|
Name |
Accession |
Description |
Interval |
E-value |
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
141-579 |
2.14e-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: 451.98 E-value: 2.14e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 141 PPYRMLSFDIECM-GEAGFPRATRDEDVILQISCVFHTAGDKSPYTQILLSLGTCEPLEGTEILEFPSEYDMLTAFFAML 219
Cdd:smart00486 1 PPLKILSFDIETYtDGGNFPDAEIFDDEIIQISLVINDGDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEFI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 220 RDYDVEFLTGYNIANFDLPYIITRATQVYNIDLKNFTKIKTGSVFEVHEPTGGGGGFLRSQSKVKISGIAPIDMYQVCRD 299
Cdd:smart00486 81 KKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGLRIPNKKPLFGSKSFGLSDIKVYIKGRLVIDLYRLYKN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 300 KLSLSDYKLDTVAKKCLGKQKDDISYRDIPPLFRSGAAGRAKIGRYCIIDSVLVMDLLRMFQTHVEIAEIARLAKIPTRR 379
Cdd:smart00486 161 KLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLRR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 380 VLTDGQQIRVFSCLLEAAAKEGYILPV----------PRGDATGGYQGATVISPIPGFYDDPVLVVDFASLYPSIIQAHN 449
Cdd:smart00486 241 TLYYGSQIRVESLLLREAKKNNYILPSkelydfkgsePDLKKKVKYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHN 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 450 LCYSTLI-PQGALPAHPELRPDDYETFVLSEG-PVHFVKKHVRESLLSKLLATWLSKRKDIRRTLASCADP--TMRTILD 525
Cdd:smart00486 321 LCYSTLVgVGEVVIKGDLIIPEDLLTIKYEKGnKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDEseELKKLLD 400
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....
gi 6469146 526 KQQLAIKVTCNAVYGFTGVASGILPCLNIAETVTLQGRKMLERSQAFVEAISPS 579
Cdd:smart00486 401 SRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGYP 454
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
6-574 |
5.50e-131 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 409.42 E-value: 5.50e-131
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 6 YFYTRAPPGV------NLLHVL-----QQAVQAAYGRTpcAFTTELVKKKILRVYDTKTY-DVYKVVLSSSPMMATL--- 70
Cdd:PTZ00166 99 YFYIEAPPNFlpedsqKLKRELnaqlsEQSQFKKYQNT--VLDIEIVKKESLMYYKGNGEkDFLKITVQLPKMVPRLrsl 176
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 71 -SDRLAACGCE--------VFESNVDATRRFVLDREFSTFGWYACTHPEPRLSGRDSWT---QLEFDCGWEDLQLRPERQ 138
Cdd:PTZ00166 177 iESGVVVCGGGwdgirlfqTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRPPKKKTstcQIEVDCSYEDLIPLPPEG 256
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 139 EW---PPYRMLSFDIECMGEAG--FPRATRDEdvILQISCVFHTAGDKS-PYTQILLSLGTCEPLEGTEILEFPSEYDML 212
Cdd:PTZ00166 257 EYltiAPLRILSFDIECIKLKGlgFPEAENDP--VIQISSVVTNQGDEEePLTKFIFTLKECASIAGANVLSFETEKELL 334
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 213 TAFFAMLRDYDVEFLTGYNIANFDLPYIITRATQVYNIDLKNFTKIKtgSVFEVHEPTgggggflRSQSK---------V 283
Cdd:PTZ00166 335 LAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIK--STRSVIKDS-------KFSSKqmgtreskeI 405
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 284 KISGIAPIDMYQVCRDKLSLSDYKLDTVAKKCLGKQKDDISYRDIPPLFRSGAAGRAKIGRYCIIDSVLVMDLLRMFQTH 363
Cdd:PTZ00166 406 NIEGRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLI 485
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 364 VEIAEIARLAKIPTRRVLTDGQQIRVFSCLLEAAAKEGYILPVPRGDATG---GYQGATVISPIPGFYDDPVLVVDFASL 440
Cdd:PTZ00166 486 YNYVEMARVTGTPIGWLLTRGQQIKVTSQLLRKCKKLNYVIPTVKYSGGGseeKYEGATVLEPKKGFYDEPIATLDFASL 565
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 441 YPSIIQAHNLCYSTLIPQGALPAHPElrpddyETFVLSEGPVHFVKKHVRESLLSKLLATWLSKRKDIRRTLASCADPTM 520
Cdd:PTZ00166 566 YPSIMIAHNLCYSTLVPPNDANNYPE------DTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLL 639
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*
gi 6469146 521 RTILDKQQLAIKVTCNAVYGFTGVAS-GILPCLNIAETVTLQGRKMLERSQAFVE 574
Cdd:PTZ00166 640 KKVLNGRQLALKISANSVYGYTGAQVgGQLPCLEVSTSITSFGRQMIDKTKELVE 694
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
375-581 |
1.97e-101 |
|
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: 314.55 E-value: 1.97e-101
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 375 IPTRRVLTDGQQIRVFSCLLEAAAKEGYILPVPRGDA--TGGYQGATVISPIPGFYDDPVLVVDFASLYPSIIQAHNLCY 452
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRPSAKgdEDGYQGATVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 453 STLIPQGAlpAHPELRPDDYE-TFVLSEGPVHFVKKHVRESLLSKLLATWLSKRKDIRRTLASCADPTMRTILDKQQLAI 531
Cdd:pfam00136 81 TTLVRSVD--EANNLPPEDNLiTVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFERAILDKQQLAL 158
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 6469146 532 KVTCNAVYGFTGVASGILPCLNIAETVTLQGRKMLERSQAFVEAISPSGL 581
Cdd:pfam00136 159 KITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYNF 208
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
1-311 |
1.41e-95 |
|
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: 295.87 E-value: 1.41e-95
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 1 FRQRCYFYTRAPPGVNLLHVLQQaVQAAYGRTPCAFTTELVKKKILRVYDTKTYDVYKVVLSSSPMMATLSDRL-AACGC 79
Cdd:pfam03104 13 FGFKPYFYCLAPDGKELEEVIEE-IKELYEGLDKIEKIELKLKKSLYGYEEDPVPYLKVSFANPRPLLKIRKYLsPENIS 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 80 EVFESNVDATRRFVLDREFSTFGWYACTHPEPRLSGRDSWTQLEFDCGWEDLQLRPERQEWPPYRMLSFDIECMGEAG-F 158
Cdd:pfam03104 92 DVYEYDVDYLERFLIDNDIVGFGWYKVKVYPFRAEGRISNCDVEIDCDSPDLISVPFEKEWPPLRVLSFDIECTSLPGkF 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 159 PRATRDEDVILQISCVFHTAGDKSPYTQILLSLGTCEPL-------------EGTEILEFPSEYDMLTAFFAMLRDYDVE 225
Cdd:pfam03104 172 PDAENVKDPIIQISCMLDGQGEPEPEPRFLFTLRECDSEdiedfeytpkpiyPGVKVFEFPSEKELLRRFFEFIRQYDPD 251
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 226 FLTGYNIANFDLPYIITRATQVYNIDLKNFTKIKTGSVFEVHEPtgggGGFLRSQSKVKISGIAPIDMYQVCRDKLSLSD 305
Cdd:pfam03104 252 IITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNRGGRSKVREI----GFGTRSYEKVKISGRLHLDLYRVIKRDYKLPS 327
|
....*.
gi 6469146 306 YKLDTV 311
Cdd:pfam03104 328 YKLNAV 333
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
2-576 |
3.75e-83 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 276.71 E-value: 3.75e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 2 RQRCYFYTRAPPGVNLLHVLQQAVQAAygrtpcafTTELVKKKIlrvYDTKTYDVYKVVLSSSPMMATLSDRLAACGCEV 81
Cdd:COG0417 39 GFRPYFYVPLPDEEKLEELLRDIKEIT--------EVEPVKLKS---FFGEPVPVLKIYTRDPRDVRELRDRLKEGGIDV 107
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 82 FESNVDATRRFVLDREFSTFGWYacthpeprlSGRDSWTQLEFDC-GWEDLQLRPErQEWPPYRMLSFDIECMGEAGFPR 160
Cdd:COG0417 108 YEADIRFHDRYLIDRFLTPGVWY---------EGEVEEDGGKLDYeVKENPRLKPE-DYRPKLKVLSFDIEVSTPRGFPD 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 161 ATRDEDVILqISCvfhtAGDKSPYTQILLSlgtcEPLEGTEILEFPSEYDMLTAFFAMLRDYDVEFLTGYNIANFDLPYI 240
Cdd:COG0417 178 PERDGPIIS-IGL----AGSDGEKKVLMLG----REGVDFEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNFDLPYL 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 241 ITRAtQVYNIDLkNFTKiktgsvfEVHEPTGGGGGFlrsQSKVKISGIAPIDMYQ-VCRDKLSLSDYKLDTVAKKCLGKQ 319
Cdd:COG0417 249 QKRA-ERLGIPL-DLGR-------DGSEPSWREHGG---QGFASIPGRVVIDLYDaLKSATYKFKSYSLDAVAEELLGEG 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 320 KDDISYRDIPPLFRSgaaGRAKIGRYCIIDSVLVMDLLRMFQTHVEIAEIARLAKIPTRRVLTDGQQIRVFSCLLEAAAK 399
Cdd:COG0417 317 KLIVDGGEIERLWDD---DKPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHR 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 400 EGYILPvPRGDATG-GYQGATVISPIPGFYDDpVLVVDFASLYPSIIQAHNLCYSTLIpqgalpahPELRPDDYETFVLS 478
Cdd:COG0417 394 RGYLAP-NKGEIKGeAYPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPETLV--------EGGEEPCGDEDVAP 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 479 EGPVHFVKKhvRESLLSKLLATWLSKRKDIRRTLASCA-DPTMRTILDKQQLAIKVTCNAVYGFTGvASGI-LPCLNIAE 556
Cdd:COG0417 464 GFGHRFCRE--PKGILPSILEELWDERDEAKKKMKKAKpDSEEYRLYDALQQALKILMNSFYGVLG-SEGCrFYDPELAE 540
|
570 580
....*....|....*....|
gi 6469146 557 TVTLQGRKMLERSQAFVEAI 576
Cdd:COG0417 541 SITARGREIIKQTIEKAEEL 560
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
414-576 |
5.78e-55 |
|
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: 191.33 E-value: 5.78e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 414 GYQGATVISPIPGFYDDPVLVVDFASLYPSIIQAHNLCYSTLIPqgalPAHPELRPDdyETFVLSEGPVHFVKKHVRESL 493
Cdd:cd05533 2 QYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLN----KNTAKKLPP--EDYIKTPNGDYFVKSSVRKGL 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 494 LSKLLATWLSKRKDIRRTLASCADPTMRTILDKQQLAIKVTCNAVYGFTGVASGILPCLNIAETVTLQGRKMLERSQAFV 573
Cdd:cd05533 76 LPEILEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLV 155
|
...
gi 6469146 574 EAI 576
Cdd:cd05533 156 EEK 158
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
141-357 |
1.08e-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: 163.90 E-value: 1.08e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 141 PPYRMLSFDIECMGEAG-FPRATRDEdvILQISCVFHTAGDKSPYTQILLSLGTCEPLEGTEILEFPSEYDMLTAFFAML 219
Cdd:cd05777 5 APLRILSFDIECAGRKGvFPEPEKDP--VIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWRDFV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 220 RDYDVEFLTGYNIANFDLPYIITRATQvynIDLKNF----------TKIKTGSV----FEVHEPTgggggflrsqsKVKI 285
Cdd:cd05777 83 QEVDPDIITGYNICNFDLPYLLERAKA---LKLNTFpflgriknikSTIKDTTFsskqMGTRETK-----------EINI 148
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6469146 286 SGIAPIDMYQVCRDKLSLSDYKLDTVAKKCLGKQKDDISYRDIPPLFRSGAAGRAKIGRYCIIDSVLVMDLL 357
Cdd:cd05777 149 EGRIQFDLLQVIQRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLL 220
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
384-574 |
2.91e-40 |
|
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: 152.37 E-value: 2.91e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 384 GQQIRVFSCLLEAAAKEGYILPVPrGDATGGYQGAT-----VISPIPGFYDDPVLVVDFASLYPSIIQAHNLCYST---- 454
Cdd:cd05534 1 GSQFRVESMLLRLAKPENYILPSP-SRQQVAQQRALeclplVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTclgr 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 455 ------------LIPQGALPAHPELRPDDYETFVLSEGPVHFVKKHVRESLLSKLLATWLSKRKDIRRTLASCA-DPTMR 521
Cdd:cd05534 80 veelngggkfgfLGVKLYLPPPPLDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKdDKKLQ 159
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 6469146 522 TILDKQQLAIKVTCNAVYGFTGV-ASGILPCLNIAETVTLQGRKMLERSQAFVE 574
Cdd:cd05534 160 RILDARQLALKLLANVTYGYTAAsFSGRMPCVEIADSIVQTGRETLERAIELIE 213
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
70-575 |
1.58e-39 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 154.63 E-value: 1.58e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 70 LSDRLAACGCEVFESNVDATRRFVLDREFSTFGWYacthpeprlSGRDSWTQLEFDcgWEDLQLRPERQEWPPYRMLSFD 149
Cdd:PRK05762 93 LPKRLREGGVDVYEADIRFPERYLMERFITPCVWF---------SGEVEQYTTDGV--LRNARLKPAPDYRPPLKVVSLD 161
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 150 IECmGEAGfpratrdedvilQISCVfhtAGDKSPYTQILLsLGTCEPLEGTEILEFPSEYDMLTAFFAMLRDYDVEFLTG 229
Cdd:PRK05762 162 IET-SNKG------------ELYSI---GLEGCGQRPVIM-LGPPNGEALDFLEYVADEKALLEKFNAWFAEHDPDVIIG 224
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 230 YNIANFDLPYIITRAtQVYNIDLkNFTKiKTGSVFEVHEPTGGGGGFLRSQSKVKISGIapidmyqvcrDKL-----SLS 304
Cdd:PRK05762 225 WNVVQFDLRLLQERA-ERYGIPL-RLGR-DGSELEWREHPFRSGYGFASVPGRLVLDGI----------DALksatwVFD 291
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 305 DYKLDTVAKKCL--GKQKDDISYR--DIPPLFRSgaaGRAKIGRYCIIDSVLVMDLLRmfQTHV-EIA-EIARLAKIPTR 378
Cdd:PRK05762 292 SFSLEYVSQRLLgeGKAIDDPYDRmdEIDRRFAE---DKPALARYNLKDCELVTRIFE--KTKLlPFLlERATVTGLPLD 366
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 379 RVltdGQQIRVF-SCLLEAAAKEGYILPVPRGDATGGYQGATVISPIPGFYDDpVLVVDFASLYPSIIQAHNLCYSTLIP 457
Cdd:PRK05762 367 RV---GGSVAAFeHLYLPRAHRAGYVAPNLGERPGEASPGGYVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDGLVE 442
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 458 QGALPahpelrPDDYetfVLSEGPVHFVKKHvreSLLSKLLATWLSKRKDIRRtlascadpTMRTILdkQQlAIKVTCNA 537
Cdd:PRK05762 443 GLAQP------PEES---VAGFLGARFSREK---HFLPEIVERLWEGRDEAKR--------EMNKPL--SQ-AIKIIMNA 499
|
490 500 510
....*....|....*....|....*....|....*....
gi 6469146 538 VYGFTGvASGI-LPCLNIAETVTLQGRKMLERSQAFVEA 575
Cdd:PRK05762 500 FYGVLG-SSGCrFFDPRLASSITMRGHEIMKQTRELIEA 537
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
57-574 |
8.63e-32 |
|
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: 131.72 E-value: 8.63e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 57 YKVVLSSSPMMATLSDRLAACGCEVFESNVDATRRFVLDREFSTFGWYACTHPEPRLSGRDSWTQLEFDCGWEDLQLRPE 136
Cdd:TIGR00592 420 YELGKEFAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVKGPDELEYPRRSWCKYEGGYVKPPNVEKGL 499
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 137 RQEWPPYRMLSFDIECMgeagFPRATRDEDVILQISCVFHTAGDKS---PYTQILLSLGT----CePLEGTEILEFP--- 206
Cdd:TIGR00592 500 DKTPPPLVVLDFSMKSL----NPSIIRNEIVSIPDTLHREFALDKPppePPYDVHPCVGTrpkdC-SFPLDLKGEFPgkk 574
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 207 --------SEYDMLTAFFAMLRDYDVEFLTGYNIANFDLPYIITRATqvyniDLKNFTKIKTGsvfEVHEPTGGGGGFLR 278
Cdd:TIGR00592 575 pslvedlaTERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRIN-----DLKIPTWSKIG---RLRRSPKFGRRFGE 646
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 279 SQSKVKISGIApIDMYQVCRDKlslsDYKLDTVAKKCLGKQKDDISYRDIPPLFRSGAAgRAKIGRYCIIDSVLVMDLLR 358
Cdd:TIGR00592 647 RTCGRMICDVE-ISAKELIRCK----SYDLSELVQQILKTERKVIPIDNINNMYSESSS-LTYLLEHTWKDAMFILQIMC 720
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 359 MFQTHVEIAEIARLAKIPTRRVLTDGQQIRVFSCLLEAAAKEGYILP-------------------VPRGDATGGYQGAT 419
Cdd:TIGR00592 721 ELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPdkqifrkqqklgdedeeidGYKKGKKAAYAGGL 800
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 420 VISPIPGFYDDPVLVVDFASLYPSIIQAHNLCYSTLIPQGALPAHPELRPDDYETFVLSegpvhfvkkhvresllsKLLA 499
Cdd:TIGR00592 801 VLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQKVDEDELPELPDSELEMGILP-----------------RELR 863
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6469146 500 TWLSKRKDIRRTLASCADPTMRTILDKQQLAIKVTCNAVYGFTGVASGILPCLNIAETVTLQGRKMLERSQAFVE 574
Cdd:TIGR00592 864 KLVERRKEVKKLMKQDLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVE 938
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
413-574 |
1.05e-31 |
|
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: 125.18 E-value: 1.05e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 413 GGYQGATVISPIPGFYDdPVLVVDFASLYPSIIQAHNLCYSTLIPQGALPAHPelrpddyetfvlSEGPVHFVKKHVRES 492
Cdd:cd00145 1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPE------------DYIGVGFRSPKDRKG 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 493 LLSKLLATWLSKRKDI-RRTLASCADPTMRTILDKQQLAIKVTCNAVYGFTGVASGILPCLNIAETVTLQGRKMLERSQA 571
Cdd:cd00145 68 LLPRILEELLNFRDEAkKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIA 147
|
...
gi 6469146 572 FVE 574
Cdd:cd00145 148 LVE 150
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
145-358 |
1.67e-29 |
|
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: 115.53 E-value: 1.67e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 145 MLSFDIECMGEAGFPRATRDEdvILQISCVFHTAGDKSPYTQILLSLGTCEP-LEGTEILEFPSEYDMLTAFFAMLRDYD 223
Cdd:cd05160 1 VLSFDIETTPPVGGPEPDRDP--IICITYADSFDGVKVVFLLKTSTVGDDIEfIDGIEVEYFADEKELLKRFFDIIREYD 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 224 VEFLTGYNIANFDLPYIITRAtQVYNIDLKNFTKIKTgsvfevheptgGGGGFLRSQSKVKISGIAPIDMYQVCRDKLSL 303
Cdd:cd05160 79 PDILTGYNIDDFDLPYLLKRA-EALGIKLTDGIYRRS-----------GGEKSSGSTERIAVKGRVVFDLLAAYKRDFKL 146
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 6469146 304 SDYKLDTVAKKCLGKQKDDISYRDIPPLfrSGAAGRAKIGRYCIIDSVLVMDLLR 358
Cdd:cd05160 147 KSYTLDAVAEELLGEGKEKVDGEIIEDA--EWEEDPERLIEYNLKDAELTLQILE 199
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
207-566 |
9.90e-28 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 118.64 E-value: 9.90e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 207 SEYDMLTAFFAMLRDYDVEFLtgYNIANFDLPYIITRATQVynidlknftkiktgsvfevheptgggGGFLRSQSKVKIS 286
Cdd:PRK05761 209 SEKELLAELFDIILEYPPVVT--FNGDNFDLPYLYNRALKL--------------------------GIPKEEIPIEPGR 260
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 287 GIAPIDMYQVCRD----------KLSLSDYKLDTVAKKCLGKQKDDISYRDipplfrsGAAGRAKIGRYCIIDSVLVMDL 356
Cdd:PRK05761 261 AGIHIDLYKFFQNkavrsyafygKYRHREARLDAVGRALLGISKVELETNI-------SELDLEELAEYNFRDAEITLKL 333
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 357 LRMFQTHV--EIAEIARLAKIPTRRV--LTDGQQIRvfSCLLEAAAKEGYILP----VPRGDATG---------GYQGAT 419
Cdd:PRK05761 334 TFFNNELVlkLILLLSRISKLPIEELsrATISTWIS--NLEYWEHRKRGWLIPwkedILRLDHEVykkaiikgkKYRGGL 411
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 420 VISPIPGFYDDpVLVVDFASLYPSIIQAHNLCYSTLipqgalpahpELRPDDYETFVLSEGPVHFVKKHvRESLLSKLLA 499
Cdd:PRK05761 412 VFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPETV----------RIPECKCHYDDEVPELGHSVCDD-RPGLTSVLVG 479
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6469146 500 TWLSKRKDIRRTLASCADPT--MRTILDKQQLAIKVTCNAVYGFTGVASGILPCLNIAETVTLQGRKML 566
Cdd:PRK05761 480 LLRDFRVKIYKKKAKDPNLDeeRRAWYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESITALGREIL 548
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
415-577 |
6.88e-27 |
|
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: 113.06 E-value: 6.88e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 415 YQGATVISPIPGFYDDPVLVVDFASLYPSIIQAHNLCYSTLipqgalpahpELRPDDYEtfvlSEGPVHFVKKHVRESLL 494
Cdd:cd05532 8 YAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTV----------DRADPDDE----DDEEPPLPPSDQEKGIL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 495 SKLLATWLSKRKDIRRTLASCADPTMRTILDKQQLAIKVTCNAVYGFTGVASGILPCLNIAETVTLQGRKMLERSQAFVE 574
Cdd:cd05532 74 PRIIRKLVERRRQVKKLMKSEKDPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVE 153
|
...
gi 6469146 575 AIS 577
Cdd:cd05532 154 KMN 156
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
141-351 |
3.76e-22 |
|
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: 94.34 E-value: 3.76e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 141 PPYRMLSFDIECMGEAGFPRATRDEdvILQISC-------VFHTAGDKSPYTQILlslgtceplegteilefPSEYDMLT 213
Cdd:cd05780 1 EDLKILSFDIEVLNHEGEPNPEKDP--IIMISFadeggnkVITWKKFDLPFVEVV-----------------KTEKEMIK 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 214 AFFAMLRDYDVEFLTGYNIANFDLPYIITRAtQVYNIDL---KNFTKIKTgsvfevhepTGGGGGFlrsqsKVKISGIAP 290
Cdd:cd05780 62 RFIEIVKEKDPDVIYTYNGDNFDFPYLKKRA-EKLGIELdlgRDGSEIKI---------QRGGFNN-----ASEIKGRIH 126
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6469146 291 IDMYQVCRDKLSLSDYKLDTVAKKCLGKQKDDISYRDIPPLFRSGaAGRAKIGRYCIIDSV 351
Cdd:cd05780 127 VDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSG-ENLERLFRYSMEDAK 186
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
144-456 |
9.14e-21 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 97.07 E-value: 9.14e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 144 RMLSFDIECMGEAGFPRATRDEDVILQIsCVFHTAGDKSpytqILLSLGTCEPLEGT------EILE------FPSEYDM 211
Cdd:PHA02528 107 RIANLDIEVTAEDGFPDPEEAKYEIDAI-THYDSIDDRF----YVFDLGSVEEWDAKgdevpqEILDkvvympFDTEREM 181
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 212 LTAFFAMLRDYDVEFLTGYNIANFDLPYIITRATQVYNIDLKN-FTKIKTGSVFEVHEPTGggggflRSQSKVKISGIAP 290
Cdd:PHA02528 182 LLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGEKTAKrLSPWGKVKERTIENMYG------REEIAYDISGISI 255
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 291 IDMYQVCRdKLSLSD---YKLDTVAKKCLGKQKDDISYRDIPPLFRSgaaGRAKIGRYCIIDSVLVMDLLRMFQTHVEIA 367
Cdd:PHA02528 256 LDYLDLYK-KFTFTNqpsYRLDYIAEVELGKKKLDYSDGPFKKFRET---DHQKYIEYNIIDVELVDRLDDKRKLIELVL 331
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 368 EIARLAKIPTRRVLTdgqQIR-----VFSCLLEaaakEGYILPVPRGDATGGYQGATVISPIPGFYdDPVLVVDFASLYP 442
Cdd:PHA02528 332 SMAYYAKINFEDVFS---PIKtwdaiIFNSLKE----EKIVIPENKSHKKQKYAGAFVKEPVPGAY-RWVVSFDLTSLYP 403
|
330
....*....|....
gi 6469146 443 SIIQAHNLCYSTLI 456
Cdd:PHA02528 404 SIIRQVNISPETIA 417
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
141-536 |
4.20e-19 |
|
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: 92.04 E-value: 4.20e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 141 PPYRMLSFDIECM---GEAGFPRATRDEDVILQIS----CVFHTAGDKSPYTQILLSLGTCEPLEGTEILEFPSEYDMLT 213
Cdd:TIGR00592 196 PELKLASFDIETYfhdGKDFFPGDENPADEEIMISttpvIAKQWDYESEPEARVVTWKKPDKPTTGSYVESVSEEISMIK 275
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 214 AFFAMLRDYDVEFLTGYNIANFDLPYIITRATQVYNIDLKNFTKIKTGSVF------EVHEPTGGGGGFLRSQSKVKISG 287
Cdd:TIGR00592 276 RFWDVIDQEDTDVEITVNGDNFDLVYLADRQVFQFYWDAYEDPAEKLGVVLlfgrdvDHVSPCVQVKGINRDLFFLPREG 355
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 288 IAPIDMYQVCRDKLSLSDYKLDTVAKKCLGKQKDDISYRDIPPLFRSGAAGRakIGRYCIIDSVLVMDLLRMFQTHVEIA 367
Cdd:TIGR00592 356 KIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIAKKYEFEAPDI--DAPYSSEYLEVTYELGKEFAPMEALP 433
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 368 EIARLAKIPTRRVLTDGQQIRVFSCLL-----EAAAKEGYILPVPRgDATGGYQGATV----ISPIPGFYDDPVLVVDFA 438
Cdd:TIGR00592 434 SDLKGQTFWHVFGSNTGNLERFLLLRKikgpcWLAVKGPDELEYPR-RSWCKYEGGYVkppnVEKGLDKTPPPLVVLDFS 512
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 439 --SLYPSIIQAHNLCYSTL----------IPQGALPAHPEL--RPDDYeTFVLSEGpvhFVKKHVRESLLSKLlatwLSK 504
Cdd:TIGR00592 513 mkSLNPSIIRNEIVSIPDTlhrefaldkpPPEPPYDVHPCVgtRPKDC-SFPLDLK---GEFPGKKPSLVEDL----ATE 584
|
410 420 430
....*....|....*....|....*....|....
gi 6469146 505 RKDIRRTLASC--ADPTMRTILDKQQLAIKVTCN 536
Cdd:TIGR00592 585 RALIKKFMAKVkkIDPDEIVGHDYQQRALKVLAN 618
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
412-567 |
5.85e-19 |
|
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: 88.92 E-value: 5.85e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 412 TGGYQGATVISPIPGFYDDpVLVVDFASLYPSIIQAHNLCYSTLIpqgalpahpelRPDDYETFVlsEGPV-HFVKKHvR 490
Cdd:cd05536 1 RESYEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLV-----------REGCEDCDV--EPQVgHKFRKD-P 65
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6469146 491 ESLLSKLLATWLSKRKDIRRTLASCADPTM-RTILDKQQLAIKVTCNAVYGFTGVASGILPCLNIAETVTLQGRKMLE 567
Cdd:cd05536 66 PGFIPSVLEDLLEERRRIKEKMKKLDPESEeYKLLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIK 143
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
414-566 |
6.77e-17 |
|
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: 82.78 E-value: 6.77e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 414 GYQGATVISPIPGFYDDpVLVVDFASLYPSIIQAHNLCYSTLIPQgalpahpelrPDDYETFVLSEGPVHFVKKhvRESL 493
Cdd:cd05530 12 KYRGAIVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYETVNCP----------HCECKTNEVPEVGHWVCKK--RPGI 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6469146 494 LSKLLATWLSKRKDIRRTLA--SCADPTMRTILDKQQLAIKVTCNAVYGFTGVASGILPCLNIAETVTLQGRKML 566
Cdd:cd05530 79 TSQIIGLLRDLRVKIYKKKAkdKSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYII 153
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
146-567 |
8.16e-13 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 71.59 E-value: 8.16e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 146 LSFDIECMGEAGFPRATRDEdvILQISCVFHtagDKSPyTQILLSLGTCEPLEGTEILE--------------------- 204
Cdd:PHA03036 163 LFLDIECHFDKKFPSVFINP--VSHISCCYI---DLSG-KEKRFTLINEDMLSEDEIEEavkrgyyeieslldmdyskel 236
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 205 -FPSEYDMLTAFFAMLR-DYDveFLTGYNIANFDLPYIITRatqvynIDLKNFTKIKTGSVF---EVH--------EPTG 271
Cdd:PHA03036 237 iLCSEIVLLRIAKKLLElEFD--YVVTFNGHNFDLRYISNR------LELLTGEKIIFRSPDgkeTVHlciyernlSSHK 308
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 272 GGGGFlrSQSKVKI---SGIAPIDMYQVCRDKLSLSDYKLDTVAK----------------------------------- 313
Cdd:PHA03036 309 GVGGV--ANTTYHInnnNGTIFFDLYTFIQKTEKLDSYKLDSISKnafncnakvlsennnevtfigdnttdakgkasifs 386
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 314 -----------------KCLGKQ---------------------------KDDISYRDIPPLFRSGAAgrAKIGRYCIID 349
Cdd:PHA03036 387 evlstgnyvtindddicKILDKDiiensftvkvicknnyipgdtytlsfgKDDVDLSDMYKNYNLEIA--LEMARYCIHD 464
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 350 SVLVMDLLRMFQTHVEIAEIAR----------------LAKIPTRRVLTDGQQIrvfscLLEAAAKEGYilpvprgdatg 413
Cdd:PHA03036 465 ACLCKYLWEYYGIETKIDAGAStyllpqsmvfeyrastLIKGPLLKLLLEEKTI-----LVRSETKNKF----------- 528
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 414 GYQGATVISPIPGFYDDPVLVVDFASLYPSIIQAHNLCYSTLI-----------------------PQGALPAHPELRPD 470
Cdd:PHA03036 529 PYEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVgvvvndnrleaeinkqelrrkypYPRYIYVHCEPRSP 608
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 471 DYetfvLSEGPVhFVKKhvRESLLSKLLATWLSKRKDIRRTLASCADPTMRTILDKQQLAIKVTCNAVYGFTGVASGILP 550
Cdd:PHA03036 609 DL----VSEIAV-FDRR--IEGIIPKLLKTFLEERARYKKLLKEATSSVEKAIYDSMQYTYKIVANSVYGLMGFRNSALY 681
|
570
....*....|....*..
gi 6469146 551 CLNIAETVTLQGRKMLE 567
Cdd:PHA03036 682 SYASAKSCTAIGRNMIK 698
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
141-356 |
3.51e-11 |
|
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: 62.58 E-value: 3.51e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 141 PPYRMLSFDIECmgeagfpratrDEDVILqISCVFHTAGDKspytqILLSLGTCEPLEGTEILEFPSEYDMLTAFFAMLR 220
Cdd:cd05784 1 PKLKVVSLDIET-----------SMDGEL-YSIGLYGEGQE-----RVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFA 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 221 DYDVEFLTGYNIANFDLPYIITRATQvYNIDLknftKI-KTGSVFEVHEPTGGGGGFLRSQSKVKISGIapidmyqvcrD 299
Cdd:cd05784 64 QYDPDIIIGWNVINFDLRLLQRRAEA-HGLPL----RLgRGGSPLNWRQSGKPGQGFLSLPGRVVLDGI----------D 128
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6469146 300 KL-----SLSDYKLDTVAKKCLGKQK--DDISYR--DIPPLFRSgaaGRAKIGRYCIIDSVLVMDL 356
Cdd:cd05784 129 ALktatyHFESFSLENVAQELLGEGKliHDVDDRgaEIERLFRE---DKLALARYNLQDCELVWRI 191
|
|
| 43A |
PHA02524 |
DNA polymerase subunit A; Provisional |
197-450 |
4.01e-11 |
|
DNA polymerase subunit A; Provisional
Pssm-ID: 164925 [Multi-domain] Cd Length: 498 Bit Score: 65.41 E-value: 4.01e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 197 LEGTEILEFPSEYDMLTAFFAMLRDYDVEFLTGYNIANFDLPYIITRATQVYNIDLKN----FTKIKTGSVFEVHEptgg 272
Cdd:PHA02524 169 LDNVVYMPFEDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNILGEKAANqlspYGKITSKTITNLYG---- 244
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 273 gggflrSQSKVKISGIAPIDMYQVCRdKLSLS---DYKLDTVAKKCLgkQKDDISYRDipPLFRSGAAGRAKIGRYCIID 349
Cdd:PHA02524 245 ------EKIIYKIHGIALMDYMDVFK-KFSFTpmpDYKLGNVGYREV--KADKLDYEG--PINKFRKADHQRYVDYCVRD 313
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 350 S--VLVMDLLRMFQTHveIAEIARLAKIPTRRVLTdgqQIRVF-SCLLEAAAKEGYILPVPRGDATGGYQGATVISPIPG 426
Cdd:PHA02524 314 TdiILLIDGRRCFIDL--ILSLSYYAKIRFDDVLG---TIKVWdSIIFNSLVESNVVIPAMKASPKQSFPGAYVKEPVPG 388
|
250 260
....*....|....*....|....
gi 6469146 427 FYDDPvLVVDFASLYPSIIQAHNL 450
Cdd:PHA02524 389 GYRYG-LSFDLTSLYPSILRLLNI 411
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
291-574 |
7.64e-11 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 65.26 E-value: 7.64e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 291 IDMYQVCRDK---LSLSDYKLDTVAKKCLGKQK-----------DDISYRDIPPLFRSGAAGRAKIGRYCIIDSVLVMDL 356
Cdd:PHA03334 472 IDLMRVCNTKsikAKCSSRKLDTVARLIISKSKphknppkigkmDDVKYTEMDGMFTAGGAALARYLIYNLVDSELLIRI 551
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 357 LRMFQTHVE-------------------------------IAEIARL-AKIPTRRVLTDGQQiRVFSCLLEAAAKEGYIL 404
Cdd:PHA03334 552 AKNLDPVIEflnrlratynidyvahgrgvmnfcgfvqstkSVEVPLLkARLRIGIFVATGRI-AESLCMPEKYARDCRQK 630
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 405 PVPRgdatGGYqgatVISPIPGF-----YDDPVLVVDFASLYPSiiqahNLCYSTLIPQGAL-PAHPEL----------- 467
Cdd:PHA03334 631 IKLK----GGY----VFAPLTGLtfagpYQGTELTLDFASLYPS-----NMCDANISPEAIVdPDCTARvrgwvvfdwkk 697
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 468 RPDDYETF-----VLSEGPVHfVKKHVRESLLSKLLATWLSKRKDIRRTLASCADPTMRTILDKQQLAIKVTCNAVYgft 542
Cdd:PHA03334 698 IDRGFGKAtlmytILRTKPEE-PSWRRFTTYTTSSLNHYLSMRTEYKGAMKQAKDPKLKSYHNQLQNEMKICANSHY--- 773
|
330 340 350
....*....|....*....|....*....|..
gi 6469146 543 GVASGILPCLniaetVTLQGRKMLERSQAFVE 574
Cdd:PHA03334 774 GVAPHACQHL-----ITTLGRHKIKLVEEFIK 800
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
174-357 |
6.48e-10 |
|
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: 59.56 E-value: 6.48e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 174 VFHTAGDKSPYTQILLSLGtcepleGTEILEFPSEYDMLTAFFAMLRDYDVEFLTGYNIANFDLPYIITRATQVYNIDL- 252
Cdd:cd05778 53 IVDELKSNASNGRIRSGLS------GIPVEVVESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLl 126
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 253 KNFTKIKTGSvfEVHEPTGGGGGFLRSQSKVKISGIAPIDMYQVCRDKLSLSDYKLDTVAKKCLGKQKDDISYRDIPPLF 332
Cdd:cd05778 127 DEISRVPSDS--NGKFGDRDDEWGYTHTSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWY 204
|
170 180
....*....|....*....|....*.
gi 6469146 333 RSG-AAGRAKIGRYCIIDSVLVMDLL 357
Cdd:cd05778 205 KSGsASERWRVLEYYLKRVRLNLEIL 230
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
415-599 |
2.43e-09 |
|
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: 59.28 E-value: 2.43e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 415 YQGATVISPIPGFYDDpVLVVDFASLYPSIIQAHNLCYSTLipqGALpaHPELRPDDYetfvlseGPVHFVKKhvRESLL 494
Cdd:cd05531 5 DRGGLVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPETI---NCR--CCECRDHVY-------LGHRICLK--RRGFL 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 495 SKLLATWLSKRKDIRRTLASCADPTMRtildkqQLAIK---VTCnavYGFTGVASGILPCLNIAETVTLQGRKMLERSQA 571
Cdd:cd05531 70 PEVLEPLLERRLEYKRLKKEEDPYAGR------QKALKwilVTS---FGYLGYKNAKFGRIEVHEAITAYGRKILLRAKE 140
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 6469146 572 FVEA--------------ISPSGLSHLLQRQITAGTEAHFKV 599
Cdd:cd05531 141 IAEEmgfrvlhgivdslwIQGRGDIEELAREIEERTGIPLKL 182
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
141-312 |
6.45e-09 |
|
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarchaea. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B-DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.
Pssm-ID: 99824 [Multi-domain] Cd Length: 188 Bit Score: 55.80 E-value: 6.45e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 141 PPYRMLSFDIECMGEAGFPRATRDEDVILQIScvfhtagDKSPYTQILLSLGTceplegteilefpSEYDMLTAFFAMLR 220
Cdd:cd05781 1 PDLKTLAFDIEVYSKYGTPNPRRDPIIVISLA-------TSNGDVEFILAEGL-------------DDRKIIREFVKYVK 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 221 DYDVEFLTGYNIANFDLPYIITRAtQVYNIDLKnftkiktgsvfevhepTGGGGGFLRSQSK---VKISGIAPIDMYQVC 297
Cdd:cd05781 61 EYDPDIIVGYNSNAFDWPYLVERA-RVLGVKLD----------------VGRRGGSEPSTGVyghYSITGRLNVDLYDFA 123
|
170
....*....|....*
gi 6469146 298 RDKLSLSDYKLDTVA 312
Cdd:cd05781 124 EEIPEVKVKTLENVA 138
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
144-349 |
5.45e-08 |
|
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: 53.57 E-value: 5.45e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 144 RMLSFDIE--CMGEAGFPRATRDEDVILQIScvfhtAGDKSPYTQILLSLGTceplegteilefpSEYDMLTAFFAMLRD 221
Cdd:cd05785 10 RRLQLDIEtySLPGFFFSNPDRGDDRIIIVA-----LRDNRGWEEVLHAEDA-------------AEKELLEELVAIIRE 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 222 YDVEFLTGYNIANFDLPYIITRAtQVYNIDlknFTKIKTGSVFEVHEPTGGGGGFLRSQSKVKISGIAPIDMY-QVCRDK 300
Cdd:cd05785 72 RDPDVIEGHNIFRFDLPYLRRRC-RRHGVP---LAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYfLVQLFD 147
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 6469146 301 LS---LSDYKLDTVAKKcLGKQKDD---ISYRDIPPLFRSgaaGRAKIGRYCIID 349
Cdd:cd05785 148 VSsrdLPSYGLKAVAKH-FGLASPDrtyIDGRQIAEVWRS---DPARLLAYALDD 198
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
413-575 |
1.31e-07 |
|
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: 53.81 E-value: 1.31e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 413 GGYqgatVISPIPGFYDDpVLVVDFASLYPSIIQahnlcySTLI-PQGALPAHPELRPDDyetfvLSEGPVH--FVKKHv 489
Cdd:cd05537 5 GGY----VMDSKPGLYKN-VLVLDFKSLYPSIIR------TFLIdPLGLIEGLKAPDPED-----LIPGFLGarFSREK- 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 490 reSLLSKLLATWLSKRKDIRRTlascADPTMrtildkqQLAIKVTCNAVYGFTGvASGilpCL----NIAETVTLQGRKM 565
Cdd:cd05537 68 --HILPDLIARLWAARDEAKRE----KNAPL-------SQAIKIIMNSFYGVLG-STG---CRffdpRLASSITLRGHEI 130
|
170
....*....|
gi 6469146 566 LERSQAFVEA 575
Cdd:cd05537 131 MKQTRAWIEQ 140
|
|
| DNA_polB_B1_exo |
cd05783 |
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ... |
198-320 |
5.85e-07 |
|
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: 50.40 E-value: 5.85e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 198 EGTEILEFPSEYDMLTAFFAMLRDYdvEFLTGYNIANFDLPYIITRAtqvynidlknftkIKTGsVFEVHEPtgggggFL 277
Cdd:cd05783 63 EGAEVEFFDSEKELIREAFKIISEY--PIVLTFNGDNFDLPYLYNRA-------------LKLG-IPKEEIP------IY 120
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 6469146 278 RSQSKVKISGIAPIDMYQVCRDKL--------SLSDYKLDTVAKKCLGKQK 320
Cdd:cd05783 121 LKRDYATLKHGIHIDLYKFFSNRAiqvyafgnKYREYTLDAVAKALLGEGK 171
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
200-364 |
4.49e-06 |
|
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis. This explains why in most organisms, that no specific repair role, other than check point control, has been assigned to this enzyme. The exonuclease domain may have a structural role.
Pssm-ID: 99819 [Multi-domain] Cd Length: 234 Bit Score: 48.38 E-value: 4.49e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 200 TEILEFPSEYDMLTAFFAMLRDYDVEFLTGYNIANFDLPYIITRAtqvynIDLK--NFTKIktgsvfevheptgggGGFL 277
Cdd:cd05776 74 TKVRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRI-----QELKvpHWSRI---------------GRLK 133
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 278 RSQSKVKISGIAPI-----------DMYQVCRDKLSLSDYKLDTVAKKCLGKQKDDISYRDIPPLFRSgAAGRAKIGRYC 346
Cdd:cd05776 134 RSVWPKKKGGGKFGereltagrllcDTYLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYND-SESLLKLLEHT 212
|
170
....*....|....*...
gi 6469146 347 IIDSVLVMDLlrMFQTHV 364
Cdd:cd05776 213 EKDAYLILQL--MFKLNI 228
|
|
| DNA_polB_epsilon_exo |
cd05779 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ... |
144-252 |
2.12e-05 |
|
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: 45.71 E-value: 2.12e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 144 RMLSFDIECMG-EAGFPRATRDEdvILQISCVFhtagDKSPYtqillsLGTCEPLEGTEILEF----------------- 205
Cdd:cd05779 3 RVLAFDIETTKlPLKFPDAETDQ--IMMISYMI----DGQGY------LIVNREIVSEDIEDFeytpkpeyegpfkvfne 70
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90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 6469146 206 PSEYDMLTAFFAMLRDYDVEFLTGYNIANFDLPYIITRATqVYNIDL 252
Cdd:cd05779 71 PDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAA-IHGLSM 116
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| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
413-567 |
2.94e-03 |
|
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Pssm-ID: 99921 Cd Length: 347 Bit Score: 40.16 E-value: 2.94e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6469146 413 GGYQGATVISPIPGFYDdPVLVVDFASLYPSIIQAHNLCystlipqgalPAHPELRpddyetfvlsegpvhfvkkhVRES 492
Cdd:cd05538 1 GKFEGGYAYVFITGVLG-PIVHADVASLYPSIMLAYRIC----------PARDSLG--------------------IFLA 49
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90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6469146 493 LLSKLLATWLSKRKDIRrtlaSCADPTMRTILDKQQLAIKVTCNAVYGFTGVASGILPCLNIAETVTLQGRKMLE 567
Cdd:cd05538 50 LLKYLVELRLAAKESAR----AAARPAERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLK 120
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