|
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 1737442406 2 TQAQEGFLLTRHWRDTPQGTEVEFWLATDSGPLHVTLPPQESVAFIPESHVEKVKQLLRGENGWRITPLELKDFHRQPVY 81
Cdd:PRK05762 1 MMLQQGFILTRHYRDTPGGPEVELWLATDEGPRVVLLDPQFRPYFIPAEQDERAESLLAGEIGVRLSPLALKDFHRRPVL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 82 GLYCRAHRQLMRYEKLLREAGVTLYEADIRPPERFLMERFITAPVWVDGTAQ----NGRLVNARLKPNPGYRPPLKWVSL 157
Cdd:PRK05762 81 GLYCRQHRQLTRLPKRLREGGVDVYEADIRFPERYLMERFITPCVWFSGEVEqyttDGVLRNARLKPAPDYRPPLKVVSL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 158 DIETTRHGELYCIGLEGCGDRIVYMLGPPNGDssALDFrLEYVNSRPQLLEKLNQWFADYDPDVLIGWNVVQFDLRVLQK 237
Cdd:PRK05762 161 DIETSNKGELYSIGLEGCGQRPVIMLGPPNGE--ALDF-LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQE 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 238 HAERYRIPLILGRGNSELEWREHGFKNGVFFAQANGRLIIDGIEALKSAFWNFSSFSLEAVAQALLGEGKSIDNPWDRMD 317
Cdd:PRK05762 238 RAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATWVFDSFSLEYVSQRLLGEGKAIDDPYDRMD 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 318 EIDRRFNEDKPALATYNLKDCELVTQIFHKTEIMPFLLERATVNGLAADRHGGSVAAFSHLYFPRMHRAGYVAPNLGDVP 397
Cdd:PRK05762 318 EIDRRFAEDKPALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLPLDRVGGSVAAFEHLYLPRAHRAGYVAPNLGERP 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 398 PQASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTYLIDPVGLVEGMAQPDDaHSTEGFLGARFSREKHCLPEIVGNIWH 477
Cdd:PRK05762 398 GEASPGGYVMDSKPGLYDSVLVLDFKSLYPSIIRTFNIDPDGLVEGLAQPPE-ESVAGFLGARFSREKHFLPEIVERLWE 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 478 GRDEAKRHGNKPLSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHEIMRQTKALIESRGYDVIYGDTDSTFVWLKA 557
Cdd:PRK05762 477 GRDEAKREMNKPLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQGYQVIYGDTDSTFVWLGG 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 558 AHSEEDAARIGKELVAFVNAWWRESLQKE-RLTSTLELEFETHFARFLMPTIRGTDQGSKKRYAGLIQEGD-TQRMVFKG 635
Cdd:PRK05762 557 AHDEEDAAKIGRALVQEINQWWQEHLQQEfGLESALELEFEKHYRRFFMPTIRGAEEGSKKRYAGLIQEGDgDGRIVFKG 636
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 636 LETVRTDWTPLAQQFQQTLYLRVFRNEPYQDYVRETIASLMAGELDNQLVYRKRLRRPLAEYQRNVPPHVRAARLADEEN 715
Cdd:PRK05762 637 LETVRTDWTPLAKEFQQELYERIFRGEPYVDYVREVIDKLRAGELDEKLVYRKRLRRPLDEYQRNVPPHVRAARLADEMG 716
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 716 VKRGRAPQYQNRGTIKYVWTINGPEPVDYQYSPLDYDHYLTRQLQPVADGILPFIDDDFATLVTGQLGLF 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: 1053.66 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 4 AQEGFLLTRHWRDTPQGTEVEFWLATDSGP-LHVTLPPQESVAFIPESHVEKVKQLLRGENGW-RITPLELKDFHRQ--P 79
Cdd:COG0417 2 KIPGFLLDRSYRDEDGKPVIELWGRTEDGPsVLLDVTGFRPYFYVPLPDEEKLEELLRDIKEItEVEPVKLKSFFGEpvP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 80 VYGLYCRAHRQLMRYEKLLREAGVTLYEADIRPPERFLMERFITAPVWVDGTAQNGRLV-------NARLKPNPgYRPPL 152
Cdd:COG0417 82 VLKIYTRDPRDVRELRDRLKEGGIDVYEADIRFHDRYLIDRFLTPGVWYEGEVEEDGGKldyevkeNPRLKPED-YRPKL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 153 KWVSLDIETT---------RHGELYCIGLEGC-GDRIVYMLGPPNgdssaLDFRLEYVNSRPQLLEKLNQWFADYDPDVL 222
Cdd:COG0417 161 KVLSFDIEVStprgfpdpeRDGPIISIGLAGSdGEKKVLMLGREG-----VDFEVEYFDDEKALLEAFFEIIREYDPDII 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 223 IGWNVVQFDLRVLQKHAERYRIPLILGRGNSELEWREHGfknGVFFAQANGRLIIDGIEALKSAFWNFSSFSLEAVAQAL 302
Cdd:COG0417 236 IGWNVDNFDLPYLQKRAERLGIPLDLGRDGSEPSWREHG---GQGFASIPGRVVIDLYDALKSATYKFKSYSLDAVAEEL 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 303 LGEGKSIDNpwdrMDEIDRRFNEDKPALATYNLKDCELVTQIFHKTEIMPFLLERATVNGLAADRHG--GSVAAFSHLYF 380
Cdd:COG0417 313 LGEGKLIVD----GGEIERLWDDDKPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGraGSSAAFENLLL 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 381 PRMHRAGYVAPNLGDVPPQASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTYLIDPVGLVEGMAQP-DDAHSTEGFlGA 459
Cdd:COG0417 389 PEAHRRGYLAPNKGEIKGEAYPGGYVLDPKPGLYENVLVLDFKSLYPSIIRTFNISPETLVEGGEEPcGDEDVAPGF-GH 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 460 RFSRE-KHCLPEIVGNIWHGRDEAKRHGNK------------PLSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGH 526
Cdd:COG0417 468 RFCREpKGILPSILEELWDERDEAKKKMKKakpdseeyrlydALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGR 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 527 EIMRQTKALIESRGYDVIYGDTDSTFVWLKaAHSEEDAARIGKELVAFVNAWWReslqkerltSTLELEFETHFARFLMP 606
Cdd:COG0417 548 EIIKQTIEKAEELGYKVIYGDTDSLFVWLP-KASLEEAIEIGKELAEEINAWWP---------SGLELEFEKHYRRFFFP 617
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 607 TirgtdqgSKKRYAGLIQEGdtqRMVFKGLETVRTDWTPLAQQFQQTLYLRVFRNEPYQ---DYVRETIASLMAGELD-N 682
Cdd:COG0417 618 G-------SKKRYAGLTEDG---KIDIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEkavEYVRDVIEKLRAGEVDlD 687
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 683 QLVYRKRLRRPLAEYQRNVPPHVRAARLADEenvkRGRApqYQNRGTIKYVWTINGPEPVDYQY-----SPLDYDHYLTR 757
Cdd:COG0417 688 DLVIRKRLRKPLSEYEKNVPPHVRAARKLDE----RGRP--YQRGDKISYVITKGGGRVEPVELakereSEIDYDYYIEK 761
|
810 820 830
....*....|....*....|....*....|
gi 1737442406 758 QLQPVADGILPFIDDDFATLVTG--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: 695.55 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 399 QASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTYLIDPVGLVEGMAQPDDAHSTEGFLGARFSREKHCLPEIVGNIWHG 478
Cdd:cd05537 1 ISSPGGYVMDSKPGLYKNVLVLDFKSLYPSIIRTFLIDPLGLIEGLKAPDPEDLIPGFLGARFSREKHILPDLIARLWAA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 479 RDEAKRHGNKPLSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHEIMRQTKALIESRGYDVIYGDTDSTFVWLKAA 558
Cdd:cd05537 81 RDEAKREKNAPLSQAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQVIYGDTDSTFVWLGEE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 559 HSEEDAARIGKELVAFVNAWWRESLQKER-LTSTLELEFETHFARFLMPTIRGTDQGSKKRYAGLIQEGDTQRMVFKGLE 637
Cdd:cd05537 161 LDAAEAQAIGKELASQINQWWAQKLKEEFgLESFLEIEFETHYSRFFMPTIRGSDEGSKKRYAGLKSTDGGDELVFKGLE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 638 TVRTDWTPLAQQFQQTLYLRVFRNEPYQDYVRETIASLMAGELDNQLVYRKRLRRPLAEYQRNVPPHVRAARLADEENVK 717
Cdd:cd05537 241 TVRSDWTPLARQFQKELYERVFNDEPYEGFIKETVEELLAGELDELLVYRKRLRRPLSEYTKNVPPHVQAARLADQINRE 320
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....
gi 1737442406 718 RGRAPQYQNrgtIKYVWTINGPEPVDYQYSPLDYDHYLTRQLQPVADGILPFID 771
Cdd:cd05537 321 LGRPRQYQW---IEYVITVNGPEPLEYRTSPLDYQHYIDKQLKPIADSILPFLG 371
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
399-768 |
5.27e-106 |
|
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: 327.79 E-value: 5.27e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 399 QASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTYLIDPVGLVEGMAQPDDAHSTeGFLGARFSREKHCLPEIVGNIWHG 478
Cdd:cd00145 1 EPYEGGYVFDPIPGLYENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYI-GVGFRSPKDRKGLLPRILEELLNF 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 479 RDEAK------------RHGNKPLSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHEIMRQTKALIESRGYDVIYG 546
Cdd:cd00145 80 RDEAKkrmkaaklapeeRVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGARVIYG 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 547 DTDSTFVWLKAAHSEEDaarigkelvafVNAWWRESLQKERLTSTLELEFETHFARFLMptirgtdqGSKKRYAGLIQE- 625
Cdd:cd00145 160 DTDSIFVSLPKMGTKED-----------AIKEGREILQELADEHLLELEFEKVYLPFFL--------GKKKRYAGLDIWk 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 626 -GDTQRMVFKGLETVRTDWTPLAQQFQQTLYLRVFRNEPYQDYVRETIASLMageldnqlvyrkrlrrplaeyqrnvpph 704
Cdd:cd00145 221 gQDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEERKVEAVKEYIDELD---------------------------- 272
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1737442406 705 vraarlADEENVKRGRAPQYQNRGTikyvwtiNGPEPVDYQYSPLDYDHYLTRQLQPVADGILP 768
Cdd:cd00145 273 ------KVKYVVTRGGKGVPDYERA-------DPPLEDLDKRHRIDYEYYLERLLQPPLERIFE 323
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
150-346 |
6.52e-105 |
|
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: 319.90 E-value: 6.52e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 150 PPLKWVSLDIETTRHGELYCIGLEGCGDRIVYMLGPPNGDSsalDFRLEYVNSRPQLLEKLNQWFADYDPDVLIGWNVVQ 229
Cdd:cd05784 1 PKLKVVSLDIETSMDGELYSIGLYGEGQERVLMVGDPEDDA---PDNIEWFADEKSLLLALIAWFAQYDPDIIIGWNVIN 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 230 FDLRVLQKHAERYRIPLILGRGNSELEWREHGfKNGVFFAQANGRLIIDGIEALKSAFWNFSSFSLEAVAQALLGEGKSI 309
Cdd:cd05784 78 FDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSG-KPGQGFLSLPGRVVLDGIDALKTATYHFESFSLENVAQELLGEGKLI 156
|
170 180 190
....*....|....*....|....*....|....*..
gi 1737442406 310 DNPWDRMDEIDRRFNEDKPALATYNLKDCELVTQIFH 346
Cdd:cd05784 157 HDVDDRGAEIERLFREDKLALARYNLQDCELVWRIFE 193
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
150-556 |
2.47e-78 |
|
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: 260.16 E-value: 2.47e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 150 PPLKWVSLDIETTRHG-----------ELYCIGLEGCGD-------RIVYMLGPpngDSSALDFRLEYVNSRPQLLEKLN 211
Cdd:smart00486 1 PPLKILSFDIETYTDGgnfpdaeifddEIIQISLVINDGdkkganrRILFTLGT---CKEIDGIEVYEFNNEKELLLAFF 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 212 QWFADYDPDVLIGWNVVQFDLRVLQKHAERYRIPLI--LGRGNSELEWREHGFKNGV-------FFAQANGRLIIDGIEA 282
Cdd:smart00486 78 EFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLskIGRLKIGLRIPNKKPLFGSksfglsdIKVYIKGRLVIDLYRL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 283 LKSAFwNFSSFSLEAVAQALLGEGKsIDNPWDRMDEIDRRFNEDKPALATYNLKDCELVTQIFHKTEIMPFLLERATVNG 362
Cdd:smart00486 158 YKNKL-KLPSYKLDTVAEYLLGKEK-DDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAG 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 363 LAADR--HGGSVAAFSHLYFPRMHRAGYVAPNLGDVPPQAS----------PGGYVMDSRPGLYDS-VLVLDYKSLYPSI 429
Cdd:smart00486 236 IPLRRtlYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSepdlkkkvkyEGGKVLEPKKGFYDNpVLVLDFNSLYPSI 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 430 IRTYLIDP--VGLVEGMAQPDDAHSTEGFL---------GARFSREKH--CLPEIVGNIWHGRDEAKRH----------- 485
Cdd:smart00486 316 IIAHNLCYstLVGVGEVVIKGDLIIPEDLLtikyekgnkYRFVKKNIRkgILPKLLKKLLDKRKEIKKLmkkekdeseel 395
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1737442406 486 --GNKPLSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHEIMRQTKALIESRGYD-----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 |
1.62e-53 |
|
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: 189.84 E-value: 1.62e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 399 QASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTYLIDPVGLVEGmaqPDDAHSTEGFLGARFSREKHCL-PEIVGNIWH 477
Cdd:cd05536 2 ESYEGGIVLEPEKGLHENIVVLDFSSLYPSIMIKYNISPDTLVRE---GCEDCDVEPQVGHKFRKDPPGFiPSVLEDLLE 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 478 GRDEAKR---------HGNKPLS---QALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHEIMRQTKALIESRGYDVIY 545
Cdd:cd05536 79 ERRRIKEkmkkldpesEEYKLLDerqRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAEEKGFKVIY 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 546 GDTDSTFV-WLKAAHSEEDAarigKELVAFVNawwreslqkERLtsTLELEFETHFARFLMPTirgtdqgsKKRYAGLIQ 624
Cdd:cd05536 159 GDTDSLFVkIDGADAVKKKV----KKLLKYIN---------EEL--PLELEIEKFYKRGFFVT--------KKRYAGLTE 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 625 EGdtqRMVFKGLETVRTDWTPLAQQFQQTLYLRVFRN---EPYQDYVRETIASLMAGELD-NQLVYRKRLRRPLAEYqRN 700
Cdd:cd05536 216 DG---KIDVVGLEVVRRDWSEIAKETQARVLEAILKEgdvEEAVKIVKEVIEKLKRGEVPpEKLVIWKQLTKDLSEY-KA 291
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1737442406 701 VPPHVRAARLADEENVKRGRApqyqnrGTIKYVwTINGP-------EPVDYQYSPLDYD--HYLTRQLQPVADGIL 767
Cdd:cd05536 292 TGPHVAAAKKLAKRGYKVRPG------TKIGYV-IVKGSgkisdraYPYDMVDEKHKYDaeYYIDNQVLPAVLRIL 360
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
382-767 |
1.73e-50 |
|
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: 183.20 E-value: 1.73e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 382 RMHRAGYVAPN----LGDVPpqASPGGYVMDSRPGLYDS-VLVLDYKSLYPSIIRTY------LIDPVGLVEGMAQPDDA 450
Cdd:pfam00136 22 LALEEGFILPDrpsaKGDED--GYQGATVIEPKKGFYDKpVLVLDFNSLYPSIIQAHnlcyttLVRSVDEANNLPPEDNL 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 451 HS-TEGFLGARF---SREKHCLPEIVGNIWHGRDEAKRHGNKPLS-----------QALKIIMNAFYGVLGTSACRFFDP 515
Cdd:pfam00136 100 ITvECTPRGVYFvkdHVREGLLPKLLKDLLAKRKAIKKLLKEETDpferaildkqqLALKITANSVYGFTGFANGRLPCL 179
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 516 RLASSITMRGHEIMRQTKALIESR---GYDVIYGDTDSTFVWLKAAhSEEDAARIGKELVAFVNawwreslqKERLTSTL 592
Cdd:pfam00136 180 PIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTDSVFIEFGGK-DVEEAMKIGDELAEHVN--------QDLFKSPI 250
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 593 ELEFETHFARFLMPtirgtdqgSKKRYAGLIQEGDTQ--RMVFKGLETVRTDWTPLAQQFQQTLYLRVFRNEPYQD---Y 667
Cdd:pfam00136 251 KLEFEKVYKPLLLI--------SKKKYAGLKYTAPSNfnKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSDRGLPVgleF 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 668 VRETIAS----LMAGELD-NQLVYRKRLRRPLAEYQRNVPPHVRAARladEENVKRGRAPQYQNRgtIKYVWTINGPEPV 742
Cdd:pfam00136 323 VISILNDarsdLRNNKVPlEKFVISKELSKPPDNYKSKNLPHVEVAL---RMNKRNGEAPEVGDR--IPYVIVKAAKGLK 397
|
410 420 430
....*....|....*....|....*....|....*....
gi 1737442406 743 D---YQYS-----------PLDYDHYLTRQLQPVADGIL 767
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 ... |
154-346 |
2.86e-50 |
|
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: 174.85 E-value: 2.86e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 154 WVSLDIETTRH--------GELYCIGLEG--CGDRIVYMLGPPNGD---SSALDFRLEYVNSRPQLLEKLNQWFADYDPD 220
Cdd:cd05160 1 VLSFDIETTPPvggpepdrDPIICITYADsfDGVKVVFLLKTSTVGddiEFIDGIEVEYFADEKELLKRFFDIIREYDPD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 221 VLIGWNVVQFDLRVLQKHAERYRIPLilgRGNSELEWREHGFKNGVFFAQANGRLIIDGIEALKSAFWnFSSFSLEAVAQ 300
Cdd:cd05160 81 ILTGYNIDDFDLPYLLKRAEALGIKL---TDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFK-LKSYTLDAVAE 156
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 1737442406 301 ALLGEGKSIDNPWDRMDEidrRFNEDKPALATYNLKDCELVTQIFH 346
Cdd:cd05160 157 ELLGEGKEKVDGEIIEDA---EWEEDPERLIEYNLKDAELTLQILE 199
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
114-767 |
8.33e-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: 177.56 E-value: 8.33e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 114 ERFLMERFITAPVWVD------------------GTAQNGRLVNARLKPNPgyrPPLKWVSLDIET-------------- 161
Cdd:TIGR00592 453 ERFLLLRKIKGPCWLAvkgpdeleyprrswckyeGGYVKPPNVEKGLDKTP---PPLVVLDFSMKSlnpsiirneivsip 529
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 162 -TRHGELYCIGLEGCGDRIVYM--LGPPNGDSSALDFRLEYVNSRPQLLEKLN------QWF-ADY---DPDVLIGWNVV 228
Cdd:TIGR00592 530 dTLHREFALDKPPPEPPYDVHPcvGTRPKDCSFPLDLKGEFPGKKPSLVEDLAteraliKKFmAKVkkiDPDEIVGHDYQ 609
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 229 QFDLRVLQKHAERYRIPLILGRGnselEWREHGFKNGVFFAQANGRLIIDGIEALKSAFWNFSSFSLEAVAQALLGEGKS 308
Cdd:TIGR00592 610 QRALKVLANRINDLKIPTWSKIG----RLRRSPKFGRRFGERTCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKV 685
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 309 IDnpwdrMDEIDRRFNEDKP--ALATYNLKDCELVTQIFHKTEIMPFLLERATVNGLAADR--HGGSVAAFSHLYFPRMH 384
Cdd:TIGR00592 686 IP-----IDNINNMYSESSSltYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRtlMGGRSERNEFLLLHAFY 760
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 385 RAGYVAPN---------LGDVPPQAS----------PGGYVMDSRPGLYDS-VLVLDYKSLYPSIIRTYLI------DPV 438
Cdd:TIGR00592 761 ENNYIVPDkqifrkqqkLGDEDEEIDgykkgkkaayAGGLVLEPKVGLYDKyVLLMDFNSLYPSIIQEFNIcfttvqQKV 840
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 439 GLVEGMAQPDDahstegflgarfSREKHCLPEIVGNIWHGRDEAKRHGNKPLS-----------QALKIIMNAFYGVLGT 507
Cdd:TIGR00592 841 DEDELPELPDS------------ELEMGILPRELRKLVERRKEVKKLMKQDLNpdlrlqydirqKALKLTANSMYGCLGY 908
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 508 SACRFFDPRLASSITMRGHEIMRQTKALIESRGYDVIYGDTDSTFVWLKAAHSEEdAARIGKELVAFVNAWWReslqker 587
Cdd:TIGR00592 909 SKSRFYAKPLAALVTAKGREILEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEE-VFKIGKEFKSEVNKLYK------- 980
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 588 ltsTLELEFETHFARFLMPTirgtdqgsKKRYAGLIQEGD-----TQRMVFKGLETVRTDWTPLAQQFQQTLYLRVFRNE 662
Cdd:TIGR00592 981 ---LLELDIDGVFKRLLLLK--------KKKYAAIKVEGDsdgnyTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDK 1049
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 663 P-------YQDYVRETIASLMAGELD-NQLVYRKRLRRPLAEY-QRNVPPHVRAA-RLADEEN--VKRGRAPQY---QNR 727
Cdd:TIGR00592 1050 DveeaveeVQEVLEKIGKNVLNGEVPlEKFVINKQLTRDPKDYpDGASLPHVHVAlRINARGGrkVKAGDVVSYvicKDG 1129
|
730 740 750 760
....*....|....*....|....*....|....*....|..
gi 1737442406 728 GTIKYVWTINGPEPVDYQYSPLDYD--HYLTRQLQPVADGIL 767
Cdd:TIGR00592 1130 GNLSARQRAYALEELQRKHNNLIYDtqYYLEHQIHPVVLRIL 1171
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
18-781 |
9.90e-46 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 175.65 E-value: 9.90e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 18 PQGTEVEFWL-ATDSGPLHVTLPPQESVAFIPEshVEKVKQLLRGENGWRITPLELKDFHRQPVYG---LYCRAHRQLMR 93
Cdd:PRK05761 40 PETGKIYKWYdRTGHKPYFLTDLDPDEIDKIPK--ILRHPSFDHLEIVEKYDGLRDKKVKVTKIVVkdpLAVRRLRLSVR 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 94 yeKLLReagvtLYEADIRPPERFLMERFITAPVWVDGTAQNGRLVN---------------------ARLKPNPGyrPPL 152
Cdd:PRK05761 118 --DIPR-----AWEADIKYEFRYIYDNGLIPGMPYDVKNGLESVEPeilveeikkafkderklaedwLPIFEAPI--PKI 188
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 153 KWVSLDIETTRHGElyciglegcgDRIvymlgpPNGDSSALDfrleyvnsrPQLLEKLnqwfADYDPDVLIgwNVVQFDL 232
Cdd:PRK05761 189 KRIAIDIEVYTPAK----------GRI------PDDSEKELL---------AELFDII----LEYPPVVTF--NGDNFDL 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 233 RVLQKHAERY-----RIPLILGRGnselewREHGFKNGVFFaqangrliidgIEALKS-AFWN---FSSFSLEAVAQALL 303
Cdd:PRK05761 238 PYLYNRALKLgipkeEIPIEPGRA------GIHIDLYKFFQ-----------NKAVRSyAFYGkyrHREARLDAVGRALL 300
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 304 GEGK-SIDNPWDRMDEIDrrfnedkpaLATYNLKDCELVTQ--IFHKTEIMPFLLERATVNGLA---ADRHGGSvAAFSH 377
Cdd:PRK05761 301 GISKvELETNISELDLEE---------LAEYNFRDAEITLKltFFNNELVLKLILLLSRISKLPieeLSRATIS-TWISN 370
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 378 LYFPRMHRAGYVAPNLGDVPPQASP-------------GGYVMDSRPGLYDSVLVLDYKSLYPSIIRTYLIDP--VGlVE 442
Cdd:PRK05761 371 LEYWEHRKRGWLIPWKEDILRLDHEvykkaiikgkkyrGGLVFQPPPGIFFNVYVLDFASLYPSIIVKWNLSPetVR-IP 449
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 443 GMAQPDDAHSTEgfLGARFSREKHCLPE-IVGNIwhgRDE-----AKRHGNKPLSQ-----------ALKIIMNAFYGVL 505
Cdd:PRK05761 450 ECKCHYDDEVPE--LGHSVCDDRPGLTSvLVGLL---RDFrvkiyKKKAKDPNLDEerrawydvvqrALKVFLNASYGVF 524
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 506 GTSACRFFDPRLASSITMRGHEIMRQTKALIESRGYDVIYGDTDSTFVWlkaAHSEEDAarigKELVAFVnawwreslqK 585
Cdd:PRK05761 525 GAENFKLYRIEVAESITALGREILLSTKKKAEELGLKVLYGDTDSLFVW---GPTKESL----EELIKEI---------E 588
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 586 ERLtsTLELEFETHFaRFLMPTirgtdqGSKKRYAGLIQEGDtqrMVFKGLETVRTDWTPLAQQFQQTLyLRVFRN---- 661
Cdd:PRK05761 589 ERT--GIDLEVDKTY-DWVAFS------GLKKNYFGVLKDGK---VKIKGIVAKKRNTPEFVKELQREV-LEVLKSirsp 655
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 662 -------EPYQDYVRETIASLMAGELD-NQLVYRKRLRRPLAEYQRNVPPHVRAARLADEE--NVKRGRAPQY---QNRG 728
Cdd:PRK05761 656 edvekvkDEIEDVLKRYYEKLRAKDYPlDELAIRVRLSKPLDEYTKNTPQHVKAALQLRDYgvEVSPGDIISYvkvDDKR 735
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|...
gi 1737442406 729 TIKYVWTINGPEpVDYQYspldYDHYLTRQLQPvadgILPFIDDDFATLVTGQ 781
Cdd:PRK05761 736 GVKPVQLAKLSE-IDVEK----YIELLRSALEQ----ILSALGVSWDDIRGTT 779
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
403-762 |
2.29e-43 |
|
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: 161.98 E-value: 2.29e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 403 GGYVMDSRPGLYDS-VLVLDYKSLYPSIIRTYLI----------DPVGLVEGMAQPDDAHSteGFLgarfsrekhclPEI 471
Cdd:cd05532 10 GGLVLEPKKGLYDKfILLLDFNSLYPSIIQEYNIcfttvdradpDDEDDEEPPLPPSDQEK--GIL-----------PRI 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 472 VGNIWHGRDEAKRHGNKPLS-----------QALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHEIMRQTKALIESRG 540
Cdd:cd05532 77 IRKLVERRRQVKKLMKSEKDpdkkaqldirqLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKMN 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 541 YDVIYGDTDSTFVwlkaaH----SEEDAARIGKELVAFVNAWWREslqkerltstLELEFETHFARFLMPtirgtdqgSK 616
Cdd:cd05532 157 LEVIYGDTDSIMI-----NtgttDYEEAKKLGNKIKKEVNKSYKK----------LEIDIDGVFKRLLLL--------KK 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 617 KRYAGLIQEGDTQRMV---FKGLETVRTDWTPLAQQFQQTLYLRVFRNEPY-------QDYVRETIASLMAGELD-NQLV 685
Cdd:cd05532 214 KKYAALKVVDDDKGKLkkeVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSRediveniHEYLRKINEDLRNGKIPlEKFI 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 686 YRKRLRRPLAEY-QRNVPPHVRAA-RLADE-ENVKRGRapqyqnrgTIKYVWTING--PEPVDYQYSP----------LD 750
Cdd:cd05532 294 ITKQLTKNPEEYpDKKSLPHVQVAlRMNKRgRKVKAGD--------TIPYIICKDGssKSLADRAYHPdevkknenlkID 365
|
410
....*....|..
gi 1737442406 751 YDHYLTRQLQPV 762
Cdd:cd05532 366 IEYYLSQQILPP 377
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
106-780 |
9.41e-41 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 161.73 E-value: 9.41e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 106 YEADIRPPERFLMERFITAPVWVDGTAQNGRLVNARLKP-------NPGYR--------------PPLKWVSLDIEttrh 164
Cdd:PTZ00166 197 YESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRPPKKKTstcqievDCSYEdliplppegeyltiAPLRILSFDIE---- 272
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 165 gelyCIGLEGCG------------DRIVYMLGPPNGDSSALDFRLEYVNSRP-----------QLLEKLNQWFADYDPDV 221
Cdd:PTZ00166 273 ----CIKLKGLGfpeaendpviqiSSVVTNQGDEEEPLTKFIFTLKECASIAganvlsfetekELLLAWAEFVIAVDPDF 348
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 222 LIGWNVVQFDLRVLQKHAERYRIP--LILGRGNSElewrEHGFKNGVFFAQA-----------NGRLIIDGIEALKSAFw 288
Cdd:PTZ00166 349 LTGYNIINFDLPYLLNRAKALKLNdfKYLGRIKST----RSVIKDSKFSSKQmgtreskeiniEGRIQFDVMDLIRRDY- 423
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 289 NFSSFSLEAVAQALLGEGKSiDNPWDRMDEIDRRFNEDKPALATYNLKDCELVTQIFHKTEIMPFLLERATVNGLAAD-- 366
Cdd:PTZ00166 424 KLKSYSLNYVSFEFLKEQKE-DVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGwl 502
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 367 -RHGGSVAAFSHLYfpRMHRA-GYVAP---NLGDVPPQASPGGYVMDSRPGLYDS-VLVLDYKSLYPSIIRTYLIDPVGL 440
Cdd:PTZ00166 503 lTRGQQIKVTSQLL--RKCKKlNYVIPtvkYSGGGSEEKYEGATVLEPKKGFYDEpIATLDFASLYPSIMIAHNLCYSTL 580
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 441 V---EGMAQPDDAhSTEGFLGARF---SREKHCLPEIVGNIWHGRDEAKRHGNK---PLSQ--------ALKIIMNAFYG 503
Cdd:PTZ00166 581 VppnDANNYPEDT-YVTTPTGDKFvkkEVRKGILPLIVEELIAARKKAKKEMKDekdPLLKkvlngrqlALKISANSVYG 659
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 504 VLGTSACRFFdPRL--ASSITMRGHEIMRQTKALIESR-----GYD----VIYGDTDStfVWLKAAHSE-EDAARIGKEL 571
Cdd:PTZ00166 660 YTGAQVGGQL-PCLevSTSITSFGRQMIDKTKELVEKHytkanGYKhdatVIYGDTDS--VMVKFGTDDiQEAMDLGKEA 736
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 572 VAFVNawwreslqkERLTSTLELEFETHFARFLMPtirgtdqgSKKRYAGLI----QEGDtqRMVFKGLETVRTDWTPLA 647
Cdd:PTZ00166 737 AERIS---------KKFLKPIKLEFEKVYCPYLLM--------NKKRYAGLLytnpEKYD--KIDCKGIETVRRDNCLLV 797
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 648 QQFQQTL--YLRVFRN-EPYQDYVRETIASLMAGELD-NQLVYRKRLRRplAEYqrnvpphvrAARLADEENVKR----- 718
Cdd:PTZ00166 798 QQMVETVlnKILIEKDvESAIEFTKGKISDLLQNRIDiSLLVITKSLGK--DDY---------EGRLAHVELAKKlrqrd 866
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1737442406 719 -GRAPQYQNRgtIKYVwTINGP--EPvdyQYS-------------PLDYDHYLtRQLQPVADGILPFIDDDFATLVTG 780
Cdd:PTZ00166 867 pGSAPNVGDR--VSYV-IVKGAkgAP---QYEraedplyvlenniPIDTQYYL-DQIKNPLLRIFEGVMDNPDSLFSG 937
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
384-775 |
1.32e-34 |
|
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: 137.73 E-value: 1.32e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 384 HRAGYVA--PNLGDV----PPQASPggYVMDSRPGLY-DSVLVLDYKSLYPSIIRTY----------------------- 433
Cdd:cd05534 15 KPENYILpsPSRQQVaqqrALECLP--LVMEPESGFYsDPVIVLDFQSLYPSIMIAYnycystclgrveelngggkfgfl 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 434 ---LIDPVGLVEGMAQPDDAH-STEGFLGARFSREKHCLPEIVGNIWHGRDEAKR------HGNKPLSQ------ALKII 497
Cdd:cd05534 93 gvkLYLPPPPLDLLLLKDDVTiSPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKamkkykDDKKLQRIldarqlALKLL 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 498 MNAFYGVlgTSACrfFDPR-----LASSITMRGHEIMRQTKALIESRGY---DVIYGDTDSTFVWLKAAhSEEDAARIGK 569
Cdd:cd05534 173 ANVTYGY--TAAS--FSGRmpcveIADSIVQTGRETLERAIELIESTPKwgaKVVYGDTDSLFVLLPGR-TKEEAFKIGK 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 570 ELVAFVNAwwreslqkeRLTSTLELEFE-THFARFLMptirgtdqgSKKRYAGLIQEGDTQRMVF---KGLETVRTDWTP 645
Cdd:cd05534 248 EIAEAVTA---------ANPSPIKLKFEkVYHPCVLV---------TKKRYVGYKYESPDQTEPTfdaKGIETVRRDGCP 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 646 LAQQFQQTLYLRVFRNepyQD------YVRETIASLMAGELDNQ-LVYRKRLRRPLAEYQRNVPPHVRAARLadEENVKR 718
Cdd:cd05534 310 AVQKILEKSLRILFET---KDlstvksYLQRQWSKLLQGRVSIQdFIFAKEVRLGTYKEGATLPAGAIVALR--RMEKDP 384
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 719 GRAPQYQNRgtIKYVwTINGP----------EPVDYQYSP---LDYDHYLTRQLQPVADGILPFIDDDFA 775
Cdd:cd05534 385 RAEPQYGER--VPYV-VVRGEpgsrlidlvvSPEEFLADPslrLDAEYYITKQIIPALDRLFNLVGVDVQ 451
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
403-755 |
5.51e-32 |
|
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: 128.24 E-value: 5.51e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 403 GGYVMDSRPGLYDSVLVLDYKSLYPSIIRTY-----LIDPVglvegmaQPDDAHSTEGFLGARFSREKHCL-PEIVGNIw 476
Cdd:cd05530 15 GAIVLEPPPGIFFNVVVLDFASLYPSIIKVWnlsyeTVNCP-------HCECKTNEVPEVGHWVCKKRPGItSQIIGLL- 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 477 hgRD--------EAKRHGNKP--------LSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHEIMRQTKALIESRG 540
Cdd:cd05530 87 --RDlrvkiykkKAKDKSLDEemrqwydvVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIITSTIKKARELG 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 541 YDVIYGDTDSTFVWLKAAHSEEDAARigkelvafvnaWWRESLQkerltstLELEFETHFaRFLMPTirgtdqGSKKRYA 620
Cdd:cd05530 165 LKVLYGDTDSLFLWNPPQEQLEDLVE-----------WVEKELG-------LDLELDKEY-RYVVFS------GLKKNYL 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 621 GLIQEGDtqrMVFKGLeTVRTDWTP--LAQQFQQTL-YLRVFRNEPYQDYVRETIASLMAG----------ELDnQLVYR 687
Cdd:cd05530 220 GVTKDGS---VDIKGL-LGKKRNTPefVKELFYEVIeILSAVNSPEDFEKAREKIRDIVKGvykrlkkkeyTLD-QLAFK 294
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1737442406 688 KRLRRPLAEYQRNVPPHVRAARLADEE--NVKRGRApqyqnrgtIKYVWTIN--GPEPVDY-QYSPLDYDHYL 755
Cdd:cd05530 295 VMLSKPPEEYTKNTPQHVKAARQLEKYgrNVEAGDI--------ISYVKVKGkeGVKPVQLaRLDEVDVEKYV 359
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
403-761 |
9.37e-32 |
|
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: 128.15 E-value: 9.37e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 403 GGYVMDSRPGLYDS-VLVLDYKSLYPSII------RTYLIDPVGLVEGMaqPDDAHST-EGFLGARFSREKHCLPEIVGN 474
Cdd:cd05533 5 GATVIEPIKGYYDVpIATLDFASLYPSIMmahnlcYTTLLNKNTAKKLP--PEDYIKTpNGDYFVKSSVRKGLLPEILEE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 475 IWHGRDEAKRHGNK---PLSQ--------ALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHEIMRQTKALIESR---- 539
Cdd:cd05533 83 LLAARKRAKKDLKEetdPFKKavldgrqlALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEKytka 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 540 -GY----DVIYGDTDSTFVWLKAAHSEEdAARIGKELVAFVNAwwreslqkeRLTSTLELEFE-THFARFLMptirgtdq 613
Cdd:cd05533 163 nGYshdaKVIYGDTDSVMVKFGVSDVEE-AMKLGKEAAEYVSK---------KFIKPIKLEFEkVYFPYLLI-------- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 614 gSKKRYAGLI----QEGDtqRMVFKGLETVRTDWTPLAQQFQQTL--YLRVFRNEP-YQDYVRETIASLMAGELD-NQLV 685
Cdd:cd05533 225 -NKKRYAGLLwtnpDKHD--KMDTKGIETVRRDNCLLVQNVVETClnKILIERDVEgAIEFVKGVISDLLQNKIDiSLLV 301
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 686 YRKRLRRPLAEYQRNVpPHVR-AARLAdeenvKR--GRAPQYQNRgtIKYVwTINGPEPVD-YQYS-----------PLD 750
Cdd:cd05533 302 ITKALTKTADDYAGKQ-AHVElAERMR-----KRdpGSAPNVGDR--VPYV-IIKGAKGAKaYEKAedpiyvlenniPID 372
|
410
....*....|.
gi 1737442406 751 YDHYLTRQLQP 761
Cdd:cd05533 373 TQYYLENQLSK 383
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
403-762 |
2.12e-31 |
|
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: 126.30 E-value: 2.12e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 403 GGYVMDSRPGLYDSVLVLDYKSLYPSIIRTYLIDPvglvEGMAQPDDAHSTEGFLGARFSR-EKHCLPEIVGNIWHGRDE 481
Cdd:cd05531 7 GGLVFQPEPGLYENVAQIDFSSMYPSIIVKYNISP----ETINCRCCECRDHVYLGHRICLkRRGFLPEVLEPLLERRLE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 482 AK-----RHGNKPLSQALKIIMNAFYGVLGTSACRFfdPRLAS--SITMRGHEIMRQTKALIESRGYDVIYGDTDSTFVW 554
Cdd:cd05531 83 YKrlkkeEDPYAGRQKALKWILVTSFGYLGYKNAKF--GRIEVheAITAYGRKILLRAKEIAEEMGFRVLHGIVDSLWIQ 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 555 LKAAHsEEDAARIGKElvafvnawwreslqkerltSTLELEFETHFaRFL--MPTIRGTdqGSKKRYAGLIQEGDtqrMV 632
Cdd:cd05531 161 GRGDI-EELAREIEER-------------------TGIPLKLEGHY-DWIvfLPERDGL--GAPNRYFGRLSDGE---MK 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 633 FKGLETVRTDWTPLAQQFQQTLY--LRVFRN--------EPYQDYVRETIASLMAGELdNQLVYRKRLRRPLAEYQrNVP 702
Cdd:cd05531 215 VRGIELRRRDTPPFVKKFQEEALdiLASAKTpeellklrEEALDLFRRYLQRLREGDL-EDLIIEKKISKRSSEYK-VLA 292
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 703 PHVRAARLADEENVKRGRAPQYQNRGTIKYVWTINGPEPVDYQYspldYDHYLTRQLQPV 762
Cdd:cd05531 293 STALKALRAKGVSVVPGMKIEYIVRDGKRPVPDLGNDEGYDTKY----YRELLERAAEEL 348
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
177-670 |
8.14e-24 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 107.47 E-value: 8.14e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 177 DRIVYMLgppngdssaldFRLEYvnsrpQLLEKLNQWFADYDPDVLIGWNVVQFDLRVLQKhaeryRIPLILGR--GNSE 254
Cdd:PHA02528 168 DKVVYMP-----------FDTER-----EMLLEYINFWEENTPVIFTGWNVELFDVPYIIN-----RIKNILGEktAKRL 226
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 255 LEWREHGFKNGVF-FAQANGRLIIDGIEAL-------KSAFWNFSSFSLEAVAQALLGEGKsidnpWDRMDEIDRRFNED 326
Cdd:PHA02528 227 SPWGKVKERTIENmYGREEIAYDISGISILdyldlykKFTFTNQPSYRLDYIAEVELGKKK-----LDYSDGPFKKFRET 301
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 327 KPAL-ATYNLKDCELVTQIFHKTEIMPFLLE---RATVNglaadrhggsvaaFSHLYFP-RMHRA---------GYVAPN 392
Cdd:PHA02528 302 DHQKyIEYNIIDVELVDRLDDKRKLIELVLSmayYAKIN-------------FEDVFSPiKTWDAiifnslkeeKIVIPE 368
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 393 LGDVPPQASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTYLIDPvglvEGMAQPDDAHSTEGFL--------------- 457
Cdd:PHA02528 369 NKSHKKQKYAGAFVKEPVPGAYRWVVSFDLTSLYPSIIRQVNISP----ETIAGTFHVAPVHEYInktaprpsdeyscsp 444
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 458 -GARFSREKH-CLPEIVGNIWHGRDEAKR-----------------HGNKPLSQ-------------------------- 492
Cdd:PHA02528 445 nGWMYRKDIRgVIPTEIKKVFDQRKIYKKkmlaaernaeliktileDLNDSVDTpidvdyyfdfsdefkaelktltkssl 524
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 493 -------------------ALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHE----IMRQT----KALIESRGYD-VI 544
Cdd:PHA02528 525 kalleecekeialcntiqmARKILINSLYGALGNEHFRYYDLRNAEAITLFGQLaiqwIERKMneylNKLCKTEDEDyVI 604
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 545 YGDTDSTFVWLKAAHSE--EDAARIGKELVAFVNAWWRESLQKERLTSTLEL-EFETHFARfLMPTIRGT--DQG---SK 616
Cdd:PHA02528 605 YGDTDSIYVNLDPLVEKvgEDKFKDTNHWVDFLDKFCKERMEPYIDSSYRELcEYMNNYEH-LMFMDREAiaGPGfwtAK 683
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1737442406 617 KRYAGLIQEGDTQR-----MVFKGLETVRTDwTPLAqqFQQTLY--LRVFRNE---PYQDYVRE 670
Cdd:PHA02528 684 KRYALNVWDSEGTRyaepkLKIMGIETQRSS-TPKA--VQKALKeaIRRILQEgeeSLQEYIKE 744
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
399-692 |
5.09e-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: 83.30 E-value: 5.09e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 399 QASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTYLIDPVGLVEGMAQPddahstegfLGARFSREKHCLPEIVGNiwhG 478
Cdd:cd05538 1 GKFEGGYAYVFITGVLGPIVHADVASLYPSIMLAYRICPARDSLGIFLA---------LLKYLVELRLAAKESARA---A 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 479 RDEAKRHGNKPLSQALKIIMNAFYGVLGTSACRFFDPRLASSITMRGHEIMRQTKALIESRGYDVIYGDTDSTFVWLKAA 558
Cdd:cd05538 69 ARPAERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRRRGATPVEVDTDGIYFIPPNG 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 559 HSEEDAARigkELVAfvnawwreslqkeRLTSTL----ELEFETHFARFLmptIRGTdqgskKRYAGLIQEGdtqRMVFK 634
Cdd:cd05538 149 VDTEDEEE---ELVR-------------ELSSTLpkgiTVEFDGRYRAMF---SYKI-----KNYALLDYDG---KLIVK 201
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 1737442406 635 GLETVRTDWTPlaqqfqqtlYLRVFRNEpyqdYVRETIASLMAGELDNQLVYRKRLRR 692
Cdd:cd05538 202 GSAFRSRGIEP---------FLREFLRE----AVRLLLQGDGAGVHDLYEDYLRRLRS 246
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
150-335 |
2.35e-14 |
|
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: 72.39 E-value: 2.35e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 150 PPLKWVSLDIETTRH--------GELYCIGLegCGDRIVYMLGPPNGDssaLDFrLEYVNSRPQLLEKLNQWFADYDPDV 221
Cdd:cd05780 1 EDLKILSFDIEVLNHegepnpekDPIIMISF--ADEGGNKVITWKKFD---LPF-VEVVKTEKEMIKRFIEIVKEKDPDV 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 222 LIGWNVVQFDLRVLQKHAERYRIPLILGRGNSELEWREHGFKNGVFFaqaNGRLIIDgIEALKSAFWNFSSFSLEAVAQA 301
Cdd:cd05780 75 IYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEI---KGRIHVD-LYPVARRTLNLTRYTLERVYEE 150
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 1737442406 302 LLGEGK------SIDNPWDRMDEIDRRFN---EDkpALATYNL 335
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 ... |
95-298 |
3.39e-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: 65.52 E-value: 3.39e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 95 EKLLREAGVTLYEADIRPPERFLMERFITAPVW--VDGTAQN--GRLVNARL-----------KPNPGYRPPLKWVSLDI 159
Cdd:pfam03104 83 KYLSPENISDVYEYDVDYLERFLIDNDIVGFGWykVKVYPFRaeGRISNCDVeidcdspdlisVPFEKEWPPLRVLSFDI 162
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 160 ETTRHGE------------------LYCIGLEGCGDRIVYMLGPPN-GDSSALDFRLEYVNSRPQLL----EK--LNQWF 214
Cdd:pfam03104 163 ECTSLPGkfpdaenvkdpiiqiscmLDGQGEPEPEPRFLFTLRECDsEDIEDFEYTPKPIYPGVKVFefpsEKelLRRFF 242
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 215 A---DYDPDVLIGWNVVQFDLRVLQKHAERYRIPLILGRGnselEWREHGFKNG---VFFAQA------NGRLIIDgIEA 282
Cdd:pfam03104 243 EfirQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIG----RLNRGGRSKVreiGFGTRSyekvkiSGRLHLD-LYR 317
|
250
....*....|....*.
gi 1737442406 283 LKSAFWNFSSFSLEAV 298
Cdd:pfam03104 318 VIKRDYKLPSYKLNAV 333
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
150-347 |
7.55e-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: 56.82 E-value: 7.55e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 150 PPLKWVSLDIEttrhgelyCIGLEGC-------------------GD-----RIVYMLGP--PNGDSSALDFRLEyvnsr 203
Cdd:cd05777 5 APLRILSFDIE--------CAGRKGVfpepekdpviqianvvtrqGEgepfiRNIFTLKTcaPIVGAQVFSFETE----- 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 204 PQLLEKLNQWFADYDPDVLIGWNVVQFDLRVLQKHAERYRIPLI--LGR-GNSELEWREHGFKN---GVFFAQA---NGR 274
Cdd:cd05777 72 EELLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFpfLGRiKNIKSTIKDTTFSSkqmGTRETKEiniEGR 151
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1737442406 275 LIIDGIEALKSAFwNFSSFSLEAVAQALLGEGK-----SIDNPWDRMDEIDRRfnedkpALATYNLKDCELVTQIFHK 347
Cdd:cd05777 152 IQFDLLQVIQRDY-KLRSYSLNSVSAHFLGEQKedvhySIITDLQNGNPETRR------RLAVYCLKDAYLPLRLLDK 222
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
152-326 |
3.29e-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: 54.72 E-value: 3.29e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 152 LKWVSLDIETTRHGELYCIGLEGCGDRIVyMLGPPNGDSSALDFRLEYVNSRpQLLEKLNQWFADYDPDVLIGWNVVQFD 231
Cdd:cd05785 9 LRRLQLDIETYSLPGFFFSNPDRGDDRII-IVALRDNRGWEEVLHAEDAAEK-ELLEELVAIIRERDPDVIEGHNIFRFD 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 232 LRVLQKHAERYRIPLILGRGNSELEWREHGFKngvfFAQ---------ANGRLIIDGIEALKS---AFWNFSSFSLEAVA 299
Cdd:cd05785 87 LPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFR----FAErlidyprydIPGRHVIDTYFLVQLfdvSSRDLPSYGLKAVA 162
|
170 180 190
....*....|....*....|....*....|....*.
gi 1737442406 300 QaLLG---------EGKSIDNPWDRMDEIDRRFNED 326
Cdd:cd05785 163 K-HFGlaspdrtyiDGRQIAEVWRSDPARLLAYALD 197
|
|
| 43A |
PHA02524 |
DNA polymerase subunit A; Provisional |
206-469 |
4.47e-08 |
|
DNA polymerase subunit A; Provisional
Pssm-ID: 164925 [Multi-domain] Cd Length: 498 Bit Score: 56.55 E-value: 4.47e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 206 LLEKLNQWFADyDPDVLIGWNVVQFDLRVLQKhaeryRIPLILGRGNSElEWREHGFKNGVFFAQANGRLIIDGIE--AL 283
Cdd:PHA02524 184 LLNYIQLWKAN-TPDLVFGWNSEGFDIPYIIT-----RITNILGEKAAN-QLSPYGKITSKTITNLYGEKIIYKIHgiAL 256
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 284 KSAFWNFSSFSLEAVAQALLGEGKSIDNPWDRMD---EIDRRFNEDKPALATYNLKDCELVTQIFHKTEIMPFLLERATV 360
Cdd:PHA02524 257 MDYMDVFKKFSFTPMPDYKLGNVGYREVKADKLDyegPINKFRKADHQRYVDYCVRDTDIILLIDGRRCFIDLILSLSYY 336
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 361 NGLAADRHGGSVAAFSHLYFPRMHRAGYVAPNLGDVPPQASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTYLIDPvGL 440
Cdd:PHA02524 337 AKIRFDDVLGTIKVWDSIIFNSLVESNVVIPAMKASPKQSFPGAYVKEPVPGGYRYGLSFDLTSLYPSILRLLNISP-EM 415
|
250 260
....*....|....*....|....*....
gi 1737442406 441 VEGMAQPDDAHSTEGFLGARFSREKHCLP 469
Cdd:PHA02524 416 IAGMFSPARLEDYINKVAPKPSDQFSCAP 444
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
150-335 |
9.53e-06 |
|
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: 46.94 E-value: 9.53e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 150 PPLKWVSLDIET-TRHGE-------LYCIGLEGCGDRIVYMLGPPNGDSSALDFRLEYVNSrpqlleklnqwfadYDPDV 221
Cdd:cd05781 1 PDLKTLAFDIEVySKYGTpnprrdpIIVISLATSNGDVEFILAEGLDDRKIIREFVKYVKE--------------YDPDI 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 222 LIGWNVVQFDLRVLQKHAERYRIPLILGR-GNSELEWREHGfKNGVffaqaNGRLIIDgieaLKSAFWNFSSF---SLEA 297
Cdd:cd05781 67 IVGYNSNAFDWPYLVERARVLGVKLDVGRrGGSEPSTGVYG-HYSI-----TGRLNVD----LYDFAEEIPEVkvkTLEN 136
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 1737442406 298 VAQAL---------LGEGKSIDNPWDRMD--EIDRRFNEDKpALATYNL 335
Cdd:cd05781 137 VAEYLgvmkkservLIEWYRIYEYWDDEKkrDILLKYNRDD-ARSTYGL 184
|
|
| 43B |
PHA02523 |
DNA polymerase subunit B; Provisional |
479-649 |
1.10e-05 |
|
DNA polymerase subunit B; Provisional
Pssm-ID: 164924 Cd Length: 391 Bit Score: 48.55 E-value: 1.10e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 479 RDEAKRHGNKpLSQalKIIMNAFYGVLGTSACRFFDPRLASSITMRGHEIMRQTKA--------LIESRGYD-VIYGDTD 549
Cdd:PHA02523 34 KEEQKRNTNQ-LNR--KILINSLYGALGNNWFRYFDLRNAEAITTYGQLAIRWIERklneyineLVKTTGVDyVCYIDTD 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 550 STFVWLKAAHSEEDAARIG--KELVAFVNAWWRESLQKERLTSTLELE----FETHFARFLMPTIRGTDQGS-------- 615
Cdd:PHA02523 111 SVYLNMEAVVNRVGIDKFRdtNHLIDFLDNLGSKKLEPFIDDSYKELEeymnHDHHLLLMDREAIFGAPLGSdgiggfwt 190
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 1737442406 616 -KKRYAGLIQEGDTQR-----MVFKGLETVRTDwTPLAQQ 649
Cdd:PHA02523 191 gKKRYALNVYDMEGTRyaephLKIMGLETQRSS-TPLACQ 229
|
|
| YprB |
COG3359 |
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function ... |
150-248 |
2.99e-04 |
|
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function prediction only];
Pssm-ID: 442587 [Multi-domain] Cd Length: 198 Bit Score: 42.62 E-value: 2.99e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 150 PPLKWVSLDIETTrhgelyciGLEGCGDRIvYMLGPPNGDSSALDFR---LEYVNSRPQLLEKLNQWFADYdpDVLIGWN 226
Cdd:COG3359 13 PSEDLLFFDIETT--------GLSGGGTVI-FLIGLADGEGDGFVVRqyfGEDPGEEAALLEAFLEWLADY--KLLVTYN 81
|
90 100
....*....|....*....|..
gi 1737442406 227 VVQFDLRVLQKHAERYRIPLIL 248
Cdd:COG3359 82 GKSFDLPFLKTRFTLHRLPPPL 103
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
218-451 |
4.00e-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: 44.28 E-value: 4.00e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 218 DPDVLIGWNVVQFDLRVLQK----------HAERYRIP---LILGRG--NSELEWREHGFKNGVFFAQANGRLIIDGIEA 282
Cdd:TIGR00592 285 DTDVEITVNGDNFDLVYLADrqvfqfywdaYEDPAEKLgvvLLFGRDvdHVSPCVQVKGINRDLFFLPREGKIDFDLGKV 364
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 283 LKSAFwNFSSFSLEAVAQALLGEGKSidnpWDRMDEIDRRFNEDKPA-LATYNLKDCELVTQIFHKTEIMPFLLERATVN 361
Cdd:TIGR00592 365 TRRTI-NLPDYYLEFVSELALGYKKE----KFRAKPIAKKYEFEAPDiDAPYSSEYLEVTYELGKEFAPMEALPSDLKGQ 439
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 362 GLaADRHGGSVAAFSHLYFPRMHRA-GYVAPNLGDVPPQ------ASPGGYVMDS--RPGLYDS-----VLVLDYKSLYP 427
Cdd:TIGR00592 440 TF-WHVFGSNTGNLERFLLLRKIKGpCWLAVKGPDELEYprrswcKYEGGYVKPPnvEKGLDKTppplvVLDFSMKSLNP 518
|
250 260
....*....|....*....|....
gi 1737442406 428 SIIRTylidpvglvEGMAQPDDAH 451
Cdd:TIGR00592 519 SIIRN---------EIVSIPDTLH 533
|
|
| DNA_polB_B1_exo |
cd05783 |
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ... |
150-340 |
4.51e-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: 42.31 E-value: 4.51e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 150 PPLKWVSLDIE--TTRHG----------ELYCIGLEGC-GDRIVYMLGPPN--GDSSAL--DFRLEYVNSRPQLLEKLNQ 212
Cdd:cd05783 3 PKLKRIAIDIEvyTPIKGripdpktaeyPVISVALAGSdGLKRVLVLKREGveGLEGLLpeGAEVEFFDSEKELIREAFK 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 213 WFADYdPdVLIGWNVVQFDLRVLQKHAER-----YRIPLILGRGNSELEwreHGFKngvffaqangrliID-----GIEA 282
Cdd:cd05783 83 IISEY-P-IVLTFNGDNFDLPYLYNRALKlgipkEEIPIYLKRDYATLK---HGIH-------------IDlykffSNRA 144
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1737442406 283 LKS-AFWN-FSSFSLEAVAQALLGEGK-SIDNPWDRMDeidrrFNEdkpaLATYNLKDCEL 340
Cdd:cd05783 145 IQVyAFGNkYREYTLDAVAKALLGEGKvELEKNISELN-----LYE----LAEYNYRDAEL 196
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
206-352 |
2.48e-03 |
|
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: 40.29 E-value: 2.48e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 206 LLEKLNQWFADYDPDVLIGWNVVQFDLRVLQKHAERYRIPLI--LGRgnseL---EWRE---HGFKNGVFFAQanGRLII 277
Cdd:cd05776 85 LLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWsrIGR----LkrsVWPKkkgGGKFGERELTA--GRLLC 158
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737442406 278 D----GIEALKSafwnfSSFSLEAVAQALLGegksidnpwdrmdeIDRRFNEDKPALATY------------NLKDCELV 341
Cdd:cd05776 159 DtylsAKELIRC-----KSYDLTELSQQVLG--------------IERQDIDPEEILNMYndsesllkllehTEKDAYLI 219
|
170
....*....|.
gi 1737442406 342 TQIFHKTEIMP 352
Cdd:cd05776 220 LQLMFKLNILP 230
|
|
| |
