|
Name |
Accession |
Description |
Interval |
E-value |
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
1302-1627 |
0e+00 |
|
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: 635.41 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1302 GSQYRVESMLLRLAHTQNYLAISPGNQQVASQPAMECVPLVMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKL 1381
Cdd:cd05534 1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1382 AHLK-MNTLGVSSYSL-----DLDVLQDLNQILQTPNSVMYVPPEVRRGILPRLLEEILSTRIMVKKAMKKlTPSEAVLH 1455
Cdd:cd05534 81 EELNgGGKFGFLGVKLylpppPLDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKK-YKDDKKLQ 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1456 RIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNANDNWNARVVYGDTDSMFVLLKGRTV 1535
Cdd:cd05534 160 RILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLFVLLPGRTK 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1536 KEAFVVGQEIASAITEMNPHPVTLKMEKVYHPCFLLTKKRYVGYSYESPNQREPIFDAKGIETVRRDTCEAVAKTMEQSL 1615
Cdd:cd05534 240 EEAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAVQKILEKSL 319
|
330
....*....|..
gi 1063695169 1616 RLFFEQKNISKV 1627
Cdd:cd05534 320 RILFETKDLSTV 331
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
1031-1532 |
2.59e-102 |
|
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: 336.81 E-value: 2.59e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1031 QLTILSIEVHAESRGDLRPDPR--FDSVNVIALVVQNDDSFVAEVFvllfspDSIDQRNVDGLSGCKLSVFLEERQLFRY 1108
Cdd:smart00486 2 PLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANRR------ILFTLGTCKEIDGIEVYEFNNEKELLLA 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1109 FIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFLNNISR-TPSPTTTNNSDNKRKLGNNllpdplvanpaqveevv 1187
Cdd:smart00486 76 FFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRlKIGLRIPNKKPLFGSKSFG----------------- 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1188 iedewgrTHASGVHVGGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPaGARYRCIEYVIRR 1267
Cdd:smart00486 139 -------LSDIKVYIKGRLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNY-EERDELLRYCIQD 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1268 ANLNLEIMSQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNQQVASQPAMECVP------L 1341
Cdd:smart00486 211 AVLTLKLFNKLNVIPLIIELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEPDLKKKvkyeggK 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1342 VMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKlahlkmntlGVSSYSLDLDVLQDLNQI-LQTPNSVMYVPPE 1420
Cdd:smart00486 291 VLEPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGV---------GEVVIKGDLIIPEDLLTIkYEKGNKYRFVKKN 361
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1421 VRRGILPRLLEEILSTRIMVKKAMKKLTPSEAVLHRIFNARQLALKLIANVTYGYTAAgFSGRMPCAELADSIVQCGRST 1500
Cdd:smart00486 362 IRKGILPKLLKKLLDKRKEIKKLMKKEKDESEELKKLLDSRQLALKLTANSVYGYLGF-TNSRLPCKPLAASVTALGREI 440
|
490 500 510
....*....|....*....|....*....|....
gi 1063695169 1501 LEKAISFVNAN--DNWNARVVYGDTDSMFVLLKG 1532
Cdd:smart00486 441 LEKTKELIEENgyPKPGFKVIYGDTDSIFVTKPG 474
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
1032-1624 |
3.64e-94 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 330.07 E-value: 3.64e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1032 LTILSIEVHAESR-GDLRPDPRFDSVNVIALVVQN----DDSFVAEVFVLlfspdsidqRNVDGLSGCKLSVFLEERQLF 1106
Cdd:PTZ00166 264 LRILSFDIECIKLkGLGFPEAENDPVIQISSVVTNqgdeEEPLTKFIFTL---------KECASIAGANVLSFETEKELL 334
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1107 RYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFLNNISRTPSPTTT--NNSDNKRKLGNNllpdplvanpaQVE 1184
Cdd:PTZ00166 335 LAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVikDSKFSSKQMGTR-----------ESK 403
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1185 EVVIEdewgrthasgvhvgGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSsGPAGARYRCIEYV 1264
Cdd:PTZ00166 404 EINIE--------------GRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQN-GSPETRRRIAVYC 468
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1265 IRRANLNLEIMSQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNQQVASQPAMECVpLVME 1344
Cdd:PTZ00166 469 LKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRGQQIKVTSQLLRKCKKLNYVIPTVKYSGGGSEEKYEGA-TVLE 547
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1345 PESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKLAHLKMNTlgvssysldldvlqdlNQILQTPNSVMYVPPEVRRG 1424
Cdd:PTZ00166 548 PKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDANNYPE----------------DTYVTTPTGDKFVKKEVRKG 611
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1425 ILPRLLEEILSTRIMVKKAMKKLTpsEAVLHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKA 1504
Cdd:PTZ00166 612 ILPLIVEELIAARKKAKKEMKDEK--DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQLPCLEVSTSITSFGRQMIDKT 689
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1505 ISFV-----NAND-NWNARVVYGDTDSMFVLLKGRTVKEAFVVGQEIASAITEMNPHPVTLKMEKVYHPCFLLTKKRYVG 1578
Cdd:PTZ00166 690 KELVekhytKANGyKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAG 769
|
570 580 590 600
....*....|....*....|....*....|....*....|....*.
gi 1063695169 1579 YSYESPNQREPIfDAKGIETVRRDTCEAVAKTMEQSLRLFFEQKNI 1624
Cdd:PTZ00166 770 LLYTNPEKYDKI-DCKGIETVRRDNCLLVQQMVETVLNKILIEKDV 814
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
1293-1628 |
5.11e-90 |
|
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: 300.30 E-value: 5.11e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1293 IDFFSVLSRGSQYRVESMLLRLAHTQNYlaISPG-NQQVASQPAMECVpLVMEPESAFYDDPVIVLDFQSLYPSMIIAYN 1371
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGF--ILPDrPSAKGDEDGYQGA-TVIEPKKGFYDKPVLVLDFNSLYPSIIQAHN 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1372 LCFSTCLGKlahlkmntlGVSSYSLDLDVlqDLNQILQTPNSVMYVPPEVRRGILPRLLEEILSTRIMVKKAMKklTPSE 1451
Cdd:pfam00136 78 LCYTTLVRS---------VDEANNLPPED--NLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLK--EETD 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1452 AVLHRIFNARQLALKLIANVTYGYTaaGFS-GRMPCAELADSIVQCGRSTLEKAISFVNANDNWNARVVYGDTDSMFVLL 1530
Cdd:pfam00136 145 PFERAILDKQQLALKITANSVYGFT--GFAnGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYNFRVIYGDTDSVFIEF 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1531 KGRTVKEAFVVGQEIASAITEMN-PHPVTLKMEKVYHPCFLLTKKRYVGYSYESPNQREPiFDAKGIETVRRDTCEAVAK 1609
Cdd:pfam00136 223 GGKDVEEAMKIGDELAEHVNQDLfKSPIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFNK-LDMKGVDLVRRDNCPLVKE 301
|
330
....*....|....*....
gi 1063695169 1610 TMEQSLRLFFEQKNISKVQ 1628
Cdd:pfam00136 302 VIKKVLDLLLSDRGLPVGL 320
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
1029-1276 |
6.13e-83 |
|
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: 271.80 E-value: 6.13e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1029 GQQLTILSIEVHAESRGDLRPDPRFDSVNVIALVVQNDDS----FVAEVFVLLFSPDSIDQRN---VDGLSGCKLSVFLE 1101
Cdd:cd05778 1 HQHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSpfilDANKVGVIIVDELKSNASNgriRSGLSGIPVEVVES 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1102 ERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIR-FLNNISRTPSPTTTNNSDNkrklgnnllpdplvanp 1180
Cdd:cd05778 81 ELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDdLLDEISRVPSDSNGKFGDR----------------- 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1181 aqveevviEDEWGRTHASGVHVGGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPAGARYRC 1260
Cdd:cd05778 144 --------DDEWGYTHTSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRV 215
|
250
....*....|....*.
gi 1063695169 1261 IEYVIRRANLNLEIMS 1276
Cdd:cd05778 216 LEYYLKRVRLNLEILD 231
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
1032-1627 |
4.24e-80 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 282.49 E-value: 4.24e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1032 LTILS--IEVHAESRgdlRPDPRFDS-VNVIALVVQNDDSfvaEVFVLLFSPDSIDqrnvdglsgckLSVFLEERQLFRY 1108
Cdd:COG0417 160 LKVLSfdIEVSTPRG---FPDPERDGpIISIGLAGSDGEK---KVLMLGREGVDFE-----------VEYFDDEKALLEA 222
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1109 FIETLCKWDPDVLLGWDIqggsIGF----LAERAAQLGIRFlnNISRTPSPTTTnnsdnkRKLGnnllpdplvanpaqve 1184
Cdd:COG0417 223 FFEIIREYDPDIIIGWNV----DNFdlpyLQKRAERLGIPL--DLGRDGSEPSW------REHG---------------- 274
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1185 evviedewGRTHASgvhVGGRIVLNAWRLIR-GEVKLNMYTIEAVSEAVL-RQKVPSIPYKVLTEWFSSgpagaRYRCIE 1262
Cdd:COG0417 275 --------GQGFAS---IPGRVVIDLYDALKsATYKFKSYSLDAVAEELLgEGKLIVDGGEIERLWDDD-----KPALAE 338
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1263 YVIRRANLNLEIMSQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNQQVASQP-AmecvpL 1341
Cdd:COG0417 339 YNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGYLAPNKGEIKGEAYPgG-----Y 413
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1342 VMEPESAFYDDpVIVLDFQSLYPSMIIAYNLCFSTclgklahlkmntlgvssysldldvlqdLNQILQTPNSVMYVPPEV 1421
Cdd:COG0417 414 VLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPET---------------------------LVEGGEEPCGDEDVAPGF 465
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1422 -------RRGILPRLLEEILSTRIMVKKAMKKLTPSEAvLHRIFNARQLALKLIANVTYGYTAAGFSgRMPCAELADSIV 1494
Cdd:COG0417 466 ghrfcrePKGILPSILEELWDERDEAKKKMKKAKPDSE-EYRLYDALQQALKILMNSFYGVLGSEGC-RFYDPELAESIT 543
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1495 QCGRSTLEKAISFVNANdnwNARVVYGDTDSMFVLLKGRTVKEAFVVGQEIASAITEMNPHPVTLKMEKVYHPCFLLT-K 1573
Cdd:COG0417 544 ARGREIIKQTIEKAEEL---GYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRRFFFPGsK 620
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....
gi 1063695169 1574 KRYVGYSYESpnqrEPIFdaKGIETVRRDTCEAVAKTMEQSLRLFFEQKNISKV 1627
Cdd:COG0417 621 KRYAGLTEDG----KIDI--KGLEAVRSDWTELAKEFQQEVYERILKEEDVEKA 668
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
1095-1615 |
2.47e-44 |
|
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: 176.79 E-value: 2.47e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1095 KLSVFLEERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFLNNISRTPSptttnnsdnKRKLGNNLlpd 1174
Cdd:TIGR00592 577 LVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRR---------SPKFGRRF--- 644
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1175 plvanpaqveevviedewgrthasGVHVGGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPA 1254
Cdd:TIGR00592 645 ------------------------GERTCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESSS 700
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1255 GARYrcIEYVIRRANLNLEIMSQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYlaISPGNQQVASQ- 1333
Cdd:TIGR00592 701 LTYL--LEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNY--IVPDKQIFRKQq 776
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1334 ----------------PAMECVPLVMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKlahlkmntlgvssysld 1397
Cdd:TIGR00592 777 klgdedeeidgykkgkKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQK----------------- 839
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1398 ldvlQDLNQILQTPnsvmyvPPEVRRGILPRLLEEILSTRIMVKKAMKKLTPSEAVLHriFNARQLALKLIANVTYGYTa 1477
Cdd:TIGR00592 840 ----VDEDELPELP------DSELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQ--YDIRQKALKLTANSMYGCL- 906
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1478 aGFS-GRMPCAELADSIVQCGRSTLEKAISFVnanDNWNARVVYGDTDSMFVLLKGRTVKEAFVVGQEIASAITEMNPhP 1556
Cdd:TIGR00592 907 -GYSkSRFYAKPLAALVTAKGREILEHTRQLV---EEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYK-L 981
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063695169 1557 VTLKMEKVYHPCFLLTKKRYVGYSYESPNQREPIF--DAKGIETVRRDTCEAVAKTMEQSL 1615
Cdd:TIGR00592 982 LELDIDGVFKRLLLLKKKKYAAIKVEGDSDGNYTTkqEVKGLDIVRRDWSPLAKETGKKVL 1042
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
15-212 |
1.03e-17 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 89.70 E-value: 1.03e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 15 IVSIDYY------MASPIPGYNicyssfqGSEVNEVPVIRIYGSTPAGQKTCLHIHRALPYLYIPCSEIPLEHHkgvdgs 88
Cdd:PTZ00166 46 QLDADYTekddksQGNPHNTVS-------GVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNFLPED------ 112
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 89 TLALSLELEKALKLKGNAASKRQHIHDCEIVRAKKFYGYH-STEEAFVKIYLYHPPDVARAASLLLAGAVLGKSL----- 162
Cdd:PTZ00166 113 SQKLKRELNAQLSEQSQFKKYQNTVLDIEIVKKESLMYYKgNGEKDFLKITVQLPKMVPRLRSLIESGVVVCGGGwdgir 192
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 1063695169 163 --QPYESHIPFILQFLVDYNLYGMGHVHISKMKFrspvphHFRPRRFDLDDC 212
Cdd:PTZ00166 193 lfQTYESNVPFVLRFLIDNNITGGSWLTLPKGKY------KIRPPKKKTSTC 238
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
39-184 |
2.22e-09 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 62.54 E-value: 2.22e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 39 SEVNEVPVIRIYGSTPAGQKTCLHIHRALPYLYIPCSEiplehhkgvdgstlalSLELEKALKLKGNaaskrqhIHDCEI 118
Cdd:COG0417 13 RDEDGKPVIELWGRTEDGPSVLLDVTGFRPYFYVPLPD----------------EEKLEELLRDIKE-------ITEVEP 69
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063695169 119 VRAKKFYGyhsTEEAFVKIYLYHPPDVARAASLLLAGavlgkSLQPYESHIPFILQFLVDYNLYGM 184
Cdd:COG0417 70 VKLKSFFG---EPVPVLKIYTRDPRDVRELRDRLKEG-----GIDVYEADIRFHDRYLIDRFLTPG 127
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
60-221 |
9.90e-09 |
|
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: 58.97 E-value: 9.90e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 60 CLHIHRALPYLYIPCSeiplehhkgvDGSTLAlslELEKALKLKGNAASKrqhIHDCEIVRAKKFYGYHSTEEAFVKIYL 139
Cdd:pfam03104 9 CVNVFGFKPYFYCLAP----------DGKELE---EVIEEIKELYEGLDK---IEKIELKLKKSLYGYEEDPVPYLKVSF 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 140 YHPPDVARAASLLLAGAVLgkslQPYESHIPFILQFLVDYNLYGMGHVHISKMKFRSPVPHHFRPRRFDLDDCPGQRIDE 219
Cdd:pfam03104 73 ANPRPLLKIRKYLSPENIS----DVYEYDVDYLERFLIDNDIVGFGWYKVKVYPFRAEGRISNCDVEIDCDSPDLISVPF 148
|
..
gi 1063695169 220 VA 221
Cdd:pfam03104 149 EK 150
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
1032-1228 |
1.73e-06 |
|
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: 52.03 E-value: 1.73e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1032 LTILSIEVHAESRGDLRPDPRF--DSVNVIALVVQNDDSFVAEVfVLLFSPDSIDQRNVDGLS--------GCKLSVFLE 1101
Cdd:pfam03104 155 LRVLSFDIECTSLPGKFPDAENvkDPIIQISCMLDGQGEPEPEP-RFLFTLRECDSEDIEDFEytpkpiypGVKVFEFPS 233
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1102 ERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGI---RFLNNISRTPSPTTTNNSDNKRKLGNNLLPdplva 1178
Cdd:pfam03104 234 EKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIvklSSIGRLNRGGRSKVREIGFGTRSYEKVKIS----- 308
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1179 npaqveevviedewgrthasgvhvgGRIVLNAWRLIRGEVKLNMYTIEAV 1228
Cdd:pfam03104 309 -------------------------GRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
1302-1627 |
0e+00 |
|
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: 635.41 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1302 GSQYRVESMLLRLAHTQNYLAISPGNQQVASQPAMECVPLVMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKL 1381
Cdd:cd05534 1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1382 AHLK-MNTLGVSSYSL-----DLDVLQDLNQILQTPNSVMYVPPEVRRGILPRLLEEILSTRIMVKKAMKKlTPSEAVLH 1455
Cdd:cd05534 81 EELNgGGKFGFLGVKLylpppPLDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKK-YKDDKKLQ 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1456 RIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNANDNWNARVVYGDTDSMFVLLKGRTV 1535
Cdd:cd05534 160 RILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLFVLLPGRTK 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1536 KEAFVVGQEIASAITEMNPHPVTLKMEKVYHPCFLLTKKRYVGYSYESPNQREPIFDAKGIETVRRDTCEAVAKTMEQSL 1615
Cdd:cd05534 240 EEAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAVQKILEKSL 319
|
330
....*....|..
gi 1063695169 1616 RLFFEQKNISKV 1627
Cdd:cd05534 320 RILFETKDLSTV 331
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
1031-1532 |
2.59e-102 |
|
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: 336.81 E-value: 2.59e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1031 QLTILSIEVHAESRGDLRPDPR--FDSVNVIALVVQNDDSFVAEVFvllfspDSIDQRNVDGLSGCKLSVFLEERQLFRY 1108
Cdd:smart00486 2 PLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANRR------ILFTLGTCKEIDGIEVYEFNNEKELLLA 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1109 FIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFLNNISR-TPSPTTTNNSDNKRKLGNNllpdplvanpaqveevv 1187
Cdd:smart00486 76 FFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRlKIGLRIPNKKPLFGSKSFG----------------- 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1188 iedewgrTHASGVHVGGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPaGARYRCIEYVIRR 1267
Cdd:smart00486 139 -------LSDIKVYIKGRLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNY-EERDELLRYCIQD 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1268 ANLNLEIMSQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNQQVASQPAMECVP------L 1341
Cdd:smart00486 211 AVLTLKLFNKLNVIPLIIELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEPDLKKKvkyeggK 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1342 VMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKlahlkmntlGVSSYSLDLDVLQDLNQI-LQTPNSVMYVPPE 1420
Cdd:smart00486 291 VLEPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGV---------GEVVIKGDLIIPEDLLTIkYEKGNKYRFVKKN 361
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1421 VRRGILPRLLEEILSTRIMVKKAMKKLTPSEAVLHRIFNARQLALKLIANVTYGYTAAgFSGRMPCAELADSIVQCGRST 1500
Cdd:smart00486 362 IRKGILPKLLKKLLDKRKEIKKLMKKEKDESEELKKLLDSRQLALKLTANSVYGYLGF-TNSRLPCKPLAASVTALGREI 440
|
490 500 510
....*....|....*....|....*....|....
gi 1063695169 1501 LEKAISFVNAN--DNWNARVVYGDTDSMFVLLKG 1532
Cdd:smart00486 441 LEKTKELIEENgyPKPGFKVIYGDTDSIFVTKPG 474
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
1032-1624 |
3.64e-94 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 330.07 E-value: 3.64e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1032 LTILSIEVHAESR-GDLRPDPRFDSVNVIALVVQN----DDSFVAEVFVLlfspdsidqRNVDGLSGCKLSVFLEERQLF 1106
Cdd:PTZ00166 264 LRILSFDIECIKLkGLGFPEAENDPVIQISSVVTNqgdeEEPLTKFIFTL---------KECASIAGANVLSFETEKELL 334
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1107 RYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFLNNISRTPSPTTT--NNSDNKRKLGNNllpdplvanpaQVE 1184
Cdd:PTZ00166 335 LAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVikDSKFSSKQMGTR-----------ESK 403
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1185 EVVIEdewgrthasgvhvgGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSsGPAGARYRCIEYV 1264
Cdd:PTZ00166 404 EINIE--------------GRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQN-GSPETRRRIAVYC 468
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1265 IRRANLNLEIMSQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNQQVASQPAMECVpLVME 1344
Cdd:PTZ00166 469 LKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRGQQIKVTSQLLRKCKKLNYVIPTVKYSGGGSEEKYEGA-TVLE 547
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1345 PESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKLAHLKMNTlgvssysldldvlqdlNQILQTPNSVMYVPPEVRRG 1424
Cdd:PTZ00166 548 PKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDANNYPE----------------DTYVTTPTGDKFVKKEVRKG 611
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1425 ILPRLLEEILSTRIMVKKAMKKLTpsEAVLHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKA 1504
Cdd:PTZ00166 612 ILPLIVEELIAARKKAKKEMKDEK--DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQLPCLEVSTSITSFGRQMIDKT 689
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1505 ISFV-----NAND-NWNARVVYGDTDSMFVLLKGRTVKEAFVVGQEIASAITEMNPHPVTLKMEKVYHPCFLLTKKRYVG 1578
Cdd:PTZ00166 690 KELVekhytKANGyKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAG 769
|
570 580 590 600
....*....|....*....|....*....|....*....|....*.
gi 1063695169 1579 YSYESPNQREPIfDAKGIETVRRDTCEAVAKTMEQSLRLFFEQKNI 1624
Cdd:PTZ00166 770 LLYTNPEKYDKI-DCKGIETVRRDNCLLVQQMVETVLNKILIEKDV 814
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
1293-1628 |
5.11e-90 |
|
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: 300.30 E-value: 5.11e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1293 IDFFSVLSRGSQYRVESMLLRLAHTQNYlaISPG-NQQVASQPAMECVpLVMEPESAFYDDPVIVLDFQSLYPSMIIAYN 1371
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGF--ILPDrPSAKGDEDGYQGA-TVIEPKKGFYDKPVLVLDFNSLYPSIIQAHN 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1372 LCFSTCLGKlahlkmntlGVSSYSLDLDVlqDLNQILQTPNSVMYVPPEVRRGILPRLLEEILSTRIMVKKAMKklTPSE 1451
Cdd:pfam00136 78 LCYTTLVRS---------VDEANNLPPED--NLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLK--EETD 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1452 AVLHRIFNARQLALKLIANVTYGYTaaGFS-GRMPCAELADSIVQCGRSTLEKAISFVNANDNWNARVVYGDTDSMFVLL 1530
Cdd:pfam00136 145 PFERAILDKQQLALKITANSVYGFT--GFAnGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYNFRVIYGDTDSVFIEF 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1531 KGRTVKEAFVVGQEIASAITEMN-PHPVTLKMEKVYHPCFLLTKKRYVGYSYESPNQREPiFDAKGIETVRRDTCEAVAK 1609
Cdd:pfam00136 223 GGKDVEEAMKIGDELAEHVNQDLfKSPIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFNK-LDMKGVDLVRRDNCPLVKE 301
|
330
....*....|....*....
gi 1063695169 1610 TMEQSLRLFFEQKNISKVQ 1628
Cdd:pfam00136 302 VIKKVLDLLLSDRGLPVGL 320
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
1029-1276 |
6.13e-83 |
|
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: 271.80 E-value: 6.13e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1029 GQQLTILSIEVHAESRGDLRPDPRFDSVNVIALVVQNDDS----FVAEVFVLLFSPDSIDQRN---VDGLSGCKLSVFLE 1101
Cdd:cd05778 1 HQHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSpfilDANKVGVIIVDELKSNASNgriRSGLSGIPVEVVES 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1102 ERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIR-FLNNISRTPSPTTTNNSDNkrklgnnllpdplvanp 1180
Cdd:cd05778 81 ELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDdLLDEISRVPSDSNGKFGDR----------------- 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1181 aqveevviEDEWGRTHASGVHVGGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPAGARYRC 1260
Cdd:cd05778 144 --------DDEWGYTHTSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRV 215
|
250
....*....|....*.
gi 1063695169 1261 IEYVIRRANLNLEIMS 1276
Cdd:cd05778 216 LEYYLKRVRLNLEILD 231
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
1032-1627 |
4.24e-80 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 282.49 E-value: 4.24e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1032 LTILS--IEVHAESRgdlRPDPRFDS-VNVIALVVQNDDSfvaEVFVLLFSPDSIDqrnvdglsgckLSVFLEERQLFRY 1108
Cdd:COG0417 160 LKVLSfdIEVSTPRG---FPDPERDGpIISIGLAGSDGEK---KVLMLGREGVDFE-----------VEYFDDEKALLEA 222
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1109 FIETLCKWDPDVLLGWDIqggsIGF----LAERAAQLGIRFlnNISRTPSPTTTnnsdnkRKLGnnllpdplvanpaqve 1184
Cdd:COG0417 223 FFEIIREYDPDIIIGWNV----DNFdlpyLQKRAERLGIPL--DLGRDGSEPSW------REHG---------------- 274
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1185 evviedewGRTHASgvhVGGRIVLNAWRLIR-GEVKLNMYTIEAVSEAVL-RQKVPSIPYKVLTEWFSSgpagaRYRCIE 1262
Cdd:COG0417 275 --------GQGFAS---IPGRVVIDLYDALKsATYKFKSYSLDAVAEELLgEGKLIVDGGEIERLWDDD-----KPALAE 338
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1263 YVIRRANLNLEIMSQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNQQVASQP-AmecvpL 1341
Cdd:COG0417 339 YNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGYLAPNKGEIKGEAYPgG-----Y 413
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1342 VMEPESAFYDDpVIVLDFQSLYPSMIIAYNLCFSTclgklahlkmntlgvssysldldvlqdLNQILQTPNSVMYVPPEV 1421
Cdd:COG0417 414 VLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPET---------------------------LVEGGEEPCGDEDVAPGF 465
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1422 -------RRGILPRLLEEILSTRIMVKKAMKKLTPSEAvLHRIFNARQLALKLIANVTYGYTAAGFSgRMPCAELADSIV 1494
Cdd:COG0417 466 ghrfcrePKGILPSILEELWDERDEAKKKMKKAKPDSE-EYRLYDALQQALKILMNSFYGVLGSEGC-RFYDPELAESIT 543
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1495 QCGRSTLEKAISFVNANdnwNARVVYGDTDSMFVLLKGRTVKEAFVVGQEIASAITEMNPHPVTLKMEKVYHPCFLLT-K 1573
Cdd:COG0417 544 ARGREIIKQTIEKAEEL---GYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRRFFFPGsK 620
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....
gi 1063695169 1574 KRYVGYSYESpnqrEPIFdaKGIETVRRDTCEAVAKTMEQSLRLFFEQKNISKV 1627
Cdd:COG0417 621 KRYAGLTEDG----KIDI--KGLEAVRSDWTELAKEFQQEVYERILKEEDVEKA 668
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
1342-1624 |
1.38e-74 |
|
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: 254.11 E-value: 1.38e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1342 VMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKLahlkmntlgvssyslDLDVLQDLnQILQTPNSVMYVPPEV 1421
Cdd:cd05533 8 VIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKN---------------TAKKLPPE-DYIKTPNGDYFVKSSV 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1422 RRGILPRLLEEILSTRIMVKKAMKKLTPSEavLHRIFNARQLALKLIANVTYGYTAAGfSGRMPCAELADSIVQCGRSTL 1501
Cdd:cd05533 72 RKGLLPEILEELLAARKRAKKDLKEETDPF--KKAVLDGRQLALKISANSVYGFTGAT-VGKLPCLEISSSVTSFGRQMI 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1502 EKAISFVNANDN------WNARVVYGDTDSMFVLLKGRTVKEAFVVGQEIASAITEMNPHPVTLKMEKVYHPCFLLTKKR 1575
Cdd:cd05533 149 EKTKKLVEEKYTkangysHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLINKKR 228
|
250 260 270 280
....*....|....*....|....*....|....*....|....*....
gi 1063695169 1576 YVGYSYESPNQREPIfDAKGIETVRRDTCEAVAKTMEQSLRLFFEQKNI 1624
Cdd:cd05533 229 YAGLLWTNPDKHDKM-DTKGIETVRRDNCLLVQNVVETCLNKILIERDV 276
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
1338-1624 |
1.18e-70 |
|
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: 240.35 E-value: 1.18e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1338 CVPLVMEPEsAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKLAHLKMNTlgvssysldldvlqdlnqilqtPNSVMYV 1417
Cdd:cd00145 4 EGGYVFDPI-PGLYENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPED----------------------YIGVGFR 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1418 PPEVRRGILPRLLEEILSTRIMVKKAMKKLTPSEAvLHRIFNARQLALKLIANVTYGYTAAGFSgRMPCAELADSIVQCG 1497
Cdd:cd00145 61 SPKDRKGLLPRILEELLNFRDEAKKRMKAAKLAPE-ERVLYDNRQQALKVLANSFYGYLGAKFF-RFYDPEVAASITSFG 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1498 RSTLEKAISFVNANdnwNARVVYGDTDSMFVLLKGRTVKE-AFVVGQEIASAITEMnpHPVTLKMEKVYHPCFLLTKKRY 1576
Cdd:cd00145 139 REIIQDTIALVEEH---GARVIYGDTDSIFVSLPKMGTKEdAIKEGREILQELADE--HLLELEFEKVYLPFFLGKKKRY 213
|
250 260 270 280
....*....|....*....|....*....|....*....|....*...
gi 1063695169 1577 VGYsYESPNQREPIFDAKGIETVRRDTCEAVAKTMEQSLRLFFEQKNI 1624
Cdd:cd00145 214 AGL-DIWKGQDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEERK 260
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
1099-1626 |
5.94e-52 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 197.77 E-value: 5.94e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1099 FLE----ERQLFRYFIETLCKWDPDVLLGWDIqggsIGF----LAERAAQLGIRFlnnisrtpsptttnnsdnkrKLGNN 1170
Cdd:PRK05762 196 FLEyvadEKALLEKFNAWFAEHDPDVIIGWNV----VQFdlrlLQERAERYGIPL--------------------RLGRD 251
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1171 LLPDPLVANPAQVeevviedewGRTHASgvhVGGRIVLNAWRLIRGEV-KLNMYTIEAVSEAVLRQ-KVPSIPYKVLTE- 1247
Cdd:PRK05762 252 GSELEWREHPFRS---------GYGFAS---VPGRLVLDGIDALKSATwVFDSFSLEYVSQRLLGEgKAIDDPYDRMDEi 319
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1248 ---WFSSGPAGARYrcieyVIRRANLNLEIMSQLDMINRTSELARVFGIDffsvLSR--GSQYRVESMLLRLAHTQNYLA 1322
Cdd:PRK05762 320 drrFAEDKPALARY-----NLKDCELVTRIFEKTKLLPFLLERATVTGLP----LDRvgGSVAAFEHLYLPRAHRAGYVA 390
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1323 isPGNQQVASQPAmecvP--LVMEPESAFYDDpVIVLDFQSLYPSMIIAYNLCFSTCLGKLAHLKMNTlgvssysldldv 1400
Cdd:PRK05762 391 --PNLGERPGEAS----PggYVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDGLVEGLAQPPEES------------ 451
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1401 lqdlnqilqtpnsvmyVPPEV------RRGILPRLLEEILSTRIMVKKAMKKltpseavlhrifnARQLALKLIANVTYG 1474
Cdd:PRK05762 452 ----------------VAGFLgarfsrEKHFLPEIVERLWEGRDEAKREMNK-------------PLSQAIKIIMNAFYG 502
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1475 YTAAGFSgRMPCAELADSIVQCGRSTLEKAISFVNANdnwNARVVYGDTDSMFVLLKG-RTVKEAFVVGQEIASAI---- 1549
Cdd:PRK05762 503 VLGSSGC-RFFDPRLASSITMRGHEIMKQTRELIEAQ---GYQVIYGDTDSTFVWLGGaHDEEDAAKIGRALVQEInqww 578
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1550 -----TEMN-PHPVTLKMEKVYHPCFLLT--------KKRYVGYSYESPNQREPIFdaKGIETVRRDTCEaVAKTMEQSL 1615
Cdd:PRK05762 579 qehlqQEFGlESALELEFEKHYRRFFMPTirgaeegsKKRYAGLIQEGDGDGRIVF--KGLETVRTDWTP-LAKEFQQEL 655
|
570
....*....|..
gi 1063695169 1616 -RLFFEQKNISK 1626
Cdd:PRK05762 656 yERIFRGEPYVD 667
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
1341-1605 |
1.22e-45 |
|
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: 170.45 E-value: 1.22e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1341 LVMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTClgklahlkmntlgvssyslDLDVLQDlnqilQTPNSVMYVPPE 1420
Cdd:cd05532 12 LVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTV-------------------DRADPDD-----EDDEEPPLPPSD 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1421 VRRGILPRLLEEILSTRIMVKKAMKklTPSEAVLHRIFNARQLALKLIANVTYGYTaaGFSG-RMPCAELADSIVQCGRS 1499
Cdd:cd05532 68 QEKGILPRIIRKLVERRRQVKKLMK--SEKDPDKKAQLDIRQLALKLTANSMYGCL--GFSYsRFYAKPLAALITSKGRE 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1500 TLEKAISFVNandNWNARVVYGDTDSMFVLLKGRTVKEAFVVGQEIASAITEMNPHpVTLKMEKVYHPCFLLTKKRYVGY 1579
Cdd:cd05532 144 ILQKTKDLVE---KMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKK-LEIDIDGVFKRLLLLKKKKYAAL 219
|
250 260
....*....|....*....|....*.
gi 1063695169 1580 SYESPNQREPIFDAKGIETVRRDTCE 1605
Cdd:cd05532 220 KVVDDDKGKLKKEVKGLDIVRRDWCP 245
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
1095-1615 |
2.47e-44 |
|
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: 176.79 E-value: 2.47e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1095 KLSVFLEERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFLNNISRTPSptttnnsdnKRKLGNNLlpd 1174
Cdd:TIGR00592 577 LVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRR---------SPKFGRRF--- 644
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1175 plvanpaqveevviedewgrthasGVHVGGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPA 1254
Cdd:TIGR00592 645 ------------------------GERTCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESSS 700
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1255 GARYrcIEYVIRRANLNLEIMSQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYlaISPGNQQVASQ- 1333
Cdd:TIGR00592 701 LTYL--LEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNY--IVPDKQIFRKQq 776
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1334 ----------------PAMECVPLVMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKlahlkmntlgvssysld 1397
Cdd:TIGR00592 777 klgdedeeidgykkgkKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQK----------------- 839
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1398 ldvlQDLNQILQTPnsvmyvPPEVRRGILPRLLEEILSTRIMVKKAMKKLTPSEAVLHriFNARQLALKLIANVTYGYTa 1477
Cdd:TIGR00592 840 ----VDEDELPELP------DSELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQ--YDIRQKALKLTANSMYGCL- 906
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1478 aGFS-GRMPCAELADSIVQCGRSTLEKAISFVnanDNWNARVVYGDTDSMFVLLKGRTVKEAFVVGQEIASAITEMNPhP 1556
Cdd:TIGR00592 907 -GYSkSRFYAKPLAALVTAKGREILEHTRQLV---EEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYK-L 981
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063695169 1557 VTLKMEKVYHPCFLLTKKRYVGYSYESPNQREPIF--DAKGIETVRRDTCEAVAKTMEQSL 1615
Cdd:TIGR00592 982 LELDIDGVFKRLLLLKKKKYAAIKVEGDSDGNYTTkqEVKGLDIVRRDWSPLAKETGKKVL 1042
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
1341-1627 |
6.35e-37 |
|
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: 144.00 E-value: 6.35e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1341 LVMEPESAFYDDpVIVLDFQSLYPSMIIAYNlcfstclgklahlkmntlgVSSYSLDLDVLQDLNQILQTPNSVMYVPPe 1420
Cdd:cd05536 8 IVLEPEKGLHEN-IVVLDFSSLYPSIMIKYN-------------------ISPDTLVREGCEDCDVEPQVGHKFRKDPP- 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1421 vrrGILPRLLEEILSTRIMVKKAMKKLTPsEAVLHRIFNARQLALKLIANVTYGYTaaGFSG-RMPCAELADSIVQCGRS 1499
Cdd:cd05536 67 ---GFIPSVLEDLLEERRRIKEKMKKLDP-ESEEYKLLDERQRAIKILANSFYGYM--GWANaRWYCKECAEAVTAWGRE 140
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1500 TLEKAISFVNANdnwNARVVYGDTDSMFVllkgrTVKEAFVVGQEIASAITEMNPH-PVTLKMEKVYHPCFLLTKKRYVG 1578
Cdd:cd05536 141 YIKTTIKIAEEK---GFKVIYGDTDSLFV-----KIDGADAVKKKVKKLLKYINEElPLELEIEKFYKRGFFVTKKRYAG 212
|
250 260 270 280
....*....|....*....|....*....|....*....|....*....
gi 1063695169 1579 YSyespnqREPIFDAKGIETVRRDTCEAVAKTMEQSLRLFFEQKNISKV 1627
Cdd:cd05536 213 LT------EDGKIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEA 255
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
1341-1609 |
1.14e-23 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 108.62 E-value: 1.14e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1341 LVMEPESAFYDDpVIVLDFQSLYPSMIIAYNLCFSTclgklahlkmntlgvssysldLDVLQDLNQILQTPNSVMYVPPE 1420
Cdd:PRK05761 411 LVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPET---------------------VRIPECKCHYDDEVPELGHSVCD 468
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1421 VRRGILPRLLEEILSTRIMVKKAMKKLTPSEAVLHRIFNARQLALKLIANVTYGYTaaGFS----GRMPCAEladSIVQC 1496
Cdd:PRK05761 469 DRPGLTSVLVGLLRDFRVKIYKKKAKDPNLDEERRAWYDVVQRALKVFLNASYGVF--GAEnfklYRIEVAE---SITAL 543
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1497 GRSTLEKAISFVNANdNWnaRVVYGDTDSMFVllKGRTVKEAfvvgQEIASAITEMnpHPVTLKMEKVYHPC-FLLTKKR 1575
Cdd:PRK05761 544 GREILLSTKKKAEEL-GL--KVLYGDTDSLFV--WGPTKESL----EELIKEIEER--TGIDLEVDKTYDWVaFSGLKKN 612
|
250 260 270
....*....|....*....|....*....|....
gi 1063695169 1576 YVGYSYESPnqrepiFDAKGIETVRRDTCEAVAK 1609
Cdd:PRK05761 613 YFGVLKDGK------VKIKGIVAKKRNTPEFVKE 640
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
1049-1275 |
5.83e-22 |
|
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon and zeta), and eukaryotic viral and plasmid-borne enzymes. Nuclear DNA polymerases alpha and zeta lack the four conserved acidic metal-binding residues. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Pssm-ID: 176646 [Multi-domain] Cd Length: 199 Bit Score: 95.50 E-value: 5.83e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1049 PDPRFDSVNVIALVVQNDDSFVaeVFVLLFSPDSIDQRNVDGLsgcKLSVFLEERQLFRYFIETLCKWDPDVLLGWDIQG 1128
Cdd:cd05160 15 PEPDRDPIICITYADSFDGVKV--VFLLKTSTVGDDIEFIDGI---EVEYFADEKELLKRFFDIIREYDPDILTGYNIDD 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1129 GSIGFLAERAAQLGIRFLNNISRTPsptttNNSDNKRklgnnllpdplvanpaqveevviedEWGRthasgVHVGGRIVL 1208
Cdd:cd05160 90 FDLPYLLKRAEALGIKLTDGIYRRS-----GGEKSSG-------------------------STER-----IAVKGRVVF 134
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063695169 1209 NAWRLIRGEVKLNMYTIEAVSEAVL-RQKVPSIPykvlTEWFSSGPAGARYRCIEYVIRRANLNLEIM 1275
Cdd:cd05160 135 DLLAAYKRDFKLKSYTLDAVAEELLgEGKEKVDG----EIIEDAEWEEDPERLIEYNLKDAELTLQIL 198
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
1342-1629 |
2.08e-19 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 95.09 E-value: 2.08e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1342 VMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKLahlkmntlgVSSYSLDLDV-LQDLNQILQTPNsVMYVPPE 1420
Cdd:PHA03036 535 VFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVV---------VNDNRLEAEInKQELRRKYPYPR-YIYVHCE 604
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1421 VR---------------RGILPRLLEEILSTRIMVKKAMKKltPSEAVLHRIFNARQLALKLIANVTYG----YTAAGFS 1481
Cdd:PHA03036 605 PRspdlvseiavfdrriEGIIPKLLKTFLEERARYKKLLKE--ATSSVEKAIYDSMQYTYKIVANSVYGlmgfRNSALYS 682
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1482 ----------GRMpCAELADSIV---------------------QCGRSTLEKAISFVNANDNWNARVVYGDTDSMFVLL 1530
Cdd:PHA03036 683 yasaksctaiGRN-MIKYLNSVLngsklingklilancpinpffKDDRSIDTNYDTNLPVEYNFTFRSVYGDTDSVFLEI 761
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1531 KGRTVKEAFVVGQEIASAI-TEMNPHPVTLKMEKVYHPCFLLTKKRYVGYSY--ESPNQREPIFDAKGIETVRRDtCEAV 1607
Cdd:PHA03036 762 NTKDVDKSIKIAKELERIInEKVLFDNFKIEFEAVYKNLIMQSKKKYTTLKYiaSSTDGSVPERVNKGTSETRRD-VSKF 840
|
330 340
....*....|....*....|....*.
gi 1063695169 1608 AKTMEQS----LRLFFEQKNISKVQI 1629
Cdd:PHA03036 841 HKYMIKIyktrLLDMLSEGNMNSNQV 866
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
1341-1624 |
3.09e-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: 91.56 E-value: 3.09e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1341 LVMEPESAFYDDpVIVLDFQSLYPSMIIAYNLcfsTCLGKLAHLKMntlgvssysldldvlQDLNQILQTPNSVMYvppE 1420
Cdd:cd05537 7 YVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLI---DPLGLIEGLKA---------------PDPEDLIPGFLGARF---S 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1421 VRRGILPRLLEEILSTRIMVKKAMkkltpseavlhrifNAR-QLALKLIANVTYGytAAGFSG-RMPCAELADSIVQCGR 1498
Cdd:cd05537 65 REKHILPDLIARLWAARDEAKREK--------------NAPlSQAIKIIMNSFYG--VLGSTGcRFFDPRLASSITLRGH 128
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1499 STLEKAISFVNANdnwNARVVYGDTDSMFVLLKGR-TVKEAFVVGQEIASAITEMNPHPVT----------LKMEKVYHP 1567
Cdd:cd05537 129 EIMKQTRAWIEQQ---GYQVIYGDTDSTFVWLGEElDAAEAQAIGKELASQINQWWAQKLKeefglesfleIEFETHYSR 205
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063695169 1568 CFLLT--------KKRYVGYSyESPNQREPIFdaKGIETVRRDTCEaVAKTMEQSL-RLFFEQKNI 1624
Cdd:cd05537 206 FFMPTirgsdegsKKRYAGLK-STDGGDELVF--KGLETVRSDWTP-LARQFQKELyERVFNDEPY 267
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
15-212 |
1.03e-17 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 89.70 E-value: 1.03e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 15 IVSIDYY------MASPIPGYNicyssfqGSEVNEVPVIRIYGSTPAGQKTCLHIHRALPYLYIPCSEIPLEHHkgvdgs 88
Cdd:PTZ00166 46 QLDADYTekddksQGNPHNTVS-------GVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNFLPED------ 112
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 89 TLALSLELEKALKLKGNAASKRQHIHDCEIVRAKKFYGYH-STEEAFVKIYLYHPPDVARAASLLLAGAVLGKSL----- 162
Cdd:PTZ00166 113 SQKLKRELNAQLSEQSQFKKYQNTVLDIEIVKKESLMYYKgNGEKDFLKITVQLPKMVPRLRSLIESGVVVCGGGwdgir 192
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 1063695169 163 --QPYESHIPFILQFLVDYNLYGMGHVHISKMKFrspvphHFRPRRFDLDDC 212
Cdd:PTZ00166 193 lfQTYESNVPFVLRFLIDNNITGGSWLTLPKGKY------KIRPPKKKTSTC 238
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
1341-1628 |
1.15e-17 |
|
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: 86.63 E-value: 1.15e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1341 LVMEPESAFYDDpVIVLDFQSLYPSMIIAYNLCFSTclgklahlkMNTlgvsSYSLDLDVLQDLNQILQTpnsvmyvppe 1420
Cdd:cd05531 9 LVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPET---------INC----RCCECRDHVYLGHRICLK---------- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1421 vRRGILPRLLEEILSTRIMVKKAMKKLTPSEAvlhrifnaRQLALKLIANVTYGYTaaGFS----GRMPCAEladSIVQC 1496
Cdd:cd05531 65 -RRGFLPEVLEPLLERRLEYKRLKKEEDPYAG--------RQKALKWILVTSFGYL--GYKnakfGRIEVHE---AITAY 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1497 GRSTLEKAISFVNANdnwNARVVYGDTDSMFVllKGRTVKEAFVvgQEIaSAITEMNphpvtLKMEKVYH-PCFLLTK-- 1573
Cdd:cd05531 131 GRKILLRAKEIAEEM---GFRVLHGIVDSLWI--QGRGDIEELA--REI-EERTGIP-----LKLEGHYDwIVFLPERdg 197
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*....
gi 1063695169 1574 ----KRYVGYSYESPnqrepiFDAKGIETVRRDTCEAVAKTMEQSLRLFFEQKNISKVQ 1628
Cdd:cd05531 198 lgapNRYFGRLSDGE------MKVRGIELRRRDTPPFVKKFQEEALDILASAKTPEELL 250
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
1341-1628 |
2.93e-13 |
|
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: 73.54 E-value: 2.93e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1341 LVMEPESAFYDDpVIVLDFQSLYPSMIIAYNLCFSTclgklahlkmntlgvssysldLDVLQDLNQILQTPNSVMYVPPE 1420
Cdd:cd05530 17 IVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYET---------------------VNCPHCECKTNEVPEVGHWVCKK 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1421 vRRGILPRLLEEI--LSTRIMVKKAM-KKLTPSEAVLhriFNARQLALKLIANVTYG-YTAAGFSgrMPCAELADSIVQC 1496
Cdd:cd05530 75 -RPGITSQIIGLLrdLRVKIYKKKAKdKSLDEEMRQW---YDVVQSAMKVFINASYGvFGAENFP--LYCPPVAESTTAL 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1497 GR----STLEKAISFvnandnwNARVVYGDTDSMFvlLKGRTvkeafvvgQEIASAITE--MNPHPVTLKMEKVY-HPCF 1569
Cdd:cd05530 149 GRyiitSTIKKAREL-------GLKVLYGDTDSLF--LWNPP--------QEQLEDLVEwvEKELGLDLELDKEYrYVVF 211
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1570 LLTKKRYVGySYESPNqrepiFDAKGIETVRRDTCEAVAKtmeqslrLFFEQKNI-SKVQ 1628
Cdd:cd05530 212 SGLKKNYLG-VTKDGS-----VDIKGLLGKKRNTPEFVKE-------LFYEVIEIlSAVN 258
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
1098-1617 |
2.69e-10 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 65.48 E-value: 2.69e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1098 VFLEERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAaqlgirflnnisrtpsptttnnsdnKRKLGNNllpdplV 1177
Cdd:PHA02528 174 PFDTEREMLLEYINFWEENTPVIFTGWNVELFDVPYIINRI-------------------------KNILGEK------T 222
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1178 AN---P-AQVEEVVIEDEWGRTHAsGVHVGGRIVLNAWRLIRGEVKLNM--YTIEAVSEAVLRQKVPSIPYKVLTEWFSS 1251
Cdd:PHA02528 223 AKrlsPwGKVKERTIENMYGREEI-AYDISGISILDYLDLYKKFTFTNQpsYRLDYIAEVELGKKKLDYSDGPFKKFRET 301
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1252 GPAgaRYrcIEYVIRRANLNLEIMSQLDMINRTSELARVFGIDFFSVLSrgsQYRVESmllrlAHTQNYLA----ISPGN 1327
Cdd:PHA02528 302 DHQ--KY--IEYNIIDVELVDRLDDKRKLIELVLSMAYYAKINFEDVFS---PIKTWD-----AIIFNSLKeekiVIPEN 369
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1328 QQVASQPAMECvpLVMEPESAFYDdPVIVLDFQSLYPSMIIAYNLCFSTCLGKLAHLKMNTLGVSSYSLDLDVLQdlnqi 1407
Cdd:PHA02528 370 KSHKKQKYAGA--FVKEPVPGAYR-WVVSFDLTSLYPSIIRQVNISPETIAGTFHVAPVHEYINKTAPRPSDEYS----- 441
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1408 lQTPNSVMYvpPEVRRGILPRLLEEILSTRIMVKKAM---------------------------------------KKLT 1448
Cdd:PHA02528 442 -CSPNGWMY--RKDIRGVIPTEIKKVFDQRKIYKKKMlaaernaeliktiledlndsvdtpidvdyyfdfsdefkaELKT 518
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1449 PSEAVLHRI----------FNARQLALKLIANVTYG--------Y------TAAGFSGRMpcaeladSIVQCGRSTLEKA 1504
Cdd:PHA02528 519 LTKSSLKALleecekeialCNTIQMARKILINSLYGalgnehfrYydlrnaEAITLFGQL-------AIQWIERKMNEYL 591
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1505 ISFVNANDnwNARVVYGDTDSMFVLL----------KGRTvKEAFV-----VGQE-----IASAITE----MN--PHPVT 1558
Cdd:PHA02528 592 NKLCKTED--EDYVIYGDTDSIYVNLdplvekvgedKFKD-TNHWVdfldkFCKErmepyIDSSYRElceyMNnyEHLMF 668
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063695169 1559 LKMEKVYHPCFLLTKKRYVGYSYESPNQR--EPIFDAKGIETVRRDTCEAVAKTMEQSLRL 1617
Cdd:PHA02528 669 MDREAIAGPGFWTAKKRYALNVWDSEGTRyaEPKLKIMGIETQRSSTPKAVQKALKEAIRR 729
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
1032-1278 |
1.38e-09 |
|
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: 60.28 E-value: 1.38e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1032 LTILSIEVHAESRGDLRPDPRFDSVNVIALVVQN---DDSFVAEVFVLlfspdsidqRNVDGLSGCKLSVFLEERQL--- 1105
Cdd:cd05777 7 LRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRqgeGEPFIRNIFTL---------KTCAPIVGAQVFSFETEEELlla 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1106 FRYFIETLckwDPDVLLGWDIQGGSIGFLAERAAQLGIR---FLNNISRTPSpTTTNNSDNKRKLGNnllPDPlvanpaq 1182
Cdd:cd05777 78 WRDFVQEV---DPDIITGYNICNFDLPYLLERAKALKLNtfpFLGRIKNIKS-TIKDTTFSSKQMGT---RET------- 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1183 vEEVVIEdewgrthasgvhvgGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPAGaRYRCIE 1262
Cdd:cd05777 144 -KEINIE--------------GRIQFDLLQVIQRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPET-RRRLAV 207
|
250
....*....|....*.
gi 1063695169 1263 YVIRRANLNLEIMSQL 1278
Cdd:cd05777 208 YCLKDAYLPLRLLDKL 223
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
39-184 |
2.22e-09 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 62.54 E-value: 2.22e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 39 SEVNEVPVIRIYGSTPAGQKTCLHIHRALPYLYIPCSEiplehhkgvdgstlalSLELEKALKLKGNaaskrqhIHDCEI 118
Cdd:COG0417 13 RDEDGKPVIELWGRTEDGPSVLLDVTGFRPYFYVPLPD----------------EEKLEELLRDIKE-------ITEVEP 69
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063695169 119 VRAKKFYGyhsTEEAFVKIYLYHPPDVARAASLLLAGavlgkSLQPYESHIPFILQFLVDYNLYGM 184
Cdd:COG0417 70 VKLKSFFG---EPVPVLKIYTRDPRDVRELRDRLKEG-----GIDVYEADIRFHDRYLIDRFLTPG 127
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
1204-1506 |
9.71e-09 |
|
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: 60.45 E-value: 9.71e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1204 GRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPAG--ARYRCiEYvirranLNLEIMSQLDMI 1281
Cdd:TIGR00592 355 GKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIAKKYEFEAPDidAPYSS-EY------LEVTYELGKEFA 427
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1282 NRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAisPGNQQVASQPAME-CVPLVM-------EPESAFYDDP 1353
Cdd:TIGR00592 428 PMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLA--VKGPDELEYPRRSwCKYEGGyvkppnvEKGLDKTPPP 505
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1354 VIVLDF--QSLYPSMIIAYNLCFSTCLGKLAHLKmNTLGVSSYSLDLDVLQDLNQILQTPNSVMYVPpevrrGILPRLLE 1431
Cdd:TIGR00592 506 LVVLDFsmKSLNPSIIRNEIVSIPDTLHREFALD-KPPPEPPYDVHPCVGTRPKDCSFPLDLKGEFP-----GKKPSLVE 579
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1432 EILSTRIMVKKAMKKLTPSEAVLHRIFNARQLALKLIANVTYGYTAAGFS--GRMPCAELADS---IVQCGRSTLEKAIS 1506
Cdd:TIGR00592 580 DLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSkiGRLRRSPKFGRrfgERTCGRMICDVEIS 659
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
60-221 |
9.90e-09 |
|
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: 58.97 E-value: 9.90e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 60 CLHIHRALPYLYIPCSeiplehhkgvDGSTLAlslELEKALKLKGNAASKrqhIHDCEIVRAKKFYGYHSTEEAFVKIYL 139
Cdd:pfam03104 9 CVNVFGFKPYFYCLAP----------DGKELE---EVIEEIKELYEGLDK---IEKIELKLKKSLYGYEEDPVPYLKVSF 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 140 YHPPDVARAASLLLAGAVLgkslQPYESHIPFILQFLVDYNLYGMGHVHISKMKFRSPVPHHFRPRRFDLDDCPGQRIDE 219
Cdd:pfam03104 73 ANPRPLLKIRKYLSPENIS----DVYEYDVDYLERFLIDNDIVGFGWYKVKVYPFRAEGRISNCDVEIDCDSPDLISVPF 148
|
..
gi 1063695169 220 VA 221
Cdd:pfam03104 149 EK 150
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
1035-1145 |
1.70e-06 |
|
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: 50.40 E-value: 1.70e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1035 LSIEVHAESRgdlRPDPRFDSVNVIALVVQNDDsfvaevfVLLFSPDSIDQRNVdglsgcklsvfleerqlFRYFIETLC 1114
Cdd:cd05781 8 FDIEVYSKYG---TPNPRRDPIIVISLATSNGD-------VEFILAEGLDDRKI-----------------IREFVKYVK 60
|
90 100 110
....*....|....*....|....*....|.
gi 1063695169 1115 KWDPDVLLGWDIQGGSIGFLAERAAQLGIRF 1145
Cdd:cd05781 61 EYDPDIIVGYNSNAFDWPYLVERARVLGVKL 91
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
1032-1228 |
1.73e-06 |
|
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: 52.03 E-value: 1.73e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1032 LTILSIEVHAESRGDLRPDPRF--DSVNVIALVVQNDDSFVAEVfVLLFSPDSIDQRNVDGLS--------GCKLSVFLE 1101
Cdd:pfam03104 155 LRVLSFDIECTSLPGKFPDAENvkDPIIQISCMLDGQGEPEPEP-RFLFTLRECDSEDIEDFEytpkpiypGVKVFEFPS 233
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1102 ERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGI---RFLNNISRTPSPTTTNNSDNKRKLGNNLLPdplva 1178
Cdd:pfam03104 234 EKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIvklSSIGRLNRGGRSKVREIGFGTRSYEKVKIS----- 308
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1179 npaqveevviedewgrthasgvhvgGRIVLNAWRLIRGEVKLNMYTIEAV 1228
Cdd:pfam03104 309 -------------------------GRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
1095-1281 |
4.74e-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: 49.53 E-value: 4.74e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1095 KLSVFLEERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFLNNISR---TPSPtttnnsdnKRKLGNNL 1171
Cdd:cd05776 75 KVRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRlkrSVWP--------KKKGGGKF 146
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1172 LPDPLVAnpaqveevviedewgrthasgvhvgGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSS 1251
Cdd:cd05776 147 GERELTA-------------------------GRLLCDTYLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYND 201
|
170 180 190
....*....|....*....|....*....|
gi 1063695169 1252 gpAGARYRCIEYVIRRANLNLEIMSQLDMI 1281
Cdd:cd05776 202 --SESLLKLLEHTEKDAYLILQLMFKLNIL 229
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
1353-1581 |
2.85e-05 |
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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: 48.25 E-value: 2.85e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1353 PVIVLDFQSLYPSMIIAYNLCfstclgklahlkmntlgvssysldldvlqdlnqilqtpnsvmyvPPEVRRGILPRLLEE 1432
Cdd:cd05538 18 PIVHADVASLYPSIMLAYRIC--------------------------------------------PARDSLGIFLALLKY 53
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90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1433 ILSTRImvkkAMKKLTPSEAVLHR--IFNARQLALKLIANVTYGYTAAGfSGRMPCAELADSIVQCGRSTLEKAISFVNA 1510
Cdd:cd05538 54 LVELRL----AAKESARAAARPAErdAFKAKQAAFKVLINSFYGYLGTG-LHAFSDPEAAAEVTRLGRELLKLMIRWLRR 128
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170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063695169 1511 NdnwNARVVYGDTDSMFVllkgrTVKEAFVVGQEIASAITEMN---PHPVTLKMEKVYHPCFLLTKKRYVGYSY 1581
Cdd:cd05538 129 R---GATPVEVDTDGIYF-----IPPNGVDTEDEEEELVRELSstlPKGITVEFDGRYRAMFSYKIKNYALLDY 194
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| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
1030-1278 |
2.94e-05 |
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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: 46.58 E-value: 2.94e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1030 QQLTILS--IEVHAESRgdlRPDPRFDSVNVIalvvqnddSFVAEVFVLLFSPDSIDQRNVDGLSgcklsvflEERQLFR 1107
Cdd:cd05780 1 EDLKILSfdIEVLNHEG---EPNPEKDPIIMI--------SFADEGGNKVITWKKFDLPFVEVVK--------TEKEMIK 61
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90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1108 YFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFlnnisrtpsptttnnsdnkrKLGNNllpdplvanpaqVEEVV 1187
Cdd:cd05780 62 RFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIEL--------------------DLGRD------------GSEIK 109
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170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063695169 1188 IEDewgRTHASGVHVGGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPagARYRCIEYVIRR 1267
Cdd:cd05780 110 IQR---GGFNNASEIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGE--NLERLFRYSMED 184
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250
....*....|.
gi 1063695169 1268 ANLNLEIMSQL 1278
Cdd:cd05780 185 AKYTYEIGKEF 195
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| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
1099-1146 |
1.40e-04 |
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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: 44.48 E-value: 1.40e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 1063695169 1099 FLEERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFL 1146
Cdd:cd05784 48 FADEKSLLLALIAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPLR 95
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