|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
1-783 |
0e+00 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 1421.16 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 1 MAQAGFILTRHWRDTPQGTEVSFWLATDNGPLQVTLAPQESVAFIPADQVPRAQHILRGEQGFRLTPLALKDFHRQPVYG 80
Cdd:PRK05762 2 MLQQGFILTRHYRDTPGGPEVELWLATDEGPRVVLLDPQFRPYFIPAEQDERAESLLAGEIGVRLSPLALKDFHRRPVLG 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 81 LYCRAHRQLMNYEKRLREGGVTVYEADVRPPERYLMERFITSPVWVEGDMH----NGAIVNARLKPHPDYRPPLKWVSID 156
Cdd:PRK05762 82 LYCRQHRQLTRLPKRLREGGVDVYEADIRFPERYLMERFITPCVWFSGEVEqyttDGVLRNARLKPAPDYRPPLKVVSLD 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 157 IETTRHGELYCIGLEGCGQRIVYMLGPENGDAsaLDFeLEYVASRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKH 236
Cdd:PRK05762 162 IETSNKGELYSIGLEGCGQRPVIMLGPPNGEA--LDF-LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQER 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 237 AERYRIPLRLGRDNSELEWREHGFKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEGKSIDNPWDRMDE 316
Cdd:PRK05762 239 AERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATWVFDSFSLEYVSQRLLGEGKAIDDPYDRMDE 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 317 IDRRFAEDKPALATYNLKDCELVTQIFHKTEIMPFLLERATVNGLPVDRHGGSVAAFGHLYFPRMHRAGYVAPNLGEVPP 396
Cdd:PRK05762 319 IDRRFAEDKPALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLPLDRVGGSVAAFEHLYLPRAHRAGYVAPNLGERPG 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 397 HASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDpEHSTEGFLDAWFSREKHCLPEIVTNIWHG 476
Cdd:PRK05762 399 EASPGGYVMDSKPGLYDSVLVLDFKSLYPSIIRTFNIDPDGLVEGLAQPP-EESVAGFLGARFSREKHFLPEIVERLWEG 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 477 RDEAKRQGNKPLSQALKIIMNAFYGVLGTTACRFFDPRLVSSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGA 556
Cdd:PRK05762 478 RDEAKREMNKPLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQGYQVIYGDTDSTFVWLGGA 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 557 HSEEEATKIGRALVQHVNVWWAETLQKQ-QLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGLIQEGD-KQRMVFKGL 634
Cdd:PRK05762 558 HDEEDAAKIGRALVQEINQWWQEHLQQEfGLESALELEFEKHYRRFFMPTIRGAEEGSKKRYAGLIQEGDgDGRIVFKGL 637
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 635 ETVRTDWTPLAQQFQQELYLRIFRNEPYQEYFRETIDKLMAGELDARLVYRKRLRRPLSEYQRNVPPHVRAARLADEENQ 714
Cdd:PRK05762 638 ETVRTDWTPLAKEFQQELYERIFRGEPYVDYVREVIDKLRAGELDEKLVYRKRLRRPLDEYQRNVPPHVRAARLADEMGY 717
|
730 740 750 760 770 780
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15829318 715 KRGRPLQYQNRGTIKYVWTTNGPEPLDYQRSPLDYEHYLTRQLQPVAEGILPFIEDNFATLMTGQLGLF 783
Cdd:PRK05762 718 KVGRPLQYQNGGKIGYVITVNGPEPLEYRKSPIDYDYYIEKQLQPVADRILPFFGDDFATLKTGQLGLF 786
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
1-783 |
0e+00 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 1051.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 1 MAQAGFILTRHWRDTPQGTEVSFWLATDNGP-LQVTLAPQESVAFIPADQVPRAQHILRGEQGF-RLTPLALKDFHRQ-- 76
Cdd:COG0417 1 MKIPGFLLDRSYRDEDGKPVIELWGRTEDGPsVLLDVTGFRPYFYVPLPDEEKLEELLRDIKEItEVEPVKLKSFFGEpv 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 77 PVYGLYCRAHRQLMNYEKRLREGGVTVYEADVRPPERYLMERFITSPVWVEGDMHNGAIV-------NARLKPHpDYRPP 149
Cdd:COG0417 81 PVLKIYTRDPRDVRELRDRLKEGGIDVYEADIRFHDRYLIDRFLTPGVWYEGEVEEDGGKldyevkeNPRLKPE-DYRPK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 150 LKWVSIDIETT---------RHGELYCIGLEGC-GQRIVYMLGPENgdasaLDFELEYVASRPQLLEKLNAWFANYDPDV 219
Cdd:COG0417 160 LKVLSFDIEVStprgfpdpeRDGPIISIGLAGSdGEKKVLMLGREG-----VDFEVEYFDDEKALLEAFFEIIREYDPDI 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 220 IIGWNVVQFDLRMLQKHAERYRIPLRLGRDNSELEWREHGfknGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQE 299
Cdd:COG0417 235 IIGWNVDNFDLPYLQKRAERLGIPLDLGRDGSEPSWREHG---GQGFASIPGRVVIDLYDALKSATYKFKSYSLDAVAEE 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 300 LLGEGKSIDNpwdrMDEIDRRFAEDKPALATYNLKDCELVTQIFHKTEIMPFLLERATVNGLPVDRHG--GSVAAFGHLY 377
Cdd:COG0417 312 LLGEGKLIVD----GGEIERLWDDDKPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGraGSSAAFENLL 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 378 FPRMHRAGYVAPNLGEVPPHASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGMAQP-DPEHSTEGFlD 456
Cdd:COG0417 388 LPEAHRRGYLAPNKGEIKGEAYPGGYVLDPKPGLYENVLVLDFKSLYPSIIRTFNISPETLVEGGEEPcGDEDVAPGF-G 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 457 AWFSRE-KHCLPEIVTNIWHGRDEAKRQGNK------------PLSQALKIIMNAFYGVLGTTACRFFDPRLVSSITMRG 523
Cdd:COG0417 467 HRFCREpKGILPSILEELWDERDEAKKKMKKakpdseeyrlydALQQALKILMNSFYGVLGSEGCRFYDPELAESITARG 546
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 524 HQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGaHSEEEATKIGRALVQHVNVWWaetlqkqqlTSALELEYETHFCRFLM 603
Cdd:COG0417 547 REIIKQTIEKAEELGYKVIYGDTDSLFVWLPK-ASLEEAIEIGKELAEEINAWW---------PSGLELEFEKHYRRFFF 616
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 604 PTirgadtgSKKRYAGLIQEGdkqRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQ---EYFRETIDKLMAGELD- 679
Cdd:COG0417 617 PG-------SKKRYAGLTEDG---KIDIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEkavEYVRDVIEKLRAGEVDl 686
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 680 ARLVYRKRLRRPLSEYQRNVPPHVRAARLADEenqkRGRPlqYQNRGTIKYVWTTNG--PEPLDY---QRSPLDYEHYLT 754
Cdd:COG0417 687 DDLVIRKRLRKPLSEYEKNVPPHVRAARKLDE----RGRP--YQRGDKISYVITKGGgrVEPVELakeRESEIDYDYYIE 760
|
810 820 830
....*....|....*....|....*....|.
gi 15829318 755 RQLQPVAEGILPFIEDNFATLMTG--QLGLF 783
Cdd:COG0417 761 KQLKPTADRILEAFGVSFDELKGGskQLGLF 791
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
397-769 |
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: 717.51 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 397 HASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHG 476
Cdd:cd05537 1 ISSPGGYVMDSKPGLYKNVLVLDFKSLYPSIIRTFLIDPLGLIEGLKAPDPEDLIPGFLGARFSREKHILPDLIARLWAA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 477 RDEAKRQGNKPLSQALKIIMNAFYGVLGTTACRFFDPRLVSSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGA 556
Cdd:cd05537 81 RDEAKREKNAPLSQAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQVIYGDTDSTFVWLGEE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 557 HSEEEATKIGRALVQHVNVWWAETLQKQ-QLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGLIQEGDKQRMVFKGLE 635
Cdd:cd05537 161 LDAAEAQAIGKELASQINQWWAQKLKEEfGLESFLEIEFETHYSRFFMPTIRGSDEGSKKRYAGLKSTDGGDELVFKGLE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 636 TVRTDWTPLAQQFQQELYLRIFRNEPYQEYFRETIDKLMAGELDARLVYRKRLRRPLSEYQRNVPPHVRAARLADEENQK 715
Cdd:cd05537 241 TVRSDWTPLARQFQKELYERVFNDEPYEGFIKETVEELLAGELDELLVYRKRLRRPLSEYTKNVPPHVQAARLADQINRE 320
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....
gi 15829318 716 RGRPLQYQNrgtIKYVWTTNGPEPLDYQRSPLDYEHYLTRQLQPVAEGILPFIE 769
Cdd:cd05537 321 LGRPRQYQW---IEYVITVNGPEPLEYRTSPLDYQHYIDKQLKPIADSILPFLG 371
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
397-766 |
1.79e-112 |
|
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: 344.35 E-value: 1.79e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 397 HASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDPEHSTeGFLDAWFSREKHCLPEIVTNIWHG 476
Cdd:cd00145 1 EPYEGGYVFDPIPGLYENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYI-GVGFRSPKDRKGLLPRILEELLNF 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 477 RDEAKRQ------------GNKPLSQALKIIMNAFYGVLGTTACRFFDPRLVSSITMRGHQIMRQTKALIEAQGYDVIYG 544
Cdd:cd00145 80 RDEAKKRmkaaklapeervLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGARVIYG 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 545 DTDSTFVWLKGAHSEEEATKigralvqhvnvWWAETLQKQQLTSALELEYETHFCRFLMptirgadtGSKKRYAGLIQE- 623
Cdd:cd00145 160 DTDSIFVSLPKMGTKEDAIK-----------EGREILQELADEHLLELEFEKVYLPFFL--------GKKKRYAGLDIWk 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 624 -GDKQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQEYFRETIDKLMageldarlvyrkrlrrplseyqrnvpph 702
Cdd:cd00145 221 gQDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEERKVEAVKEYIDELD---------------------------- 272
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15829318 703 vraarlADEENQKRGRPLQYQNRGtikyvwtTNGPEPLDYQRSPLDYEHYLTRQLQPVAEGILP 766
Cdd:cd00145 273 ------KVKYVVTRGGKGVPDYER-------ADPPLEDLDKRHRIDYEYYLERLLQPPLERIFE 323
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
148-344 |
8.50e-107 |
|
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: 324.91 E-value: 8.50e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 148 PPLKWVSIDIETTRHGELYCIGLEGCGQRIVYMLGPENGDAsalDFELEYVASRPQLLEKLNAWFANYDPDVIIGWNVVQ 227
Cdd:cd05784 1 PKLKVVSLDIETSMDGELYSIGLYGEGQERVLMVGDPEDDA---PDNIEWFADEKSLLLALIAWFAQYDPDIIIGWNVIN 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 228 FDLRMLQKHAERYRIPLRLGRDNSELEWREHGfKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEGKSI 307
Cdd:cd05784 78 FDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSG-KPGQGFLSLPGRVVLDGIDALKTATYHFESFSLENVAQELLGEGKLI 156
|
170 180 190
....*....|....*....|....*....|....*..
gi 15829318 308 DNPWDRMDEIDRRFAEDKPALATYNLKDCELVTQIFH 344
Cdd:cd05784 157 HDVDDRGAEIERLFREDKLALARYNLQDCELVWRIFE 193
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
148-555 |
2.24e-83 |
|
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: 273.64 E-value: 2.24e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 148 PPLKWVSIDIETTRHG-----------ELYCIGLEGCGQ-------RIVYMLGPengDASALDFELEYVASRPQLLEKLN 209
Cdd:smart00486 1 PPLKILSFDIETYTDGgnfpdaeifddEIIQISLVINDGdkkganrRILFTLGT---CKEIDGIEVYEFNNEKELLLAFF 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 210 AWFANYDPDVIIGWNVVQFDLRMLQKHAERYRIP--LRLGRDNSELEWREHGFKNGV-------FFAQAKGRLIIDGIEA 280
Cdd:smart00486 78 EFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDplSKIGRLKIGLRIPNKKPLFGSksfglsdIKVYIKGRLVIDLYRL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 281 LKSAFwNFSSFSLETVAQELLGEGKsIDNPWDRMDEIDRRFAEDKPALATYNLKDCELVTQIFHKTEIMPFLLERATVNG 360
Cdd:smart00486 158 YKNKL-KLPSYKLDTVAEYLLGKEK-DDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAG 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 361 LPVDR--HGGSVAAFGHLYFPRMHRAGYVAPNLGEVP----------PHASPGGYVMDSRPGLYDS-VLVLDYKSLYPSI 427
Cdd:smart00486 236 IPLRRtlYYGSQIRVESLLLREAKKNNYILPSKELYDfkgsepdlkkKVKYEGGKVLEPKKGFYDNpVLVLDFNSLYPSI 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 428 IRTFLIDP--VGLVEGMAQPDPEHSTEGFLD---------AWFSREKH--CLPEIVTNIWHGRDEAK------------- 481
Cdd:smart00486 316 IIAHNLCYstLVGVGEVVIKGDLIIPEDLLTikyekgnkyRFVKKNIRkgILPKLLKKLLDKRKEIKklmkkekdeseel 395
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15829318 482 RQGNKPLSQALKIIMNAFYGVLGTTACRFFDPRLVSSITMRGHQIMRQTKALIEAQGYD-----VIYGDTDSTFVWLKG 555
Cdd:smart00486 396 KKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGYPkpgfkVIYGDTDSIFVTKPG 474
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
380-765 |
3.71e-53 |
|
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: 190.52 E-value: 3.71e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 380 RMHRAGYVAPN----LGEVPPHasPGGYVMDSRPGLYDS-VLVLDYKSLYPSIIR-------TFLIDPVGLVEGMAQPDP 447
Cdd:pfam00136 22 LALEEGFILPDrpsaKGDEDGY--QGATVIEPKKGFYDKpVLVLDFNSLYPSIIQahnlcytTLVRSVDEANNLPPEDNL 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 448 E--HSTEGFLDAWFSREKHC-LPEIVTNIWHGRDEAK---RQGNKPL--------SQALKIIMNAFYGVLGTTACRFFDP 513
Cdd:pfam00136 100 ItvECTPRGVYFVKDHVREGlLPKLLKDLLAKRKAIKkllKEETDPFeraildkqQLALKITANSVYGFTGFANGRLPCL 179
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 514 RLVSSITMRGHQIMRQTKALIEAQ---GYDVIYGDTDSTFVWLKGAhSEEEATKIGRALVQHVNvwwaetlqKQQLTSAL 590
Cdd:pfam00136 180 PIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTDSVFIEFGGK-DVEEAMKIGDELAEHVN--------QDLFKSPI 250
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 591 ELEYETHFCRFLMPtirgadtgSKKRYAGLIQEGDKQ--RMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQE---Y 665
Cdd:pfam00136 251 KLEFEKVYKPLLLI--------SKKKYAGLKYTAPSNfnKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSDRGLPVgleF 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 666 FRETI----DKLMAGELDAR-LVYRKRLRRPLSEYQRNVPPHVRAARladEENQKRGRPLQYQNRgtIKYVWTTNGPEP- 739
Cdd:pfam00136 323 VISILndarSDLRNNKVPLEkFVISKELSKPPDNYKSKNLPHVEVAL---RMNKRNGEAPEVGDR--IPYVIVKAAKGLk 397
|
410 420 430
....*....|....*....|....*....|....*....
gi 15829318 740 --LDYQRS-----------PLDYEHYLTRQLQPVAEGIL 765
Cdd:pfam00136 398 nlLIYERAedpeyvlennlPIDYEYYFSNQLIPPVARLL 436
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
152-344 |
2.74e-52 |
|
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: 180.24 E-value: 2.74e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 152 WVSIDIETTRH--------GELYCIGLEG--CGQRIVYMLGPENGDASA---LDFELEYVASRPQLLEKLNAWFANYDPD 218
Cdd:cd05160 1 VLSFDIETTPPvggpepdrDPIICITYADsfDGVKVVFLLKTSTVGDDIefiDGIEVEYFADEKELLKRFFDIIREYDPD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 219 VIIGWNVVQFDLRMLQKHAERYRIPLrlgRDNSELEWREHGFKNGVFFAQAKGRLIIDGIEALKSAFWnFSSFSLETVAQ 298
Cdd:cd05160 81 ILTGYNIDDFDLPYLLKRAEALGIKL---TDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFK-LKSYTLDAVAE 156
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 15829318 299 ELLGEGKSIDNPWDRMDEidrRFAEDKPALATYNLKDCELVTQIFH 344
Cdd:cd05160 157 ELLGEGKEKVDGEIIEDA---EWEEDPERLIEYNLKDAELTLQILE 199
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
401-765 |
2.03e-51 |
|
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: 183.68 E-value: 2.03e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 401 GGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGmaqPDPEHSTEGFLDAWFSREKHCL-PEIVTNIWHGRDE 479
Cdd:cd05536 6 GGIVLEPEKGLHENIVVLDFSSLYPSIMIKYNISPDTLVRE---GCEDCDVEPQVGHKFRKDPPGFiPSVLEDLLEERRR 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 480 AKRQGNK--PLS----------QALKIIMNAFYGVLGTTACRFFDPRLVSSITMRGHQIMRQTKALIEAQGYDVIYGDTD 547
Cdd:cd05536 83 IKEKMKKldPESeeykllderqRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAEEKGFKVIYGDTD 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 548 STFVWLKGAHSEEEATKigrALVQHVNvwwaETLqkqqltsALELEYETHFCRFLMPTirgadtgsKKRYAGLIQEGdkq 627
Cdd:cd05536 163 SLFVKIDGADAVKKKVK---KLLKYIN----EEL-------PLELEIEKFYKRGFFVT--------KKRYAGLTEDG--- 217
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 628 RMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQE---YFRETIDKLMAGELDAR-LVYRKRLRRPLSEYqRNVPPHV 703
Cdd:cd05536 218 KIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEavkIVKEVIEKLKRGEVPPEkLVIWKQLTKDLSEY-KATGPHV 296
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15829318 704 RAARLAdeenQKRGRPLQyqnRGT-IKYVwTTNGP-------EPLDYQRSP--LDYEHYLTRQLQPVAEGIL 765
Cdd:cd05536 297 AAAKKL----AKRGYKVR---PGTkIGYV-IVKGSgkisdraYPYDMVDEKhkYDAEYYIDNQVLPAVLRIL 360
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
401-769 |
5.80e-47 |
|
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: 172.38 E-value: 5.80e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 401 GGYVMDSRPGLYDS-VLVLDYKSLYPSIIRTFLI-------DPVGLVEGMAQPDPEHSTEgfldawfsreKHCLPEIVTN 472
Cdd:cd05532 10 GGLVLEPKKGLYDKfILLLDFNSLYPSIIQEYNIcfttvdrADPDDEDDEEPPLPPSDQE----------KGILPRIIRK 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 473 IWHGRDEAKRQGNKPLS-----------QALKIIMNAFYGVLGTTACRFFDPRLVSSITMRGHQIMRQTKALIEAQGYDV 541
Cdd:cd05532 80 LVERRRQVKKLMKSEKDpdkkaqldirqLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKMNLEV 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 542 IYGDTDSTFVWlKGAHSEEEATKIGRALVQHVNvwwaetlqkqQLTSALELEYETHFCRFLMPtirgadtgSKKRYAGLI 621
Cdd:cd05532 160 IYGDTDSIMIN-TGTTDYEEAKKLGNKIKKEVN----------KSYKKLEIDIDGVFKRLLLL--------KKKKYAALK 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 622 QEGDKQRMV---FKGLETVRTDWTPLAQQFQQELYLRIFRNEPY-------QEYFRETIDKLMAGELDAR-LVYRKRLRR 690
Cdd:cd05532 221 VVDDDKGKLkkeVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSRediveniHEYLRKINEDLRNGKIPLEkFIITKQLTK 300
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 691 PLSEY-QRNVPPHVRAA-RLadeenQKRGRplQYQNRGTIKYVWTTNGPEPLDYQR--SP----------LDYEHYLTRQ 756
Cdd:cd05532 301 NPEEYpDKKSLPHVQVAlRM-----NKRGR--KVKAGDTIPYIICKDGSSKSLADRayHPdevkknenlkIDIEYYLSQQ 373
|
410
....*....|...
gi 15829318 757 LQPVAEGILPFIE 769
Cdd:cd05532 374 ILPPISRLCEPIE 386
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
191-765 |
3.19e-46 |
|
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: 178.71 E-value: 3.19e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 191 LDFELEYVASRPQLLEKLNA------WF-ANY---DPDVIIGWNVVQFDLRMLQKHAERYRIPL--RLGRdnseleWREH 258
Cdd:TIGR00592 564 LDLKGEFPGKKPSLVEDLATeralikKFmAKVkkiDPDEIVGHDYQQRALKVLANRINDLKIPTwsKIGR------LRRS 637
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 259 GFKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEGKSIDnpwdrMDEIDRRFAEDKP--ALATYNLKDC 336
Cdd:TIGR00592 638 PKFGRRFGERTCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIP-----IDNINNMYSESSSltYLLEHTWKDA 712
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 337 ELVTQIFHKTEIMPFLLERATVNGLPVDR--HGGSVAAFGHLYFPRMHRAGYVAPNLGEVPPH----------------- 397
Cdd:TIGR00592 713 MFILQIMCELNVLPLALQITNIAGNIMSRtlMGGRSERNEFLLLHAFYENNYIVPDKQIFRKQqklgdedeeidgykkgk 792
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 398 --ASPGGYVMDSRPGLYDS-VLVLDYKSLYPSIIRTFLI------DPVGLVEGMAQPDPEhSTEGFLDAWFSREKHCLPE 468
Cdd:TIGR00592 793 kaAYAGGLVLEPKVGLYDKyVLLMDFNSLYPSIIQEFNIcfttvqQKVDEDELPELPDSE-LEMGILPRELRKLVERRKE 871
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 469 IVTNIWHGRDEAKRQGNKPLSQALKIIMNAFYGVLGTTACRFFDPRLVSSITMRGHQIMRQTKALIEAQGYDVIYGDTDS 548
Cdd:TIGR00592 872 VKKLMKQDLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEMNLEVIYGDTDS 951
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 549 TFVWLKGAHSeEEATKIGRALVQHVNvwwaetlqkqQLTSALELEYETHFCRFLMPTirgadtgsKKRYAGLIQEGDKQ- 627
Cdd:TIGR00592 952 IMINTPGTKY-EEVFKIGKEFKSEVN----------KLYKLLELDIDGVFKRLLLLK--------KKKYAAIKVEGDSDg 1012
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 628 ----RMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEP-------YQEYFRETIDKLMAGELD-ARLVYRKRLRRPLSEY 695
Cdd:TIGR00592 1013 nyttKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDveeaveeVQEVLEKIGKNVLNGEVPlEKFVINKQLTRDPKDY 1092
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 696 -QRNVPPHVRAA-RLadeeNQKRGRPlqYQNRGTIKYVWTTNGPEPLDYQRS-------------PLDYEHYLTRQLQPV 760
Cdd:TIGR00592 1093 pDGASLPHVHVAlRI----NARGGRK--VKAGDVVSYVICKDGGNLSARQRAyaleelqrkhnnlIYDTQYYLEHQIHPV 1166
|
....*
gi 15829318 761 AEGIL 765
Cdd:TIGR00592 1167 VLRIL 1171
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
103-778 |
5.43e-45 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 174.83 E-value: 5.43e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 103 VYEADVRPPERYLMERFITSPVWVEGDMHNGAIVNARLK----------------PHP---DYR--PPLKWVSIDIEttr 161
Cdd:PTZ00166 196 TYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRPPKKKtstcqievdcsyedliPLPpegEYLtiAPLRILSFDIE--- 272
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 162 hgelyCIGLEGCG------------QRIVYMLGPENGDASALDFELEYVASRP-----------QLLEKLNAWFANYDPD 218
Cdd:PTZ00166 273 -----CIKLKGLGfpeaendpviqiSSVVTNQGDEEEPLTKFIFTLKECASIAganvlsfetekELLLAWAEFVIAVDPD 347
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 219 VIIGWNVVQFDLRMLQKHAERYRIP--LRLGRDNSElewrEHGFKNGVFFAQA-----------KGRLIIDGIEALKSAF 285
Cdd:PTZ00166 348 FLTGYNIINFDLPYLLNRAKALKLNdfKYLGRIKST----RSVIKDSKFSSKQmgtreskeiniEGRIQFDVMDLIRRDY 423
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 286 wNFSSFSLETVAQELLGEGKSiDNPWDRMDEIDRRFAEDKPALATYNLKDCELVTQIFHKTEIMPFLLERATVNGLPVD- 364
Cdd:PTZ00166 424 -KLKSYSLNYVSFEFLKEQKE-DVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGw 501
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 365 --RHGGSVAAFGHLYfpRMHRA-GYVAP---NLGEVPPHASPGGYVMDSRPGLYDS-VLVLDYKSLYPSII------RTF 431
Cdd:PTZ00166 502 llTRGQQIKVTSQLL--RKCKKlNYVIPtvkYSGGGSEEKYEGATVLEPKKGFYDEpIATLDFASLYPSIMiahnlcYST 579
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 432 LIDPvglvEGMAQPDPEHSTEGFLDAWF---SREKHCLPEIVTNIWHGRDEAKRQGNK---PLSQ--------ALKIIMN 497
Cdd:PTZ00166 580 LVPP----NDANNYPEDTYVTTPTGDKFvkkEVRKGILPLIVEELIAARKKAKKEMKDekdPLLKkvlngrqlALKISAN 655
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 498 AFYGVLGTTACRFFdPRL--VSSITMRGHQIMRQTKALIE-----AQGYD----VIYGDTDSTFVWLkGAHSEEEATKIG 566
Cdd:PTZ00166 656 SVYGYTGAQVGGQL-PCLevSTSITSFGRQMIDKTKELVEkhytkANGYKhdatVIYGDTDSVMVKF-GTDDIQEAMDLG 733
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 567 RALvqhvnvwwAETLQKQQLtSALELEYETHFCRFLMPtirgadtgSKKRYAGLI-QEGDK-QRMVFKGLETVRTDWTPL 644
Cdd:PTZ00166 734 KEA--------AERISKKFL-KPIKLEFEKVYCPYLLM--------NKKRYAGLLyTNPEKyDKIDCKGIETVRRDNCLL 796
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 645 AQQFQQEL--YLRIFRN-EPYQEYFRETIDKLMAGELD-ARLVYRKRLRRplSEYqrnvpphvrAARLADEENQKRGR-- 718
Cdd:PTZ00166 797 VQQMVETVlnKILIEKDvESAIEFTKGKISDLLQNRIDiSLLVITKSLGK--DDY---------EGRLAHVELAKKLRqr 865
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15829318 719 -PLQYQNRGT-IKYVWT--TNGpEPLdYQRS-----------PLDYEHYLtRQLQPVAEGILPFIEDNFATLMTG 778
Cdd:PTZ00166 866 dPGSAPNVGDrVSYVIVkgAKG-APQ-YERAedplyvlenniPIDTQYYL-DQIKNPLLRIFEGVMDNPDSLFSG 937
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
103-783 |
5.67e-45 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 173.34 E-value: 5.67e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 103 VYEADVRPPERYLMERFITSPVWVEGDMHNGAIVNARLKPH------PDYRPPLKWVSIDIETTRHGELYCIGLEgcgqr 176
Cdd:PRK05761 122 AWEADIKYEFRYIYDNGLIPGMPYDVKNGLESVEPEILVEEikkafkDERKLAEDWLPIFEAPIPKIKRIAIDIE----- 196
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 177 iVYmlGPENGDASAlDFELEyvasrpqLLEKLNAWFANYDPDVIIgwNVVQFDLRMLqkhaerYRIPLRLGRDNSEL--- 253
Cdd:PRK05761 197 -VY--TPAKGRIPD-DSEKE-------LLAELFDIILEYPPVVTF--NGDNFDLPYL------YNRALKLGIPKEEIpie 257
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 254 --EWREHGFKNGVFFaqakgrliidgIEALKS-AFWN---FSSFSLETVAQELLGEGK-SIDNPWDRMDEIDrrfaedkp 326
Cdd:PRK05761 258 pgRAGIHIDLYKFFQ-----------NKAVRSyAFYGkyrHREARLDAVGRALLGISKvELETNISELDLEE-------- 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 327 aLATYNLKDCELVTQ--IFHKTEIMPFLLERATVNGLPVD---RHggSVAAFGHLYFPRMHRA-GYVAPNLGEVPPHASP 400
Cdd:PRK05761 319 -LAEYNFRDAEITLKltFFNNELVLKLILLLSRISKLPIEelsRA--TISTWISNLEYWEHRKrGWLIPWKEDILRLDHE 395
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 401 -------------GGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDP--VGLVEGMAQPDPEhstEGFLDAWFSREKHC 465
Cdd:PRK05761 396 vykkaiikgkkyrGGLVFQPPPGIFFNVYVLDFASLYPSIIVKWNLSPetVRIPECKCHYDDE---VPELGHSVCDDRPG 472
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 466 LPEIVTNIWhgRDE-----AKRQGNKPLSQ-----------ALKIIMNAFYGVLGTTACRFFDPRLVSSITMRGHQIMRQ 529
Cdd:PRK05761 473 LTSVLVGLL--RDFrvkiyKKKAKDPNLDEerrawydvvqrALKVFLNASYGVFGAENFKLYRIEVAESITALGREILLS 550
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 530 TKALIEAQGYDVIYGDTDSTFVWlkgAHSEEEATKIGRalvqhvnvWWAETLQkqqltsaLELEYETHFcRFLmptirgA 609
Cdd:PRK05761 551 TKKKAEELGLKVLYGDTDSLFVW---GPTKESLEELIK--------EIEERTG-------IDLEVDKTY-DWV------A 605
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 610 DTGSKKRYAGLIQEGDkqrMVFKGLETVRTDWTPLAQQFQQELyLRIFRN-----------EPYQEYFRETIDKLMAGEL 678
Cdd:PRK05761 606 FSGLKKNYFGVLKDGK---VKIKGIVAKKRNTPEFVKELQREV-LEVLKSirspedvekvkDEIEDVLKRYYEKLRAKDY 681
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 679 D-ARLVYRKRLRRPLSEYQRNVPPHVRAARLADEENqkrgrpLQYQNRGTIKYVWTTN--GPEPLDYQR-SPLDYEHYLt 754
Cdd:PRK05761 682 PlDELAIRVRLSKPLDEYTKNTPQHVKAALQLRDYG------VEVSPGDIISYVKVDDkrGVKPVQLAKlSEIDVEKYI- 754
|
730 740 750
....*....|....*....|....*....|
gi 15829318 755 RQLQPVAEGILPFIEDNFATL-MTGQLGLF 783
Cdd:PRK05761 755 ELLRSALEQILSALGVSWDDIrGTTRLDSF 784
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
382-759 |
3.89e-32 |
|
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: 130.41 E-value: 3.89e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 382 HRAGYVA--PNLGEV----PPHASPggYVMDSRPGLY-DSVLVLDYKSLYPSII-------RTFLidpvGLVEGMAQ--- 444
Cdd:cd05534 15 KPENYILpsPSRQQVaqqrALECLP--LVMEPESGFYsDPVIVLDFQSLYPSIMiaynycySTCL----GRVEELNGggk 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 445 -----------PDPEHSTE------------GFLDAwfSREKHCLPEIVTNIWHGRDEAKR------QGNKPLSQ----- 490
Cdd:cd05534 89 fgflgvklylpPPPLDLLLlkddvtispngvMFVKK--SVRKGILPKMLEEILDTRIMVKKamkkykDDKKLQRIldarq 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 491 -ALKIIMNAFYGVLGTTacrfFDPR-----LVSSITMRGHQIMRQTKALIEAQGY---DVIYGDTDSTFVWLKGAhSEEE 561
Cdd:cd05534 167 lALKLLANVTYGYTAAS----FSGRmpcveIADSIVQTGRETLERAIELIESTPKwgaKVVYGDTDSLFVLLPGR-TKEE 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 562 ATKIGRALVQHVNvwwaetlqkQQLTSALELEYET--HFCrFLMptirgadtgSKKRYAGLIQEGDKQRMVF---KGLET 636
Cdd:cd05534 242 AFKIGKEIAEAVT---------AANPSPIKLKFEKvyHPC-VLV---------TKKRYVGYKYESPDQTEPTfdaKGIET 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 637 VRTDWTPLAQQFQQELYLRIFRN---EPYQEYFRETIDKLMAGELDAR-LVYRKRLRRPLSEYQRNVPPHVRAARLADEE 712
Cdd:cd05534 303 VRRDGCPAVQKILEKSLRILFETkdlSTVKSYLQRQWSKLLQGRVSIQdFIFAKEVRLGTYKEGATLPAGAIVALRRMEK 382
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*....
gi 15829318 713 NQkRGRPlQYQNRgtIKYVWTTNGP---------EPLDYQRSP---LDYEHYLTRQLQP 759
Cdd:cd05534 383 DP-RAEP-QYGER--VPYVVVRGEPgsrlidlvvSPEEFLADPslrLDAEYYITKQIIP 437
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
401-753 |
1.55e-31 |
|
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: 127.08 E-value: 1.55e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 401 GGYVMDSRPGLYDSVLVLDYKSLYPSIIRTF-----LIDPVGlVEGMAQPDPEhstegfLDAWFSREKHCL-PEIV---- 470
Cdd:cd05530 15 GAIVLEPPPGIFFNVVVLDFASLYPSIIKVWnlsyeTVNCPH-CECKTNEVPE------VGHWVCKKRPGItSQIIgllr 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 471 ---TNIWHGR------DEAKRQGNKPLSQALKIIMNAFYGVLGTTACRFFDPRLVSSITMRGHQIMRQTKALIEAQGYDV 541
Cdd:cd05530 88 dlrVKIYKKKakdkslDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIITSTIKKARELGLKV 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 542 IYGDTDSTFVWlkgAHSEEEATKIgralVQHVnvwwaetlqKQQLTSALELEYETHFCRFlmptirgadTGSKKRYAGLI 621
Cdd:cd05530 168 LYGDTDSLFLW---NPPQEQLEDL----VEWV---------EKELGLDLELDKEYRYVVF---------SGLKKNYLGVT 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 622 QEGDkqrMVFKGLeTVRTDWTPlaqQFQQELY------LRIFRNEPYQEYFRETIDKLMAG----------ELDaRLVYR 685
Cdd:cd05530 223 KDGS---VDIKGL-LGKKRNTP---EFVKELFyevieiLSAVNSPEDFEKAREKIRDIVKGvykrlkkkeyTLD-QLAFK 294
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15829318 686 KRLRRPLSEYQRNVPPHVRAARLAdeenQKRGRPLqyqNRG-TIKYVWTTN--GPEPLDYQRSP-LDYEHYL 753
Cdd:cd05530 295 VMLSKPPEEYTKNTPQHVKAARQL----EKYGRNV---EAGdIISYVKVKGkeGVKPVQLARLDeVDVEKYV 359
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
401-765 |
3.89e-31 |
|
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: 126.23 E-value: 3.89e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 401 GGYVMDSRPGLYDS-VLVLDYKSLYPSII------RTFLIDPVGLVEGMaqpdPEHSTEGFLDAWF---SREKHCLPEIV 470
Cdd:cd05533 5 GATVIEPIKGYYDVpIATLDFASLYPSIMmahnlcYTTLLNKNTAKKLP----PEDYIKTPNGDYFvksSVRKGLLPEIL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 471 TNIWHGRDEAKRQGNK---PLSQ--------ALKIIMNAFYGVLGTTACRFFDPRLVSSITMRGHQIMRQTKALIE---- 535
Cdd:cd05533 81 EELLAARKRAKKDLKEetdPFKKavldgrqlALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEekyt 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 536 -AQGY----DVIYGDTDSTFVWLkGAHSEEEATKIGRALVQHVNvwwaetlqkQQLTSALELEYETHFCRFLMPtirgad 610
Cdd:cd05533 161 kANGYshdaKVIYGDTDSVMVKF-GVSDVEEAMKLGKEAAEYVS---------KKFIKPIKLEFEKVYFPYLLI------ 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 611 tgSKKRYAGLI----QEGDKqrMVFKGLETVRTDWTPLAQQFQQEL--YLRIFRNEP-YQEYFRETIDKLMAGELD-ARL 682
Cdd:cd05533 225 --NKKRYAGLLwtnpDKHDK--MDTKGIETVRRDNCLLVQNVVETClnKILIERDVEgAIEFVKGVISDLLQNKIDiSLL 300
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 683 VYRKRLRRPLSEYQRNVpPHVR-AARLadeenQKRGrPLQYQNRGT-IKYVWTTNGPEPLDYQRS-----------PLDY 749
Cdd:cd05533 301 VITKALTKTADDYAGKQ-AHVElAERM-----RKRD-PGSAPNVGDrVPYVIIKGAKGAKAYEKAedpiyvlenniPIDT 373
|
410 420
....*....|....*....|
gi 15829318 750 EHYLTRQLQP----VAEGIL 765
Cdd:cd05533 374 QYYLENQLSKpllrIFEPIL 393
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
401-760 |
2.53e-30 |
|
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: 122.84 E-value: 2.53e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 401 GGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPvglvEGMAQPDPEHSTEGFLDAWFSR-EKHCLPEIVTNIWHGRDE 479
Cdd:cd05531 7 GGLVFQPEPGLYENVAQIDFSSMYPSIIVKYNISP----ETINCRCCECRDHVYLGHRICLkRRGFLPEVLEPLLERRLE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 480 AKRQG-----NKPLSQALKIIMNAFYGVLGTTACRFFDPRLVSSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLK 554
Cdd:cd05531 83 YKRLKkeedpYAGRQKALKWILVTSFGYLGYKNAKFGRIEVHEAITAYGRKILLRAKEIAEEMGFRVLHGIVDSLWIQGR 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 555 GAHsEEEATKIGRalvqhvnvwwaETlqkqqltsALELEYETHfCRFL--MPTIRGadTGSKKRYAGLIQEGDkqrMVFK 632
Cdd:cd05531 163 GDI-EELAREIEE-----------RT--------GIPLKLEGH-YDWIvfLPERDG--LGAPNRYFGRLSDGE---MKVR 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 633 GLETVRTDWTPLAQQFQQELyLRIFRN-----------EPYQEYFRETIDKLMAGELDaRLVYRKRLRRPLSEYQrNVPP 701
Cdd:cd05531 217 GIELRRRDTPPFVKKFQEEA-LDILASaktpeellklrEEALDLFRRYLQRLREGDLE-DLIIEKKISKRSSEYK-VLAS 293
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*....
gi 15829318 702 HVRAARLADEENQKRGRPLQYQNRGTIKYVWTTNGPEPLDYQRspldYEHYLTRQLQPV 760
Cdd:cd05531 294 TALKALRAKGVSVVPGMKIEYIVRDGKRPVPDLGNDEGYDTKY----YRELLERAAEEL 348
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
78-668 |
1.69e-21 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 100.15 E-value: 1.69e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 78 VYGLYCRAH-----RQLMNYEKRLREGGVTVYEadvrpperylMERFITSPVwveGDMHNGAIVNARLKphpdyrppLKW 152
Cdd:PHA02528 50 IYGKNCRPKkfdsmRDARKWMKRMKDVGFEALG----------MDDFKLQYI---SDTYPGEIKYDRSK--------IRI 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 153 VSIDIETTRHG----------ELYCIGLEGC--GQRIVYMLGPENGDASALDF-------ELEYVASRPQ---LLEKLNA 210
Cdd:PHA02528 109 ANLDIEVTAEDgfpdpeeakyEIDAITHYDSidDRFYVFDLGSVEEWDAKGDEvpqeildKVVYMPFDTEremLLEYINF 188
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 211 WFANYdPDVIIGWNVVQFDLRMLqkhAERYRiplRLGRDNSELEWREHGFKNGVFFAQAKGRLI----IDGIEAL----- 281
Cdd:PHA02528 189 WEENT-PVIFTGWNVELFDVPYI---INRIK---NILGEKTAKRLSPWGKVKERTIENMYGREEiaydISGISILdyldl 261
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 282 --KSAFWNFSSFSLETVAQELLGEGKsidnpWDRMDEIDRRFAEDKPAL-ATYNLKDCELVTQIFHKTEIMPFLLERATV 358
Cdd:PHA02528 262 ykKFTFTNQPSYRLDYIAEVELGKKK-----LDYSDGPFKKFRETDHQKyIEYNIIDVELVDRLDDKRKLIELVLSMAYY 336
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 359 NGLPVDRHGGSVAAFGHLYFPRMHRAGYVAPNLGEVPPHASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIR--------- 429
Cdd:PHA02528 337 AKINFEDVFSPIKTWDAIIFNSLKEEKIVIPENKSHKKQKYAGAFVKEPVPGAYRWVVSFDLTSLYPSIIRqvnispeti 416
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 430 --TFLIDPV-GLVEGMAQ-PDPEHS--TEGfldAWFSREKH-CLPEIVTNIWHGRD-------EAKRQG----------- 484
Cdd:PHA02528 417 agTFHVAPVhEYINKTAPrPSDEYScsPNG---WMYRKDIRgVIPTEIKKVFDQRKiykkkmlAAERNAeliktiledln 493
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 485 ---NKPLS-----------------------------------------QALKIIMNAFYGVLGTTACRFFDPRLVSSIT 520
Cdd:PHA02528 494 dsvDTPIDvdyyfdfsdefkaelktltksslkalleecekeialcntiqMARKILINSLYGALGNEHFRYYDLRNAEAIT 573
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 521 MRGH----QIMRQT----KALIEAQGYD-VIYGDTDSTFVWLkgahsEEEATKIGRALVQHVNVW--WAETLQKQQLTSA 589
Cdd:PHA02528 574 LFGQlaiqWIERKMneylNKLCKTEDEDyVIYGDTDSIYVNL-----DPLVEKVGEDKFKDTNHWvdFLDKFCKERMEPY 648
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 590 LELEYEtHFCRF------LMPTIRG--ADTG---SKKRYAGLIQ--EG---DKQRMVFKGLETVRTDWTPLAQQFQQELY 653
Cdd:PHA02528 649 IDSSYR-ELCEYmnnyehLMFMDREaiAGPGfwtAKKRYALNVWdsEGtryAEPKLKIMGIETQRSSTPKAVQKALKEAI 727
|
730
....*....|....*..
gi 15829318 654 LRIFR--NEPYQEYFRE 668
Cdd:PHA02528 728 RRILQegEESLQEYIKE 744
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
401-761 |
6.09e-17 |
|
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: 82.92 E-value: 6.09e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 401 GGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPdpehstegfLDAWFSREKHCLPEIVTNiwhGRDEA 480
Cdd:cd05538 5 GGYAYVFITGVLGPIVHADVASLYPSIMLAYRICPARDSLGIFLA---------LLKYLVELRLAAKESARA---AARPA 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 481 KRQGNKPLSQALKIIMNAFYGVLGTTACRFFDPRLVSSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGAHSEE 560
Cdd:cd05538 73 ERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRRRGATPVEVDTDGIYFIPPNGVDTE 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 561 EATKIGRALVQhvnvwwaetlqkQQLTSALELEYETHFCRFLmptIRGadtgsKKRYAGLIQEGdkqRMVFKGLETVRTD 640
Cdd:cd05538 153 DEEEELVRELS------------STLPKGITVEFDGRYRAMF---SYK-----IKNYALLDYDG---KLIVKGSAFRSRG 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 641 WTPLAQQFQQELYLRIFRNEPYQ--EYFRETIDKLMAGELDARLVYR-KRLRRPLSEYQRNVPPHVRAARLADEENQKRG 717
Cdd:cd05538 210 IEPFLREFLREAVRLLLQGDGAGvhDLYEDYLRRLRSHELPISDLARtETLKESPEEYLQKVRAGKRNPAAAYEIALARP 289
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|...
gi 15829318 718 RPLQYQNRGTIKYVWT-------TNGPEPLDYQRSPLDY--EHYLTRQLQPVA 761
Cdd:cd05538 290 REWRAGDRVTYYVSGTgkgvsvyENCRLVADYDPAHPDEntGFYAERLLQLAA 342
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
148-333 |
5.59e-16 |
|
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: 77.01 E-value: 5.59e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 148 PPLKWVSIDIETTRH--------GELYCIGLegCGQRIVYMLGPENGDasaLDFeLEYVASRPQLLEKLNAWFANYDPDV 219
Cdd:cd05780 1 EDLKILSFDIEVLNHegepnpekDPIIMISF--ADEGGNKVITWKKFD---LPF-VEVVKTEKEMIKRFIEIVKEKDPDV 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 220 IIGWNVVQFDLRMLQKHAERYRIPLRLGRDNSELEWREHGFKNGVFFaqaKGRLIIDgIEALKSAFWNFSSFSLETVAQE 299
Cdd:cd05780 75 IYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEI---KGRIHVD-LYPVARRTLNLTRYTLERVYEE 150
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 15829318 300 LLGEGK------SIDNPWDRMDEIDRRF---AEDkpALATYNL 333
Cdd:cd05780 151 LFGIEKedvpgeEIAEAWDSGENLERLFrysMED--AKYTYEI 191
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
96-296 |
1.31e-11 |
|
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: 66.67 E-value: 1.31e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 96 LREGGVTVYEADVRPPERYLMERFITSPVWVEGDMH----NGAIVNARL---KPHPDY--------RPPLKWVSIDIETT 160
Cdd:pfam03104 86 SPENISDVYEYDVDYLERFLIDNDIVGFGWYKVKVYpfraEGRISNCDVeidCDSPDLisvpfekeWPPLRVLSFDIECT 165
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 161 RHGE------------------LYCIGLEGCGQRIVYMLGP-ENGDASALDFELEYVASRPQLL----EK--LNAWFA-- 213
Cdd:pfam03104 166 SLPGkfpdaenvkdpiiqiscmLDGQGEPEPEPRFLFTLREcDSEDIEDFEYTPKPIYPGVKVFefpsEKelLRRFFEfi 245
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 214 -NYDPDVIIGWNVVQFDLRMLQKHAERYRIP--LRLGRDNSelewreHGFKNG---VFFAQA------KGRLIIDgIEAL 281
Cdd:pfam03104 246 rQYDPDIITGYNGDNFDWPYILNRAKELYIVklSSIGRLNR------GGRSKVreiGFGTRSyekvkiSGRLHLD-LYRV 318
|
250
....*....|....*
gi 15829318 282 KSAFWNFSSFSLETV 296
Cdd:pfam03104 319 IKRDYKLPSYKLNAV 333
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
150-324 |
7.14e-11 |
|
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: 62.43 E-value: 7.14e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 150 LKWVSIDIETTRHGELYCIGLEGCGQRIVYMLGPENGDASALDFELEyvASRPQLLEKLNAWFANYDPDVIIGWNVVQFD 229
Cdd:cd05785 9 LRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEVLHAED--AAEKELLEELVAIIRERDPDVIEGHNIFRFD 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 230 LRMLQKHAERYRIPLRLGRDNSELEWREHGFKngvfFAQ---------AKGRLIIDGIEALKS---AFWNFSSFSLETVA 297
Cdd:cd05785 87 LPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFR----FAErlidyprydIPGRHVIDTYFLVQLfdvSSRDLPSYGLKAVA 162
|
170 180 190
....*....|....*....|....*....|....*
gi 15829318 298 QEL--------LGEGKSIDNPWDRMDEIDRRFAED 324
Cdd:cd05785 163 KHFglaspdrtYIDGRQIAEVWRSDPARLLAYALD 197
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
148-345 |
4.22e-09 |
|
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The 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 contain four conserved acidic residues necessary for metal binding and 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.
Pssm-ID: 99820 [Multi-domain] Cd Length: 230 Bit Score: 57.59 E-value: 4.22e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 148 PPLKWVSIDIET----------------------TRHGELYCIglegcgQRIVYMLG---PENGdASALDFELEyvasrP 202
Cdd:cd05777 5 APLRILSFDIECagrkgvfpepekdpviqianvvTRQGEGEPF------IRNIFTLKtcaPIVG-AQVFSFETE-----E 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 203 QLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRIPL--RLGR-DNSELEWREHGFkngvffaQAK--------- 270
Cdd:cd05777 73 ELLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTfpFLGRiKNIKSTIKDTTF-------SSKqmgtretke 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 271 ----GRLIIDGIEALKSAFwNFSSFSLETVAQELLGEGK-----SIDNPWDRMDEIDRRfaedkpALATYNLKDCELVTQ 341
Cdd:cd05777 146 inieGRIQFDLLQVIQRDY-KLRSYSLNSVSAHFLGEQKedvhySIITDLQNGNPETRR------RLAVYCLKDAYLPLR 218
|
....
gi 15829318 342 IFHK 345
Cdd:cd05777 219 LLDK 222
|
|
| 43A |
PHA02524 |
DNA polymerase subunit A; Provisional |
204-445 |
5.93e-08 |
|
DNA polymerase subunit A; Provisional
Pssm-ID: 164925 [Multi-domain] Cd Length: 498 Bit Score: 56.16 E-value: 5.93e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 204 LLEKLNAWFANyDPDVIIGWNVVQFDLRMLQKhaeryRIPLRLGRDNSElEWREHGFKNGVFFAQAKGRLIIDGIE--AL 281
Cdd:PHA02524 184 LLNYIQLWKAN-TPDLVFGWNSEGFDIPYIIT-----RITNILGEKAAN-QLSPYGKITSKTITNLYGEKIIYKIHgiAL 256
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 282 KSAFWNFSSFSLETVAQELLGEGKSIDNPWDRMD---EIDRRFAEDKPALATYNLKDCELVTQIFHKTEIMPFLLERATV 358
Cdd:PHA02524 257 MDYMDVFKKFSFTPMPDYKLGNVGYREVKADKLDyegPINKFRKADHQRYVDYCVRDTDIILLIDGRRCFIDLILSLSYY 336
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 359 NGLPVDRHGGSVAAFGHLYFPRMHRAGYVAPNLGEVPPHASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPvGL 438
Cdd:PHA02524 337 AKIRFDDVLGTIKVWDSIIFNSLVESNVVIPAMKASPKQSFPGAYVKEPVPGGYRYGLSFDLTSLYPSILRLLNISP-EM 415
|
....*..
gi 15829318 439 VEGMAQP 445
Cdd:PHA02524 416 IAGMFSP 422
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
214-333 |
8.34e-07 |
|
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: 50.02 E-value: 8.34e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 214 NYDPDVIIGWNVVQFDLRMLQKHAERYRIPLRLGRD-NSELEWREHGfKNGVffaqaKGRLIIDgieaLKSAFWNFSSF- 291
Cdd:cd05781 61 EYDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRgGSEPSTGVYG-HYSI-----TGRLNVD----LYDFAEEIPEVk 130
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*
gi 15829318 292 --SLETVAQEL---------LGEGKSIDNPWDRMD--EIDRRFAEDKpALATYNL 333
Cdd:cd05781 131 vkTLENVAEYLgvmkkservLIEWYRIYEYWDDEKkrDILLKYNRDD-ARSTYGL 184
|
|
| 43B |
PHA02523 |
DNA polymerase subunit B; Provisional |
477-666 |
3.33e-05 |
|
DNA polymerase subunit B; Provisional
Pssm-ID: 164924 Cd Length: 391 Bit Score: 47.01 E-value: 3.33e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 477 RDEAKRQGNKpLSQalKIIMNAFYGVLGTTACRFFDPRLVSSITMRGHQIMRQTKA--------LIEAQGYD-VIYGDTD 547
Cdd:PHA02523 34 KEEQKRNTNQ-LNR--KILINSLYGALGNNWFRYFDLRNAEAITTYGQLAIRWIERklneyineLVKTTGVDyVCYIDTD 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 548 STFVwlkgaHSEEEATKIGRALVQHVN--VWWAETLQKQQLTSALELEYET---------HFCRFLMPTIRGADTGS--- 613
Cdd:PHA02523 111 SVYL-----NMEAVVNRVGIDKFRDTNhlIDFLDNLGSKKLEPFIDDSYKEleeymnhdhHLLLMDREAIFGAPLGSdgi 185
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15829318 614 ------KKRYAGLIQEGDKQR-----MVFKGLETVRTDwTPLAQQFQQELYLRIFRNE---PYQEYF 666
Cdd:PHA02523 186 ggfwtgKKRYALNVYDMEGTRyaephLKIMGLETQRSS-TPLACQKSLKESIRRLLQEgesSLQDYF 251
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
204-350 |
5.21e-05 |
|
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: 45.30 E-value: 5.21e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 204 LLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRIPL--RLGR-DNSelEWREhgFKNGVFFAQ---AKGRLIID- 276
Cdd:cd05776 85 LLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHwsRIGRlKRS--VWPK--KKGGGKFGErelTAGRLLCDt 160
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 277 ---GIEALKSafwnfSSFSLETVAQELLG-EGKSIDNpwdrmDEIdRRFAEDKPALATY---NLKDCELVTQIFHKTEIM 349
Cdd:cd05776 161 ylsAKELIRC-----KSYDLTELSQQVLGiERQDIDP-----EEI-LNMYNDSESLLKLlehTEKDAYLILQLMFKLNIL 229
|
.
gi 15829318 350 P 350
Cdd:cd05776 230 P 230
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
216-430 |
1.29e-04 |
|
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: 45.82 E-value: 1.29e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 216 DPDVIIGWNVVQFDLR------MLQKHAERYRIPLR-------LGR--DNSELEWREHGFKNGVFFAQAKGRLIIDGIEA 280
Cdd:TIGR00592 285 DTDVEITVNGDNFDLVyladrqVFQFYWDAYEDPAEklgvvllFGRdvDHVSPCVQVKGINRDLFFLPREGKIDFDLGKV 364
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 281 LKSAFwNFSSFSLETVaqELLGEGKSIDNPwdRMDEIDRRFAEDKPA-LATYNLKDCELVTQIFHKTEIMPFLLERATVN 359
Cdd:TIGR00592 365 TRRTI-NLPDYYLEFV--SELALGYKKEKF--RAKPIAKKYEFEAPDiDAPYSSEYLEVTYELGKEFAPMEALPSDLKGQ 439
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 360 GLPVDrHGGSVAAFGHLYFPRMHRA----GYVAPNLGEVPPH---ASPGGYVMDS--RPGLYDS-----VLVLDYKSLYP 425
Cdd:TIGR00592 440 TFWHV-FGSNTGNLERFLLLRKIKGpcwlAVKGPDELEYPRRswcKYEGGYVKPPnvEKGLDKTppplvVLDFSMKSLNP 518
|
....*
gi 15829318 426 SIIRT 430
Cdd:TIGR00592 519 SIIRN 523
|
|
| DNA_polB_B1_exo |
cd05783 |
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ... |
148-338 |
2.15e-04 |
|
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: 43.08 E-value: 2.15e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 148 PPLKWVSIDIE--TTRHG----------ELYCIGLEGC-GQRIVYML---------GPENGDASALDFELEYvasrpQLL 205
Cdd:cd05783 3 PKLKRIAIDIEvyTPIKGripdpktaeyPVISVALAGSdGLKRVLVLkregvegleGLLPEGAEVEFFDSEK-----ELI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829318 206 EKLNAWFANYdPdVIIGWNVVQFDLRMLQKHAER-----YRIPLRLGRDNSELEwreHGFKngvffaqakgrliID---- 276
Cdd:cd05783 78 REAFKIISEY-P-IVLTFNGDNFDLPYLYNRALKlgipkEEIPIYLKRDYATLK---HGIH-------------IDlykf 139
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15829318 277 -GIEALKS-AFWN-FSSFSLETVAQELLGEGKSidnpwdrmdEIDRRFAEDKPA-LATYNLKDCEL 338
Cdd:cd05783 140 fSNRAIQVyAFGNkYREYTLDAVAKALLGEGKV---------ELEKNISELNLYeLAEYNYRDAEL 196
|
|
| |
