|
Name |
Accession |
Description |
Interval |
E-value |
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
523-994 |
0e+00 |
|
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: 620.01 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 523 IPCRRVLDDGQQIRVFSCLLAAAQKENFILP-MPSA-SDRDGYQGATVIQPLSGFYNSPVLVVDFASLYPSIIQAHNLCY 600
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPdRPSAkGDEDGYQGATVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 601 STMITPGEEHRlaGLRPGEDYESFRLTGGVYHFVKKHVHESFLASLLTSWLAKRKAIKKLLAACEDPRQRTILDKQQLAI 680
Cdd:pfam00136 81 TTLVRSVDEAN--NLPPEDNLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFERAILDKQQLAL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 681 KCTCNAVYGFTGVANGLFPCLSIAETVTLQGRTMLERAKAFVEALSPANlqalapspdawaplnpegqLRVIYGDTDSLF 760
Cdd:pfam00136 159 KITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYN-------------------FRVIYGDTDSVF 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 761 IECRGFSESETLRFAEALAAHTTRSLFVAPISLEAEKTFSCLMLITKKRYVGVLTD-----GKTLMKGVELVRKTACKFV 835
Cdd:pfam00136 220 IEFGGKDVEEAMKIGDELAEHVNQDLFKSPIKLEFEKVYKPLLLISKKKYAGLKYTapsnfNKLDMKGVDLVRRDNCPLV 299
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 836 QTRCRRVLDLVLADarvkeaasllshrpfqesftQGLPVGFLPVIDILNQAYTDLREGRVPMGELCFSTELSRKLSAYKS 915
Cdd:pfam00136 300 KEVIKKVLDLLLSD--------------------RGLPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNYKS 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 916 TQMPHLAVYQKFVERNEELPQIHDRIQYVFVEPKGGVKGARKTEMAEDPAYAERHGVPVAVDHYFD-KLLQGAANILQCL 994
Cdd:pfam00136 360 KNLPHVEVALRMNKRNGEAPEVGDRIPYVIVKAAKGLKNLLIYERAEDPEYVLENNLPIDYEYYFSnQLIPPVARLLEPI 439
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
78-983 |
6.62e-167 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 517.66 E-value: 6.62e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 78 EGTARPEADTHGSPLDFhVYDILETVYTHEKCAVIPSDKQGYVVPCGI---VIKLLGRRKaDGASVCVNVFGQQAYFYAS 154
Cdd:PTZ00166 26 FSKLRRPLPPISLQKDL-VFFQLDADYTEKDDKSQGNPHNTVSGVRHVevpIIRLYGVTK-EGHSVLVNVHNFFPYFYIE 103
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 155 APQGLDVEFAVL------SALKASTFDRRTPCRV-SVEKVTRRSIMGY-GNHAGDYHKITLSHPNSVCHVATWLQD---- 222
Cdd:PTZ00166 104 APPNFLPEDSQKlkrelnAQLSEQSQFKKYQNTVlDIEIVKKESLMYYkGNGEKDFLKITVQLPKMVPRLRSLIESgvvv 183
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 223 --KHGCRI-----FEANVDATRRFVLDNDFVTFGWYSCRRA---IPRLQHRDSYAELEYDCEVGDLSVRREDSSW---PS 289
Cdd:PTZ00166 184 cgGGWDGIrlfqtYESNVPFVLRFLIDNNITGGSWLTLPKGkykIRPPKKKTSTCQIEVDCSYEDLIPLPPEGEYltiAP 263
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 290 YQALAFDIECLGE--EGFPTATNeaDLILQISCVLWSTGEEAGRYRRILLTLGTCEDIEGVEVYEFPSELDMLYAFFQLI 367
Cdd:PTZ00166 264 LRILSFDIECIKLkgLGFPEAEN--DPVIQISSVVTNQGDEEEPLTKFIFTLKECASIAGANVLSFETEKELLLAWAEFV 341
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 368 RDLSVEIVTGYNVANFDWPYILDRARHIYSINPASLGKIRaGGVCEVRRPHDAGKGF-LRANTKVRITGLIPIDMYAVCR 446
Cdd:PTZ00166 342 IAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIK-STRSVIKDSKFSSKQMgTRESKEINIEGRIQFDVMDLIR 420
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 447 DKLSLSDYKLDTVARHLLGAKKEDVHYKEIPRLFAAGPEGRRRLGMYCVQDSALVMDLLNHFVIHVEVAEIAKIAHIPCR 526
Cdd:PTZ00166 421 RDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIG 500
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 527 RVLDDGQQIRVFSCLLAAAQKENFILP---MPSASDRDGYQGATVIQPLSGFYNSPVLVVDFASLYPSIIQAHNLCYSTM 603
Cdd:PTZ00166 501 WLLTRGQQIKVTSQLLRKCKKLNYVIPtvkYSGGGSEEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTL 580
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 604 ITPGEehrLAGLRPgedyESFRLTGGVYHFVKKHVHESFLASLLTSWLAKRKAIKKLLAACEDPRQRTILDKQQLAIKCT 683
Cdd:PTZ00166 581 VPPND---ANNYPE----DTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLLKKVLNGRQLALKIS 653
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 684 CNAVYGFTG-VANGLFPCLSIAETVTLQGRTMLERAKAFVEALSPanlQALAPSPDAwaplnpegqlRVIYGDTDSLFIE 762
Cdd:PTZ00166 654 ANSVYGYTGaQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKHYT---KANGYKHDA----------TVIYGDTDSVMVK 720
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 763 CRGFSESETLRFAEAlAAHTTRSLFVAPISLEAEKTFSCLMLITKKRYVGVL-----TDGKTLMKGVELVRKTACKFVQT 837
Cdd:PTZ00166 721 FGTDDIQEAMDLGKE-AAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAGLLytnpeKYDKIDCKGIETVRRDNCLLVQQ 799
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 838 RCRRVLDLVLADARVKEAasllshrpfqESFTQGlpvgflpVIdilnqayTDLREGRVPMGELCFSTELSRklSAYKsTQ 917
Cdd:PTZ00166 800 MVETVLNKILIEKDVESA----------IEFTKG-------KI-------SDLLQNRIDISLLVITKSLGK--DDYE-GR 852
|
890 900 910 920 930 940
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1386448495 918 MPHLAVYQKFVERNE-ELPQIHDRIQYVFVEpkgGVKGARKTEMAEDPAYAERHGVPVAVDHYFDKL 983
Cdd:PTZ00166 853 LAHVELAKKLRQRDPgSAPNVGDRVSYVIVK---GAKGAPQYERAEDPLYVLENNIPIDTQYYLDQI 916
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
288-765 |
6.63e-166 |
|
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: 495.13 E-value: 6.63e-166
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 288 PSYQALAFDIECL-GEEGFPTATNEADLILQISCVLWStGEEAGRYRRILLTLGTCEDIEGVEVYEFPSELDMLYAFFQL 366
Cdd:smart00486 1 PPLKILSFDIETYtDGGNFPDAEIFDDEIIQISLVIND-GDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEF 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 367 IRDLSVEIVTGYNVANFDWPYILDRARHIYSINPASLGKIRAGGVCEVRRPHDAGKGFLRANTKVRITGLIPIDMYAVCR 446
Cdd:smart00486 80 IKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGLRIPNKKPLFGSKSFGLSDIKVYIKGRLVIDLYRLYK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 447 DKLSLSDYKLDTVARHLLGAKKEDVHYKEIPRLFAAGPEGRRRLGMYCVQDSALVMDLLNHFVIHVEVAEIAKIAHIPCR 526
Cdd:smart00486 160 NKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLR 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 527 RVLDDGQQIRVFSCLLAAAQKENFILPMPSASDRD----------GYQGATVIQPLSGFYNSPVLVVDFASLYPSIIQAH 596
Cdd:smart00486 240 RTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKgsepdlkkkvKYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAH 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 597 NLCYSTMITPGEEHRLAGLRPGEDYESFRLTGG-VYHFVKKHVHESFLASLLTSWLAKRKAIKKLLAACEDP--RQRTIL 673
Cdd:smart00486 320 NLCYSTLVGVGEVVIKGDLIIPEDLLTIKYEKGnKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDEseELKKLL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 674 DKQQLAIKCTCNAVYGFTGVANGLFPCLSIAETVTLQGRTMLERAKAFVEALSpanlqalapspdawaplNPEGQLRVIY 753
Cdd:smart00486 400 DSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENG-----------------YPKPGFKVIY 462
|
490
....*....|..
gi 1386448495 754 GDTDSLFIECRG 765
Cdd:smart00486 463 GDTDSIFVTKPG 474
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
124-994 |
1.73e-132 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 419.23 E-value: 1.73e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 124 GIVIKLLGRRkADGASVCVNVFGQQAYFYASAPQGLDVEfAVLSALKAstfdrrtpcRVSVEKVTRRSIMGygnHAGDYH 203
Cdd:COG0417 18 KPVIELWGRT-EDGPSVLLDVTGFRPYFYVPLPDEEKLE-ELLRDIKE---------ITEVEPVKLKSFFG---EPVPVL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 204 KITLSHPNSVCHVATWLQDkHGCRIFEANVDATRRFVLDNDFVTFGWYSCRRaiprlQHRDSYAELEYDCEVGDlsvrRE 283
Cdd:COG0417 84 KIYTRDPRDVRELRDRLKE-GGIDVYEADIRFHDRYLIDRFLTPGVWYEGEV-----EEDGGKLDYEVKENPRL----KP 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 284 DSSWPSYQALAFDIECLGEEGFPTATNEADLILqIScvLWStgeEAGRYRRILLTlgtcEDIEGVEVYEFPSELDMLYAF 363
Cdd:COG0417 154 EDYRPKLKVLSFDIEVSTPRGFPDPERDGPIIS-IG--LAG---SDGEKKVLMLG----REGVDFEVEYFDDEKALLEAF 223
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 364 FQLIRDLSVEIVTGYNVANFDWPYILDRARhIYSINPAsLGkiRAGGVCEVRRPhdagkgflRANTKVRITGLIPIDMY- 442
Cdd:COG0417 224 FEIIREYDPDIIIGWNVDNFDLPYLQKRAE-RLGIPLD-LG--RDGSEPSWREH--------GGQGFASIPGRVVIDLYd 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 443 AVCRDKLSLSDYKLDTVARHLLGAKKEDVHYKEIPRLFAagpEGRRRLGMYCVQDSALVMDLLNH-----FVIhvevaEI 517
Cdd:COG0417 292 ALKSATYKFKSYSLDAVAEELLGEGKLIVDGGEIERLWD---DDKPALAEYNLRDAELTLRIFEKtlllpFLI-----EL 363
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 518 AKIAHIPCRRVLDDGQQIRVFSCLLAAAQKENFILPMPSASDRDGYQGATVIQPLSGFYNSpVLVVDFASLYPSIIQAHN 597
Cdd:COG0417 364 SRITGLPLDDVGRAGSSAAFENLLLPEAHRRGYLAPNKGEIKGEAYPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFN 442
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 598 LCYSTMITPGEEhrlaglRPGEDYESfrlTGGVYHFVKKHVHesFLASLLTSWLAKRKAIKKLLA-ACEDPRQRTILDKQ 676
Cdd:COG0417 443 ISPETLVEGGEE------PCGDEDVA---PGFGHRFCREPKG--ILPSILEELWDERDEAKKKMKkAKPDSEEYRLYDAL 511
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 677 QLAIKCTCNAVYGFTGVANGLFPCLSIAETVTLQGRTMLERAKAFVEALspanlqalapspdawaplnpeGqLRVIYGDT 756
Cdd:COG0417 512 QQALKILMNSFYGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEEL---------------------G-YKVIYGDT 569
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 757 DSLFIECRGFSESETLRFAEALAAHTTRSLfVAPISLEAEKTFS-CLMLITKKRYVGVLTDGKTLMKGVELVRKTACKFV 835
Cdd:COG0417 570 DSLFVWLPKASLEEAIEIGKELAEEINAWW-PSGLELEFEKHYRrFFFPGSKKRYAGLTEDGKIDIKGLEAVRSDWTELA 648
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 836 QTRCRRVLDLVLADARVKEAasllshrpfqesftqglpvgflpvIDILNQAYTDLREGRVPMGELCFSTELSRKLSAYKS 915
Cdd:COG0417 649 KEFQQEVYERILKEEDVEKA------------------------VEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSEYEK 704
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 916 TQMPHLAVYQKFVERNEElPQIHDRIQYVFVEPKGGVkgarktemaEDPAYAERHGVPVAVDHYFDKLLQGAAN-ILQCL 994
Cdd:COG0417 705 NVPPHVRAARKLDERGRP-YQRGDKISYVITKGGGRV---------EPVELAKERESEIDYDYYIEKQLKPTADrILEAF 774
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
136-459 |
8.86e-115 |
|
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: 356.73 E-value: 8.86e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 136 DGASVCVNVFGQQAYFYASAPQGLDVEfAVLSALKASTFDRRTPcrVSVEKVTRRSIMGYGNHAGDYHKITLSHPNSVCH 215
Cdd:pfam03104 4 EGVSVCVNVFGFKPYFYCLAPDGKELE-EVIEEIKELYEGLDKI--EKIELKLKKSLYGYEEDPVPYLKVSFANPRPLLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 216 VATWLQDKHGCRIFEANVDATRRFVLDNDFVTFGWYSCRRAIPRLQHRDSYAELEYDCEVGDLSVRREDSSWPSYQALAF 295
Cdd:pfam03104 81 IRKYLSPENISDVYEYDVDYLERFLIDNDIVGFGWYKVKVYPFRAEGRISNCDVEIDCDSPDLISVPFEKEWPPLRVLSF 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 296 DIECLGEEG-FPTATNEADLILQISCVLWSTGeEAGRYRRILLTLGTCE-------------DIEGVEVYEFPSELDMLY 361
Cdd:pfam03104 161 DIECTSLPGkFPDAENVKDPIIQISCMLDGQG-EPEPEPRFLFTLRECDsediedfeytpkpIYPGVKVFEFPSEKELLR 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 362 AFFQLIRDLSVEIVTGYNVANFDWPYILDRARHIYSINPASLGKIRAGGVCEVRRPHDagkgFLRANTKVRITGLIPIDM 441
Cdd:pfam03104 240 RFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNRGGRSKVREIGF----GTRSYEKVKISGRLHLDL 315
|
330
....*....|....*...
gi 1386448495 442 YAVCRDKLSLSDYKLDTV 459
Cdd:pfam03104 316 YRVIKRDYKLPSYKLNAV 333
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
561-985 |
5.37e-90 |
|
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: 293.02 E-value: 5.37e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 561 DGYQGATVIQPLSGFYNSPVLVVDFASLYPSIIQAHNLCYSTMITPGEEHRLaglrPGEDYEsfrLTGGVYHFVKKHVHE 640
Cdd:cd05533 1 EQYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKL----PPEDYI---KTPNGDYFVKSSVRK 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 641 SFLASLLTSWLAKRKAIKKLLAACEDPRQRTILDKQQLAIKCTCNAVYGFTGVANGLFPCLSIAETVTLQGRTMLERAKA 720
Cdd:cd05533 74 GLLPEILEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKK 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 721 FVEAL-SPANlqalAPSPDAwaplnpegqlRVIYGDTDSLFIEcrgFSESetlRFAEAL-----AAHTTRSLFVAPISLE 794
Cdd:cd05533 154 LVEEKyTKAN----GYSHDA----------KVIYGDTDSVMVK---FGVS---DVEEAMklgkeAAEYVSKKFIKPIKLE 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 795 AEKTFSCLMLITKKRYVGVL-----TDGKTLMKGVELVRKTACKFVQTRCRRVLDLVLADARVKEAasllshrpfqESFT 869
Cdd:cd05533 214 FEKVYFPYLLINKKRYAGLLwtnpdKHDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGA----------IEFV 283
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 870 QGlpvgflpVIDilnqaytDLREGRVPMGELCFSTELSRKLSAYKSTQmPHLAVYQKFVERNE-ELPQIHDRIQYVFVep 948
Cdd:cd05533 284 KG-------VIS-------DLLQNKIDISLLVITKALTKTADDYAGKQ-AHVELAERMRKRDPgSAPNVGDRVPYVII-- 346
|
410 420 430
....*....|....*....|....*....|....*..
gi 1386448495 949 kGGVKGARKTEMAEDPAYAERHGVPVAVDHYFDKLLQ 985
Cdd:cd05533 347 -KGAKGAKAYEKAEDPIYVLENNIPIDTQYYLENQLS 382
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
293-507 |
1.29e-50 |
|
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: 178.15 E-value: 1.29e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 293 LAFDIECLGEEG-FPTATNeaDLILQISCVLWSTGEEAGRYRRILlTLGTCEDIEGVEVYEFPSELDMLYAFFQLIRDLS 371
Cdd:cd05777 10 LSFDIECAGRKGvFPEPEK--DPVIQIANVVTRQGEGEPFIRNIF-TLKTCAPIVGAQVFSFETEEELLLAWRDFVQEVD 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 372 VEIVTGYNVANFDWPYILDRARHIYSINPASLGKIRaGGVCEVRRPHDAGKGFLRANTK-VRITGLIPIDMY-AVCRDKl 449
Cdd:cd05777 87 PDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIK-NIKSTIKDTTFSSKQMGTRETKeINIEGRIQFDLLqVIQRDY- 164
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*...
gi 1386448495 450 SLSDYKLDTVARHLLGAKKEDVHYKEIPRLFAAGPEGRRRLGMYCVQDSALVMDLLNH 507
Cdd:cd05777 165 KLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDK 222
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
58-968 |
1.12e-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: 182.18 E-value: 1.12e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 58 LTVVGGDEDGKGMWWRQRAQEGTarpeadthgspldfhvyDILETVYTHEKCAVIPSDKQ-------GYVVPCGIV-IKL 129
Cdd:TIGR00592 264 VESVSEEISMIKRFWDVIDQEDT-----------------DVEITVNGDNFDLVYLADRQvfqfywdAYEDPAEKLgVVL 326
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 130 LGRRKADGASVCVNVFGQQAYFYAsapqgLDVEFAVLSALKASTFDRRTPCRVSVEKV-------------TRRSIMGYG 196
Cdd:TIGR00592 327 LFGRDVDHVSPCVQVKGINRDLFF-----LPREGKIDFDLGKVTRRTINLPDYYLEFVselalgykkekfrAKPIAKKYE 401
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 197 NHAG--------DYHKITLSHPNSVCHVATWLQDKHG---CRIFEANVDATRRFVLDNDFVTFGWYSCRRAIPRLQHRDS 265
Cdd:TIGR00592 402 FEAPdidapyssEYLEVTYELGKEFAPMEALPSDLKGqtfWHVFGSNTGNLERFLLLRKIKGPCWLAVKGPDELEYPRRS 481
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 266 YAELEYDCEVGDLSVRREDSSWPSYQALAFDIECLgeegFP------------TATNEADLILQISCVLWSTGEEAG-RY 332
Cdd:TIGR00592 482 WCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMKSL----NPsiirneivsipdTLHREFALDKPPPEPPYDVHPCVGtRP 557
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 333 RRILLTLGTCEDIEGV---EVYEFPSELDMLYAFFQLIRDLSVEIVTGYNVANFDWPYILDRARHIYSINPASLGKIRag 409
Cdd:TIGR00592 558 KDCSFPLDLKGEFPGKkpsLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLR-- 635
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 410 gvcevrRPHDAGKGFLrantkVRITGLIPIDMYAVCRDKLSLSDYKLDTVARHLLGAKKEDVHYKEIPRLFAAGpEGRRR 489
Cdd:TIGR00592 636 ------RSPKFGRRFG-----ERTCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSES-SSLTY 703
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 490 LGMYCVQDSALVMDLLNHFVIHVEVAEIAKIAHIPCRRVLDDGQQIRVFSCLLAAAQKENFILP---------------- 553
Cdd:TIGR00592 704 LLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPdkqifrkqqklgdede 783
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 554 ---MPSASDRDGYQGATVIQPLSGFYNSPVLVVDFASLYPSIIQAHNLCYSTMITPGEEHRLAGLRPGEdyesfrltggv 630
Cdd:TIGR00592 784 eidGYKKGKKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQKVDEDELPELPDSE----------- 852
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 631 yhfvkkhVHESFLASLLTSWLAKRKAIKKLLAACEDPRQRTILDKQQLAIKCTCNAVYGFTGVANGLFPCLSIAETVTLQ 710
Cdd:TIGR00592 853 -------LEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAK 925
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 711 GRTMLERAKAFVEALSpanlqalapspdawaplnpegqLRVIYGDTDSLFIECRGFSESETLRFAEALAAHTTRSLfvAP 790
Cdd:TIGR00592 926 GREILEHTRQLVEEMN----------------------LEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLY--KL 981
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 791 ISLEAEKTFSCLMLITKKRYVGVLTDG--------KTLMKGVELVRKTACKFVQTRCRRVLDLVLADARVKEAASLlshr 862
Cdd:TIGR00592 982 LELDIDGVFKRLLLLKKKKYAAIKVEGdsdgnyttKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEE---- 1057
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 863 pfqesftqglpvgflpVIDILNQAYTDLREGRVPMGELCFSTELSRKLSAYKSTQ-MPHLAVYQKFVERNEELPQIHDRI 941
Cdd:TIGR00592 1058 ----------------VQEVLEKIGKNVLNGEVPLEKFVINKQLTRDPKDYPDGAsLPHVHVALRINARGGRKVKAGDVV 1121
|
970 980
....*....|....*....|....*..
gi 1386448495 942 QYVFVEPKGGVKGARKTEMAEDPAYAE 968
Cdd:TIGR00592 1122 SYVICKDGGNLSARQRAYALEELQRKH 1148
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
523-994 |
0e+00 |
|
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: 620.01 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 523 IPCRRVLDDGQQIRVFSCLLAAAQKENFILP-MPSA-SDRDGYQGATVIQPLSGFYNSPVLVVDFASLYPSIIQAHNLCY 600
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPdRPSAkGDEDGYQGATVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 601 STMITPGEEHRlaGLRPGEDYESFRLTGGVYHFVKKHVHESFLASLLTSWLAKRKAIKKLLAACEDPRQRTILDKQQLAI 680
Cdd:pfam00136 81 TTLVRSVDEAN--NLPPEDNLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFERAILDKQQLAL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 681 KCTCNAVYGFTGVANGLFPCLSIAETVTLQGRTMLERAKAFVEALSPANlqalapspdawaplnpegqLRVIYGDTDSLF 760
Cdd:pfam00136 159 KITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYN-------------------FRVIYGDTDSVF 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 761 IECRGFSESETLRFAEALAAHTTRSLFVAPISLEAEKTFSCLMLITKKRYVGVLTD-----GKTLMKGVELVRKTACKFV 835
Cdd:pfam00136 220 IEFGGKDVEEAMKIGDELAEHVNQDLFKSPIKLEFEKVYKPLLLISKKKYAGLKYTapsnfNKLDMKGVDLVRRDNCPLV 299
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 836 QTRCRRVLDLVLADarvkeaasllshrpfqesftQGLPVGFLPVIDILNQAYTDLREGRVPMGELCFSTELSRKLSAYKS 915
Cdd:pfam00136 300 KEVIKKVLDLLLSD--------------------RGLPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNYKS 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 916 TQMPHLAVYQKFVERNEELPQIHDRIQYVFVEPKGGVKGARKTEMAEDPAYAERHGVPVAVDHYFD-KLLQGAANILQCL 994
Cdd:pfam00136 360 KNLPHVEVALRMNKRNGEAPEVGDRIPYVIVKAAKGLKNLLIYERAEDPEYVLENNLPIDYEYYFSnQLIPPVARLLEPI 439
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
78-983 |
6.62e-167 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 517.66 E-value: 6.62e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 78 EGTARPEADTHGSPLDFhVYDILETVYTHEKCAVIPSDKQGYVVPCGI---VIKLLGRRKaDGASVCVNVFGQQAYFYAS 154
Cdd:PTZ00166 26 FSKLRRPLPPISLQKDL-VFFQLDADYTEKDDKSQGNPHNTVSGVRHVevpIIRLYGVTK-EGHSVLVNVHNFFPYFYIE 103
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 155 APQGLDVEFAVL------SALKASTFDRRTPCRV-SVEKVTRRSIMGY-GNHAGDYHKITLSHPNSVCHVATWLQD---- 222
Cdd:PTZ00166 104 APPNFLPEDSQKlkrelnAQLSEQSQFKKYQNTVlDIEIVKKESLMYYkGNGEKDFLKITVQLPKMVPRLRSLIESgvvv 183
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 223 --KHGCRI-----FEANVDATRRFVLDNDFVTFGWYSCRRA---IPRLQHRDSYAELEYDCEVGDLSVRREDSSW---PS 289
Cdd:PTZ00166 184 cgGGWDGIrlfqtYESNVPFVLRFLIDNNITGGSWLTLPKGkykIRPPKKKTSTCQIEVDCSYEDLIPLPPEGEYltiAP 263
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 290 YQALAFDIECLGE--EGFPTATNeaDLILQISCVLWSTGEEAGRYRRILLTLGTCEDIEGVEVYEFPSELDMLYAFFQLI 367
Cdd:PTZ00166 264 LRILSFDIECIKLkgLGFPEAEN--DPVIQISSVVTNQGDEEEPLTKFIFTLKECASIAGANVLSFETEKELLLAWAEFV 341
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 368 RDLSVEIVTGYNVANFDWPYILDRARHIYSINPASLGKIRaGGVCEVRRPHDAGKGF-LRANTKVRITGLIPIDMYAVCR 446
Cdd:PTZ00166 342 IAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIK-STRSVIKDSKFSSKQMgTRESKEINIEGRIQFDVMDLIR 420
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 447 DKLSLSDYKLDTVARHLLGAKKEDVHYKEIPRLFAAGPEGRRRLGMYCVQDSALVMDLLNHFVIHVEVAEIAKIAHIPCR 526
Cdd:PTZ00166 421 RDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIG 500
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 527 RVLDDGQQIRVFSCLLAAAQKENFILP---MPSASDRDGYQGATVIQPLSGFYNSPVLVVDFASLYPSIIQAHNLCYSTM 603
Cdd:PTZ00166 501 WLLTRGQQIKVTSQLLRKCKKLNYVIPtvkYSGGGSEEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTL 580
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 604 ITPGEehrLAGLRPgedyESFRLTGGVYHFVKKHVHESFLASLLTSWLAKRKAIKKLLAACEDPRQRTILDKQQLAIKCT 683
Cdd:PTZ00166 581 VPPND---ANNYPE----DTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLLKKVLNGRQLALKIS 653
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 684 CNAVYGFTG-VANGLFPCLSIAETVTLQGRTMLERAKAFVEALSPanlQALAPSPDAwaplnpegqlRVIYGDTDSLFIE 762
Cdd:PTZ00166 654 ANSVYGYTGaQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKHYT---KANGYKHDA----------TVIYGDTDSVMVK 720
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 763 CRGFSESETLRFAEAlAAHTTRSLFVAPISLEAEKTFSCLMLITKKRYVGVL-----TDGKTLMKGVELVRKTACKFVQT 837
Cdd:PTZ00166 721 FGTDDIQEAMDLGKE-AAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAGLLytnpeKYDKIDCKGIETVRRDNCLLVQQ 799
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 838 RCRRVLDLVLADARVKEAasllshrpfqESFTQGlpvgflpVIdilnqayTDLREGRVPMGELCFSTELSRklSAYKsTQ 917
Cdd:PTZ00166 800 MVETVLNKILIEKDVESA----------IEFTKG-------KI-------SDLLQNRIDISLLVITKSLGK--DDYE-GR 852
|
890 900 910 920 930 940
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1386448495 918 MPHLAVYQKFVERNE-ELPQIHDRIQYVFVEpkgGVKGARKTEMAEDPAYAERHGVPVAVDHYFDKL 983
Cdd:PTZ00166 853 LAHVELAKKLRQRDPgSAPNVGDRVSYVIVK---GAKGAPQYERAEDPLYVLENNIPIDTQYYLDQI 916
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
288-765 |
6.63e-166 |
|
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: 495.13 E-value: 6.63e-166
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 288 PSYQALAFDIECL-GEEGFPTATNEADLILQISCVLWStGEEAGRYRRILLTLGTCEDIEGVEVYEFPSELDMLYAFFQL 366
Cdd:smart00486 1 PPLKILSFDIETYtDGGNFPDAEIFDDEIIQISLVIND-GDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEF 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 367 IRDLSVEIVTGYNVANFDWPYILDRARHIYSINPASLGKIRAGGVCEVRRPHDAGKGFLRANTKVRITGLIPIDMYAVCR 446
Cdd:smart00486 80 IKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGLRIPNKKPLFGSKSFGLSDIKVYIKGRLVIDLYRLYK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 447 DKLSLSDYKLDTVARHLLGAKKEDVHYKEIPRLFAAGPEGRRRLGMYCVQDSALVMDLLNHFVIHVEVAEIAKIAHIPCR 526
Cdd:smart00486 160 NKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLR 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 527 RVLDDGQQIRVFSCLLAAAQKENFILPMPSASDRD----------GYQGATVIQPLSGFYNSPVLVVDFASLYPSIIQAH 596
Cdd:smart00486 240 RTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKgsepdlkkkvKYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAH 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 597 NLCYSTMITPGEEHRLAGLRPGEDYESFRLTGG-VYHFVKKHVHESFLASLLTSWLAKRKAIKKLLAACEDP--RQRTIL 673
Cdd:smart00486 320 NLCYSTLVGVGEVVIKGDLIIPEDLLTIKYEKGnKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDEseELKKLL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 674 DKQQLAIKCTCNAVYGFTGVANGLFPCLSIAETVTLQGRTMLERAKAFVEALSpanlqalapspdawaplNPEGQLRVIY 753
Cdd:smart00486 400 DSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENG-----------------YPKPGFKVIY 462
|
490
....*....|..
gi 1386448495 754 GDTDSLFIECRG 765
Cdd:smart00486 463 GDTDSIFVTKPG 474
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
124-994 |
1.73e-132 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 419.23 E-value: 1.73e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 124 GIVIKLLGRRkADGASVCVNVFGQQAYFYASAPQGLDVEfAVLSALKAstfdrrtpcRVSVEKVTRRSIMGygnHAGDYH 203
Cdd:COG0417 18 KPVIELWGRT-EDGPSVLLDVTGFRPYFYVPLPDEEKLE-ELLRDIKE---------ITEVEPVKLKSFFG---EPVPVL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 204 KITLSHPNSVCHVATWLQDkHGCRIFEANVDATRRFVLDNDFVTFGWYSCRRaiprlQHRDSYAELEYDCEVGDlsvrRE 283
Cdd:COG0417 84 KIYTRDPRDVRELRDRLKE-GGIDVYEADIRFHDRYLIDRFLTPGVWYEGEV-----EEDGGKLDYEVKENPRL----KP 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 284 DSSWPSYQALAFDIECLGEEGFPTATNEADLILqIScvLWStgeEAGRYRRILLTlgtcEDIEGVEVYEFPSELDMLYAF 363
Cdd:COG0417 154 EDYRPKLKVLSFDIEVSTPRGFPDPERDGPIIS-IG--LAG---SDGEKKVLMLG----REGVDFEVEYFDDEKALLEAF 223
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 364 FQLIRDLSVEIVTGYNVANFDWPYILDRARhIYSINPAsLGkiRAGGVCEVRRPhdagkgflRANTKVRITGLIPIDMY- 442
Cdd:COG0417 224 FEIIREYDPDIIIGWNVDNFDLPYLQKRAE-RLGIPLD-LG--RDGSEPSWREH--------GGQGFASIPGRVVIDLYd 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 443 AVCRDKLSLSDYKLDTVARHLLGAKKEDVHYKEIPRLFAagpEGRRRLGMYCVQDSALVMDLLNH-----FVIhvevaEI 517
Cdd:COG0417 292 ALKSATYKFKSYSLDAVAEELLGEGKLIVDGGEIERLWD---DDKPALAEYNLRDAELTLRIFEKtlllpFLI-----EL 363
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 518 AKIAHIPCRRVLDDGQQIRVFSCLLAAAQKENFILPMPSASDRDGYQGATVIQPLSGFYNSpVLVVDFASLYPSIIQAHN 597
Cdd:COG0417 364 SRITGLPLDDVGRAGSSAAFENLLLPEAHRRGYLAPNKGEIKGEAYPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFN 442
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 598 LCYSTMITPGEEhrlaglRPGEDYESfrlTGGVYHFVKKHVHesFLASLLTSWLAKRKAIKKLLA-ACEDPRQRTILDKQ 676
Cdd:COG0417 443 ISPETLVEGGEE------PCGDEDVA---PGFGHRFCREPKG--ILPSILEELWDERDEAKKKMKkAKPDSEEYRLYDAL 511
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 677 QLAIKCTCNAVYGFTGVANGLFPCLSIAETVTLQGRTMLERAKAFVEALspanlqalapspdawaplnpeGqLRVIYGDT 756
Cdd:COG0417 512 QQALKILMNSFYGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEEL---------------------G-YKVIYGDT 569
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 757 DSLFIECRGFSESETLRFAEALAAHTTRSLfVAPISLEAEKTFS-CLMLITKKRYVGVLTDGKTLMKGVELVRKTACKFV 835
Cdd:COG0417 570 DSLFVWLPKASLEEAIEIGKELAEEINAWW-PSGLELEFEKHYRrFFFPGSKKRYAGLTEDGKIDIKGLEAVRSDWTELA 648
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 836 QTRCRRVLDLVLADARVKEAasllshrpfqesftqglpvgflpvIDILNQAYTDLREGRVPMGELCFSTELSRKLSAYKS 915
Cdd:COG0417 649 KEFQQEVYERILKEEDVEKA------------------------VEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSEYEK 704
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 916 TQMPHLAVYQKFVERNEElPQIHDRIQYVFVEPKGGVkgarktemaEDPAYAERHGVPVAVDHYFDKLLQGAAN-ILQCL 994
Cdd:COG0417 705 NVPPHVRAARKLDERGRP-YQRGDKISYVITKGGGRV---------EPVELAKERESEIDYDYYIEKQLKPTADrILEAF 774
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
136-459 |
8.86e-115 |
|
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: 356.73 E-value: 8.86e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 136 DGASVCVNVFGQQAYFYASAPQGLDVEfAVLSALKASTFDRRTPcrVSVEKVTRRSIMGYGNHAGDYHKITLSHPNSVCH 215
Cdd:pfam03104 4 EGVSVCVNVFGFKPYFYCLAPDGKELE-EVIEEIKELYEGLDKI--EKIELKLKKSLYGYEEDPVPYLKVSFANPRPLLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 216 VATWLQDKHGCRIFEANVDATRRFVLDNDFVTFGWYSCRRAIPRLQHRDSYAELEYDCEVGDLSVRREDSSWPSYQALAF 295
Cdd:pfam03104 81 IRKYLSPENISDVYEYDVDYLERFLIDNDIVGFGWYKVKVYPFRAEGRISNCDVEIDCDSPDLISVPFEKEWPPLRVLSF 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 296 DIECLGEEG-FPTATNEADLILQISCVLWSTGeEAGRYRRILLTLGTCE-------------DIEGVEVYEFPSELDMLY 361
Cdd:pfam03104 161 DIECTSLPGkFPDAENVKDPIIQISCMLDGQG-EPEPEPRFLFTLRECDsediedfeytpkpIYPGVKVFEFPSEKELLR 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 362 AFFQLIRDLSVEIVTGYNVANFDWPYILDRARHIYSINPASLGKIRAGGVCEVRRPHDagkgFLRANTKVRITGLIPIDM 441
Cdd:pfam03104 240 RFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNRGGRSKVREIGF----GTRSYEKVKISGRLHLDL 315
|
330
....*....|....*...
gi 1386448495 442 YAVCRDKLSLSDYKLDTV 459
Cdd:pfam03104 316 YRVIKRDYKLPSYKLNAV 333
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
561-985 |
5.37e-90 |
|
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: 293.02 E-value: 5.37e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 561 DGYQGATVIQPLSGFYNSPVLVVDFASLYPSIIQAHNLCYSTMITPGEEHRLaglrPGEDYEsfrLTGGVYHFVKKHVHE 640
Cdd:cd05533 1 EQYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKL----PPEDYI---KTPNGDYFVKSSVRK 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 641 SFLASLLTSWLAKRKAIKKLLAACEDPRQRTILDKQQLAIKCTCNAVYGFTGVANGLFPCLSIAETVTLQGRTMLERAKA 720
Cdd:cd05533 74 GLLPEILEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKK 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 721 FVEAL-SPANlqalAPSPDAwaplnpegqlRVIYGDTDSLFIEcrgFSESetlRFAEAL-----AAHTTRSLFVAPISLE 794
Cdd:cd05533 154 LVEEKyTKAN----GYSHDA----------KVIYGDTDSVMVK---FGVS---DVEEAMklgkeAAEYVSKKFIKPIKLE 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 795 AEKTFSCLMLITKKRYVGVL-----TDGKTLMKGVELVRKTACKFVQTRCRRVLDLVLADARVKEAasllshrpfqESFT 869
Cdd:cd05533 214 FEKVYFPYLLINKKRYAGLLwtnpdKHDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGA----------IEFV 283
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 870 QGlpvgflpVIDilnqaytDLREGRVPMGELCFSTELSRKLSAYKSTQmPHLAVYQKFVERNE-ELPQIHDRIQYVFVep 948
Cdd:cd05533 284 KG-------VIS-------DLLQNKIDISLLVITKALTKTADDYAGKQ-AHVELAERMRKRDPgSAPNVGDRVPYVII-- 346
|
410 420 430
....*....|....*....|....*....|....*..
gi 1386448495 949 kGGVKGARKTEMAEDPAYAERHGVPVAVDHYFDKLLQ 985
Cdd:cd05533 347 -KGAKGAKAYEKAEDPIYVLENNIPIDTQYYLENQLS 382
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
532-953 |
2.42e-73 |
|
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: 249.82 E-value: 2.42e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 532 GQQIRVFSCLLAAAQKENFILPMPSASDRdGYQGAT-----VIQPLSGFYNSPVLVVDFASLYPSIIQAHNLCYSTMITP 606
Cdd:cd05534 1 GSQFRVESMLLRLAKPENYILPSPSRQQV-AQQRALeclplVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 607 GEEHRLAGL---------RPGEDYESFRLTGGVY------HFVKKHVHESFLASLLTSWLAKRKAIKKLLAACEDPR--Q 669
Cdd:cd05534 80 VEELNGGGKfgflgvklyLPPPPLDLLLLKDDVTispngvMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDDKklQ 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 670 RtILDKQQLAIKCTCNAVYGFTGvAN--GLFPCLSIAETVTLQGRTMLERAKAFVEAlspanlqalapspdawaplNPEG 747
Cdd:cd05534 160 R-ILDARQLALKLLANVTYGYTA-ASfsGRMPCVEIADSIVQTGRETLERAIELIES-------------------TPKW 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 748 QLRVIYGDTDSLFIECRGFSESETLRFAEALAAHTTrSLFVAPISLEAEKTFSCLMLITKKRYVGVL------TDGKTLM 821
Cdd:cd05534 219 GAKVVYGDTDSLFVLLPGRTKEEAFKIGKEIAEAVT-AANPSPIKLKFEKVYHPCVLVTKKRYVGYKyespdqTEPTFDA 297
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 822 KGVELVRKTACKFVQTRCRRVLDLVLADARVKEaasllshrpfqesftqglpvgflpVIDILNQAYTDLREGRVPMGELC 901
Cdd:cd05534 298 KGIETVRRDGCPAVQKILEKSLRILFETKDLST------------------------VKSYLQRQWSKLLQGRVSIQDFI 353
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*..
gi 1386448495 902 FSTELsrKLSAYKSTQM--PHLAVYQKFVE---RNEelPQIHDRIQYVFVEPKGGVK 953
Cdd:cd05534 354 FAKEV--RLGTYKEGATlpAGAIVALRRMEkdpRAE--PQYGERVPYVVVRGEPGSR 406
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
115-991 |
2.72e-64 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 232.82 E-value: 2.72e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 115 DKQGYVVPCGIVIKLLGrrKADGASVCVNVFGQQA-YFYASAPQGldvefAVLSALKASTFDRRTPcrVSVEKVTRRSIM 193
Cdd:PRK05762 10 TRHYRDTPGGPEVELWL--ATDEGPRVVLLDPQFRpYFIPAEQDE-----RAESLLAGEIGVRLSP--LALKDFHRRPVL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 194 GYgnhagdYHKItlshpNSVCHVATWLQDKHGCRIFEANVDATRRFVLDNDFVTFGWYSCrraiprlQHRDSYAELEY-D 272
Cdd:PRK05762 81 GL------YCRQ-----HRQLTRLPKRLREGGVDVYEADIRFPERYLMERFITPCVWFSG-------EVEQYTTDGVLrN 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 273 CEVGDLSVRRedsswPSYQALAFDIEClGEEGfptatneadlilqiscVLWSTGEEAGRYRRILLtLGTCEDIEGVEVYE 352
Cdd:PRK05762 143 ARLKPAPDYR-----PPLKVVSLDIET-SNKG----------------ELYSIGLEGCGQRPVIM-LGPPNGEALDFLEY 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 353 FPSELDMLYAFFQLIRDLSVEIVTGYNVANFDWPYILDRARHiYSInPASLGkiRAGGVCEVRR-PHDAGKGFlrantkV 431
Cdd:PRK05762 200 VADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAER-YGI-PLRLG--RDGSELEWREhPFRSGYGF------A 269
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 432 RITGLIPIDMYAVCRDKL-SLSDYKLDTVARHLLGAKKE--DVHYK--EIPRLFAagpEGRRRLGMYCVQDSALVMDLLN 506
Cdd:PRK05762 270 SVPGRLVLDGIDALKSATwVFDSFSLEYVSQRLLGEGKAidDPYDRmdEIDRRFA---EDKPALARYNLKDCELVTRIFE 346
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 507 H-----FVIhvEVAEIAKIAhipcrrvLDD--GQQIRVFSCLLAAAQKENFILPMPSASDRDGYQGATVIQPLSGFYNSp 579
Cdd:PRK05762 347 KtkllpFLL--ERATVTGLP-------LDRvgGSVAAFEHLYLPRAHRAGYVAPNLGERPGEASPGGYVMDSKPGLYDS- 416
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 580 VLVVDFASLYPSIIQAHNLCYSTMItPGEEHRlaglrPGEDYESFRltGGVyhFVKKHvHesFLASLLTSWLAKRKAIKK 659
Cdd:PRK05762 417 VLVLDFKSLYPSIIRTFNIDPDGLV-EGLAQP-----PEESVAGFL--GAR--FSREK-H--FLPEIVERLWEGRDEAKR 483
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 660 LLAAcedPRQRtildkqqlAIKCTCNAVYGFTGVANGLFPCLSIAETVTLQGRTMLERAKAFVEALSpanlqalapspda 739
Cdd:PRK05762 484 EMNK---PLSQ--------AIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQG------------- 539
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 740 waplnpegqLRVIYGDTDSLFIECRGF-SESETLRFAEALAAH-------TTRSLFVAP--ISLEAEKTFSCLMLIT--- 806
Cdd:PRK05762 540 ---------YQVIYGDTDSTFVWLGGAhDEEDAAKIGRALVQEinqwwqeHLQQEFGLEsaLELEFEKHYRRFFMPTirg 610
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 807 -----KKRYVGVLT----DGKTLMKGVELVRKTACKFVQTRCRRVLDLVLADarvkeaasllshrpfqesftqglpvgfL 877
Cdd:PRK05762 611 aeegsKKRYAGLIQegdgDGRIVFKGLETVRTDWTPLAKEFQQELYERIFRG---------------------------E 663
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 878 PVIDILNQAYTDLREGRVPmGELCFSTELSRKLSAYKSTQMPHLAVYQKFVERNEEL-----PQIHDRIQYVFVepkggV 952
Cdd:PRK05762 664 PYVDYVREVIDKLRAGELD-EKLVYRKRLRRPLDEYQRNVPPHVRAARLADEMGYKVgrplqYQNGGKIGYVIT-----V 737
|
890 900 910 920
....*....|....*....|....*....|....*....|
gi 1386448495 953 KGARKTEmaedpayaERHgVPVAVDHYFDKLLQGAAN-IL 991
Cdd:PRK05762 738 NGPEPLE--------YRK-SPIDYDYYIEKQLQPVADrIL 768
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
293-507 |
1.29e-50 |
|
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: 178.15 E-value: 1.29e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 293 LAFDIECLGEEG-FPTATNeaDLILQISCVLWSTGEEAGRYRRILlTLGTCEDIEGVEVYEFPSELDMLYAFFQLIRDLS 371
Cdd:cd05777 10 LSFDIECAGRKGvFPEPEK--DPVIQIANVVTRQGEGEPFIRNIF-TLKTCAPIVGAQVFSFETEEELLLAWRDFVQEVD 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 372 VEIVTGYNVANFDWPYILDRARHIYSINPASLGKIRaGGVCEVRRPHDAGKGFLRANTK-VRITGLIPIDMY-AVCRDKl 449
Cdd:cd05777 87 PDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIK-NIKSTIKDTTFSSKQMGTRETKeINIEGRIQFDLLqVIQRDY- 164
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*...
gi 1386448495 450 SLSDYKLDTVARHLLGAKKEDVHYKEIPRLFAAGPEGRRRLGMYCVQDSALVMDLLNH 507
Cdd:cd05777 165 KLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDK 222
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
562-856 |
5.45e-50 |
|
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: 179.87 E-value: 5.45e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 562 GYQGATVIQPlSGFYNSPVLVVDFASLYPSIIQAHNLCYSTMITPGEEHrlaglrpgeDYESFRLTGGVYHFVKKHVHES 641
Cdd:cd00145 2 PYEGGYVFDP-IPGLYENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIA---------APEDYIGVGFRSPKDRKGLLPR 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 642 FLASLLTSwlakRKAIKKL-LAACEDPRQRTILDKQQLAIKCTCNAVYGFTGVANGLFPCLSIAETVTLQGRTMLERAKA 720
Cdd:cd00145 72 ILEELLNF----RDEAKKRmKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIA 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 721 FVEalspanlqalapspdawaplnpEGQLRVIYGDTDSLFIEcrgFSESETLRFAEALAAHTTRSLFVA-PISLEAEKTF 799
Cdd:cd00145 148 LVE----------------------EHGARVIYGDTDSIFVS---LPKMGTKEDAIKEGREILQELADEhLLELEFEKVY 202
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1386448495 800 SCLMLITKKRYVGVL-----TDGKTLMKGVELVRKTACKFVQTRCRRVLDLVLADARVKEAA 856
Cdd:cd00145 203 LPFFLGKKKRYAGLDiwkgqDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEERKVEAV 264
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
145-970 |
3.77e-49 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 187.97 E-value: 3.77e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 145 FGQQAYFYASAPQGLDVEFAVLsaLKASTFDRrtpcrvsVEKVTRRSimGYGNHAGDYHKITLSHPNSVCHVATWLQDKH 224
Cdd:PRK05761 52 TGHKPYFLTDLDPDEIDKIPKI--LRHPSFDH-------LEIVEKYD--GLRDKKVKVTKIVVKDPLAVRRLRLSVRDIP 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 225 gcRIFEANVDATRRFVLDNDFVTFGWYSCRRAIPRLQHRDSYAELEY----DCEVGDLSVRREDSSWPSYQALAFDIECL 300
Cdd:PRK05761 121 --RAWEADIKYEFRYIYDNGLIPGMPYDVKNGLESVEPEILVEEIKKafkdERKLAEDWLPIFEAPIPKIKRIAIDIEVY 198
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 301 GEegfptatneadlilqiscvlwstgeeagryrrillTLGTCEDiegvevyefPSELDMLYAFFQLIRDLSVEIVtgYNV 380
Cdd:PRK05761 199 TP-----------------------------------AKGRIPD---------DSEKELLAELFDIILEYPPVVT--FNG 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 381 ANFDWPYILDRARHIysinpaslgkiragGVcevrrphdaGKGFLRANTKVRItglIPIDMYAVCRD----------KLS 450
Cdd:PRK05761 233 DNFDLPYLYNRALKL--------------GI---------PKEEIPIEPGRAG---IHIDLYKFFQNkavrsyafygKYR 286
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 451 LSDYKLDTVARHLLGAKKEDvHYKEIPRLfaagpeGRRRLGMYCVQD-----------SALVMDLlnhfvihveVAEIAK 519
Cdd:PRK05761 287 HREARLDAVGRALLGISKVE-LETNISEL------DLEELAEYNFRDaeitlkltffnNELVLKL---------ILLLSR 350
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 520 IAHIP----CRRVLddGQQIRvfSCLLAAAQKENFILPM-------------PSASDRDGYQGATVIQPLSGFYNSpVLV 582
Cdd:PRK05761 351 ISKLPieelSRATI--STWIS--NLEYWEHRKRGWLIPWkedilrldhevykKAIIKGKKYRGGLVFQPPPGIFFN-VYV 425
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 583 VDFASLYPSIIQAHNLCYSTMITPGEEHRLAGLRPGEDYESFRLTGGvyhfvkkhvhesFLASLLTSWLAKRKAIKKLLA 662
Cdd:PRK05761 426 LDFASLYPSIIVKWNLSPETVRIPECKCHYDDEVPELGHSVCDDRPG------------LTSVLVGLLRDFRVKIYKKKA 493
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 663 ACEDPR--QRTILDKQQLAIKCTCNAVYGFTGVANGLFPCLSIAETVTLQGRTMLERAKAFVEALSpanlqalapspdaw 740
Cdd:PRK05761 494 KDPNLDeeRRAWYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESITALGREILLSTKKKAEELG-------------- 559
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 741 aplnpegqLRVIYGDTDSLFIecRGFSEsETLrfaEALAAHTTRSLfvaPISLEAEKTFSCLMLI-TKKRYVGVLTDGKT 819
Cdd:PRK05761 560 --------LKVLYGDTDSLFV--WGPTK-ESL---EELIKEIEERT---GIDLEVDKTYDWVAFSgLKKNYFGVLKDGKV 622
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 820 LMKGVELVRKTA---CKFVQTRCRRVLdlvladarvKEAASllshrpfqesfTQGLPVGFLPVIDILNQAYTDLREGRVP 896
Cdd:PRK05761 623 KIKGIVAKKRNTpefVKELQREVLEVL---------KSIRS-----------PEDVEKVKDEIEDVLKRYYEKLRAKDYP 682
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1386448495 897 MGELCFSTELSRKLSAYKSTQMPHLAVYQKFVERNEELpQIHDRIQYVFVEPKGGVKGARKTEMAE-DPAYAERH 970
Cdd:PRK05761 683 LDELAIRVRLSKPLDEYTKNTPQHVKAALQLRDYGVEV-SPGDIISYVKVDDKRGVKPVQLAKLSEiDVEKYIEL 756
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
560-982 |
7.44e-49 |
|
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: 177.90 E-value: 7.44e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 560 RDGYQGATVIQPLSGFYNSpVLVVDFASLYPSIIQAHNLCYSTMItpgeehrlaglRPGEDYESFRLTGGvYHFVKKHvh 639
Cdd:cd05536 1 RESYEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLV-----------REGCEDCDVEPQVG-HKFRKDP-- 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 640 ESFLASLLTSWLAKRKAIKKLLAACEDPR-QRTILDKQQLAIKCTCNAVYGFTGVANGLFPCLSIAETVTLQGRTMLERA 718
Cdd:cd05536 66 PGFIPSVLEDLLEERRRIKEKMKKLDPESeEYKLLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTT 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 719 KAFVEalspanlqalapspdawaplnpEGQLRVIYGDTDSLFIECRGfsESETLRFAEALAAHTTRSLfvaPISLEAEKT 798
Cdd:cd05536 146 IKIAE----------------------EKGFKVIYGDTDSLFVKIDG--ADAVKKKVKKLLKYINEEL---PLELEIEKF 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 799 FSCLMLITKKRYVGVLTDGKTLMKGVELVRKTAC---KFVQtrcRRVLDLVLADARVKEAasllshrpfqesftqglpvg 875
Cdd:cd05536 199 YKRGFFVTKKRYAGLTEDGKIDVVGLEVVRRDWSeiaKETQ---ARVLEAILKEGDVEEA-------------------- 255
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 876 flpvIDILNQAYTDLREGRVPMGELCFSTELSRKLSAYKSTQmPHLAVYQKFVERNEELPqIHDRIQYVFvepkggVKGA 955
Cdd:cd05536 256 ----VKIVKEVIEKLKRGEVPPEKLVIWKQLTKDLSEYKATG-PHVAAAKKLAKRGYKVR-PGTKIGYVI------VKGS 323
|
410 420
....*....|....*....|....*...
gi 1386448495 956 RK-TEMAEdPAYAERHGVPVAVDHYFDK 982
Cdd:cd05536 324 GKiSDRAY-PYDMVDEKHKYDAEYYIDN 350
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
58-968 |
1.12e-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: 182.18 E-value: 1.12e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 58 LTVVGGDEDGKGMWWRQRAQEGTarpeadthgspldfhvyDILETVYTHEKCAVIPSDKQ-------GYVVPCGIV-IKL 129
Cdd:TIGR00592 264 VESVSEEISMIKRFWDVIDQEDT-----------------DVEITVNGDNFDLVYLADRQvfqfywdAYEDPAEKLgVVL 326
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 130 LGRRKADGASVCVNVFGQQAYFYAsapqgLDVEFAVLSALKASTFDRRTPCRVSVEKV-------------TRRSIMGYG 196
Cdd:TIGR00592 327 LFGRDVDHVSPCVQVKGINRDLFF-----LPREGKIDFDLGKVTRRTINLPDYYLEFVselalgykkekfrAKPIAKKYE 401
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 197 NHAG--------DYHKITLSHPNSVCHVATWLQDKHG---CRIFEANVDATRRFVLDNDFVTFGWYSCRRAIPRLQHRDS 265
Cdd:TIGR00592 402 FEAPdidapyssEYLEVTYELGKEFAPMEALPSDLKGqtfWHVFGSNTGNLERFLLLRKIKGPCWLAVKGPDELEYPRRS 481
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 266 YAELEYDCEVGDLSVRREDSSWPSYQALAFDIECLgeegFP------------TATNEADLILQISCVLWSTGEEAG-RY 332
Cdd:TIGR00592 482 WCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMKSL----NPsiirneivsipdTLHREFALDKPPPEPPYDVHPCVGtRP 557
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 333 RRILLTLGTCEDIEGV---EVYEFPSELDMLYAFFQLIRDLSVEIVTGYNVANFDWPYILDRARHIYSINPASLGKIRag 409
Cdd:TIGR00592 558 KDCSFPLDLKGEFPGKkpsLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLR-- 635
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 410 gvcevrRPHDAGKGFLrantkVRITGLIPIDMYAVCRDKLSLSDYKLDTVARHLLGAKKEDVHYKEIPRLFAAGpEGRRR 489
Cdd:TIGR00592 636 ------RSPKFGRRFG-----ERTCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSES-SSLTY 703
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 490 LGMYCVQDSALVMDLLNHFVIHVEVAEIAKIAHIPCRRVLDDGQQIRVFSCLLAAAQKENFILP---------------- 553
Cdd:TIGR00592 704 LLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPdkqifrkqqklgdede 783
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 554 ---MPSASDRDGYQGATVIQPLSGFYNSPVLVVDFASLYPSIIQAHNLCYSTMITPGEEHRLAGLRPGEdyesfrltggv 630
Cdd:TIGR00592 784 eidGYKKGKKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQKVDEDELPELPDSE----------- 852
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 631 yhfvkkhVHESFLASLLTSWLAKRKAIKKLLAACEDPRQRTILDKQQLAIKCTCNAVYGFTGVANGLFPCLSIAETVTLQ 710
Cdd:TIGR00592 853 -------LEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAK 925
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 711 GRTMLERAKAFVEALSpanlqalapspdawaplnpegqLRVIYGDTDSLFIECRGFSESETLRFAEALAAHTTRSLfvAP 790
Cdd:TIGR00592 926 GREILEHTRQLVEEMN----------------------LEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLY--KL 981
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 791 ISLEAEKTFSCLMLITKKRYVGVLTDG--------KTLMKGVELVRKTACKFVQTRCRRVLDLVLADARVKEAASLlshr 862
Cdd:TIGR00592 982 LELDIDGVFKRLLLLKKKKYAAIKVEGdsdgnyttKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEE---- 1057
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 863 pfqesftqglpvgflpVIDILNQAYTDLREGRVPMGELCFSTELSRKLSAYKSTQ-MPHLAVYQKFVERNEELPQIHDRI 941
Cdd:TIGR00592 1058 ----------------VQEVLEKIGKNVLNGEVPLEKFVINKQLTRDPKDYPDGAsLPHVHVALRINARGGRKVKAGDVV 1121
|
970 980
....*....|....*....|....*..
gi 1386448495 942 QYVFVEPKGGVKGARKTEMAEDPAYAE 968
Cdd:TIGR00592 1122 SYVICKDGGNLSARQRAYALEELQRKH 1148
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
563-944 |
2.42e-46 |
|
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: 171.61 E-value: 2.42e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 563 YQGATVIQPLSGFYNSPVLVVDFASLYPSIIQAHNLCYSTmITPGEEHRLAGLRPGEDYESfrltggvyhfvkkhVHESF 642
Cdd:cd05532 8 YAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTT-VDRADPDDEDDEEPPLPPSD--------------QEKGI 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 643 LASLLTSWLAKRKAIKKLLAACEDPRQRTILDKQQLAIKCTCNAVYGFTGVANGLFPCLSIAETVTLQGRTMLERAKAFV 722
Cdd:cd05532 73 LPRIIRKLVERRRQVKKLMKSEKDPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLV 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 723 EALSpanlqalapspdawaplnpegqLRVIYGDTDSLFIECRGFSESETLRFAEALAAHTTRSLFVapISLEAEKTFSCL 802
Cdd:cd05532 153 EKMN----------------------LEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKK--LEIDIDGVFKRL 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 803 MLITKKRYVGV-LTDGKTL-----MKGVELVRKTACKFVQTRCRRVLDLVLADaRVKEAASLLSHrpfqesftqglpvgf 876
Cdd:cd05532 209 LLLKKKKYAALkVVDDDKGklkkeVKGLDIVRRDWCPLSKEIGNYVLDQILSD-KSREDIVENIH--------------- 272
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1386448495 877 lpviDILNQAYTDLREGRVPMGELCFSTELSRKLSAYKSTQ-MPHLAVYQKFVERNEELPQiHDRIQYV 944
Cdd:cd05532 273 ----EYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPDKKsLPHVQVALRMNKRGRKVKA-GDTIPYI 336
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
562-963 |
2.45e-32 |
|
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Pssm-ID: 99913 Cd Length: 372 Bit Score: 129.78 E-value: 2.45e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 562 GYQGATVIQPLSG-FYNspVLVVDFASLYPSIIQAHNLCYSTMITPGEEHRLaglrpgedyesfRLTGGVYHFVKKhvHE 640
Cdd:cd05530 12 KYRGAIVLEPPPGiFFN--VVVLDFASLYPSIIKVWNLSYETVNCPHCECKT------------NEVPEVGHWVCK--KR 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 641 SFLASLLTSWLA-------KRKAIKKLLaaceDPRQRTILDKQQLAIKCTCNAVYGFTGVANglFP--CLSIAETVTLQG 711
Cdd:cd05530 76 PGITSQIIGLLRdlrvkiyKKKAKDKSL----DEEMRQWYDVVQSAMKVFINASYGVFGAEN--FPlyCPPVAESTTALG 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 712 RtmleraKAFVEALSPANlqalapspdawaplnpEGQLRVIYGDTDSLFIecRGFSEsETLrfaEALAAHTTRSLfvaPI 791
Cdd:cd05530 150 R------YIITSTIKKAR----------------ELGLKVLYGDTDSLFL--WNPPQ-EQL---EDLVEWVEKEL---GL 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 792 SLEAEKTFSCLMLI-TKKRYVGVLTDGKTLMKGVELVRKTACKFVQTRCRRVLDLVLADARVKEaasllshrpFQESFTQ 870
Cdd:cd05530 199 DLELDKEYRYVVFSgLKKNYLGVTKDGSVDIKGLLGKKRNTPEFVKELFYEVIEILSAVNSPED---------FEKAREK 269
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 871 glpvgflpVIDILNQAYTDLREGRVPMGELCFSTELSRKLSAYKSTQMPH------LAVYQKFVERNeelpqihDRIQYV 944
Cdd:cd05530 270 --------IRDIVKGVYKRLKKKEYTLDQLAFKVMLSKPPEEYTKNTPQHvkaarqLEKYGRNVEAG-------DIISYV 334
|
410 420
....*....|....*....|..
gi 1386448495 945 FVEPKGGVKG---ARKTEMAED 963
Cdd:cd05530 335 KVKGKEGVKPvqlARLDEVDVE 356
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
293-505 |
6.32e-30 |
|
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: 117.84 E-value: 6.32e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 293 LAFDIECLGEEGFPTatNEADLILQISCVLWSTGEeagRYRRILLTLGTCEDIE---GVEVYEFPSELDMLYAFFQLIRD 369
Cdd:cd05160 2 LSFDIETTPPVGGPE--PDRDPIICITYADSFDGV---KVVFLLKTSTVGDDIEfidGIEVEYFADEKELLKRFFDIIRE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 370 LSVEIVTGYNVANFDWPYILDRARhIYSINPASLGKIRAGgvcevrrphdaGKGFLRANTKVRITGLIPIDMYAVCRDKL 449
Cdd:cd05160 77 YDPDILTGYNIDDFDLPYLLKRAE-ALGIKLTDGIYRRSG-----------GEKSSGSTERIAVKGRVVFDLLAAYKRDF 144
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 1386448495 450 SLSDYKLDTVARHLLGAKKEDVHYKEIPRLFAAgpEGRRRLGMYCVQDSALVMDLL 505
Cdd:cd05160 145 KLKSYTLDAVAEELLGEGKEKVDGEIIEDAEWE--EDPERLIEYNLKDAELTLQIL 198
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
288-497 |
1.37e-24 |
|
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: 102.43 E-value: 1.37e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 288 PSYQALAFDIECLGEEGFPTAtnEADLILQIScvLWStgeeaGRYRRILLTLGtcEDIEGVEVYEfpSELDMLYAFFQLI 367
Cdd:cd05780 1 EDLKILSFDIEVLNHEGEPNP--EKDPIIMIS--FAD-----EGGNKVITWKK--FDLPFVEVVK--TEKEMIKRFIEIV 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 368 RDLSVEIVTGYNVANFDWPYILDRARhIYSIN-----PASLGKIRAGGVcevrrphdagkgflraNTKVRITGLIPIDMY 442
Cdd:cd05780 68 KEKDPDVIYTYNGDNFDFPYLKKRAE-KLGIEldlgrDGSEIKIQRGGF----------------NNASEIKGRIHVDLY 130
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 1386448495 443 AVCRDKLSLSDYKLDTVARHLLGAKKEDVHYKEIPRLFAAGpEGRRRLGMYCVQD 497
Cdd:cd05780 131 PVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSG-ENLERLFRYSMED 184
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
557-851 |
1.51e-22 |
|
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: 100.50 E-value: 1.51e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 557 ASDRDGYqgatVIQPLSGFYNSpVLVVDFASLYPSIIQAHNLCYSTMITPGEEHRLAGlrpgedyesfrltGGVYHFVKK 636
Cdd:cd05531 3 LADRGGL----VFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPETINCRCCECRDHV-------------YLGHRICLK 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 637 hvHESFLASLLTSWLAKRKAIKKLLaacedpRQRTILDKQQLAIKCTCNAVYGFTGVANGLFPCLSIAETVTLQGRTMLE 716
Cdd:cd05531 65 --RRGFLPEVLEPLLERRLEYKRLK------KEEDPYAGRQKALKWILVTSFGYLGYKNAKFGRIEVHEAITAYGRKILL 136
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 717 RAKAFVEalspanlqalapspdawaplnpEGQLRVIYGDTDSLFIECRGFSEsetlRFAEALAAHTTRslfvaPISLEAE 796
Cdd:cd05531 137 RAKEIAE----------------------EMGFRVLHGIVDSLWIQGRGDIE----ELAREIEERTGI-----PLKLEGH 185
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 797 KTFSCLM-----LITKKRYVGVLTDGKTLMKGVELVRKTACKFVQTRCRRVLDlVLADAR 851
Cdd:cd05531 186 YDWIVFLperdgLGAPNRYFGRLSDGEMKVRGIELRRRDTPPFVKKFQEEALD-ILASAK 244
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
289-950 |
1.65e-22 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 104.33 E-value: 1.65e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 289 SYqaLAFDIECLGEEGFPTA----------------TNEADLILqISCVLWSTGEEAGRYRRILLTLGTCEDIEGVEVYE 352
Cdd:PHA03036 161 SY--LFLDIECHFDKKFPSVfinpvshisccyidlsGKEKRFTL-INEDMLSEDEIEEAVKRGYYEIESLLDMDYSKELI 237
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 353 FPSELDMLYaFFQLIRDLSVEIVTGYNVANFDWPYILDR-----ARHIYSINPASLGKIRaggVCEVRR---PHDAGKGF 424
Cdd:PHA03036 238 LCSEIVLLR-IAKKLLELEFDYVVTFNGHNFDLRYISNRlelltGEKIIFRSPDGKETVH---LCIYERnlsSHKGVGGV 313
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 425 lrANTKVRI---TGLIPIDMYAVCRDKLSLSDYKLDTVAR---HLLGAKKE--DVHYKEIP----------RLFA----- 481
Cdd:PHA03036 314 --ANTTYHInnnNGTIFFDLYTFIQKTEKLDSYKLDSISKnafNCNAKVLSenNNEVTFIGdnttdakgkaSIFSevlst 391
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 482 ---------------------------------AGPEGRRRL------------------------GMYCVQDSALVMDL 504
Cdd:PHA03036 392 gnyvtindddickildkdiiensftvkvicknnYIPGDTYTLsfgkddvdlsdmyknynleialemARYCIHDACLCKYL 471
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 505 LNHFVIHVEVAEIAKIAHIPCRRVLD-------DGQQIRVfscLLaaaqkENFILPMPSASDRDG-YQGATVIQPLSGFY 576
Cdd:PHA03036 472 WEYYGIETKIDAGASTYLLPQSMVFEyrastliKGPLLKL---LL-----EEKTILVRSETKNKFpYEGGKVFAPKQKMF 543
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 577 NSPVLVVDFASLYPSIIQAHNLCYSTMI-TPGEEHRLAG------LR---PGEDYESF----RLTGGVYHF-VKKHVHES 641
Cdd:PHA03036 544 DNNVLIFDYNSLYPNVCIFGNLSPETLVgVVVNDNRLEAeinkqeLRrkyPYPRYIYVhcepRSPDLVSEIaVFDRRIEG 623
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 642 FLASLLTSWLAKRKAIKKLLAACEDPRQRTILDKQQLAIKCTCNAVYGFTGVANGLFPCLSIAETVTLQGRTMLE----- 716
Cdd:PHA03036 624 IIPKLLKTFLEERARYKKLLKEATSSVEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCTAIGRNMIKylnsv 703
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 717 ------RAKAFVEALSPAN-----LQALAPSPDAWAPLNPEGQLRVIYGDTDSLFIECRGFSESETLRFAEALAAHTTRS 785
Cdd:PHA03036 704 lngsklINGKLILANCPINpffkdDRSIDTNYDTNLPVEYNFTFRSVYGDTDSVFLEINTKDVDKSIKIAKELERIINEK 783
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 786 LFVAPISLEAEKTFSCLMLITKKRYVGV-----LTDGKTLM---KGVELVRKTACKFVQTRCRRVLDLVLAdarvkeaas 857
Cdd:PHA03036 784 VLFDNFKIEFEAVYKNLIMQSKKKYTTLkyiasSTDGSVPErvnKGTSETRRDVSKFHKYMIKIYKTRLLD--------- 854
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 858 LLShrpfqESFTQGLPVgflpVIDILNQAYTDLREGrvpmgelcFSTE--------LSRKLSA-YKSTQMPHLAVYQKFV 928
Cdd:PHA03036 855 MLS-----EGNMNSNQV----CIDILRSLEKDLIIE--------FDSRsaplemflLSRTHHCnYKSPDNPNMYLVNEYN 917
|
810 820
....*....|....*....|..
gi 1386448495 929 ERNEELPQIHDRIQYVFVEPKG 950
Cdd:PHA03036 918 KNNPEKIEIGERYYFAYICPIN 939
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
565-994 |
2.84e-22 |
|
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: 100.03 E-value: 2.84e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 565 GATVIQPLSGFYNSpVLVVDFASLYPSIIQAHNLCYSTMITPGEEHRLAGLRPGEDYESFRLTggvyhfvkkhvhESFLA 644
Cdd:cd05537 5 GGYVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLIDPLGLIEGLKAPDPEDLIPGFLGARFSRE------------KHILP 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 645 SLLTSWLAKRKAIKKllaacedprqrtilDKQQL---AIKCTCNAVYGFTGVANGLFPCLSIAETVTLQGRTMLERAKAF 721
Cdd:cd05537 72 DLIARLWAARDEAKR--------------EKNAPlsqAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAW 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 722 VEALspanlqalapspdawaplnpegQLRVIYGDTDSLFIECR-GFSESETLRFAEALAAH---------TTRSLFVAPI 791
Cdd:cd05537 138 IEQQ----------------------GYQVIYGDTDSTFVWLGeELDAAEAQAIGKELASQinqwwaqklKEEFGLESFL 195
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 792 SLEAEKTFSCLMLIT--------KKRYVGVL-TDGKTLM--KGVELVRKTACKFVQTRCRRVLDLVLADArvkeaasllS 860
Cdd:cd05537 196 EIEFETHYSRFFMPTirgsdegsKKRYAGLKsTDGGDELvfKGLETVRSDWTPLARQFQKELYERVFNDE---------P 266
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 861 HRPFQESFTQglpvgflpvidilnqaytDLREGRVPmGELCFSTELSRKLSAYKSTQMPHLAVYQKFVERNEEL--PQIH 938
Cdd:cd05537 267 YEGFIKETVE------------------ELLAGELD-ELLVYRKRLRRPLSEYTKNVPPHVQAARLADQINRELgrPRQY 327
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*..
gi 1386448495 939 DRIQYVFVepkggVKGarktemaedPAYAERHGVPVAVDHYFDKLLQGAAN-ILQCL 994
Cdd:cd05537 328 QWIEYVIT-----VNG---------PEPLEYRTSPLDYQHYIDKQLKPIADsILPFL 370
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
294-665 |
6.62e-19 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 92.45 E-value: 6.62e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 294 AFDIECLGEEGFP---TATNEADLIL-------QISCVLWSTGEEAGRYRRILLTlgtcEDIEGVEVYEFPSELDMLYAF 363
Cdd:PHA02528 110 NLDIEVTAEDGFPdpeEAKYEIDAIThydsiddRFYVFDLGSVEEWDAKGDEVPQ----EILDKVVYMPFDTEREMLLEY 185
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 364 FQLIRDLSVEIVTGYNVANFDWPYILDRARHIYsinpaslgkiragGVCEVRR--PHdagkGFLRANTKVRITG--LIPI 439
Cdd:PHA02528 186 INFWEENTPVIFTGWNVELFDVPYIINRIKNIL-------------GEKTAKRlsPW----GKVKERTIENMYGreEIAY 248
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 440 DMYAV-CRDKLSL---------SDYKLDTVARHLLGAKKEDVHYKEIPRLFAAGPEgrrRLGMYCVQDSALVMDL---LN 506
Cdd:PHA02528 249 DISGIsILDYLDLykkftftnqPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQ---KYIEYNIIDVELVDRLddkRK 325
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 507 HFVIHVEVAEIAKiahIPCRRVLddgQQIR-----VFSCLLaaaqKENFILPMPSASDRDGYQGATVIQPLSGFYNSpVL 581
Cdd:PHA02528 326 LIELVLSMAYYAK---INFEDVF---SPIKtwdaiIFNSLK----EEKIVIPENKSHKKQKYAGAFVKEPVPGAYRW-VV 394
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 582 VVDFASLYPSIIQAHNLCYSTMITPGEEHRLAGL------RPGEDYeSFRLTGGVYhfvKKHVHeSFLASLLTSWLAKRK 655
Cdd:PHA02528 395 SFDLTSLYPSIIRQVNISPETIAGTFHVAPVHEYinktapRPSDEY-SCSPNGWMY---RKDIR-GVIPTEIKKVFDQRK 469
|
410
....*....|
gi 1386448495 656 AIKKLLAACE 665
Cdd:PHA02528 470 IYKKKMLAAE 479
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
428-763 |
7.77e-19 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 92.61 E-value: 7.77e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 428 NTKVRITGLIPIDMYAVCRDK---LSLSDYKLDTVARHLLG-----------AKKEDVHYKEIPRLFAAGPEGRRRLGMY 493
Cdd:PHA03334 461 NSTSHGFGAHIIDLMRVCNTKsikAKCSSRKLDTVARLIISkskphknppkiGKMDDVKYTEMDGMFTAGGAALARYLIY 540
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 494 CVQDSALVMDLLNHFVIHVE-------------------------VAEIAKIAHIPCRRV-LDDGqqiRVFScllAAAQK 547
Cdd:PHA03334 541 NLVDSELLIRIAKNLDPVIEflnrlratynidyvahgrgvmnfcgFVQSTKSVEVPLLKArLRIG---IFVA---TGRIA 614
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 548 ENFILPMPSASD---RDGYQGATVIQPLSGF-----YNSPVLVVDFASLYPSIIQAHNLCYSTMITPGEEHRLAGL---- 615
Cdd:PHA03334 615 ESLCMPEKYARDcrqKIKLKGGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCDANISPEAIVDPDCTARVRGWvvfd 694
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 616 --RPGEDYESFRLTGGVYHFVKKHV----HESFLASLLTSWLAKRKAIKKLLAACEDPRQRTILDKQQLAIKCTCNAVYg 689
Cdd:PHA03334 695 wkKIDRGFGKATLMYTILRTKPEEPswrrFTTYTTSSLNHYLSMRTEYKGAMKQAKDPKLKSYHNQLQNEMKICANSHY- 773
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1386448495 690 ftGVANGLFPCLsiaetVTLQGRTMLERAKAFVEAlspanlqalapspdawaplnpEGQLRVIYGDTDSLFIEC 763
Cdd:PHA03334 774 --GVAPHACQHL-----ITTLGRHKIKLVEEFIKK---------------------EPGMTVNYGDTDSVMFQL 819
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
288-504 |
1.65e-16 |
|
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: 78.76 E-value: 1.65e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 288 PSYQALAFDIEClGEEGfptatneadlilqiscVLWSTGEEAGRYRRILLtLGTCEDIEGVEVYEFPSELDMLYAFFQLI 367
Cdd:cd05784 1 PKLKVVSLDIET-SMDG----------------ELYSIGLYGEGQERVLM-VGDPEDDAPDNIEWFADEKSLLLALIAWF 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 368 RDLSVEIVTGYNVANFDWPYILDRARHiYSInPASLGkiRAGGVCEVRRPHDAGKGFLRANTKVRITGlipIDMYAVCrd 447
Cdd:cd05784 63 AQYDPDIIIGWNVINFDLRLLQRRAEA-HGL-PLRLG--RGGSPLNWRQSGKPGQGFLSLPGRVVLDG---IDALKTA-- 133
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1386448495 448 KLSLSDYKLDTVARHLLGAKK--EDVHYK--EIPRLFAagpEGRRRLGMYCVQDSALVMDL 504
Cdd:cd05784 134 TYHFESFSLENVAQELLGEGKliHDVDDRgaEIERLFR---EDKLALARYNLQDCELVWRI 191
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
293-681 |
6.85e-16 |
|
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: 82.80 E-value: 6.85e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 293 LAFDIEC---LGEEGFPTATNEADLILQISCVLWSTGEEAGR---YRRILltlgTCEDI----EGVEVYEFPSELDMLYA 362
Cdd:TIGR00592 201 ASFDIETyfhDGKDFFPGDENPADEEIMISTTPVIAKQWDYEsepEARVV----TWKKPdkptTGSYVESVSEEISMIKR 276
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 363 FFQLIRDLSVEIVTGYNVANFDWPYILDR--------ARHIYSINPASL---GKIRAGGVCEVRRphdagKGFLRANTKV 431
Cdd:TIGR00592 277 FWDVIDQEDTDVEITVNGDNFDLVYLADRqvfqfywdAYEDPAEKLGVVllfGRDVDHVSPCVQV-----KGINRDLFFL 351
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 432 RITGLIPIDMYAVCRDKLSLSDYKLDTVARHLLGAKKEDVHYKEIPRLFAAGPEGrrRLGMYCVQDSALVMDLLNHFVIH 511
Cdd:TIGR00592 352 PREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIAKKYEFEAPD--IDAPYSSEYLEVTYELGKEFAPM 429
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 512 VEVAEIAKIAHIPCRRVLDDGQQIRVFSCLLAAAQKENFI-----LPMPSASdRDGYQGATV----IQPLSGFYNSPVLV 582
Cdd:TIGR00592 430 EALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVkgpdeLEYPRRS-WCKYEGGYVkppnVEKGLDKTPPPLVV 508
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 583 VDFA--SLYPSIIQAHNLcySTMITPGEEHRLAGLRPGEDYESFRLTG---GVYHFVKKHVHE--SFLASLLTSWLAKRK 655
Cdd:TIGR00592 509 LDFSmkSLNPSIIRNEIV--SIPDTLHREFALDKPPPEPPYDVHPCVGtrpKDCSFPLDLKGEfpGKKPSLVEDLATERA 586
|
410 420
....*....|....*....|....*...
gi 1386448495 656 AIKKLLAAC--EDPRQRTILDKQQLAIK 681
Cdd:TIGR00592 587 LIKKFMAKVkkIDPDEIVGHDYQQRALK 614
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
347-506 |
2.12e-12 |
|
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: 67.64 E-value: 2.12e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 347 GVEVYEFPSELDMLYAFFQLIRDLSVEIVTGYNVANFDWPYILDRARHIYSIN---------PASLGKIRAGGVcEVRRP 417
Cdd:cd05778 72 GIPVEVVESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDlldeisrvpSDSNGKFGDRDD-EWGYT 150
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 418 HDAGkgflrantkVRITGLIPIDMYAVCRDKLSLSDYKLDTVARHLLGAKKEDVHYKEIPRLFAAG-PEGRRRLGMYCVQ 496
Cdd:cd05778 151 HTSG---------IKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGsASERWRVLEYYLK 221
|
170
....*....|
gi 1386448495 497 DSALVMDLLN 506
Cdd:cd05778 222 RVRLNLEILD 231
|
|
| DNA_polB_epsilon_exo |
cd05779 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ... |
293-394 |
1.62e-11 |
|
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon 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 delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal 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. DNA polymerase epsilon also carries a unique large C-terminal domain with an unknown function. Phylogenetic analyses indicate that it is orthologous to the archaeal DNA polymerase B3 rather than to the eukaryotic alpha, delta, or zeta polymerases. 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
Pssm-ID: 99822 [Multi-domain] Cd Length: 204 Bit Score: 64.59 E-value: 1.62e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 293 LAFDIECLGEE-GFPTAtnEADLILQISCVLWSTGeeagryrrILLTLGTC--EDIEGVE------------VYEFPSEL 357
Cdd:cd05779 5 LAFDIETTKLPlKFPDA--ETDQIMMISYMIDGQG--------YLIVNREIvsEDIEDFEytpkpeyegpfkVFNEPDEK 74
|
90 100 110
....*....|....*....|....*....|....*..
gi 1386448495 358 DMLYAFFQLIRDLSVEIVTGYNVANFDWPYILDRARH 394
Cdd:cd05779 75 ALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAI 111
|
|
| DNA_polB_B1_exo |
cd05783 |
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ... |
288-506 |
9.51e-11 |
|
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: 62.34 E-value: 9.51e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 288 PSYQALAFDIECLGE-EGFPTATNEADLILqISCVLWSTgeeAGRYRRILLTLGTCEDIE-----GVEVYEFPSELDMLY 361
Cdd:cd05783 3 PKLKRIAIDIEVYTPiKGRIPDPKTAEYPV-ISVALAGS---DGLKRVLVLKREGVEGLEgllpeGAEVEFFDSEKELIR 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 362 AFFQLIRDLSveIVTGYNVANFDWPYILDRARHIysinpaslgkiragGVCEVRRPHDAGKGflrantKVRITGLIPIDM 441
Cdd:cd05783 79 EAFKIISEYP--IVLTFNGDNFDLPYLYNRALKL--------------GIPKEEIPIYLKRD------YATLKHGIHIDL 136
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1386448495 442 YAVCRDKlSL---------SDYKLDTVARHLLGAKKEDVHyKEIPRLfaagpeGRRRLGMYCVQDSALVMDLLN 506
Cdd:cd05783 137 YKFFSNR-AIqvyafgnkyREYTLDAVAKALLGEGKVELE-KNISEL------NLYELAEYNYRDAELTLELTT 202
|
|
| 43A |
PHA02524 |
DNA polymerase subunit A; Provisional |
345-663 |
1.09e-10 |
|
DNA polymerase subunit A; Provisional
Pssm-ID: 164925 [Multi-domain] Cd Length: 498 Bit Score: 65.41 E-value: 1.09e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 345 IEGVEVYEFPSELDMLYAFFQLIRDLSVEIVTGYNVANFDWPYILDRARHIYSINPAS----LGKIRAGGVCEVrrphda 420
Cdd:PHA02524 169 LDNVVYMPFEDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNILGEKAANqlspYGKITSKTITNL------ 242
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 421 gkgfLRANTKVRITGLIPIDMYAVCRdKLSLS---DYKLDTVARHLLGAKKEDvHYKEIPRLFAAgpeGRRRLGMYCVQD 497
Cdd:PHA02524 243 ----YGEKIIYKIHGIALMDYMDVFK-KFSFTpmpDYKLGNVGYREVKADKLD-YEGPINKFRKA---DHQRYVDYCVRD 313
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 498 S--ALVMDLLNHFV-IHVEVAEIAKIahipcrRVLDDGQQIRVF-SCLLAAAQKENFILPMPSASDRDGYQGATVIQPLS 573
Cdd:PHA02524 314 TdiILLIDGRRCFIdLILSLSYYAKI------RFDDVLGTIKVWdSIIFNSLVESNVVIPAMKASPKQSFPGAYVKEPVP 387
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 574 GFYNSPvLVVDFASLYPSIIQAHNLC---YSTMITPGE-EHRLAGL--RPGEDYE----SFRLTGGVYHFVKKHVHESFL 643
Cdd:PHA02524 388 GGYRYG-LSFDLTSLYPSILRLLNISpemIAGMFSPARlEDYINKVapKPSDQFScapnGMMYKKGVVGVLPNETEKVFL 466
|
330 340
....*....|....*....|....*
gi 1386448495 644 -----ASLLTSWLAKRKAIKKLLAA 663
Cdd:PHA02524 467 qrkseKKMMLAAIRNQEAIKKILAS 491
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
288-478 |
1.81e-08 |
|
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: 55.41 E-value: 1.81e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 288 PSYQALAFDIECLGEEGFPTAtnEADLILQIScvLWSTGeeagryrrilltlGTCEDIEGvevyEFPSELDMLYAFFQLI 367
Cdd:cd05781 1 PDLKTLAFDIEVYSKYGTPNP--RRDPIIVIS--LATSN-------------GDVEFILA----EGLDDRKIIREFVKYV 59
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 368 RDLSVEIVTGYNVANFDWPYILDRARhiysinpaSLG-KIRAG--GVCEVRRP---HdagkgflrantkVRITGLIPIDM 441
Cdd:cd05781 60 KEYDPDIIVGYNSNAFDWPYLVERAR--------VLGvKLDVGrrGGSEPSTGvygH------------YSITGRLNVDL 119
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 1386448495 442 YAVCRDKLSLSDYKLDTVARHLLGAKKE---DVHYKEIPR 478
Cdd:cd05781 120 YDFAEEIPEVKVKTLENVAEYLGVMKKServLIEWYRIYE 159
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
293-489 |
3.41e-06 |
|
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: 48.95 E-value: 3.41e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 293 LAFDIECLGEEGFPTATNEA--DLILQISCvlwstgEEAGRYRRILLTlgtcEDIegvevyefpSELDMLYAFFQLIRDL 370
Cdd:cd05785 12 LQLDIETYSLPGFFFSNPDRgdDRIIIVAL------RDNRGWEEVLHA----EDA---------AEKELLEELVAIIRER 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 371 SVEIVTGYNVANFDWPYILDRARhIYSInPASLGKIRAggvceVRRPHDAGKGF---LRANTKVRITGLIPIDMY-AVCR 446
Cdd:cd05785 73 DPDVIEGHNIFRFDLPYLRRRCR-RHGV-PLAIGRDGS-----IPRQRPSRFRFaerLIDYPRYDIPGRHVIDTYfLVQL 145
|
170 180 190 200
....*....|....*....|....*....|....*....|....*...
gi 1386448495 447 DKLS---LSDYKLDTVARH--LLGAKKEDVHYKEIPRLFAAGPEGRRR 489
Cdd:cd05785 146 FDVSsrdLPSYGLKAVAKHfgLASPDRTYIDGRQIAEVWRSDPARLLA 193
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
350-507 |
6.20e-06 |
|
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: 48.76 E-value: 6.20e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386448495 350 VYEFPSELDMLYAFFQLIRDLSVEIVTGYNVANFDWPYILDRARHIYSINPASLGKIRaggvceVRRPHDAGKGFLRANT 429
Cdd:cd05776 76 VRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLK------RSVWPKKKGGGKFGER 149
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1386448495 430 KVrITGLIPIDMYAVCRDKLSLSDYKLDTVARHLLGAKKEDVHYKEIPRLFAAgPEGRRRLGMYCVQDSALVMDLLNH 507
Cdd:cd05776 150 EL-TAGRLLCDTYLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYND-SESLLKLLEHTEKDAYLILQLMFK 225
|
|
| |
