|
Name |
Accession |
Description |
Interval |
E-value |
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
1303-1751 |
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: 834.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1303 GSQYRVESMLLRLAHTQNYLAISPGNQQVASQPAMECVPLVMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKL 1382
Cdd:cd05534 1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1383 AHLK-MNTLGVSSYSL-----DLDVLQDLNQILQTPNSVMYVPPEVRRGILPRLLEEILSTRIMVKKAMKKlTPSEAVLH 1456
Cdd:cd05534 81 EELNgGGKFGFLGVKLylpppPLDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKK-YKDDKKLQ 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1457 RIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNANDNWNARVVYGDTDSMFVLLKGRTV 1536
Cdd:cd05534 160 RILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLFVLLPGRTK 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1537 KEAFVVGQEIASAITEMNPHPVTLKMEKVYHPCFLLTKKRYVGYSYESPNQREPIFDAKGIETVRRDTCEAVAKTMEQSL 1616
Cdd:cd05534 240 EEAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAVQKILEKSL 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1617 RLFFEQKNISKVKSYLYRQWKRILSGRVSLQDFIFAKEVRLGTYStrDSSLLPPAAIVATKSMKADPRTEPRYAERVPYV 1696
Cdd:cd05534 320 RILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLGTYK--EGATLPAGAIVALRRMEKDPRAEPQYGERVPYV 397
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*
gi 42563023 1697 VIHGEPGARLVDMVVDPLVLLDvDTPYRLNDLYYINKQIIPALQRVFGLVGADLN 1751
Cdd:cd05534 398 VVRGEPGSRLIDLVVSPEEFLA-DPSLRLDAEYYITKQIIPALDRLFNLVGVDVQ 451
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
1033-1869 |
9.95e-119 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 403.25 E-value: 9.95e-119
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1033 LTILSIEVHAESR-GDLRPDPRFDSVNVIALVVQN----DDSFVAEVFVLlfspdsidqRNVDGLSGCKLSVFLEERQLF 1107
Cdd:PTZ00166 264 LRILSFDIECIKLkGLGFPEAENDPVIQISSVVTNqgdeEEPLTKFIFTL---------KECASIAGANVLSFETEKELL 334
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1108 RYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFLNNISRTPSPTTT--NNSDNKRKLGNNllpdplvanpaQVE 1185
Cdd:PTZ00166 335 LAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVikDSKFSSKQMGTR-----------ESK 403
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1186 EVVIEdewgrthasgvhvgGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSsGPAGARYRCIEYV 1265
Cdd:PTZ00166 404 EINIE--------------GRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQN-GSPETRRRIAVYC 468
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1266 IRRANLNLEIMSQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNQQVASQPAMECVpLVME 1345
Cdd:PTZ00166 469 LKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRGQQIKVTSQLLRKCKKLNYVIPTVKYSGGGSEEKYEGA-TVLE 547
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1346 PESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKLAHLKMNTlgvssysldldvlqdlNQILQTPNSVMYVPPEVRRG 1425
Cdd:PTZ00166 548 PKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDANNYPE----------------DTYVTTPTGDKFVKKEVRKG 611
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1426 ILPRLLEEILSTRIMVKKAMKKLTpsEAVLHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKA 1505
Cdd:PTZ00166 612 ILPLIVEELIAARKKAKKEMKDEK--DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQLPCLEVSTSITSFGRQMIDKT 689
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1506 ISFV-----NAND-NWNARVVYGDTDSMFVLLKGRTVKEAFVVGQEIASAITEMNPHPVTLKMEKVYHPCFLLTKKRYVG 1579
Cdd:PTZ00166 690 KELVekhytKANGyKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAG 769
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1580 YSYESPNQREPIfDAKGIETVRRDTCEAVAKTMEQSLRLFFEQKNISKVKSYLYRQWKRILSGRVSLQDFIFAKEVRLGT 1659
Cdd:PTZ00166 770 LLYTNPEKYDKI-DCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRIDISLLVITKSLGKDD 848
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1660 YSTRdsslLPPAAIvATKSMKADPRTEPRYAERVPYVVIHGEPGARLVDMVVDPLVLLDVDTPYRLNdlYYINkQIIPAL 1739
Cdd:PTZ00166 849 YEGR----LAHVEL-AKKLRQRDPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVLENNIPIDTQ--YYLD-QIKNPL 920
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1740 QRVFGLVGADLNQWFL-EMPR-LTRSSLGQRPLNSknshktridyfYLSK--HCILCGEVVQESAqLCNRCLQNKSAAA- 1814
Cdd:PTZ00166 921 LRIFEGVMDNPDSLFSgEHTRhITISSSSKGGLSK-----------FVKKqlQCLGCKSVIKEGA-LCDNCNQNKEPSIy 988
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*
gi 42563023 1815 ATIVWKTSKLEREMQHLATICRHCGGGdwvVQSGVKCNSLACSVFYERRKVQKEL 1869
Cdd:PTZ00166 989 GKKLAKRRHKEAEYSQLWTQCQRCQGS---LHQEVICTNRDCPIFYRRKKVQKDL 1040
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
1294-1743 |
1.62e-109 |
|
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: 356.54 E-value: 1.62e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1294 IDFFSVLSRGSQYRVESMLLRLAHTQNYlaISPG-NQQVASQPAMECVpLVMEPESAFYDDPVIVLDFQSLYPSMIIAYN 1372
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGF--ILPDrPSAKGDEDGYQGA-TVIEPKKGFYDKPVLVLDFNSLYPSIIQAHN 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1373 LCFSTCLGKlahlkmntlGVSSYSLDLDVlqDLNQILQTPNSVMYVPPEVRRGILPRLLEEILSTRIMVKKAMKklTPSE 1452
Cdd:pfam00136 78 LCYTTLVRS---------VDEANNLPPED--NLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLK--EETD 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1453 AVLHRIFNARQLALKLIANVTYGYTaaGFS-GRMPCAELADSIVQCGRSTLEKAISFVNANDNWNARVVYGDTDSMFVLL 1531
Cdd:pfam00136 145 PFERAILDKQQLALKITANSVYGFT--GFAnGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYNFRVIYGDTDSVFIEF 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1532 KGRTVKEAFVVGQEIASAITEMN-PHPVTLKMEKVYHPCFLLTKKRYVGYSYESPNQREPiFDAKGIETVRRDTCEAVAK 1610
Cdd:pfam00136 223 GGKDVEEAMKIGDELAEHVNQDLfKSPIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFNK-LDMKGVDLVRRDNCPLVKE 301
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1611 TMEQSLRLFFEQKN----ISKVKSYLYRQWKRILSGRVSLQDFIFAKEVRLGT--YSTRDssllPPAAIVATKSMKADPR 1684
Cdd:pfam00136 302 VIKKVLDLLLSDRGlpvgLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPdnYKSKN----LPHVEVALRMNKRNGE 377
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 42563023 1685 tEPRYAERVPYVVI---HGEPGARLVDMVVDPLVLLDVDTPyrLNDLYYINKQIIPALQRVF 1743
Cdd:pfam00136 378 -APEVGDRIPYVIVkaaKGLKNLLIYERAEDPEYVLENNLP--IDYEYYFSNQLIPPVARLL 436
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
1032-1533 |
5.72e-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: 336.42 E-value: 5.72e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1032 QLTILSIEVHAESRGDLRPDPR--FDSVNVIALVVQNDDSFVAEVFvllfspDSIDQRNVDGLSGCKLSVFLEERQLFRY 1109
Cdd:smart00486 2 PLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANRR------ILFTLGTCKEIDGIEVYEFNNEKELLLA 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1110 FIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFLNNISR-TPSPTTTNNSDNKRKLGNNllpdplvanpaqveevv 1188
Cdd:smart00486 76 FFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRlKIGLRIPNKKPLFGSKSFG----------------- 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1189 iedewgrTHASGVHVGGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPaGARYRCIEYVIRR 1268
Cdd:smart00486 139 -------LSDIKVYIKGRLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNY-EERDELLRYCIQD 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1269 ANLNLEIMSQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNQQVASQPAMECVP------L 1342
Cdd:smart00486 211 AVLTLKLFNKLNVIPLIIELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEPDLKKKvkyeggK 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1343 VMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKlahlkmntlGVSSYSLDLDVLQDLNQI-LQTPNSVMYVPPE 1421
Cdd:smart00486 291 VLEPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGV---------GEVVIKGDLIIPEDLLTIkYEKGNKYRFVKKN 361
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1422 VRRGILPRLLEEILSTRIMVKKAMKKLTPSEAVLHRIFNARQLALKLIANVTYGYTAAgFSGRMPCAELADSIVQCGRST 1501
Cdd:smart00486 362 IRKGILPKLLKKLLDKRKEIKKLMKKEKDESEELKKLLDSRQLALKLTANSVYGYLGF-TNSRLPCKPLAASVTALGREI 440
|
490 500 510
....*....|....*....|....*....|....
gi 42563023 1502 LEKAISFVNAN--DNWNARVVYGDTDSMFVLLKG 1533
Cdd:smart00486 441 LEKTKELIEENgyPKPGFKVIYGDTDSIFVTKPG 474
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
1033-1749 |
1.48e-96 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 331.41 E-value: 1.48e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1033 LTILS--IEVHAESRgdlRPDPRFDS-VNVIALVVQNDDSfvaEVFVLLFSPDSIDqrnvdglsgckLSVFLEERQLFRY 1109
Cdd:COG0417 160 LKVLSfdIEVSTPRG---FPDPERDGpIISIGLAGSDGEK---KVLMLGREGVDFE-----------VEYFDDEKALLEA 222
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1110 FIETLCKWDPDVLLGWDIqggsIGF----LAERAAQLGIRFlnNISRTPSPTTTnnsdnkRKLGnnllpdplvanpaqve 1185
Cdd:COG0417 223 FFEIIREYDPDIIIGWNV----DNFdlpyLQKRAERLGIPL--DLGRDGSEPSW------REHG---------------- 274
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1186 evviedewGRTHASgvhVGGRIVLNAWRLIR-GEVKLNMYTIEAVSEAVL-RQKVPSIPYKVLTEWFSSgpagaRYRCIE 1263
Cdd:COG0417 275 --------GQGFAS---IPGRVVIDLYDALKsATYKFKSYSLDAVAEELLgEGKLIVDGGEIERLWDDD-----KPALAE 338
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1264 YVIRRANLNLEIMSQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNQQVASQP-AmecvpL 1342
Cdd:COG0417 339 YNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGYLAPNKGEIKGEAYPgG-----Y 413
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1343 VMEPESAFYDDpVIVLDFQSLYPSMIIAYNLCFSTclgklahlkmntlgvssysldldvlqdLNQILQTPNSVMYVPPEV 1422
Cdd:COG0417 414 VLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPET---------------------------LVEGGEEPCGDEDVAPGF 465
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1423 -------RRGILPRLLEEILSTRIMVKKAMKKLTPSEAvLHRIFNARQLALKLIANVTYGYTAAGFSgRMPCAELADSIV 1495
Cdd:COG0417 466 ghrfcrePKGILPSILEELWDERDEAKKKMKKAKPDSE-EYRLYDALQQALKILMNSFYGVLGSEGC-RFYDPELAESIT 543
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1496 QCGRSTLEKAISFVNANdnwNARVVYGDTDSMFVLLKGRTVKEAFVVGQEIASAITEMNPHPVTLKMEKVYHPCFLLT-K 1574
Cdd:COG0417 544 ARGREIIKQTIEKAEEL---GYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRRFFFPGsK 620
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1575 KRYVGYSYESpnqrEPIFdaKGIETVRRDTCEAVAKTMEQSLRLFFEQKNISKVKSYLYRQWKRILSGRVSLQDFIFAKE 1654
Cdd:COG0417 621 KRYAGLTEDG----KIDI--KGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDLVIRKR 694
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1655 VR--LGTYSTRDssllPPAAIVATKSMKADPRTEPRyaERVPYVVIHGEPGARLVDMVVDPLVLLDVDtpyrlndlYYIN 1732
Cdd:COG0417 695 LRkpLSEYEKNV----PPHVRAARKLDERGRPYQRG--DKISYVITKGGGRVEPVELAKERESEIDYD--------YYIE 760
|
730
....*....|....*..
gi 42563023 1733 KQIIPALQRVFGLVGAD 1749
Cdd:COG0417 761 KQLKPTADRILEAFGVS 777
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
1030-1277 |
8.74e-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: 271.42 E-value: 8.74e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1030 GQQLTILSIEVHAESRGDLRPDPRFDSVNVIALVVQNDDS----FVAEVFVLLFSPDSIDQRN---VDGLSGCKLSVFLE 1102
Cdd:cd05778 1 HQHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSpfilDANKVGVIIVDELKSNASNgriRSGLSGIPVEVVES 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1103 ERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIR-FLNNISRTPSPTTTNNSDNkrklgnnllpdplvanp 1181
Cdd:cd05778 81 ELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDdLLDEISRVPSDSNGKFGDR----------------- 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1182 aqveevviEDEWGRTHASGVHVGGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPAGARYRC 1261
Cdd:cd05778 144 --------DDEWGYTHTSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRV 215
|
250
....*....|....*.
gi 42563023 1262 IEYVIRRANLNLEIMS 1277
Cdd:cd05778 216 LEYYLKRVRLNLEILD 231
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
1096-1743 |
2.40e-51 |
|
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: 199.51 E-value: 2.40e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1096 KLSVFLEERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFLNNISRTPSptttnnsdnKRKLGNNLlpd 1175
Cdd:TIGR00592 577 LVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRR---------SPKFGRRF--- 644
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1176 plvanpaqveevviedewgrthasGVHVGGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPA 1255
Cdd:TIGR00592 645 ------------------------GERTCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESSS 700
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1256 GARYrcIEYVIRRANLNLEIMSQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYlaISPGNQQVASQ- 1334
Cdd:TIGR00592 701 LTYL--LEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNY--IVPDKQIFRKQq 776
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1335 ----------------PAMECVPLVMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKlahlkmntlgvssysld 1398
Cdd:TIGR00592 777 klgdedeeidgykkgkKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQK----------------- 839
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1399 ldvlQDLNQILQTPnsvmyvPPEVRRGILPRLLEEILSTRIMVKKAMKKLTPSEAVLHriFNARQLALKLIANVTYGYTa 1478
Cdd:TIGR00592 840 ----VDEDELPELP------DSELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQ--YDIRQKALKLTANSMYGCL- 906
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1479 aGFS-GRMPCAELADSIVQCGRSTLEKAISFVnanDNWNARVVYGDTDSMFVLLKGRTVKEAFVVGQEIASAITEMNPhP 1557
Cdd:TIGR00592 907 -GYSkSRFYAKPLAALVTAKGREILEHTRQLV---EEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYK-L 981
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1558 VTLKMEKVYHPCFLLTKKRYVGYSYESPNQREPIF--DAKGIETVRRDTCEAVAKTMEQSLRLFFEQKNISK----VKSY 1631
Cdd:TIGR00592 982 LELDIDGVFKRLLLLKKKKYAAIKVEGDSDGNYTTkqEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEaveeVQEV 1061
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1632 LYRQWKRILSGRVSLQDFIFAKEVRLGTYSTRDSSLLPPAAiVATKSMKADPRTEPRyAERVPYVVIHGEPGARLVDMVV 1711
Cdd:TIGR00592 1062 LEKIGKNVLNGEVPLEKFVINKQLTRDPKDYPDGASLPHVH-VALRINARGGRKVKA-GDVVSYVICKDGGNLSARQRAY 1139
|
650 660 670
....*....|....*....|....*....|..
gi 42563023 1712 DPLVLLDVDTPYRLNDLYYINKQIIPALQRVF 1743
Cdd:TIGR00592 1140 ALEELQRKHNNLIYDTQYYLEHQIHPVVLRIL 1171
|
|
| zf-C4pol |
pfam14260 |
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ... |
1789-1862 |
1.11e-18 |
|
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1.
Pssm-ID: 464119 Cd Length: 68 Bit Score: 81.65 E-value: 1.11e-18
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 42563023 1789 CILCGEVvqeSAQLCNRCLQNKSAAAATIVWKTSKLEREMQHLATICRHCGGGdwvVQSGVKCNSLACSVFYER 1862
Cdd:pfam14260 1 CLGCGAP---EEPLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGS---LHEEVLCDSRDCPVFYMR 68
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
15-213 |
6.75e-17 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 87.39 E-value: 6.75e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 15 IVSIDYY------MASPIPGYNicyssfqGSEVNEVPVIRIYGSTPAGQKTCLHIHRALPYLYIPCSEIPLEHHkgvdgs 88
Cdd:PTZ00166 46 QLDADYTekddksQGNPHNTVS-------GVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNFLPED------ 112
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 89 TLALSLELEKALKLKGNAASKRQHIHDCEIVRAKKFYGYH-STEEAFVKIYLSYhPPDVARAASLLLAGAVLGKSL---- 163
Cdd:PTZ00166 113 SQKLKRELNAQLSEQSQFKKYQNTVLDIEIVKKESLMYYKgNGEKDFLKITVQL-PKMVPRLRSLIESGVVVCGGGwdgi 191
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 42563023 164 ---QPYESHIPFILQFLVDYNLYGMGHVHISKMKFrspvphHFRPRRFDLDDC 213
Cdd:PTZ00166 192 rlfQTYESNVPFVLRFLIDNNITGGSWLTLPKGKY------KIRPPKKKTSTC 238
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
60-222 |
2.88e-08 |
|
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: 57.81 E-value: 2.88e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 60 CLHIHRALPYLYIPCSeiplehhkgvDGSTLAlslELEKALKLKGNAASKrqhIHDCEIVRAKKFYGYHSTEEAFVKIYL 139
Cdd:pfam03104 9 CVNVFGFKPYFYCLAP----------DGKELE---EVIEEIKELYEGLDK---IEKIELKLKKSLYGYEEDPVPYLKVSF 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 140 SYhPPDVARAASLLLAGAVLgkslQPYESHIPFILQFLVDYNLYGMGHVHISKMKFRSPVPHHFRPRRFDLDDCPGQRID 219
Cdd:pfam03104 73 AN-PRPLLKIRKYLSPENIS----DVYEYDVDYLERFLIDNDIVGFGWYKVKVYPFRAEGRISNCDVEIDCDSPDLISVP 147
|
...
gi 42563023 220 EVA 222
Cdd:pfam03104 148 FEK 150
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
39-185 |
5.94e-08 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 57.91 E-value: 5.94e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 39 SEVNEVPVIRIYGSTPAGQKTCLHIHRALPYLYIPCSEiplehhkgvdgstlalSLELEKALKLKGNaaskrqhIHDCEI 118
Cdd:COG0417 13 RDEDGKPVIELWGRTEDGPSVLLDVTGFRPYFYVPLPD----------------EEKLEELLRDIKE-------ITEVEP 69
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 42563023 119 VRAKKFYGyhsTEEAFVKIYLSyHPPDVARAASLLLAGavlgkSLQPYESHIPFILQFLVDYNLYGM 185
Cdd:COG0417 70 VKLKSFFG---EPVPVLKIYTR-DPRDVRELRDRLKEG-----GIDVYEADIRFHDRYLIDRFLTPG 127
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
1033-1229 |
1.99e-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: 1.99e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1033 LTILSIEVHAESRGDLRPDPRF--DSVNVIALVVQNDDSFVAEVfVLLFSPDSIDQRNVDGLS--------GCKLSVFLE 1102
Cdd:pfam03104 155 LRVLSFDIECTSLPGKFPDAENvkDPIIQISCMLDGQGEPEPEP-RFLFTLRECDSEDIEDFEytpkpiypGVKVFEFPS 233
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1103 ERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGI---RFLNNISRTPSPTTTNNSDNKRKLGNNLLPdplva 1179
Cdd:pfam03104 234 EKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIvklSSIGRLNRGGRSKVREIGFGTRSYEKVKIS----- 308
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 42563023 1180 npaqveevviedewgrthasgvhvgGRIVLNAWRLIRGEVKLNMYTIEAV 1229
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 ... |
1303-1751 |
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: 834.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1303 GSQYRVESMLLRLAHTQNYLAISPGNQQVASQPAMECVPLVMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKL 1382
Cdd:cd05534 1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1383 AHLK-MNTLGVSSYSL-----DLDVLQDLNQILQTPNSVMYVPPEVRRGILPRLLEEILSTRIMVKKAMKKlTPSEAVLH 1456
Cdd:cd05534 81 EELNgGGKFGFLGVKLylpppPLDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKK-YKDDKKLQ 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1457 RIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNANDNWNARVVYGDTDSMFVLLKGRTV 1536
Cdd:cd05534 160 RILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLFVLLPGRTK 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1537 KEAFVVGQEIASAITEMNPHPVTLKMEKVYHPCFLLTKKRYVGYSYESPNQREPIFDAKGIETVRRDTCEAVAKTMEQSL 1616
Cdd:cd05534 240 EEAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAVQKILEKSL 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1617 RLFFEQKNISKVKSYLYRQWKRILSGRVSLQDFIFAKEVRLGTYStrDSSLLPPAAIVATKSMKADPRTEPRYAERVPYV 1696
Cdd:cd05534 320 RILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLGTYK--EGATLPAGAIVALRRMEKDPRAEPQYGERVPYV 397
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*
gi 42563023 1697 VIHGEPGARLVDMVVDPLVLLDvDTPYRLNDLYYINKQIIPALQRVFGLVGADLN 1751
Cdd:cd05534 398 VVRGEPGSRLIDLVVSPEEFLA-DPSLRLDAEYYITKQIIPALDRLFNLVGVDVQ 451
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
1033-1869 |
9.95e-119 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 403.25 E-value: 9.95e-119
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1033 LTILSIEVHAESR-GDLRPDPRFDSVNVIALVVQN----DDSFVAEVFVLlfspdsidqRNVDGLSGCKLSVFLEERQLF 1107
Cdd:PTZ00166 264 LRILSFDIECIKLkGLGFPEAENDPVIQISSVVTNqgdeEEPLTKFIFTL---------KECASIAGANVLSFETEKELL 334
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1108 RYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFLNNISRTPSPTTT--NNSDNKRKLGNNllpdplvanpaQVE 1185
Cdd:PTZ00166 335 LAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVikDSKFSSKQMGTR-----------ESK 403
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1186 EVVIEdewgrthasgvhvgGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSsGPAGARYRCIEYV 1265
Cdd:PTZ00166 404 EINIE--------------GRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQN-GSPETRRRIAVYC 468
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1266 IRRANLNLEIMSQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNQQVASQPAMECVpLVME 1345
Cdd:PTZ00166 469 LKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRGQQIKVTSQLLRKCKKLNYVIPTVKYSGGGSEEKYEGA-TVLE 547
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1346 PESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKLAHLKMNTlgvssysldldvlqdlNQILQTPNSVMYVPPEVRRG 1425
Cdd:PTZ00166 548 PKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDANNYPE----------------DTYVTTPTGDKFVKKEVRKG 611
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1426 ILPRLLEEILSTRIMVKKAMKKLTpsEAVLHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKA 1505
Cdd:PTZ00166 612 ILPLIVEELIAARKKAKKEMKDEK--DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQLPCLEVSTSITSFGRQMIDKT 689
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1506 ISFV-----NAND-NWNARVVYGDTDSMFVLLKGRTVKEAFVVGQEIASAITEMNPHPVTLKMEKVYHPCFLLTKKRYVG 1579
Cdd:PTZ00166 690 KELVekhytKANGyKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAG 769
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1580 YSYESPNQREPIfDAKGIETVRRDTCEAVAKTMEQSLRLFFEQKNISKVKSYLYRQWKRILSGRVSLQDFIFAKEVRLGT 1659
Cdd:PTZ00166 770 LLYTNPEKYDKI-DCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRIDISLLVITKSLGKDD 848
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1660 YSTRdsslLPPAAIvATKSMKADPRTEPRYAERVPYVVIHGEPGARLVDMVVDPLVLLDVDTPYRLNdlYYINkQIIPAL 1739
Cdd:PTZ00166 849 YEGR----LAHVEL-AKKLRQRDPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVLENNIPIDTQ--YYLD-QIKNPL 920
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1740 QRVFGLVGADLNQWFL-EMPR-LTRSSLGQRPLNSknshktridyfYLSK--HCILCGEVVQESAqLCNRCLQNKSAAA- 1814
Cdd:PTZ00166 921 LRIFEGVMDNPDSLFSgEHTRhITISSSSKGGLSK-----------FVKKqlQCLGCKSVIKEGA-LCDNCNQNKEPSIy 988
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*
gi 42563023 1815 ATIVWKTSKLEREMQHLATICRHCGGGdwvVQSGVKCNSLACSVFYERRKVQKEL 1869
Cdd:PTZ00166 989 GKKLAKRRHKEAEYSQLWTQCQRCQGS---LHQEVICTNRDCPIFYRRKKVQKDL 1040
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
1294-1743 |
1.62e-109 |
|
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: 356.54 E-value: 1.62e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1294 IDFFSVLSRGSQYRVESMLLRLAHTQNYlaISPG-NQQVASQPAMECVpLVMEPESAFYDDPVIVLDFQSLYPSMIIAYN 1372
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGF--ILPDrPSAKGDEDGYQGA-TVIEPKKGFYDKPVLVLDFNSLYPSIIQAHN 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1373 LCFSTCLGKlahlkmntlGVSSYSLDLDVlqDLNQILQTPNSVMYVPPEVRRGILPRLLEEILSTRIMVKKAMKklTPSE 1452
Cdd:pfam00136 78 LCYTTLVRS---------VDEANNLPPED--NLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLK--EETD 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1453 AVLHRIFNARQLALKLIANVTYGYTaaGFS-GRMPCAELADSIVQCGRSTLEKAISFVNANDNWNARVVYGDTDSMFVLL 1531
Cdd:pfam00136 145 PFERAILDKQQLALKITANSVYGFT--GFAnGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYNFRVIYGDTDSVFIEF 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1532 KGRTVKEAFVVGQEIASAITEMN-PHPVTLKMEKVYHPCFLLTKKRYVGYSYESPNQREPiFDAKGIETVRRDTCEAVAK 1610
Cdd:pfam00136 223 GGKDVEEAMKIGDELAEHVNQDLfKSPIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFNK-LDMKGVDLVRRDNCPLVKE 301
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1611 TMEQSLRLFFEQKN----ISKVKSYLYRQWKRILSGRVSLQDFIFAKEVRLGT--YSTRDssllPPAAIVATKSMKADPR 1684
Cdd:pfam00136 302 VIKKVLDLLLSDRGlpvgLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPdnYKSKN----LPHVEVALRMNKRNGE 377
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 42563023 1685 tEPRYAERVPYVVI---HGEPGARLVDMVVDPLVLLDVDTPyrLNDLYYINKQIIPALQRVF 1743
Cdd:pfam00136 378 -APEVGDRIPYVIVkaaKGLKNLLIYERAEDPEYVLENNLP--IDYEYYFSNQLIPPVARLL 436
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
1032-1533 |
5.72e-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: 336.42 E-value: 5.72e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1032 QLTILSIEVHAESRGDLRPDPR--FDSVNVIALVVQNDDSFVAEVFvllfspDSIDQRNVDGLSGCKLSVFLEERQLFRY 1109
Cdd:smart00486 2 PLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANRR------ILFTLGTCKEIDGIEVYEFNNEKELLLA 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1110 FIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFLNNISR-TPSPTTTNNSDNKRKLGNNllpdplvanpaqveevv 1188
Cdd:smart00486 76 FFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRlKIGLRIPNKKPLFGSKSFG----------------- 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1189 iedewgrTHASGVHVGGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPaGARYRCIEYVIRR 1268
Cdd:smart00486 139 -------LSDIKVYIKGRLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNY-EERDELLRYCIQD 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1269 ANLNLEIMSQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNQQVASQPAMECVP------L 1342
Cdd:smart00486 211 AVLTLKLFNKLNVIPLIIELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEPDLKKKvkyeggK 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1343 VMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKlahlkmntlGVSSYSLDLDVLQDLNQI-LQTPNSVMYVPPE 1421
Cdd:smart00486 291 VLEPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGV---------GEVVIKGDLIIPEDLLTIkYEKGNKYRFVKKN 361
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1422 VRRGILPRLLEEILSTRIMVKKAMKKLTPSEAVLHRIFNARQLALKLIANVTYGYTAAgFSGRMPCAELADSIVQCGRST 1501
Cdd:smart00486 362 IRKGILPKLLKKLLDKRKEIKKLMKKEKDESEELKKLLDSRQLALKLTANSVYGYLGF-TNSRLPCKPLAASVTALGREI 440
|
490 500 510
....*....|....*....|....*....|....
gi 42563023 1502 LEKAISFVNAN--DNWNARVVYGDTDSMFVLLKG 1533
Cdd:smart00486 441 LEKTKELIEENgyPKPGFKVIYGDTDSIFVTKPG 474
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
1033-1749 |
1.48e-96 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 331.41 E-value: 1.48e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1033 LTILS--IEVHAESRgdlRPDPRFDS-VNVIALVVQNDDSfvaEVFVLLFSPDSIDqrnvdglsgckLSVFLEERQLFRY 1109
Cdd:COG0417 160 LKVLSfdIEVSTPRG---FPDPERDGpIISIGLAGSDGEK---KVLMLGREGVDFE-----------VEYFDDEKALLEA 222
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1110 FIETLCKWDPDVLLGWDIqggsIGF----LAERAAQLGIRFlnNISRTPSPTTTnnsdnkRKLGnnllpdplvanpaqve 1185
Cdd:COG0417 223 FFEIIREYDPDIIIGWNV----DNFdlpyLQKRAERLGIPL--DLGRDGSEPSW------REHG---------------- 274
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1186 evviedewGRTHASgvhVGGRIVLNAWRLIR-GEVKLNMYTIEAVSEAVL-RQKVPSIPYKVLTEWFSSgpagaRYRCIE 1263
Cdd:COG0417 275 --------GQGFAS---IPGRVVIDLYDALKsATYKFKSYSLDAVAEELLgEGKLIVDGGEIERLWDDD-----KPALAE 338
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1264 YVIRRANLNLEIMSQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNQQVASQP-AmecvpL 1342
Cdd:COG0417 339 YNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGYLAPNKGEIKGEAYPgG-----Y 413
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1343 VMEPESAFYDDpVIVLDFQSLYPSMIIAYNLCFSTclgklahlkmntlgvssysldldvlqdLNQILQTPNSVMYVPPEV 1422
Cdd:COG0417 414 VLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPET---------------------------LVEGGEEPCGDEDVAPGF 465
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1423 -------RRGILPRLLEEILSTRIMVKKAMKKLTPSEAvLHRIFNARQLALKLIANVTYGYTAAGFSgRMPCAELADSIV 1495
Cdd:COG0417 466 ghrfcrePKGILPSILEELWDERDEAKKKMKKAKPDSE-EYRLYDALQQALKILMNSFYGVLGSEGC-RFYDPELAESIT 543
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1496 QCGRSTLEKAISFVNANdnwNARVVYGDTDSMFVLLKGRTVKEAFVVGQEIASAITEMNPHPVTLKMEKVYHPCFLLT-K 1574
Cdd:COG0417 544 ARGREIIKQTIEKAEEL---GYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRRFFFPGsK 620
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1575 KRYVGYSYESpnqrEPIFdaKGIETVRRDTCEAVAKTMEQSLRLFFEQKNISKVKSYLYRQWKRILSGRVSLQDFIFAKE 1654
Cdd:COG0417 621 KRYAGLTEDG----KIDI--KGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDLVIRKR 694
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1655 VR--LGTYSTRDssllPPAAIVATKSMKADPRTEPRyaERVPYVVIHGEPGARLVDMVVDPLVLLDVDtpyrlndlYYIN 1732
Cdd:COG0417 695 LRkpLSEYEKNV----PPHVRAARKLDERGRPYQRG--DKISYVITKGGGRVEPVELAKERESEIDYD--------YYIE 760
|
730
....*....|....*..
gi 42563023 1733 KQIIPALQRVFGLVGAD 1749
Cdd:COG0417 761 KQLKPTADRILEAFGVS 777
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
1343-1743 |
4.25e-89 |
|
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: 296.10 E-value: 4.25e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1343 VMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKLahlkmntlgvssyslDLDVLQDLnQILQTPNSVMYVPPEV 1422
Cdd:cd05533 8 VIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKN---------------TAKKLPPE-DYIKTPNGDYFVKSSV 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1423 RRGILPRLLEEILSTRIMVKKAMKKLTPSEavLHRIFNARQLALKLIANVTYGYTAAGfSGRMPCAELADSIVQCGRSTL 1502
Cdd:cd05533 72 RKGLLPEILEELLAARKRAKKDLKEETDPF--KKAVLDGRQLALKISANSVYGFTGAT-VGKLPCLEISSSVTSFGRQMI 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1503 EKAISFVNANDN------WNARVVYGDTDSMFVLLKGRTVKEAFVVGQEIASAITEMNPHPVTLKMEKVYHPCFLLTKKR 1576
Cdd:cd05533 149 EKTKKLVEEKYTkangysHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLINKKR 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1577 YVGYSYESPNQREPIfDAKGIETVRRDTCEAVAKTMEQSLRLFFEQKNISKVKSYLYRQWKRILSGRVSLQDFIFAKEVr 1656
Cdd:cd05533 229 YAGLLWTNPDKHDKM-DTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLLQNKIDISLLVITKAL- 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1657 lgTYSTRDSSLLPPAAIVATKSMKADPRTEPRYAERVPYVVIHGEPGARLVDMVVDPLVLLDVDTPYRLNdlYYINKQII 1736
Cdd:cd05533 307 --TKTADDYAGKQAHVELAERMRKRDPGSAPNVGDRVPYVIIKGAKGAKAYEKAEDPIYVLENNIPIDTQ--YYLENQLS 382
|
....*..
gi 42563023 1737 PALQRVF 1743
Cdd:cd05533 383 KPLLRIF 389
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
1030-1277 |
8.74e-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: 271.42 E-value: 8.74e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1030 GQQLTILSIEVHAESRGDLRPDPRFDSVNVIALVVQNDDS----FVAEVFVLLFSPDSIDQRN---VDGLSGCKLSVFLE 1102
Cdd:cd05778 1 HQHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSpfilDANKVGVIIVDELKSNASNgriRSGLSGIPVEVVES 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1103 ERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIR-FLNNISRTPSPTTTNNSDNkrklgnnllpdplvanp 1181
Cdd:cd05778 81 ELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDdLLDEISRVPSDSNGKFGDR----------------- 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1182 aqveevviEDEWGRTHASGVHVGGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPAGARYRC 1261
Cdd:cd05778 144 --------DDEWGYTHTSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRV 215
|
250
....*....|....*.
gi 42563023 1262 IEYVIRRANLNLEIMS 1277
Cdd:cd05778 216 LEYYLKRVRLNLEILD 231
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
1339-1743 |
7.67e-74 |
|
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: 249.59 E-value: 7.67e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1339 CVPLVMEPEsAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKLAHLKMNTlgvssysldldvlqdlnqilqtPNSVMYV 1418
Cdd:cd00145 4 EGGYVFDPI-PGLYENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPED----------------------YIGVGFR 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1419 PPEVRRGILPRLLEEILSTRIMVKKAMKKLTPSEAvLHRIFNARQLALKLIANVTYGYTAAGFSgRMPCAELADSIVQCG 1498
Cdd:cd00145 61 SPKDRKGLLPRILEELLNFRDEAKKRMKAAKLAPE-ERVLYDNRQQALKVLANSFYGYLGAKFF-RFYDPEVAASITSFG 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1499 RSTLEKAISFVNANdnwNARVVYGDTDSMFVLLKGRTVKE-AFVVGQEIASAITEMnpHPVTLKMEKVYHPCFLLTKKRY 1577
Cdd:cd00145 139 REIIQDTIALVEEH---GARVIYGDTDSIFVSLPKMGTKEdAIKEGREILQELADE--HLLELEFEKVYLPFFLGKKKRY 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1578 VGYsYESPNQREPIFDAKGIETVRRDTCEAVAKTMEQSLRLFFEQKNISK-VKSYLYRqwkrilsgrvslqdfifakevr 1656
Cdd:cd00145 214 AGL-DIWKGQDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEERKVEaVKEYIDE---------------------- 270
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1657 lgtystrdssllppaaivatksmkadprtepryAERVPYVVIHGEPGARLVDMVVDPLVLLDVDTpyRLNDLYYINKQII 1736
Cdd:cd00145 271 ---------------------------------LDKVKYVVTRGGKGVPDYERADPPLEDLDKRH--RIDYEYYLERLLQ 315
|
....*..
gi 42563023 1737 PALQRVF 1743
Cdd:cd00145 316 PPLERIF 322
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
1100-1752 |
2.23e-60 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 223.58 E-value: 2.23e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1100 FLE----ERQLFRYFIETLCKWDPDVLLGWDIqggsIGF----LAERAAQLGIRFlnnisrtpsptttnnsdnkrKLGNN 1171
Cdd:PRK05762 196 FLEyvadEKALLEKFNAWFAEHDPDVIIGWNV----VQFdlrlLQERAERYGIPL--------------------RLGRD 251
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1172 LLPDPLVANPAQVeevviedewGRTHASgvhVGGRIVLNAWRLIRGEV-KLNMYTIEAVSEAVLRQ-KVPSIPYKVLTE- 1248
Cdd:PRK05762 252 GSELEWREHPFRS---------GYGFAS---VPGRLVLDGIDALKSATwVFDSFSLEYVSQRLLGEgKAIDDPYDRMDEi 319
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1249 ---WFSSGPAGARYrcieyVIRRANLNLEIMSQLDMINRTSELARVFGIDffsvLSR--GSQYRVESMLLRLAHTQNYLA 1323
Cdd:PRK05762 320 drrFAEDKPALARY-----NLKDCELVTRIFEKTKLLPFLLERATVTGLP----LDRvgGSVAAFEHLYLPRAHRAGYVA 390
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1324 isPGNQQVASQPAmecvP--LVMEPESAFYDDpVIVLDFQSLYPSMIIAYNLCFSTCLGKLAHLKMNTlgvssysldldv 1401
Cdd:PRK05762 391 --PNLGERPGEAS----PggYVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDGLVEGLAQPPEES------------ 451
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1402 lqdlnqilqtpnsvmyVPPEV------RRGILPRLLEEILSTRIMVKKAMKKltpseavlhrifnARQLALKLIANVTYG 1475
Cdd:PRK05762 452 ----------------VAGFLgarfsrEKHFLPEIVERLWEGRDEAKREMNK-------------PLSQAIKIIMNAFYG 502
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1476 YTAAGFSgRMPCAELADSIVQCGRSTLEKAISFVNANdnwNARVVYGDTDSMFVLLKG-RTVKEAFVVGQEIASAI---- 1550
Cdd:PRK05762 503 VLGSSGC-RFFDPRLASSITMRGHEIMKQTRELIEAQ---GYQVIYGDTDSTFVWLGGaHDEEDAAKIGRALVQEInqww 578
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1551 -----TEMN-PHPVTLKMEKVYHPCFLLT--------KKRYVGYSYESPNQREPIFdaKGIETVRRDTCEaVAKTMEQSL 1616
Cdd:PRK05762 579 qehlqQEFGlESALELEFEKHYRRFFMPTirgaeegsKKRYAGLIQEGDGDGRIVF--KGLETVRTDWTP-LAKEFQQEL 655
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1617 --RLFFEQKNISKVKSYLyrqwKRILSGRVSlQDFIFAKEVR--LGTYsTRDSsllPPAAIVATKSMKADPR-TEPRYAE 1691
Cdd:PRK05762 656 yeRIFRGEPYVDYVREVI----DKLRAGELD-EKLVYRKRLRrpLDEY-QRNV---PPHVRAARLADEMGYKvGRPLQYQ 726
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 42563023 1692 R---VPYVVIHGEPGarlvdmvvdPL----VLLDVDtpyrlndlYYINKQIIPALQRVFGLVGADLNQ 1752
Cdd:PRK05762 727 NggkIGYVITVNGPE---------PLeyrkSPIDYD--------YYIEKQLQPVADRILPFFGDDFAT 777
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
1342-1744 |
1.58e-53 |
|
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: 193.56 E-value: 1.58e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1342 LVMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTClgklahlkmntlgvssyslDLDVLQDlnqilQTPNSVMYVPPE 1421
Cdd:cd05532 12 LVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTV-------------------DRADPDD-----EDDEEPPLPPSD 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1422 VRRGILPRLLEEILSTRIMVKKAMKklTPSEAVLHRIFNARQLALKLIANVTYGYTaaGFSG-RMPCAELADSIVQCGRS 1500
Cdd:cd05532 68 QEKGILPRIIRKLVERRRQVKKLMK--SEKDPDKKAQLDIRQLALKLTANSMYGCL--GFSYsRFYAKPLAALITSKGRE 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1501 TLEKAISFVNandNWNARVVYGDTDSMFVLLKGRTVKEAFVVGQEIASAITEMNPHpVTLKMEKVYHPCFLLTKKRYVGY 1580
Cdd:cd05532 144 ILQKTKDLVE---KMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKK-LEIDIDGVFKRLLLLKKKKYAAL 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1581 SYESPNQREPIFDAKGIETVRRDTCEAVAKTMEQSLRLFFEQKN----ISKVKSYLYRQWKRILSGRVSLQDFIFAKevR 1656
Cdd:cd05532 220 KVVDDDKGKLKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSrediVENIHEYLRKINEDLRNGKIPLEKFIITK--Q 297
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1657 LG----TYSTRDSSllpPAAIVATKSMKADPRTEPryAERVPYVVIHGEPGARLVD-----MVVDPLVLLDVDTpyrlnd 1727
Cdd:cd05532 298 LTknpeEYPDKKSL---PHVQVALRMNKRGRKVKA--GDTIPYIICKDGSSKSLADrayhpDEVKKNENLKIDI------ 366
|
410
....*....|....*..
gi 42563023 1728 LYYINKQIIPALQRVFG 1744
Cdd:cd05532 367 EYYLSQQILPPISRLCE 383
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
1096-1743 |
2.40e-51 |
|
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: 199.51 E-value: 2.40e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1096 KLSVFLEERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFLNNISRTPSptttnnsdnKRKLGNNLlpd 1175
Cdd:TIGR00592 577 LVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRR---------SPKFGRRF--- 644
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1176 plvanpaqveevviedewgrthasGVHVGGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPA 1255
Cdd:TIGR00592 645 ------------------------GERTCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESSS 700
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1256 GARYrcIEYVIRRANLNLEIMSQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYlaISPGNQQVASQ- 1334
Cdd:TIGR00592 701 LTYL--LEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNY--IVPDKQIFRKQq 776
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1335 ----------------PAMECVPLVMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKlahlkmntlgvssysld 1398
Cdd:TIGR00592 777 klgdedeeidgykkgkKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQK----------------- 839
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1399 ldvlQDLNQILQTPnsvmyvPPEVRRGILPRLLEEILSTRIMVKKAMKKLTPSEAVLHriFNARQLALKLIANVTYGYTa 1478
Cdd:TIGR00592 840 ----VDEDELPELP------DSELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQ--YDIRQKALKLTANSMYGCL- 906
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1479 aGFS-GRMPCAELADSIVQCGRSTLEKAISFVnanDNWNARVVYGDTDSMFVLLKGRTVKEAFVVGQEIASAITEMNPhP 1557
Cdd:TIGR00592 907 -GYSkSRFYAKPLAALVTAKGREILEHTRQLV---EEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYK-L 981
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1558 VTLKMEKVYHPCFLLTKKRYVGYSYESPNQREPIF--DAKGIETVRRDTCEAVAKTMEQSLRLFFEQKNISK----VKSY 1631
Cdd:TIGR00592 982 LELDIDGVFKRLLLLKKKKYAAIKVEGDSDGNYTTkqEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEaveeVQEV 1061
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1632 LYRQWKRILSGRVSLQDFIFAKEVRLGTYSTRDSSLLPPAAiVATKSMKADPRTEPRyAERVPYVVIHGEPGARLVDMVV 1711
Cdd:TIGR00592 1062 LEKIGKNVLNGEVPLEKFVINKQLTRDPKDYPDGASLPHVH-VALRINARGGRKVKA-GDVVSYVICKDGGNLSARQRAY 1139
|
650 660 670
....*....|....*....|....*....|..
gi 42563023 1712 DPLVLLDVDTPYRLNDLYYINKQIIPALQRVF 1743
Cdd:TIGR00592 1140 ALEELQRKHNNLIYDTQYYLEHQIHPVVLRIL 1171
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
1342-1747 |
1.41e-49 |
|
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.
Pssm-ID: 99919 Cd Length: 371 Bit Score: 181.37 E-value: 1.41e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1342 LVMEPESAFYDDpVIVLDFQSLYPSMIIAYNlcfstclgklahlkmntlgVSSYSLDLDVLQDLNQILQTPNSVMYVPPe 1421
Cdd:cd05536 8 IVLEPEKGLHEN-IVVLDFSSLYPSIMIKYN-------------------ISPDTLVREGCEDCDVEPQVGHKFRKDPP- 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1422 vrrGILPRLLEEILSTRIMVKKAMKKLTPsEAVLHRIFNARQLALKLIANVTYGYTaaGFSG-RMPCAELADSIVQCGRS 1500
Cdd:cd05536 67 ---GFIPSVLEDLLEERRRIKEKMKKLDP-ESEEYKLLDERQRAIKILANSFYGYM--GWANaRWYCKECAEAVTAWGRE 140
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1501 TLEKAISFVNANdnwNARVVYGDTDSMFVllkgrTVKEAFVVGQEIASAITEMNPH-PVTLKMEKVYHPCFLLTKKRYVG 1579
Cdd:cd05536 141 YIKTTIKIAEEK---GFKVIYGDTDSLFV-----KIDGADAVKKKVKKLLKYINEElPLELEIEKFYKRGFFVTKKRYAG 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1580 YSyespnqREPIFDAKGIETVRRDTCEAVAKTMEQSLRLFFEQKNISKVKSYLYRQWKRILSGRVSLQDFIFAKEVrlgT 1659
Cdd:cd05536 213 LT------EDGKIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVIEKLKRGEVPPEKLVIWKQL---T 283
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1660 YSTRDSSLLPPAAIVATKSMKADPRTEPryAERVPYVVIHGePG-----ARLVDMvvdplvlldVDTPYRLNDLYYINKQ 1734
Cdd:cd05536 284 KDLSEYKATGPHVAAAKKLAKRGYKVRP--GTKIGYVIVKG-SGkisdrAYPYDM---------VDEKHKYDAEYYIDNQ 351
|
410
....*....|...
gi 42563023 1735 IIPALQRVFGLVG 1747
Cdd:cd05536 352 VLPAVLRILEAFG 364
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
1342-1721 |
1.66e-25 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 114.79 E-value: 1.66e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1342 LVMEPESAFYDDpVIVLDFQSLYPSMIIAYNLCFSTclgklahlkmntlgvssysldLDVLQDLNQILQTPNSVMYVPPE 1421
Cdd:PRK05761 411 LVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPET---------------------VRIPECKCHYDDEVPELGHSVCD 468
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1422 VRRGILPRLLEEILSTRIMVKKAMKKLTPSEAVLHRIFNARQLALKLIANVTYGYTaaGFS----GRMPCAEladSIVQC 1497
Cdd:PRK05761 469 DRPGLTSVLVGLLRDFRVKIYKKKAKDPNLDEERRAWYDVVQRALKVFLNASYGVF--GAEnfklYRIEVAE---SITAL 543
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1498 GRSTLEKAISFVNANdNWnaRVVYGDTDSMFVllKGRTVKEAfvvgQEIASAITEMnpHPVTLKMEKVYHPC-FLLTKKR 1576
Cdd:PRK05761 544 GREILLSTKKKAEEL-GL--KVLYGDTDSLFV--WGPTKESL----EELIKEIEER--TGIDLEVDKTYDWVaFSGLKKN 612
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1577 YVGYSYESPnqrepiFDAKGIETVRRDTCEAVAKTMEQSLRLFFE-------QKNISKVKSYLYRQWKRILSGRVSLQDF 1649
Cdd:PRK05761 613 YFGVLKDGK------VKIKGIVAKKRNTPEFVKELQREVLEVLKSirspedvEKVKDEIEDVLKRYYEKLRAKDYPLDEL 686
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 42563023 1650 IFAKEV--RLGTYSTRdsslLPPAAIVATKSMKADPRTEPRyaERVPYVVIHGEPGarlvdmvVDPLVLLDVDT 1721
Cdd:PRK05761 687 AIRVRLskPLDEYTKN----TPQHVKAALQLRDYGVEVSPG--DIISYVKVDDKRG-------VKPVQLAKLSE 747
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
1050-1276 |
6.85e-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: 6.85e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1050 PDPRFDSVNVIALVVQNDDSFVaeVFVLLFSPDSIDQRNVDGLsgcKLSVFLEERQLFRYFIETLCKWDPDVLLGWDIQG 1129
Cdd:cd05160 15 PEPDRDPIICITYADSFDGVKV--VFLLKTSTVGDDIEFIDGI---EVEYFADEKELLKRFFDIIREYDPDILTGYNIDD 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1130 GSIGFLAERAAQLGIRFLNNISRTPsptttNNSDNKRklgnnllpdplvanpaqveevviedEWGRthasgVHVGGRIVL 1209
Cdd:cd05160 90 FDLPYLLKRAEALGIKLTDGIYRRS-----GGEKSSG-------------------------STER-----IAVKGRVVF 134
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 42563023 1210 NAWRLIRGEVKLNMYTIEAVSEAVL-RQKVPSIPykvlTEWFSSGPAGARYRCIEYVIRRANLNLEIM 1276
Cdd:cd05160 135 DLLAAYKRDFKLKSYTLDAVAEELLgEGKEKVDG----EIIEDAEWEEDPERLIEYNLKDAELTLQIL 198
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
1342-1747 |
1.44e-21 |
|
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: 98.88 E-value: 1.44e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1342 LVMEPESAFYDDpVIVLDFQSLYPSMIIAYNLcfsTCLGKLAHLKMntlgvssysldldvlQDLNQILQTPNSVMYvppE 1421
Cdd:cd05537 7 YVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLI---DPLGLIEGLKA---------------PDPEDLIPGFLGARF---S 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1422 VRRGILPRLLEEILSTRIMVKKAMkkltpseavlhrifNAR-QLALKLIANVTYGytAAGFSG-RMPCAELADSIVQCGR 1499
Cdd:cd05537 65 REKHILPDLIARLWAARDEAKREK--------------NAPlSQAIKIIMNSFYG--VLGSTGcRFFDPRLASSITLRGH 128
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1500 STLEKAISFVNANdnwNARVVYGDTDSMFVLLKGR-TVKEAFVVGQEIASAITEMNPHPVT----------LKMEKVYHP 1568
Cdd:cd05537 129 EIMKQTRAWIEQQ---GYQVIYGDTDSTFVWLGEElDAAEAQAIGKELASQINQWWAQKLKeefglesfleIEFETHYSR 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1569 CFLLT--------KKRYVGYSyESPNQREPIFdaKGIETVRRDTCEaVAKTMEQSL-RLFFEQKNISK-VKSYLyrqwKR 1638
Cdd:cd05537 206 FFMPTirgsdegsKKRYAGLK-STDGGDELVF--KGLETVRSDWTP-LARQFQKELyERVFNDEPYEGfIKETV----EE 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1639 ILSGRVSLQdFIFAKEVR--LGTYsTRDSsllPP---AAIVAtkSMKADPRTEPRYAERVPYVVIhgEPGARLVDMVVDP 1713
Cdd:cd05537 278 LLAGELDEL-LVYRKRLRrpLSEY-TKNV---PPhvqAARLA--DQINRELGRPRQYQWIEYVIT--VNGPEPLEYRTSP 348
|
410 420 430
....*....|....*....|....*....|....
gi 42563023 1714 lvlLDVDtpyrlndlYYINKQIIPALQRVFGLVG 1747
Cdd:cd05537 349 ---LDYQ--------HYIDKQLKPIADSILPFLG 371
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
1343-1633 |
2.38e-19 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 95.47 E-value: 2.38e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1343 VMEPESAFYDDPVIVLDFQSLYPSMIIAYNLCFSTCLGKLahlkmntlgVSSYSLDLDV-LQDLNQILQTPNsVMYVPPE 1421
Cdd:PHA03036 535 VFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVV---------VNDNRLEAEInKQELRRKYPYPR-YIYVHCE 604
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1422 VR---------------RGILPRLLEEILSTRIMVKKAMKKltPSEAVLHRIFNARQLALKLIANVTYG----YTAAGFS 1482
Cdd:PHA03036 605 PRspdlvseiavfdrriEGIIPKLLKTFLEERARYKKLLKE--ATSSVEKAIYDSMQYTYKIVANSVYGlmgfRNSALYS 682
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1483 ----------GRMpCAELADSIV---------------------QCGRSTLEKAISFVNANDNWNARVVYGDTDSMFVLL 1531
Cdd:PHA03036 683 yasaksctaiGRN-MIKYLNSVLngsklingklilancpinpffKDDRSIDTNYDTNLPVEYNFTFRSVYGDTDSVFLEI 761
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1532 KGRTVKEAFVVGQEIASAI-TEMNPHPVTLKMEKVYHPCFLLTKKRYVGYSY--ESPNQREPIFDAKGIETVRRDTC--- 1605
Cdd:PHA03036 762 NTKDVDKSIKIAKELERIInEKVLFDNFKIEFEAVYKNLIMQSKKKYTTLKYiaSSTDGSVPERVNKGTSETRRDVSkfh 841
|
330 340
....*....|....*....|....*....
gi 42563023 1606 -EAVAKTMEQSLRLFFEQKNISKVKSYLY 1633
Cdd:PHA03036 842 kYMIKIYKTRLLDMLSEGNMNSNQVCIDI 870
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
1342-1701 |
2.89e-19 |
|
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: 91.64 E-value: 2.89e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1342 LVMEPESAFYDDpVIVLDFQSLYPSMIIAYNLCFSTclgklahlkMNTlgvsSYSLDLDVLQDLNQILQTpnsvmyvppe 1421
Cdd:cd05531 9 LVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPET---------INC----RCCECRDHVYLGHRICLK---------- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1422 vRRGILPRLLEEILSTRIMVKKAMKKLTPSEAvlhrifnaRQLALKLIANVTYGYTaaGFS----GRMPCAEladSIVQC 1497
Cdd:cd05531 65 -RRGFLPEVLEPLLERRLEYKRLKKEEDPYAG--------RQKALKWILVTSFGYL--GYKnakfGRIEVHE---AITAY 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1498 GRSTLEKAISFVNANdnwNARVVYGDTDSMFVllKGRTVKEAFVvgQEIaSAITEMNphpvtLKMEKVYH-PCFLLTK-- 1574
Cdd:cd05531 131 GRKILLRAKEIAEEM---GFRVLHGIVDSLWI--QGRGDIEELA--REI-EERTGIP-----LKLEGHYDwIVFLPERdg 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1575 ----KRYVGYSYESPnqrepiFDAKGIETVRRDTCEAVAKTMEQSLRLFFEQKNISKVK-------SYLYRQWKRILSGR 1643
Cdd:cd05531 198 lgapNRYFGRLSDGE------MKVRGIELRRRDTPPFVKKFQEEALDILASAKTPEELLklreealDLFRRYLQRLREGD 271
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*...
gi 42563023 1644 vsLQDFIFAKEVRLGTYSTRdssllPPAAIVATKSMKADprTEPRYAERVPYVVIHGE 1701
Cdd:cd05531 272 --LEDLIIEKKISKRSSEYK-----VLASTALKALRAKG--VSVVPGMKIEYIVRDGK 320
|
|
| zf-C4pol |
pfam14260 |
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ... |
1789-1862 |
1.11e-18 |
|
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1.
Pssm-ID: 464119 Cd Length: 68 Bit Score: 81.65 E-value: 1.11e-18
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 42563023 1789 CILCGEVvqeSAQLCNRCLQNKSAAAATIVWKTSKLEREMQHLATICRHCGGGdwvVQSGVKCNSLACSVFYER 1862
Cdd:pfam14260 1 CLGCGAP---EEPLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGS---LHEEVLCDSRDCPVFYMR 68
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
15-213 |
6.75e-17 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 87.39 E-value: 6.75e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 15 IVSIDYY------MASPIPGYNicyssfqGSEVNEVPVIRIYGSTPAGQKTCLHIHRALPYLYIPCSEIPLEHHkgvdgs 88
Cdd:PTZ00166 46 QLDADYTekddksQGNPHNTVS-------GVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNFLPED------ 112
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 89 TLALSLELEKALKLKGNAASKRQHIHDCEIVRAKKFYGYH-STEEAFVKIYLSYhPPDVARAASLLLAGAVLGKSL---- 163
Cdd:PTZ00166 113 SQKLKRELNAQLSEQSQFKKYQNTVLDIEIVKKESLMYYKgNGEKDFLKITVQL-PKMVPRLRSLIESGVVVCGGGwdgi 191
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 42563023 164 ---QPYESHIPFILQFLVDYNLYGMGHVHISKMKFrspvphHFRPRRFDLDDC 213
Cdd:PTZ00166 192 rlfQTYESNVPFVLRFLIDNNITGGSWLTLPKGKY------KIRPPKKKTSTC 238
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
1342-1630 |
1.82e-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: 74.31 E-value: 1.82e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1342 LVMEPESAFYDDpVIVLDFQSLYPSMIIAYNLCFSTclgklahlkmntlgvssysldLDVLQDLNQILQTPNSVMYVPPE 1421
Cdd:cd05530 17 IVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYET---------------------VNCPHCECKTNEVPEVGHWVCKK 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1422 vRRGILPRLLEEI--LSTRIMVKKAM-KKLTPSEAVLhriFNARQLALKLIANVTYG-YTAAGFSgrMPCAELADSIVQC 1497
Cdd:cd05530 75 -RPGITSQIIGLLrdLRVKIYKKKAKdKSLDEEMRQW---YDVVQSAMKVFINASYGvFGAENFP--LYCPPVAESTTAL 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1498 GR----STLEKAISFvnandnwNARVVYGDTDSMFvlLKGRTvkeafvvgQEIASAITE--MNPHPVTLKMEKVY-HPCF 1570
Cdd:cd05530 149 GRyiitSTIKKAREL-------GLKVLYGDTDSLF--LWNPP--------QEQLEDLVEwvEKELGLDLELDKEYrYVVF 211
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 42563023 1571 LLTKKRYVGySYESPNqrepiFDAKGIETVRRDTCEAVAKtmeqslrLFFEQKNI-SKVKS 1630
Cdd:cd05530 212 SGLKKNYLG-VTKDGS-----VDIKGLLGKKRNTPEFVKE-------LFYEVIEIlSAVNS 259
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
1099-1660 |
4.96e-11 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 68.18 E-value: 4.96e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1099 VFLEERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAaqlgirflnnisrtpsptttnnsdnKRKLGNNllpdplV 1178
Cdd:PHA02528 174 PFDTEREMLLEYINFWEENTPVIFTGWNVELFDVPYIINRI-------------------------KNILGEK------T 222
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1179 AN---P-AQVEEVVIEDEWGRTHAsGVHVGGRIVLNAWRLIRGEVKLNM--YTIEAVSEAVLRQKVPSIPYKVLTEWFSS 1252
Cdd:PHA02528 223 AKrlsPwGKVKERTIENMYGREEI-AYDISGISILDYLDLYKKFTFTNQpsYRLDYIAEVELGKKKLDYSDGPFKKFRET 301
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1253 GPAgaRYrcIEYVIRRANLNLEIMSQLDMINRTSELARVFGIDFFSVLSrgsQYRVESmllrlAHTQNYLA----ISPGN 1328
Cdd:PHA02528 302 DHQ--KY--IEYNIIDVELVDRLDDKRKLIELVLSMAYYAKINFEDVFS---PIKTWD-----AIIFNSLKeekiVIPEN 369
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1329 QQVASQPAMECvpLVMEPESAFYDdPVIVLDFQSLYPSMIIAYNLCFSTCLGKLAHLKMNTLGVSSYSLDLDVLQdlnqi 1408
Cdd:PHA02528 370 KSHKKQKYAGA--FVKEPVPGAYR-WVVSFDLTSLYPSIIRQVNISPETIAGTFHVAPVHEYINKTAPRPSDEYS----- 441
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1409 lQTPNSVMYvpPEVRRGILPRLLEEILSTRIMVKKAM---------------------------------------KKLT 1449
Cdd:PHA02528 442 -CSPNGWMY--RKDIRGVIPTEIKKVFDQRKIYKKKMlaaernaeliktiledlndsvdtpidvdyyfdfsdefkaELKT 518
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1450 PSEAVLHRI----------FNARQLALKLIANVTYG--------Y------TAAGFSGRMpcaeladSIVQCGRSTLEKA 1505
Cdd:PHA02528 519 LTKSSLKALleecekeialCNTIQMARKILINSLYGalgnehfrYydlrnaEAITLFGQL-------AIQWIERKMNEYL 591
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1506 ISFVNANDnwNARVVYGDTDSMFVLL----------KGRTvKEAFV-----VGQE-----IASAITE----MN--PHPVT 1559
Cdd:PHA02528 592 NKLCKTED--EDYVIYGDTDSIYVNLdplvekvgedKFKD-TNHWVdfldkFCKErmepyIDSSYRElceyMNnyEHLMF 668
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1560 LKMEKVYHPCFLLTKKRYVGYSYESPNQR--EPIFDAKGIETVRRDTCEAVAKTMEQSLRlffeqkniskvksylyrqwk 1637
Cdd:PHA02528 669 MDREAIAGPGFWTAKKRYALNVWDSEGTRyaEPKLKIMGIETQRSSTPKAVQKALKEAIR-------------------- 728
|
650 660
....*....|....*....|....*.
gi 42563023 1638 RILS-GRVSLQDFI--FAKEVRLGTY 1660
Cdd:PHA02528 729 RILQeGEESLQEYIkeFEKEFRKLDY 754
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
1033-1279 |
1.60e-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: 1.60e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1033 LTILSIEVHAESRGDLRPDPRFDSVNVIALVVQN---DDSFVAEVFVLlfspdsidqRNVDGLSGCKLSVFLEERQL--- 1106
Cdd:cd05777 7 LRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRqgeGEPFIRNIFTL---------KTCAPIVGAQVFSFETEEELlla 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1107 FRYFIETLckwDPDVLLGWDIQGGSIGFLAERAAQLGIR---FLNNISRTPSpTTTNNSDNKRKLGNnllPDPlvanpaq 1183
Cdd:cd05777 78 WRDFVQEV---DPDIITGYNICNFDLPYLLERAKALKLNtfpFLGRIKNIKS-TIKDTTFSSKQMGT---RET------- 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1184 vEEVVIEdewgrthasgvhvgGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPAGaRYRCIE 1263
Cdd:cd05777 144 -KEINIE--------------GRIQFDLLQVIQRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPET-RRRLAV 207
|
250
....*....|....*.
gi 42563023 1264 YVIRRANLNLEIMSQL 1279
Cdd:cd05777 208 YCLKDAYLPLRLLDKL 223
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
1205-1507 |
9.03e-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: 60.84 E-value: 9.03e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1205 GRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPAG--ARYRCiEYvirranLNLEIMSQLDMI 1282
Cdd:TIGR00592 355 GKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIAKKYEFEAPDidAPYSS-EY------LEVTYELGKEFA 427
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1283 NRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAisPGNQQVASQPAME-CVPLVM-------EPESAFYDDP 1354
Cdd:TIGR00592 428 PMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLA--VKGPDELEYPRRSwCKYEGGyvkppnvEKGLDKTPPP 505
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1355 VIVLDF--QSLYPSMIIAYNLCFSTCLGKLAHLKmNTLGVSSYSLDLDVLQDLNQILQTPNSVMYVPpevrrGILPRLLE 1432
Cdd:TIGR00592 506 LVVLDFsmKSLNPSIIRNEIVSIPDTLHREFALD-KPPPEPPYDVHPCVGTRPKDCSFPLDLKGEFP-----GKKPSLVE 579
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1433 EILSTRIMVKKAMKKLTPSEAVLHRIFNARQLALKLIANVTYGYTAAGFS--GRMPCAELADS---IVQCGRSTLEKAIS 1507
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 ... |
60-222 |
2.88e-08 |
|
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: 57.81 E-value: 2.88e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 60 CLHIHRALPYLYIPCSeiplehhkgvDGSTLAlslELEKALKLKGNAASKrqhIHDCEIVRAKKFYGYHSTEEAFVKIYL 139
Cdd:pfam03104 9 CVNVFGFKPYFYCLAP----------DGKELE---EVIEEIKELYEGLDK---IEKIELKLKKSLYGYEEDPVPYLKVSF 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 140 SYhPPDVARAASLLLAGAVLgkslQPYESHIPFILQFLVDYNLYGMGHVHISKMKFRSPVPHHFRPRRFDLDDCPGQRID 219
Cdd:pfam03104 73 AN-PRPLLKIRKYLSPENIS----DVYEYDVDYLERFLIDNDIVGFGWYKVKVYPFRAEGRISNCDVEIDCDSPDLISVP 147
|
...
gi 42563023 220 EVA 222
Cdd:pfam03104 148 FEK 150
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
39-185 |
5.94e-08 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 57.91 E-value: 5.94e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 39 SEVNEVPVIRIYGSTPAGQKTCLHIHRALPYLYIPCSEiplehhkgvdgstlalSLELEKALKLKGNaaskrqhIHDCEI 118
Cdd:COG0417 13 RDEDGKPVIELWGRTEDGPSVLLDVTGFRPYFYVPLPD----------------EEKLEELLRDIKE-------ITEVEP 69
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 42563023 119 VRAKKFYGyhsTEEAFVKIYLSyHPPDVARAASLLLAGavlgkSLQPYESHIPFILQFLVDYNLYGM 185
Cdd:COG0417 70 VKLKSFFG---EPVPVLKIYTR-DPRDVRELRDRLKEG-----GIDVYEADIRFHDRYLIDRFLTPG 127
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
1033-1229 |
1.99e-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: 1.99e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1033 LTILSIEVHAESRGDLRPDPRF--DSVNVIALVVQNDDSFVAEVfVLLFSPDSIDQRNVDGLS--------GCKLSVFLE 1102
Cdd:pfam03104 155 LRVLSFDIECTSLPGKFPDAENvkDPIIQISCMLDGQGEPEPEP-RFLFTLRECDSEDIEDFEytpkpiypGVKVFEFPS 233
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1103 ERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGI---RFLNNISRTPSPTTTNNSDNKRKLGNNLLPdplva 1179
Cdd:pfam03104 234 EKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIvklSSIGRLNRGGRSKVREIGFGTRSYEKVKIS----- 308
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 42563023 1180 npaqveevviedewgrthasgvhvgGRIVLNAWRLIRGEVKLNMYTIEAV 1229
Cdd:pfam03104 309 -------------------------GRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
1036-1146 |
1.99e-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: 1.99e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1036 LSIEVHAESRgdlRPDPRFDSVNVIALVVQNDDsfvaevfVLLFSPDSIDQRNVdglsgcklsvfleerqlFRYFIETLC 1115
Cdd:cd05781 8 FDIEVYSKYG---TPNPRRDPIIVISLATSNGD-------VEFILAEGLDDRKI-----------------IREFVKYVK 60
|
90 100 110
....*....|....*....|....*....|.
gi 42563023 1116 KWDPDVLLGWDIQGGSIGFLAERAAQLGIRF 1146
Cdd:cd05781 61 EYDPDIIVGYNSNAFDWPYLVERARVLGVKL 91
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
1096-1282 |
5.22e-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: 49.92 E-value: 5.22e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1096 KLSVFLEERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFLNNISR---TPSPtttnnsdnKRKLGNNL 1172
Cdd:cd05776 75 KVRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRlkrSVWP--------KKKGGGKF 146
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1173 LPDPLVAnpaqveevviedewgrthasgvhvgGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSS 1252
Cdd:cd05776 147 GERELTA-------------------------GRLLCDTYLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYND 201
|
170 180 190
....*....|....*....|....*....|
gi 42563023 1253 gpAGARYRCIEYVIRRANLNLEIMSQLDMI 1282
Cdd:cd05776 202 --SESLLKLLEHTEKDAYLILQLMFKLNIL 229
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
1354-1659 |
2.50e-05 |
|
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Pssm-ID: 99921 Cd Length: 347 Bit Score: 48.64 E-value: 2.50e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1354 PVIVLDFQSLYPSMIIAYNLCfstclgklahlkmntlgvssysldldvlqdlnqilqtpnsvmyvPPEVRRGILPRLLEE 1433
Cdd:cd05538 18 PIVHADVASLYPSIMLAYRIC--------------------------------------------PARDSLGIFLALLKY 53
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1434 ILSTRImvkkAMKKLTPSEAVLHR--IFNARQLALKLIANVTYGYTAAGfSGRMPCAELADSIVQCGRSTLEKAISFVNA 1511
Cdd:cd05538 54 LVELRL----AAKESARAAARPAErdAFKAKQAAFKVLINSFYGYLGTG-LHAFSDPEAAAEVTRLGRELLKLMIRWLRR 128
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1512 NdnwNARVVYGDTDSMFVllkgrTVKEAFVVGQEIASAITEMN---PHPVTLKMEKVYHPCFLLTKKRYVGYSY-ESPNQ 1587
Cdd:cd05538 129 R---GATPVEVDTDGIYF-----IPPNGVDTEDEEEELVRELSstlPKGITVEFDGRYRAMFSYKIKNYALLDYdGKLIV 200
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42563023 1588 REPIFDAKGIETVRRDtceavakTMEQSLRLFFeQKNISKVKSYlYRQWK-RILSGRVSLQDfiFAKEVRLGT 1659
Cdd:cd05538 201 KGSAFRSRGIEPFLRE-------FLREAVRLLL-QGDGAGVHDL-YEDYLrRLRSHELPISD--LARTETLKE 262
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
1031-1279 |
3.45e-05 |
|
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: 3.45e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1031 QQLTILS--IEVHAESRgdlRPDPRFDSVNVIalvvqnddSFVAEVFVLLFSPDSIDQRNVDGLSgcklsvflEERQLFR 1108
Cdd:cd05780 1 EDLKILSfdIEVLNHEG---EPNPEKDPIIMI--------SFADEGGNKVITWKKFDLPFVEVVK--------TEKEMIK 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1109 YFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFlnnisrtpsptttnnsdnkrKLGNNllpdplvanpaqVEEVV 1188
Cdd:cd05780 62 RFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIEL--------------------DLGRD------------GSEIK 109
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563023 1189 IEDewgRTHASGVHVGGRIVLNAWRLIRGEVKLNMYTIEAVSEAVLRQKVPSIPYKVLTEWFSSGPagARYRCIEYVIRR 1268
Cdd:cd05780 110 IQR---GGFNNASEIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGE--NLERLFRYSMED 184
|
250
....*....|.
gi 42563023 1269 ANLNLEIMSQL 1279
Cdd:cd05780 185 AKYTYEIGKEF 195
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
1100-1147 |
1.65e-04 |
|
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: 1.65e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 42563023 1100 FLEERQLFRYFIETLCKWDPDVLLGWDIQGGSIGFLAERAAQLGIRFL 1147
Cdd:cd05784 48 FADEKSLLLALIAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPLR 95
|
|
| |
