|
Name |
Accession |
Description |
Interval |
E-value |
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
81-1126 |
0e+00 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 1474.88 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 81 RPTPPalDPQTEPLIFQQLEIDHYVG----PAQPVPGGPPPSRGSVPVLRAFGVTDEGFSVCCHIHGFAPYFYTPAPPGF 156
Cdd:PTZ00166 31 RPLPP--ISLQKDLVFFQLDADYTEKddksQGNPHNTVSGVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNF 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 157 GPEHMGDLQRELNLAISRDSRGGRelTGPAVLAVELCSRESMFGYHGHGPSPFLRITVALPRLVAPARRLLEQGIRV--- 233
Cdd:PTZ00166 109 LPEDSQKLKRELNAQLSEQSQFKK--YQNTVLDIEIVKKESLMYYKGNGEKDFLKITVQLPKMVPRLRSLIESGVVVcgg 186
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 234 AGLGTPSFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKYALR-LKEKATQCQLEADVLWSDVVSHPPEGPWQRIAPLRV 312
Cdd:PTZ00166 187 GWDGIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRpPKKKTSTCQIEVDCSYEDLIPLPPEGEYLTIAPLRI 266
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 313 LSFDIECAGRKGI-FPEPERDPVIQICSLGLRWGEPE-PFLRLALTLRPCAPILGAKVQSYEKEEDLLQAWSTFIRIMDP 390
Cdd:PTZ00166 267 LSFDIECIKLKGLgFPEAENDPVIQISSVVTNQGDEEePLTKFIFTLKECASIAGANVLSFETEKELLLAWAEFVIAVDP 346
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 391 DVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRVAGLCSNIRDSSFQSKQTGRRDTKVVSMVGRVQMDMLQVLLREYKLR 470
Cdd:PTZ00166 347 DFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLK 426
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 471 SYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPLSYLLSRG 550
Cdd:PTZ00166 427 SYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRG 506
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 551 QQVKVVSQLLRQAMHEGLLMPVVKSEGG---EDYTGATVIEPLKGvrpqdragaawellaltpgrgcspprYYDVPIATL 627
Cdd:PTZ00166 507 QQIKVTSQLLRKCKKLNYVIPTVKYSGGgseEKYEGATVLEPKKG--------------------------FYDEPIATL 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 628 DFSSLYPSIMMAHNLCYTTLLRPGTAQKlgLTEDQFIRTPTGDEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPL 707
Cdd:PTZ00166 561 DFASLYPSIMIAHNLCYSTLVPPNDANN--YPEDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPL 638
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 708 RRQVLDGRQLALKVSANSVYGFTGAQV-GKLPCLEISQSVTGFGRQMIEKTKQLVESKYTVENGYSTSAKVVYGDTDSVM 786
Cdd:PTZ00166 639 LKKVLNGRQLALKISANSVYGYTGAQVgGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVM 718
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 787 CRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKGLEAVRRDNCPLV 866
Cdd:PTZ00166 719 VKFGTDDIQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAGLLY-TNPEKYDKIDCKGIETVRRDNCLLV 797
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 867 ANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRaaSDYAGKQAHVELAERMRKRDPGSAPSLGD 946
Cdd:PTZ00166 798 QQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRIDISLLVITKSLGK--DDYEGRLAHVELAKKLRQRDPGSAPNVGD 875
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 947 RVPYVIISAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEqQLAKPLLRIFEPILGEgraEAVLLRGDHTRCKTVLTGKVG 1026
Cdd:PTZ00166 876 RVSYVIVKGAKGAPQYERAEDPLYVLENNIPIDTQYYLD-QIKNPLLRIFEGVMDN---PDSLFSGEHTRHITISSSSKG 951
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 1027 GLLAFAKRRNCCIGCRTVLShQGAVCEFC-QPRESELYQKEVSHLNALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIF 1105
Cdd:PTZ00166 952 GLSKFVKKQLQCLGCKSVIK-EGALCDNCnQNKEPSIYGKKLAKRRHKEAEYSQLWTQCQRCQGSLHQEVICTNRDCPIF 1030
|
1050 1060
....*....|....*....|.
gi 821174304 1106 YMRKKVRKDLEDQEQLLRRFG 1126
Cdd:PTZ00166 1031 YRRKKVQKDLAELQELLSRFG 1051
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
579-1000 |
0e+00 |
|
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: 815.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 579 EDYTGATVIEPLKGvrpqdragaawellaltpgrgcspprYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGl 658
Cdd:cd05533 1 EQYEGATVIEPIKG--------------------------YYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKLP- 53
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 659 tEDQFIRTPTGDEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLP 738
Cdd:cd05533 54 -PEDYIKTPNGDYFVKSSVRKGLLPEILEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLP 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 739 CLEISQSVTGFGRQMIEKTKQLVESKYTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRL 818
Cdd:cd05533 133 CLEISSSVTSFGRQMIEKTKKLVEEKYTKANGYSHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKL 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 819 EFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQDVISDLL 898
Cdd:cd05533 213 EFEKVYFPYLLINKKRYAGLLW-TNPDKHDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLL 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 899 CNRIDISQLVITKELTRAASDYAGKQAHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVLEHSLPI 978
Cdd:cd05533 292 QNKIDISLLVITKALTKTADDYAGKQAHVELAERMRKRDPGSAPNVGDRVPYVIIKGAKGAKAYEKAEDPIYVLENNIPI 371
|
410 420
....*....|....*....|..
gi 821174304 979 DTQYYLEQQLAKPLLRIFEPIL 1000
Cdd:cd05533 372 DTQYYLENQLSKPLLRIFEPIL 393
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
541-999 |
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: 562.62 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 541 VPLSYLLSRGQQVKVVSQLLRQAMHEGLLMPVVKSEGG--EDYTGATVIEPLKGvrpqdragaawellaltpgrgcsppr 618
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRPSAKGdeDGYQGATVIEPKKG-------------------------- 54
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 619 YYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTA---QKLGLTEDQFIRTPTGDEFVKTSVRKGLLPQILENLLSARKR 695
Cdd:pfam00136 55 FYDKPVLVLDFNSLYPSIIQAHNLCYTTLVRSVDEannLPPEDNLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKA 134
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 696 AKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKYTvengysTSA 775
Cdd:pfam00136 135 IKKLLKEETDPFERAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYT------YNF 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 776 KVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGH-FPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKG 854
Cdd:pfam00136 209 RVIYGDTDSVFIEFGGKDVEEAMKIGDELAEHVNQDlFKSPIKLEFEKVYKPLLLISKKKYAGLKY-TAPSNFNKLDMKG 287
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 855 LEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQDVI----SDLLCNRIDISQLVITKELTRAASDYAGKQ-AHVEL 929
Cdd:pfam00136 288 VDLVRRDNCPLVKEVIKKVLDLLLSDRGLPVGLEFVISILndarSDLRNNKVPLEKFVISKELSKPPDNYKSKNlPHVEV 367
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 821174304 930 AERMRKRDpGSAPSLGDRVPYVIISAAK---GVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 999
Cdd:pfam00136 368 ALRMNKRN-GEAPEVGDRIPYVIVKAAKglkNLLIYERAEDPEYVLENNLPIDYEYYFSNQLIPPVARLLEPI 439
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
119-999 |
1.15e-177 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 540.96 E-value: 1.15e-177
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 119 RGSVPVLRAFGVTDEGFSVCCHIHGFAPYFYTPAPpgfgpehmgdlQRELNLAISRDSRGgreltgpaVLAVELCSRESM 198
Cdd:COG0417 15 EDGKPVIELWGRTEDGPSVLLDVTGFRPYFYVPLP-----------DEEKLEELLRDIKE--------ITEVEPVKLKSF 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 199 FGyhghGPSPFLRITVALPRLVAPAR-RLLEQGIRVaglgtpsfapYEANVDFEIRFMVDTDIVGCNWLELPAGKYALRL 277
Cdd:COG0417 76 FG----EPVPVLKIYTRDPRDVRELRdRLKEGGIDV----------YEADIRFHDRYLIDRFLTPGVWYEGEVEEDGGKL 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 278 KEKatqcqleadvlwsdVVSHPPEGPWQRIAPLRVLSFDIECAGRKGiFPEPERD-PVIQICSlglrwgEPEPFLRLALT 356
Cdd:COG0417 142 DYE--------------VKENPRLKPEDYRPKLKVLSFDIEVSTPRG-FPDPERDgPIISIGL------AGSDGEKKVLM 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 357 LRpcAPILGAKVQSYEKEEDLLQAwstFIRIM---DPDVITGYNIQNFDLPYLISRAQTLKVqtfPF-LGRVAGLCSnIR 432
Cdd:COG0417 201 LG--REGVDFEVEYFDDEKALLEA---FFEIIreyDPDIIIGWNVDNFDLPYLQKRAERLGI---PLdLGRDGSEPS-WR 271
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 433 DSSFQSKqtgrrdtkvVSMVGRVQMDMLQVLLR-EYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQngnDQTRRRLAVY 511
Cdd:COG0417 272 EHGGQGF---------ASIPGRVVIDLYDALKSaTYKFKSYSLDAVAEELLGEGKLIVDGGEIERLW---DDDKPALAEY 339
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 512 CLKDAYLPLRLLERLMVLVNAVEMARVTGVPLsYLLSRGQQVKVVSQL-LRQAMHEGLLMPVVKSEGGEDYTGATVIEPL 590
Cdd:COG0417 340 NLRDAELTLRIFEKTLLLPFLIELSRITGLPL-DDVGRAGSSAAFENLlLPEAHRRGYLAPNKGEIKGEAYPGGYVLDPK 418
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 591 KGVrpqdragaawellaltpgrgcspprYYDVpiATLDFSSLYPSIMMAHNLCYTTLLRPGTAQklgltEDQFIRTPT-G 669
Cdd:COG0417 419 PGL-------------------------YENV--LVLDFKSLYPSIIRTFNISPETLVEGGEEP-----CGDEDVAPGfG 466
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 670 DEFVKTsvRKGLLPQILENLLSARKRAKAELAK-ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTG 748
Cdd:COG0417 467 HRFCRE--PKGILPSILEELWDERDEAKKKMKKaKPDSEEYRLYDALQQALKILMNSFYGVLGSEGCRFYDPELAESITA 544
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 749 FGRQMIEKTKQLVESKytvenGYstsaKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYL 828
Cdd:COG0417 545 RGREIIKQTIEKAEEL-----GY----KVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRRFF 615
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 829 LI-SKKRYAGLLfssrPDahDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQL 907
Cdd:COG0417 616 FPgSKKRYAGLT----ED--GKIDIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDL 689
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 908 VITKELTRAASDY-AGKQAHVELAERMRKRdpGSAPSLGDRVPYVIISAAKGVaaymksEDPLFVLEHSLPIDTQYYLEQ 986
Cdd:COG0417 690 VIRKRLRKPLSEYeKNVPPHVRAARKLDER--GRPYQRGDKISYVITKGGGRV------EPVELAKERESEIDYDYYIEK 761
|
890
....*....|...
gi 821174304 987 QLAKPLLRIFEPI 999
Cdd:COG0417 762 QLKPTADRILEAF 774
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
304-533 |
1.09e-152 |
|
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: 454.34 E-value: 1.09e-152
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 304 WQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEKEEDLLQAWST 383
Cdd:cd05777 1 WSKIAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWRD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 384 FIRIMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRVAGLCSNIRDSSFQSKQTGRRDTKVVSMVGRVQMDMLQVL 463
Cdd:cd05777 81 FVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQFDLLQVI 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 464 LREYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAV 533
Cdd:cd05777 161 QRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLMCLVNYI 230
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
309-790 |
4.14e-143 |
|
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: 439.27 E-value: 4.14e-143
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 309 PLRVLSFDIECAGRKGIFPEPE--RDPVIQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEKEEDLLQAWSTFIR 386
Cdd:smart00486 2 PLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEFIK 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 387 IMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRV-AGLCSNIRDSSFQSKQTGRRDTKVVsMVGRVQMDMLQVLLR 465
Cdd:smart00486 82 KYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLkIGLRIPNKKPLFGSKSFGLSDIKVY-IKGRLVIDLYRLYKN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 466 EYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPLSY 545
Cdd:smart00486 161 KLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLRR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 546 LLSRGQQVKVVSQLLRQAMHEGLLMPVVKSEGG----------EDYTGATVIEPLKGvrpqdragaawellaltpgrgcs 615
Cdd:smart00486 241 TLYYGSQIRVESLLLREAKKNNYILPSKELYDFkgsepdlkkkVKYEGGKVLEPKKG----------------------- 297
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 616 pprYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGLT----EDQFIRTPTG--DEFVKTSVRKGLLPQILENL 689
Cdd:smart00486 298 ---FYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKGDLiipeDLLTIKYEKGnkYRFVKKNIRKGILPKLLKKL 374
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 690 LSARKRAKAELAKETDPL--RRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKYTV 767
Cdd:smart00486 375 LDKRKEIKKLMKKEKDESeeLKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGYP 454
|
490 500
....*....|....*....|...
gi 821174304 768 ENGYstsaKVVYGDTDSVMCRFG 790
Cdd:smart00486 455 KPGF----KVIYGDTDSIFVTKP 473
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
119-1001 |
2.87e-108 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 357.24 E-value: 2.87e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 119 RGSVPVLRAFGVTDEGFSVCCHIHGFAPYFYtPAppgfgpEHMGDLQRELNLAISRDSRggreltgpavlAVELCS--RE 196
Cdd:PRK05762 16 TPGGPEVELWLATDEGPRVVLLDPQFRPYFI-PA------EQDERAESLLAGEIGVRLS-----------PLALKDfhRR 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 197 SMFGYhghgPSPFLRITVALPRlvaparRLLEQGIRVaglgtpsfapYEANVDFEIRFMVDTDIVGCNWLElpaGKYALR 276
Cdd:PRK05762 78 PVLGL----YCRQHRQLTRLPK------RLREGGVDV----------YEADIRFPERYLMERFITPCVWFS---GEVEQY 134
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 277 LKE-KATQCQLEADVLWsdvvshPPegpwqriaPLRVLSFDIECAgRKGI-----FPEPERDPVIQIcslglrwGEPEPf 350
Cdd:PRK05762 135 TTDgVLRNARLKPAPDY------RP--------PLKVVSLDIETS-NKGElysigLEGCGQRPVIML-------GPPNG- 191
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 351 lrlaltlrpCAPILGAKVQSyekEEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVqtfPF-LGRvAGLCS 429
Cdd:PRK05762 192 ---------EALDFLEYVAD---EKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGI---PLrLGR-DGSEL 255
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 430 NIRDSSFQSkqtgrrDTKVVSMVGRVQMDMLQVLLR-EYKLRSYTLNAVSFHFLGEQKEdvqhsIITDLQNGNDQTRR-- 506
Cdd:PRK05762 256 EWREHPFRS------GYGFASVPGRLVLDGIDALKSaTWVFDSFSLEYVSQRLLGEGKA-----IDDPYDRMDEIDRRfa 324
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 507 ----RLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPlsylLSR--GQQVKVVSQLLRQAMHEGLLMPVVKSEGGED 580
Cdd:PRK05762 325 edkpALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLP----LDRvgGSVAAFEHLYLPRAHRAGYVAPNLGERPGEA 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 581 YTGATVIEPLKGVrpqdragaawellaltpgrgcspprYYDVpiATLDFSSLYPSIMMAHNLCYTTLLRPgtaqkLGLTE 660
Cdd:PRK05762 401 SPGGYVMDSKPGL-------------------------YDSV--LVLDFKSLYPSIIRTFNIDPDGLVEG-----LAQPP 448
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 661 DQFIRTPTGDEFVKTsvrKGLLPQILENLLSARKRAKAELAKEtdplrrqvldgRQLALKVSANSVYGFTGAQVGKLPCL 740
Cdd:PRK05762 449 EESVAGFLGARFSRE---KHFLPEIVERLWEGRDEAKREMNKP-----------LSQAIKIIMNAFYGVLGSSGCRFFDP 514
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 741 EISQSVTGFGRQMIEKTKQLVESKytvenGYstsaKVVYGDTDSVMCRFGVS-SVAEAMALGREAADWVSGHFPSPIR-- 817
Cdd:PRK05762 515 RLASSITMRGHEIMKQTRELIEAQ-----GY----QVIYGDTDSTFVWLGGAhDEEDAAKIGRALVQEINQWWQEHLQqe 585
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 818 --------LEFEKVY----FPYLLI----SKKRYAGLLfsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDR 881
Cdd:PRK05762 586 fglesaleLEFEKHYrrffMPTIRGaeegSKKRYAGLI--QEGDGDGRIVFKGLETVRTDWTPLAKEFQQELYERIFRGE 663
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 882 DPEGAVahaQDVISDLLCNRIDiSQLVITKELTRAASDYAGKQA-HV----ELAERMRKRDPGSAPSLGDRVPYVIISAA 956
Cdd:PRK05762 664 PYVDYV---REVIDKLRAGELD-EKLVYRKRLRRPLDEYQRNVPpHVraarLADEMGYKVGRPLQYQNGGKIGYVITVNG 739
|
890 900 910 920
....*....|....*....|....*....|....*....|....*
gi 821174304 957 KGVAAYMKSedplfvlehslPIDTQYYLEQQLaKPLLRIFEPILG 1001
Cdd:PRK05762 740 PEPLEYRKS-----------PIDYDYYIEKQL-QPVADRILPFFG 772
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
550-999 |
3.40e-98 |
|
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: 319.16 E-value: 3.40e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 550 GQQVKVVSQLLRQAMHEGLLMPvvkseggedytgatviEPLKGVRPQDRAGaawELLALT--PgrgcsPPRYYDVPIATL 627
Cdd:cd05534 1 GSQFRVESMLLRLAKPENYILP----------------SPSRQQVAQQRAL---ECLPLVmeP-----ESGFYSDPVIVL 56
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 628 DFSSLYPSIMMAHNLCYTTLL-------------RPGTAQK-------LGLTEDQFIRTPTGDEFVKTSVRKGLLPQILE 687
Cdd:cd05534 57 DFQSLYPSIMIAYNYCYSTCLgrveelngggkfgFLGVKLYlppppldLLLLKDDVTISPNGVMFVKKSVRKGILPKMLE 136
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 688 NLLSAR---KRAKAELAKETDPLRRqvLDGRQLALKVSANSVYGFTGAQV-GKLPCLEISQSVTGFGRQMIEKTKQLVES 763
Cdd:cd05534 137 EILDTRimvKKAMKKYKDDKKLQRI--LDARQLALKLLANVTYGYTAASFsGRMPCVEIADSIVQTGRETLERAIELIES 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 764 kyTVENGystsAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSSR 843
Cdd:cd05534 215 --TPKWG----AKVVYGDTDSLFVLLPGRTKEEAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESP 288
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 844 PDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDYAGK 923
Cdd:cd05534 289 DQTEPTFDAKGIETVRRDGCPAVQKILEKSLRILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLGTYKEGAT 368
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 821174304 924 -QAHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDP-LFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 999
Cdd:cd05534 369 lPAGAIVALRRMEKDPRAEPQYGERVPYVVVRGEPGSRLIDLVVSPeEFLADPSLRLDAEYYITKQIIPALDRLFNLV 446
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
130-477 |
2.19e-96 |
|
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: 310.12 E-value: 2.19e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 130 VTDEGFSVCCHIHGFAPYFYTPAPPGFGPEHMGDLQRELNLAISRdsrggreltgpaVLAVELCSRESMFGYHGHgPSPF 209
Cdd:pfam03104 1 KTDEGVSVCVNVFGFKPYFYCLAPDGKELEEVIEEIKELYEGLDK------------IEKIELKLKKSLYGYEED-PVPY 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 210 LRITVALPRLVAPARRLLEQGirvaglgtPSFAPYEANVDFEIRFMVDTDIVGCNWLELPagKYALRLKEKATQCQLEAD 289
Cdd:pfam03104 68 LKVSFANPRPLLKIRKYLSPE--------NISDVYEYDVDYLERFLIDNDIVGFGWYKVK--VYPFRAEGRISNCDVEID 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 290 VLWSDVVSHPPEGPWqriAPLRVLSFDIECAGRKGIFPEPER--DPVIQICSLGLRWGEPEPFLRLALTLRPCAPI---- 363
Cdd:pfam03104 138 CDSPDLISVPFEKEW---PPLRVLSFDIECTSLPGKFPDAENvkDPIIQISCMLDGQGEPEPEPRFLFTLRECDSEdied 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 364 ---------LGAKVQSYEKEEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRVA-GLCSNIRD 433
Cdd:pfam03104 215 feytpkpiyPGVKVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNrGGRSKVRE 294
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 821174304 434 SSFqskqtGRRDTKVVSMVGRVQMDMLQVLLREYKLRSYTLNAV 477
Cdd:pfam03104 295 IGF-----GTRSYEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
253-997 |
3.92e-85 |
|
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: 300.82 E-value: 3.92e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 253 RFMVDTDIVGCNWLELpaGKYALRLKEKATQCQLEADVLWSDVVShppEGPWQRIAPLRVLSFDIECAGRKGIFPEPERD 332
Cdd:TIGR00592 454 RFLLLRKIKGPCWLAV--KGPDELEYPRRSWCKYEGGYVKPPNVE---KGLDKTPPPLVVLDFSMKSLNPSIIRNEIVSI 528
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 333 PVIQICSLGLRWGEPEPFLRLALTL--RP--CAPILG----------AKVQSYEKEEDLLQAWSTFIRIMDPDVITGYNI 398
Cdd:TIGR00592 529 PDTLHREFALDKPPPEPPYDVHPCVgtRPkdCSFPLDlkgefpgkkpSLVEDLATERALIKKFMAKVKKIDPDEIVGHDY 608
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 399 QNFDLPYLISRAQTLKVQTFPFLGRVAglcsnirdssfQSKQTGRRdtKVVSMVGRVQMDMLQVLLREYKLRSYTLNAVS 478
Cdd:TIGR00592 609 QQRALKVLANRINDLKIPTWSKIGRLR-----------RSPKFGRR--FGERTCGRMICDVEISAKELIRCKSYDLSELV 675
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 479 FHFLG-EQKEDVQHSIITDLQNGNDQTRrrLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPLSYLLSRGQQVKVVS 557
Cdd:TIGR00592 676 QQILKtERKVIPIDNINNMYSESSSLTY--LLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEF 753
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 558 QLLRQAMHEGLLMP---VVKSEGGEDYTGATVIEPLKGVRPQDRAGaawelLALTPGRGcspprYYDVPIATLDFSSLYP 634
Cdd:TIGR00592 754 LLLHAFYENNYIVPdkqIFRKQQKLGDEDEEIDGYKKGKKAAYAGG-----LVLEPKVG-----LYDKYVLLMDFNSLYP 823
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 635 SIMMAHNLCYTTLLRPgtaqklgLTEDQFIRTPtgdefvKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDG 714
Cdd:TIGR00592 824 SIIQEFNICFTTVQQK-------VDEDELPELP------DSELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDI 890
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 715 RQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKYTvengystsaKVVYGDTDSVMCRFGVSSV 794
Cdd:TIGR00592 891 RQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEMNL---------EVIYGDTDSIMINTPGTKY 961
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 795 AEAMALGREAADWVSGHFPsPIRLEFEKVYFPYLLISKKRYAGLLFS--SRPDAHDRMDCKGLEAVRRDNCPLVANLVTA 872
Cdd:TIGR00592 962 EEVFKIGKEFKSEVNKLYK-LLELDIDGVFKRLLLLKKKKYAAIKVEgdSDGNYTTKQEVKGLDIVRRDWSPLAKETGKK 1040
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 873 SLRRLLIDRDPEGAVAHAQDVISDL----LCNRIDISQLVITKELTRAASDYAGK--QAHVELAERMRKRDPGSAPSlGD 946
Cdd:TIGR00592 1041 VLDTILSDKDVEEAVEEVQEVLEKIgknvLNGEVPLEKFVINKQLTRDPKDYPDGasLPHVHVALRINARGGRKVKA-GD 1119
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|....
gi 821174304 947 RVPYVIISAAKGVAAYMKS---EDPLFvLEHSLPIDTQYYLEQQLAKPLLRIFE 997
Cdd:TIGR00592 1120 VVSYVICKDGGNLSARQRAyalEELQR-KHNNLIYDTQYYLEHQIHPVVLRILE 1172
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
579-997 |
8.72e-82 |
|
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: 270.01 E-value: 8.72e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 579 EDYTGATVIEPLKGVRPqdragaawellaltpgrgcsppryydvPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLgl 658
Cdd:cd00145 1 EPYEGGYVFDPIPGLYE---------------------------NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAP-- 51
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 659 tEDqfirtPTGDEFVKTSVRKGLLPQILENLLSARKRAKAELAK-ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKL 737
Cdd:cd00145 52 -ED-----YIGVGFRSPKDRKGLLPRILEELLNFRDEAKKRMKAaKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRF 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 738 PCLEISQSVTGFGRQMIEKTKQLVESKytvenGYstsaKVVYGDTDSVMCRFGVS-SVAEAMALGREAADWVsgHFPSPI 816
Cdd:cd00145 126 YDPEVAASITSFGREIIQDTIALVEEH-----GA----RVIYGDTDSIFVSLPKMgTKEDAIKEGREILQEL--ADEHLL 194
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 817 RLEFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQDVIsd 896
Cdd:cd00145 195 ELEFEKVYLPFFLGKKKRYAGLDI-WKGQDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEERKVEAVKEYIDEL-- 271
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 897 llcnridisqlvitkeltraasdyagkqahvelaermrkrdpgsapslgDRVPYVIISAAKGVAAYMKSEDPLFVLEHSL 976
Cdd:cd00145 272 -------------------------------------------------DKVKYVVTRGGKGVPDYERADPPLEDLDKRH 302
|
410 420
....*....|....*....|.
gi 821174304 977 PIDTQYYLEQQLAKPLLRIFE 997
Cdd:cd00145 303 RIDYEYYLERLLQPPLERIFE 323
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
581-1001 |
6.71e-79 |
|
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: 264.83 E-value: 6.71e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 581 YTGATVIEPLKGvrpqdragaawellaltpgrgcspprYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGLTE 660
Cdd:cd05532 8 YAGGLVLEPKKG--------------------------LYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEDDEEP 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 661 DQfirtptgdefVKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCL 740
Cdd:cd05532 62 PL----------PPSDQEKGILPRIIRKLVERRRQVKKLMKSEKDPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAK 131
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 741 EISQSVTGFGRQMIEKTKQLVESKytvenGYStsakVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSpIRLEF 820
Cdd:cd05532 132 PLAALITSKGREILQKTKDLVEKM-----NLE----VIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKK-LEIDI 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 821 EKVYFPYLLISKKRYAGLLFSSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAV----AHAQDVISD 896
Cdd:cd05532 202 DGVFKRLLLLKKKKYAALKVVDDDKGKLKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVenihEYLRKINED 281
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 897 LLCNRIDISQLVITKELTRAASDYAGK--QAHVELAERMRKRDPGSAPslGDRVPYVIIS--AAKGVA--AYMKSEdplF 970
Cdd:cd05532 282 LRNGKIPLEKFIITKQLTKNPEEYPDKksLPHVQVALRMNKRGRKVKA--GDTIPYIICKdgSSKSLAdrAYHPDE---V 356
|
410 420 430
....*....|....*....|....*....|.
gi 821174304 971 VLEHSLPIDTQYYLEQQLAKPLLRIFEPILG 1001
Cdd:cd05532 357 KKNENLKIDIEYYLSQQILPPISRLCEPIEG 387
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
579-997 |
2.58e-73 |
|
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: 248.01 E-value: 2.58e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 579 EDYTGATVIEPLKGVrpqdragaaWEllaltpgrgcsppryydvPIATLDFSSLYPSIMMAHNLCYTTLLRPGtaqklgl 658
Cdd:cd05536 2 ESYEGGIVLEPEKGL---------HE------------------NIVVLDFSSLYPSIMIKYNISPDTLVREG------- 47
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 659 TEDQFIRTPTGDEFVKTsvRKGLLPQILENLLSARKRAKAELaKETDP--LRRQVLDGRQLALKVSANSVYGFTGAQVGK 736
Cdd:cd05536 48 CEDCDVEPQVGHKFRKD--PPGFIPSVLEDLLEERRRIKEKM-KKLDPesEEYKLLDERQRAIKILANSFYGYMGWANAR 124
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 737 LPCLEISQSVTGFGRQMIEKTKQLVEskytvENGYstsaKVVYGDTDSVmcrFGVSSVAEA-MALGREAADWVSGHFpsP 815
Cdd:cd05536 125 WYCKECAEAVTAWGREYIKTTIKIAE-----EKGF----KVIYGDTDSL---FVKIDGADAvKKKVKKLLKYINEEL--P 190
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 816 IRLEFEKVYFPYLLISKKRYAGLlfssrpDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQDVIS 895
Cdd:cd05536 191 LELEIEKFYKRGFFVTKKRYAGL------TEDGKIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVIE 264
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 896 DLLCNRIDISQLVITKELTRAASDYAGKQAHVELAERMRKRdpGSAPSLGDRVPYVIIsaaKGVAAYMKSEDPLFVLEHS 975
Cdd:cd05536 265 KLKRGEVPPEKLVIWKQLTKDLSEYKATGPHVAAAKKLAKR--GYKVRPGTKIGYVIV---KGSGKISDRAYPYDMVDEK 339
|
410 420
....*....|....*....|..
gi 821174304 976 LPIDTQYYLEQQLAKPLLRIFE 997
Cdd:cd05536 340 HKYDAEYYIDNQVLPAVLRILE 361
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
143-1001 |
1.51e-62 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 228.81 E-value: 1.51e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 143 GFAPYFYTPAPPgfgpehmgDLQRELNLaISRDsrggreltgPAVLAVELCSRESmfGYHGHgPSPFLRITVALPRLVAP 222
Cdd:PRK05761 53 GHKPYFLTDLDP--------DEIDKIPK-ILRH---------PSFDHLEIVEKYD--GLRDK-KVKVTKIVVKDPLAVRR 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 223 ARRLLEQGIRVaglgtpsfapYEANVDFEIRFMVDTDIVGCNWLELPAGKYALRLKE------KATQCQLEADVLWSDVV 296
Cdd:PRK05761 112 LRLSVRDIPRA----------WEADIKYEFRYIYDNGLIPGMPYDVKNGLESVEPEIlveeikKAFKDERKLAEDWLPIF 181
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 297 SHPPegpwqriAPLRVLSFDIECAGrkgifPEPERDPViqicslglrwgepepflrlaltlrpcapilgakvqsyEKEED 376
Cdd:PRK05761 182 EAPI-------PKIKRIAIDIEVYT-----PAKGRIPD-------------------------------------DSEKE 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 377 LLQAWSTFIRIMDPDVItgYNIQNFDLPYLISRAQTLKVQTFPFLGRVAGLCSNIRDSSFQSKqtgrRDTKVVSMVGRvq 456
Cdd:PRK05761 213 LLAELFDIILEYPPVVT--FNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQN----KAVRSYAFYGK-- 284
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 457 mdmlqvllreYKLRSYTLNAVSFHFLGEQKEDVQHSIitdlqngNDQTRRRLAVYCLKDAYLPLRL--LERLMVLVNAVE 534
Cdd:PRK05761 285 ----------YRHREARLDAVGRALLGISKVELETNI-------SELDLEELAEYNFRDAEITLKLtfFNNELVLKLILL 347
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 535 MARVTGVPLSYLlSRGQQVKVVSQLL-RQAMHEGLLMP-----------VVKSEG--GEDYTGATVIEPLKGVrpqdrag 600
Cdd:PRK05761 348 LSRISKLPIEEL-SRATISTWISNLEyWEHRKRGWLIPwkedilrldheVYKKAIikGKKYRGGLVFQPPPGI------- 419
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 601 aawellaltpgrgcspprYYDVpiATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLgltedqfIRTPTGDEFVKTSVRKG 680
Cdd:PRK05761 420 ------------------FFNV--YVLDFASLYPSIIVKWNLSPETVRIPECKCHY-------DDEVPELGHSVCDDRPG 472
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 681 LLPQILENLLSARKRAKAELAKE--TDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTK 758
Cdd:PRK05761 473 LTSVLVGLLRDFRVKIYKKKAKDpnLDEERRAWYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESITALGREILLSTK 552
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 759 QLVEskytvENGYstsaKVVYGDTDSVMCRFGVSSVAEAMalgreaADWVSGHFpsPIRLEFEKVYfPYLLIS--KKRYA 836
Cdd:PRK05761 553 KKAE-----ELGL----KVLYGDTDSLFVWGPTKESLEEL------IKEIEERT--GIDLEVDKTY-DWVAFSglKKNYF 614
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 837 GLLFSsrpdahDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAV-------AHAQDVISDLLCNRIDISQLVI 909
Cdd:PRK05761 615 GVLKD------GKVKIKGIVAKKRNTPEFVKELQREVLEVLKSIRSPEDVEkvkdeieDVLKRYYEKLRAKDYPLDELAI 688
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 910 TKELTRAASDYA-GKQAHVELAERMRKRdpGSAPSLGDRVPYVIISAAKGVaaymkseDPLFVLEHSlPIDTQYYLEQql 988
Cdd:PRK05761 689 RVRLSKPLDEYTkNTPQHVKAALQLRDY--GVEVSPGDIISYVKVDDKRGV-------KPVQLAKLS-EIDVEKYIEL-- 756
|
890
....*....|...
gi 821174304 989 akpLLRIFEPILG 1001
Cdd:PRK05761 757 ---LRSALEQILS 766
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
312-524 |
1.46e-53 |
|
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: 185.64 E-value: 1.46e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 312 VLSFDIECAGRKGiFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPCAP-ILGAKVQSYEKEEDLLQAWSTFIRIMDP 390
Cdd:cd05160 1 VLSFDIETTPPVG-GPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDDIEfIDGIEVEYFADEKELLKRFFDIIREYDP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 391 DVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRVaglcSNIRDSSfqskqtgrRDTKVVSMVGRVQMDMLQVLLREYKLR 470
Cdd:cd05160 80 DILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRR----SGGEKSS--------GSTERIAVKGRVVFDLLAAYKRDFKLK 147
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 821174304 471 SYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDqtRRRLAVYCLKDAYLPLRLLE 524
Cdd:cd05160 148 SYTLDAVAEELLGEGKEKVDGEIIEDAEWEED--PERLIEYNLKDAELTLQILE 199
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
615-997 |
1.69e-43 |
|
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: 162.82 E-value: 1.69e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 615 SPPRYYDvPIATLDFSSLYPSIMMahnlcyTTLLRP-GTAQKL-GLTEDQFIRTPTGDEFVKTsvrKGLLPQILENLLSA 692
Cdd:cd05537 11 SKPGLYK-NVLVLDFKSLYPSIIR------TFLIDPlGLIEGLkAPDPEDLIPGFLGARFSRE---KHILPDLIARLWAA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 693 RKRAKaelaKETDPLRRQvldgrqlALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVEskytvENGYs 772
Cdd:cd05537 81 RDEAK----REKNAPLSQ-------AIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIE-----QQGY- 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 773 tsaKVVYGDTDSVMCRFG-VSSVAEAMALGREAAD----WVSGH------FPSPIRLEFEKVYFPYLLI--------SKK 833
Cdd:cd05537 144 ---QVIYGDTDSTFVWLGeELDAAEAQAIGKELASqinqWWAQKlkeefgLESFLEIEFETHYSRFFMPtirgsdegSKK 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 834 RYAGLlfsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVahaQDVISDLLCNRIDiSQLVITKEL 913
Cdd:cd05537 221 RYAGL---KSTDGGDELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGFI---KETVEELLAGELD-ELLVYRKRL 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 914 TRAASDY-AGKQAHVELAermRKRDPgSAPSLGDRVPYVIISaakgvaaYMKSEDPLFVLEH-SLPIDTQYYLEQQL--- 988
Cdd:cd05537 294 RRPLSEYtKNVPPHVQAA---RLADQ-INRELGRPRQYQWIE-------YVITVNGPEPLEYrTSPLDYQHYIDKQLkpi 362
|
....*....
gi 821174304 989 AKPLLRIFE 997
Cdd:cd05537 363 ADSILPFLG 371
|
|
| zf-C4pol |
pfam14260 |
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ... |
1038-1108 |
3.16e-30 |
|
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1.
Pssm-ID: 464119 Cd Length: 68 Bit Score: 114.01 E-value: 3.16e-30
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 821174304 1038 CIGCRTVlshQGAVCEFCQPRESELYQKEVSHLNALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMR 1108
Cdd:pfam14260 1 CLGCGAP---EEPLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYMR 68
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
597-1002 |
9.20e-30 |
|
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Pssm-ID: 99914 Cd Length: 352 Bit Score: 122.07 E-value: 9.20e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 597 DRAGaawelLALTPGRGCspprYYDVpiATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGLTEDQFIRTPtgdefvkts 676
Cdd:cd05531 5 DRGG-----LVFQPEPGL----YENV--AQIDFSSMYPSIIVKYNISPETINCRCCECRDHVYLGHRICLK--------- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 677 vRKGLLPQILENLLSARKRAKAELAKETDPlrrqvlDGRQLALKVSANSVYGFTG---AQVGKLPCLEisqSVTGFGRQM 753
Cdd:cd05531 65 -RRGFLPEVLEPLLERRLEYKRLKKEEDPY------AGRQKALKWILVTSFGYLGyknAKFGRIEVHE---AITAYGRKI 134
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 754 IEKTKQLVEskytvENGYstsaKVVYGDTDSVMCRfgVSSVAEAMALGREAadwvsghfPSPIRLEFEKVY-FPYLLISK 832
Cdd:cd05531 135 LLRAKEIAE-----EMGF----RVLHGIVDSLWIQ--GRGDIEELAREIEE--------RTGIPLKLEGHYdWIVFLPER 195
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 833 ------KRYAGLLFSsrpdahDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPE---GAVAHAQDVIS--DLLCNR 901
Cdd:cd05531 196 dglgapNRYFGRLSD------GEMKVRGIELRRRDTPPFVKKFQEEALDILASAKTPEellKLREEALDLFRryLQRLRE 269
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 902 IDISQLVITKELTRAASDYAGKQAHVelAERMRKRdpGSAPSLGDRVPYVIISAAKGVAaymksedplfVLEHSLPIDTQ 981
Cdd:cd05531 270 GDLEDLIIEKKISKRSSEYKVLASTA--LKALRAK--GVSVVPGMKIEYIVRDGKRPVP----------DLGNDEGYDTK 335
|
410 420
....*....|....*....|.
gi 821174304 982 YYLEQqlakpLLRIFEPILGE 1002
Cdd:cd05531 336 YYREL-----LERAAEELLFP 351
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
578-959 |
3.66e-26 |
|
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: 111.67 E-value: 3.66e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 578 GEDYTGATVIEPLKGVrpqdragaawellaltpgrgcspprYYDVpiATLDFSSLYPSIMMAHNLCYTTLLRPGTaqklg 657
Cdd:cd05530 10 GKKYRGAIVLEPPPGI-------------------------FFNV--VVLDFASLYPSIIKVWNLSYETVNCPHC----- 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 658 ltEDQFIRTPTGDEFVKTSvRKGLLPQILENLLSAR-----KRAKAelaKETDPLRRQVLDGRQLALKVSANSVYGFTGA 732
Cdd:cd05530 58 --ECKTNEVPEVGHWVCKK-RPGITSQIIGLLRDLRvkiykKKAKD---KSLDEEMRQWYDVVQSAMKVFINASYGVFGA 131
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 733 QVGKLPCLEISQSVTGFGRQMIEKTkqlveSKYTVENGYstsaKVVYGDTDSVMCRFGVSSVAEamalgrEAADWVSGHF 812
Cdd:cd05530 132 ENFPLYCPPVAESTTALGRYIITST-----IKKARELGL----KVLYGDTDSLFLWNPPQEQLE------DLVEWVEKEL 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 813 psPIRLEFEKVYfPYLLIS--KKRYAGLLFSSrpdahdRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEgAVAHA 890
Cdd:cd05530 197 --GLDLELDKEY-RYVVFSglKKNYLGVTKDG------SVDIKGLLGKKRNTPEFVKELFYEVIEILSAVNSPE-DFEKA 266
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 821174304 891 QDVISDL-------LCNR-IDISQLVITKELTRAASDYA-GKQAHVELAERMRKRdpGSAPSLGDRVPYVIISAAKGV 959
Cdd:cd05530 267 REKIRDIvkgvykrLKKKeYTLDQLAFKVMLSKPPEEYTkNTPQHVKAARQLEKY--GRNVEAGDIISYVKVKGKEGV 342
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
310-526 |
4.61e-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: 100.89 E-value: 4.61e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 310 LRVLSFDIECAGRKGIfPEPERDPVIQI--CSLG----LRW-GEPEPFlrlaltlrpcapilgakVQSYEKEEDLLQaws 382
Cdd:cd05780 3 LKILSFDIEVLNHEGE-PNPEKDPIIMIsfADEGgnkvITWkKFDLPF-----------------VEVVKTEKEMIK--- 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 383 TFIRIM---DPDVITGYNIQNFDLPYLISRAQTLKVQtFPfLGRVAglcSNIrdssfqsKQTGRRDTKVVSMVGRVQMDM 459
Cdd:cd05780 62 RFIEIVkekDPDVIYTYNGDNFDFPYLKKRAEKLGIE-LD-LGRDG---SEI-------KIQRGGFNNASEIKGRIHVDL 129
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 821174304 460 LQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNgNDQTRRRLAVYCLKDAYLPLRLLERL 526
Cdd:cd05780 130 YPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWD-SGENLERLFRYSMEDAKYTYEIGKEF 195
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
623-994 |
2.64e-23 |
|
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Pssm-ID: 99921 Cd Length: 347 Bit Score: 102.95 E-value: 2.64e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 623 PIATLDFSSLYPSIMMAHNLCyttllrpgtaqklgltedqfirtPTGDEFvktsvrkGLLPQILENLLSARKRAKAELAK 702
Cdd:cd05538 18 PIVHADVASLYPSIMLAYRIC-----------------------PARDSL-------GIFLALLKYLVELRLAAKESARA 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 703 ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKytvengystSAKVVYGDT 782
Cdd:cd05538 68 AARPAERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRRR---------GATPVEVDT 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 783 DSV--MCRFGVSSVAEAMALGREaadwVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSsrpdahDRMDCKGLEAVRR 860
Cdd:cd05538 139 DGIyfIPPNGVDTEDEEEELVRE----LSSTLPKGITVEFDGRYRAMFSYKIKNYALLDYD------GKLIVKGSAFRSR 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 861 DNCPLVANLVTASLRRLLIDrDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDY-----AGKQAHVELAERMRK 935
Cdd:cd05538 209 GIEPFLREFLREAVRLLLQG-DGAGVHDLYEDYLRRLRSHELPISDLARTETLKESPEEYlqkvrAGKRNPAAAYEIALA 287
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 821174304 936 RDPGSAPslGDRVPYVIISAAKGVAAYMK-SEDPLFVLEHSLpIDTQYYLEQ--QLAKPLLR 994
Cdd:cd05538 288 RPREWRA--GDRVTYYVSGTGKGVSVYENcRLVADYDPAHPD-ENTGFYAERllQLAARLLP 346
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
310-524 |
1.12e-22 |
|
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: 98.08 E-value: 1.12e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 310 LRVLSFDIECAGRKGIFPEPERDPVIQIC----------------SLGLRWGEPEPFLRLALTLRPCapiLGAKVQSYEK 373
Cdd:cd05778 4 LTILSLEVHVNTRGDLLPDPEFDPISAIFycidddvspfildankVGVIIVDELKSNASNGRIRSGL---SGIPVEVVES 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 374 EEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPF-LGRVaglcSNIRDSSFQSKQTGRRDTK--VVS 450
Cdd:cd05778 81 ELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDeISRV----PSDSNGKFGDRDDEWGYTHtsGIK 156
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 821174304 451 MVGRVQMDMLQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGND-QTRRRLAVYCLKDAYLPLRLLE 524
Cdd:cd05778 157 IVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSaSERWRVLEYYLKRVRLNLEILD 231
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
309-757 |
1.26e-22 |
|
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: 105.14 E-value: 1.26e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 309 PLRVLSFDIEC--AGRKGIFP--EPERDPVIQI----CSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEKEEDLLQA 380
Cdd:TIGR00592 197 ELKLASFDIETyfHDGKDFFPgdENPADEEIMIsttpVIAKQWDYESEPEARVVTWKKPDKPTTGSYVESVSEEISMIKR 276
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 381 WSTFIRIMDPDVITGYNIQNFDLPYLISRaqtlkvQTFPF-----------LGRVAGLCSNIRDSSFQSKQTG-RRDTKV 448
Cdd:TIGR00592 277 FWDVIDQEDTDVEITVNGDNFDLVYLADR------QVFQFywdayedpaekLGVVLLFGRDVDHVSPCVQVKGiNRDLFF 350
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 449 VSMVGRVQMDMLQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIITdlQNGNDQTRRRLAVYCLKDAYLPLRLLERLMV 528
Cdd:TIGR00592 351 LPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIA--KKYEFEAPDIDAPYSSEYLEVTYELGKEFAP 428
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 529 LVNAVEMARVTGVPLSYLLSRGQQVKVVsqLLRQAMHEGLLmpvvkseggeDYTGATViEPLKGVRPQDRAGAAWELLAL 608
Cdd:TIGR00592 429 MEALPSDLKGQTFWHVFGSNTGNLERFL--LLRKIKGPCWL----------AVKGPDE-LEYPRRSWCKYEGGYVKPPNV 495
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 609 TPGRGCSPPryydvPIATLDFS--SLYPSIMMAHNLCYTTLLRPGTAQKLGLTEDQFIRTP-TGDEFVKTSVR------- 678
Cdd:TIGR00592 496 EKGLDKTPP-----PLVVLDFSmkSLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPcVGTRPKDCSFPldlkgef 570
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 679 KGLLPQILENLLSARKRAKAELA--KETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSvtgFGRQMIEK 756
Cdd:TIGR00592 571 PGKKPSLVEDLATERALIKKFMAkvKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPK---FGRRFGER 647
|
.
gi 821174304 757 T 757
Cdd:TIGR00592 648 T 648
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
313-864 |
5.74e-22 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 102.79 E-value: 5.74e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 313 LSFDIECAGRKGiFPEPERDPV--IQICSLGLRWGEpepfLRLALT---LRPCAPILGAKVQSYEKEEDLLQAWSTFIRI 387
Cdd:PHA03036 163 LFLDIECHFDKK-FPSVFINPVshISCCYIDLSGKE----KRFTLInedMLSEDEIEEAVKRGYYEIESLLDMDYSKELI 237
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 388 ----------------MDPDVITGYNIQNFDLPYLISRAQTLKVQTF----PFLGRVAGLCSNIRDSSFQSKQTGRRDT- 446
Cdd:PHA03036 238 lcseivllriakklleLEFDYVVTFNGHNFDLRYISNRLELLTGEKIifrsPDGKETVHLCIYERNLSSHKGVGGVANTt 317
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 447 -KVVSMVGRVQMDMLQVLLREYKLRSYTLNAVS---FH--------------FLGEQKEDVQ------------------ 490
Cdd:PHA03036 318 yHINNNNGTIFFDLYTFIQKTEKLDSYKLDSISknaFNcnakvlsennnevtFIGDNTTDAKgkasifsevlstgnyvti 397
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 491 ------------------------------HSIIT--------DLQ----NGNDQTRRRLAVYCLKDAYLPLRLLERLMV 528
Cdd:PHA03036 398 ndddickildkdiiensftvkvicknnyipGDTYTlsfgkddvDLSdmykNYNLEIALEMARYCIHDACLCKYLWEYYGI 477
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 529 lvnaveMARVTGVPLSYLLSRGQQVKVVS------QLLRQAMHEGLLMPVVKSEGGEDYTGATVIEPLKgvrpqdragaa 602
Cdd:PHA03036 478 ------ETKIDAGASTYLLPQSMVFEYRAstlikgPLLKLLLEEKTILVRSETKNKFPYEGGKVFAPKQ----------- 540
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 603 wellaltpgrgcsppRYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGLTE--DQFIR-------------TP 667
Cdd:PHA03036 541 ---------------KMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVNDNRLEAEinKQELRrkypypryiyvhcEP 605
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 668 TGDEFVKTSV-----RKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEI 742
Cdd:PHA03036 606 RSPDLVSEIAvfdrrIEGIIPKLLKTFLEERARYKKLLKEATSSVEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYAS 685
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 743 SQSVTGFGRQMIE---------------------------KTKQLVESKY--TVENGYSTSAKVVYGDTDSVMCRFGVSS 793
Cdd:PHA03036 686 AKSCTAIGRNMIKylnsvlngsklingklilancpinpffKDDRSIDTNYdtNLPVEYNFTFRSVYGDTDSVFLEINTKD 765
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 821174304 794 VAEAMALGREAADWVSGH-FPSPIRLEFEKVYFPYLLISKKRYAGLLF--SSRPDAHDRMDCKGLEAVRRDNCP 864
Cdd:PHA03036 766 VDKSIKIAKELERIINEKvLFDNFKIEFEAVYKNLIMQSKKKYTTLKYiaSSTDGSVPERVNKGTSETRRDVSK 839
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
310-809 |
7.79e-22 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 102.08 E-value: 7.79e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 310 LRVLSFDIECAGRKGiFPEPERDPViQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQ----------SYEKEEDLLQ 379
Cdd:PHA02528 106 IRIANLDIEVTAEDG-FPDPEEAKY-EIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPqeildkvvymPFDTEREMLL 183
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 380 AWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLkvqtfpfLG-RVAGLCSNIRdsSFQSKQT----GRRDTKvVSMVGR 454
Cdd:PHA02528 184 EYINFWEENTPVIFTGWNVELFDVPYIINRIKNI-------LGeKTAKRLSPWG--KVKERTIenmyGREEIA-YDISGI 253
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 455 VQMDMLQVllreYK------LRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQtrrRLAVYCLKDAYLPLRLLERLMV 528
Cdd:PHA02528 254 SILDYLDL----YKkftftnQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQ---KYIEYNIIDVELVDRLDDKRKL 326
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 529 LVNAVEMARVTGVPLSYLLSrgqQVK-----VVSQLLRQamheGLLMPVVKSEGGEDYTGATVIEPLkgvrpqdragaaw 603
Cdd:PHA02528 327 IELVLSMAYYAKINFEDVFS---PIKtwdaiIFNSLKEE----KIVIPENKSHKKQKYAGAFVKEPV------------- 386
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 604 ellaltpgrgcspPRYYDVpIATLDFSSLYPSIMMAHNLCYTTLLrpGT----------AQKLGLTEDQFIRTPTGDEFV 673
Cdd:PHA02528 387 -------------PGAYRW-VVSFDLTSLYPSIIRQVNISPETIA--GTfhvapvheyiNKTAPRPSDEYSCSPNGWMYR 450
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 674 KTsvRKGLLPQILENLLSARKRAK---------AELAKET----------------------------DPLRRQVLDGR- 715
Cdd:PHA02528 451 KD--IRGVIPTEIKKVFDQRKIYKkkmlaaernAELIKTIledlndsvdtpidvdyyfdfsdefkaelKTLTKSSLKALl 528
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 716 -------------QLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIektkQLVESKYtveNGY-----STSAK- 776
Cdd:PHA02528 529 eecekeialcntiQMARKILINSLYGALGNEHFRYYDLRNAEAITLFGQLAI----QWIERKM---NEYlnklcKTEDEd 601
|
570 580 590
....*....|....*....|....*....|....*.
gi 821174304 777 -VVYGDTDSVMCRFGvsSVAEAMALGR--EAADWVS 809
Cdd:PHA02528 602 yVIYGDTDSIYVNLD--PLVEKVGEDKfkDTNHWVD 635
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
309-524 |
1.82e-18 |
|
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: 84.54 E-value: 1.82e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 309 PLRVLSFDIECagrkgifpeperDPVIQICSLGLrWGEPEpflRLALTLRPCAPILGAKVQSYEKEEDLLQAWSTFIRIM 388
Cdd:cd05784 2 KLKVVSLDIET------------SMDGELYSIGL-YGEGQ---ERVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQY 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 389 DPDVITGYNIQNFDLPYLISRAQTLKVqtfPF-LGRvAGLCSNIRDSSFQSKQTgrrdtkvVSMVGRVQMDMLQvLLRE- 466
Cdd:cd05784 66 DPDIIIGWNVINFDLRLLQRRAEAHGL---PLrLGR-GGSPLNWRQSGKPGQGF-------LSLPGRVVLDGID-ALKTa 133
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 821174304 467 -YKLRSYTLNAVSFHFLGEQKedvqhsIITDLQNGNDQTRRR-------LAVYCLKDAYLPLRLLE 524
Cdd:cd05784 134 tYHFESFSLENVAQELLGEGK------LIHDVDDRGAEIERLfredklaLARYNLQDCELVWRIFE 193
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
366-787 |
8.27e-16 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 82.98 E-value: 8.27e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 366 AKVQSYEKEEDLLQAWSTFI----RIMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPfLGRVAGLCSnIRDSSFQSKQT 441
Cdd:PHA03334 370 FKQRPHPLTKALMEAWEAFLskdpQLVPAQLLFGSDILNSNYLELLDVIESHKAQFKA-TCRKAAARK-EEIGSYMKTRD 447
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 442 GRRDTKVVSMV---------GRVQMDMLQVLLR---EYKLRSYTLNAVSFHFLGEQK-----------EDVQHSIITDLQ 498
Cdd:PHA03334 448 TVQDFNDNDKKylnstshgfGAHIIDLMRVCNTksiKAKCSSRKLDTVARLIISKSKphknppkigkmDDVKYTEMDGMF 527
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 499 NGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTgVPLSYL-LSRG--------QQVKVVS-QLLRQAMHEGL 568
Cdd:PHA03334 528 TAGGAALARYLIYNLVDSELLIRIAKNLDPVIEFLNRLRAT-YNIDYVaHGRGvmnfcgfvQSTKSVEvPLLKARLRIGI 606
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 569 LMPVVKseGGEDYTGATVIEPLKGVRPQDRAGAAWEllaltPGRGCSPPRYYDVPIATLDFSSLYPSIMMAHNLCYTTLL 648
Cdd:PHA03334 607 FVATGR--IAESLCMPEKYARDCRQKIKLKGGYVFA-----PLTGLTFAGPYQGTELTLDFASLYPSNMCDANISPEAIV 679
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 649 RPGTA---------------QKLGLTEDQFIRTPTGDEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLD 713
Cdd:PHA03334 680 DPDCTarvrgwvvfdwkkidRGFGKATLMYTILRTKPEEPSWRRFTTYTTSSLNHYLSMRTEYKGAMKQAKDPKLKSYHN 759
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 821174304 714 GRQLALKVSANSVYGftgaqVGKLPCleiSQSVTGFGRQMIektkQLVESKYTVENGYStsakVVYGDTDSVMC 787
Cdd:PHA03334 760 QLQNEMKICANSHYG-----VAPHAC---QHLITTLGRHKI----KLVEEFIKKEPGMT----VNYGDTDSVMF 817
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
309-483 |
9.86e-16 |
|
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: 76.60 E-value: 9.86e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 309 PLRVLSFDIECAGRKGiFPEPERDPVIQIcSLGLRWGEPEPFLrlaltlrpcapilgakvQSYEKEEDLLQAWSTFIRIM 388
Cdd:cd05781 2 DLKTLAFDIEVYSKYG-TPNPRRDPIIVI-SLATSNGDVEFIL-----------------AEGLDDRKIIREFVKYVKEY 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 389 DPDVITGYNIQNFDLPYLISRAQTLKVQTfpFLGRVAGlcsnirDSSFQSKqTGRrdtkvVSMVGRVQMDMLQVLLREYK 468
Cdd:cd05781 63 DPDIIVGYNSNAFDWPYLVERARVLGVKL--DVGRRGG------SEPSTGV-YGH-----YSITGRLNVDLYDFAEEIPE 128
|
170
....*....|....*
gi 821174304 469 LRSYTLNAVSfHFLG 483
Cdd:cd05781 129 VKVKTLENVA-EYLG 142
|
|
| DNA_polB_B1_exo |
cd05783 |
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ... |
307-522 |
2.46e-15 |
|
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: 75.82 E-value: 2.46e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 307 IAPLRVLSFDIEC-AGRKGIFPEPERD--PVIQIC---SLGLRwgepepflRLALTLRPCAPIL------GAKVQSYEKE 374
Cdd:cd05783 2 IPKLKRIAIDIEVyTPIKGRIPDPKTAeyPVISVAlagSDGLK--------RVLVLKREGVEGLegllpeGAEVEFFDSE 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 375 EDLLQAwstFIRIMD--PDVITgYNIQNFDLPYLISRAQTLKV--QTFPFLGRvaglcsniRDSsfqskqtgrrdtkvVS 450
Cdd:cd05783 74 KELIRE---AFKIISeyPIVLT-FNGDNFDLPYLYNRALKLGIpkEEIPIYLK--------RDY--------------AT 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 451 MVGRVQMDM--------LQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIitdlqngNDQTRRRLAVYCLKDAYLPLRL 522
Cdd:cd05783 128 LKHGIHIDLykffsnraIQVYAFGNKYREYTLDAVAKALLGEGKVELEKNI-------SELNLYELAEYNYRDAELTLEL 200
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|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
310-515 |
3.11e-13 |
|
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: 69.75 E-value: 3.11e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 310 LRVLSFDIECAGRKGIF---PEPERDPVIQIcslGLRwgEPEPFlRLALTLRPCApilgakvqsyekEEDLLQAWSTFIR 386
Cdd:cd05785 9 LRRLQLDIETYSLPGFFfsnPDRGDDRIIIV---ALR--DNRGW-EEVLHAEDAA------------EKELLEELVAIIR 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 387 IMDPDVITGYNIQNFDLPYLISRAQTLKVqtfPF-LGRVaGLCSNIRDSSFQSKQtGRRDTKVVSMVGRVQMDMLQVLLR 465
Cdd:cd05785 71 ERDPDVIEGHNIFRFDLPYLRRRCRRHGV---PLaIGRD-GSIPRQRPSRFRFAE-RLIDYPRYDIPGRHVIDTYFLVQL 145
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 821174304 466 ----EYKLRSYTLNAVSFHF--LGEQKEDVQHSIITDLQNGNdqtRRRLAVYCLKD 515
Cdd:cd05785 146 fdvsSRDLPSYGLKAVAKHFglASPDRTYIDGRQIAEVWRSD---PARLLAYALDD 198
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|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
327-529 |
4.34e-13 |
|
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: 69.95 E-value: 4.34e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 327 PEPERDPVIQICSLGL---RWGEPEPFLRLALTLRPcapilgaKVQSYEKEEDLLQAWSTFIRIMDPDVITGYNIQNFDL 403
Cdd:cd05776 39 PTPPPPFQSHTCTLTRplgRSPPPDLFEKNAKKKKT-------KVRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDL 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 404 PYLISRAQTLKVQTFPFLGRVaglcsnIRDSSFQSKQTGRRDTKVVsMVGRVQMDMlQVLLRE-YKLRSYTLNAVSFHFL 482
Cdd:cd05776 112 DVLLSRIQELKVPHWSRIGRL------KRSVWPKKKGGGKFGEREL-TAGRLLCDT-YLSAKElIRCKSYDLTELSQQVL 183
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 821174304 483 GEQKEDVqhsIITDLQNGNDQTRR--RLAVYCLKDAYLPLRLLERLMVL 529
Cdd:cd05776 184 GIERQDI---DPEEILNMYNDSESllKLLEHTEKDAYLILQLMFKLNIL 229
|
|
| DNA_polB_epsilon_exo |
cd05779 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ... |
309-413 |
7.29e-06 |
|
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: 48.03 E-value: 7.29e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821174304 309 PLRVLSFDIECAGRKGIFPEPERDPVIQIcSLGLrwgEPEPFLrlaLTLRPcapILGAKVQSYE---------------- 372
Cdd:cd05779 1 DPRVLAFDIETTKLPLKFPDAETDQIMMI-SYMI---DGQGYL---IVNRE---IVSEDIEDFEytpkpeyegpfkvfne 70
|
90 100 110 120
....*....|....*....|....*....|....*....|..
gi 821174304 373 -KEEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTL 413
Cdd:cd05779 71 pDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIH 112
|
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