|
Name |
Accession |
Description |
Interval |
E-value |
| 43 |
PHA02528 |
DNA polymerase; Provisional |
33-879 |
6.28e-163 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 497.68 E-value: 6.28e-163
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 33 GKRKWVQKDFSPNLFVRDTEGKDAIDIYGHPLKRVDLGSISEARDFVKMLDEASRDLFGYRKYETQFIcqagyRESTPEE 112
Cdd:PHA02528 24 GKERSRKVKYEPTLFVHANEESKYKDIYGKNCRPKKFDSMRDARKWMKRMKDVGFEALGMDDFKLQYI-----SDTYPGE 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 113 ysIVYH---------DIETEVHDGFPDPSVAKEPINMITLLQRGGKRFAL-----------TTCEVKKEKIDEefgIETM 172
Cdd:PHA02528 99 --IKYDrskirianlDIEVTAEDGFPDPEEAKYEIDAITHYDSIDDRFYVfdlgsveewdaKGDEVPQEILDK---VVYM 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 173 MFSSEAEMLRHFIYLFTEVLEvDIFVGWNSEKFDLPYIVNRIKRILGGDMAKKLSPFGEVYIRSFIDDFGDEAVTAEILG 252
Cdd:PHA02528 174 PFDTEREMLLEYINFWEENTP-VIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISG 252
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 253 VSHVDMLQFYKKFSHESQESYSLDNIAKVELGVGKLVHESGiPGHLLYHEYPTDGLRYNIVDVVRLEEIDEKKGIIDLAI 332
Cdd:PHA02528 253 ISILDYLDLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDG-PFKKFRETDHQKYIEYNIIDVELVDRLDDKRKLIELVL 331
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 333 TVANMSKTNVSDTMFSTRLWMSMIYDYLSQRGRYFEfSRERNEYRKIEGGFVSCNSPGLHDYITSYDYASLYPSTMMALN 412
Cdd:PHA02528 332 SMAYYAKINFEDVFSPIKTWDAIIFNSLKEEKIVIP-ENKSHKKQKYAGAFVKEPVPGAYRWVVSFDLTSLYPSIIRQVN 410
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 413 IGIESKRQKIeDINPQYLIDNPEFNAPEN-LAMGANGQCYAKDKKSFLNEIISHGYDLRKKYKALKLFYQNLETKTDEGL 491
Cdd:PHA02528 411 ISPETIAGTF-HVAPVHEYINKTAPRPSDeYSCSPNGWMYRKDIRGVIPTEIKKVFDQRKIYKKKMLAAERNAELIKTIL 489
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 492 IEAVKTHL------REKKKDQGLLEELARIDSMSLEKARKEVTRLAKLYDSYDKSIKTILNSCYGALAEKNFFFYDPDMA 565
Cdd:PHA02528 490 EDLNDSVDtpidvdYYFDFSDEFKAELKTLTKSSLKALLEECEKEIALCNTIQMARKILINSLYGALGNEHFRYYDLRNA 569
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 566 ESITMTGQFMV----RNLGETFVKLL-TKNYgkgTYLLNQDTDSCYLTLKSAVDKHFGDRdvsEKEKIEW---LCKFADG 637
Cdd:PHA02528 570 EAITLFGQLAIqwieRKMNEYLNKLCkTEDE---DYVIYGDTDSIYVNLDPLVEKVGEDK---FKDTNHWvdfLDKFCKE 643
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 638 PMKKVVQIANDIANKRLGSYEPERFdADREAVCRRGVFIKKKMYALAISDMEGVHYEKPKLKIVGLQAKKKSTPAFFRSK 717
Cdd:PHA02528 644 RMEPYIDSSYRELCEYMNNYEHLMF-MDREAIAGPGFWTAKKRYALNVWDSEGTRYAEPKLKIMGIETQRSSTPKAVQKA 722
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 718 MEIFFNILLGEGDkKKASEHVIDVENEFRNSPLDEIAGNFSVSDIsSKIDDSEKGYVKGVHINARAAIVSNRVVASDEKa 797
Cdd:PHA02528 723 LKEAIRRILQEGE-ESLQEYIKEFEKEFRKLDYEEIAFVSSANNI-AKYSDDKGIPGKGCPIHIRGALLYNRAVKGTLG- 799
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 798 rlyIEPIRNGDKIKMLPLRLPNPTKENIIAW--KEDFPDVFREkKIDQYIDWNSQFTKAFMNPLKNIFTVCGIRPDIKEE 875
Cdd:PHA02528 800 ---YPPIQEGEKVMVLPLKEPNPIGENCIAWpsGTELPKEIRS-DLLKWVDYNLLFEKSFIKPLKNITEAIGWDYEKKAS 875
|
....
gi 2438090180 876 LDIF 879
Cdd:PHA02528 876 LEDL 879
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
119-811 |
2.52e-62 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 225.48 E-value: 2.52e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 119 DIETEVHDGFPDPSVAkEPINMITLLQRGGKR--FALTTcevkkekidEEFGIETMMFSSEAEMLRHFIYLFTEvLEVDI 196
Cdd:COG0417 166 DIEVSTPRGFPDPERD-GPIISIGLAGSDGEKkvLMLGR---------EGVDFEVEYFDDEKALLEAFFEIIRE-YDPDI 234
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 197 FVGWNSEKFDLPYIVNRIKR-----ILGGDMakklspfGEVYIRSFIDDFgdeavTAEILGVSHVDMLQFYKKFSHESqE 271
Cdd:COG0417 235 IIGWNVDNFDLPYLQKRAERlgiplDLGRDG-------SEPSWREHGGQG-----FASIPGRVVIDLYDALKSATYKF-K 301
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 272 SYSLDNIAKVELGVGKLVHESGIPGHLlYHEYPTDGLRYNIVDVVRLEEIDEKKGIIDLAITVANMSKTNVSDTMFSTR- 350
Cdd:COG0417 302 SYSLDAVAEELLGEGKLIVDGGEIERL-WDDDKPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSs 380
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 351 LWMSMIYDYLSQRGRYFEFSRERNEYRKIEGGFVSCNSPGLHDYITSYDYASLYPSTMMALNIGIESKrqkiedINPQYL 430
Cdd:COG0417 381 AAFENLLLPEAHRRGYLAPNKGEIKGEAYPGGYVLDPKPGLYENVLVLDFKSLYPSIIRTFNISPETL------VEGGEE 454
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 431 IDNPEFNAPEnlamgaNGQCYAKDKKSFLNEIISHGYDLRKKYKalklfyqnletktdeglieavkthlREKKKDQGLLE 510
Cdd:COG0417 455 PCGDEDVAPG------FGHRFCREPKGILPSILEELWDERDEAK-------------------------KKMKKAKPDSE 503
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 511 ELARIDSMSlekarkevtrlaklydsydKSIKTILNSCYGALAEKNFFFYDPDMAESITMTGQF-------MVRNLGETF 583
Cdd:COG0417 504 EYRLYDALQ-------------------QALKILMNSFYGVLGSEGCRFYDPELAESITARGREiikqtieKAEELGYKV 564
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 584 VklltknYGkgtyllnqDTDSCYLTLKSAvdkhfgdrdvSEKEKIEwlckfadgpmkKVVQIANDIaNKRLGSYeperFD 663
Cdd:COG0417 565 I------YG--------DTDSLFVWLPKA----------SLEEAIE-----------IGKELAEEI-NAWWPSG----LE 604
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 664 ADREAVCRRGVFI-KKKMYAlaisdmeGVhYEKPKLKIVGLQAKKKSTPAFFRSKMEIFFNILLGEGDKKKASEHVIDVE 742
Cdd:COG0417 605 LEFEKHYRRFFFPgSKKRYA-------GL-TEDGKIDIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVEYVRDVI 676
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2438090180 743 NEFRN--SPLDEIAgnFSVSdISSKIDDsekgYVKGVHINARAAivsnrvvasdEKARLYIEPIRNGDKIK 811
Cdd:COG0417 677 EKLRAgeVDLDDLV--IRKR-LRKPLSE----YEKNVPPHVRAA----------RKLDERGRPYQRGDKIS 730
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
112-610 |
6.70e-39 |
|
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: 151.14 E-value: 6.70e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 112 EYSIVYHDIETEV-HDGFPDPSVAKEPINMITL-LQRGGKRFALTTCEVKKEKIDEEFGIETMMFSSEAEMLRHFIYLFT 189
Cdd:smart00486 2 PLKILSFDIETYTdGGNFPDAEIFDDEIIQISLvINDGDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEFIK 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 190 EVlEVDIFVGWNSEKFDLPYIVNRIKRILGGDMA-----KKLSPFGEVYIRSFIDDFGDEAVTAEILGVSHVDMLQFYKK 264
Cdd:smart00486 82 KY-DPDIIYGHNISNFDLPYIISRLEKLKIDPLSkigrlKIGLRIPNKKPLFGSKSFGLSDIKVYIKGRLVIDLYRLYKN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 265 FSheSQESYSLDNIAKVELGVGKLvhesGIPGHLLYHEYPTDG------LRYNIVDVVRLEEIDEKKGIIDLAITVANMS 338
Cdd:smart00486 161 KL--KLPSYKLDTVAEYLLGKEKD----DLPYKDIPELYNGNYeerdelLRYCIQDAVLTLKLFNKLNVIPLIIELARIA 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 339 KTNVSDTMFSTR--------LWMSMIYDYL---SQRGRYFEFSRERNEYRKIEGGFVSCNSPGLHD-YITSYDYASLYPS 406
Cdd:smart00486 235 GIPLRRTLYYGSqirvesllLREAKKNNYIlpsKELYDFKGSEPDLKKKVKYEGGKVLEPKKGFYDnPVLVLDFNSLYPS 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 407 TMMALNIGIESKRQKIEDINPQYLIDNPEFNAPENLAmGANGQCYAKDK-KSFLNEIISHGYDLRKKYKALKLFYQNlet 485
Cdd:smart00486 315 IIIAHNLCYSTLVGVGEVVIKGDLIIPEDLLTIKYEK-GNKYRFVKKNIrKGILPKLLKKLLDKRKEIKKLMKKEKD--- 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 486 ktdeglieavkthlrekkkdqglleelaridsmslekarkEVTRLAKLYDSYDKSIKTILNSCYGALAEKNFFFYDPDMA 565
Cdd:smart00486 391 ----------------------------------------ESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLA 430
|
490 500 510 520
....*....|....*....|....*....|....*....|....*...
gi 2438090180 566 ESITMTGQFMVRNlgetfVKLLTKNYGKGTYLLNQ---DTDSCYLTLK 610
Cdd:smart00486 431 ASVTALGREILEK-----TKELIEENGYPKPGFKViygDTDSIFVTKP 473
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
119-323 |
1.16e-22 |
|
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: 96.66 E-value: 1.16e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 119 DIETEVHDGFPDPSvaKEPINMITLL--QRGGKRFALTTCEVKKEKIDEEFGIETMMFSSEAEMLRHFIYLFTEVlEVDI 196
Cdd:cd05160 5 DIETTPPVGGPEPD--RDPIICITYAdsFDGVKVVFLLKTSTVGDDIEFIDGIEVEYFADEKELLKRFFDIIREY-DPDI 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 197 FVGWNSEKFDLPYIVNRIKRIlggdmakKLSPFGEVYIRSFIDDFGDEAVTAEILGVSHVDMLQFYKKFSHesQESYSLD 276
Cdd:cd05160 82 LTGYNIDDFDLPYLLKRAEAL-------GIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFK--LKSYTLD 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 2438090180 277 NIAKVELGVGKLVHESGIPGHLLYHEYPTDGLRYNIVDVVRLEEIDE 323
Cdd:cd05160 153 AVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQILE 199
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
107-278 |
4.40e-17 |
|
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: 83.62 E-value: 4.40e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 107 ESTPEEYSIVYHDIETEVHDG-FPDPSVAKEPINMITLLQRGGKR--------FALTTC--------EVKKEKIDEEFGI 169
Cdd:pfam03104 149 EKEWPPLRVLSFDIECTSLPGkFPDAENVKDPIIQISCMLDGQGEpepeprflFTLRECdsediedfEYTPKPIYPGVKV 228
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 170 ETmmFSSEAEMLRHFIYLFTEVlEVDIFVGWNSEKFDLPYIVNRIK--RILGGDMAKKLSPFGEVYIRSFIDDFgDEAVT 247
Cdd:pfam03104 229 FE--FPSEKELLRRFFEFIRQY-DPDIITGYNGDNFDWPYILNRAKelYIVKLSSIGRLNRGGRSKVREIGFGT-RSYEK 304
|
170 180 190
....*....|....*....|....*....|.
gi 2438090180 248 AEILGVSHVDMLQFYKKFSHESqeSYSLDNI 278
Cdd:pfam03104 305 VKISGRLHLDLYRVIKRDYKLP--SYKLNAV 333
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
415-793 |
2.21e-05 |
|
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA polymerases.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273159 [Multi-domain] Cd Length: 1172 Bit Score: 48.51 E-value: 2.21e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 415 IESKRQKIEDinpqyliDNPEFNAPENLAMGANGQCYAKDKKSFLNEIISHGYDLRKKYKALKLFYQNLETKTDEGLIEA 494
Cdd:TIGR00592 771 IFRKQQKLGD-------EDEEIDGYKKGKKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQKVDED 843
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 495 VKTHLREKKKDQGLLEELARidsmSLEKARKEVTRLAKL---------YDSYDKSIKTILNSCYGALAEKNFFFYDPDMA 565
Cdd:TIGR00592 844 ELPELPDSELEMGILPRELR----KLVERRKEVKKLMKQdlnpdlrlqYDIRQKALKLTANSMYGCLGYSKSRFYAKPLA 919
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 566 ESITMTGQFMVRNLGETFVKLLTKN-YGkgtyllnqDTDSCYLTLKSavdkhfgdrdvsekEKIEwlckfadgpmkKVVQ 644
Cdd:TIGR00592 920 ALVTAKGREILEHTRQLVEEMNLEViYG--------DTDSIMINTPG--------------TKYE-----------EVFK 966
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 645 IANDIANKRLGSYEPErfDADREAVCRRGVFIKKKMYALAISDMEGVHYEKPKLKIVGLQAKKKSTPAFFRSKMEIFFNI 724
Cdd:TIGR00592 967 IGKEFKSEVNKLYKLL--ELDIDGVFKRLLLLKKKKYAAIKVEGDSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDT 1044
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2438090180 725 LLGEGDKKKASEHVIDVENEFRNSPLDeiaGNFSVS--DISSKIDDSEKGYVKG-----VHINARAAIVSNRVVAS 793
Cdd:TIGR00592 1045 ILSDKDVEEAVEEVQEVLEKIGKNVLN---GEVPLEkfVINKQLTRDPKDYPDGaslphVHVALRINARGGRKVKA 1117
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| 43 |
PHA02528 |
DNA polymerase; Provisional |
33-879 |
6.28e-163 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 497.68 E-value: 6.28e-163
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 33 GKRKWVQKDFSPNLFVRDTEGKDAIDIYGHPLKRVDLGSISEARDFVKMLDEASRDLFGYRKYETQFIcqagyRESTPEE 112
Cdd:PHA02528 24 GKERSRKVKYEPTLFVHANEESKYKDIYGKNCRPKKFDSMRDARKWMKRMKDVGFEALGMDDFKLQYI-----SDTYPGE 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 113 ysIVYH---------DIETEVHDGFPDPSVAKEPINMITLLQRGGKRFAL-----------TTCEVKKEKIDEefgIETM 172
Cdd:PHA02528 99 --IKYDrskirianlDIEVTAEDGFPDPEEAKYEIDAITHYDSIDDRFYVfdlgsveewdaKGDEVPQEILDK---VVYM 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 173 MFSSEAEMLRHFIYLFTEVLEvDIFVGWNSEKFDLPYIVNRIKRILGGDMAKKLSPFGEVYIRSFIDDFGDEAVTAEILG 252
Cdd:PHA02528 174 PFDTEREMLLEYINFWEENTP-VIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISG 252
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 253 VSHVDMLQFYKKFSHESQESYSLDNIAKVELGVGKLVHESGiPGHLLYHEYPTDGLRYNIVDVVRLEEIDEKKGIIDLAI 332
Cdd:PHA02528 253 ISILDYLDLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDG-PFKKFRETDHQKYIEYNIIDVELVDRLDDKRKLIELVL 331
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 333 TVANMSKTNVSDTMFSTRLWMSMIYDYLSQRGRYFEfSRERNEYRKIEGGFVSCNSPGLHDYITSYDYASLYPSTMMALN 412
Cdd:PHA02528 332 SMAYYAKINFEDVFSPIKTWDAIIFNSLKEEKIVIP-ENKSHKKQKYAGAFVKEPVPGAYRWVVSFDLTSLYPSIIRQVN 410
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 413 IGIESKRQKIeDINPQYLIDNPEFNAPEN-LAMGANGQCYAKDKKSFLNEIISHGYDLRKKYKALKLFYQNLETKTDEGL 491
Cdd:PHA02528 411 ISPETIAGTF-HVAPVHEYINKTAPRPSDeYSCSPNGWMYRKDIRGVIPTEIKKVFDQRKIYKKKMLAAERNAELIKTIL 489
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 492 IEAVKTHL------REKKKDQGLLEELARIDSMSLEKARKEVTRLAKLYDSYDKSIKTILNSCYGALAEKNFFFYDPDMA 565
Cdd:PHA02528 490 EDLNDSVDtpidvdYYFDFSDEFKAELKTLTKSSLKALLEECEKEIALCNTIQMARKILINSLYGALGNEHFRYYDLRNA 569
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 566 ESITMTGQFMV----RNLGETFVKLL-TKNYgkgTYLLNQDTDSCYLTLKSAVDKHFGDRdvsEKEKIEW---LCKFADG 637
Cdd:PHA02528 570 EAITLFGQLAIqwieRKMNEYLNKLCkTEDE---DYVIYGDTDSIYVNLDPLVEKVGEDK---FKDTNHWvdfLDKFCKE 643
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 638 PMKKVVQIANDIANKRLGSYEPERFdADREAVCRRGVFIKKKMYALAISDMEGVHYEKPKLKIVGLQAKKKSTPAFFRSK 717
Cdd:PHA02528 644 RMEPYIDSSYRELCEYMNNYEHLMF-MDREAIAGPGFWTAKKRYALNVWDSEGTRYAEPKLKIMGIETQRSSTPKAVQKA 722
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 718 MEIFFNILLGEGDkKKASEHVIDVENEFRNSPLDEIAGNFSVSDIsSKIDDSEKGYVKGVHINARAAIVSNRVVASDEKa 797
Cdd:PHA02528 723 LKEAIRRILQEGE-ESLQEYIKEFEKEFRKLDYEEIAFVSSANNI-AKYSDDKGIPGKGCPIHIRGALLYNRAVKGTLG- 799
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 798 rlyIEPIRNGDKIKMLPLRLPNPTKENIIAW--KEDFPDVFREkKIDQYIDWNSQFTKAFMNPLKNIFTVCGIRPDIKEE 875
Cdd:PHA02528 800 ---YPPIQEGEKVMVLPLKEPNPIGENCIAWpsGTELPKEIRS-DLLKWVDYNLLFEKSFIKPLKNITEAIGWDYEKKAS 875
|
....
gi 2438090180 876 LDIF 879
Cdd:PHA02528 876 LEDL 879
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
119-811 |
2.52e-62 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 225.48 E-value: 2.52e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 119 DIETEVHDGFPDPSVAkEPINMITLLQRGGKR--FALTTcevkkekidEEFGIETMMFSSEAEMLRHFIYLFTEvLEVDI 196
Cdd:COG0417 166 DIEVSTPRGFPDPERD-GPIISIGLAGSDGEKkvLMLGR---------EGVDFEVEYFDDEKALLEAFFEIIRE-YDPDI 234
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 197 FVGWNSEKFDLPYIVNRIKR-----ILGGDMakklspfGEVYIRSFIDDFgdeavTAEILGVSHVDMLQFYKKFSHESqE 271
Cdd:COG0417 235 IIGWNVDNFDLPYLQKRAERlgiplDLGRDG-------SEPSWREHGGQG-----FASIPGRVVIDLYDALKSATYKF-K 301
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 272 SYSLDNIAKVELGVGKLVHESGIPGHLlYHEYPTDGLRYNIVDVVRLEEIDEKKGIIDLAITVANMSKTNVSDTMFSTR- 350
Cdd:COG0417 302 SYSLDAVAEELLGEGKLIVDGGEIERL-WDDDKPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSs 380
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 351 LWMSMIYDYLSQRGRYFEFSRERNEYRKIEGGFVSCNSPGLHDYITSYDYASLYPSTMMALNIGIESKrqkiedINPQYL 430
Cdd:COG0417 381 AAFENLLLPEAHRRGYLAPNKGEIKGEAYPGGYVLDPKPGLYENVLVLDFKSLYPSIIRTFNISPETL------VEGGEE 454
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 431 IDNPEFNAPEnlamgaNGQCYAKDKKSFLNEIISHGYDLRKKYKalklfyqnletktdeglieavkthlREKKKDQGLLE 510
Cdd:COG0417 455 PCGDEDVAPG------FGHRFCREPKGILPSILEELWDERDEAK-------------------------KKMKKAKPDSE 503
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 511 ELARIDSMSlekarkevtrlaklydsydKSIKTILNSCYGALAEKNFFFYDPDMAESITMTGQF-------MVRNLGETF 583
Cdd:COG0417 504 EYRLYDALQ-------------------QALKILMNSFYGVLGSEGCRFYDPELAESITARGREiikqtieKAEELGYKV 564
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 584 VklltknYGkgtyllnqDTDSCYLTLKSAvdkhfgdrdvSEKEKIEwlckfadgpmkKVVQIANDIaNKRLGSYeperFD 663
Cdd:COG0417 565 I------YG--------DTDSLFVWLPKA----------SLEEAIE-----------IGKELAEEI-NAWWPSG----LE 604
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 664 ADREAVCRRGVFI-KKKMYAlaisdmeGVhYEKPKLKIVGLQAKKKSTPAFFRSKMEIFFNILLGEGDKKKASEHVIDVE 742
Cdd:COG0417 605 LEFEKHYRRFFFPgSKKRYA-------GL-TEDGKIDIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVEYVRDVI 676
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2438090180 743 NEFRN--SPLDEIAgnFSVSdISSKIDDsekgYVKGVHINARAAivsnrvvasdEKARLYIEPIRNGDKIK 811
Cdd:COG0417 677 EKLRAgeVDLDDLV--IRKR-LRKPLSE----YEKNVPPHVRAA----------RKLDERGRPYQRGDKIS 730
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
112-610 |
6.70e-39 |
|
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: 151.14 E-value: 6.70e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 112 EYSIVYHDIETEV-HDGFPDPSVAKEPINMITL-LQRGGKRFALTTCEVKKEKIDEEFGIETMMFSSEAEMLRHFIYLFT 189
Cdd:smart00486 2 PLKILSFDIETYTdGGNFPDAEIFDDEIIQISLvINDGDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEFIK 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 190 EVlEVDIFVGWNSEKFDLPYIVNRIKRILGGDMA-----KKLSPFGEVYIRSFIDDFGDEAVTAEILGVSHVDMLQFYKK 264
Cdd:smart00486 82 KY-DPDIIYGHNISNFDLPYIISRLEKLKIDPLSkigrlKIGLRIPNKKPLFGSKSFGLSDIKVYIKGRLVIDLYRLYKN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 265 FSheSQESYSLDNIAKVELGVGKLvhesGIPGHLLYHEYPTDG------LRYNIVDVVRLEEIDEKKGIIDLAITVANMS 338
Cdd:smart00486 161 KL--KLPSYKLDTVAEYLLGKEKD----DLPYKDIPELYNGNYeerdelLRYCIQDAVLTLKLFNKLNVIPLIIELARIA 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 339 KTNVSDTMFSTR--------LWMSMIYDYL---SQRGRYFEFSRERNEYRKIEGGFVSCNSPGLHD-YITSYDYASLYPS 406
Cdd:smart00486 235 GIPLRRTLYYGSqirvesllLREAKKNNYIlpsKELYDFKGSEPDLKKKVKYEGGKVLEPKKGFYDnPVLVLDFNSLYPS 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 407 TMMALNIGIESKRQKIEDINPQYLIDNPEFNAPENLAmGANGQCYAKDK-KSFLNEIISHGYDLRKKYKALKLFYQNlet 485
Cdd:smart00486 315 IIIAHNLCYSTLVGVGEVVIKGDLIIPEDLLTIKYEK-GNKYRFVKKNIrKGILPKLLKKLLDKRKEIKKLMKKEKD--- 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 486 ktdeglieavkthlrekkkdqglleelaridsmslekarkEVTRLAKLYDSYDKSIKTILNSCYGALAEKNFFFYDPDMA 565
Cdd:smart00486 391 ----------------------------------------ESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLA 430
|
490 500 510 520
....*....|....*....|....*....|....*....|....*...
gi 2438090180 566 ESITMTGQFMVRNlgetfVKLLTKNYGKGTYLLNQ---DTDSCYLTLK 610
Cdd:smart00486 431 ASVTALGREILEK-----TKELIEENGYPKPGFKViygDTDSIFVTKP 473
|
|
| 43B |
PHA02523 |
DNA polymerase subunit B; Provisional |
509-862 |
4.54e-32 |
|
DNA polymerase subunit B; Provisional
Pssm-ID: 164924 Cd Length: 391 Bit Score: 129.44 E-value: 4.54e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 509 LEELARIDSMSLEKARKEVTRLAKLYDSYDKSIKTILNSCYGALAEKNFFFYDPDMAESITMTGQFMVRNLgETFVKLLT 588
Cdd:PHA02523 14 LTYLNTLSTDELQQMIARCEKEEQKRNTNQLNRKILINSLYGALGNNWFRYFDLRNAEAITTYGQLAIRWI-ERKLNEYI 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 589 KNYGKGT---YLLNQDTDSCYLTLKSAVDKhfgdRDVSEKEKIEWLCKFADGPMKKVVQIANDIANKRLGSY---EPERF 662
Cdd:PHA02523 93 NELVKTTgvdYVCYIDTDSVYLNMEAVVNR----VGIDKFRDTNHLIDFLDNLGSKKLEPFIDDSYKELEEYmnhDHHLL 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 663 DADREAVCRR--------GVFIKKKMYALAISDMEGVHYEKPKLKIVGLQAKKKSTPAFFRSKMEIFFNILLGEGDkKKA 734
Cdd:PHA02523 169 LMDREAIFGAplgsdgigGFWTGKKRYALNVYDMEGTRYAEPHLKIMGLETQRSSTPLACQKSLKESIRRLLQEGE-SSL 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 735 SEHVIDVENEFRNSPLDEIAGNFSVSDISSKIDDSekGY-VKGVHINARAAIVSNRVVASDEKarlyIEPIRNGDKIKML 813
Cdd:PHA02523 248 QDYFKEFKDEFKNIPYQDVAAVSSANNIGKNGDAL--GFpIKGTPYHVKGVLAYNRIAKTDTA----IPMISEGEKVMVL 321
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|.
gi 2438090180 814 PLRLPNPTKENIIAWKE--DFPDVFrEKKIDQYIDWNSQFTKAFMNPLKNI 862
Cdd:PHA02523 322 PLRDRNPFNEACFAWPSgtPIPPAV-EADVLKYLDINKLFDKTFVKPLSSI 371
|
|
| 43A |
PHA02524 |
DNA polymerase subunit A; Provisional |
31-416 |
4.54e-31 |
|
DNA polymerase subunit A; Provisional
Pssm-ID: 164925 [Multi-domain] Cd Length: 498 Bit Score: 128.19 E-value: 4.54e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 31 RQGKRKWVQKDFSPNLFVRDTEGKDAI--DIYGHPLKRVDLGSISEARDFVKMLDEASRDLFGYRKYETQFICQA--GYR 106
Cdd:PHA02524 20 DNGKRQTRKVAYQPTLFQHAAPGVQTKhkDIYGRFCVPKKHENIWEAKQWIKRMEEVGMDAMGMDDYGISYISDTyrGVI 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 107 ESTPEEYSIVYHDIETEVHDgFPDPSVAKEPINMIT--LLQRGGKRFALTTC-------EVKKEKIDEEF--GIETMMFS 175
Cdd:PHA02524 100 DFDRDDVVIDVVDIEVTAPE-FPEPKYAKYEIDMIShvRLHNGKKTYYIFDLvkdvghwDPKKSVLEKYIldNVVYMPFE 178
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 176 SEAEMLRHFIYLFTEVLEvDIFVGWNSEKFDLPYIVNRIKRILGGDMAKKLSPFGEVYIRSFIDDFGdEAVTAEILGVSH 255
Cdd:PHA02524 179 DEVDLLLNYIQLWKANTP-DLVFGWNSEGFDIPYIITRITNILGEKAANQLSPYGKITSKTITNLYG-EKIIYKIHGIAL 256
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 256 VDMLQFYKKFSHESQESYSLDNIAKVELGVGKLVHESGI-----PGHLLYHEYPTDGlryniVDVVRLeeIDEKKGIIDL 330
Cdd:PHA02524 257 MDYMDVFKKFSFTPMPDYKLGNVGYREVKADKLDYEGPInkfrkADHQRYVDYCVRD-----TDIILL--IDGRRCFIDL 329
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 331 AITVANMSKTNVSDTMFSTRLWMSMIYDYLSQRGRYFEFSRERNEyRKIEGGFVSCNSPGLHDYITSYDYASLYPSTMMA 410
Cdd:PHA02524 330 ILSLSYYAKIRFDDVLGTIKVWDSIIFNSLVESNVVIPAMKASPK-QSFPGAYVKEPVPGGYRYGLSFDLTSLYPSILRL 408
|
....*.
gi 2438090180 411 LNIGIE 416
Cdd:PHA02524 409 LNISPE 414
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
174-615 |
5.68e-25 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 111.49 E-value: 5.68e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 174 FSSEAEMLRHFIYLFTEvLEVDIFVGWNSEKFDLPYIVNRIKRI--------LGGDMAKKLSPFGEVYirsfiddfgdea 245
Cdd:PRK05762 200 VADEKALLEKFNAWFAE-HDPDVIIGWNVVQFDLRLLQERAERYgiplrlgrDGSELEWREHPFRSGY------------ 266
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 246 VTAEILGVSHVDMLQFYKKFSHeSQESYSLDNIAKVELGVGKLVHESGIPGHLLYHEYPTDG---LRYNIVDVVRLEEID 322
Cdd:PRK05762 267 GFASVPGRLVLDGIDALKSATW-VFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKpalARYNLKDCELVTRIF 345
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 323 EKKGIIDLAITVANMSKTNVSDTMFS----TRLWMSMIYdylsqRGRYFEFSRERNEYRKIEGGFVSCNSPGLHDYITSY 398
Cdd:PRK05762 346 EKTKLLPFLLERATVTGLPLDRVGGSvaafEHLYLPRAH-----RAGYVAPNLGERPGEASPGGYVMDSKPGLYDSVLVL 420
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 399 DYASLYPSTMMALNIGieskrqkiedinPQYLIDNPEFNAPENLAmGANGQCYAKdKKSFLNEIIshgydlrkkykalkl 478
Cdd:PRK05762 421 DFKSLYPSIIRTFNID------------PDGLVEGLAQPPEESVA-GFLGARFSR-EKHFLPEIV--------------- 471
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 479 fyqnletktdEGLIEAvkthlREKKKDQGlleelaridsmslEKARKevtrlaklydsydKSIKTILNSCYGALAEKNFF 558
Cdd:PRK05762 472 ----------ERLWEG-----RDEAKREM-------------NKPLS-------------QAIKIIMNAFYGVLGSSGCR 510
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2438090180 559 FYDPDMAESITMTG-QFM------VRNLGETFVklltknYGkgtyllnqDTDSCYLTLKSAVDK 615
Cdd:PRK05762 511 FFDPRLASSITMRGhEIMkqtrelIEAQGYQVI------YG--------DTDSTFVWLGGAHDE 560
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
119-323 |
1.16e-22 |
|
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: 96.66 E-value: 1.16e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 119 DIETEVHDGFPDPSvaKEPINMITLL--QRGGKRFALTTCEVKKEKIDEEFGIETMMFSSEAEMLRHFIYLFTEVlEVDI 196
Cdd:cd05160 5 DIETTPPVGGPEPD--RDPIICITYAdsFDGVKVVFLLKTSTVGDDIEFIDGIEVEYFADEKELLKRFFDIIREY-DPDI 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 197 FVGWNSEKFDLPYIVNRIKRIlggdmakKLSPFGEVYIRSFIDDFGDEAVTAEILGVSHVDMLQFYKKFSHesQESYSLD 276
Cdd:cd05160 82 LTGYNIDDFDLPYLLKRAEAL-------GIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFK--LKSYTLD 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 2438090180 277 NIAKVELGVGKLVHESGIPGHLLYHEYPTDGLRYNIVDVVRLEEIDE 323
Cdd:cd05160 153 AVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQILE 199
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
380-740 |
2.18e-22 |
|
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: 98.98 E-value: 2.18e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 380 EGGFVSCNSPGLHDYITSYDYASLYPSTMMALNIGIESkrqkiedINPQYLIDNPEFNAPenlamgaNGQCYAKDKKSFL 459
Cdd:cd00145 4 EGGYVFDPIPGLYENVIVLDFKSLYPSIIITYNLSPTT-------LVGNGEIAAPEDYIG-------VGFRSPKDRKGLL 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 460 NEIISHGYDLRKKYKALKlfyqnletktdeglieavkthlrekkkdqglleelaridsmsleKARKEVTRLAKLYDSYDK 539
Cdd:cd00145 70 PRILEELLNFRDEAKKRM--------------------------------------------KAAKLAPEERVLYDNRQQ 105
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 540 SIKTILNSCYGALAEKNFFFYDPDMAESITMTGQFMVRNLgetfVKLLTKNYGKGTYLlnqDTDSCYLTLKSAVDKHFGD 619
Cdd:cd00145 106 ALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDT----IALVEEHGARVIYG---DTDSIFVSLPKMGTKEDAI 178
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 620 RDVSE-KEKIEwlckfadgpmkkvvqiandiankrlgsyEPERFDADREAVCRRGVFIKKKMYALAISDMEGVHyekPKL 698
Cdd:cd00145 179 KEGREiLQELA----------------------------DEHLLELEFEKVYLPFFLGKKKRYAGLDIWKGQDE---GKI 227
|
330 340 350 360
....*....|....*....|....*....|....*....|..
gi 2438090180 699 KIVGLQAKKKSTPAFFRSKMEIFFNILLGEGDKKKASEHVID 740
Cdd:cd00145 228 DIKGLETRRRDSPPLVKKFQKEVLELILEEERKVEAVKEYID 269
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
107-278 |
4.40e-17 |
|
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: 83.62 E-value: 4.40e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 107 ESTPEEYSIVYHDIETEVHDG-FPDPSVAKEPINMITLLQRGGKR--------FALTTC--------EVKKEKIDEEFGI 169
Cdd:pfam03104 149 EKEWPPLRVLSFDIECTSLPGkFPDAENVKDPIIQISCMLDGQGEpepeprflFTLRECdsediedfEYTPKPIYPGVKV 228
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 170 ETmmFSSEAEMLRHFIYLFTEVlEVDIFVGWNSEKFDLPYIVNRIK--RILGGDMAKKLSPFGEVYIRSFIDDFgDEAVT 247
Cdd:pfam03104 229 FE--FPSEKELLRRFFEFIRQY-DPDIITGYNGDNFDWPYILNRAKelYIVKLSSIGRLNRGGRSKVREIGFGT-RSYEK 304
|
170 180 190
....*....|....*....|....*....|.
gi 2438090180 248 AEILGVSHVDMLQFYKKFSHESqeSYSLDNI 278
Cdd:pfam03104 305 VKISGRLHLDLYRVIKRDYKLP--SYKLNAV 333
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
176-784 |
3.86e-14 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 76.65 E-value: 3.86e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 176 SEAEMLRHfiyLFTEVLEVDIFVGWNSEKFDLPYIVNRikrilggdmAKKLSPFGEVYIRSFIDDFGdeavtaeilgvsH 255
Cdd:PRK05761 209 SEKELLAE---LFDIILEYPPVVTFNGDNFDLPYLYNR---------ALKLGIPKEEIPIEPGRAGI------------H 264
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 256 VDMlqfYKKFSHESQESY-----------SLDNIAKVELGVGKLVHESGIPGHLLYHEyptdgLRYNIVDVVRLEEID-- 322
Cdd:PRK05761 265 IDL---YKFFQNKAVRSYafygkyrhreaRLDAVGRALLGISKVELETNISELDLEEL-----AEYNFRDAEITLKLTff 336
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 323 EKKGIIDLAITVANMSKTNVSDTmfsTRL----WMSMIYDYLSQRGRYF-----EFSRERNE-YRKIE-------GGFVS 385
Cdd:PRK05761 337 NNELVLKLILLLSRISKLPIEEL---SRAtistWISNLEYWEHRKRGWLipwkeDILRLDHEvYKKAIikgkkyrGGLVF 413
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 386 CNSPGLHDYITSYDYASLYPSTMMALNIGIESkrqkiedinpqylIDNPEFNAPENLAMGANGQCYAKDKKSFLNEIISH 465
Cdd:PRK05761 414 QPPPGIFFNVYVLDFASLYPSIIVKWNLSPET-------------VRIPECKCHYDDEVPELGHSVCDDRPGLTSVLVGL 480
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 466 GYDLRKKYKalklfyqnletktdeglieavkthlREKKKDQGLLEELARidsmslekarkevtrlakLYDSYDKSIKTIL 545
Cdd:PRK05761 481 LRDFRVKIY-------------------------KKKAKDPNLDEERRA------------------WYDVVQRALKVFL 517
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 546 NSCYGALAEKNFFFYDPDMAESITMTGQFMvrnLGETfVKLLTKNygkGTYLLNQDTDSCYLTlksavdkhfgdrdVSEK 625
Cdd:PRK05761 518 NASYGVFGAENFKLYRIEVAESITALGREI---LLST-KKKAEEL---GLKVLYGDTDSLFVW-------------GPTK 577
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 626 EKIEWLCKFADgpmkkvvqiandianKRLGsyeperFDADREAVCRRGVF--IKKKMYalaisdmeGVHYEKpKLKIVGL 703
Cdd:PRK05761 578 ESLEELIKEIE---------------ERTG------IDLEVDKTYDWVAFsgLKKNYF--------GVLKDG-KVKIKGI 627
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 704 QAKKKSTPAF----FRSKMEIFFNILLGEgDKKKASEHVIDVENEFRNS------PLDEIAgnfsvsdISSKIDDSEKGY 773
Cdd:PRK05761 628 VAKKRNTPEFvkelQREVLEVLKSIRSPE-DVEKVKDEIEDVLKRYYEKlrakdyPLDELA-------IRVRLSKPLDEY 699
|
650
....*....|.
gi 2438090180 774 VKGVHINARAA 784
Cdd:PRK05761 700 TKNTPQHVKAA 710
|
|
| DNA_polB_B1_exo |
cd05783 |
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ... |
119-294 |
5.60e-13 |
|
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: 68.50 E-value: 5.60e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 119 DIE--TEVHDGFPDPSVAKEPINMITLLQRGGKR--FALTTCEVKKEKIDEEFGIETMMFSSEAEMLRHFiylFTEVLEV 194
Cdd:cd05783 11 DIEvyTPIKGRIPDPKTAEYPVISVALAGSDGLKrvLVLKREGVEGLEGLLPEGAEVEFFDSEKELIREA---FKIISEY 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 195 DIFVGWNSEKFDLPYIVNRIKRiLGgdMAKKLSPfgevyirsfIDDFGDEavtAEILGVSHVDMlqfYKKFSHESQESY- 273
Cdd:cd05783 88 PIVLTFNGDNFDLPYLYNRALK-LG--IPKEEIP---------IYLKRDY---ATLKHGIHIDL---YKFFSNRAIQVYa 149
|
170 180
....*....|....*....|....*....
gi 2438090180 274 --------SLDNIAKVELGVGKLVHESGI 294
Cdd:cd05783 150 fgnkyreyTLDAVAKALLGEGKVELEKNI 178
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
380-846 |
6.56e-13 |
|
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: 71.20 E-value: 6.56e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 380 EGGFVSCNSPGLHDYITSYDYASLYPSTMMALNIGieskrqkiedinPQYLIDNPEFNAPENLAMGangqcyakdkksfl 459
Cdd:cd05536 5 EGGIVLEPEKGLHENIVVLDFSSLYPSIMIKYNIS------------PDTLVREGCEDCDVEPQVG-------------- 58
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 460 neiishgYDLRKKYKAlklFYQNLEtktdEGLIEavkthLREKKKdqgllEELARIDSMSLEKarkevtrlaKLYDSYDK 539
Cdd:cd05536 59 -------HKFRKDPPG---FIPSVL----EDLLE-----ERRRIK-----EKMKKLDPESEEY---------KLLDERQR 105
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 540 SIKTILNSCYGALAEKNFFFYDPDMAESITMTGqfmvRNLGETFVKLLTKnygKGTYLLNQDTDSCYLTLKSavdkhfgd 619
Cdd:cd05536 106 AIKILANSFYGYMGWANARWYCKECAEAVTAWG----REYIKTTIKIAEE---KGFKVIYGDTDSLFVKIDG-------- 170
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 620 rdvsekekiewlckfADGPMKKVVQIANDIaNKRLGsyeperFDADREAVCRRGVFIKKKMYALAISDmegvhyekPKLK 699
Cdd:cd05536 171 ---------------ADAVKKKVKKLLKYI-NEELP------LELEIEKFYKRGFFVTKKRYAGLTED--------GKID 220
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 700 IVGLQAKKKSTPAFFRSKMEIFFNILLGEGDKKKASEHVIDVENEFRNspldeiaGNFSVSD--ISSKIDDSEKGY-VKG 776
Cdd:cd05536 221 VVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVIEKLKR-------GEVPPEKlvIWKQLTKDLSEYkATG 293
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2438090180 777 VHInaraaivsnrVVASDEKARLYIepIRNGDKIKMLPLRLPNPTKENIIAwkedfPDVFREKK---IDQYID 846
Cdd:cd05536 294 PHV----------AAAKKLAKRGYK--VRPGTKIGYVIVKGSGKISDRAYP-----YDMVDEKHkydAEYYID 349
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
111-258 |
9.40e-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: 61.99 E-value: 9.40e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 111 EEYSIVYHDIETEVHDGFPDPsvAKEPINMITLLQRGGKRfALTTcevkkEKIDEEFgIETMmfSSEAEMLRHFIYLFTE 190
Cdd:cd05780 1 EDLKILSFDIEVLNHEGEPNP--EKDPIIMISFADEGGNK-VITW-----KKFDLPF-VEVV--KTEKEMIKRFIEIVKE 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 191 VlEVDIFVGWNSEKFDLPYIVNR-----IKRILGGD----------MAKKLSPFGEVYI------RSFI--DDFGDEAVT 247
Cdd:cd05780 70 K-DPDVIYTYNGDNFDFPYLKKRaeklgIELDLGRDgseikiqrggFNNASEIKGRIHVdlypvaRRTLnlTRYTLERVY 148
|
170
....*....|.
gi 2438090180 248 AEILGVSHVDM 258
Cdd:cd05780 149 EELFGIEKEDV 159
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
353-746 |
1.92e-10 |
|
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: 64.17 E-value: 1.92e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 353 MSMIYDYLSQRGR-YFEFSRERNEYRKIEGGFVSCNSPGLHD-YITSYDYASLYPSTMMALNI--------GIESKRQKI 422
Cdd:pfam00136 16 ESCLLRLALEEGFiLPDRPSAKGDEDGYQGATVIEPKKGFYDkPVLVLDFNSLYPSIIQAHNLcyttlvrsVDEANNLPP 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 423 EDINPQYLIdnpefnapenlamGANGQCYAKD--KKSFLNEIISHGYDLRKKYKALklfyqnLETKTDEglieavkthlr 500
Cdd:pfam00136 96 EDNLITVEC-------------TPRGVYFVKDhvREGLLPKLLKDLLAKRKAIKKL------LKEETDP----------- 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 501 ekkkdqglleelaridsmslekarkevtRLAKLYDSYDKSIKTILNSCYGALAEKNFFFYDPDMAESITMTGQFMVRNLG 580
Cdd:pfam00136 146 ----------------------------FERAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTK 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 581 ETFVKLLTKN----YGkgtyllnqDTDSCYLtlksavdkHFGDRDvsekekiewlckfadgpMKKVVQIANDIA---NKR 653
Cdd:pfam00136 198 DLVEGMYTYNfrviYG--------DTDSVFI--------EFGGKD-----------------VEEAMKIGDELAehvNQD 244
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 654 LGsyePERFDADREAVCRRGVFIKKKMYAlaisdmeGVHYEKP----KLKIVGLQAKKKSTPAFFRSKMEIFFNILLGEG 729
Cdd:pfam00136 245 LF---KSPIKLEFEKVYKPLLLISKKKYA-------GLKYTAPsnfnKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSDR 314
|
410
....*....|....*..
gi 2438090180 730 DKKKASEHVIDVENEFR 746
Cdd:pfam00136 315 GLPVGLEFVISILNDAR 331
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
381-614 |
6.13e-09 |
|
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: 58.82 E-value: 6.13e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 381 GGFVSCNSPGLHDYITSYDYASLYPSTMMALNigieskrqkiedINPQYLIDNPEFNAPENLAMGANGQCYAKDkKSFLN 460
Cdd:cd05537 5 GGYVMDSKPGLYKNVLVLDFKSLYPSIIRTFL------------IDPLGLIEGLKAPDPEDLIPGFLGARFSRE-KHILP 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 461 EIISHgydlrkkykalkLFyqnletktdeglieavktHLREKKKDQGlleelariDSMsLEKArkevtrlaklydsydks 540
Cdd:cd05537 72 DLIAR------------LW------------------AARDEAKREK--------NAP-LSQA----------------- 95
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 541 IKTILNSCYGALAEKNFFFYDPDMAESITMTGQFMVR-------NLGETFVklltknYGkgtyllnqDTDSCYLTLKSAV 613
Cdd:cd05537 96 IKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKqtrawieQQGYQVI------YG--------DTDSTFVWLGEEL 161
|
.
gi 2438090180 614 D 614
Cdd:cd05537 162 D 162
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
377-754 |
9.20e-09 |
|
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: 58.52 E-value: 9.20e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 377 RKIEGGFVSCNSPGLHDYITSYDYASLYPSTMMALNIGIESkrqkiedINPQYLiDNPEFNAPENlamganGQCYAKDKK 456
Cdd:cd05530 11 KKYRGAIVLEPPPGIFFNVVVLDFASLYPSIIKVWNLSYET-------VNCPHC-ECKTNEVPEV------GHWVCKKRP 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 457 SFLNEIISHGYDLR-KKYKalklfyqnletktdeglieavkthlrEKKKDQGLLEElaridsmslEKArkevtrlakLYD 535
Cdd:cd05530 77 GITSQIIGLLRDLRvKIYK--------------------------KKAKDKSLDEE---------MRQ---------WYD 112
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 536 SYDKSIKTILNSCYGALAEKNFFFYDPDMAESITMTGQFMVRNLGETFVKL-LTKNYGkgtyllnqDTDSCYLtlksavd 614
Cdd:cd05530 113 VVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIITSTIKKARELgLKVLYG--------DTDSLFL------- 177
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 615 khfgdRDVSEkEKIEWLCKFADgpmkkvvqiandianKRLGsyeperFDADREAVCRRGVFIK-KKMYAlaisdmeGVhY 693
Cdd:cd05530 178 -----WNPPQ-EQLEDLVEWVE---------------KELG------LDLELDKEYRYVVFSGlKKNYL-------GV-T 222
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 694 EKPKLKIVGLQAKKKSTPAFFRSKMEIFFNILLG-------EGDKKKASEHVIDVENEFRNS--PLDEIA 754
Cdd:cd05530 223 KDGSVDIKGLLGKKRNTPEFVKELFYEVIEILSAvnspedfEKAREKIRDIVKGVYKRLKKKeyTLDQLA 292
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
119-315 |
1.60e-07 |
|
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarchaea. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B-DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.
Pssm-ID: 99824 [Multi-domain] Cd Length: 188 Bit Score: 52.33 E-value: 1.60e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 119 DIETEVHDGFPDPSvaKEPINMITLLQRGGKRFALTTcevkkEKIDEEfgietmmfsseaEMLRHFIYLFTEvLEVDIFV 198
Cdd:cd05781 9 DIEVYSKYGTPNPR--RDPIIVISLATSNGDVEFILA-----EGLDDR------------KIIREFVKYVKE-YDPDIIV 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 199 GWNSEKFDLPYIVNRIKRI-LGGDMAKKLS--PFGEVYirsfiddfGDEAVTaeilGVSHVDMLQFYKKFSheSQESYSL 275
Cdd:cd05781 69 GYNSNAFDWPYLVERARVLgVKLDVGRRGGsePSTGVY--------GHYSIT----GRLNVDLYDFAEEIP--EVKVKTL 134
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 2438090180 276 DNIAKvELGVGKLVHESGIPGHLLYhEYPTDG------LRYNIVDV 315
Cdd:cd05781 135 ENVAE-YLGVMKKSERVLIEWYRIY-EYWDDEkkrdilLKYNRDDA 178
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
119-215 |
1.83e-07 |
|
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: 52.96 E-value: 1.83e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 119 DIETEVHDG-FPDPsvAKEPI----NMITLLQRGGKR----FALTTCEvkkeKIdeeFGIETMMFSSEAEMLRHFIYLFT 189
Cdd:cd05777 13 DIECAGRKGvFPEP--EKDPViqiaNVVTRQGEGEPFirniFTLKTCA----PI---VGAQVFSFETEEELLLAWRDFVQ 83
|
90 100
....*....|....*....|....*.
gi 2438090180 190 EVlEVDIFVGWNSEKFDLPYIVNRIK 215
Cdd:cd05777 84 EV-DPDIITGYNICNFDLPYLLERAK 108
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
174-321 |
2.31e-06 |
|
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: 49.10 E-value: 2.31e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 174 FSSEAEMLRHFIYLFTEVlEVDIFVGWNSEKFDLPYIVNRIKRiLGgdMAKKLSPFGEV-YIRSfiDDFGDEAvTAEILG 252
Cdd:cd05784 48 FADEKSLLLALIAWFAQY-DPDIIIGWNVINFDLRLLQRRAEA-HG--LPLRLGRGGSPlNWRQ--SGKPGQG-FLSLPG 120
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2438090180 253 ---VSHVDMLQ--FYkKFshesqESYSLDNIAKVELGVGKLVHESGIPGHL---LYHEYPTDGLRYNIVDVVRLEEI 321
Cdd:cd05784 121 rvvLDGIDALKtaTY-HF-----ESFSLENVAQELLGEGKLIHDVDDRGAEierLFREDKLALARYNLQDCELVWRI 191
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
398-576 |
1.11e-05 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 49.25 E-value: 1.11e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 398 YDYASLYPSTMMALN------IGIESKRQKIE-DINPQYLIDNpeFNAPENLAMgangQCyAKDKKSFLNEIIShgYDLR 470
Cdd:PHA03036 550 FDYNSLYPNVCIFGNlspetlVGVVVNDNRLEaEINKQELRRK--YPYPRYIYV----HC-EPRSPDLVSEIAV--FDRR 620
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 471 KkykalklfyqnletktdEGLI-EAVKTHLREKKKDQGLLEElariDSMSLEKArkevtrlakLYDSYDKSIKTILNSCY 549
Cdd:PHA03036 621 I-----------------EGIIpKLLKTFLEERARYKKLLKE----ATSSVEKA---------IYDSMQYTYKIVANSVY 670
|
170 180
....*....|....*....|....*..
gi 2438090180 550 GALAEKNFFFYDPDMAESITMTGQFMV 576
Cdd:PHA03036 671 GLMGFRNSALYSYASAKSCTAIGRNMI 697
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
109-476 |
1.32e-05 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 49.25 E-value: 1.32e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 109 TPEEYSIVYHDIETEVHDG--FPDPSvaKEPINMI-TLLQRGGKR--------FALTTCevkkekiDEEFGIETMMFSSE 177
Cdd:PTZ00166 260 TIAPLRILSFDIECIKLKGlgFPEAE--NDPVIQIsSVVTNQGDEeepltkfiFTLKEC-------ASIAGANVLSFETE 330
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 178 AEMLRHFIYLFTEVlEVDIFVGWNSEKFDLPYIVNRIKrilggdmAKKLSPFGEV-YIRSFIDDFGDEAVTAEILGvshv 256
Cdd:PTZ00166 331 KELLLAWAEFVIAV-DPDFLTGYNIINFDLPYLLNRAK-------ALKLNDFKYLgRIKSTRSVIKDSKFSSKQMG---- 398
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 257 dmlqfykkfSHESQE----------------------SYSLDNIAKVELGVGKL-VHESGIPGhlLYHEYPTDGLR---Y 310
Cdd:PTZ00166 399 ---------TRESKEiniegriqfdvmdlirrdyklkSYSLNYVSFEFLKEQKEdVHYSIISD--LQNGSPETRRRiavY 467
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 311 NIVD-VVRLEEIDEkkgiidLAITVANMSKTNVSDTMFSTRLW-------MSMIYDYLSQRGRY---FEFSRERNEyRKI 379
Cdd:PTZ00166 468 CLKDaILPLRLLDK------LLLIYNYVEMARVTGTPIGWLLTrgqqikvTSQLLRKCKKLNYViptVKYSGGGSE-EKY 540
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 380 EGGFVSCNSPGLHDY-ITSYDYASLYPSTMMALNIGIES--KRQKIEDINPQYLIDNPefnapenlamgaNGQCYAKD-- 454
Cdd:PTZ00166 541 EGATVLEPKKGFYDEpIATLDFASLYPSIMIAHNLCYSTlvPPNDANNYPEDTYVTTP------------TGDKFVKKev 608
|
410 420
....*....|....*....|..
gi 2438090180 455 KKSFLNEIISHGYDLRKKYKAL 476
Cdd:PTZ00166 609 RKGILPLIVEELIAARKKAKKE 630
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
415-793 |
2.21e-05 |
|
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA polymerases.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273159 [Multi-domain] Cd Length: 1172 Bit Score: 48.51 E-value: 2.21e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 415 IESKRQKIEDinpqyliDNPEFNAPENLAMGANGQCYAKDKKSFLNEIISHGYDLRKKYKALKLFYQNLETKTDEGLIEA 494
Cdd:TIGR00592 771 IFRKQQKLGD-------EDEEIDGYKKGKKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQKVDED 843
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 495 VKTHLREKKKDQGLLEELARidsmSLEKARKEVTRLAKL---------YDSYDKSIKTILNSCYGALAEKNFFFYDPDMA 565
Cdd:TIGR00592 844 ELPELPDSELEMGILPRELR----KLVERRKEVKKLMKQdlnpdlrlqYDIRQKALKLTANSMYGCLGYSKSRFYAKPLA 919
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 566 ESITMTGQFMVRNLGETFVKLLTKN-YGkgtyllnqDTDSCYLTLKSavdkhfgdrdvsekEKIEwlckfadgpmkKVVQ 644
Cdd:TIGR00592 920 ALVTAKGREILEHTRQLVEEMNLEViYG--------DTDSIMINTPG--------------TKYE-----------EVFK 966
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 645 IANDIANKRLGSYEPErfDADREAVCRRGVFIKKKMYALAISDMEGVHYEKPKLKIVGLQAKKKSTPAFFRSKMEIFFNI 724
Cdd:TIGR00592 967 IGKEFKSEVNKLYKLL--ELDIDGVFKRLLLLKKKKYAAIKVEGDSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDT 1044
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2438090180 725 LLGEGDKKKASEHVIDVENEFRNSPLDeiaGNFSVS--DISSKIDDSEKGYVKG-----VHINARAAIVSNRVVAS 793
Cdd:TIGR00592 1045 ILSDKDVEEAVEEVQEVLEKIGKNVLN---GEVPLEkfVINKQLTRDPKDYPDGaslphVHVALRINARGGRKVKA 1117
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
123-227 |
8.66e-05 |
|
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase 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. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 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.
Pssm-ID: 99821 [Multi-domain] Cd Length: 231 Bit Score: 44.92 E-value: 8.66e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 123 EVH-----DGFPDPsvAKEPINMI---------TLLQRGGKRFALTTCEVKKEKIDEEF-----GIETMMFSSEAEMLRH 183
Cdd:cd05778 10 EVHvntrgDLLPDP--EFDPISAIfycidddvsPFILDANKVGVIIVDELKSNASNGRIrsglsGIPVEVVESELELFEE 87
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 2438090180 184 FIYLFtEVLEVDIFVGWNSEKFDLPYIVNRIKRILGGDMAKKLS 227
Cdd:cd05778 88 LIDLV-RRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDEIS 130
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
381-477 |
7.85e-04 |
|
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: 42.72 E-value: 7.85e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 381 GGFVSCNSPGLHDYITSYDYASLYPSTMMALNIGIESkrqkiedinpqylIDNPEfnaPENLAMGANGQCYAKDKKSFLN 460
Cdd:cd05531 7 GGLVFQPEPGLYENVAQIDFSSMYPSIIVKYNISPET-------------INCRC---CECRDHVYLGHRICLKRRGFLP 70
|
90
....*....|....*..
gi 2438090180 461 EIISHGYDLRKKYKALK 477
Cdd:cd05531 71 EVLEPLLERRLEYKRLK 87
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
508-844 |
1.46e-03 |
|
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: 41.70 E-value: 1.46e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 508 LLEELARIDSMSLEKARKEVTRLAKLY-DSYDKSIKTILNSCYGALAEKNFFFYDPDMAESITMTGQFMVRNLGETFVKl 586
Cdd:cd05538 50 LLKYLVELRLAAKESARAAARPAERDAfKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRR- 128
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 587 ltknygKGTYLLNQDTDSCYLTLKSAVDKhfgdrdvseKEKIEWLCKFADGPMKKVVQIANDiankrlgsyepERFDAdr 666
Cdd:cd05538 129 ------RGATPVEVDTDGIYFIPPNGVDT---------EDEEEELVRELSSTLPKGITVEFD-----------GRYRA-- 180
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 667 eavcrrgVFI-KKKMYALAISDmegvhyekPKLKIVGLQAKKKSTPAFFRSKMEIFFNILLgEGDKKKASEHVIDVENEF 745
Cdd:cd05538 181 -------MFSyKIKNYALLDYD--------GKLIVKGSAFRSRGIEPFLREFLREAVRLLL-QGDGAGVHDLYEDYLRRL 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 746 RNSpldeiagNFSVSDISS--KIDDSEKGYVKGVHINARaaivsNRVVASdEKARLYIEPIRNGDKIKMLPLRLPNPTK- 822
Cdd:cd05538 245 RSH-------ELPISDLARteTLKESPEEYLQKVRAGKR-----NPAAAY-EIALARPREWRAGDRVTYYVSGTGKGVSv 311
|
330 340
....*....|....*....|....*....
gi 2438090180 823 -ENI--IA-WKEDFPDV---FREKKIDQY 844
Cdd:cd05538 312 yENCrlVAdYDPAHPDEntgFYAERLLQL 340
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
377-489 |
4.48e-03 |
|
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: 40.33 E-value: 4.48e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 377 RKIEGGFVSCNSPGLHDY-ITSYDYASLYPSTMMALNIGIESkrqkiedinpqyLIDNPEFN--APENLAMGANGQCYAK 453
Cdd:cd05533 1 EQYEGATVIEPIKGYYDVpIATLDFASLYPSIMMAHNLCYTT------------LLNKNTAKklPPEDYIKTPNGDYFVK 68
|
90 100 110
....*....|....*....|....*....|....*...
gi 2438090180 454 D--KKSFLNEIISHGYDLRKKYKALklfyqnLETKTDE 489
Cdd:cd05533 69 SsvRKGLLPEILEELLAARKRAKKD------LKEETDP 100
|
|
| DNA_polB_like1_exo |
cd05782 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
115-213 |
4.87e-03 |
|
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: 99825 [Multi-domain] Cd Length: 208 Bit Score: 39.15 E-value: 4.87e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2438090180 115 IVYHDIET-------EVHDGFPDPSVAKEPINMITLLQRGGKRFAL--------TTCEVKKEKIDEEFGIETMMFSSEAE 179
Cdd:cd05782 1 ILVFDIETvpdvdlgRRLYLLLELDDLEVLEKRFAQRLEKSGSDFLplpfhkvvSISALYRDDDGGFLKVRTLDGADEKE 80
|
90 100 110
....*....|....*....|....*....|....
gi 2438090180 180 MLRHFIYLFTEVLEVdiFVGWNSEKFDLPYIVNR 213
Cdd:cd05782 81 LLEDFFQLIEKKNPR--LVSFNGRGFDLPVLHLR 112
|
|
| |
