|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
2-792 |
0e+00 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 1389.19 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 2 TAFEQGFILTRHWRDTASGIEIEFWLATGHGPRRVRLRSQEAVAFIPAEQQALAERTLAGERDAELRPLALRDFRQRPVL 81
Cdd:PRK05762 1 MMLQQGFILTRHYRDTPGGPEVELWLATDEGPRVVLLDPQFRPYFIPAEQDERAESLLAGEIGVRLSPLALKDFHRRPVL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 82 GLYCKRYRHLSGLQKRLAAAGVDVYEADVQPPDRYAMERFITACVEFRGQP---GRDGTLTGGELKPATGYRPALRCVSL 158
Cdd:PRK05762 81 GLYCRQHRQLTRLPKRLREGGVDVYEADIRFPERYLMERFITPCVWFSGEVeqyTTDGVLRNARLKPAPDYRPPLKVVSL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 159 DIETSVHGELYSIALEGCGQRQVYMLGPPNGDERDgtgtldfNLDYCDSRPAMLARLNDWFDEHDPDAVIGWNLVQFDLR 238
Cdd:PRK05762 161 DIETSNKGELYSIGLEGCGQRPVIMLGPPNGEALD-------FLEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLR 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 239 ILHAHAEQYGVPLKLGRGGSVLDWRAHGQQPDHFFAGAAGRLILDGIDMLKSATWTFPSFSLEYVSQSLLGEGKSIDNPY 318
Cdd:PRK05762 234 LLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATWVFDSFSLEYVSQRLLGEGKAIDDPY 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 319 QRMDEIQRRFDHDKPALARYNLKDCELVTRIFDKADLLSFALERASVTGLAADRTGGSVAAFTHLYLPRMHRLGYVAPNL 398
Cdd:PRK05762 314 DRMDEIDRRFAEDKPALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLPLDRVGGSVAAFEHLYLPRAHRAGYVAPNL 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 399 GDVTGQNSPGGFVMDSRPGLYDSVLVFDYKSLYPSIIRTFLIDPVGLIEGLAHPaDETSVPGFLGARFSRTAHCLPDIVR 478
Cdd:PRK05762 394 GERPGEASPGGYVMDSKPGLYDSVLVLDFKSLYPSIIRTFNIDPDGLVEGLAQP-PEESVAGFLGARFSREKHFLPEIVE 472
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 479 RVWEGRDDAKRQRNAPLSQALKIIMNSFYGVLGSTGCRFFDPRLASSITMRGHEIMHRTRKLIEAQGYEVIYGDTDSTFV 558
Cdd:PRK05762 473 RLWEGRDEAKREMNKPLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQGYQVIYGDTDSTFV 552
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 559 WLGRAHDDDEAGAKGRALVEHVNRWWQAHLREQFGLDSALELQYERHYRRFLMPTVRGAEEGSKKRYAGLAATADGGEDL 638
Cdd:PRK05762 553 WLGGAHDEEDAAKIGRALVQEINQWWQEHLQQEFGLESALELEFEKHYRRFFMPTIRGAEEGSKKRYAGLIQEGDGDGRI 632
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 639 VFKGLETVRTDWTPLAQQFQRELYRRVFSREPYQDFIRDYVRRTLAGEFDDQLVYRKRVRRPLREYERNVPPHVRAARIA 718
Cdd:PRK05762 633 VFKGLETVRTDWTPLAKEFQQELYERIFRGEPYVDYVREVIDKLRAGELDEKLVYRKRLRRPLDEYQRNVPPHVRAARLA 712
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1144870178 719 DEFNHAQGRPLQYQRGGWISYVMTTAGPEPLETMRSPIDYAFYLSRQLQPVADAILPFLRDDFERVISGQGQLF 792
Cdd:PRK05762 713 DEMGYKVGRPLQYQNGGKIGYVITVNGPEPLEYRKSPIDYDYYIEKQLQPVADRILPFFGDDFATLKTGQLGLF 786
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
5-791 |
0e+00 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 1020.14 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 5 EQGFILTRHWRDTASGIEIEFWLATGHGPR-RVRLRSQEAVAFIPAEQQALAERTLAGERD-AELRPLALRDFRQR--PV 80
Cdd:COG0417 3 IPGFLLDRSYRDEDGKPVIELWGRTEDGPSvLLDVTGFRPYFYVPLPDEEKLEELLRDIKEiTEVEPVKLKSFFGEpvPV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 81 LGLYCKRYRHLSGLQKRLAAAGVDVYEADVQPPDRYAMERFITACVEFRGQPGRDGTLTGGE------LKPATgYRPALR 154
Cdd:COG0417 83 LKIYTRDPRDVRELRDRLKEGGIDVYEADIRFHDRYLIDRFLTPGVWYEGEVEEDGGKLDYEvkenprLKPED-YRPKLK 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 155 CVSLDIETS---------VHGELYSIALEGC-GQRQVYMLGPPNgderdgtgtLDFNLDYCDSRPAMLARLNDWFDEHDP 224
Cdd:COG0417 162 VLSFDIEVStprgfpdpeRDGPIISIGLAGSdGEKKVLMLGREG---------VDFEVEYFDDEKALLEAFFEIIREYDP 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 225 DAVIGWNLVQFDLRILHAHAEQYGVPLKLGRGGSVLDWRAHGqqpDHFFAGAAGRLILDGIDMLKSATWTFPSFSLEYVS 304
Cdd:COG0417 233 DIIIGWNVDNFDLPYLQKRAERLGIPLDLGRDGSEPSWREHG---GQGFASIPGRVVIDLYDALKSATYKFKSYSLDAVA 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 305 QSLLGEGKSIDNpyqrMDEIQRRFDHDKPALARYNLKDCELVTRIFDKADLLSFALERASVTGLAADRTG--GSVAAFTH 382
Cdd:COG0417 310 EELLGEGKLIVD----GGEIERLWDDDKPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGraGSSAAFEN 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 383 LYLPRMHRLGYVAPNLGDVTGQNSPGGFVMDSRPGLYDSVLVFDYKSLYPSIIRTFLIDPVGLIEGLAHPADET-SVPGF 461
Cdd:COG0417 386 LLLPEAHRRGYLAPNKGEIKGEAYPGGYVLDPKPGLYENVLVLDFKSLYPSIIRTFNISPETLVEGGEEPCGDEdVAPGF 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 462 lGARFSRTA-HCLPDIVRRVWEGRDDAKRQRN------------APLSQALKIIMNSFYGVLGSTGCRFFDPRLASSITM 528
Cdd:COG0417 466 -GHRFCREPkGILPSILEELWDERDEAKKKMKkakpdseeyrlyDALQQALKILMNSFYGVLGSEGCRFYDPELAESITA 544
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 529 RGHEIMHRTRKLIEAQGYEVIYGDTDSTFVWLGRaHDDDEAGAKGRALVEHVNRWWQahlreqfgldSALELQYERHYRR 608
Cdd:COG0417 545 RGREIIKQTIEKAEELGYKVIYGDTDSLFVWLPK-ASLEEAIEIGKELAEEINAWWP----------SGLELEFEKHYRR 613
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 609 FLMPTvrgaeegSKKRYAGLaaTADGGedLVFKGLETVRTDWTPLAQQFQRELYRRVFSREPYQ---DFIRDYVRRTLAG 685
Cdd:COG0417 614 FFFPG-------SKKRYAGL--TEDGK--IDIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEkavEYVRDVIEKLRAG 682
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 686 EFD-DQLVYRKRVRRPLREYERNVPPHVRAARIADEfnhaQGRPlqYQRGGWISYVMTTAG--PEPLETMR---SPIDYA 759
Cdd:COG0417 683 EVDlDDLVIRKRLRKPLSEYEKNVPPHVRAARKLDE----RGRP--YQRGDKISYVITKGGgrVEPVELAKereSEIDYD 756
|
810 820 830
....*....|....*....|....*....|..
gi 1144870178 760 FYLSRQLQPVADAILPFLRDDFERVISGQGQL 791
Cdd:COG0417 757 YYIEKQLKPTADRILEAFGVSFDELKGGSKQL 788
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
404-777 |
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: 720.98 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 404 QNSPGGFVMDSRPGLYDSVLVFDYKSLYPSIIRTFLIDPVGLIEGLAHPADETSVPGFLGARFSRTAHCLPDIVRRVWEG 483
Cdd:cd05537 1 ISSPGGYVMDSKPGLYKNVLVLDFKSLYPSIIRTFLIDPLGLIEGLKAPDPEDLIPGFLGARFSREKHILPDLIARLWAA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 484 RDDAKRQRNAPLSQALKIIMNSFYGVLGSTGCRFFDPRLASSITMRGHEIMHRTRKLIEAQGYEVIYGDTDSTFVWLGRA 563
Cdd:cd05537 81 RDEAKREKNAPLSQAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQVIYGDTDSTFVWLGEE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 564 HDDDEAGAKGRALVEHVNRWWQAHLREQFGLDSALELQYERHYRRFLMPTVRGAEEGSKKRYAGLAATaDGGEDLVFKGL 643
Cdd:cd05537 161 LDAAEAQAIGKELASQINQWWAQKLKEEFGLESFLEIEFETHYSRFFMPTIRGSDEGSKKRYAGLKST-DGGDELVFKGL 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 644 ETVRTDWTPLAQQFQRELYRRVFSREPYQDFIRDYVRRTLAGEFDDQLVYRKRVRRPLREYERNVPPHVRAARIADEFNH 723
Cdd:cd05537 240 ETVRSDWTPLARQFQKELYERVFNDEPYEGFIKETVEELLAGELDELLVYRKRLRRPLSEYTKNVPPHVQAARLADQINR 319
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....
gi 1144870178 724 AQGRPLQYQrggWISYVMTTAGPEPLETMRSPIDYAFYLSRQLQPVADAILPFL 777
Cdd:cd05537 320 ELGRPRQYQ---WIEYVITVNGPEPLEYRTSPLDYQHYIDKQLKPIADSILPFL 370
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
151-351 |
1.08e-104 |
|
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: 319.51 E-value: 1.08e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 151 PALRCVSLDIETSVHGELYSIALEGCGQRQVYMLGPPNGDerdgtgtLDFNLDYCDSRPAMLARLNDWFDEHDPDAVIGW 230
Cdd:cd05784 1 PKLKVVSLDIETSMDGELYSIGLYGEGQERVLMVGDPEDD-------APDNIEWFADEKSLLLALIAWFAQYDPDIIIGW 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 231 NLVQFDLRILHAHAEQYGVPLKLGRGGSVLDWRAHGQqPDHFFAGAAGRLILDGIDMLKSATWTFPSFSLEYVSQSLLGE 310
Cdd:cd05784 74 NVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGK-PGQGFLSLPGRVVLDGIDALKTATYHFESFSLENVAQELLGE 152
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 1144870178 311 GKSIDNPYQRMDEIQRRFDHDKPALARYNLKDCELVTRIFD 351
Cdd:cd05784 153 GKLIHDVDDRGAEIERLFREDKLALARYNLQDCELVWRIFE 193
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
407-775 |
2.75e-86 |
|
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: 276.56 E-value: 2.75e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 407 PGGFVMDSRPGLYDSVLVFDYKSLYPSIIRTFLIDPVGLIEGLAHPADETSVpGFLGARFSRTAHCLPDIVRRVWEGRDD 486
Cdd:cd00145 4 EGGYVFDPIPGLYENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYI-GVGFRSPKDRKGLLPRILEELLNFRDE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 487 AKRQRNAP------------LSQALKIIMNSFYGVLGSTGCRFFDPRLASSITMRGHEIMHRTRKLIEAQGYEVIYGDTD 554
Cdd:cd00145 83 AKKRMKAAklapeervlydnRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGARVIYGDTD 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 555 STFVWLGrahdddeagakGRALVEHVNRWWQaHLREQFGLDSALELQYERHYRRFLMptvrgaeeGSKKRYAGLAATADG 634
Cdd:cd00145 163 SIFVSLP-----------KMGTKEDAIKEGR-EILQELADEHLLELEFEKVYLPFFL--------GKKKRYAGLDIWKGQ 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 635 GED-LVFKGLETVRTDWTPLAQQFQRELYRRVFSREPYQDFIRDYVRRTLAgefddqlVYRKRVRRPlreyeRNVPphvr 713
Cdd:cd00145 223 DEGkIDIKGLETRRRDSPPLVKKFQKEVLELILEEERKVEAVKEYIDELDK-------VKYVVTRGG-----KGVP---- 286
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1144870178 714 aariadefnhaqgrplQYQRggwisyvmtTAGPEPLETMRSPIDYAFYLSRQLQPVADAILP 775
Cdd:cd00145 287 ----------------DYER---------ADPPLEDLDKRHRIDYEYYLERLLQPPLERIFE 323
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
151-561 |
5.46e-67 |
|
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: 230.11 E-value: 5.46e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 151 PALRCVSLDIET-----------SVHGELYSIALEGCGQ-------RQVYMLGPPngDERDGTgtldfNLDYCDSRPAML 212
Cdd:smart00486 1 PPLKILSFDIETytdggnfpdaeIFDDEIIQISLVINDGdkkganrRILFTLGTC--KEIDGI-----EVYEFNNEKELL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 213 ARLNDWFDEHDPDAVIGWNLVQFDLRILHAHAEQYGVP--LKLGRGGSVLDWRAHGQQPDHFFAG-------AAGRLILD 283
Cdd:smart00486 74 LAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDplSKIGRLKIGLRIPNKKPLFGSKSFGlsdikvyIKGRLVID 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 284 GIDMLKSATwTFPSFSLEYVSQSLLGEGKsIDNPYQRMDEIQRRFDHDKPALARYNLKDCELVTRIFDKADLLSFALERA 363
Cdd:smart00486 154 LYRLYKNKL-KLPSYKLDTVAEYLLGKEK-DDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELA 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 364 SVTGLAADRT--GGSVAAFTHLYLPRMHRLGYVAPNLGDVTGQNS----------PGGFVMDSRPGLYDS-VLVFDYKSL 430
Cdd:smart00486 232 RIAGIPLRRTlyYGSQIRVESLLLREAKKNNYILPSKELYDFKGSepdlkkkvkyEGGKVLEPKKGFYDNpVLVLDFNSL 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 431 YPSIIRTFLIDPVGLI-EGLAHPADETSVP----------GFLGARFSRTAH--CLPDIVRRVWEGRDDAKRQRNA---- 493
Cdd:smart00486 312 YPSIIIAHNLCYSTLVgVGEVVIKGDLIIPedlltikyekGNKYRFVKKNIRkgILPKLLKKLLDKRKEIKKLMKKekde 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 494 ---------PLSQALKIIMNSFYGVLGSTGCRFFDPRLASSITMRGHEIMHRTRKLIEAQGY-----EVIYGDTDSTFVW 559
Cdd:smart00486 392 seelkklldSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGYpkpgfKVIYGDTDSIFVT 471
|
..
gi 1144870178 560 LG 561
Cdd:smart00486 472 KP 473
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
385-774 |
3.33e-51 |
|
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: 185.51 E-value: 3.33e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 385 LPRMHRLGYVAPN----LGDVTGQnsPGGFVMDSRPGLYDS-VLVFDYKSLYPSIIR------TFLIDPVGLIEGLAHPA 453
Cdd:pfam00136 20 LRLALEEGFILPDrpsaKGDEDGY--QGATVIEPKKGFYDKpVLVLDFNSLYPSIIQahnlcyTTLVRSVDEANNLPPED 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 454 DETSV---PGFLGARFSRTAHC-LPDIVRRVWEGRDDAKRQRNAPLS-----------QALKIIMNSFYGVLGSTGCRFF 518
Cdd:pfam00136 98 NLITVectPRGVYFVKDHVREGlLPKLLKDLLAKRKAIKKLLKEETDpferaildkqqLALKITANSVYGFTGFANGRLP 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 519 DPRLASSITMRGHEIMHRTRKLIEAQ---GYEVIYGDTDSTFVWLGrAHDDDEAGAKGRALVEHVNRwwqaHLreqfgLD 595
Cdd:pfam00136 178 CLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTDSVFIEFG-GKDVEEAMKIGDELAEHVNQ----DL-----FK 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 596 SALELQYERHYRRFLMPtvrgaeegSKKRYAGLAATADGGED-LVFKGLETVRTDWTPLAQQFQRELYRRVFSREPYQDf 674
Cdd:pfam00136 248 SPIKLEFEKVYKPLLLI--------SKKKYAGLKYTAPSNFNkLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSDRGLPV- 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 675 IRDYVRRTLAGEFDD---------QLVYRKRVRRPLREYERNVPPHVRAARiadEFNHAQGRPLQYqrGGWISYVMTTAG 745
Cdd:pfam00136 319 GLEFVISILNDARSDlrnnkvpleKFVISKELSKPPDNYKSKNLPHVEVAL---RMNKRNGEAPEV--GDRIPYVIVKAA 393
|
410 420 430 440
....*....|....*....|....*....|....*....|...
gi 1144870178 746 --------------PEPLETMRSPIDYAFYLSRQLQPVADAIL 774
Cdd:pfam00136 394 kglknlliyeraedPEYVLENNLPIDYEYYFSNQLIPPVARLL 436
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
408-774 |
1.75e-50 |
|
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: 181.37 E-value: 1.75e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 408 GGFVMDSRPGLYDSVLVFDYKSLYPSIIRTFLIDPVGLIEGlahPADETSVPGFLGARFSRTAHCL-PDIVRRVWEGRDD 486
Cdd:cd05536 6 GGIVLEPEKGLHENIVVLDFSSLYPSIMIKYNISPDTLVRE---GCEDCDVEPQVGHKFRKDPPGFiPSVLEDLLEERRR 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 487 AK------------------RQRnaplsqALKIIMNSFYGVLGSTGCRFFDPRLASSITMRGHEIMHRTRKLIEAQGYEV 548
Cdd:cd05536 83 IKekmkkldpeseeyklldeRQR------AIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAEEKGFKV 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 549 IYGDTDSTFVWLGrahDDDEAGAKGRALVEHVNrwwqahlrEQFGldsaLELQYERHYRRFLMPTvrgaeegsKKRYAGL 628
Cdd:cd05536 157 IYGDTDSLFVKID---GADAVKKKVKKLLKYIN--------EELP----LELEIEKFYKRGFFVT--------KKRYAGL 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 629 aaTADGgeDLVFKGLETVRTDWTPLAQQFQRELYRRVF-SREPYQ--DFIRDYVRRTLAGEFD-DQLVYRKRVRRPLREY 704
Cdd:cd05536 214 --TEDG--KIDVVGLEVVRRDWSEIAKETQARVLEAILkEGDVEEavKIVKEVIEKLKRGEVPpEKLVIWKQLTKDLSEY 289
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1144870178 705 ErNVPPHVRAARIADEfnhaqgRPLQYQRGGWISYVMTT-AGP-----EPLETMRSP--IDYAFYLSRQLQPVADAIL 774
Cdd:cd05536 290 K-ATGPHVAAAKKLAK------RGYKVRPGTKIGYVIVKgSGKisdraYPYDMVDEKhkYDAEYYIDNQVLPAVLRIL 360
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
14-789 |
4.23e-47 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 179.88 E-value: 4.23e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 14 WRDTASGiEIEFWL-ATGHGPRRVRLRSQEAVAFIP--AEQQALAERTLAGERDAelrplaLRDfRQRPVLGLYCKRYRH 90
Cdd:PRK05761 37 LYDPETG-KIYKWYdRTGHKPYFLTDLDPDEIDKIPkiLRHPSFDHLEIVEKYDG------LRD-KKVKVTKIVVKDPLA 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 91 LSGLQKRLAAAGvDVYEADVQPPDRYAMERFITACVEF---RGQPGRDGTLTGGELKPATGYR---------------PA 152
Cdd:PRK05761 109 VRRLRLSVRDIP-RAWEADIKYEFRYIYDNGLIPGMPYdvkNGLESVEPEILVEEIKKAFKDErklaedwlpifeapiPK 187
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 153 LRCVSLDIE--TSVHGELysialegcgqrqvymlgpPNGDERDgtgtldfnldycdsrpaMLARLNDWFDEHDPDavIGW 230
Cdd:PRK05761 188 IKRIAIDIEvyTPAKGRI------------------PDDSEKE-----------------LLAELFDIILEYPPV--VTF 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 231 NLVQFDLRILHAHAEQYGV-----PLKLGRGGSVLDWRAhgqqpdhFFAGAAGRlildgidmlksaTWTF------PSFS 299
Cdd:PRK05761 231 NGDNFDLPYLYNRALKLGIpkeeiPIEPGRAGIHIDLYK-------FFQNKAVR------------SYAFygkyrhREAR 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 300 LEYVSQSLLGEGKsidnpyqrMDEIQRRFDHDKPALARYNLKDCELVTR--IFDKADLLSFALERASVTGLA---ADRTG 374
Cdd:PRK05761 292 LDAVGRALLGISK--------VELETNISELDLEELAEYNFRDAEITLKltFFNNELVLKLILLLSRISKLPieeLSRAT 363
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 375 GSvAAFTHLYLPRMHRLGYVAPNLGDVTGQNSP-------------GGFVMDSRPGLYDSVLVFDYKSLYPSIIRTFLID 441
Cdd:PRK05761 364 IS-TWISNLEYWEHRKRGWLIPWKEDILRLDHEvykkaiikgkkyrGGLVFQPPPGIFFNVYVLDFASLYPSIIVKWNLS 442
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 442 P------------VGLIEGLAHpADETSVPGFLGArfsrtahcLPDIVR--RVWEGRDDAKRQRNAP--------LSQAL 499
Cdd:PRK05761 443 PetvripeckchyDDEVPELGH-SVCDDRPGLTSV--------LVGLLRdfRVKIYKKKAKDPNLDEerrawydvVQRAL 513
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 500 KIIMNSFYGVLGSTGCRFFDPRLASSITMRGHEIMHRTRKLIEAQGYEVIYGDTDSTFVWlGRAHDDDEagakgrALVEH 579
Cdd:PRK05761 514 KVFLNASYGVFGAENFKLYRIEVAESITALGREILLSTKKKAEELGLKVLYGDTDSLFVW-GPTKESLE------ELIKE 586
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 580 VnrwwqahlREQFGLDsaleLQYERHYrRFLMPTvrgaeeGSKKRYAGLaaTADGGEDLvfKGLETVRTDWTPLAQQFQR 659
Cdd:PRK05761 587 I--------EERTGID----LEVDKTY-DWVAFS------GLKKNYFGV--LKDGKVKI--KGIVAKKRNTPEFVKELQR 643
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 660 EL------YRRVFSREPYQDFIRDYVRRTL----AGEFD-DQLVYRKRVRRPLREYERNVPPHVRAARIADEFNhaqgrp 728
Cdd:PRK05761 644 EVlevlksIRSPEDVEKVKDEIEDVLKRYYeklrAKDYPlDELAIRVRLSKPLDEYTKNTPQHVKAALQLRDYG------ 717
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1144870178 729 LQYQRGGWISYVMTTA--GPEPLETMR-SPIDYAFYLsRQLQPVADAILPFLRDDFERVISGQG 789
Cdd:PRK05761 718 VEVSPGDIISYVKVDDkrGVKPVQLAKlSEIDVEKYI-ELLRSALEQILSALGVSWDDIRGTTR 780
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
198-774 |
1.76e-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: 179.87 E-value: 1.76e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 198 LDFNLDYCDSRPAMLARLND------WF----DEHDPDAVIGWNLVQFDLRILhahaEQYGVPLKLGRGGSVLDWRAHGQ 267
Cdd:TIGR00592 564 LDLKGEFPGKKPSLVEDLATeralikKFmakvKKIDPDEIVGHDYQQRALKVL----ANRINDLKIPTWSKIGRLRRSPK 639
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 268 QPDHFFAGAAGRLILDGIDMLKSATWTFPSFSLEYVSQSLLGEGKSIDNPYQRMdeiQRRFDHDKPALARYNLKDCELVT 347
Cdd:TIGR00592 640 FGRRFGERTCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINN---MYSESSSLTYLLEHTWKDAMFIL 716
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 348 RIFDKADLLSFALERASVTGLAADRT--GGSVAAFTHLYLPRMHRLGYVAPNLGDVTGQNS------------------- 406
Cdd:TIGR00592 717 QIMCELNVLPLALQITNIAGNIMSRTlmGGRSERNEFLLLHAFYENNYIVPDKQIFRKQQKlgdedeeidgykkgkkaay 796
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 407 PGGFVMDSRPGLYDS-VLVFDYKSLYPSIIRTFLIdpvgLIEGLAHPADETSVPGFLGARFSRTAhcLPDIVRRVWEGRD 485
Cdd:TIGR00592 797 AGGLVLEPKVGLYDKyVLLMDFNSLYPSIIQEFNI----CFTTVQQKVDEDELPELPDSELEMGI--LPRELRKLVERRK 870
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 486 DAKRQRNAPLS-----------QALKIIMNSFYGVLGSTGCRFFDPRLASSITMRGHEIMHRTRKLIEAQGYEVIYGDTD 554
Cdd:TIGR00592 871 EVKKLMKQDLNpdlrlqydirqKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEMNLEVIYGDTD 950
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 555 STFVWLGRAhDDDEAGAKGRALVEHVNrwwqahlrEQFGLdsaLELQYERHYRRFLMPTvrgaeegsKKRYAGL--AATA 632
Cdd:TIGR00592 951 SIMINTPGT-KYEEVFKIGKEFKSEVN--------KLYKL---LELDIDGVFKRLLLLK--------KKKYAAIkvEGDS 1010
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 633 DGGEDLV--FKGLETVRTDWTPLAQQFQRELYRRVFSREP-------YQDFIRDYVRRTLAGEFD-DQLVYRKRVRRPLR 702
Cdd:TIGR00592 1011 DGNYTTKqeVKGLDIVRRDWSPLAKETGKKVLDTILSDKDveeaveeVQEVLEKIGKNVLNGEVPlEKFVINKQLTRDPK 1090
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 703 EY-ERNVPPHVraaRIADEFNHAQGRPlqYQRGGWISYVMTTAGPEPLETMRS-------------PIDYAFYLSRQLQP 768
Cdd:TIGR00592 1091 DYpDGASLPHV---HVALRINARGGRK--VKAGDVVSYVICKDGGNLSARQRAyaleelqrkhnnlIYDTQYYLEHQIHP 1165
|
....*.
gi 1144870178 769 VADAIL 774
Cdd:TIGR00592 1166 VVLRIL 1171
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
408-769 |
5.80e-42 |
|
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: 158.13 E-value: 5.80e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 408 GGFVMDSRPGLYDS-VLVFDYKSLYPSIIRTFLI-----------DPVGLIEGLAHPADETSVpgflgarfsrtahcLPD 475
Cdd:cd05532 10 GGLVLEPKKGLYDKfILLLDFNSLYPSIIQEYNIcfttvdradpdDEDDEEPPLPPSDQEKGI--------------LPR 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 476 IVRRVWEGRDDAKRQRNAPLS-----------QALKIIMNSFYGVLGSTGCRFFDPRLASSITMRGHEIMHRTRKLIEAQ 544
Cdd:cd05532 76 IIRKLVERRRQVKKLMKSEKDpdkkaqldirqLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKM 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 545 GYEVIYGDTDSTFVWLGRAhDDDEAGAKGRALVEHVNRwwqahlreqfgLDSALELQYERHYRRFLMPtvrgaeegSKKR 624
Cdd:cd05532 156 NLEVIYGDTDSIMINTGTT-DYEEAKKLGNKIKKEVNK-----------SYKKLEIDIDGVFKRLLLL--------KKKK 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 625 YAGLAATADGGEDLV--FKGLETVRTDWTPLAQQFQRELYRRVFSREPY-------QDFIRDYVRRTLAGEFD-DQLVYR 694
Cdd:cd05532 216 YAALKVVDDDKGKLKkeVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSRediveniHEYLRKINEDLRNGKIPlEKFIIT 295
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 695 KRVRRPLREY-ERNVPPHVRAA-RIadefnHAQGRplQYQRGGWISYVMTTAGPEPLETMR--SP----------IDYAF 760
Cdd:cd05532 296 KQLTKNPEEYpDKKSLPHVQVAlRM-----NKRGR--KVKAGDTIPYIICKDGSSKSLADRayHPdevkknenlkIDIEY 368
|
....*....
gi 1144870178 761 YLSRQLQPV 769
Cdd:cd05532 369 YLSQQILPP 377
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
156-350 |
1.04e-37 |
|
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: 139.80 E-value: 1.04e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 156 VSLDIETSVH--------GELYSIALEG--CGQRQVYMLGPPNGDErDGTGTLDFNLDYCDSRPAMLARLNDWFDEHDPD 225
Cdd:cd05160 2 LSFDIETTPPvggpepdrDPIICITYADsfDGVKVVFLLKTSTVGD-DIEFIDGIEVEYFADEKELLKRFFDIIREYDPD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 226 AVIGWNLVQFDLRILHAHAEQYGVPLKLGRGGsvlDWRAHGQQPDHFFAGAAGRLILDGIDMLKSATWtFPSFSLEYVSQ 305
Cdd:cd05160 81 ILTGYNIDDFDLPYLLKRAEALGIKLTDGIYR---RSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFK-LKSYTLDAVAE 156
|
170 180 190 200
....*....|....*....|....*....|....*....|....*
gi 1144870178 306 SLLGEGKSIdnpYQRMDEIQRRFDHDKPALARYNLKDCELVTRIF 350
Cdd:cd05160 157 ELLGEGKEK---VDGEIIEDAEWEEDPERLIEYNLKDAELTLQIL 198
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
188-792 |
4.64e-36 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 147.10 E-value: 4.64e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 188 NGDERDGTGTLDFNLDYCDSRP-----------AMLARLNDWFDEHDPDAVIGWNLVQFDLRILHAHAEQYGVP--LKLG 254
Cdd:PTZ00166 299 QGDEEEPLTKFIFTLKECASIAganvlsfetekELLLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNdfKYLG 378
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 255 RGGSVldwraHGQQPDHFFAGAA------------GRLILDGIDMLKSATwTFPSFSLEYVSQSLLGEGKSiDNPYQRMD 322
Cdd:PTZ00166 379 RIKST-----RSVIKDSKFSSKQmgtreskeinieGRIQFDVMDLIRRDY-KLKSYSLNYVSFEFLKEQKE-DVHYSIIS 451
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 323 EIQRRFDHDKPALARYNLKDCELVTRIFDKADLLSFALERASVTGLAAD---RTGGSVAAFTHLYlPRMHRLGYVAPNLG 399
Cdd:PTZ00166 452 DLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGwllTRGQQIKVTSQLL-RKCKKLNYVIPTVK 530
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 400 DVTGQNSP---GGFVMDSRPGLYDS-VLVFDYKSLYPSII------RTFLIDPvgliEGLAHPADETSVPGFLGARFSRt 469
Cdd:PTZ00166 531 YSGGGSEEkyeGATVLEPKKGFYDEpIATLDFASLYPSIMiahnlcYSTLVPP----NDANNYPEDTYVTTPTGDKFVK- 605
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 470 AHC----LPDIVRRVWEGRDDAKRQRNA---PLSQ--------ALKIIMNSFYGVLGSTGCRFFdPRL--ASSITMRGHE 532
Cdd:PTZ00166 606 KEVrkgiLPLIVEELIAARKKAKKEMKDekdPLLKkvlngrqlALKISANSVYGYTGAQVGGQL-PCLevSTSITSFGRQ 684
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 533 IMHRTRKLIE-----AQGYE----VIYGDTDSTFVWLGrahDDD--EAGAKGRALVEHVNrwwqahlrEQFglDSALELQ 601
Cdd:PTZ00166 685 MIDKTKELVEkhytkANGYKhdatVIYGDTDSVMVKFG---TDDiqEAMDLGKEAAERIS--------KKF--LKPIKLE 751
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 602 YERHYRRFLMPtvrgaeegSKKRYAGLAAT-ADGGEDLVFKGLETVRTDWTPLAQQFQRELYRRVF---SREPYQDFIRD 677
Cdd:PTZ00166 752 FEKVYCPYLLM--------NKKRYAGLLYTnPEKYDKIDCKGIETVRRDNCLLVQQMVETVLNKILiekDVESAIEFTKG 823
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 678 YVRRTLAGEFD-DQLVYRKRVRRplREYERNVpPHV------------RAARIADEFNH-----AQGRPlQYQRggwisy 739
Cdd:PTZ00166 824 KISDLLQNRIDiSLLVITKSLGK--DDYEGRL-AHVelakklrqrdpgSAPNVGDRVSYvivkgAKGAP-QYER------ 893
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*
gi 1144870178 740 vmttaGPEPLETMRS--PIDYAFYLsrqlqpvaDAILPFLRDDFERVISGQGQLF 792
Cdd:PTZ00166 894 -----AEDPLYVLENniPIDTQYYL--------DQIKNPLLRIFEGVMDNPDSLF 935
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
408-762 |
7.09e-34 |
|
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Pssm-ID: 99913 Cd Length: 372 Bit Score: 134.02 E-value: 7.09e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 408 GGFVMDSRPGLYDSVLVFDYKSLYPSIIRTF-----LIDPVglieglaHPADETSVPGFLGARF--------SRTAHCLP 474
Cdd:cd05530 15 GAIVLEPPPGIFFNVVVLDFASLYPSIIKVWnlsyeTVNCP-------HCECKTNEVPEVGHWVckkrpgitSQIIGLLR 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 475 DIVRRVWEGR------DDAKRQRNAPLSQALKIIMNSFYGVLGSTGCRFFDPRLASSITMRGHEIMHRTRKLIEAQGYEV 548
Cdd:cd05530 88 DLRVKIYKKKakdkslDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIITSTIKKARELGLKV 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 549 IYGDTDSTFVWlgrahddDEAGAKGRALVEHVnrwwqahlREQFGLDSALELQYerhyrRFLMPTvrgaeeGSKKRYAGL 628
Cdd:cd05530 168 LYGDTDSLFLW-------NPPQEQLEDLVEWV--------EKELGLDLELDKEY-----RYVVFS------GLKKNYLGV 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 629 aaTADGGEDLvfKGLeTVRTDWTPlaqQFQRELYRRVF--------------SREPYQDFIRDYVRRTLAGEFD-DQLVY 693
Cdd:cd05530 222 --TKDGSVDI--KGL-LGKKRNTP---EFVKELFYEVIeilsavnspedfekAREKIRDIVKGVYKRLKKKEYTlDQLAF 293
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1144870178 694 RKRVRRPLREYERNVPPHVRAARIADEFNhaqgrpLQYQRGGWISYVMTTA--GPEPLETMRSP-IDYAFYL 762
Cdd:cd05530 294 KVMLSKPPEEYTKNTPQHVKAARQLEKYG------RNVEAGDIISYVKVKGkeGVKPVQLARLDeVDVEKYV 359
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
116-678 |
1.07e-29 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 126.34 E-value: 1.07e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 116 YAMERFITACV--EFRGQPGRDgtltggelkpatgyRPALRCVSLDIETSVHG----------ELYSIALEGCGQRQVYM 183
Cdd:PHA02528 81 LGMDDFKLQYIsdTYPGEIKYD--------------RSKIRIANLDIEVTAEDgfpdpeeakyEIDAITHYDSIDDRFYV 146
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 184 LGPPNGDERDGTGTLDF-----NLDY--CDSRPAMLARLNDWFDEHDPDAVIGWNLVQFDL-----RILHAHAEQYG--- 248
Cdd:PHA02528 147 FDLGSVEEWDAKGDEVPqeildKVVYmpFDTEREMLLEYINFWEENTPVIFTGWNVELFDVpyiinRIKNILGEKTAkrl 226
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 249 VPLKLGRGGSVLDwrAHGQQpdHFFAGAAGRLILDGIDMLKSATWT-FPSFSLEYVSQSLLGEGKsIDNPYQRMDEIQRR 327
Cdd:PHA02528 227 SPWGKVKERTIEN--MYGRE--EIAYDISGISILDYLDLYKKFTFTnQPSYRLDYIAEVELGKKK-LDYSDGPFKKFRET 301
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 328 fDHDKpaLARYNLKDCELVTRIFDKADLLSFALERASVTGLAADRTGGSVA---AFTHLYLPRMHRlgyVAPNLGDVTGQ 404
Cdd:PHA02528 302 -DHQK--YIEYNIIDVELVDRLDDKRKLIELVLSMAYYAKINFEDVFSPIKtwdAIIFNSLKEEKI---VIPENKSHKKQ 375
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 405 NSPGGFVMDSRPGLYDSVLVFDYKSLYPSIIR-----------TFLIDPV-GLIEGLAH-PADETSV-PGflGARFSRTA 470
Cdd:PHA02528 376 KYAGAFVKEPVPGAYRWVVSFDLTSLYPSIIRqvnispetiagTFHVAPVhEYINKTAPrPSDEYSCsPN--GWMYRKDI 453
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 471 H-CLPDIVRRVWEGRDDAKR-----QRNAPLSQ----------------------------------------------- 497
Cdd:PHA02528 454 RgVIPTEIKKVFDQRKIYKKkmlaaERNAELIKtiledlndsvdtpidvdyyfdfsdefkaelktltksslkalleecek 533
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 498 ----------ALKIIMNSFYGVLGSTGCRFFDPRLASSITMRGH-EIMHRTRKL---------IEAQGYeVIYGDTDSTF 557
Cdd:PHA02528 534 eialcntiqmARKILINSLYGALGNEHFRYYDLRNAEAITLFGQlAIQWIERKMneylnklckTEDEDY-VIYGDTDSIY 612
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 558 VWLG---------RAHDDDeagakgrALVEHVNRWWQAHLrEQFGLDSALEL-QYERHYRRfLMPTVRGAEEG-----SK 622
Cdd:PHA02528 613 VNLDplvekvgedKFKDTN-------HWVDFLDKFCKERM-EPYIDSSYRELcEYMNNYEH-LMFMDREAIAGpgfwtAK 683
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1144870178 623 KRYaglAATADGGEDLVFK-------GLETVRTDWTPLAQQFQRELYRRVFSR--EPYQDFIRDY 678
Cdd:PHA02528 684 KRY---ALNVWDSEGTRYAepklkimGIETQRSSTPKAVQKALKEAIRRILQEgeESLQEYIKEF 745
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
408-762 |
3.69e-29 |
|
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: 119.37 E-value: 3.69e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 408 GGFVMDSRPGLYDSVLVFDYKSLYPSIIRTFLIDPvgliEGLAHPADETSVPGFLGARFSRTAH-CLPDIVRRVWEGRDD 486
Cdd:cd05531 7 GGLVFQPEPGLYENVAQIDFSSMYPSIIVKYNISP----ETINCRCCECRDHVYLGHRICLKRRgFLPEVLEPLLERRLE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 487 AKRQ-----RNAPLSQALKIIMNSFYGVLGSTGCRFfdPRLAS--SITMRGHEIMHRTRKLIEAQGYEVIYGDTDSTFVw 559
Cdd:cd05531 83 YKRLkkeedPYAGRQKALKWILVTSFGYLGYKNAKF--GRIEVheAITAYGRKILLRAKEIAEEMGFRVLHGIVDSLWI- 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 560 lgrahdddeagaKGRALVEHVNRwwqaHLREQFGLDsaleLQYERHYRRFL-MPTVRGAeeGSKKRYAGLaaTADGGedL 638
Cdd:cd05531 160 ------------QGRGDIEELAR----EIEERTGIP----LKLEGHYDWIVfLPERDGL--GAPNRYFGR--LSDGE--M 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 639 VFKGLETVRTDWTPLAQQFQRELYRRVFS----------REPYQDFIRDYVRRTLAGEFDDqLVYRKRVRRPLREYERNV 708
Cdd:cd05531 214 KVRGIELRRRDTPPFVKKFQEEALDILASaktpeellklREEALDLFRRYLQRLREGDLED-LIIEKKISKRSSEYKVLA 292
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*
gi 1144870178 709 PPHVRAARiadefnhAQGRPlqYQRGGWISYVMTTAG-PEPLETMRSPIDYAFYL 762
Cdd:cd05531 293 STALKALR-------AKGVS--VVPGMKIEYIVRDGKrPVPDLGNDEGYDTKYYR 338
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
382-768 |
1.18e-25 |
|
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: 111.15 E-value: 1.18e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 382 HLYLPRMHRLGYVA--PNLGDVTGQNSPGG--FVMDSRPGLY-DSVLVFDYKSLYPSII--------------------- 435
Cdd:cd05534 8 SMLLRLAKPENYILpsPSRQQVAQQRALEClpLVMEPESGFYsDPVIVLDFQSLYPSIMiaynycystclgrveelnggg 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 436 -----RTFLIDPVGLIEGLAHPADETSVPgfLGARFSRTA---HCLPDIVRRVWEGR-----------DDAKRQRNAPLS 496
Cdd:cd05534 88 kfgflGVKLYLPPPPLDLLLLKDDVTISP--NGVMFVKKSvrkGILPKMLEEILDTRimvkkamkkykDDKKLQRILDAR 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 497 Q-ALKIIMNSFYGVLGSTgcrfFDPR-----LASSITMRGHEIMHRTRKLIEAQGY---EVIYGDTDSTFVWL-GRAHdd 566
Cdd:cd05534 166 QlALKLLANVTYGYTAAS----FSGRmpcveIADSIVQTGRETLERAIELIESTPKwgaKVVYGDTDSLFVLLpGRTK-- 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 567 DEAGAKGRALVEHVNrwwqahlrEQFglDSALELQYERHYRR-FLMptvrgaeegSKKRYAGLA-ATADGGEDlVF--KG 642
Cdd:cd05534 240 EEAFKIGKEIAEAVT--------AAN--PSPIKLKFEKVYHPcVLV---------TKKRYVGYKyESPDQTEP-TFdaKG 299
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 643 LETVRTDWTPLAQQFQRELYRRVFSRepyQDF--IRDYV----RRTLAGEFD-DQLVYRKRVRRPLREYERNVPPHVRAA 715
Cdd:cd05534 300 IETVRRDGCPAVQKILEKSLRILFET---KDLstVKSYLqrqwSKLLQGRVSiQDFIFAKEVRLGTYKEGATLPAGAIVA 376
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1144870178 716 RIADEfNHAQGRPLQYQRggwISYVMTTAGP---------EPLETMRSP---IDYAFYLSRQLQP 768
Cdd:cd05534 377 LRRME-KDPRAEPQYGER---VPYVVVRGEPgsrlidlvvSPEEFLADPslrLDAEYYITKQIIP 437
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
408-785 |
3.39e-24 |
|
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: 105.81 E-value: 3.39e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 408 GGFVMDSRPGLYDS-VLVFDYKSLYPSII------RTFLIDPVGLIEGLahPADETSVP-GFLGARFSRTAHCLPDIVRR 479
Cdd:cd05533 5 GATVIEPIKGYYDVpIATLDFASLYPSIMmahnlcYTTLLNKNTAKKLP--PEDYIKTPnGDYFVKSSVRKGLLPEILEE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 480 VWEGRDDAKRQRNA---PLSQ--------ALKIIMNSFYGVLGSTGCRFFDPRLASSITMRGHEIMHRTRKLIE-----A 543
Cdd:cd05533 83 LLAARKRAKKDLKEetdPFKKavldgrqlALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEekytkA 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 544 QGY----EVIYGDTDSTFVWLGRAhDDDEAGAKGRALVEHVNrwwqahlrEQFglDSALELQYERHYRRFLMPtvrgaee 619
Cdd:cd05533 163 NGYshdaKVIYGDTDSVMVKFGVS-DVEEAMKLGKEAAEYVS--------KKF--IKPIKLEFEKVYFPYLLI------- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 620 gSKKRYAGLAAT-ADGGEDLVFKGLETVRTDWTPLAQQFQRE-LYRRVFSREP--YQDFIRDYVRRTLAGEFD-DQLVYR 694
Cdd:cd05533 225 -NKKRYAGLLWTnPDKHDKMDTKGIETVRRDNCLLVQNVVETcLNKILIERDVegAIEFVKGVISDLLQNKIDiSLLVIT 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 695 KRVRRPLREYERNVpPHVRAARIADEFNHAQGRPLqyqrGGWISYVMTTAGP---------EPLETMRS--PIDYAFYLS 763
Cdd:cd05533 304 KALTKTADDYAGKQ-AHVELAERMRKRDPGSAPNV----GDRVPYVIIKGAKgakayekaeDPIYVLENniPIDTQYYLE 378
|
410 420
....*....|....*....|..
gi 1144870178 764 RQLQPvadailPFLRdDFERVI 785
Cdd:cd05533 379 NQLSK------PLLR-IFEPIL 393
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
408-745 |
3.99e-15 |
|
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: 77.53 E-value: 3.99e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 408 GGFVMDSRPGLYDSVLVFDYKSLYPSIIRTFLIDPVGLIEGLAHPADETSVPGFLGARfsrtahclpdivRRVWEGRDDA 487
Cdd:cd05538 5 GGYAYVFITGVLGPIVHADVASLYPSIMLAYRICPARDSLGIFLALLKYLVELRLAAK------------ESARAAARPA 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 488 KRQRNAPLSQALKIIMNSFYGVLGSTGCRFFDPRLASSITMRGHEIMHRTRKLIEAQGYEVIYGDTDSTFVWLGRAHDDD 567
Cdd:cd05538 73 ERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRRRGATPVEVDTDGIYFIPPNGVDTE 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 568 EagaKGRALVEHVNRwwqahlreqfGLDSALELQYERHYRRFLmptVRGaeegsKKRYAGLaataDGGEDLVFKGLETVR 647
Cdd:cd05538 153 D---EEEELVRELSS----------TLPKGITVEFDGRYRAMF---SYK-----IKNYALL----DYDGKLIVKGSAFRS 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 648 TDWTPLAQQFQRELYRRVFSREPYQ--DFIRDYVRRTLAGEFDDQLVYRKRVrrpLREYERNVPPHVRAAR--IADEFNH 723
Cdd:cd05538 208 RGIEPFLREFLREAVRLLLQGDGAGvhDLYEDYLRRLRSHELPISDLARTET---LKESPEEYLQKVRAGKrnPAAAYEI 284
|
330 340
....*....|....*....|..
gi 1144870178 724 AQGRPLQYQRGGWISYVMTTAG 745
Cdd:cd05538 285 ALARPREWRAGDRVTYYVSGTG 306
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
151-349 |
5.00e-11 |
|
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: 62.76 E-value: 5.00e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 151 PALRCVSLDIETSVHGELYSIAlegcgQRQVYMLGPPNGDERDGTGTLDFNLDYCDSRP---AMLARLNDWFDEHDPDAV 227
Cdd:cd05780 1 EDLKILSFDIEVLNHEGEPNPE-----KDPIIMISFADEGGNKVITWKKFDLPFVEVVKtekEMIKRFIEIVKEKDPDVI 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 228 IGWNLVQFDLRILHAHAEQYGVPLKLGRGGSVLDWRAHGqqpDHFFAGAAGRLildGIDMLKSA--TWTFPSFSLEYVSQ 305
Cdd:cd05780 76 YTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGG---FNNASEIKGRI---HVDLYPVArrTLNLTRYTLERVYE 149
|
170 180 190 200
....*....|....*....|....*....|....*....|....
gi 1144870178 306 SLLGEGKsIDNPYQRMDEIQRRfDHDKPALARYNLKDCELVTRI 349
Cdd:cd05780 150 ELFGIEK-EDVPGEEIAEAWDS-GENLERLFRYSMEDAKYTYEI 191
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
153-349 |
2.15e-10 |
|
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: 60.89 E-value: 2.15e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 153 LRCVSLDIETSVHGElYSIALEGCGQRQVYMLGppngdERDGTGTLDFNLDYCDSRPAMLARLNDWFDEHDPDAVIGWNL 232
Cdd:cd05785 9 LRRLQLDIETYSLPG-FFFSNPDRGDDRIIIVA-----LRDNRGWEEVLHAEDAAEKELLEELVAIIRERDPDVIEGHNI 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 233 VQFDLRILHAHAEQYGVPLKLGRGGSVL-----DWRAHGQQPDHFFAGAAGRLILDGIDMLKS---ATWTFPSFSLEYVS 304
Cdd:cd05785 83 FRFDLPYLRRRCRRHGVPLAIGRDGSIPrqrpsRFRFAERLIDYPRYDIPGRHVIDTYFLVQLfdvSSRDLPSYGLKAVA 162
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 1144870178 305 QSL-LGEGKSIDNPYQRMDEIqrrFDHDKPALARYNLKDCELVTRI 349
Cdd:cd05785 163 KHFgLASPDRTYIDGRQIAEV---WRSDPARLLAYALDDVRETEGL 205
|
|
| 43A |
PHA02524 |
DNA polymerase subunit A; Provisional |
224-475 |
2.87e-08 |
|
DNA polymerase subunit A; Provisional
Pssm-ID: 164925 [Multi-domain] Cd Length: 498 Bit Score: 56.93 E-value: 2.87e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 224 PDAVIGWNLVQFDL-----RILHAHAEQYGVPLK-LGRGGSVLDWRAHGQQPDHFFAGAAgrlILDGIDMLKSATWT-FP 296
Cdd:PHA02524 196 PDLVFGWNSEGFDIpyiitRITNILGEKAANQLSpYGKITSKTITNLYGEKIIYKIHGIA---LMDYMDVFKKFSFTpMP 272
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 297 SFSLEYVS-QSLLGEGKSIDNPYQRMdeiqRRFDHDKpaLARYNLKDCELVTRIFDKADLLSFALERASVTGLAADRTGG 375
Cdd:PHA02524 273 DYKLGNVGyREVKADKLDYEGPINKF----RKADHQR--YVDYCVRDTDIILLIDGRRCFIDLILSLSYYAKIRFDDVLG 346
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 376 SVAAFTHLYLPRMHRLGYVAPNLGDVTGQNSPGGFVMDSRPGLYDSVLVFDYKSLYPSIIRTFLIDPvGLIEGLAHPADE 455
Cdd:PHA02524 347 TIKVWDSIIFNSLVESNVVIPAMKASPKQSFPGAYVKEPVPGGYRYGLSFDLTSLYPSILRLLNISP-EMIAGMFSPARL 425
|
250 260
....*....|....*....|
gi 1144870178 456 TSVPGFLGARFSRTAHCLPD 475
Cdd:PHA02524 426 EDYINKVAPKPSDQFSCAPN 445
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
200-358 |
3.26e-08 |
|
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: 54.89 E-value: 3.26e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 200 FNLDYCDSRP-----------AMLARLNDWFDEHDPDAVIGWNLVQFDLRILHAHAEQYGVPL--KLGR----GGSVLDW 262
Cdd:cd05777 52 FTLKTCAPIVgaqvfsfeteeELLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTfpFLGRikniKSTIKDT 131
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 263 RAHGQQ---PDHFFAGAAGRLILDGIDMLKSATWTFpSFSLEYVSQSLLGEGK-----SIDNPYQRMDEIQRRfdhdkpA 334
Cdd:cd05777 132 TFSSKQmgtRETKEINIEGRIQFDLLQVIQRDYKLR-SYSLNSVSAHFLGEQKedvhySIITDLQNGNPETRR------R 204
|
170 180
....*....|....*....|....
gi 1144870178 335 LARYNLKDCELVTRIFDKadLLSF 358
Cdd:cd05777 205 LAVYCLKDAYLPLRLLDK--LMCL 226
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
83-303 |
3.56e-08 |
|
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: 55.89 E-value: 3.56e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 83 LYCKRY----RHLSGLQKRL-AAAGVDVYEADVQPPDRYAMERFIT--ACVEFRGQPGRD---GTLTGGEL--------- 143
Cdd:pfam03104 66 PYLKVSfanpRPLLKIRKYLsPENISDVYEYDVDYLERFLIDNDIVgfGWYKVKVYPFRAegrISNCDVEIdcdspdlis 145
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 144 KPATGYRPALRCVSLDIETSvHGELY--------------SIALEGCGQ-----RQVYMLGPPNGDERDGTGTLDFNLDY 204
Cdd:pfam03104 146 VPFEKEWPPLRVLSFDIECT-SLPGKfpdaenvkdpiiqiSCMLDGQGEpepepRFLFTLRECDSEDIEDFEYTPKPIYP 224
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 205 ------CDSRPAMLarlNDWFD---EHDPDAVIGWNLVQFDLRILHAHAEQYGVP-----LKLGRGGSVLDWRAHGQQPD 270
Cdd:pfam03104 225 gvkvfeFPSEKELL---RRFFEfirQYDPDIITGYNGDNFDWPYILNRAKELYIVklssiGRLNRGGRSKVREIGFGTRS 301
|
250 260 270
....*....|....*....|....*....|...
gi 1144870178 271 HFFAGAAGRLILDGIDMLKsATWTFPSFSLEYV 303
Cdd:pfam03104 302 YEKVKISGRLHLDLYRVIK-RDYKLPSYKLNAV 333
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
211-437 |
1.72e-06 |
|
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: 51.98 E-value: 1.72e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 211 MLARLNDWFDEHDPDAVIGWNLVQFDLRILH-------------AHAEQYGVPLKLGRG--GSVLDWRAHGQQPDHFFAG 275
Cdd:TIGR00592 273 MIKRFWDVIDQEDTDVEITVNGDNFDLVYLAdrqvfqfywdayeDPAEKLGVVLLFGRDvdHVSPCVQVKGINRDLFFLP 352
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 276 AAGRLILDGIDMLKSaTWTFPSFSLEYVSQSLLGEGKSidnpYQRMDEIQRRFDHDKPA-LARYNLKDCELvtrifdkad 354
Cdd:TIGR00592 353 REGKIDFDLGKVTRR-TINLPDYYLEFVSELALGYKKE----KFRAKPIAKKYEFEAPDiDAPYSSEYLEV--------- 418
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 355 LLSFALERASVTGLAADRTGGSVA----AFT-HLYLPRMHRLGYvAPNLGDVTG-----------QNSPGGFVMDS--RP 416
Cdd:TIGR00592 419 TYELGKEFAPMEALPSDLKGQTFWhvfgSNTgNLERFLLLRKIK-GPCWLAVKGpdeleyprrswCKYEGGYVKPPnvEK 497
|
250 260
....*....|....*....|....*.
gi 1144870178 417 GLYDS-----VLVFDYKSLYPSIIRT 437
Cdd:TIGR00592 498 GLDKTppplvVLDFSMKSLNPSIIRN 523
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
185-309 |
2.37e-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: 46.45 E-value: 2.37e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 185 GPPNGDERDGTGTLDFNLDYCDSRPAMLARLNDWFDEHDPDAVIGWNLVQFDLRILHAHAEQYGVPL--KLGRggsvldw 262
Cdd:cd05776 59 SPPPDLFEKNAKKKKTKVRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHwsRIGR------- 131
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 1144870178 263 RAHGQQPDHFFAGA-------AGRLILD----GIDMLKSatwtfPSFSLEYVSQSLLG 309
Cdd:cd05776 132 LKRSVWPKKKGGGKfgereltAGRLLCDtylsAKELIRC-----KSYDLTELSQQVLG 184
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
203-342 |
9.26e-04 |
|
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarchaea. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B-DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.
Pssm-ID: 99824 [Multi-domain] Cd Length: 188 Bit Score: 41.16 E-value: 9.26e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 203 DYCDSRpaMLARLNDWFDEHDPDAVIGWNLVQFDLRILHAHAEQYGVPLKLGR-GGSVLDWRAHGqqpdHFfaGAAGRLI 281
Cdd:cd05781 45 GLDDRK--IIREFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRrGGSEPSTGVYG----HY--SITGRLN 116
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1144870178 282 LDGIDMLKSATwTFPSFSLEYVSQsLLGEGKSIDNPYQRMDEIQRRFDHDK--PALARYNLKD 342
Cdd:cd05781 117 VDLYDFAEEIP-EVKVKTLENVAE-YLGVMKKSERVLIEWYRIYEYWDDEKkrDILLKYNRDD 177
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
408-664 |
1.17e-03 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 42.70 E-value: 1.17e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 408 GGFVMDSRPGLYDS-VLVFDYKSLYPSIIRTFLIDP---VGL---------------IEGLAHPAD------ETSVPGFL 462
Cdd:PHA03036 532 GGKVFAPKQKMFDNnVLIFDYNSLYPNVCIFGNLSPetlVGVvvndnrleaeinkqeLRRKYPYPRyiyvhcEPRSPDLV 611
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 463 G--ARFSRTAHCL-PDIVRRVWEGRDDAKRQRNAPLS---QAL--------KIIMNSFYGVLGSTGCRFFDPRLASSITM 528
Cdd:PHA03036 612 SeiAVFDRRIEGIiPKLLKTFLEERARYKKLLKEATSsveKAIydsmqytyKIVANSVYGLMGFRNSALYSYASAKSCTA 691
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 529 RGHEIMHRTR-----------KLIEAQ---------------------------GYEVIYGDTDSTFVWLGRAhdDDEAG 570
Cdd:PHA03036 692 IGRNMIKYLNsvlngsklingKLILANcpinpffkddrsidtnydtnlpveynfTFRSVYGDTDSVFLEINTK--DVDKS 769
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 571 AK-GRALVEHVNrwwQAHLREQFgldsalELQYERHYRRFLMPtvrgaeegSKKRYAGLAATADGGEDL----VFKGLET 645
Cdd:PHA03036 770 IKiAKELERIIN---EKVLFDNF------KIEFEAVYKNLIMQ--------SKKKYTTLKYIASSTDGSvperVNKGTSE 832
|
330
....*....|....*....
gi 1144870178 646 VRTDWTPlaqqFQRELYRR 664
Cdd:PHA03036 833 TRRDVSK----FHKYMIKI 847
|
|
| DNA_polB_B1_exo |
cd05783 |
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ... |
151-350 |
1.63e-03 |
|
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are unique in that they are able to recognize the presence of uracil in the template strand, leading to the stalling of DNA synthesis. This is an additional safeguard mechanism against increased levels of deaminated bases during genome duplication at high temperatures. S. solfataricus B1 also interacts with DNA polymerase Y and may contribute to genome stability mechanisms.
Pssm-ID: 99826 [Multi-domain] Cd Length: 204 Bit Score: 40.38 E-value: 1.63e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 151 PALRCVSLDIE--TSVHG----------ELYSIALEGC-GQRQVYMLGPPNGDERDGTGTLDFNLDYCDSRPAMLARLND 217
Cdd:cd05783 3 PKLKRIAIDIEvyTPIKGripdpktaeyPVISVALAGSdGLKRVLVLKREGVEGLEGLLPEGAEVEFFDSEKELIREAFK 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1144870178 218 WFDEHdPdAVIGWNLVQFDLRILHAHAEQYGV-----PLKLGRGGSVLDwraHGQQPD--HFFAGAAGRLILDGidmlks 290
Cdd:cd05783 83 IISEY-P-IVLTFNGDNFDLPYLYNRALKLGIpkeeiPIYLKRDYATLK---HGIHIDlyKFFSNRAIQVYAFG------ 151
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1144870178 291 atWTFPSFSLEYVSQSLLGEGK-SIDNPYQRMDEIQrrfdhdkpaLARYNLKDCELVTRIF 350
Cdd:cd05783 152 --NKYREYTLDAVAKALLGEGKvELEKNISELNLYE---------LAEYNYRDAELTLELT 201
|
|
| |
