKPGLYKNVLVLDFKSLYPSIIRTFLIDPLGLIEGLKAPDPEDLIPGFLGARFSREKHILPDLIARLWAA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 479 RDEAKRQHNKPLSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHAIMRQTKALIEAQGYDVIYGDTDSTFVWLKRP 558
Cdd:cd05537 81 RDEAKREKNAPLSQAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQVIYGDTDSTFVWLGEE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 559 HSEAQAAEIGRKLVAYVNDWWAQELGKS-QLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGMIQEGDAQRMVFKGLE 637
Cdd:cd05537 161 LDAAEAQAIGKELASQINQWWAQKLKEEfGLESFLEIEFETHYSRFFMPTIRGSDEGSKKRYAGLKSTDGGDELVFKGLE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 638 TVRTDWTPLAQQFQQELYLRIFRHQPYQDYVRETIARLMNGELDEQLVYRKRLRRPLAEYQRNVPPHVRAARLADEHNVK 717
Cdd:cd05537 241 TVRSDWTPLARQFQKELYERVFNDEPYEGFIKETVEELLAGELDELLVYRKRLRRPLSEYTKNVPPHVQAARLADQINRE 320
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....
gi 1994014905 718 LGRAQQYQQrgtIKYVWTTGGPEPVDYQQSPLDYDHYLSKQLQPVAEGILPFVN 771
Cdd:cd05537 321 LGRPRQYQW---IEYVITVNGPEPLEYRTSPLDYQHYIDKQLKPIADSILPFLG 371
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
150-556 |
2.39e-73 |
|
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Pssm-ID: 214691 [Multi-domain] Cd Length: 474 Bit Score: 247.06 E-value: 2.39e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 150 PPLKWVSLDIET-SRHG----------ELYCIGLEGCGQ-------RVVYMLGPepaTPPDVGFSLVYVASRPLLLEKLN 211
Cdd:smart00486 1 PPLKILSFDIETyTDGGnfpdaeifddEIIQISLVINDGdkkganrRILFTLGT---CKEIDGIEVYEFNNEKELLLAFF 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 212 AWFAEHDPDVLIGWNVVQFDLRVLQKHAERYRIPLL--LGRGNSELEWREHGFKNGV-------FFAQANGRLIIDGIEA 282
Cdd:smart00486 78 EFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLskIGRLKIGLRIPNKKPLFGSksfglsdIKVYIKGRLVIDLYRL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 283 LKSAFwNFSSFSLEAVARELLGEGKaIDNPWDRMDEIDRRFHEDKPALATYNLQDCELVTRIFHKTEIMPFLLERATVNG 362
Cdd:smart00486 158 YKNKL-KLPSYKLDTVAEYLLGKEK-DDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAG 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 363 LPADR--HGGSVAAFSHLYFPRMHRLGYVAPNLGEIPPQAS----------PGGYVMDSRPGLYDS-VLVLDYKSLYPSI 429
Cdd:smart00486 236 IPLRRtlYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSepdlkkkvkyEGGKVLEPKKGFYDNpVLVLDFNSLYPSI 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 430 IRTFLIDP--VGLVEGLAQPDDRHSTEGFL---------GARFSREKH--CLPGIVGQIWHGRDEAKRQHNK-------- 488
Cdd:smart00486 316 IIAHNLCYstLVGVGEVVIKGDLIIPEDLLtikyekgnkYRFVKKNIRkgILPKLLKKLLDKRKEIKKLMKKekdeseel 395
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1994014905 489 -----PLSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHAIMRQTKALIEAQGYD-----VIYGDTDSTFVWLK 556
Cdd:smart00486 396 kklldSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGYPkpgfkVIYGDTDSIFVTKP 473
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
382-767 |
1.41e-48 |
|
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.
Pssm-ID: 395085 Cd Length: 439 Bit Score: 177.80 E-value: 1.41e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 382 RMHRLGYVAPNlgeiPPQAS------PGGYVMDSRPGLYDS-VLVLDYKSLYPSIIR------TFLIDPVGLVEGLAQPD 448
Cdd:pfam00136 22 LALEEGFILPD----RPSAKgdedgyQGATVIEPKKGFYDKpVLVLDFNSLYPSIIQahnlcyTTLVRSVDEANNLPPED 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 449 DRHS-TEGFLGARF---SREKHCLPGIVGQIWHGRDEAK---RQHNKPL--------SQALKIIMNAFYGVLGTSACRFF 513
Cdd:pfam00136 98 NLITvECTPRGVYFvkdHVREGLLPKLLKDLLAKRKAIKkllKEETDPFeraildkqQLALKITANSVYGFTGFANGRLP 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 514 DPRLASSITMRGHAIMRQTKALIEAQ---GYDVIYGDTDSTFVWLkRPHSEAQAAEIGRKLVAYVNdwwaqelgKSQLTS 590
Cdd:pfam00136 178 CLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTDSVFIEF-GGKDVEEAMKIGDELAEHVN--------QDLFKS 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 591 ALELEYETHFCRFLMPtirgadtgSKKRYAGMIQEGDAQ--RMVFKGLETVRTDWTPLAQQFQQELYLRIFRHQPYQD-- 666
Cdd:pfam00136 249 PIKLEFEKVYKPLLLI--------SKKKYAGLKYTAPSNfnKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSDRGLPVgl 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 667 -YVRETI----ARLMNGELD-EQLVYRKRLRRPLAEYQRNVPPHVRAA-RLADEHnvklGRAQQYQQRgtIKYVWTTGGP 739
Cdd:pfam00136 321 eFVISILndarSDLRNNKVPlEKFVISKELSKPPDNYKSKNLPHVEVAlRMNKRN----GEAPEVGDR--IPYVIVKAAK 394
|
410 420 430 440
....*....|....*....|....*....|....*....|..
gi 1994014905 740 EPVD---YQQS-----------PLDYDHYLSKQLQPVAEGIL 767
Cdd:pfam00136 395 GLKNlliYERAedpeyvlennlPIDYEYYFSNQLIPPVARLL 436
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
204-767 |
1.04e-44 |
|
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA polymerases.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: 273159 [Multi-domain] Cd Length: 1172 Bit Score: 174.09 E-value: 1.04e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 204 PLLLEKLNA------WF----AEHDPDVLIGWNVVQFDLRVLQKHAERYRIPLLLGRGnselEWREHGFKNGVFFAQANG 273
Cdd:TIGR00592 575 PSLVEDLATeralikKFmakvKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIG----RLRRSPKFGRRFGERTCG 650
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 274 RLIIDGIEALKSAFWNFSSFSLEAVARELLGEGKAIDnpwdrMDEIDRRFHEDKP--ALATYNLQDCELVTRIFHKTEIM 351
Cdd:TIGR00592 651 RMICDVEISAKELIRCKSYDLSELVQQILKTERKVIP-----IDNINNMYSESSSltYLLEHTWKDAMFILQIMCELNVL 725
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 352 PFLLERATVNGLPADR--HGGSVAAFSHLYFPRMHRLGYVAPNLGEIPPQ-------------------ASPGGYVMDSR 410
Cdd:TIGR00592 726 PLALQITNIAGNIMSRtlMGGRSERNEFLLLHAFYENNYIVPDKQIFRKQqklgdedeeidgykkgkkaAYAGGLVLEPK 805
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 411 PGLYDS-VLVLDYKSLYPSIIRTFLI------DPVGLVEGLAQPDDrhstegflgarfSREKHCLPGIVGQIWHGRDEAK 483
Cdd:TIGR00592 806 VGLYDKyVLLMDFNSLYPSIIQEFNIcfttvqQKVDEDELPELPDS------------ELEMGILPRELRKLVERRKEVK 873
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 484 RQHNKPLS-----------QALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHAIMRQTKALIEAQGYDVIYGDTDStf 552
Cdd:TIGR00592 874 KLMKQDLNpdlrlqydirqKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEMNLEVIYGDTDS-- 951
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 553 VWLKRPHSE-AQAAEIGRKLVAYVNdwwaqelgksQLTSALELEYETHFCRFLMPTirgadtgsKKRYAGMIQEGDAQ-- 629
Cdd:TIGR00592 952 IMINTPGTKyEEVFKIGKEFKSEVN----------KLYKLLELDIDGVFKRLLLLK--------KKKYAAIKVEGDSDgn 1013
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 630 ---RMVFKGLETVRTDWTPLAQQFQQELYLRIFRHQPYQDYVRETIARL-------MNGELD-EQLVYRKRLRRPLAEY- 697
Cdd:TIGR00592 1014 yttKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLekigknvLNGEVPlEKFVINKQLTRDPKDYp 1093
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 698 QRNVPPHVRAA-RLADEHNVKlgraqqYQQRGTIKYVWTTGG-----------PEPVDYQQSPLDYD--HYLSKQLQPVA 763
Cdd:TIGR00592 1094 DGASLPHVHVAlRINARGGRK------VKAGDVVSYVICKDGgnlsarqrayaLEELQRKHNNLIYDtqYYLEHQIHPVV 1167
|
....
gi 1994014905 764 EGIL 767
Cdd:TIGR00592 1168 LRIL 1171
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
2-785 |
0e+00 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 1413.85 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 2 TQPQAGFLLTRHWRDTPLGTELAFWLATDNGPLQVTLPPQESVAFIPEAQRPQAERLLQGENGYRLAQLALKDFHRQPVF 81
Cdd:PRK05762 1 MMLQQGFILTRHYRDTPGGPEVELWLATDEGPRVVLLDPQFRPYFIPAEQDERAESLLAGEIGVRLSPLALKDFHRRPVL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 82 GLYCRGHRQLMRLEKKLRENGVTVYEGDIRPPERYLMERFITAPVWVEGETRGSQ----LVNARMKPHPDYRPPLKWVSL 157
Cdd:PRK05762 81 GLYCRQHRQLTRLPKRLREGGVDVYEADIRFPERYLMERFITPCVWFSGEVEQYTtdgvLRNARLKPAPDYRPPLKVVSL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 158 DIETSRHGELYCIGLEGCGQRVVYMLGPEPATPPDvgfSLVYVASRPLLLEKLNAWFAEHDPDVLIGWNVVQFDLRVLQK 237
Cdd:PRK05762 161 DIETSNKGELYSIGLEGCGQRPVIMLGPPNGEALD---FLEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQE 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 238 HAERYRIPLLLGRGNSELEWREHGFKNGVFFAQANGRLIIDGIEALKSAFWNFSSFSLEAVARELLGEGKAIDNPWDRMD 317
Cdd:PRK05762 238 RAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATWVFDSFSLEYVSQRLLGEGKAIDDPYDRMD 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 318 EIDRRFHEDKPALATYNLQDCELVTRIFHKTEIMPFLLERATVNGLPADRHGGSVAAFSHLYFPRMHRLGYVAPNLGEIP 397
Cdd:PRK05762 318 EIDRRFAEDKPALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLPLDRVGGSVAAFEHLYLPRAHRAGYVAPNLGERP 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 398 PQASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGLAQPDDrHSTEGFLGARFSREKHCLPGIVGQIWH 477
Cdd:PRK05762 398 GEASPGGYVMDSKPGLYDSVLVLDFKSLYPSIIRTFNIDPDGLVEGLAQPPE-ESVAGFLGARFSREKHFLPEIVERLWE 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 478 GRDEAKRQHNKPLSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHAIMRQTKALIEAQGYDVIYGDTDSTFVWLKR 557
Cdd:PRK05762 477 GRDEAKREMNKPLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQGYQVIYGDTDSTFVWLGG 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 558 PHSEAQAAEIGRKLVAYVNDWWAQELGKS-QLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGMIQEGD-AQRMVFKG 635
Cdd:PRK05762 557 AHDEEDAAKIGRALVQEINQWWQEHLQQEfGLESALELEFEKHYRRFFMPTIRGAEEGSKKRYAGLIQEGDgDGRIVFKG 636
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 636 LETVRTDWTPLAQQFQQELYLRIFRHQPYQDYVRETIARLMNGELDEQLVYRKRLRRPLAEYQRNVPPHVRAARLADEHN 715
Cdd:PRK05762 637 LETVRTDWTPLAKEFQQELYERIFRGEPYVDYVREVIDKLRAGELDEKLVYRKRLRRPLDEYQRNVPPHVRAARLADEMG 716
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 716 VKLGRAQQYQQRGTIKYVWTTGGPEPVDYQQSPLDYDHYLSKQLQPVAEGILPFVNDDFATIVTGQLGLF 785
Cdd:PRK05762 717 YKVGRPLQYQNGGKIGYVITVNGPEPLEYRKSPIDYDYYIEKQLQPVADRILPFFGDDFATLKTGQLGLF 786
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
4-785 |
0e+00 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 1056.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 4 PQAGFLLTRHWRDTPLGTELAFWLATDNGP-LQVTLPPQESVAFIPEAQRPQAERLLQGENG-YRLAQLALKDFHRQ--P 79
Cdd:COG0417 2 KIPGFLLDRSYRDEDGKPVIELWGRTEDGPsVLLDVTGFRPYFYVPLPDEEKLEELLRDIKEiTEVEPVKLKSFFGEpvP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 80 VFGLYCRGHRQLMRLEKKLRENGVTVYEGDIRPPERYLMERFITAPVWVEGETRGSQLV-------NARMKPHpDYRPPL 152
Cdd:COG0417 82 VLKIYTRDPRDVRELRDRLKEGGIDVYEADIRFHDRYLIDRFLTPGVWYEGEVEEDGGKldyevkeNPRLKPE-DYRPKL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 153 KWVSLDIETS---------RHGELYCIGLEGC-GQRVVYMLGPepatpPDVGFSLVYVASRPLLLEKLNAWFAEHDPDVL 222
Cdd:COG0417 161 KVLSFDIEVStprgfpdpeRDGPIISIGLAGSdGEKKVLMLGR-----EGVDFEVEYFDDEKALLEAFFEIIREYDPDII 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 223 IGWNVVQFDLRVLQKHAERYRIPLLLGRGNSELEWREHGfknGVFFAQANGRLIIDGIEALKSAFWNFSSFSLEAVAREL 302
Cdd:COG0417 236 IGWNVDNFDLPYLQKRAERLGIPLDLGRDGSEPSWREHG---GQGFASIPGRVVIDLYDALKSATYKFKSYSLDAVAEEL 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 303 LGEGKAIDNpwdrMDEIDRRFHEDKPALATYNLQDCELVTRIFHKTEIMPFLLERATVNGLPADRHG--GSVAAFSHLYF 380
Cdd:COG0417 313 LGEGKLIVD----GGEIERLWDDDKPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGraGSSAAFENLLL 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 381 PRMHRLGYVAPNLGEIPPQASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGLAQP-DDRHSTEGFlGA 459
Cdd:COG0417 389 PEAHRRGYLAPNKGEIKGEAYPGGYVLDPKPGLYENVLVLDFKSLYPSIIRTFNISPETLVEGGEEPcGDEDVAPGF-GH 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 460 RFSRE-KHCLPGIVGQIWHGRDEAKRQHNK------------PLSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGH 526
Cdd:COG0417 468 RFCREpKGILPSILEELWDERDEAKKKMKKakpdseeyrlydALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGR 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 527 AIMRQTKALIEAQGYDVIYGDTDSTFVWLKrPHSEAQAAEIGRKLVAYVNDWWaqelgksqlTSALELEYETHFCRFLMP 606
Cdd:COG0417 548 EIIKQTIEKAEELGYKVIYGDTDSLFVWLP-KASLEEAIEIGKELAEEINAWW---------PSGLELEFEKHYRRFFFP 617
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 607 TirgadtgSKKRYAGMIQEGdaqRMVFKGLETVRTDWTPLAQQFQQELYLRIFRHQPYQ---DYVRETIARLMNGELD-E 682
Cdd:COG0417 618 G-------SKKRYAGLTEDG---KIDIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEkavEYVRDVIEKLRAGEVDlD 687
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 683 QLVYRKRLRRPLAEYQRNVPPHVRAARLADEHNVKlgraqqYQQRGTIKYVWTTGG--PEPVDY---QQSPLDYDHYLSK 757
Cdd:COG0417 688 DLVIRKRLRKPLSEYEKNVPPHVRAARKLDERGRP------YQRGDKISYVITKGGgrVEPVELakeRESEIDYDYYIEK 761
|
810 820 830
....*....|....*....|....*....|
gi 1994014905 758 QLQPVAEGILPFVNDDFATIVTG--QLGLF 785
Cdd:COG0417 762 QLKPTADRILEAFGVSFDELKGGskQLGLF 791
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
399-771 |
0e+00 |
|
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Pssm-ID: 99920 Cd Length: 371 Bit Score: 687.46 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 399 QASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGLAQPDDRHSTEGFLGARFSREKHCLPGIVGQIWHG 478
Cdd:cd05537 1 ISSPGGYVMDSKPGLYKNVLVLDFKSLYPSIIRTFLIDPLGLIEGLKAPDPEDLIPGFLGARFSREKHILPDLIARLWAA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 479 RDEAKRQHNKPLSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHAIMRQTKALIEAQGYDVIYGDTDSTFVWLKRP 558
Cdd:cd05537 81 RDEAKREKNAPLSQAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQVIYGDTDSTFVWLGEE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 559 HSEAQAAEIGRKLVAYVNDWWAQELGKS-QLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGMIQEGDAQRMVFKGLE 637
Cdd:cd05537 161 LDAAEAQAIGKELASQINQWWAQKLKEEfGLESFLEIEFETHYSRFFMPTIRGSDEGSKKRYAGLKSTDGGDELVFKGLE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 638 TVRTDWTPLAQQFQQELYLRIFRHQPYQDYVRETIARLMNGELDEQLVYRKRLRRPLAEYQRNVPPHVRAARLADEHNVK 717
Cdd:cd05537 241 TVRSDWTPLARQFQKELYERVFNDEPYEGFIKETVEELLAGELDELLVYRKRLRRPLSEYTKNVPPHVQAARLADQINRE 320
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....
gi 1994014905 718 LGRAQQYQQrgtIKYVWTTGGPEPVDYQQSPLDYDHYLSKQLQPVAEGILPFVN 771
Cdd:cd05537 321 LGRPRQYQW---IEYVITVNGPEPLEYRTSPLDYQHYIDKQLKPIADSILPFLG 371
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
150-346 |
1.47e-106 |
|
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged by UV irradiation or oxidation. It plays a pivotal role in replication-restart, a process that bypasses DNA damage in an error-free manner. Pol II is also involved in lagging strand synthesis.
Pssm-ID: 99827 [Multi-domain] Cd Length: 193 Bit Score: 324.14 E-value: 1.47e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 150 PPLKWVSLDIETSRHGELYCIGLEGCGQRVVYMLGPEPatpPDVGFSLVYVASRPLLLEKLNAWFAEHDPDVLIGWNVVQ 229
Cdd:cd05784 1 PKLKVVSLDIETSMDGELYSIGLYGEGQERVLMVGDPE---DDAPDNIEWFADEKSLLLALIAWFAQYDPDIIIGWNVIN 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 230 FDLRVLQKHAERYRIPLLLGRGNSELEWREHGfKNGVFFAQANGRLIIDGIEALKSAFWNFSSFSLEAVARELLGEGKAI 309
Cdd:cd05784 78 FDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSG-KPGQGFLSLPGRVVLDGIDALKTATYHFESFSLENVAQELLGEGKLI 156
|
170 180 190
....*....|....*....|....*....|....*..
gi 1994014905 310 DNPWDRMDEIDRRFHEDKPALATYNLQDCELVTRIFH 346
Cdd:cd05784 157 HDVDDRGAEIERLFREDKLALARYNLQDCELVWRIFE 193
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
399-768 |
1.53e-100 |
|
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis.
Pssm-ID: 99912 [Multi-domain] Cd Length: 323 Bit Score: 313.54 E-value: 1.53e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 399 QASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGLAQPDDRHSTeGFLGARFSREKHCLPGIVGQIWHG 478
Cdd:cd00145 1 EPYEGGYVFDPIPGLYENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYI-GVGFRSPKDRKGLLPRILEELLNF 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 479 RDEAKRQHNKP------------LSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHAIMRQTKALIEAQGYDVIYG 546
Cdd:cd00145 80 RDEAKKRMKAAklapeervlydnRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGARVIYG 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 547 DTDSTFVWLKRPHSEAQAAEIGRKLVAYVNDwwaqelgksqlTSALELEYETHFCRFLMptirgadtGSKKRYAGMIQE- 625
Cdd:cd00145 160 DTDSIFVSLPKMGTKEDAIKEGREILQELAD-----------EHLLELEFEKVYLPFFL--------GKKKRYAGLDIWk 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 626 -GDAQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRHQPYQDYVRETIARLMngeldeqlvyrkrlrrplaeyqrnvpph 704
Cdd:cd00145 221 gQDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEERKVEAVKEYIDELD---------------------------- 272
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1994014905 705 vraarlADEHNVKLGRAQQYQQRGTIkyvwttgGPEPVDYQQSPLDYDHYLSKQLQPVAEGILP 768
Cdd:cd00145 273 ------KVKYVVTRGGKGVPDYERAD-------PPLEDLDKRHRIDYEYYLERLLQPPLERIFE 323
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
150-556 |
2.39e-73 |
|
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Pssm-ID: 214691 [Multi-domain] Cd Length: 474 Bit Score: 247.06 E-value: 2.39e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 150 PPLKWVSLDIET-SRHG----------ELYCIGLEGCGQ-------RVVYMLGPepaTPPDVGFSLVYVASRPLLLEKLN 211
Cdd:smart00486 1 PPLKILSFDIETyTDGGnfpdaeifddEIIQISLVINDGdkkganrRILFTLGT---CKEIDGIEVYEFNNEKELLLAFF 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 212 AWFAEHDPDVLIGWNVVQFDLRVLQKHAERYRIPLL--LGRGNSELEWREHGFKNGV-------FFAQANGRLIIDGIEA 282
Cdd:smart00486 78 EFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLskIGRLKIGLRIPNKKPLFGSksfglsdIKVYIKGRLVIDLYRL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 283 LKSAFwNFSSFSLEAVARELLGEGKaIDNPWDRMDEIDRRFHEDKPALATYNLQDCELVTRIFHKTEIMPFLLERATVNG 362
Cdd:smart00486 158 YKNKL-KLPSYKLDTVAEYLLGKEK-DDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAG 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 363 LPADR--HGGSVAAFSHLYFPRMHRLGYVAPNLGEIPPQAS----------PGGYVMDSRPGLYDS-VLVLDYKSLYPSI 429
Cdd:smart00486 236 IPLRRtlYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSepdlkkkvkyEGGKVLEPKKGFYDNpVLVLDFNSLYPSI 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 430 IRTFLIDP--VGLVEGLAQPDDRHSTEGFL---------GARFSREKH--CLPGIVGQIWHGRDEAKRQHNK-------- 488
Cdd:smart00486 316 IIAHNLCYstLVGVGEVVIKGDLIIPEDLLtikyekgnkYRFVKKNIRkgILPKLLKKLLDKRKEIKKLMKKekdeseel 395
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1994014905 489 -----PLSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHAIMRQTKALIEAQGYD-----VIYGDTDSTFVWLK 556
Cdd:smart00486 396 kklldSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGYPkpgfkVIYGDTDSIFVTKP 473
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
399-767 |
3.22e-58 |
|
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.
Pssm-ID: 99919 Cd Length: 371 Bit Score: 202.55 E-value: 3.22e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 399 QASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGlaqPDDRHSTEGFLGARFSREKHCL-PGIVGQIWH 477
Cdd:cd05536 2 ESYEGGIVLEPEKGLHENIVVLDFSSLYPSIMIKYNISPDTLVRE---GCEDCDVEPQVGHKFRKDPPGFiPSVLEDLLE 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 478 GRDEAK---RQHNKPLS---------QALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHAIMRQTKALIEAQGYDVIY 545
Cdd:cd05536 79 ERRRIKekmKKLDPESEeykllderqRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAEEKGFKVIY 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 546 GDTDSTFVwlKRPHSEAQAAEIgRKLVAYVNdwwaQELGksqltsaLELEYETHFCRFLMPTirgadtgsKKRYAGMIQE 625
Cdd:cd05536 159 GDTDSLFV--KIDGADAVKKKV-KKLLKYIN----EELP-------LELEIEKFYKRGFFVT--------KKRYAGLTED 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 626 GdaqRMVFKGLETVRTDWTPLAQQFQQELYLRIFRHQPYQ---DYVRETIARLMNGELD-EQLVYRKRLRRPLAEYqRNV 701
Cdd:cd05536 217 G---KIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEeavKIVKEVIEKLKRGEVPpEKLVIWKQLTKDLSEY-KAT 292
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1994014905 702 PPHVRAARLADEHNVKLGRAQqyqqrgTIKYVWTTG-GP-----EPVDYQQSPLDYD--HYLSKQLQPVAEGIL 767
Cdd:cd05536 293 GPHVAAAKKLAKRGYKVRPGT------KIGYVIVKGsGKisdraYPYDMVDEKHKYDaeYYIDNQVLPAVLRIL 360
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
92-781 |
4.83e-50 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 188.74 E-value: 4.83e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 92 MRLEKKLRENGvTVYEGDIRPPERYLMERFITAPVWVEGETRGSQLVNARMKPH------PDYRPPLKWVSLDIETSRHG 165
Cdd:PRK05761 110 RRLRLSVRDIP-RAWEADIKYEFRYIYDNGLIPGMPYDVKNGLESVEPEILVEEikkafkDERKLAEDWLPIFEAPIPKI 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 166 ELYCIGLEgcgqrvVYmlGPEPATPPDVGfslvyvaSRPLLLEKLNAwFAEHDPDVLIgwNVVQFDLRVLQKHAERYRIP 245
Cdd:PRK05761 189 KRIAIDIE------VY--TPAKGRIPDDS-------EKELLAELFDI-ILEYPPVVTF--NGDNFDLPYLYNRALKLGIP 250
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 246 lllgRGNSELEWRE---HGFKNGVFFaqangrliidgIEALKS-AFWN---FSSFSLEAVARELLGEGKA-IDNPWDRMD 317
Cdd:PRK05761 251 ----KEEIPIEPGRagiHIDLYKFFQ-----------NKAVRSyAFYGkyrHREARLDAVGRALLGISKVeLETNISELD 315
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 318 EIDrrfhedkpaLATYNLQDCELVTR--IFHKTEIMPFLLERATVNGLP---ADRHGGSvAAFSHLYFPRMHRLGYVAPN 392
Cdd:PRK05761 316 LEE---------LAEYNFRDAEITLKltFFNNELVLKLILLLSRISKLPieeLSRATIS-TWISNLEYWEHRKRGWLIPW 385
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 393 LGEIPPQASP-------------GGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDP--VGlVEGLAQPDDRHSTEgfL 457
Cdd:PRK05761 386 KEDILRLDHEvykkaiikgkkyrGGLVFQPPPGIFFNVYVLDFASLYPSIIVKWNLSPetVR-IPECKCHYDDEVPE--L 462
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 458 GARFSREKhclPGIVGQIwHG--RDE-----AKRQHNKPLSQ-----------ALKIIMNAFYGVLGTSACRFFDPRLAS 519
Cdd:PRK05761 463 GHSVCDDR---PGLTSVL-VGllRDFrvkiyKKKAKDPNLDEerrawydvvqrALKVFLNASYGVFGAENFKLYRIEVAE 538
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 520 SITMRGHAIMRQTKALIEAQGYDVIYGDTDSTFVWlkrPHSEAQAaeigRKLVAYVNDwwaqELGksqltsaLELEYETH 599
Cdd:PRK05761 539 SITALGREILLSTKKKAEELGLKVLYGDTDSLFVW---GPTKESL----EELIKEIEE----RTG-------IDLEVDKT 600
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 600 FcRFLmptirgADTGSKKRYAGMIQEGDaqrMVFKGLETVRTDWTPLAQQFQQELyLRIFR-----------HQPYQDYV 668
Cdd:PRK05761 601 Y-DWV------AFSGLKKNYFGVLKDGK---VKIKGIVAKKRNTPEFVKELQREV-LEVLKsirspedvekvKDEIEDVL 669
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 669 RETIARLMNGELD-EQLVYRKRLRRPLAEYQRNVPPHVRAARLADEHNVKLGRAQQyqqrgtIKYVWTTG--GPEPVDYQ 745
Cdd:PRK05761 670 KRYYEKLRAKDYPlDELAIRVRLSKPLDEYTKNTPQHVKAALQLRDYGVEVSPGDI------ISYVKVDDkrGVKPVQLA 743
|
730 740 750
....*....|....*....|....*....|....*..
gi 1994014905 746 Q-SPLDYDHYLsKQLQPVAEGILPFVNDDFATIVTGQ 781
Cdd:PRK05761 744 KlSEIDVEKYI-ELLRSALEQILSALGVSWDDIRGTT 779
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
382-767 |
1.41e-48 |
|
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.
Pssm-ID: 395085 Cd Length: 439 Bit Score: 177.80 E-value: 1.41e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 382 RMHRLGYVAPNlgeiPPQAS------PGGYVMDSRPGLYDS-VLVLDYKSLYPSIIR------TFLIDPVGLVEGLAQPD 448
Cdd:pfam00136 22 LALEEGFILPD----RPSAKgdedgyQGATVIEPKKGFYDKpVLVLDFNSLYPSIIQahnlcyTTLVRSVDEANNLPPED 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 449 DRHS-TEGFLGARF---SREKHCLPGIVGQIWHGRDEAK---RQHNKPL--------SQALKIIMNAFYGVLGTSACRFF 513
Cdd:pfam00136 98 NLITvECTPRGVYFvkdHVREGLLPKLLKDLLAKRKAIKkllKEETDPFeraildkqQLALKITANSVYGFTGFANGRLP 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 514 DPRLASSITMRGHAIMRQTKALIEAQ---GYDVIYGDTDSTFVWLkRPHSEAQAAEIGRKLVAYVNdwwaqelgKSQLTS 590
Cdd:pfam00136 178 CLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTDSVFIEF-GGKDVEEAMKIGDELAEHVN--------QDLFKS 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 591 ALELEYETHFCRFLMPtirgadtgSKKRYAGMIQEGDAQ--RMVFKGLETVRTDWTPLAQQFQQELYLRIFRHQPYQD-- 666
Cdd:pfam00136 249 PIKLEFEKVYKPLLLI--------SKKKYAGLKYTAPSNfnKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSDRGLPVgl 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 667 -YVRETI----ARLMNGELD-EQLVYRKRLRRPLAEYQRNVPPHVRAA-RLADEHnvklGRAQQYQQRgtIKYVWTTGGP 739
Cdd:pfam00136 321 eFVISILndarSDLRNNKVPlEKFVISKELSKPPDNYKSKNLPHVEVAlRMNKRN----GEAPEVGDR--IPYVIVKAAK 394
|
410 420 430 440
....*....|....*....|....*....|....*....|..
gi 1994014905 740 EPVD---YQQS-----------PLDYDHYLSKQLQPVAEGIL 767
Cdd:pfam00136 395 GLKNlliYERAedpeyvlennlPIDYEYYFSNQLIPPVARLL 436
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
154-346 |
2.08e-46 |
|
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D 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 exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon and zeta), and eukaryotic viral and plasmid-borne enzymes. Nuclear DNA polymerases alpha and zeta lack the four conserved acidic metal-binding residues. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Pssm-ID: 176646 [Multi-domain] Cd Length: 199 Bit Score: 164.07 E-value: 2.08e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 154 WVSLDIETSRH--------GELYCIGLEG--CGQRVVYMLGPEPAT---PPDVGFSLVYVASRPLLLEKLNAWFAEHDPD 220
Cdd:cd05160 1 VLSFDIETTPPvggpepdrDPIICITYADsfDGVKVVFLLKTSTVGddiEFIDGIEVEYFADEKELLKRFFDIIREYDPD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 221 VLIGWNVVQFDLRVLQKHAERYRIPLllgRGNSELEWREHGFKNGVFFAQANGRLIIDGIEALKSAFWnFSSFSLEAVAR 300
Cdd:cd05160 81 ILTGYNIDDFDLPYLLKRAEALGIKL---TDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFK-LKSYTLDAVAE 156
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 1994014905 301 ELLGEGKAIDNPWDRMDEidrRFHEDKPALATYNLQDCELVTRIFH 346
Cdd:cd05160 157 ELLGEGKEKVDGEIIEDA---EWEEDPERLIEYNLKDAELTLQILE 199
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
204-767 |
1.04e-44 |
|
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA polymerases.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: 273159 [Multi-domain] Cd Length: 1172 Bit Score: 174.09 E-value: 1.04e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 204 PLLLEKLNA------WF----AEHDPDVLIGWNVVQFDLRVLQKHAERYRIPLLLGRGnselEWREHGFKNGVFFAQANG 273
Cdd:TIGR00592 575 PSLVEDLATeralikKFmakvKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIG----RLRRSPKFGRRFGERTCG 650
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 274 RLIIDGIEALKSAFWNFSSFSLEAVARELLGEGKAIDnpwdrMDEIDRRFHEDKP--ALATYNLQDCELVTRIFHKTEIM 351
Cdd:TIGR00592 651 RMICDVEISAKELIRCKSYDLSELVQQILKTERKVIP-----IDNINNMYSESSSltYLLEHTWKDAMFILQIMCELNVL 725
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 352 PFLLERATVNGLPADR--HGGSVAAFSHLYFPRMHRLGYVAPNLGEIPPQ-------------------ASPGGYVMDSR 410
Cdd:TIGR00592 726 PLALQITNIAGNIMSRtlMGGRSERNEFLLLHAFYENNYIVPDKQIFRKQqklgdedeeidgykkgkkaAYAGGLVLEPK 805
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 411 PGLYDS-VLVLDYKSLYPSIIRTFLI------DPVGLVEGLAQPDDrhstegflgarfSREKHCLPGIVGQIWHGRDEAK 483
Cdd:TIGR00592 806 VGLYDKyVLLMDFNSLYPSIIQEFNIcfttvqQKVDEDELPELPDS------------ELEMGILPRELRKLVERRKEVK 873
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 484 RQHNKPLS-----------QALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHAIMRQTKALIEAQGYDVIYGDTDStf 552
Cdd:TIGR00592 874 KLMKQDLNpdlrlqydirqKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEMNLEVIYGDTDS-- 951
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 553 VWLKRPHSE-AQAAEIGRKLVAYVNdwwaqelgksQLTSALELEYETHFCRFLMPTirgadtgsKKRYAGMIQEGDAQ-- 629
Cdd:TIGR00592 952 IMINTPGTKyEEVFKIGKEFKSEVN----------KLYKLLELDIDGVFKRLLLLK--------KKKYAAIKVEGDSDgn 1013
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 630 ---RMVFKGLETVRTDWTPLAQQFQQELYLRIFRHQPYQDYVRETIARL-------MNGELD-EQLVYRKRLRRPLAEY- 697
Cdd:TIGR00592 1014 yttKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLekigknvLNGEVPlEKFVINKQLTRDPKDYp 1093
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 698 QRNVPPHVRAA-RLADEHNVKlgraqqYQQRGTIKYVWTTGG-----------PEPVDYQQSPLDYD--HYLSKQLQPVA 763
Cdd:TIGR00592 1094 DGASLPHVHVAlRINARGGRK------VKAGDVVSYVICKDGgnlsarqrayaLEELQRKHNNLIYDtqYYLEHQIHPVV 1167
|
....
gi 1994014905 764 EGIL 767
Cdd:TIGR00592 1168 LRIL 1171
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
403-762 |
4.63e-41 |
|
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than check point control, has been assigned to this enzyme. Pol alpha contains both polymerase and exonuclease domains, but lacks exonuclease activity suggesting that the exonuclease domain may be for structural purposes only.
Pssm-ID: 99915 Cd Length: 400 Bit Score: 155.43 E-value: 4.63e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 403 GGYVMDSRPGLYDS-VLVLDYKSLYPSIIRTFLID------PVGLVEGLAQPDDRHSTEgflgarfsrEKHCLPGIVGQI 475
Cdd:cd05532 10 GGLVLEPKKGLYDKfILLLDFNSLYPSIIQEYNICfttvdrADPDDEDDEEPPLPPSDQ---------EKGILPRIIRKL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 476 WHGRDEAKRQHNKPLS-----------QALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHAIMRQTKALIEAQGYDVI 544
Cdd:cd05532 81 VERRRQVKKLMKSEKDpdkkaqldirqLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKMNLEVI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 545 YGDTDSTFVwlkrpH----SEAQAAEIGRKLVAYVNDwwaqelgksqLTSALELEYETHFCRFLMPtirgadtgSKKRYA 620
Cdd:cd05532 161 YGDTDSIMI-----NtgttDYEEAKKLGNKIKKEVNK----------SYKKLEIDIDGVFKRLLLL--------KKKKYA 217
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 621 GMIQEGDAQRMV---FKGLETVRTDWTPLAQQFQQELYLRIFRHQPY-------QDYVRETIARLMNGELD-EQLVYRKR 689
Cdd:cd05532 218 ALKVVDDDKGKLkkeVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSRediveniHEYLRKINEDLRNGKIPlEKFIITKQ 297
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 690 LRRPLAEY-QRNVPPHVRAA-RLADE-HNVKLGRaqqyqqrgTIKYVWTTGGPE---------PVDYQQSP---LDYDHY 754
Cdd:cd05532 298 LTKNPEEYpDKKSLPHVQVAlRMNKRgRKVKAGD--------TIPYIICKDGSSksladrayhPDEVKKNEnlkIDIEYY 369
|
....*...
gi 1994014905 755 LSKQLQPV 762
Cdd:cd05532 370 LSQQILPP 377
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
96-768 |
1.51e-37 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 151.72 E-value: 1.51e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 96 KKLRENGVTV-------------YEGDIRPPERYLMERFITAPVWVEGETRGSQLVNARMK----------------PHP 146
Cdd:PTZ00166 174 RSLIESGVVVcgggwdgirlfqtYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRPPKKKtstcqievdcsyedliPLP 253
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 147 ---DYR--PPLKWVSLDIEtsrhgelyCIGLEGCG------------QRVVYMLGPEPATPPDVGFSLVYVASRP----- 204
Cdd:PTZ00166 254 pegEYLtiAPLRILSFDIE--------CIKLKGLGfpeaendpviqiSSVVTNQGDEEEPLTKFIFTLKECASIAganvl 325
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 205 ------LLLEKLNAWFAEHDPDVLIGWNVVQFDLRVLQKHAERYRIP--LLLGRGNSElewrEHGFKNGVFFAQA----- 271
Cdd:PTZ00166 326 sfetekELLLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNdfKYLGRIKST----RSVIKDSKFSSKQmgtre 401
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 272 ------NGRLIIDGIEALKSAFwNFSSFSLEAVARELLGEGKAiDNPWDRMDEIDRRFHEDKPALATYNLQDCELVTRIF 345
Cdd:PTZ00166 402 skeiniEGRIQFDVMDLIRRDY-KLKSYSLNYVSFEFLKEQKE-DVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLL 479
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 346 HKTEIMPFLLERATVNGLPAD---RHGGSVAAFSHLYfPRMHRLGYVAP---NLGEIPPQASPGGYVMDSRPGLYDS-VL 418
Cdd:PTZ00166 480 DKLLLIYNYVEMARVTGTPIGwllTRGQQIKVTSQLL-RKCKKLNYVIPtvkYSGGGSEEKYEGATVLEPKKGFYDEpIA 558
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 419 VLDYKSLYPSII------RTFLIDPVGLVegLAQPDDRhsTEGFLGARF---SREKHCLPGIVGQIWHGRDEAKRQHNK- 488
Cdd:PTZ00166 559 TLDFASLYPSIMiahnlcYSTLVPPNDAN--NYPEDTY--VTTPTGDKFvkkEVRKGILPLIVEELIAARKKAKKEMKDe 634
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 489 --PLSQ--------ALKIIMNAFYGVLGTSACRFFdPRL--ASSITMRGHAIMRQTKALIE-----AQGYD----VIYGD 547
Cdd:PTZ00166 635 kdPLLKkvlngrqlALKISANSVYGYTGAQVGGQL-PCLevSTSITSFGRQMIDKTKELVEkhytkANGYKhdatVIYGD 713
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 548 TDStfVWLKRPHSE-AQAAEIGRKlvayvndwwAQELGKSQLTSALELEYETHFCRFLMPtirgadtgSKKRYAGMI--- 623
Cdd:PTZ00166 714 TDS--VMVKFGTDDiQEAMDLGKE---------AAERISKKFLKPIKLEFEKVYCPYLLM--------NKKRYAGLLytn 774
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 624 -QEGDaqRMVFKGLETVRTDWTPLAQQFQQELYLRIFRHQPYQ---DYVRETIARLMNGELD-EQLVYRKRLRRplAEYQ 698
Cdd:PTZ00166 775 pEKYD--KIDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVEsaiEFTKGKISDLLQNRIDiSLLVITKSLGK--DDYE 850
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 699 RNVpPHVRAARladehnvKL-----GRAQQYQQRgtIKYVWTTGGPEPVDYQQS-----------PLDYDHYLsKQLQP- 761
Cdd:PTZ00166 851 GRL-AHVELAK-------KLrqrdpGSAPNVGDR--VSYVIVKGAKGAPQYERAedplyvlenniPIDTQYYL-DQIKNp 919
|
810
....*....|
gi 1994014905 762 ---VAEGILP 768
Cdd:PTZ00166 920 llrIFEGVMD 929
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
403-755 |
4.69e-34 |
|
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Pssm-ID: 99913 Cd Length: 372 Bit Score: 134.40 E-value: 4.69e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 403 GGYVMDSRPGLYDSVLVLDYKSLYPSIIRTF-----LIDPVglveglaQPDDRHSTEGFLGARFSREKhclPGIVGQIWh 477
Cdd:cd05530 15 GAIVLEPPPGIFFNVVVLDFASLYPSIIKVWnlsyeTVNCP-------HCECKTNEVPEVGHWVCKKR---PGITSQII- 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 478 G--RD--------EAKRQHNKP--------LSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHAIMRQTKALIEAQ 539
Cdd:cd05530 84 GllRDlrvkiykkKAKDKSLDEemrqwydvVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIITSTIKKAREL 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 540 GYDVIYGDTDSTFVWlkRPhSEAQAAEIgrklvayvNDWWAQELGksqltsaLELEYETHFcRFLMPtirgadTGSKKRY 619
Cdd:cd05530 164 GLKVLYGDTDSLFLW--NP-PQEQLEDL--------VEWVEKELG-------LDLELDKEY-RYVVF------SGLKKNY 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 620 AGMIQEGDaqrMVFKGLeTVRTDWTPlaqQFQQELYLRIFR--------------HQPYQDYVRETIARLMNGELD-EQL 684
Cdd:cd05530 219 LGVTKDGS---VDIKGL-LGKKRNTP---EFVKELFYEVIEilsavnspedfekaREKIRDIVKGVYKRLKKKEYTlDQL 291
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1994014905 685 VYRKRLRRPLAEYQRNVPPHVRAARLADEHNVKLGRAQqyqqrgTIKYVWTTG--GPEPVDYQQSP-LDYDHYL 755
Cdd:cd05530 292 AFKVMLSKPPEEYTKNTPQHVKAARQLEKYGRNVEAGD------IISYVKVKGkeGVKPVQLARLDeVDVEKYV 359
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
384-761 |
4.74e-30 |
|
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.
Pssm-ID: 99917 Cd Length: 451 Bit Score: 124.25 E-value: 4.74e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 384 HRLGYVA--PNLGEI----PPQASPggYVMDSRPGLY-DSVLVLDYKSLYPSII-------------------------- 430
Cdd:cd05534 15 KPENYILpsPSRQQVaqqrALECLP--LVMEPESGFYsDPVIVLDFQSLYPSIMiaynycystclgrveelngggkfgfl 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 431 RTFLIDPVGLVEGLAQPDDRH-STEGFLGARFSREKHCLPGIVGQIWHGRDEAKR-----QHNKPLSQ-------ALKII 497
Cdd:cd05534 93 GVKLYLPPPPLDLLLLKDDVTiSPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKamkkyKDDKKLQRildarqlALKLL 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 498 MNAFYGVlgTSACrfFDPR-----LASSITMRGHAIMRQTKALIEAQGY---DVIYGDTDSTFVWLKrPHSEAQAAEIGR 569
Cdd:cd05534 173 ANVTYGY--TAAS--FSGRmpcveIADSIVQTGRETLERAIELIESTPKwgaKVVYGDTDSLFVLLP-GRTKEEAFKIGK 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 570 KLVAYVNdwwaqelgkSQLTSALELEYET--HFCrFLMptirgadtgSKKRYAGMIQEGDAQRMVF---KGLETVRTDWT 644
Cdd:cd05534 248 EIAEAVT---------AANPSPIKLKFEKvyHPC-VLV---------TKKRYVGYKYESPDQTEPTfdaKGIETVRRDGC 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 645 PLAQQFQQELYLRIFRHqpyQD------YVRETIARLMNGELDEQ-LVYRKRLRRPLAEYQRNVPPHVRAARLADEHNVk 717
Cdd:cd05534 309 PAVQKILEKSLRILFET---KDlstvksYLQRQWSKLLQGRVSIQdFIFAKEVRLGTYKEGATLPAGAIVALRRMEKDP- 384
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*.
gi 1994014905 718 lGRAQQYQQRgtIKYVWTTGGP---------EPVDYQQSP---LDYDHYLSKQLQP 761
Cdd:cd05534 385 -RAEPQYGER--VPYVVVRGEPgsrlidlvvSPEEFLADPslrLDAEYYITKQIIP 437
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
403-767 |
2.27e-28 |
|
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Pssm-ID: 99914 Cd Length: 352 Bit Score: 117.06 E-value: 2.27e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 403 GGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPvglvEGLAQPDDRHSTEGFLGARFSREKhclPGIVGQIWHG---- 478
Cdd:cd05531 7 GGLVFQPEPGLYENVAQIDFSSMYPSIIVKYNISP----ETINCRCCECRDHVYLGHRICLKR---RGFLPEVLEPller 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 479 RDEAKRQ-----HNKPLSQALKIIMNAFYGVLGTSACRFfdPRLAS--SITMRGHAIMRQTKALIEAQGYDVIYGDTDST 551
Cdd:cd05531 80 RLEYKRLkkeedPYAGRQKALKWILVTSFGYLGYKNAKF--GRIEVheAITAYGRKILLRAKEIAEEMGFRVLHGIVDSL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 552 FVWlKRPHSEAQAAEIGRKlvayvndwwaqelgksqltSALELEYETHfCRFL--MPTIRGadTGSKKRYAGMIQEGDaq 629
Cdd:cd05531 158 WIQ-GRGDIEELAREIEER-------------------TGIPLKLEGH-YDWIvfLPERDG--LGAPNRYFGRLSDGE-- 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 630 rMVFKGLETVRTDWTPLAQQFQQELyLRIF-----------RHQPYQDYVRETIARLMNGELdEQLVYRKRLRRPLAEYQ 698
Cdd:cd05531 213 -MKVRGIELRRRDTPPFVKKFQEEA-LDILasaktpeellkLREEALDLFRRYLQRLREGDL-EDLIIEKKISKRSSEYK 289
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 699 RNVPPHVRAARLADEHnvklgraqqYQQRGTIKYVWTTGG-PEPVDYQQSPLDYDHYLsKQLQPVAEGIL 767
Cdd:cd05531 290 VLASTALKALRAKGVS---------VVPGMKIEYIVRDGKrPVPDLGNDEGYDTKYYR-ELLERAAEELL 349
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
403-767 |
4.50e-28 |
|
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.
Pssm-ID: 99916 Cd Length: 393 Bit Score: 117.37 E-value: 4.50e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 403 GGYVMDSRPGLYDS-VLVLDYKSLYPSII------RTFLIDPVGLVEGLaqPDDRHST-EGFLGARFSREKHCLPGIVGQ 474
Cdd:cd05533 5 GATVIEPIKGYYDVpIATLDFASLYPSIMmahnlcYTTLLNKNTAKKLP--PEDYIKTpNGDYFVKSSVRKGLLPEILEE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 475 IWHGRDEAKRQHNK---PLSQ--------ALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHAIMRQTKALIE-----A 538
Cdd:cd05533 83 LLAARKRAKKDLKEetdPFKKavldgrqlALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEekytkA 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 539 QGY----DVIYGDTDSTFVWLKRPhSEAQAAEIGRKLVAYVNdwwaqelgkSQLTSALELEYETHFCRFLMPtirgadtg 614
Cdd:cd05533 163 NGYshdaKVIYGDTDSVMVKFGVS-DVEEAMKLGKEAAEYVS---------KKFIKPIKLEFEKVYFPYLLI-------- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 615 SKKRYAGMI----QEGDaqRMVFKGLETVRTDWTPLAQQFQQELYLRIFRHQPYQ---DYVRETIARLMNGELD-EQLVY 686
Cdd:cd05533 225 NKKRYAGLLwtnpDKHD--KMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEgaiEFVKGVISDLLQNKIDiSLLVI 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 687 RKRLRRPLAEYQRNVpPHVRAA---RLADEhnvklGRAQQYQQRgtIKYVWTTGGPEPVDYQQS-----------PLDYD 752
Cdd:cd05533 303 TKALTKTADDYAGKQ-AHVELAermRKRDP-----GSAPNVGDR--VPYVIIKGAKGAKAYEKAedpiyvlenniPIDTQ 374
|
410
....*....|....*....
gi 1994014905 753 HYLSKQLQP----VAEGIL 767
Cdd:cd05533 375 YYLENQLSKpllrIFEPIL 393
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
203-683 |
2.11e-24 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 109.39 E-value: 2.11e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 203 RPLLLEKLNaWFAEHDPDVLIGWNVVQFDLRVLQKhaeryRIPLLLGR--GNSELEWREHGFKNGVF-FAQANGRLIIDG 279
Cdd:PHA02528 179 REMLLEYIN-FWEENTPVIFTGWNVELFDVPYIIN-----RIKNILGEktAKRLSPWGKVKERTIENmYGREEIAYDISG 252
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 280 IEAL-------KSAFWNFSSFSLEAVARELLGEGKAidnpwDRMDEIDRRFHEDKPAL-ATYNLQDCELVTRIFHKTEIM 351
Cdd:PHA02528 253 ISILdyldlykKFTFTNQPSYRLDYIAEVELGKKKL-----DYSDGPFKKFRETDHQKyIEYNIIDVELVDRLDDKRKLI 327
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 352 PFLLERATVNGLPADRHGGSVAAFSHLYFPRMHRLGYVAPNLGEIPPQASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIR 431
Cdd:PHA02528 328 ELVLSMAYYAKINFEDVFSPIKTWDAIIFNSLKEEKIVIPENKSHKKQKYAGAFVKEPVPGAYRWVVSFDLTSLYPSIIR 407
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 432 -----------TFLIDPV-GLVEGLAQ-PDDRHSTEGFlGARFSREKH-CLPGIVGQIWHGRD-------EAKRQ----- 485
Cdd:PHA02528 408 qvnispetiagTFHVAPVhEYINKTAPrPSDEYSCSPN-GWMYRKDIRgVIPTEIKKVFDQRKiykkkmlAAERNaelik 486
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 486 ---------HNKPLS-----------------------------------------QALKIIMNAFYGVLGTSACRFFDP 515
Cdd:PHA02528 487 tiledlndsVDTPIDvdyyfdfsdefkaelktltksslkalleecekeialcntiqMARKILINSLYGALGNEHFRYYDL 566
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 516 RLASSITMRGHA----IMRQT----KALIEAQGYD-VIYGDTDSTFVWLkrphsEAQAAEIGRKLVAYVNDW--WAQELG 584
Cdd:PHA02528 567 RNAEAITLFGQLaiqwIERKMneylNKLCKTEDEDyVIYGDTDSIYVNL-----DPLVEKVGEDKFKDTNHWvdFLDKFC 641
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 585 KSQLTSALELEYEtHFCRF------LMPTIRG--ADTG---SKKRYAGMIQEGDAQR-----MVFKGLETVRTDwTPlaq 648
Cdd:PHA02528 642 KERMEPYIDSSYR-ELCEYmnnyehLMFMDREaiAGPGfwtAKKRYALNVWDSEGTRyaepkLKIMGIETQRSS-TP--- 716
|
570 580 590
....*....|....*....|....*....|....*.
gi 1994014905 649 qfqqelylrifrhQPYQDYVRETIARLMN-GELDEQ 683
Cdd:PHA02528 717 -------------KAVQKALKEAIRRILQeGEESLQ 739
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
399-763 |
1.78e-14 |
|
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Pssm-ID: 99921 Cd Length: 347 Bit Score: 75.60 E-value: 1.78e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 399 QASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGLAQPD-DRHSTEGFLGARFSREkhclpgivgqiwh 477
Cdd:cd05538 1 GKFEGGYAYVFITGVLGPIVHADVASLYPSIMLAYRICPARDSLGIFLALlKYLVELRLAAKESARA------------- 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 478 GRDEAKRQHNKPLSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHAIMRQTKALIEAQGYDVIYGDTDStfVWLKR 557
Cdd:cd05538 68 AARPAERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRRRGATPVEVDTDG--IYFIP 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 558 PHSEAQAAEIgRKLVAYVNdwwaqelgkSQLTSALELEYETHFCRFLmptIRGadtgsKKRYAGMIQEGdaqRMVFKGLE 637
Cdd:cd05538 146 PNGVDTEDEE-EELVRELS---------STLPKGITVEFDGRYRAMF---SYK-----IKNYALLDYDG---KLIVKGSA 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 638 TVRTDWTPLAQQFQQELYLRIFRHQPYQ--DYVRETIARLMNGELDEQLVYR-KRLRRPLAEYQRNV------PPHVRAA 708
Cdd:cd05538 205 FRSRGIEPFLREFLREAVRLLLQGDGAGvhDLYEDYLRRLRSHELPISDLARtETLKESPEEYLQKVragkrnPAAAYEI 284
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*...
gi 1994014905 709 RLADEHNVKLGRAQQYQQRGTIK-YVWTTGGPEPVDYQQSPLDYD--HYLSKQLQPVA 763
Cdd:cd05538 285 ALARPREWRAGDRVTYYVSGTGKgVSVYENCRLVADYDPAHPDENtgFYAERLLQLAA 342
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
150-344 |
2.93e-12 |
|
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show similarity to eukaryotic DNA polymerases involved in DNA replication. Some archaea possess multiple family-B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family-B DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.
Pssm-ID: 99823 [Multi-domain] Cd Length: 195 Bit Score: 66.22 E-value: 2.93e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 150 PPLKWVSLDIET-SRHGElyciglegcgqrvvymlgPEPATPP-------DVGFSLV------------YVASRPLLLEK 209
Cdd:cd05780 1 EDLKILSFDIEVlNHEGE------------------PNPEKDPiimisfaDEGGNKVitwkkfdlpfveVVKTEKEMIKR 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 210 LNAWFAEHDPDVLIGWNVVQFDLRVLQKHAERYRIPLLLGRGNSELEWREHGFKNGVFFaqaNGRLIIDgIEALKSAFWN 289
Cdd:cd05780 63 FIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEI---KGRIHVD-LYPVARRTLN 138
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1994014905 290 FSSFSLEAVARELLGEGKA------IDNPWDRMDEIDRrfhedkpaLATYNLQDCELVTRI 344
Cdd:cd05780 139 LTRYTLERVYEELFGIEKEdvpgeeIAEAWDSGENLER--------LFRYSMEDAKYTYEI 191
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
89-298 |
5.81e-12 |
|
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold.
Pssm-ID: 397292 Cd Length: 333 Bit Score: 67.83 E-value: 5.81e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 89 RQLMRL-EKKLRENGVTVYEGDIRPPERYLMERFITAPVW-------VEGETRGSQLVNARMKPHPDY--------RPPL 152
Cdd:pfam03104 76 RPLLKIrKYLSPENISDVYEYDVDYLERFLIDNDIVGFGWykvkvypFRAEGRISNCDVEIDCDSPDLisvpfekeWPPL 155
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 153 KWVSLDIET-SRHGE-----------------LYCIGLEGCGQRVVYMLGpEPATPPDVGFSLVYVASRPLL-------- 206
Cdd:pfam03104 156 RVLSFDIECtSLPGKfpdaenvkdpiiqiscmLDGQGEPEPEPRFLFTLR-ECDSEDIEDFEYTPKPIYPGVkvfefpse 234
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 207 LEKLNAWFA---EHDPDVLIGWNVVQFDLRVLQKHAERYRIPLLLGRGnselEWREHGFKNG---VFFAQA------NGR 274
Cdd:pfam03104 235 KELLRRFFEfirQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIG----RLNRGGRSKVreiGFGTRSyekvkiSGR 310
|
250 260
....*....|....*....|....
gi 1994014905 275 LIIDgIEALKSAFWNFSSFSLEAV 298
Cdd:pfam03104 311 LHLD-LYRVIKRDYKLPSYKLNAV 333
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
206-326 |
8.09e-08 |
|
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Pssm-ID: 99828 [Multi-domain] Cd Length: 207 Bit Score: 53.57 E-value: 8.09e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 206 LLEKLNAWFAEHDPDVLIGWNVVQFDLRVLQKHAERYRIPLLLGRGNSELEWREHGFKngvfFAQ---------ANGRLI 276
Cdd:cd05785 61 LLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFR----FAErlidyprydIPGRHV 136
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1994014905 277 IDGIEALKS---AFWNFSSFSLEAVAREL--------LGEGKAIDNPWDRMDEIDRRFHED 326
Cdd:cd05785 137 IDTYFLVQLfdvSSRDLPSYGLKAVAKHFglaspdrtYIDGRQIAEVWRSDPARLLAYALD 197
|
|
| 43A |
PHA02524 |
DNA polymerase subunit A; Provisional |
205-447 |
1.65e-07 |
|
DNA polymerase subunit A; Provisional
Pssm-ID: 164925 [Multi-domain] Cd Length: 498 Bit Score: 54.62 E-value: 1.65e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 205 LLLEKLNAWFAeHDPDVLIGWNVVQFDL--------RVLQKHAERYRIPLllGRGNSELEWREHGFKngvFFAQANGRLI 276
Cdd:PHA02524 183 LLLNYIQLWKA-NTPDLVFGWNSEGFDIpyiitritNILGEKAANQLSPY--GKITSKTITNLYGEK---IIYKIHGIAL 256
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 277 IDGIEALKS-AFWNFSSFSLEAVA-RELLGEGKAIDNPWDRMDEIDRRFHEDkpalatYNLQDCELVTRIFHKTEIMPFL 354
Cdd:PHA02524 257 MDYMDVFKKfSFTPMPDYKLGNVGyREVKADKLDYEGPINKFRKADHQRYVD------YCVRDTDIILLIDGRRCFIDLI 330
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 355 LERATVNGLPADRHGGSVAAFSHLYFPRMHRLGYVAPNLGEIPPQASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFL 434
Cdd:PHA02524 331 LSLSYYAKIRFDDVLGTIKVWDSIIFNSLVESNVVIPAMKASPKQSFPGAYVKEPVPGGYRYGLSFDLTSLYPSILRLLN 410
|
250
....*....|...
gi 1994014905 435 IDPvGLVEGLAQP 447
Cdd:PHA02524 411 ISP-EMIAGMFSP 422
|
|
| 43B |
PHA02523 |
DNA polymerase subunit B; Provisional |
479-649 |
2.34e-06 |
|
DNA polymerase subunit B; Provisional
Pssm-ID: 164924 Cd Length: 391 Bit Score: 50.48 E-value: 2.34e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 479 RDEAKRQHNKpLSQalKIIMNAFYGVLGTSACRFFDPRLASSITMRGHAIMRQTKA--------LIEAQGYD-VIYGDTD 549
Cdd:PHA02523 34 KEEQKRNTNQ-LNR--KILINSLYGALGNNWFRYFDLRNAEAITTYGQLAIRWIERklneyineLVKTTGVDyVCYIDTD 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 550 STFVwlkrpHSEAQAAEIGRKLVAYVNDW--WAQELGKSQLTSALELEYET---------HFCRFLMPTIRGADTGS--- 615
Cdd:PHA02523 111 SVYL-----NMEAVVNRVGIDKFRDTNHLidFLDNLGSKKLEPFIDDSYKEleeymnhdhHLLLMDREAIFGAPLGSdgi 185
|
170 180 190 200
....*....|....*....|....*....|....*....|....*
gi 1994014905 616 ------KKRYAGMIQEGDAQR-----MVFKGLETVRTDwTPLAQQ 649
Cdd:PHA02523 186 ggfwtgKKRYALNVYDMEGTRyaephLKIMGLETQRSS-TPLACQ 229
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
93-432 |
3.46e-05 |
|
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA polymerases.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: 273159 [Multi-domain] Cd Length: 1172 Bit Score: 47.74 E-value: 3.46e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 93 RLEKKLRENGVTVYEGDIRPP--ERYLMERfITAPVWVEGETRGSQLVnarmKPHPDyrPPLKWVSLDIETSRH------ 164
Cdd:TIGR00592 144 AINDFSNHHPAVVDIVKKAIPvsTRYLLEK-ILIPVPLKRAEFAGGDV----QMEGD--PELKLASFDIETYFHdgkdff 216
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 165 -------GELYCIGLEGCGQRVVYMlGPEPAT------PPDVGFSLVYVASRPLLLEKLNAWFA---EHDPDVLIGWNVV 228
Cdd:TIGR00592 217 pgdenpaDEEIMISTTPVIAKQWDY-ESEPEArvvtwkKPDKPTTGSYVESVSEEISMIKRFWDvidQEDTDVEITVNGD 295
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 229 QFDLRVLQK----------HAERYRIP---LLLGRG--NSELEWREHGFKNGVFFAQANGRLIIDGIEALKSAFwNFSSF 293
Cdd:TIGR00592 296 NFDLVYLADrqvfqfywdaYEDPAEKLgvvLLFGRDvdHVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTI-NLPDY 374
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 294 SLEAVarELLGEGKAIDNPwdRMDEIDRRF-HEDKPALATYNLQDCELVTRIFHKTEIMPFLLERATVNGLPaDRHGGSV 372
Cdd:TIGR00592 375 YLEFV--SELALGYKKEKF--RAKPIAKKYeFEAPDIDAPYSSEYLEVTYELGKEFAPMEALPSDLKGQTFW-HVFGSNT 449
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1994014905 373 AAFSHLYFPR--MHR--LGYVAPNLGEIPPQ---ASPGGYVMDS--RPGLYDS-----VLVLDYKSLYPSIIRT 432
Cdd:TIGR00592 450 GNLERFLLLRkiKGPcwLAVKGPDELEYPRRswcKYEGGYVKPPnvEKGLDKTppplvVLDFSMKSLNPSIIRN 523
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
150-335 |
1.12e-04 |
|
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarchaea. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B-DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.
Pssm-ID: 99824 [Multi-domain] Cd Length: 188 Bit Score: 43.85 E-value: 1.12e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 150 PPLKWVSLDIET-SRHGElyciglegcgqrvvymlgPEPATPPDVGFSlVYVASRP---LLLEKLN-----AWFA----E 216
Cdd:cd05781 1 PDLKTLAFDIEVySKYGT------------------PNPRRDPIIVIS-LATSNGDvefILAEGLDdrkiiREFVkyvkE 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 217 HDPDVLIGWNVVQFDLRVLQKHAERYRIPLLLGR-GNSELEWREHGfKNGVffaqaNGRLIIDgieaLKSAFWNFSSF-- 293
Cdd:cd05781 62 YDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRrGGSEPSTGVYG-HYSI-----TGRLNVD----LYDFAEEIPEVkv 131
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 1994014905 294 -SLEAVAREL---------LGEGKAIDNPWDRMD--EIDRRFHEDKpALATYNL 335
Cdd:cd05781 132 kTLENVAEYLgvmkkservLIEWYRIYEYWDDEKkrDILLKYNRDD-ARSTYGL 184
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
206-352 |
7.51e-04 |
|
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis. This explains why in most organisms, that no specific repair role, other than check point control, has been assigned to this enzyme. The exonuclease domain may have a structural role.
Pssm-ID: 99819 [Multi-domain] Cd Length: 234 Bit Score: 41.83 E-value: 7.51e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 206 LLEKLNAWFAEHDPDVLIGWNVVQFDLRVLQKHAERYRIPLL--LGRgnseL---EWRE---HGFKNGVFFAQanGRLII 277
Cdd:cd05776 85 LLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWsrIGR----LkrsVWPKkkgGGKFGERELTA--GRLLC 158
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 278 D----GIEALKSafwnfSSFSLEAVARELLG-EGKAIDNpwdrmDEIdRRFHEDKPALATY---NLQDCELVTRIFHKTE 349
Cdd:cd05776 159 DtylsAKELIRC-----KSYDLTELSQQVLGiERQDIDP-----EEI-LNMYNDSESLLKLlehTEKDAYLILQLMFKLN 227
|
...
gi 1994014905 350 IMP 352
Cdd:cd05776 228 ILP 230
|
|
| DNA_polB_B1_exo |
cd05783 |
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ... |
150-345 |
1.90e-03 |
|
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are unique in that they are able to recognize the presence of uracil in the template strand, leading to the stalling of DNA synthesis. This is an additional safeguard mechanism against increased levels of deaminated bases during genome duplication at high temperatures. S. solfataricus B1 also interacts with DNA polymerase Y and may contribute to genome stability mechanisms.
Pssm-ID: 99826 [Multi-domain] Cd Length: 204 Bit Score: 40.38 E-value: 1.90e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 150 PPLKWVSLDIE--TSRHG----------ELYCIGLEGC-GQRVVYML------GPEPATPPDVGFsLVYVASRPLLLEKL 210
Cdd:cd05783 3 PKLKRIAIDIEvyTPIKGripdpktaeyPVISVALAGSdGLKRVLVLkregveGLEGLLPEGAEV-EFFDSEKELIREAF 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1994014905 211 NAwFAEHdPdVLIGWNVVQFDLRVLQKHAER-----YRIPLLLGRGNSELEwreHGFKngvffaqangrliID-----GI 280
Cdd:cd05783 82 KI-ISEY-P-IVLTFNGDNFDLPYLYNRALKlgipkEEIPIYLKRDYATLK---HGIH-------------IDlykffSN 142
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1994014905 281 EALKS-AFWN-FSSFSLEAVARELLGEGKAidnpwdrmdEIDRRFHEDKPA-LATYNLQDCELVTRIF 345
Cdd:cd05783 143 RAIQVyAFGNkYREYTLDAVAKALLGEGKV---------ELEKNISELNLYeLAEYNYRDAELTLELT 201
|
|
| |
