|
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 ... |
521-985 |
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: 597.67 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 521 IPTRRVLTDGQQIRVFSCLLDVAGREGYILPV--DRHADAEGYQGATVIDPSPGFYNTPVLVVDFASLYPTIIQAHNLCY 598
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDrpSAKGDEDGYQGATVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 599 STMIPGDRLCLHphLGPGDYE-TFELASGPVHFVKKHKAVSLLATLLNVWLAKRKAIRRELATVSDEAVRTILDKQQLAI 677
Cdd:pfam00136 81 TTLVRSVDEANN--LPPEDNLiTVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFERAILDKQQLAL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 678 KVTCNAVYGFTGVASGILPCLKIAETVTFQGRRMLENSKRYIEGVTPegladilgrrvecapdASFKVIYGDTDSLFIHC 757
Cdd:pfam00136 159 KITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYT----------------YNFRVIYGDTDSVFIEF 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 758 RGYRPEQVTGFCDELAAHMTRTLFVDPIKLEAEKTFKCLILLTKKRYIGMMTT-----DRLLMKGVDLVRKTACRFVQET 832
Cdd:pfam00136 223 GGKDVEEAMKIGDELAEHVNQDLFKSPIKLEFEKVYKPLLLISKKKYAGLKYTapsnfNKLDMKGVDLVRRDNCPLVKEV 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 833 TKAILDLVMGDeavraaaerlcamrveevcaRGPPVGFLKVVDILNDSYRKLRLNRVPVGQLSFSTELSRPISYYKTLTL 912
Cdd:pfam00136 303 IKKVLDLLLSD--------------------RGLPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNYKSKNL 362
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1706512 913 PHLVVYHKIMQRNEELPQIHDRIAYVFVQSPKGK---LRSEMAEDPAYAAQHNIPPAVDLYFD-KVIHGAANILQCL 985
Cdd:pfam00136 363 PHVEVALRMNKRNGEAPEVGDRIPYVIVKAAKGLknlLIYERAEDPEYVLENNLPIDYEYYFSnQLIPPVARLLEPI 439
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
287-759 |
6.80e-154 |
|
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: 463.93 E-value: 6.80e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 287 PGYNVLSFDIECL-GENGFPNASRDEDMILQISCVIWKAGSGEAPRSVLLNLGTCEEIEGVEVYQCPSELDLLYLFFTMI 365
Cdd:smart00486 1 PPLKILSFDIETYtDGGNFPDAEIFDDEIIQISLVINDGDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEFI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 366 RDADVEFVTGYNISNFDFPYVIDRATQVYNLNLKEFTRVRSSSIFEVHKPKNSSAGFMRAVSKVKVAGVVPIDMYQVCRD 445
Cdd:smart00486 81 KKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGLRIPNKKPLFGSKSFGLSDIKVYIKGRLVIDLYRLYKN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 446 KLSLSNYKLDTVAGECVGAKKEDVSYKEIPHLFRQGPGGRARLGLYCVKDSALVLDLLRYFMTHVEISEIAKIAKIPTRR 525
Cdd:smart00486 161 KLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLRR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 526 VLTDGQQIRVFSCLLDVAGREGYILPVDRHADA----------EGYQGATVIDPSPGFYNTPVLVVDFASLYPTIIQAHN 595
Cdd:smart00486 241 TLYYGSQIRVESLLLREAKKNNYILPSKELYDFkgsepdlkkkVKYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHN 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 596 LCYSTMI-PGDRLCLHPHLGPGDYETFELASG-PVHFVKKHKAVSLLATLLNVWLAKRKAIRRELATVSD--EAVRTILD 671
Cdd:smart00486 321 LCYSTLVgVGEVVIKGDLIIPEDLLTIKYEKGnKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDesEELKKLLD 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 672 KQQLAIKVTCNAVYGFTGVASGILPCLKIAETVTFQGRRMLENSKRYIEGvtpegladilgrrvECAPDASFKVIYGDTD 751
Cdd:smart00486 401 SRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEE--------------NGYPKPGFKVIYGDTD 466
|
....*...
gi 1706512 752 SLFIHCRG 759
Cdd:smart00486 467 SIFVTKPG 474
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
127-972 |
3.19e-152 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 478.75 E-value: 3.19e-152
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 127 VLKLLGRTSDDRSVCVNVFRQELYFYVRVPEGLKLDFLIQQCSRENFNFSQgRYRYEKTSKRVLREYCVEAR-------- 198
Cdd:PTZ00166 76 IIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNFLPEDSQKLKRELNAQLSE-QSQFKKYQNTVLDIEIVKKEslmyykgn 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 199 ---EVYRVFASSQGFV----DLLAGGLTAAGCE--------VFETNVDAARRFIIDNGFSTFGWYSC-AAAVPRQGGAAR 262
Cdd:PTZ00166 155 gekDFLKITVQLPKMVprlrSLIESGVVVCGGGwdgirlfqTYESNVPFVLRFLIDNNITGGSWLTLpKGKYKIRPPKKK 234
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 263 DSWTELEYDCAAGDLEFHAGRADW---PGYNVLSFDIECLGENG--FPNASRDEdmILQISCVIWKAGSGEAPRS-VLLN 336
Cdd:PTZ00166 235 TSTCQIEVDCSYEDLIPLPPEGEYltiAPLRILSFDIECIKLKGlgFPEAENDP--VIQISSVVTNQGDEEEPLTkFIFT 312
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 337 LGTCEEIEGVEVYQCPSELDLLYLFFTMIRDADVEFVTGYNISNFDFPYVIDRATQvynLNLKEFTRV-RSSSIFEVHKP 415
Cdd:PTZ00166 313 LKECASIAGANVLSFETEKELLLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKA---LKLNDFKYLgRIKSTRSVIKD 389
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 416 KNSSAGFM--RAVSKVKVAGVVPIDMYQVCRDKLSLSNYKLDTVAGECVGAKKEDVSYKEIPHLFRQGPGGRARLGLYCV 493
Cdd:PTZ00166 390 SKFSSKQMgtRESKEINIEGRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCL 469
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 494 KDSALVLDLLRYFMTHVEISEIAKIAKIPTRRVLTDGQQIRVFSCLLDVAGREGYILPVDRHA---DAEGYQGATVIDPS 570
Cdd:PTZ00166 470 KDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRGQQIKVTSQLLRKCKKLNYVIPTVKYSgggSEEKYEGATVLEPK 549
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 571 PGFYNTPVLVVDFASLYPTIIQAHNLCYSTMIPGDRLCLHPHlgpgdyETFELASGPVHFVKKHKAVSLLATLLNVWLAK 650
Cdd:PTZ00166 550 KGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDANNYPE------DTYVTTPTGDKFVKKEVRKGILPLIVEELIAA 623
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 651 RKAIRRELATVSDEAVRTILDKQQLAIKVTCNAVYGFTGVAS-GILPCLKIAETVTFQGRRMLENSKRYIEgvtpeglaD 729
Cdd:PTZ00166 624 RKKAKKEMKDEKDPLLKKVLNGRQLALKISANSVYGYTGAQVgGQLPCLEVSTSITSFGRQMIDKTKELVE--------K 695
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 730 ILGRRVECAPDAsfKVIYGDTDSLFIHCRGYRPEQVTGFCDElAAHMTRTLFVDPIKLEAEKTFKCLILLTKKRYIGMMT 809
Cdd:PTZ00166 696 HYTKANGYKHDA--TVIYGDTDSVMVKFGTDDIQEAMDLGKE-AAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAGLLY 772
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 810 T-----DRLLMKGVDLVRKTACRFVQETTKAILDLVMGDEAVRAAAErlcamrveevcargppvgFLKVVdilndsYRKL 884
Cdd:PTZ00166 773 TnpekyDKIDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIE------------------FTKGK------ISDL 828
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 885 RLNRVPVGQLSFSTELSRpiSYYKTlTLPHLVVYHKIMQRNE-ELPQIHDRIAYVFVQSPKGKLRSEMAEDPAYAAQHNI 963
Cdd:PTZ00166 829 LQNRIDISLLVITKSLGK--DDYEG-RLAHVELAKKLRQRDPgSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVLENNI 905
|
....*....
gi 1706512 964 PPAVDLYFD 972
Cdd:PTZ00166 906 PIDTQYYLD 914
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
116-985 |
7.61e-118 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 380.33 E-value: 7.61e-118
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 116 QFQTDIIPSGTVLKLLGRTSDDRSVCVNVFRQELYFYVRVPEGLKLDFLIQQcsrenfnfSQGRYRYEKTSKRVLREycv 195
Cdd:COG0417 9 DRSYRDEDGKPVIELWGRTEDGPSVLLDVTGFRPYFYVPLPDEEKLEELLRD--------IKEITEVEPVKLKSFFG--- 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 196 EAREVYRVFASSQGFVDLLAGGLTAAGCEVFETNVDAARRFIIDNGFSTFGWYScaaavprqGGAARDSWTELEYDCAAG 275
Cdd:COG0417 78 EPVPVLKIYTRDPRDVRELRDRLKEGGIDVYEADIRFHDRYLIDRFLTPGVWYE--------GEVEEDGGKLDYEVKENP 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 276 DLEFHAGRadwPGYNVLSFDIECLGENGFPNASRDEDMILqISCviwkagSGEAPRSVLLNLGTCEEIEGVEVyqCPSEL 355
Cdd:COG0417 150 RLKPEDYR---PKLKVLSFDIEVSTPRGFPDPERDGPIIS-IGL------AGSDGEKKVLMLGREGVDFEVEY--FDDEK 217
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 356 DLLYLFFTMIRDADVEFVTGYNISNFDFPYVIDRAtQVYNLNLKeFTRVRSssifevhKPKNSSAGFMRAVSkvkVAGVV 435
Cdd:COG0417 218 ALLEAFFEIIREYDPDIIIGWNVDNFDLPYLQKRA-ERLGIPLD-LGRDGS-------EPSWREHGGQGFAS---IPGRV 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 436 PIDMYQ-VCRDKLSLSNYKLDTVAGECVGAKKEDVSYKEIPHLFRQGpggRARLGLYCVKDSALVLDLLRYFMTHVEISE 514
Cdd:COG0417 286 VIDLYDaLKSATYKFKSYSLDAVAEELLGEGKLIVDGGEIERLWDDD---KPALAEYNLRDAELTLRIFEKTLLLPFLIE 362
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 515 IAKIAKIPTRRVLTDGQQIRVFSCLLDVAGREGYILPVDRHADAEGYQGATVIDPSPGFYNTpVLVVDFASLYPTIIQAH 594
Cdd:COG0417 363 LSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGYLAPNKGEIKGEAYPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTF 441
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 595 NLCYSTMIPGDRLClhphlgpgDYETFELASGPVHFVKKHKAvsLLATLLNVWLAKRKAIRRELA-TVSDEAVRTILDKQ 673
Cdd:COG0417 442 NISPETLVEGGEEP--------CGDEDVAPGFGHRFCREPKG--ILPSILEELWDERDEAKKKMKkAKPDSEEYRLYDAL 511
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 674 QLAIKVTCNAVYGFTGvASGI-LPCLKIAETVTFQGRRMLENSKRYIEGvtpegladiLGrrvecapdasFKVIYGDTDS 752
Cdd:COG0417 512 QQALKILMNSFYGVLG-SEGCrFYDPELAESITARGREIIKQTIEKAEE---------LG----------YKVIYGDTDS 571
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 753 LFIHCRGYRPEQVTGFCDELAAHMTRTLfVDPIKLEAEKTFKCLILLT-KKRYIGMMTTDRLLMKGVDLVRKTACRFVQE 831
Cdd:COG0417 572 LFVWLPKASLEEAIEIGKELAEEINAWW-PSGLELEFEKHYRRFFFPGsKKRYAGLTEDGKIDIKGLEAVRSDWTELAKE 650
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 832 TTKAILDLVMGDEAVRaaaerlcamrveevcargppvgflKVVDILNDSYRKLRLNRVPVGQLSFSTELSRPISYYKTLT 911
Cdd:COG0417 651 FQQEVYERILKEEDVE------------------------KAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSEYEKNV 706
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1706512 912 LPHLVVYHKIMQRNEElPQIHDRIAYVFVqspKGKLRsemAEDPAYAAQHNIPPAVDLYFDKVIHGAAN-ILQCL 985
Cdd:COG0417 707 PPHVRAARKLDERGRP-YQRGDKISYVIT---KGGGR---VEPVELAKERESEIDYDYYIEKQLKPTADrILEAF 774
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
133-457 |
3.48e-86 |
|
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: 280.46 E-value: 3.48e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 133 RTSDDRSVCVNVFRQELYFYVRVPEGLKLDFLIQQCsRENFNFSQGRYRYEKTSKRVLREYCVEAREVYRVFASSQGFVD 212
Cdd:pfam03104 1 KTDEGVSVCVNVFGFKPYFYCLAPDGKELEEVIEEI-KELYEGLDKIEKIELKLKKSLYGYEEDPVPYLKVSFANPRPLL 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 213 LLAGGLTAA-GCEVFETNVDAARRFIIDNGFSTFGWYSCAAAVPRQGGaaRDSWTELEYDCAAGDLEFHAGRADWPGYNV 291
Cdd:pfam03104 80 KIRKYLSPEnISDVYEYDVDYLERFLIDNDIVGFGWYKVKVYPFRAEG--RISNCDVEIDCDSPDLISVPFEKEWPPLRV 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 292 LSFDIECLGENG-FPNASRDEDMILQISCVIWKAGSGEAPRSVLLNLGTCE-------------EIEGVEVYQCPSELDL 357
Cdd:pfam03104 158 LSFDIECTSLPGkFPDAENVKDPIIQISCMLDGQGEPEPEPRFLFTLRECDsediedfeytpkpIYPGVKVFEFPSEKEL 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 358 LYLFFTMIRDADVEFVTGYNISNFDFPYVIDRATQVYNLNLKEFTRVRSSSIFEVHKPKNSsagfMRAVSKVKVAGVVPI 437
Cdd:pfam03104 238 LRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNRGGRSKVREIGFG----TRSYEKVKISGRLHL 313
|
330 340
....*....|....*....|
gi 1706512 438 DMYQVCRDKLSLSNYKLDTV 457
Cdd:pfam03104 314 DLYRVIKRDYKLPSYKLNAV 333
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
559-987 |
2.01e-85 |
|
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: 280.69 E-value: 2.01e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 559 EGYQGATVIDPSPGFYNTPVLVVDFASLYPTIIQAHNLCYSTMIPGDRLCLhphLGPGDYETfelasGPVH--FVKKHKA 636
Cdd:cd05533 1 EQYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKK---LPPEDYIK-----TPNGdyFVKSSVR 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 637 VSLLATLLNVWLAKRKAIRRELATVSDEAVRTILDKQQLAIKVTCNAVYGFTGVASGILPCLKIAETVTFQGRRMLENSK 716
Cdd:cd05533 73 KGLLPEILEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTK 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 717 RYIEgvtpeglaDILGRRVECAPDAsfKVIYGDTDSLFIHCRGYRPEQVTGFCDELAAHMTrTLFVDPIKLEAEKTFKCL 796
Cdd:cd05533 153 KLVE--------EKYTKANGYSHDA--KVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVS-KKFIKPIKLEFEKVYFPY 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 797 ILLTKKRYIGMMTT-----DRLLMKGVDLVRKTACRFVQETTKAILDLVMGDEAVRAAAErlcamrveevcargppvgFL 871
Cdd:cd05533 222 LLINKKRYAGLLWTnpdkhDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIE------------------FV 283
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 872 KvvDILNDsyrkLRLNRVPVGQLSFSTELSRPISYYKTlTLPHLVVYHKIMQRNE-ELPQIHDRIAYVFVQSPKGKLRSE 950
Cdd:cd05533 284 K--GVISD----LLQNKIDISLLVITKALTKTADDYAG-KQAHVELAERMRKRDPgSAPNVGDRVPYVIIKGAKGAKAYE 356
|
410 420 430
....*....|....*....|....*....|....*..
gi 1706512 951 MAEDPAYAAQHNIPPAVDLYFDKVIhgaANILQCLFE 987
Cdd:cd05533 357 KAEDPIYVLENNIPIDTQYYLENQL---SKPLLRIFE 390
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
125-976 |
3.41e-47 |
|
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: 184.10 E-value: 3.41e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 125 GTVLkLLGRTSDDRSVCVNVFRQELYFYVrVPEGLKLDFLIQQCSRENFNFSQgrYRYEKTSKRVLREYC--VEAREVYR 202
Cdd:TIGR00592 323 GVVL-LFGRDVDHVSPCVQVKGINRDLFF-LPREGKIDFDLGKVTRRTINLPD--YYLEFVSELALGYKKekFRAKPIAK 398
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 203 VFASSQGFVD----------LLAGGLTAAGCE-------------VFETNVDAARRFIIDNGFSTFGWYscAAAVPRQGG 259
Cdd:TIGR00592 399 KYEFEAPDIDapysseylevTYELGKEFAPMEalpsdlkgqtfwhVFGSNTGNLERFLLLRKIKGPCWL--AVKGPDELE 476
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 260 AARDSWTELEydcAAGDLEFHAGRADW---PGYNVLSFDIECLgengFPNASRDEDMILQISCVIWKA------------ 324
Cdd:TIGR00592 477 YPRRSWCKYE---GGYVKPPNVEKGLDktpPPLVVLDFSMKSL----NPSIIRNEIVSIPDTLHREFAldkpppeppydv 549
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 325 --GSGEAPRSVLLNLGTCEEIEGVEvyqcPSELDLLYLFFTMIR---------DADVEfvTGYNISNFDFPYVIDRatqv 393
Cdd:TIGR00592 550 hpCVGTRPKDCSFPLDLKGEFPGKK----PSLVEDLATERALIKkfmakvkkiDPDEI--VGHDYQQRALKVLANR---- 619
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 394 ynlnlkeftrvrsssIFEVHKPKNSSAGFMRAVSKVKVAGVVPIDMYQVCRDKLSlsnykldtvAGECVGAKKEDVS--Y 471
Cdd:TIGR00592 620 ---------------INDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVEIS---------AKELIRCKSYDLSelV 675
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 472 KEIPHLFRQGPGGRARLGLYcvKDSALVLDLLRYFMTHVEIS--------------EIAKIAKIPTRRVLTDGQQIRVFS 537
Cdd:TIGR00592 676 QQILKTERKVIPIDNINNMY--SESSSLTYLLEHTWKDAMFIlqimcelnvlplalQITNIAGNIMSRTLMGGRSERNEF 753
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 538 CLLDVAGREGYILP-----------VDRHADAEG--------YQGATVIDPSPGFYNTPVLVVDFASLYPTIIQAHNLCY 598
Cdd:TIGR00592 754 LLLHAFYENNYIVPdkqifrkqqklGDEDEEIDGykkgkkaaYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICF 833
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 599 STMIPGDRLCLHPHLGPGDYETfelasgpvhfvkkhkavSLLATLLNVWLAKRKAIRRELATVSDEAVRTILDKQQLAIK 678
Cdd:TIGR00592 834 TTVQQKVDEDELPELPDSELEM-----------------GILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDIRQKALK 896
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 679 VTCNAVYGFTGVASGILPCLKIAETVTFQGRRMLENSKRYIEgvtpegladilgrrvecapDASFKVIYGDTDSLFIHCR 758
Cdd:TIGR00592 897 LTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVE-------------------EMNLEVIYGDTDSIMINTP 957
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 759 GYRPEQVTGFCDELAAHMTRTLfvDPIKLEAEKTFKCLILLTKKRYIGMM--------TTDRLLMKGVDLVRKTACRFVQ 830
Cdd:TIGR00592 958 GTKYEEVFKIGKEFKSEVNKLY--KLLELDIDGVFKRLLLLKKKKYAAIKvegdsdgnYTTKQEVKGLDIVRRDWSPLAK 1035
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 831 ETTKAILDLVMGDEAVRAAaerlcamrVEEvcargppvgflkVVDILNDSYRKLRLNRVPVGQLSFSTELSRPISYYKTL 910
Cdd:TIGR00592 1036 ETGKKVLDTILSDKDVEEA--------VEE------------VQEVLEKIGKNVLNGEVPLEKFVINKQLTRDPKDYPDG 1095
|
890 900 910 920 930 940 950
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 911 -TLPHLVVYHKIMQRNEELPQIHDRIAYVFVQSPKG---KLRSEMAEDPAYaAQHNIPPAVDLYFDKVIH 976
Cdd:TIGR00592 1096 aSLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNlsaRQRAYALEELQR-KHNNLIYDTQYYLEHQIH 1164
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
291-507 |
6.65e-46 |
|
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: 164.67 E-value: 6.65e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 291 VLSFDIECLGENG-FPNASRDEdmILQISCVIWKAGSGEAPRSVLLNLGTCEEIEGVEVYQCPSELDLLYLFFTMIRDAD 369
Cdd:cd05777 9 ILSFDIECAGRKGvFPEPEKDP--VIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWRDFVQEVD 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 370 VEFVTGYNISNFDFPYVIDRATQvynLNLKEFTRV-RSSSIFEVHKPKN-SSAGFMRAVSK-VKVAGVVPIDMYQVCRDK 446
Cdd:cd05777 87 PDIITGYNICNFDLPYLLERAKA---LKLNTFPFLgRIKNIKSTIKDTTfSSKQMGTRETKeINIEGRIQFDLLQVIQRD 163
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1706512 447 LSLSNYKLDTVAGECVGAKKEDVSYKEIPHLFRQGPGGRARLGLYCVKDSALVLDLLRYFM 507
Cdd:cd05777 164 YKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLM 224
|
|
| |
|
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 ... |
521-985 |
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: 597.67 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 521 IPTRRVLTDGQQIRVFSCLLDVAGREGYILPV--DRHADAEGYQGATVIDPSPGFYNTPVLVVDFASLYPTIIQAHNLCY 598
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDrpSAKGDEDGYQGATVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 599 STMIPGDRLCLHphLGPGDYE-TFELASGPVHFVKKHKAVSLLATLLNVWLAKRKAIRRELATVSDEAVRTILDKQQLAI 677
Cdd:pfam00136 81 TTLVRSVDEANN--LPPEDNLiTVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFERAILDKQQLAL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 678 KVTCNAVYGFTGVASGILPCLKIAETVTFQGRRMLENSKRYIEGVTPegladilgrrvecapdASFKVIYGDTDSLFIHC 757
Cdd:pfam00136 159 KITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYT----------------YNFRVIYGDTDSVFIEF 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 758 RGYRPEQVTGFCDELAAHMTRTLFVDPIKLEAEKTFKCLILLTKKRYIGMMTT-----DRLLMKGVDLVRKTACRFVQET 832
Cdd:pfam00136 223 GGKDVEEAMKIGDELAEHVNQDLFKSPIKLEFEKVYKPLLLISKKKYAGLKYTapsnfNKLDMKGVDLVRRDNCPLVKEV 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 833 TKAILDLVMGDeavraaaerlcamrveevcaRGPPVGFLKVVDILNDSYRKLRLNRVPVGQLSFSTELSRPISYYKTLTL 912
Cdd:pfam00136 303 IKKVLDLLLSD--------------------RGLPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNYKSKNL 362
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1706512 913 PHLVVYHKIMQRNEELPQIHDRIAYVFVQSPKGK---LRSEMAEDPAYAAQHNIPPAVDLYFD-KVIHGAANILQCL 985
Cdd:pfam00136 363 PHVEVALRMNKRNGEAPEVGDRIPYVIVKAAKGLknlLIYERAEDPEYVLENNLPIDYEYYFSnQLIPPVARLLEPI 439
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
287-759 |
6.80e-154 |
|
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: 463.93 E-value: 6.80e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 287 PGYNVLSFDIECL-GENGFPNASRDEDMILQISCVIWKAGSGEAPRSVLLNLGTCEEIEGVEVYQCPSELDLLYLFFTMI 365
Cdd:smart00486 1 PPLKILSFDIETYtDGGNFPDAEIFDDEIIQISLVINDGDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEFI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 366 RDADVEFVTGYNISNFDFPYVIDRATQVYNLNLKEFTRVRSSSIFEVHKPKNSSAGFMRAVSKVKVAGVVPIDMYQVCRD 445
Cdd:smart00486 81 KKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGLRIPNKKPLFGSKSFGLSDIKVYIKGRLVIDLYRLYKN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 446 KLSLSNYKLDTVAGECVGAKKEDVSYKEIPHLFRQGPGGRARLGLYCVKDSALVLDLLRYFMTHVEISEIAKIAKIPTRR 525
Cdd:smart00486 161 KLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLRR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 526 VLTDGQQIRVFSCLLDVAGREGYILPVDRHADA----------EGYQGATVIDPSPGFYNTPVLVVDFASLYPTIIQAHN 595
Cdd:smart00486 241 TLYYGSQIRVESLLLREAKKNNYILPSKELYDFkgsepdlkkkVKYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHN 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 596 LCYSTMI-PGDRLCLHPHLGPGDYETFELASG-PVHFVKKHKAVSLLATLLNVWLAKRKAIRRELATVSD--EAVRTILD 671
Cdd:smart00486 321 LCYSTLVgVGEVVIKGDLIIPEDLLTIKYEKGnKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDesEELKKLLD 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 672 KQQLAIKVTCNAVYGFTGVASGILPCLKIAETVTFQGRRMLENSKRYIEGvtpegladilgrrvECAPDASFKVIYGDTD 751
Cdd:smart00486 401 SRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEE--------------NGYPKPGFKVIYGDTD 466
|
....*...
gi 1706512 752 SLFIHCRG 759
Cdd:smart00486 467 SIFVTKPG 474
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
127-972 |
3.19e-152 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 478.75 E-value: 3.19e-152
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 127 VLKLLGRTSDDRSVCVNVFRQELYFYVRVPEGLKLDFLIQQCSRENFNFSQgRYRYEKTSKRVLREYCVEAR-------- 198
Cdd:PTZ00166 76 IIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNFLPEDSQKLKRELNAQLSE-QSQFKKYQNTVLDIEIVKKEslmyykgn 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 199 ---EVYRVFASSQGFV----DLLAGGLTAAGCE--------VFETNVDAARRFIIDNGFSTFGWYSC-AAAVPRQGGAAR 262
Cdd:PTZ00166 155 gekDFLKITVQLPKMVprlrSLIESGVVVCGGGwdgirlfqTYESNVPFVLRFLIDNNITGGSWLTLpKGKYKIRPPKKK 234
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 263 DSWTELEYDCAAGDLEFHAGRADW---PGYNVLSFDIECLGENG--FPNASRDEdmILQISCVIWKAGSGEAPRS-VLLN 336
Cdd:PTZ00166 235 TSTCQIEVDCSYEDLIPLPPEGEYltiAPLRILSFDIECIKLKGlgFPEAENDP--VIQISSVVTNQGDEEEPLTkFIFT 312
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 337 LGTCEEIEGVEVYQCPSELDLLYLFFTMIRDADVEFVTGYNISNFDFPYVIDRATQvynLNLKEFTRV-RSSSIFEVHKP 415
Cdd:PTZ00166 313 LKECASIAGANVLSFETEKELLLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKA---LKLNDFKYLgRIKSTRSVIKD 389
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 416 KNSSAGFM--RAVSKVKVAGVVPIDMYQVCRDKLSLSNYKLDTVAGECVGAKKEDVSYKEIPHLFRQGPGGRARLGLYCV 493
Cdd:PTZ00166 390 SKFSSKQMgtRESKEINIEGRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCL 469
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 494 KDSALVLDLLRYFMTHVEISEIAKIAKIPTRRVLTDGQQIRVFSCLLDVAGREGYILPVDRHA---DAEGYQGATVIDPS 570
Cdd:PTZ00166 470 KDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRGQQIKVTSQLLRKCKKLNYVIPTVKYSgggSEEKYEGATVLEPK 549
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 571 PGFYNTPVLVVDFASLYPTIIQAHNLCYSTMIPGDRLCLHPHlgpgdyETFELASGPVHFVKKHKAVSLLATLLNVWLAK 650
Cdd:PTZ00166 550 KGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDANNYPE------DTYVTTPTGDKFVKKEVRKGILPLIVEELIAA 623
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 651 RKAIRRELATVSDEAVRTILDKQQLAIKVTCNAVYGFTGVAS-GILPCLKIAETVTFQGRRMLENSKRYIEgvtpeglaD 729
Cdd:PTZ00166 624 RKKAKKEMKDEKDPLLKKVLNGRQLALKISANSVYGYTGAQVgGQLPCLEVSTSITSFGRQMIDKTKELVE--------K 695
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 730 ILGRRVECAPDAsfKVIYGDTDSLFIHCRGYRPEQVTGFCDElAAHMTRTLFVDPIKLEAEKTFKCLILLTKKRYIGMMT 809
Cdd:PTZ00166 696 HYTKANGYKHDA--TVIYGDTDSVMVKFGTDDIQEAMDLGKE-AAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAGLLY 772
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 810 T-----DRLLMKGVDLVRKTACRFVQETTKAILDLVMGDEAVRAAAErlcamrveevcargppvgFLKVVdilndsYRKL 884
Cdd:PTZ00166 773 TnpekyDKIDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIE------------------FTKGK------ISDL 828
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 885 RLNRVPVGQLSFSTELSRpiSYYKTlTLPHLVVYHKIMQRNE-ELPQIHDRIAYVFVQSPKGKLRSEMAEDPAYAAQHNI 963
Cdd:PTZ00166 829 LQNRIDISLLVITKSLGK--DDYEG-RLAHVELAKKLRQRDPgSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVLENNI 905
|
....*....
gi 1706512 964 PPAVDLYFD 972
Cdd:PTZ00166 906 PIDTQYYLD 914
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
116-985 |
7.61e-118 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 380.33 E-value: 7.61e-118
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 116 QFQTDIIPSGTVLKLLGRTSDDRSVCVNVFRQELYFYVRVPEGLKLDFLIQQcsrenfnfSQGRYRYEKTSKRVLREycv 195
Cdd:COG0417 9 DRSYRDEDGKPVIELWGRTEDGPSVLLDVTGFRPYFYVPLPDEEKLEELLRD--------IKEITEVEPVKLKSFFG--- 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 196 EAREVYRVFASSQGFVDLLAGGLTAAGCEVFETNVDAARRFIIDNGFSTFGWYScaaavprqGGAARDSWTELEYDCAAG 275
Cdd:COG0417 78 EPVPVLKIYTRDPRDVRELRDRLKEGGIDVYEADIRFHDRYLIDRFLTPGVWYE--------GEVEEDGGKLDYEVKENP 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 276 DLEFHAGRadwPGYNVLSFDIECLGENGFPNASRDEDMILqISCviwkagSGEAPRSVLLNLGTCEEIEGVEVyqCPSEL 355
Cdd:COG0417 150 RLKPEDYR---PKLKVLSFDIEVSTPRGFPDPERDGPIIS-IGL------AGSDGEKKVLMLGREGVDFEVEY--FDDEK 217
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 356 DLLYLFFTMIRDADVEFVTGYNISNFDFPYVIDRAtQVYNLNLKeFTRVRSssifevhKPKNSSAGFMRAVSkvkVAGVV 435
Cdd:COG0417 218 ALLEAFFEIIREYDPDIIIGWNVDNFDLPYLQKRA-ERLGIPLD-LGRDGS-------EPSWREHGGQGFAS---IPGRV 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 436 PIDMYQ-VCRDKLSLSNYKLDTVAGECVGAKKEDVSYKEIPHLFRQGpggRARLGLYCVKDSALVLDLLRYFMTHVEISE 514
Cdd:COG0417 286 VIDLYDaLKSATYKFKSYSLDAVAEELLGEGKLIVDGGEIERLWDDD---KPALAEYNLRDAELTLRIFEKTLLLPFLIE 362
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 515 IAKIAKIPTRRVLTDGQQIRVFSCLLDVAGREGYILPVDRHADAEGYQGATVIDPSPGFYNTpVLVVDFASLYPTIIQAH 594
Cdd:COG0417 363 LSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGYLAPNKGEIKGEAYPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTF 441
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 595 NLCYSTMIPGDRLClhphlgpgDYETFELASGPVHFVKKHKAvsLLATLLNVWLAKRKAIRRELA-TVSDEAVRTILDKQ 673
Cdd:COG0417 442 NISPETLVEGGEEP--------CGDEDVAPGFGHRFCREPKG--ILPSILEELWDERDEAKKKMKkAKPDSEEYRLYDAL 511
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 674 QLAIKVTCNAVYGFTGvASGI-LPCLKIAETVTFQGRRMLENSKRYIEGvtpegladiLGrrvecapdasFKVIYGDTDS 752
Cdd:COG0417 512 QQALKILMNSFYGVLG-SEGCrFYDPELAESITARGREIIKQTIEKAEE---------LG----------YKVIYGDTDS 571
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 753 LFIHCRGYRPEQVTGFCDELAAHMTRTLfVDPIKLEAEKTFKCLILLT-KKRYIGMMTTDRLLMKGVDLVRKTACRFVQE 831
Cdd:COG0417 572 LFVWLPKASLEEAIEIGKELAEEINAWW-PSGLELEFEKHYRRFFFPGsKKRYAGLTEDGKIDIKGLEAVRSDWTELAKE 650
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 832 TTKAILDLVMGDEAVRaaaerlcamrveevcargppvgflKVVDILNDSYRKLRLNRVPVGQLSFSTELSRPISYYKTLT 911
Cdd:COG0417 651 FQQEVYERILKEEDVE------------------------KAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSEYEKNV 706
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1706512 912 LPHLVVYHKIMQRNEElPQIHDRIAYVFVqspKGKLRsemAEDPAYAAQHNIPPAVDLYFDKVIHGAAN-ILQCL 985
Cdd:COG0417 707 PPHVRAARKLDERGRP-YQRGDKISYVIT---KGGGR---VEPVELAKERESEIDYDYYIEKQLKPTADrILEAF 774
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
133-457 |
3.48e-86 |
|
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: 280.46 E-value: 3.48e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 133 RTSDDRSVCVNVFRQELYFYVRVPEGLKLDFLIQQCsRENFNFSQGRYRYEKTSKRVLREYCVEAREVYRVFASSQGFVD 212
Cdd:pfam03104 1 KTDEGVSVCVNVFGFKPYFYCLAPDGKELEEVIEEI-KELYEGLDKIEKIELKLKKSLYGYEEDPVPYLKVSFANPRPLL 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 213 LLAGGLTAA-GCEVFETNVDAARRFIIDNGFSTFGWYSCAAAVPRQGGaaRDSWTELEYDCAAGDLEFHAGRADWPGYNV 291
Cdd:pfam03104 80 KIRKYLSPEnISDVYEYDVDYLERFLIDNDIVGFGWYKVKVYPFRAEG--RISNCDVEIDCDSPDLISVPFEKEWPPLRV 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 292 LSFDIECLGENG-FPNASRDEDMILQISCVIWKAGSGEAPRSVLLNLGTCE-------------EIEGVEVYQCPSELDL 357
Cdd:pfam03104 158 LSFDIECTSLPGkFPDAENVKDPIIQISCMLDGQGEPEPEPRFLFTLRECDsediedfeytpkpIYPGVKVFEFPSEKEL 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 358 LYLFFTMIRDADVEFVTGYNISNFDFPYVIDRATQVYNLNLKEFTRVRSSSIFEVHKPKNSsagfMRAVSKVKVAGVVPI 437
Cdd:pfam03104 238 LRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNRGGRSKVREIGFG----TRSYEKVKISGRLHL 313
|
330 340
....*....|....*....|
gi 1706512 438 DMYQVCRDKLSLSNYKLDTV 457
Cdd:pfam03104 314 DLYRVIKRDYKLPSYKLNAV 333
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
559-987 |
2.01e-85 |
|
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: 280.69 E-value: 2.01e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 559 EGYQGATVIDPSPGFYNTPVLVVDFASLYPTIIQAHNLCYSTMIPGDRLCLhphLGPGDYETfelasGPVH--FVKKHKA 636
Cdd:cd05533 1 EQYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKK---LPPEDYIK-----TPNGdyFVKSSVR 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 637 VSLLATLLNVWLAKRKAIRRELATVSDEAVRTILDKQQLAIKVTCNAVYGFTGVASGILPCLKIAETVTFQGRRMLENSK 716
Cdd:cd05533 73 KGLLPEILEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTK 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 717 RYIEgvtpeglaDILGRRVECAPDAsfKVIYGDTDSLFIHCRGYRPEQVTGFCDELAAHMTrTLFVDPIKLEAEKTFKCL 796
Cdd:cd05533 153 KLVE--------EKYTKANGYSHDA--KVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVS-KKFIKPIKLEFEKVYFPY 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 797 ILLTKKRYIGMMTT-----DRLLMKGVDLVRKTACRFVQETTKAILDLVMGDEAVRAAAErlcamrveevcargppvgFL 871
Cdd:cd05533 222 LLINKKRYAGLLWTnpdkhDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIE------------------FV 283
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 872 KvvDILNDsyrkLRLNRVPVGQLSFSTELSRPISYYKTlTLPHLVVYHKIMQRNE-ELPQIHDRIAYVFVQSPKGKLRSE 950
Cdd:cd05533 284 K--GVISD----LLQNKIDISLLVITKALTKTADDYAG-KQAHVELAERMRKRDPgSAPNVGDRVPYVIIKGAKGAKAYE 356
|
410 420 430
....*....|....*....|....*....|....*..
gi 1706512 951 MAEDPAYAAQHNIPPAVDLYFDKVIhgaANILQCLFE 987
Cdd:cd05533 357 KAEDPIYVLENNIPIDTQYYLENQL---SKPLLRIFE 390
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
530-947 |
1.52e-60 |
|
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: 214.00 E-value: 1.52e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 530 GQQIRVFSCLLDVAGREGYILP----VDRHAdaegyQGAT-----VIDPSPGFYNTPVLVVDFASLYPTIIQAHNLCYST 600
Cdd:cd05534 1 GSQFRVESMLLRLAKPENYILPspsrQQVAQ-----QRALeclplVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYST 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 601 MI----------PGDRLCLHPHLGPGDYETfELASGPVH-------FVKKHKAVSLLATLLNVWLAKRKAIRREL-ATVS 662
Cdd:cd05534 76 CLgrveelngggKFGFLGVKLYLPPPPLDL-LLLKDDVTispngvmFVKKSVRKGILPKMLEEILDTRIMVKKAMkKYKD 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 663 DEAVRTILDKQQLAIKVTCNAVYGFTGV-ASGILPCLKIAETVTFQGRRMLENSKRYIEGvTPEGLAdilgrrvecapda 741
Cdd:cd05534 155 DKKLQRILDARQLALKLLANVTYGYTAAsFSGRMPCVEIADSIVQTGRETLERAIELIES-TPKWGA------------- 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 742 sfKVIYGDTDSLFIHCRGYRPEQVTGFCDELAAHMTRTlFVDPIKLEAEKTFKCLILLTKKRYIGMM------TTDRLLM 815
Cdd:cd05534 221 --KVVYGDTDSLFVLLPGRTKEEAFKIGKEIAEAVTAA-NPSPIKLKFEKVYHPCVLVTKKRYVGYKyespdqTEPTFDA 297
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 816 KGVDLVRKTACRFVQETTKAILDLVMGDEAVRaaaerlcamrveevcargppvgflKVVDILNDSYRKLRLNRVPVGQLS 895
Cdd:cd05534 298 KGIETVRRDGCPAVQKILEKSLRILFETKDLS------------------------TVKSYLQRQWSKLLQGRVSIQDFI 353
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*.
gi 1706512 896 FSTELsRPISYYKTLTLP-HLVVYHKIMQ---RNEelPQIHDRIAYVFVQSPKGKL 947
Cdd:cd05534 354 FAKEV-RLGTYKEGATLPaGAIVALRRMEkdpRAE--PQYGERVPYVVVRGEPGSR 406
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
117-982 |
5.38e-56 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 208.56 E-value: 5.38e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 117 FQTDIIPSGTVLKLLGRTsDDRSVCVNVFRQE-LYFYVRVPEGLKLDFLIQQCSRENF-----NFSQgryryektsKRVL 190
Cdd:PRK05762 11 RHYRDTPGGPEVELWLAT-DEGPRVVLLDPQFrPYFIPAEQDERAESLLAGEIGVRLSplalkDFHR---------RPVL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 191 REYCvearEVYRVFAssqgfvdLLAGGLTAAGCEVFETNVDAARRFIIDNGFSTFGWYScaaavprqgGaardswtelEY 270
Cdd:PRK05762 81 GLYC----RQHRQLT-------RLPKRLREGGVDVYEADIRFPERYLMERFITPCVWFS---------G---------EV 131
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 271 DCAAGDLEFHAGR----ADW-PGYNVLSFDIEClgengfpnaSRDEDMIlqiscVIWKAGSGEAPrsvLLNLGTCEEIEG 345
Cdd:PRK05762 132 EQYTTDGVLRNARlkpaPDYrPPLKVVSLDIET---------SNKGELY-----SIGLEGCGQRP---VIMLGPPNGEAL 194
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 346 VEVYQCPSELDLLYLFFTMIRDADVEFVTGYNISNFDFPYVIDRAtQVYNLNLKeFTRVRSSSIFEVHkPKNSSAGFmra 425
Cdd:PRK05762 195 DFLEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERA-ERYGIPLR-LGRDGSELEWREH-PFRSGYGF--- 268
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 426 vskVKVAGVVPIDMYqvcrDKL-----SLSNYKLDTVAGECVGAKKE--DVSYK--EIPHLFRQgpgGRARLGLYCVKDS 496
Cdd:PRK05762 269 ---ASVPGRLVLDGI----DALksatwVFDSFSLEYVSQRLLGEGKAidDPYDRmdEIDRRFAE---DKPALARYNLKDC 338
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 497 ALVLDLLRYfmTHVeIS---EIAKIAKIPTRRVltdGQQIRVF-SCLLDVAGREGYILPVDRHADAEGYQGATVIDPSPG 572
Cdd:PRK05762 339 ELVTRIFEK--TKL-LPfllERATVTGLPLDRV---GGSVAAFeHLYLPRAHRAGYVAPNLGERPGEASPGGYVMDSKPG 412
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 573 FYNTpVLVVDFASLYPTIIQAHNLCYSTMIPGDRL-CLHPHLGPGDYeTFelaSGPVHFVKKhkavsLLATLlnvwLAKR 651
Cdd:PRK05762 413 LYDS-VLVLDFKSLYPSIIRTFNIDPDGLVEGLAQpPEESVAGFLGA-RF---SREKHFLPE-----IVERL----WEGR 478
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 652 KAIRRElatvsdeavrtiLDK--QQlAIKVTCNAVYGFTGvASGI-LPCLKIAETVTFQGRRMLENSKRYIEGvtpegla 728
Cdd:PRK05762 479 DEAKRE------------MNKplSQ-AIKIIMNAFYGVLG-SSGCrFFDPRLASSITMRGHEIMKQTRELIEA------- 537
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 729 diLGrrvecapdasFKVIYGDTDSLFIHCRG-YRPEQVTGFCDELAAHM----TRTLFVDP-----IKLEAEKTFKCLIL 798
Cdd:PRK05762 538 --QG----------YQVIYGDTDSTFVWLGGaHDEEDAAKIGRALVQEInqwwQEHLQQEFglesaLELEFEKHYRRFFM 605
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 799 LT--------KKRYIGMMTTD----RLLMKGVDLVRKTACRFVQETTKAILDLVMgdeavraaaerlcamrveevcARGP 866
Cdd:PRK05762 606 PTirgaeegsKKRYAGLIQEGdgdgRIVFKGLETVRTDWTPLAKEFQQELYERIF---------------------RGEP 664
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 867 PVGFLK-VVDilndsyrKLRLNRVPvGQLSFSTELSRPISYYKTLTLPHLVVYHKIMQRNEEL-----PQIHDRIAYVFV 940
Cdd:PRK05762 665 YVDYVReVID-------KLRAGELD-EKLVYRKRLRRPLDEYQRNVPPHVRAARLADEMGYKVgrplqYQNGGKIGYVIT 736
|
890 900 910 920
....*....|....*....|....*....|....*....|...
gi 1706512 941 QSPKGKLRSEmaedpayaaqhNIPPAVDLYFDKVIHGAAN-IL 982
Cdd:PRK05762 737 VNGPEPLEYR-----------KSPIDYDYYIEKQLQPVADrIL 768
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
561-952 |
2.20e-47 |
|
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: 174.69 E-value: 2.20e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 561 YQGATVIDPSPGFYNTPVLVVDFASLYPTIIQAHNLCYSTmipgdrlclhphLGPGDYETFELASGPVHFVKKHKAV--S 638
Cdd:cd05532 8 YAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTT------------VDRADPDDEDDEEPPLPPSDQEKGIlpR 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 639 LLATLLNvwlaKRKAIRRELATVSDEAVRTILDKQQLAIKVTCNAVYGFTGVASGILPCLKIAETVTFQGRrmlenskry 718
Cdd:cd05532 76 IIRKLVE----RRRQVKKLMKSEKDPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGR--------- 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 719 iegvtpeglaDILGRRVECAPDASFKVIYGDTDSLFIHcrgyrpeqvTGFCDELAAHMTRTLFVDPI-------KLEAEK 791
Cdd:cd05532 143 ----------EILQKTKDLVEKMNLEVIYGDTDSIMIN---------TGTTDYEEAKKLGNKIKKEVnksykklEIDIDG 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 792 TFKCLILLTKKRYIGMMTTD------RLLMKGVDLVRKTACRFVQETTKAILDLVMGDEAVRAAAErlcamrveevcarg 865
Cdd:cd05532 204 VFKRLLLLKKKKYAALKVVDddkgklKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVE-------------- 269
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 866 ppvgflKVVDILNDSYRKLRLNRVPVGQLSFSTELSRPISYYK-TLTLPHLVVYHKIMQRNEELPQiHDRIAYVFVQSPK 944
Cdd:cd05532 270 ------NIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPdKKSLPHVQVALRMNKRGRKVKA-GDTIPYIICKDGS 342
|
....*...
gi 1706512 945 GKLRSEMA 952
Cdd:cd05532 343 SKSLADRA 350
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
125-976 |
3.41e-47 |
|
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: 184.10 E-value: 3.41e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 125 GTVLkLLGRTSDDRSVCVNVFRQELYFYVrVPEGLKLDFLIQQCSRENFNFSQgrYRYEKTSKRVLREYC--VEAREVYR 202
Cdd:TIGR00592 323 GVVL-LFGRDVDHVSPCVQVKGINRDLFF-LPREGKIDFDLGKVTRRTINLPD--YYLEFVSELALGYKKekFRAKPIAK 398
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 203 VFASSQGFVD----------LLAGGLTAAGCE-------------VFETNVDAARRFIIDNGFSTFGWYscAAAVPRQGG 259
Cdd:TIGR00592 399 KYEFEAPDIDapysseylevTYELGKEFAPMEalpsdlkgqtfwhVFGSNTGNLERFLLLRKIKGPCWL--AVKGPDELE 476
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 260 AARDSWTELEydcAAGDLEFHAGRADW---PGYNVLSFDIECLgengFPNASRDEDMILQISCVIWKA------------ 324
Cdd:TIGR00592 477 YPRRSWCKYE---GGYVKPPNVEKGLDktpPPLVVLDFSMKSL----NPSIIRNEIVSIPDTLHREFAldkpppeppydv 549
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 325 --GSGEAPRSVLLNLGTCEEIEGVEvyqcPSELDLLYLFFTMIR---------DADVEfvTGYNISNFDFPYVIDRatqv 393
Cdd:TIGR00592 550 hpCVGTRPKDCSFPLDLKGEFPGKK----PSLVEDLATERALIKkfmakvkkiDPDEI--VGHDYQQRALKVLANR---- 619
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 394 ynlnlkeftrvrsssIFEVHKPKNSSAGFMRAVSKVKVAGVVPIDMYQVCRDKLSlsnykldtvAGECVGAKKEDVS--Y 471
Cdd:TIGR00592 620 ---------------INDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVEIS---------AKELIRCKSYDLSelV 675
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 472 KEIPHLFRQGPGGRARLGLYcvKDSALVLDLLRYFMTHVEIS--------------EIAKIAKIPTRRVLTDGQQIRVFS 537
Cdd:TIGR00592 676 QQILKTERKVIPIDNINNMY--SESSSLTYLLEHTWKDAMFIlqimcelnvlplalQITNIAGNIMSRTLMGGRSERNEF 753
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 538 CLLDVAGREGYILP-----------VDRHADAEG--------YQGATVIDPSPGFYNTPVLVVDFASLYPTIIQAHNLCY 598
Cdd:TIGR00592 754 LLLHAFYENNYIVPdkqifrkqqklGDEDEEIDGykkgkkaaYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICF 833
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 599 STMIPGDRLCLHPHLGPGDYETfelasgpvhfvkkhkavSLLATLLNVWLAKRKAIRRELATVSDEAVRTILDKQQLAIK 678
Cdd:TIGR00592 834 TTVQQKVDEDELPELPDSELEM-----------------GILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDIRQKALK 896
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 679 VTCNAVYGFTGVASGILPCLKIAETVTFQGRRMLENSKRYIEgvtpegladilgrrvecapDASFKVIYGDTDSLFIHCR 758
Cdd:TIGR00592 897 LTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVE-------------------EMNLEVIYGDTDSIMINTP 957
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 759 GYRPEQVTGFCDELAAHMTRTLfvDPIKLEAEKTFKCLILLTKKRYIGMM--------TTDRLLMKGVDLVRKTACRFVQ 830
Cdd:TIGR00592 958 GTKYEEVFKIGKEFKSEVNKLY--KLLELDIDGVFKRLLLLKKKKYAAIKvegdsdgnYTTKQEVKGLDIVRRDWSPLAK 1035
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 831 ETTKAILDLVMGDEAVRAAaerlcamrVEEvcargppvgflkVVDILNDSYRKLRLNRVPVGQLSFSTELSRPISYYKTL 910
Cdd:TIGR00592 1036 ETGKKVLDTILSDKDVEEA--------VEE------------VQEVLEKIGKNVLNGEVPLEKFVINKQLTRDPKDYPDG 1095
|
890 900 910 920 930 940 950
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 911 -TLPHLVVYHKIMQRNEELPQIHDRIAYVFVQSPKG---KLRSEMAEDPAYaAQHNIPPAVDLYFDKVIH 976
Cdd:TIGR00592 1096 aSLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNlsaRQRAYALEELQR-KHNNLIYDTQYYLEHQIH 1164
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
559-867 |
1.59e-46 |
|
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: 169.86 E-value: 1.59e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 559 EGYQGATVIDPSPGFYNtPVLVVDFASLYPTIIQAHNLCYSTmIPGDRLCLHPHlgpgdyetfelASGPVHFVKKHKAVS 638
Cdd:cd00145 1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTT-LVGNGEIAAPE-----------DYIGVGFRSPKDRKG 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 639 LLATLLNVWLAKRKAI-RRELATVSDEAVRTILDKQQLAIKVTCNAVYGFTGVASGILPCLKIAETVTFQGRRMLENSKR 717
Cdd:cd00145 68 LLPRILEELLNFRDEAkKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIA 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 718 YIEgvtpegladilgrrvecapDASFKVIYGDTDSLFIHCRGYRP-EQVTGFCDELAAHMTRTLfvdPIKLEAEKTFKCL 796
Cdd:cd00145 148 LVE-------------------EHGARVIYGDTDSIFVSLPKMGTkEDAIKEGREILQELADEH---LLELEFEKVYLPF 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 797 ILLTKKRYIGMMTT-----DRLLMKGVDLVRKTACRFVQETTKAILDLVM----GDEAVRAAAERLcaMRVEEVCARGPP 867
Cdd:cd00145 206 FLGKKKRYAGLDIWkgqdeGKIDIKGLETRRRDSPPLVKKFQKEVLELILeeerKVEAVKEYIDEL--DKVKYVVTRGGK 283
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
291-507 |
6.65e-46 |
|
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: 164.67 E-value: 6.65e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 291 VLSFDIECLGENG-FPNASRDEdmILQISCVIWKAGSGEAPRSVLLNLGTCEEIEGVEVYQCPSELDLLYLFFTMIRDAD 369
Cdd:cd05777 9 ILSFDIECAGRKGvFPEPEKDP--VIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWRDFVQEVD 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 370 VEFVTGYNISNFDFPYVIDRATQvynLNLKEFTRV-RSSSIFEVHKPKN-SSAGFMRAVSK-VKVAGVVPIDMYQVCRDK 446
Cdd:cd05777 87 PDIITGYNICNFDLPYLLERAKA---LKLNTFPFLgRIKNIKSTIKDTTfSSKQMGTRETKeINIEGRIQFDLLQVIQRD 163
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1706512 447 LSLSNYKLDTVAGECVGAKKEDVSYKEIPHLFRQGPGGRARLGLYCVKDSALVLDLLRYFM 507
Cdd:cd05777 164 YKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLM 224
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
559-967 |
1.25e-43 |
|
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: 162.88 E-value: 1.25e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 559 EGYQGATVIDPSPGFYNTpVLVVDFASLYPTIIQAHNLCYSTMIPGdrlclhphlGPGDYETfELASGpvHFVKKHKAvS 638
Cdd:cd05536 2 ESYEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVRE---------GCEDCDV-EPQVG--HKFRKDPP-G 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 639 LLATLLNVWLAKRKAIRRELATVSDEAV-RTILDKQQLAIKVTCNAVYGFTGVASGILPCLKIAETVTFQGRRMLENSKR 717
Cdd:cd05536 68 FIPSVLEDLLEERRRIKEKMKKLDPESEeYKLLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIK 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 718 YIEgvtpegladilgrrvecapDASFKVIYGDTDSLFIHCRGYRP--EQVTGFCDELAAHMtrtlfvdPIKLEAEKTFKC 795
Cdd:cd05536 148 IAE-------------------EKGFKVIYGDTDSLFVKIDGADAvkKKVKKLLKYINEEL-------PLELEIEKFYKR 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 796 LILLTKKRYIGMMTTDRLLMKGVDLVRKTACRFVQETTKAILDLVMGDEAVRAAaerlcamrveevcargppvgflkvVD 875
Cdd:cd05536 202 GFFVTKKRYAGLTEDGKIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEA------------------------VK 257
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 876 ILNDSYRKLRLNRVPVGQLSFSTELSRPISYYKTlTLPHLVVYHKIMQRNEELPqIHDRIAYVFVQSPkGKLrSEMAE-- 953
Cdd:cd05536 258 IVKEVIEKLKRGEVPPEKLVIWKQLTKDLSEYKA-TGPHVAAAKKLAKRGYKVR-PGTKIGYVIVKGS-GKI-SDRAYpy 333
|
410 420
....*....|....*....|...
gi 1706512 954 ---------DPAYAAQHNIPPAV 967
Cdd:cd05536 334 dmvdekhkyDAEYYIDNQVLPAV 356
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
346-957 |
2.63e-39 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 157.54 E-value: 2.63e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 346 VEVYQC-------PSELDLLYLFFTMIRDADVEFVtgYNISNFDFPYVIDRATQvynLNLKEFTRVRSSSIFEVHkpkns 418
Cdd:PRK05761 195 IEVYTPakgripdDSEKELLAELFDIILEYPPVVT--FNGDNFDLPYLYNRALK---LGIPKEEIPIEPGRAGIH----- 264
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 419 sagfmravskvkvagvvpIDMYQVCRDKlSLSNY-----------KLDTVAGECVGAKKedvsykeIPHLFRQGPGGRAR 487
Cdd:PRK05761 265 ------------------IDLYKFFQNK-AVRSYafygkyrhreaRLDAVGRALLGISK-------VELETNISELDLEE 318
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 488 LGLYCVKDSALVLDLLRYF--MTHVEISEIAKIAKIPTRRV--LTDGQQIRvfSCLLDVAGREGYILP------VDRH-- 555
Cdd:PRK05761 319 LAEYNFRDAEITLKLTFFNneLVLKLILLLSRISKLPIEELsrATISTWIS--NLEYWEHRKRGWLIPwkedilRLDHev 396
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 556 ---ADAEG--YQGATVIDPSPGFYnTPVLVVDFASLYPTIIQAHNLCYSTMipgdrlcLHPHLGPGDYETFElasGPVHF 630
Cdd:PRK05761 397 ykkAIIKGkkYRGGLVFQPPPGIF-FNVYVLDFASLYPSIIVKWNLSPETV-------RIPECKCHYDDEVP---ELGHS 465
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 631 VKKHKAvSLLATLLNVWLAKRKAIRRELAT--VSDEAVRTILDKQQLAIKVTCNAVYGFTGVASGILPCLKIAETVTFQG 708
Cdd:PRK05761 466 VCDDRP-GLTSVLVGLLRDFRVKIYKKKAKdpNLDEERRAWYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESITALG 544
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 709 RRmlenskryiegvtpegladILGRRVECAPDASFKVIYGDTDSLFIhcRGYRPEQVtgfcDELAAHMTRTLFVDpikLE 788
Cdd:PRK05761 545 RE-------------------ILLSTKKKAEELGLKVLYGDTDSLFV--WGPTKESL----EELIKEIEERTGID---LE 596
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 789 AEKTFKcLILLT--KKRYIGMMTTDRLLMKGVDLVRKTACRFVQettkaildlvmgdEAVRAAAERLCAMR-VEEVcarg 865
Cdd:PRK05761 597 VDKTYD-WVAFSglKKNYFGVLKDGKVKIKGIVAKKRNTPEFVK-------------ELQREVLEVLKSIRsPEDV---- 658
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 866 pPVGFLKVVDILNDSYRKLRLNRVPVGQLSFSTELSRPISYYKTLTLPHLVVyhkIMQRNEELPQIH--DRIAYVFVQSP 943
Cdd:PRK05761 659 -EKVKDEIEDVLKRYYEKLRAKDYPLDELAIRVRLSKPLDEYTKNTPQHVKA---ALQLRDYGVEVSpgDIISYVKVDDK 734
|
650
....*....|....*...
gi 1706512 944 KGKLRSEMAE----DPAY 957
Cdd:PRK05761 735 RGVKPVQLAKlseiDVEK 752
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
560-952 |
1.05e-33 |
|
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Pssm-ID: 99913 Cd Length: 372 Bit Score: 134.02 E-value: 1.05e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 560 GYQGATVIDPSPG-FYNtpVLVVDFASLYPTIIQAHNLCYSTMIPgdrlclhPHLGPGDYETFELAsgpvHFV--KKHKA 636
Cdd:cd05530 12 KYRGAIVLEPPPGiFFN--VVVLDFASLYPSIIKVWNLSYETVNC-------PHCECKTNEVPEVG----HWVckKRPGI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 637 VSLLATLL---NVWLAKRKAIRRELatvsDEAVRTILDKQQLAIKVTCNAVYGFTGVASGILPCLKIAETVTFQGRRMLE 713
Cdd:cd05530 79 TSQIIGLLrdlRVKIYKKKAKDKSL----DEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIIT 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 714 NSkryiegvtpegladilgrrVECAPDASFKVIYGDTDSLFIhcrgYRPEQvtGFCDELAAHMTRTLFVDpikLEAEKTF 793
Cdd:cd05530 155 ST-------------------IKKARELGLKVLYGDTDSLFL----WNPPQ--EQLEDLVEWVEKELGLD---LELDKEY 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 794 KcLILLT--KKRYIGMMTTDRLLMKGVDLVRKTACRFVQETTKAILDLvmgdeavraaaerLCAMRVEE--VCARgppvg 869
Cdd:cd05530 207 R-YVVFSglKKNYLGVTKDGSVDIKGLLGKKRNTPEFVKELFYEVIEI-------------LSAVNSPEdfEKAR----- 267
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 870 fLKVVDILNDSYRKLRLNRVPVGQLSFSTELSRPISYYKTLTLPHlVVYHKIMQRNEELPQIHDRIAYVFVQSPKGKLRS 949
Cdd:cd05530 268 -EKIRDIVKGVYKRLKKKEYTLDQLAFKVMLSKPPEEYTKNTPQH-VKAARQLEKYGRNVEAGDIISYVKVKGKEGVKPV 345
|
...
gi 1706512 950 EMA 952
Cdd:cd05530 346 QLA 348
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
291-504 |
7.59e-27 |
|
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: 108.98 E-value: 7.59e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 291 VLSFDIECLGENGFPNASRDEdmILQISCVIWKAGsGEAPRSVLLNLGTCEE--IEGVEVYQCPSELDLLYLFFTMIRDA 368
Cdd:cd05160 1 VLSFDIETTPPVGGPEPDRDP--IICITYADSFDG-VKVVFLLKTSTVGDDIefIDGIEVEYFADEKELLKRFFDIIREY 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 369 DVEFVTGYNISNFDFPYVIDRAtQVYNLNLkEFTRVRsssifevhKPKNSsaGFMRAVSKVKVAGVVPIDMYQVCRDKLS 448
Cdd:cd05160 78 DPDILTGYNIDDFDLPYLLKRA-EALGIKL-TDGIYR--------RSGGE--KSSGSTERIAVKGRVVFDLLAAYKRDFK 145
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 1706512 449 LSNYKLDTVAGECVGAKKEDVSYKEIPHLFRQgpGGRARLGLYCVKDSALVLDLLR 504
Cdd:cd05160 146 LKSYTLDAVAEELLGEGKEKVDGEIIEDAEWE--EDPERLIEYNLKDAELTLQILE 199
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
287-506 |
1.05e-23 |
|
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: 99.74 E-value: 1.05e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 287 PGYNVLSFDIECLGENGFPNASRDEdmILQISCviwkAGSGEAprSVLlnlgTCEEIEGVEVYQCPSELDLLYLFFTMIR 366
Cdd:cd05780 1 EDLKILSFDIEVLNHEGEPNPEKDP--IIMISF----ADEGGN--KVI----TWKKFDLPFVEVVKTEKEMIKRFIEIVK 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 367 DADVEFVTGYNISNFDFPYVIDRAtQVYNLnlkEFTRVRSSSifevhKPKNSSAGFMRAVskvKVAGVVPIDMYQVCRDK 446
Cdd:cd05780 69 EKDPDVIYTYNGDNFDFPYLKKRA-EKLGI---ELDLGRDGS-----EIKIQRGGFNNAS---EIKGRIHVDLYPVARRT 136
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 447 LSLSNYKLDTVAGECVGAKKEDVSYKEIPHLFRQGPgGRARLGLYCVKDSALVLDLLRYF 506
Cdd:cd05780 137 LNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGE-NLERLFRYSMEDAKYTYEIGKEF 195
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
561-911 |
3.69e-20 |
|
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: 93.18 E-value: 3.69e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 561 YQGATVIDPSPGFYnTPVLVVDFASLYPTIIQAHNLCYSTmipgdrlclhphLGPGDYETFELASGPVHFVKKHKAvsLL 640
Cdd:cd05531 5 DRGGLVFQPEPGLY-ENVAQIDFSSMYPSIIVKYNISPET------------INCRCCECRDHVYLGHRICLKRRG--FL 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 641 ATLLNVWLAKRKAIRRELATVSDEAVRtildkqQLAIK---VTCnavYGFTGVASGILPCLKIAETVTFQGRRMLENSKr 717
Cdd:cd05531 70 PEVLEPLLERRLEYKRLKKEEDPYAGR------QKALKwilVTS---FGYLGYKNAKFGRIEVHEAITAYGRKILLRAK- 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 718 yiegvtpegladilgrrvECAPDASFKVIYGDTDSLFIHCRGYRPEqvtgFCDELAAHMTrtlfvdpIKLEAEKTFKCLI 797
Cdd:cd05531 140 ------------------EIAEEMGFRVLHGIVDSLWIQGRGDIEE----LAREIEERTG-------IPLKLEGHYDWIV 190
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 798 LLTKK-------RYIGMMTTDRLLMKGVDLVRKTACRFVQETTKAILDlVMGdeavraaaerlCAMRVEEVCARGPpvgf 870
Cdd:cd05531 191 FLPERdglgapnRYFGRLSDGEMKVRGIELRRRDTPPFVKKFQEEALD-ILA-----------SAKTPEELLKLRE---- 254
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 1706512 871 lKVVDILNdSYRKlRLNRVPVGQLSFSTELSRPISYYKTLT 911
Cdd:cd05531 255 -EALDLFR-RYLQ-RLREGDLEDLIIEKKISKRSSEYKVLA 292
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
563-941 |
1.31e-19 |
|
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: 91.94 E-value: 1.31e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 563 GATVIDPSPGFYNTpVLVVDFASLYPTIIQAHNLCYSTMIPG----DRLCLHPhlGPGDyetfelasgpVHFVK-KHKAV 637
Cdd:cd05537 5 GGYVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLIDPLGLIEGlkapDPEDLIP--GFLG----------ARFSReKHILP 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 638 SLLATLlnvWLAKRKAIRRelatvSDEAvrtildkQQLAIKVTCNAVYGFTGvASGilpCL----KIAETVTFQGRRMLE 713
Cdd:cd05537 72 DLIARL---WAARDEAKRE-----KNAP-------LSQAIKIIMNSFYGVLG-STG---CRffdpRLASSITLRGHEIMK 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 714 NSKRYIEgvtpegladilgrrvecapDASFKVIYGDTDSLFIHCR-GYRPEQVTGFCDELA--------AHMTRTLFVDP 784
Cdd:cd05537 133 QTRAWIE-------------------QQGYQVIYGDTDSTFVWLGeELDAAEAQAIGKELAsqinqwwaQKLKEEFGLES 193
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 785 -IKLEAEKTFKCLILLT--------KKRYIGMMTTD---RLLMKGVDLVRKTACRFVQETTKAILDLVMGDEavraaaer 852
Cdd:cd05537 194 fLEIEFETHYSRFFMPTirgsdegsKKRYAGLKSTDggdELVFKGLETVRSDWTPLARQFQKELYERVFNDE-------- 265
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 853 lcamrveevcargPPVGFLK-VVDILNDSyrklRLNrvpvGQLSFSTELSRPISYYKTLTLPHLVVYHKIMQRNEEL--P 929
Cdd:cd05537 266 -------------PYEGFIKeTVEELLAG----ELD----ELLVYRKRLRRPLSEYTKNVPPHVQAARLADQINRELgrP 324
|
410
....*....|..
gi 1706512 930 QIHDRIAYVFVQ 941
Cdd:cd05537 325 RQYQWIEYVITV 336
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
292-841 |
2.43e-18 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 90.85 E-value: 2.43e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 292 LSFDIECLGENGFPNASRDEdmILQISCViWKAGSGEAPRSVLLN--LGTCEEIEGVEVYQCP----------------- 352
Cdd:PHA03036 163 LFLDIECHFDKKFPSVFINP--VSHISCC-YIDLSGKEKRFTLINedMLSEDEIEEAVKRGYYeieslldmdyskelilc 239
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 353 SELDLLyLFFTMIRDADVEFVTGYNISNFDFPYVIDRATqvynLNLKEFTRVRSS--------SIFEVHKPKNSSAGFMR 424
Cdd:PHA03036 240 SEIVLL-RIAKKLLELEFDYVVTFNGHNFDLRYISNRLE----LLTGEKIIFRSPdgketvhlCIYERNLSSHKGVGGVA 314
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 425 AVSkVKV---AGVVPIDMYQVCRDKLSLSNYKLDTVAGE---CVGAKKE--DVSYKEIPH----------LFRQ------ 480
Cdd:PHA03036 315 NTT-YHInnnNGTIFFDLYTFIQKTEKLDSYKLDSISKNafnCNAKVLSenNNEVTFIGDnttdakgkasIFSEvlstgn 393
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 481 --------------------------------GPGGRARLGL------------------------YCVKDSALVLDLLR 504
Cdd:PHA03036 394 yvtindddickildkdiiensftvkvicknnyIPGDTYTLSFgkddvdlsdmyknynleialemarYCIHDACLCKYLWE 473
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 505 YFMTHVEISEIAK----------------IAKIPTRRVLTDGQQIRVfsclldvagreGYILPVDRHadaegYQGATVID 568
Cdd:PHA03036 474 YYGIETKIDAGAStyllpqsmvfeyrastLIKGPLLKLLLEEKTILV-----------RSETKNKFP-----YEGGKVFA 537
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 569 PSPGFYNTPVLVVDFASLYPTIIQAHNLCYSTMI-----------------------PGDRLCLHPHLGPGDYETfELAs 625
Cdd:PHA03036 538 PKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVgvvvndnrleaeinkqelrrkypYPRYIYVHCEPRSPDLVS-EIA- 615
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 626 gpvhfVKKHKAVSLLATLLNVWLAKRKAIRRELATVSDEAVRTILDKQQLAIKVTCNAVYGFTGVASGILPCLKIAETVT 705
Cdd:PHA03036 616 -----VFDRRIEGIIPKLLKTFLEERARYKKLLKEATSSVEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCT 690
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 706 FQGRRM-------LENSKrYIEGV-----TPEGLADILGRRVECAPDAS--------FKVIYGDTDSLFIHCRgyrpEQV 765
Cdd:PHA03036 691 AIGRNMikylnsvLNGSK-LINGKlilanCPINPFFKDDRSIDTNYDTNlpveynftFRSVYGDTDSVFLEIN----TKD 765
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 766 TGFCDELAAHMTRTL----FVDPIKLEAEKTFKCLILLTKKRYIGM----MTTDRL----LMKGVDLVRKTACRFVQETT 833
Cdd:PHA03036 766 VDKSIKIAKELERIInekvLFDNFKIEFEAVYKNLIMQSKKKYTTLkyiaSSTDGSvperVNKGTSETRRDVSKFHKYMI 845
|
....*...
gi 1706512 834 KAILDLVM 841
Cdd:PHA03036 846 KIYKTRLL 853
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
291-755 |
2.33e-16 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 84.36 E-value: 2.33e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 291 VLSFDIECLGENGFPNASRDEDMILQIS----------------CVIWKAGSGEAPRsvllnlgtcEEIEGVEVYQCPSE 354
Cdd:PHA02528 108 IANLDIEVTAEDGFPDPEEAKYEIDAIThydsiddrfyvfdlgsVEEWDAKGDEVPQ---------EILDKVVYMPFDTE 178
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 355 LDLLYLFFTMIRDADVEFVTGYNISNFDFPYVIDRATQVYNLNLkeftrVRSSSIFEVHKPKNSSAGFMRAVSKVKVAGV 434
Cdd:PHA02528 179 REMLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGEKT-----AKRLSPWGKVKERTIENMYGREEIAYDISGI 253
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 435 VPIDMYQVCRdKLSLSN---YKLDTVAGECVGAKKEDVSYKEIPHLFRQGPggrARLGLYCVKDSALVLDL--LRYFMTH 509
Cdd:PHA02528 254 SILDYLDLYK-KFTFTNqpsYRLDYIAEVELGKKKLDYSDGPFKKFRETDH---QKYIEYNIIDVELVDRLddKRKLIEL 329
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 510 VeISeIAKIAKIPTRRVLTdgqQIR-----VFSCLLDvagrEGYILPVDRHADAEGYQGATVIDPSPGFYNTpVLVVDFA 584
Cdd:PHA02528 330 V-LS-MAYYAKINFEDVFS---PIKtwdaiIFNSLKE----EKIVIPENKSHKKQKYAGAFVKEPVPGAYRW-VVSFDLT 399
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 585 SLYPTIIQAHNLCYSTMI------------------PGDRLCLHPH--------------------LGPGDYETFELASG 626
Cdd:PHA02528 400 SLYPSIIRQVNISPETIAgtfhvapvheyinktaprPSDEYSCSPNgwmyrkdirgvipteikkvfDQRKIYKKKMLAAE 479
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 627 PVHFVKKHKAVSLLATL-----LNVWLAKRKAIRRELATVSDEAVRTILDK----------QQLAIKVTCNAVYGFTGVA 691
Cdd:PHA02528 480 RNAELIKTILEDLNDSVdtpidVDYYFDFSDEFKAELKTLTKSSLKALLEEcekeialcntIQMARKILINSLYGALGNE 559
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1706512 692 SGILPCLKIAETVTFQGrrmlENSKRYIEGVTPEGLADILGRRvecapDASFkVIYGDTDSLFI 755
Cdd:PHA02528 560 HFRYYDLRNAEAITLFG----QLAIQWIERKMNEYLNKLCKTE-----DEDY-VIYGDTDSIYV 613
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
290-682 |
9.53e-15 |
|
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: 79.33 E-value: 9.53e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 290 NVLSFDIEC---LGENGFPNASRDEDMILQIS----CVIWKAGSGEAPRSVLLNLGTCEEIEGVEVYQCPSELDLLYLFF 362
Cdd:TIGR00592 199 KLASFDIETyfhDGKDFFPGDENPADEEIMISttpvIAKQWDYESEPEARVVTWKKPDKPTTGSYVESVSEEISMIKRFW 278
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 363 TMIRDADVEFVTGYNISNFDFPYVIDRATQV-----YNLNLKEFTRVRSSSIFEVHK-PKNSSAGFMRAVSKVKVAGVVP 436
Cdd:TIGR00592 279 DVIDQEDTDVEITVNGDNFDLVYLADRQVFQfywdaYEDPAEKLGVVLLFGRDVDHVsPCVQVKGINRDLFFLPREGKID 358
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 437 IDMYQVCRDKLSLSNYKLDTVAGECVGAKKEDVSYKEIPHLFRQGPGGraRLGLYCVKDSALVLDLLRYFMTHVEISEIA 516
Cdd:TIGR00592 359 FDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIAKKYEFEAPD--IDAPYSSEYLEVTYELGKEFAPMEALPSDL 436
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 517 KIAKIPTRRVLTDGQQIRVFSCL-------LDVAGREGYILPVDRHadaEGYQGATVIDPS--PGFYNT--PVLVVDFA- 584
Cdd:TIGR00592 437 KGQTFWHVFGSNTGNLERFLLLRkikgpcwLAVKGPDELEYPRRSW---CKYEGGYVKPPNveKGLDKTppPLVVLDFSm 513
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 585 -SLYPTIIQAHNLcystMIPgDRLCLHPHL-GPGDYETFELASGPVHFVK--------KHKAVSLLATLLNVWLAKRKAI 654
Cdd:TIGR00592 514 kSLNPSIIRNEIV----SIP-DTLHREFALdKPPPEPPYDVHPCVGTRPKdcsfpldlKGEFPGKKPSLVEDLATERALI 588
|
410 420 430
....*....|....*....|....*....|
gi 1706512 655 RRELATV--SDEAVRTILDKQQLAIKVTCN 682
Cdd:TIGR00592 589 KKFMAKVkkIDPDEIVGHDYQQRALKVLAN 618
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
427-757 |
2.27e-13 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 74.89 E-value: 2.27e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 427 SKVKVAGVVPIDMYQVCRDK---LSLSNYKLDTVAGECVG-----------AKKEDVSYKEIPHLFRQGPGGRARLGLYC 492
Cdd:PHA03334 462 STSHGFGAHIIDLMRVCNTKsikAKCSSRKLDTVARLIISkskphknppkiGKMDDVKYTEMDGMFTAGGAALARYLIYN 541
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 493 VKDSALVLDLLRYFMTHVE-ISEIAKIAKIPT----RRVLT-DG--QQIRVFSC-LLDVAGREGYILPVDRHADA----E 559
Cdd:PHA03334 542 LVDSELLIRIAKNLDPVIEfLNRLRATYNIDYvahgRGVMNfCGfvQSTKSVEVpLLKARLRIGIFVATGRIAESlcmpE 621
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 560 GY----------QGATVIDPSPGF-----YNTPVLVVDFASLYPTiiqahNLCYSTMIPG---DRLCLHPHLG------- 614
Cdd:PHA03334 622 KYardcrqkiklKGGYVFAPLTGLtfagpYQGTELTLDFASLYPS-----NMCDANISPEaivDPDCTARVRGwvvfdwk 696
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 615 --PGDYETFELasgpVHFVKKHKAV--------SLLATLLNVWLAKRKAIRRELATVSDEAVRTILDKQQLAIKVTCNAV 684
Cdd:PHA03334 697 kiDRGFGKATL----MYTILRTKPEepswrrftTYTTSSLNHYLSMRTEYKGAMKQAKDPKLKSYHNQLQNEMKICANSH 772
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1706512 685 YgftGVASGILPCLkiaetVTFQGRRMLENSKRYIEgvtpegladilgrrvecaPDASFKVIYGDTDSLFIHC 757
Cdd:PHA03334 773 Y---GVAPHACQHL-----ITTLGRHKIKLVEEFIK------------------KEPGMTVNYGDTDSVMFQL 819
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
287-502 |
3.33e-10 |
|
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: 60.66 E-value: 3.33e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 287 PGYNVLSFDIEClGENGfpnasrdedMILQIscviwkAGSGEAPRSVLLnLGTCEEIEGVEVYQCPSELDLLYLFFTMIR 366
Cdd:cd05784 1 PKLKVVSLDIET-SMDG---------ELYSI------GLYGEGQERVLM-VGDPEDDAPDNIEWFADEKSLLLALIAWFA 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 367 DADVEFVTGYNISNFDFPYVIDRATQvynLNLKeFTRVRSSSIFEVHKPKNSSAGFMRAVSKVKVAGvvpIDM-----YQ 441
Cdd:cd05784 64 QYDPDIIIGWNVINFDLRLLQRRAEA---HGLP-LRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDG---IDAlktatYH 136
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1706512 442 vcrdklsLSNYKLDTVAGECVGAKK--EDVSYK--EIPHLFRQGPggrARLGLYCVKDSALVLDL 502
Cdd:cd05784 137 -------FESFSLENVAQELLGEGKliHDVDDRgaEIERLFREDK---LALARYNLQDCELVWRI 191
|
|
| DNA_polB_epsilon_exo |
cd05779 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ... |
290-400 |
4.17e-10 |
|
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: 60.35 E-value: 4.17e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 290 NVLSFDIECLG-ENGFPNASRDEdmILQISCVIwkAGSGEaprsVLLNLGTC-EEIEGVE------------VYQCPSEL 355
Cdd:cd05779 3 RVLAFDIETTKlPLKFPDAETDQ--IMMISYMI--DGQGY----LIVNREIVsEDIEDFEytpkpeyegpfkVFNEPDEK 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 1706512 356 DLLYLFFTMIRDADVEFVTGYNISNFDFPYVIDRATqVYNLNLKE 400
Cdd:cd05779 75 ALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAA-IHGLSMEE 118
|
|
| 43A |
PHA02524 |
DNA polymerase subunit A; Provisional |
353-604 |
1.55e-08 |
|
DNA polymerase subunit A; Provisional
Pssm-ID: 164925 [Multi-domain] Cd Length: 498 Bit Score: 58.47 E-value: 1.55e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 353 SELDLLYLFFTMIRDADVEFVTGYNISNFDFPYVIDRATQVYNLN----LKEFTRVRSSSIFEVHKPKnssagfmravSK 428
Cdd:PHA02524 179 DEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNILGEKaanqLSPYGKITSKTITNLYGEK----------II 248
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 429 VKVAGVVPIDMYQVCRdKLSLS---NYKLDTVAGECVGAKKEDvsYKEIPHLFRQgpGGRARLGLYCVKDSALVL--DLL 503
Cdd:PHA02524 249 YKIHGIALMDYMDVFK-KFSFTpmpDYKLGNVGYREVKADKLD--YEGPINKFRK--ADHQRYVDYCVRDTDIILliDGR 323
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 504 RYFMTHveISEIAKIAKIPTRRVLTdgqQIRVF-SCLLDVAGREGYILPVDRHADAEGYQGATVIDPSPGFYNTPvLVVD 582
Cdd:PHA02524 324 RCFIDL--ILSLSYYAKIRFDDVLG---TIKVWdSIIFNSLVESNVVIPAMKASPKQSFPGAYVKEPVPGGYRYG-LSFD 397
|
250 260
....*....|....*....|..
gi 1706512 583 FASLYPTIIQAHNLCySTMIPG 604
Cdd:PHA02524 398 LTSLYPSILRLLNIS-PEMIAG 418
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
304-503 |
1.76e-08 |
|
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: 56.09 E-value: 1.76e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 304 FPNASRDEdmilqISCVIWKA-------------------GSGEAPRSVLLNLGTCEEIEgVEVYQcpSELDLLYLFFTM 364
Cdd:cd05778 20 LPDPEFDP-----ISAIFYCIdddvspfildankvgviivDELKSNASNGRIRSGLSGIP-VEVVE--SELELFEELIDL 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 365 IRDADVEFVTGYNISNFDFPYVIDRATQVYNLNL-KEFTRVrsssifevhkPKNSSAGFMRAV--------SKVKVAGVV 435
Cdd:cd05778 92 VRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLlDEISRV----------PSDSNGKFGDRDdewgythtSGIKIVGRH 161
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1706512 436 PIDMYQVCRDKLSLSNYKLDTVAGECVGAKKEDVSYKEIPHLFRQG-PGGRARLGLYCVKDSALVLDLL 503
Cdd:cd05778 162 ILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGsASERWRVLEYYLKRVRLNLEIL 230
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
287-475 |
3.18e-07 |
|
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarchaea. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B-DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.
Pssm-ID: 99824 [Multi-domain] Cd Length: 188 Bit Score: 51.56 E-value: 3.18e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 287 PGYNVLSFDIECLGENGFPNASRDEdmILQIScvIWkagSGEAPRSVLLNLGTceeiegvevyqcpSELDLLYLFFTMIR 366
Cdd:cd05781 1 PDLKTLAFDIEVYSKYGTPNPRRDP--IIVIS--LA---TSNGDVEFILAEGL-------------DDRKIIREFVKYVK 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 367 DADVEFVTGYNISNFDFPYVIDRATqvyNLNLK-EFTRvRSSSIfevhkPKNSSAGfmravsKVKVAGVVPIDMYQVCRD 445
Cdd:cd05781 61 EYDPDIIVGYNSNAFDWPYLVERAR---VLGVKlDVGR-RGGSE-----PSTGVYG------HYSITGRLNVDLYDFAEE 125
|
170 180 190
....*....|....*....|....*....|...
gi 1706512 446 KLSLSNYKLDTVAGEC-VGAKKEDVS--YKEIP 475
Cdd:cd05781 126 IPEVKVKTLENVAEYLgVMKKSERVLieWYRIY 158
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
292-495 |
1.00e-05 |
|
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: 47.41 E-value: 1.00e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 292 LSFDIE--CLGENGFPNASRDEDMILQIScviwkagsgeaprsVLLNLGTCEEIEGVEVyqcpSELDLLYLFFTMIRDAD 369
Cdd:cd05785 12 LQLDIEtySLPGFFFSNPDRGDDRIIIVA--------------LRDNRGWEEVLHAEDA----AEKELLEELVAIIRERD 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 370 VEFVTGYNISNFDFPYVIDRAtqvyNLNLKEFTRVRSSSIFEVHKPKNSSAGFMRAVSKVKVAGVVPIDMY-QVCRDKLS 448
Cdd:cd05785 74 PDVIEGHNIFRFDLPYLRRRC----RRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYfLVQLFDVS 149
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 1706512 449 ---LSNYKLDTVAgECVGAKKED---VSYKEIPHLFRQGPggrARLGLYCVKD 495
Cdd:cd05785 150 srdLPSYGLKAVA-KHFGLASPDrtyIDGRQIAEVWRSDP---ARLLAYALDD 198
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
577-936 |
2.48e-05 |
|
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: 47.48 E-value: 2.48e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 577 PVLVVDFASLYPTIIQAHNLCYStmipGDRLCLHPhlgpgdyetfelasgpvhfvkkhkavSLLATLLNVWLAKRKAIRR 656
Cdd:cd05538 18 PIVHADVASLYPSIMLAYRICPA----RDSLGIFL--------------------------ALLKYLVELRLAAKESARA 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 657 ElatvSDEAVRTILDKQQLAIKVTCNAVYGFTGVASGILPCLKIAETVTFQGRRMLENSKRYI--EGVTPegladilgrr 734
Cdd:cd05538 68 A----ARPAERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLrrRGATP---------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 735 VECapdasfkviygDTDSL-FIHcrgyrPEQVTGFCDE--LAAHMTRTLfvdP--IKLEAEKTFKCLILLTKKRYIGMMT 809
Cdd:cd05538 134 VEV-----------DTDGIyFIP-----PNGVDTEDEEeeLVRELSSTL---PkgITVEFDGRYRAMFSYKIKNYALLDY 194
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 810 TDRLLMKGVDLVRKTACRFVQETTKAILDLVMGDEAvrAAAERLCAMRVEEVCARGPPVGFLKVVDILNDS---YR-KLR 885
Cdd:cd05538 195 DGKLIVKGSAFRSRGIEPFLREFLREAVRLLLQGDG--AGVHDLYEDYLRRLRSHELPISDLARTETLKESpeeYLqKVR 272
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1706512 886 L-NRVPVGQLSFSTELSRP------ISYYKTLTLPHLVVY---------------HKIMQRNEELPQIHDRIA 936
Cdd:cd05538 273 AgKRNPAAAYEIALARPREwragdrVTYYVSGTGKGVSVYencrlvadydpahpdENTGFYAERLLQLAARLL 345
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
348-517 |
2.31e-04 |
|
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: 43.76 E-value: 2.31e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 348 VYQCPSELDLLYLFFTMIR--DADVefVTGYNISNFDFPYVIDRAtqvYNLNLKEFTRV----RSSsifevhKPKNSSAG 421
Cdd:cd05776 76 VRIFENERALLNFFLAKLQkiDPDV--LVGHDLEGFDLDVLLSRI---QELKVPHWSRIgrlkRSV------WPKKKGGG 144
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 422 FMRAVSkvKVAGVVPIDMYQVCRDKLSLSNYKLDTVAGECVGAKKEDVSYKEIPHLFRQgPGGRARLGLYCVKDSALVLD 501
Cdd:cd05776 145 KFGERE--LTAGRLLCDTYLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYND-SESLLKLLEHTEKDAYLILQ 221
|
170
....*....|....*.
gi 1706512 502 LlryfMTHVEISEIAK 517
Cdd:cd05776 222 L----MFKLNILPLTK 233
|
|
| DNA_polB_B1_exo |
cd05783 |
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ... |
292-390 |
8.44e-04 |
|
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are unique in that they are able to recognize the presence of uracil in the template strand, leading to the stalling of DNA synthesis. This is an additional safeguard mechanism against increased levels of deaminated bases during genome duplication at high temperatures. S. solfataricus B1 also interacts with DNA polymerase Y and may contribute to genome stability mechanisms.
Pssm-ID: 99826 [Multi-domain] Cd Length: 204 Bit Score: 41.92 E-value: 8.44e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706512 292 LSFDIECLGE--NGFPNASRDEDMILQISCviwkAGSGEAPRSVLLNLGTCEEIE-----GVEVYQCPSELDLLYLFFTM 364
Cdd:cd05783 8 IAIDIEVYTPikGRIPDPKTAEYPVISVAL----AGSDGLKRVLVLKREGVEGLEgllpeGAEVEFFDSEKELIREAFKI 83
|
90 100
....*....|....*....|....*.
gi 1706512 365 IRDadVEFVTGYNISNFDFPYVIDRA 390
Cdd:cd05783 84 ISE--YPIVLTFNGDNFDLPYLYNRA 107
|
|
| |
