|
Name |
Accession |
Description |
Interval |
E-value |
| POLBc_epsilon |
cd05535 |
DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
531-1153 |
0e+00 |
|
DNA polymerase type-B epsilon 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) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B.
Pssm-ID: 99918 Cd Length: 621 Bit Score: 1331.54 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 531 GHVLDSETYVGGHVEALESGVFRSDIPCRFRMNPAAFDFLLQRVEKTLRHALEEEEKVPVEQVTNFEEVCDEIKSKLASL 610
Cdd:cd05535 1 GHLLESETYVGGHVEALESGVFRSDIPCRFKLDPDAIQELLQNVDETLRFAIEVEGKIPLDQVENFEEVREEILEKLQSL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 611 KDVPSRIECPLIYHLDVGAMYPNIILTNRLQPSAMVDEATCAACDFNKPGANCQRKMAWQWRGEFMPASRSEYHRIQHQL 690
Cdd:cd05535 81 RDNPKRSEKPLIYHLDVAAMYPNIILTNRLQPDAIVDEDVCAACDFNKPGKTCQRRMEWAWRGEYFPASRGEYERIKQQL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 691 ESEKFPPLFPEGPARAFHELSREEQAKYEKRRLADYCRKAYKKIHITKVEERLTTICQRENSFYVDTVRAFRDRRYEFKG 770
Cdd:cd05535 161 ESEKFPPLFPGGPPKSFHELSPEEQAEELKKRLKDYSRKVYKKTHVTKEEERSTTICQRENPFYVDTVRAFRDRRYEYKG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 771 LHKVWKKKLSAAVEVGDAAEVKRCKNMEVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELI 850
Cdd:cd05535 241 LHKVWKKKLEAAKAAGDAAEIKEAKKMVVLYDSLQLAHKCILNSFYGYVMRKGSRWYSMEMAGIVCYTGANIIQMARELV 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 851 EQIGRPLELDTDGIWCVLPNSFPENFVFKTTNvkKPKVTISYPGAMLNIMVKEGFTNDQYQELAEPSSLTYVTRSENSIF 930
Cdd:cd05535 321 EQIGRPLELDTDGIWCILPKSFPENFTFKTKN--GKKVTISYPCVMLNHLVHKKFTNDQYQELVDPSTGTYETRSENSIF 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 931 FEVDGPYLAMILPASKEEGKKLKKRYAVFNEDGSLAELKGFEVKRRGELQLIKIFQSSVFEAFLKGSTLEEVYGSVAKVA 1010
Cdd:cd05535 399 FEVDGPYKAMILPASKEEGKLLKKRYAVFNEDGSLAELKGFEVKRRGELQLIKIFQSEVFDAFLKGSTLEECYAAVAAVA 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1011 DYWLDVLYSKAANMPDSELFELISENRSMSRKLEDYGEQKSTSISTAKRLAEFLGDQMVKDAGLSCRYIISRKPEGSPVT 1090
Cdd:cd05535 479 NYWLDVLDSKGENLDDEELFELISENRSMSKKLEEYGNQKSTSITTAKRLAEFLGDQMVKDKGLSCKYIISKKPEGSPVT 558
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62198237 1091 ERAIPLAIFQAEPTVRKHFLRKWLKSSSLQDFDIRAILDWDYYIERLGSAIQKIITIPAALQQ 1153
Cdd:cd05535 559 ERAIPVAIFQAEPEVRKHYLRKWLKDPSDEDLDIRDIIDWDYYIERLGSTIQKIITIPAALQG 621
|
|
| DUF1744 |
pfam08490 |
Domain of unknown function (DUF1744); This domain is found at the C-terminal of the epsilon ... |
1538-1925 |
0e+00 |
|
Domain of unknown function (DUF1744); This domain is found at the C-terminal of the epsilon catalytic subunit of DNA polymerase. It is found C terminal to pfam03104 and pfam00136.
Pssm-ID: 462493 Cd Length: 400 Bit Score: 592.60 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1538 LEKVGPELLPPPKHTFEVRAETDLKTICRAIQRFLLAYKEERRGPTLIAVQSSWELKRLASEIPVLEEFPLVPICVADK- 1616
Cdd:pfam08490 16 LEKWSGAFEYPEDMTFEVTYFTDERKAYKALSRALSKYKEEKSGPTLLVLQSPKDLSYLLSKIPILNEFPVVSIPSNDAd 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1617 INYGVLDWQRHGARRMIRHYLNLDTCLSQAFEMSRYFHIPIGNLPEDISTFGSDLFFARHLQRHNHLLWLSPTARPDLGG 1696
Cdd:pfam08490 96 SSLPALGWQSVVAKRMVNHYLSLGSWLSHLIELARYFDIPLCNLESDDPLFLIDIFYARRLKKNNIVLWWSPSPLPDLGG 175
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1697 KEADDNCLVME-FDDQATVEINSSGCYSTVCVELDLQNLAVNTILQSHHVNDMEGADSMGIsfdvIQQASLEDMITGGQA 1775
Cdd:pfam08490 176 REKDDNPNTLGlMEELDSPEINNPGAYSNVCLELDIRNLAVNTILQSALINELEGSDLSTA----FDAASHTLDEYSKGD 251
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1776 ASAPASYDETALCSNTFRILKSMVVGWVKEITQyHNIYADNQVMHFYRWLRSPSSLLHDPALHRTLHNMMKKLFLQLIAE 1855
Cdd:pfam08490 252 VNSSSTYDEDAFSSAAFRVLRSMVKSWWDDALK-GNVFADLLVDHFVRWVQSPDSLLYDPALHRHVHNLMKKAFLQLLAE 330
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1856 FKRLGSSVIYANFNRIILCTKKRRVEDAIAYVEYITSSIHSKETFHSLTISFSRCWEFLLWMDPSNYGGI 1925
Cdd:pfam08490 331 FKRLGSTVVYADFNRILLQTSKPSVENAYAYSQYIVKAIRSKPLFHFLDLKIVRYWDYLLWMDEANYGGV 400
|
|
| DNA_polB_epsilon_exo |
cd05779 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ... |
268-471 |
1.20e-154 |
|
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique large C-terminal domain with an unknown function. Phylogenetic analyses indicate that it is orthologous to the archaeal DNA polymerase B3 rather than to the eukaryotic alpha, delta, or zeta polymerases. The exonuclease domain of family-B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation
Pssm-ID: 99822 [Multi-domain] Cd Length: 204 Bit Score: 475.60 E-value: 1.20e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 268 DPVVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLITNREIVSEDIEDFEFTPKPEYEGPFCVFNEPDEAHLIQRW 347
Cdd:cd05779 1 DPRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNREIVSEDIEDFEYTPKPEYEGPFKVFNEPDEKALLQRF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 348 FEHVQETKPTIMVTYNGDFFDWPFVEARAAVHGLSMQQEIGFQKDSQGEYKAPQCIHMDCLRWVKRDSYLPVGSHNLKAA 427
Cdd:cd05779 81 FEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQGLKAV 160
|
170 180 190 200
....*....|....*....|....*....|....*....|....
gi 62198237 428 AKAKLGYDPVELDPEDMCRMATEQPQTLATYSVSDAVATYYLYM 471
Cdd:cd05779 161 TKAKLGYDPVELDPEDMVPLAREDPQTLASYSVSDAVATYYLYM 204
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
86-426 |
5.77e-85 |
|
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: 282.38 E-value: 5.77e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 86 FIQDDGSRFKVALPYKPYFYIATRKGCE-REVSSFLSKKFQGKIakveTVPKEDLDLPNHLVGLKRN---YIRLSFHTVE 161
Cdd:pfam03104 1 KTDEGVSVCVNVFGFKPYFYCLAPDGKElEEVIEEIKELYEGLD----KIEKIELKLKKSLYGYEEDpvpYLKVSFANPR 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 162 DLVKVRKEISPAvkknreqdhasdaytallssvlqrggvitdeeetskkiadqldNIVDMREYDVPYHIRLSIDLKIHVA 241
Cdd:pfam03104 77 PLLKIRKYLSPE-------------------------------------------NISDVYEYDVDYLERFLIDNDIVGF 113
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 242 HWYNVRY-------RGNAFPVEITRRDDLVER-------PDPVVLAFDIETTKLPLKFPDAE--TDQIMMISYMIDGQG- 304
Cdd:pfam03104 114 GWYKVKVypfraegRISNCDVEIDCDSPDLISvpfekewPPLRVLSFDIECTSLPGKFPDAEnvKDPIIQISCMLDGQGe 193
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 305 ------YLITNREIVSEDIEDFEFTPKPEYEGPfCVFNEPDEAHLIQRWFEHVQETKPTIMVTYNGDFFDWPFVEARAA- 377
Cdd:pfam03104 194 pepeprFLFTLRECDSEDIEDFEYTPKPIYPGV-KVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKe 272
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 62198237 378 -------------VHGLSMQQEIGFQKDSQGEYKAPQCIHMDCLRWVKRDSYLPvgSHNLKA 426
Cdd:pfam03104 273 lyivklssigrlnRGGRSKVREIGFGTRSYEKVKISGRLHLDLYRVIKRDYKLP--SYKLNA 332
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
267-870 |
2.15e-72 |
|
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: 251.30 E-value: 2.15e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 267 PDPVVLAFDIETTKLPLKFPDAE--TDQIMMISYMIDGQGYLITNReivsedIEDFEFTPKPEYEGPFCVFNEpDEAHLI 344
Cdd:smart00486 1 PPLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANR------RILFTLGTCKEIDGIEVYEFN-NEKELL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 345 QRWFEHVQETKPTIMVTYNGDFFDWPFVEARAAVHGLSMQQEIGFQKDSQG------------------EYKAPQCIHMD 406
Cdd:smart00486 74 LAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGLRipnkkplfgsksfglsdiKVYIKGRLVID 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 407 CLRWVKRDSYLPvgSHNLKAAAKAKLGYDPVELDPEDMCRM---ATEQPQTLATYSVSDAVATYYLYMKY-VHPFIFALC 482
Cdd:smart00486 154 LYRLYKNKLKLP--SYKLDTVAEYLLGKEKDDLPYKDIPELyngNYEERDELLRYCIQDAVLTLKLFNKLnVIPLIIELA 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 483 TIIPMEPDEVLRKGSGTLCEALLMVQAFHANIIFPNKQEQEFNKLTDDGHVLDSetYVGGHVEALESGVFRSDipcrfrm 562
Cdd:smart00486 232 RIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEPDLKKKVK--YEGGKVLEPKKGFYDNP------- 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 563 npaafdfllqrvektlrhaleeeekvpveqvtnfeevcdeiksklaslkdvpsriecplIYHLDVGAMYPNIILTNRLQP 642
Cdd:smart00486 303 -----------------------------------------------------------VLVLDFNSLYPSIIIAHNLCY 323
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 643 SAMVDEATCAACDFNKpgancqrkmawqwrgefmpasrseyhriqhqlesekfpplfpegparafhelsreeqakyekrr 722
Cdd:smart00486 324 STLVGVGEVVIKGDLI---------------------------------------------------------------- 339
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 723 ladyCRKAYKKIHITKVEERLTTICQRENSFYVDTVRAFRDRRYEFKGLHKVWKkklsaavevgdaaevKRCKNMEVLYD 802
Cdd:smart00486 340 ----IPEDLLTIKYEKGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEK---------------DESEELKKLLD 400
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62198237 803 SLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGRP------LELDTDGIWCVLPN 870
Cdd:smart00486 401 SRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGYPkpgfkvIYGDTDSIFVTKPG 474
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
71-1136 |
6.03e-57 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 213.92 E-value: 6.03e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 71 ILD---EDKRLGSAVDYYFIQDDGSRFKVALP-YKPYFYIATRkgcEREVSSFLsKKFQGKIAKVETVPKEDLDlpnhlv 146
Cdd:COG0417 7 LLDrsyRDEDGKPVIELWGRTEDGPSVLLDVTgFRPYFYVPLP---DEEKLEEL-LRDIKEITEVEPVKLKSFF------ 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 147 GLKRNYIRLSFHTVEDLVKVRKEISPAVKknreqdhasDAYtallssvlqrggvitdeeetskkiadqldnivdmrEYDV 226
Cdd:COG0417 77 GEPVPVLKIYTRDPRDVRELRDRLKEGGI---------DVY-----------------------------------EADI 112
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 227 PYHIRLSIDLKIHVAHWYNVRYRGNAFPVEITRRDDLVERPDPV-----VLAFDIETTkLPLKFPDAETD-QIMMISYMi 300
Cdd:COG0417 113 RFHDRYLIDRFLTPGVWYEGEVEEDGGKLDYEVKENPRLKPEDYrpklkVLSFDIEVS-TPRGFPDPERDgPIISIGLA- 190
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 301 DGQGY---LITNREIVSEDIEDFEftpkpeyegpfcvfnepDEAHLIQRWFEHVQETKPTIMVTYNGDFFDWPFVEARAA 377
Cdd:COG0417 191 GSDGEkkvLMLGREGVDFEVEYFD-----------------DEKALLEAFFEIIREYDPDIIIGWNVDNFDLPYLQKRAE 253
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 378 VHGLSM-----QQEIGFQKD-SQGEYKAPQCIHMDCLRWVKRDSY-LPvgSHNLKAAAKAKLGYDPVELDPEDMCRMATE 450
Cdd:COG0417 254 RLGIPLdlgrdGSEPSWREHgGQGFASIPGRVVIDLYDALKSATYkFK--SYSLDAVAEELLGEGKLIVDGGEIERLWDD 331
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 451 QPQTLATYSVSDAVATYYLYMK-YVHPFIFALCTIIPMEPDEVLRKGSGTLCEALLMVQAFHANIIFPNKQEQEfnkltd 529
Cdd:COG0417 332 DKPALAEYNLRDAELTLRIFEKtLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGYLAPNKGEIK------ 405
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 530 dghvldSETYVGGHVeaLES--GVFRsdipcrfrmNPAAFDFllqrvektlrhaleeeekvpveqvtnfeevcdeiKSkl 607
Cdd:COG0417 406 ------GEAYPGGYV--LDPkpGLYE---------NVLVLDF----------------------------------KS-- 432
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 608 aslkdvpsriecpliyhldvgaMYPNIILTNRLQPSAMVDEatcaacdfnkpgancqrkmawqwrgefMPASRSEYHRIq 687
Cdd:COG0417 433 ----------------------LYPSIIRTFNISPETLVEG---------------------------GEEPCGDEDVA- 462
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 688 hqlesekfpplfPEGPARafhelsreeqakyekrrladYCRkayKKIHITKveerltTIcqrensfyVDTVRAFRDRrye 767
Cdd:COG0417 463 ------------PGFGHR--------------------FCR---EPKGILP------SI--------LEELWDERDE--- 490
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 768 fkglhkvWKKKLsaavevgdaAEVKRCKNMEVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQAR 847
Cdd:COG0417 491 -------AKKKM---------KKAKPDSEEYRLYDALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGREIIKQTI 554
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 848 ELIEQIG-RPLELDTDGiwcvlpnsfpenfVFkttnVKKPKVTisypgamlnimvkEGFTNDQYQELAEpssltYVTRSE 926
Cdd:COG0417 555 EKAEELGyKVIYGDTDS-------------LF----VWLPKAS-------------LEEAIEIGKELAE-----EINAWW 599
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 927 NSIF-FEVDGPYLAMILPASkeegkklKKRYAVFNEDGSLaELKGFEVKRRGELQLIKIFQSSVFEAFLKGSTLEEVygs 1005
Cdd:COG0417 600 PSGLeLEFEKHYRRFFFPGS-------KKRYAGLTEDGKI-DIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKA--- 668
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1006 VAKVADYWLDVlysKAANMPDSELfeLISenRSMSRKLEDYgeQKSTS--ISTAKRLAEFLGDQMVKDaglSCRYIISRK 1083
Cdd:COG0417 669 VEYVRDVIEKL---RAGEVDLDDL--VIR--KRLRKPLSEY--EKNVPphVRAARKLDERGRPYQRGD---KISYVITKG 736
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|...
gi 62198237 1084 pegspvTERAIPLaifqaeptvrkhFLRKWLKSSslqdfdiraiLDWDYYIER 1136
Cdd:COG0417 737 ------GGRVEPV------------ELAKERESE----------IDYDYYIEK 761
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
714-1135 |
2.85e-15 |
|
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA polymerases.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273159 [Multi-domain] Cd Length: 1172 Bit Score: 82.41 E-value: 2.85e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 714 EQAKYEKRRLADYCRKAYKKIhITKVEERLTTICQRENsfyVDTVRAFRDRRYEFKGLHKVWKKKLSAAVEVGDAAEVKR 793
Cdd:TIGR00592 805 KVGLYDKYVLLMDFNSLYPSI-IQEFNICFTTVQQKVD---EDELPELPDSELEMGILPRELRKLVERRKEVKKLMKQDL 880
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 794 CKNMEVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGrpLEL---DTDGIWCVLPN 870
Cdd:TIGR00592 881 NPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEMN--LEViygDTDSIMINTPG 958
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 871 SFPENfVFKTTNVKKPKVTISYPgaMLNImvkegftndqyqelaepssltyvtrsensiffEVDGPYLAMILPAskeegk 950
Cdd:TIGR00592 959 TKYEE-VFKIGKEFKSEVNKLYK--LLEL--------------------------------DIDGVFKRLLLLK------ 997
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 951 klKKRYAVFNEDGSLA-------ELKGFEVKRRGELQLIKIFQSSVFEAFLKGSTLEEVygsVAKVADYWLDVLYSKAAN 1023
Cdd:TIGR00592 998 --KKKYAAIKVEGDSDgnyttkqEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEA---VEEVQEVLEKIGKNVLNG 1072
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1024 MPDSELFELiseNRSMSRKLEDYGEQKS-TSISTAKRLAEfLGDQMVKdAGLSCRYIISRkpEGSPVTERAiplAIFQAE 1102
Cdd:TIGR00592 1073 EVPLEKFVI---NKQLTRDPKDYPDGASlPHVHVALRINA-RGGRKVK-AGDVVSYVICK--DGGNLSARQ---RAYALE 1142
|
410 420 430
....*....|....*....|....*....|...
gi 62198237 1103 PTVRKHflrKWLkssslqdfdiraILDWDYYIE 1135
Cdd:TIGR00592 1143 ELQRKH---NNL------------IYDTQYYLE 1160
|
|
| YprB |
COG3359 |
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function ... |
261-472 |
1.46e-10 |
|
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function prediction only];
Pssm-ID: 442587 [Multi-domain] Cd Length: 198 Bit Score: 62.66 E-value: 1.46e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 261 DDLVERPDPVVlaFDIETTKLplkfpDAETDQIMMISYMIDGQGYLITnREIVSEDIEDfeftpkpeyegpfcvfnepdE 340
Cdd:COG3359 9 AELLPSEDLLF--FDIETTGL-----SGGGTVIFLIGLADGEGDGFVV-RQYFGEDPGE--------------------E 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 341 AHLIQRWFEHVQETKptIMVTYNGDFFDWPFVEARAAVHGLsmqqeigfqkdsqgEYKAPQCIHMDCLRWVKRDSYLPVG 420
Cdd:COG3359 61 AALLEAFLEWLADYK--LLVTYNGKSFDLPFLKTRFTLHRL--------------PPPLPEFPHLDLLHPARRLWKNRLP 124
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 62198237 421 SHNLKAAAKaKLGYDPVEldpedmcrmateqpqtlaTYSVSDAVATYYLYMK 472
Cdd:COG3359 125 SGGLKTVEE-LLGIERED------------------DLPGYEAPRLYRRYLR 157
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
790-1136 |
1.85e-08 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 59.87 E-value: 1.85e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 790 EVKRCKNMEvlydsLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGrpLEL---DTDGIwc 866
Cdd:PRK05762 480 EAKREMNKP-----LSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQG--YQViygDTDST-- 550
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 867 vlpnsfpenFVfkTTNVKKPKVTISYPGAMLNIMVKEGFTNDQYQELAEPSSLTyvtrsensIFFEVDgpYLAMILPASK 946
Cdd:PRK05762 551 ---------FV--WLGGAHDEEDAAKIGRALVQEINQWWQEHLQQEFGLESALE--------LEFEKH--YRRFFMPTIR 609
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 947 EEGKKLKKRYA--VFNEDGSLaEL--KGFEVKRRGELQLIKIFQSSVFEAFLKGStleevygsvaKVADYWLDVLYS-KA 1021
Cdd:PRK05762 610 GAEEGSKKRYAglIQEGDGDG-RIvfKGLETVRTDWTPLAKEFQQELYERIFRGE----------PYVDYVREVIDKlRA 678
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1022 ANMPDselfELISENRsMSRKLEDYgeQKSTS--ISTAKRLAEFLGDQMVKDA---GLSCRYIISRK-PEgsPVTERAIP 1095
Cdd:PRK05762 679 GELDE----KLVYRKR-LRRPLDEY--QRNVPphVRAARLADEMGYKVGRPLQyqnGGKIGYVITVNgPE--PLEYRKSP 749
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 62198237 1096 laifqaeptvrkhflrkwlkssslqdfdiraiLDWDYYIER 1136
Cdd:PRK05762 750 --------------------------------IDYDYYIEK 758
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
789-1046 |
1.06e-07 |
|
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: 56.85 E-value: 1.06e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 789 AEVKRCKN--MEVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGRP-LEL---DTD 862
Cdd:pfam00136 137 KLLKEETDpfERAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYnFRViygDTD 216
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 863 GIwcvlpnsfpenFV-FKTTNVKKpkvtisypgamlniMVKEGFtndqyqELAEpssltYVTRS--ENSIFFEVDGPYLA 939
Cdd:pfam00136 217 SV-----------FIeFGGKDVEE--------------AMKIGD------ELAE-----HVNQDlfKSPIKLEFEKVYKP 260
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 940 MILPAskeegkklKKRYA----VFNEDGSLAELKGFEVKRRGELQLIKIFQSSVFEAFLKGSTLEEVygsVAKVADYWLD 1015
Cdd:pfam00136 261 LLLIS--------KKKYAglkyTAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSDRGLPVG---LEFVISILND 329
|
250 260 270
....*....|....*....|....*....|.
gi 62198237 1016 VLYSKAANMPDSELFELiseNRSMSRKLEDY 1046
Cdd:pfam00136 330 ARSDLRNNKVPLEKFVI---SKELSKPPDNY 357
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
271-378 |
3.10e-04 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 46.17 E-value: 3.10e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 271 VLAFDIETTKLP-LKFPDAETDQIMMISYMIDGQGYLItnreivsEDIEDFEFTPKPEYEGPFC-VFNEPDEAHLIQRWF 348
Cdd:PTZ00166 266 ILSFDIECIKLKgLGFPEAENDPVIQISSVVTNQGDEE-------EPLTKFIFTLKECASIAGAnVLSFETEKELLLAWA 338
|
90 100 110
....*....|....*....|....*....|
gi 62198237 349 EHVQETKPTIMVTYNGDFFDWPFVEARAAV 378
Cdd:PTZ00166 339 EFVIAVDPDFLTGYNIINFDLPYLLNRAKA 368
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| POLBc_epsilon |
cd05535 |
DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
531-1153 |
0e+00 |
|
DNA polymerase type-B epsilon 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) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B.
Pssm-ID: 99918 Cd Length: 621 Bit Score: 1331.54 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 531 GHVLDSETYVGGHVEALESGVFRSDIPCRFRMNPAAFDFLLQRVEKTLRHALEEEEKVPVEQVTNFEEVCDEIKSKLASL 610
Cdd:cd05535 1 GHLLESETYVGGHVEALESGVFRSDIPCRFKLDPDAIQELLQNVDETLRFAIEVEGKIPLDQVENFEEVREEILEKLQSL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 611 KDVPSRIECPLIYHLDVGAMYPNIILTNRLQPSAMVDEATCAACDFNKPGANCQRKMAWQWRGEFMPASRSEYHRIQHQL 690
Cdd:cd05535 81 RDNPKRSEKPLIYHLDVAAMYPNIILTNRLQPDAIVDEDVCAACDFNKPGKTCQRRMEWAWRGEYFPASRGEYERIKQQL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 691 ESEKFPPLFPEGPARAFHELSREEQAKYEKRRLADYCRKAYKKIHITKVEERLTTICQRENSFYVDTVRAFRDRRYEFKG 770
Cdd:cd05535 161 ESEKFPPLFPGGPPKSFHELSPEEQAEELKKRLKDYSRKVYKKTHVTKEEERSTTICQRENPFYVDTVRAFRDRRYEYKG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 771 LHKVWKKKLSAAVEVGDAAEVKRCKNMEVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELI 850
Cdd:cd05535 241 LHKVWKKKLEAAKAAGDAAEIKEAKKMVVLYDSLQLAHKCILNSFYGYVMRKGSRWYSMEMAGIVCYTGANIIQMARELV 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 851 EQIGRPLELDTDGIWCVLPNSFPENFVFKTTNvkKPKVTISYPGAMLNIMVKEGFTNDQYQELAEPSSLTYVTRSENSIF 930
Cdd:cd05535 321 EQIGRPLELDTDGIWCILPKSFPENFTFKTKN--GKKVTISYPCVMLNHLVHKKFTNDQYQELVDPSTGTYETRSENSIF 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 931 FEVDGPYLAMILPASKEEGKKLKKRYAVFNEDGSLAELKGFEVKRRGELQLIKIFQSSVFEAFLKGSTLEEVYGSVAKVA 1010
Cdd:cd05535 399 FEVDGPYKAMILPASKEEGKLLKKRYAVFNEDGSLAELKGFEVKRRGELQLIKIFQSEVFDAFLKGSTLEECYAAVAAVA 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1011 DYWLDVLYSKAANMPDSELFELISENRSMSRKLEDYGEQKSTSISTAKRLAEFLGDQMVKDAGLSCRYIISRKPEGSPVT 1090
Cdd:cd05535 479 NYWLDVLDSKGENLDDEELFELISENRSMSKKLEEYGNQKSTSITTAKRLAEFLGDQMVKDKGLSCKYIISKKPEGSPVT 558
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62198237 1091 ERAIPLAIFQAEPTVRKHFLRKWLKSSSLQDFDIRAILDWDYYIERLGSAIQKIITIPAALQQ 1153
Cdd:cd05535 559 ERAIPVAIFQAEPEVRKHYLRKWLKDPSDEDLDIRDIIDWDYYIERLGSTIQKIITIPAALQG 621
|
|
| DUF1744 |
pfam08490 |
Domain of unknown function (DUF1744); This domain is found at the C-terminal of the epsilon ... |
1538-1925 |
0e+00 |
|
Domain of unknown function (DUF1744); This domain is found at the C-terminal of the epsilon catalytic subunit of DNA polymerase. It is found C terminal to pfam03104 and pfam00136.
Pssm-ID: 462493 Cd Length: 400 Bit Score: 592.60 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1538 LEKVGPELLPPPKHTFEVRAETDLKTICRAIQRFLLAYKEERRGPTLIAVQSSWELKRLASEIPVLEEFPLVPICVADK- 1616
Cdd:pfam08490 16 LEKWSGAFEYPEDMTFEVTYFTDERKAYKALSRALSKYKEEKSGPTLLVLQSPKDLSYLLSKIPILNEFPVVSIPSNDAd 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1617 INYGVLDWQRHGARRMIRHYLNLDTCLSQAFEMSRYFHIPIGNLPEDISTFGSDLFFARHLQRHNHLLWLSPTARPDLGG 1696
Cdd:pfam08490 96 SSLPALGWQSVVAKRMVNHYLSLGSWLSHLIELARYFDIPLCNLESDDPLFLIDIFYARRLKKNNIVLWWSPSPLPDLGG 175
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1697 KEADDNCLVME-FDDQATVEINSSGCYSTVCVELDLQNLAVNTILQSHHVNDMEGADSMGIsfdvIQQASLEDMITGGQA 1775
Cdd:pfam08490 176 REKDDNPNTLGlMEELDSPEINNPGAYSNVCLELDIRNLAVNTILQSALINELEGSDLSTA----FDAASHTLDEYSKGD 251
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1776 ASAPASYDETALCSNTFRILKSMVVGWVKEITQyHNIYADNQVMHFYRWLRSPSSLLHDPALHRTLHNMMKKLFLQLIAE 1855
Cdd:pfam08490 252 VNSSSTYDEDAFSSAAFRVLRSMVKSWWDDALK-GNVFADLLVDHFVRWVQSPDSLLYDPALHRHVHNLMKKAFLQLLAE 330
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1856 FKRLGSSVIYANFNRIILCTKKRRVEDAIAYVEYITSSIHSKETFHSLTISFSRCWEFLLWMDPSNYGGI 1925
Cdd:pfam08490 331 FKRLGSTVVYADFNRILLQTSKPSVENAYAYSQYIVKAIRSKPLFHFLDLKIVRYWDYLLWMDEANYGGV 400
|
|
| DNA_polB_epsilon_exo |
cd05779 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ... |
268-471 |
1.20e-154 |
|
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique large C-terminal domain with an unknown function. Phylogenetic analyses indicate that it is orthologous to the archaeal DNA polymerase B3 rather than to the eukaryotic alpha, delta, or zeta polymerases. The exonuclease domain of family-B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation
Pssm-ID: 99822 [Multi-domain] Cd Length: 204 Bit Score: 475.60 E-value: 1.20e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 268 DPVVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLITNREIVSEDIEDFEFTPKPEYEGPFCVFNEPDEAHLIQRW 347
Cdd:cd05779 1 DPRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNREIVSEDIEDFEYTPKPEYEGPFKVFNEPDEKALLQRF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 348 FEHVQETKPTIMVTYNGDFFDWPFVEARAAVHGLSMQQEIGFQKDSQGEYKAPQCIHMDCLRWVKRDSYLPVGSHNLKAA 427
Cdd:cd05779 81 FEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQGLKAV 160
|
170 180 190 200
....*....|....*....|....*....|....*....|....
gi 62198237 428 AKAKLGYDPVELDPEDMCRMATEQPQTLATYSVSDAVATYYLYM 471
Cdd:cd05779 161 TKAKLGYDPVELDPEDMVPLAREDPQTLASYSVSDAVATYYLYM 204
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
86-426 |
5.77e-85 |
|
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: 282.38 E-value: 5.77e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 86 FIQDDGSRFKVALPYKPYFYIATRKGCE-REVSSFLSKKFQGKIakveTVPKEDLDLPNHLVGLKRN---YIRLSFHTVE 161
Cdd:pfam03104 1 KTDEGVSVCVNVFGFKPYFYCLAPDGKElEEVIEEIKELYEGLD----KIEKIELKLKKSLYGYEEDpvpYLKVSFANPR 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 162 DLVKVRKEISPAvkknreqdhasdaytallssvlqrggvitdeeetskkiadqldNIVDMREYDVPYHIRLSIDLKIHVA 241
Cdd:pfam03104 77 PLLKIRKYLSPE-------------------------------------------NISDVYEYDVDYLERFLIDNDIVGF 113
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 242 HWYNVRY-------RGNAFPVEITRRDDLVER-------PDPVVLAFDIETTKLPLKFPDAE--TDQIMMISYMIDGQG- 304
Cdd:pfam03104 114 GWYKVKVypfraegRISNCDVEIDCDSPDLISvpfekewPPLRVLSFDIECTSLPGKFPDAEnvKDPIIQISCMLDGQGe 193
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 305 ------YLITNREIVSEDIEDFEFTPKPEYEGPfCVFNEPDEAHLIQRWFEHVQETKPTIMVTYNGDFFDWPFVEARAA- 377
Cdd:pfam03104 194 pepeprFLFTLRECDSEDIEDFEYTPKPIYPGV-KVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKe 272
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 62198237 378 -------------VHGLSMQQEIGFQKDSQGEYKAPQCIHMDCLRWVKRDSYLPvgSHNLKA 426
Cdd:pfam03104 273 lyivklssigrlnRGGRSKVREIGFGTRSYEKVKISGRLHLDLYRVIKRDYKLP--SYKLNA 332
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
267-870 |
2.15e-72 |
|
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: 251.30 E-value: 2.15e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 267 PDPVVLAFDIETTKLPLKFPDAE--TDQIMMISYMIDGQGYLITNReivsedIEDFEFTPKPEYEGPFCVFNEpDEAHLI 344
Cdd:smart00486 1 PPLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANR------RILFTLGTCKEIDGIEVYEFN-NEKELL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 345 QRWFEHVQETKPTIMVTYNGDFFDWPFVEARAAVHGLSMQQEIGFQKDSQG------------------EYKAPQCIHMD 406
Cdd:smart00486 74 LAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGLRipnkkplfgsksfglsdiKVYIKGRLVID 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 407 CLRWVKRDSYLPvgSHNLKAAAKAKLGYDPVELDPEDMCRM---ATEQPQTLATYSVSDAVATYYLYMKY-VHPFIFALC 482
Cdd:smart00486 154 LYRLYKNKLKLP--SYKLDTVAEYLLGKEKDDLPYKDIPELyngNYEERDELLRYCIQDAVLTLKLFNKLnVIPLIIELA 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 483 TIIPMEPDEVLRKGSGTLCEALLMVQAFHANIIFPNKQEQEFNKLTDDGHVLDSetYVGGHVEALESGVFRSDipcrfrm 562
Cdd:smart00486 232 RIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEPDLKKKVK--YEGGKVLEPKKGFYDNP------- 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 563 npaafdfllqrvektlrhaleeeekvpveqvtnfeevcdeiksklaslkdvpsriecplIYHLDVGAMYPNIILTNRLQP 642
Cdd:smart00486 303 -----------------------------------------------------------VLVLDFNSLYPSIIIAHNLCY 323
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 643 SAMVDEATCAACDFNKpgancqrkmawqwrgefmpasrseyhriqhqlesekfpplfpegparafhelsreeqakyekrr 722
Cdd:smart00486 324 STLVGVGEVVIKGDLI---------------------------------------------------------------- 339
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 723 ladyCRKAYKKIHITKVEERLTTICQRENSFYVDTVRAFRDRRYEFKGLHKVWKkklsaavevgdaaevKRCKNMEVLYD 802
Cdd:smart00486 340 ----IPEDLLTIKYEKGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEK---------------DESEELKKLLD 400
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62198237 803 SLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGRP------LELDTDGIWCVLPN 870
Cdd:smart00486 401 SRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGYPkpgfkvIYGDTDSIFVTKPG 474
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
271-471 |
1.11e-57 |
|
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: 198.35 E-value: 1.11e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 271 VLAFDIETTKLPlKFPDAETDQIMMISYMIDGQGYLITNREIVSEDIEDFEFtpkpeyEGPFCVFNEPDEAHLIQRWFEH 350
Cdd:cd05160 1 VLSFDIETTPPV-GGPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDDIEF------IDGIEVEYFADEKELLKRFFDI 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 351 VQETKPTIMVTYNGDFFDWPFVEARAAVHGLS----MQQEIGFQK--DSQGEYKAPQCIHMDCLRWVKRDSYLPvgSHNL 424
Cdd:cd05160 74 IREYDPDILTGYNIDDFDLPYLLKRAEALGIKltdgIYRRSGGEKssGSTERIAVKGRVVFDLLAAYKRDFKLK--SYTL 151
|
170 180 190 200
....*....|....*....|....*....|....*....|....*...
gi 62198237 425 KAAAKAKLGYDPVELDPEDMCR-MATEQPQTLATYSVSDAVATYYLYM 471
Cdd:cd05160 152 DAVAEELLGEGKEKVDGEIIEDaEWEEDPERLIEYNLKDAELTLQILE 199
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
71-1136 |
6.03e-57 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 213.92 E-value: 6.03e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 71 ILD---EDKRLGSAVDYYFIQDDGSRFKVALP-YKPYFYIATRkgcEREVSSFLsKKFQGKIAKVETVPKEDLDlpnhlv 146
Cdd:COG0417 7 LLDrsyRDEDGKPVIELWGRTEDGPSVLLDVTgFRPYFYVPLP---DEEKLEEL-LRDIKEITEVEPVKLKSFF------ 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 147 GLKRNYIRLSFHTVEDLVKVRKEISPAVKknreqdhasDAYtallssvlqrggvitdeeetskkiadqldnivdmrEYDV 226
Cdd:COG0417 77 GEPVPVLKIYTRDPRDVRELRDRLKEGGI---------DVY-----------------------------------EADI 112
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 227 PYHIRLSIDLKIHVAHWYNVRYRGNAFPVEITRRDDLVERPDPV-----VLAFDIETTkLPLKFPDAETD-QIMMISYMi 300
Cdd:COG0417 113 RFHDRYLIDRFLTPGVWYEGEVEEDGGKLDYEVKENPRLKPEDYrpklkVLSFDIEVS-TPRGFPDPERDgPIISIGLA- 190
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 301 DGQGY---LITNREIVSEDIEDFEftpkpeyegpfcvfnepDEAHLIQRWFEHVQETKPTIMVTYNGDFFDWPFVEARAA 377
Cdd:COG0417 191 GSDGEkkvLMLGREGVDFEVEYFD-----------------DEKALLEAFFEIIREYDPDIIIGWNVDNFDLPYLQKRAE 253
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 378 VHGLSM-----QQEIGFQKD-SQGEYKAPQCIHMDCLRWVKRDSY-LPvgSHNLKAAAKAKLGYDPVELDPEDMCRMATE 450
Cdd:COG0417 254 RLGIPLdlgrdGSEPSWREHgGQGFASIPGRVVIDLYDALKSATYkFK--SYSLDAVAEELLGEGKLIVDGGEIERLWDD 331
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 451 QPQTLATYSVSDAVATYYLYMK-YVHPFIFALCTIIPMEPDEVLRKGSGTLCEALLMVQAFHANIIFPNKQEQEfnkltd 529
Cdd:COG0417 332 DKPALAEYNLRDAELTLRIFEKtLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGYLAPNKGEIK------ 405
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 530 dghvldSETYVGGHVeaLES--GVFRsdipcrfrmNPAAFDFllqrvektlrhaleeeekvpveqvtnfeevcdeiKSkl 607
Cdd:COG0417 406 ------GEAYPGGYV--LDPkpGLYE---------NVLVLDF----------------------------------KS-- 432
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 608 aslkdvpsriecpliyhldvgaMYPNIILTNRLQPSAMVDEatcaacdfnkpgancqrkmawqwrgefMPASRSEYHRIq 687
Cdd:COG0417 433 ----------------------LYPSIIRTFNISPETLVEG---------------------------GEEPCGDEDVA- 462
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 688 hqlesekfpplfPEGPARafhelsreeqakyekrrladYCRkayKKIHITKveerltTIcqrensfyVDTVRAFRDRrye 767
Cdd:COG0417 463 ------------PGFGHR--------------------FCR---EPKGILP------SI--------LEELWDERDE--- 490
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 768 fkglhkvWKKKLsaavevgdaAEVKRCKNMEVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQAR 847
Cdd:COG0417 491 -------AKKKM---------KKAKPDSEEYRLYDALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGREIIKQTI 554
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 848 ELIEQIG-RPLELDTDGiwcvlpnsfpenfVFkttnVKKPKVTisypgamlnimvkEGFTNDQYQELAEpssltYVTRSE 926
Cdd:COG0417 555 EKAEELGyKVIYGDTDS-------------LF----VWLPKAS-------------LEEAIEIGKELAE-----EINAWW 599
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 927 NSIF-FEVDGPYLAMILPASkeegkklKKRYAVFNEDGSLaELKGFEVKRRGELQLIKIFQSSVFEAFLKGSTLEEVygs 1005
Cdd:COG0417 600 PSGLeLEFEKHYRRFFFPGS-------KKRYAGLTEDGKI-DIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKA--- 668
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1006 VAKVADYWLDVlysKAANMPDSELfeLISenRSMSRKLEDYgeQKSTS--ISTAKRLAEFLGDQMVKDaglSCRYIISRK 1083
Cdd:COG0417 669 VEYVRDVIEKL---RAGEVDLDDL--VIR--KRLRKPLSEY--EKNVPphVRAARKLDERGRPYQRGD---KISYVITKG 736
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|...
gi 62198237 1084 pegspvTERAIPLaifqaeptvrkhFLRKWLKSSslqdfdiraiLDWDYYIER 1136
Cdd:COG0417 737 ------GGRVEPV------------ELAKERESE----------IDYDYYIEK 761
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
614-1147 |
1.11e-48 |
|
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: 177.18 E-value: 1.11e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 614 PSRIECPLIYHLDVGAMYPNIILTNRLQPSAMVDEATCAACDFNKPgancqrkmawqwrgefmpasrseyhriQHQLESE 693
Cdd:cd00145 11 PIPGLYENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYIG---------------------------VGFRSPK 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 694 KFPPLFPEgparafhelsreeqakyekrrladycrkaykkihitkveerltticqrensfYVDTVRAFRDRRYEFKGLHK 773
Cdd:cd00145 64 DRKGLLPR----------------------------------------------------ILEELLNFRDEAKKRMKAAK 91
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 774 vwkkklsaavevgdaaevkRCKNMEVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQI 853
Cdd:cd00145 92 -------------------LAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEH 152
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 854 G-RPLELDTDGIWCVLPNSFPENFVFKttnvkkpkvtisypgamlnimvkegFTNDQYQELAepssltyvtrSENSIFFE 932
Cdd:cd00145 153 GaRVIYGDTDSIFVSLPKMGTKEDAIK-------------------------EGREILQELA----------DEHLLELE 197
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 933 VDGPYLAMILPAskeegkklKKRYAVFNE----DGSLAELKGFEVKRRGELQLIKIFQSSVFEAFLK-GSTLEEVYGSVA 1007
Cdd:cd00145 198 FEKVYLPFFLGK--------KKRYAGLDIwkgqDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEeERKVEAVKEYID 269
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1008 KVadywldvlyskaanmpdselfelisenrsmsrkledygeqkstsistakrlaeflgdQMVKdaglscrYIISRKPEGS 1087
Cdd:cd00145 270 EL---------------------------------------------------------DKVK-------YVVTRGGKGV 285
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1088 PVTERAIPlaifqaeptvrkhflrkwlkssSLQDFDIRAILDWDYYIERLGSAIQKIITI 1147
Cdd:cd00145 286 PDYERADP----------------------PLEDLDKRHRIDYEYYLERLLQPPLERIFE 323
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
267-469 |
2.78e-20 |
|
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: 90.88 E-value: 2.78e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 267 PDPVVLAFDIETtKLPLKFPDAETDQIMMISYMIDGQGYLITNREIVSEDIEDFEftpkpeyegpfcvfnepDEAHLIQR 346
Cdd:cd05780 1 EDLKILSFDIEV-LNHEGEPNPEKDPIIMISFADEGGNKVITWKKFDLPFVEVVK-----------------TEKEMIKR 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 347 WFEHVQETKPTIMVTYNGDFFDWPFVEARAAVHGLSM-----QQEIGFQKDSqGEYKA--PQCIHMDCLRWVKRdsYLPV 419
Cdd:cd05780 63 FIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELdlgrdGSEIKIQRGG-FNNASeiKGRIHVDLYPVARR--TLNL 139
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 62198237 420 GSHNLKAAAKAKLGYDPVELDPEDMCRM--ATEQPQTLATYSVSDAVATYYL 469
Cdd:cd05780 140 TRYTLERVYEELFGIEKEDVPGEEIAEAwdSGENLERLFRYSMEDAKYTYEI 191
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
800-1151 |
3.73e-19 |
|
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.
Pssm-ID: 99919 Cd Length: 371 Bit Score: 92.00 E-value: 3.73e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 800 LYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIG-RPLELDTDGIwcvlpnsfpenFVf 878
Cdd:cd05536 99 LLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAEEKGfKVIYGDTDSL-----------FV- 166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 879 kttnvkkpkvtiSYPGAMLNIMVKEGFTNDQYQELaepssltyvtrsenSIFFEVDGPYLAMILPAskeegkklKKRYAV 958
Cdd:cd05536 167 ------------KIDGADAVKKKVKKLLKYINEEL--------------PLELEIEKFYKRGFFVT--------KKRYAG 212
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 959 FNEDGSLaELKGFEVKRRGELQLIKIFQSSVFEAFLKgstleevYGSVAKVADYWLDVLYS-KAANMPDSELfeLISEnr 1037
Cdd:cd05536 213 LTEDGKI-DVVGLEVVRRDWSEIAKETQARVLEAILK-------EGDVEEAVKIVKEVIEKlKRGEVPPEKL--VIWK-- 280
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1038 SMSRKLEDYgEQKSTSISTAKRLAEfLGDQMVKdaGLSCRYIISRKPegSPVTERAIPLAIFQAEPTVrkhflrkwlkss 1117
Cdd:cd05536 281 QLTKDLSEY-KATGPHVAAAKKLAK-RGYKVRP--GTKIGYVIVKGS--GKISDRAYPYDMVDEKHKY------------ 342
|
330 340 350
....*....|....*....|....*....|....
gi 62198237 1118 slqdfdirailDWDYYIERlgsaiQkiiTIPAAL 1151
Cdd:cd05536 343 -----------DAEYYIDN-----Q---VLPAVL 357
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
714-1135 |
2.85e-15 |
|
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA polymerases.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273159 [Multi-domain] Cd Length: 1172 Bit Score: 82.41 E-value: 2.85e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 714 EQAKYEKRRLADYCRKAYKKIhITKVEERLTTICQRENsfyVDTVRAFRDRRYEFKGLHKVWKKKLSAAVEVGDAAEVKR 793
Cdd:TIGR00592 805 KVGLYDKYVLLMDFNSLYPSI-IQEFNICFTTVQQKVD---EDELPELPDSELEMGILPRELRKLVERRKEVKKLMKQDL 880
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 794 CKNMEVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGrpLEL---DTDGIWCVLPN 870
Cdd:TIGR00592 881 NPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEMN--LEViygDTDSIMINTPG 958
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 871 SFPENfVFKTTNVKKPKVTISYPgaMLNImvkegftndqyqelaepssltyvtrsensiffEVDGPYLAMILPAskeegk 950
Cdd:TIGR00592 959 TKYEE-VFKIGKEFKSEVNKLYK--LLEL--------------------------------DIDGVFKRLLLLK------ 997
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 951 klKKRYAVFNEDGSLA-------ELKGFEVKRRGELQLIKIFQSSVFEAFLKGSTLEEVygsVAKVADYWLDVLYSKAAN 1023
Cdd:TIGR00592 998 --KKKYAAIKVEGDSDgnyttkqEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEA---VEEVQEVLEKIGKNVLNG 1072
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1024 MPDSELFELiseNRSMSRKLEDYGEQKS-TSISTAKRLAEfLGDQMVKdAGLSCRYIISRkpEGSPVTERAiplAIFQAE 1102
Cdd:TIGR00592 1073 EVPLEKFVI---NKQLTRDPKDYPDGASlPHVHVALRINA-RGGRKVK-AGDVVSYVICK--DGGNLSARQ---RAYALE 1142
|
410 420 430
....*....|....*....|....*....|...
gi 62198237 1103 PTVRKHflrKWLkssslqdfdiraILDWDYYIE 1135
Cdd:TIGR00592 1143 ELQRKH---NNL------------IYDTQYYLE 1160
|
|
| YprB |
COG3359 |
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function ... |
261-472 |
1.46e-10 |
|
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function prediction only];
Pssm-ID: 442587 [Multi-domain] Cd Length: 198 Bit Score: 62.66 E-value: 1.46e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 261 DDLVERPDPVVlaFDIETTKLplkfpDAETDQIMMISYMIDGQGYLITnREIVSEDIEDfeftpkpeyegpfcvfnepdE 340
Cdd:COG3359 9 AELLPSEDLLF--FDIETTGL-----SGGGTVIFLIGLADGEGDGFVV-RQYFGEDPGE--------------------E 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 341 AHLIQRWFEHVQETKptIMVTYNGDFFDWPFVEARAAVHGLsmqqeigfqkdsqgEYKAPQCIHMDCLRWVKRDSYLPVG 420
Cdd:COG3359 61 AALLEAFLEWLADYK--LLVTYNGKSFDLPFLKTRFTLHRL--------------PPPLPEFPHLDLLHPARRLWKNRLP 124
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 62198237 421 SHNLKAAAKaKLGYDPVEldpedmcrmateqpqtlaTYSVSDAVATYYLYMK 472
Cdd:COG3359 125 SGGLKTVEE-LLGIERED------------------DLPGYEAPRLYRRYLR 157
|
|
| DNA_polB_like1_exo |
cd05782 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
271-472 |
1.58e-10 |
|
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Pssm-ID: 99825 [Multi-domain] Cd Length: 208 Bit Score: 63.03 E-value: 1.58e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 271 VLAFDIETTklplkfPDAETDQIMMISYMIDGQGYLITNREIVSEDIEDfEFTPKP-------------EYEGPFCVFNE 337
Cdd:cd05782 1 ILVFDIETV------PDVDLGRRLYLLLELDDLEVLEKRFAQRLEKSGS-DFLPLPfhkvvsisalyrdDDGGFLKVRTL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 338 P--DEAHLIQRWFEHVQETKPTiMVTYNGDFFDWPFVEARAAVHGLSM--QQEIGfqkDSQGEYKAPQCI-HMDCLRWVK 412
Cdd:cd05782 74 DgaDEKELLEDFFQLIEKKNPR-LVSFNGRGFDLPVLHLRALIHGVSApaYFDLG---NKDWNYRNRYSErHLDLMDLLA 149
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62198237 413 rdSYLPVGSHNLKAAAKAkLGYdPVELDPE-----DMcrMATEQPQTLATYSVSDAVATYYLYMK 472
Cdd:cd05782 150 --FYGARARASLDLLAKL-LGI-PGKMDVDgsqvwEL--YAEGKLDEIAEYCETDVLNTYLLYLR 208
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
801-1096 |
7.55e-09 |
|
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: 60.28 E-value: 7.55e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 801 YDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGrpLEL---DTDGIWcVLPNSFPENFV 877
Cdd:cd05532 103 LDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKMN--LEViygDTDSIM-INTGTTDYEEA 179
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 878 FKTTNVKKPKVtisypgamlnimvkegftNDQYQELaepssltyvtrsENsiffEVDGPYLAMILPAskeegkklKKRYA 957
Cdd:cd05532 180 KKLGNKIKKEV------------------NKSYKKL------------EI----DIDGVFKRLLLLK--------KKKYA 217
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 958 ----VFNEDGSLA-ELKGFEVKRRGELQLIKIFQSSVFEAFLKGSTLEEVygsVAKVADYWLDVLYSKAANMPDSELFEL 1032
Cdd:cd05532 218 alkvVDDDKGKLKkEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDI---VENIHEYLRKINEDLRNGKIPLEKFII 294
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1033 iseNRSMSRKLEDYGEQKST-SISTAKRL----AEFL-GDQMvkdaglscRYIISRKPEGSPVTERAIPL 1096
Cdd:cd05532 295 ---TKQLTKNPEEYPDKKSLpHVQVALRMnkrgRKVKaGDTI--------PYIICKDGSSKSLADRAYHP 353
|
|
| DNA_polB_B1_exo |
cd05783 |
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ... |
267-471 |
8.59e-09 |
|
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are unique in that they are able to recognize the presence of uracil in the template strand, leading to the stalling of DNA synthesis. This is an additional safeguard mechanism against increased levels of deaminated bases during genome duplication at high temperatures. S. solfataricus B1 also interacts with DNA polymerase Y and may contribute to genome stability mechanisms.
Pssm-ID: 99826 [Multi-domain] Cd Length: 204 Bit Score: 57.71 E-value: 8.59e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 267 PDPVVLAFDIET-TKLPLKFPDAETDQIMMISY-MIDGQGYlitnREIVSEDIEDFEFTPKPEYEGPFCVFNEpDEAHLI 344
Cdd:cd05783 3 PKLKRIAIDIEVyTPIKGRIPDPKTAEYPVISVaLAGSDGL----KRVLVLKREGVEGLEGLLPEGAEVEFFD-SEKELI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 345 QRWFEHVQETkPtIMVTYNGDFFDWPFVEARAAVHGLSMQQE-IGFQKDSqGEYKAPqcIHMDCLRWVKRDS---YLPVG 420
Cdd:cd05783 78 REAFKIISEY-P-IVLTFNGDNFDLPYLYNRALKLGIPKEEIpIYLKRDY-ATLKHG--IHIDLYKFFSNRAiqvYAFGN 152
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 62198237 421 SH---NLKAAAKAKLGYDPVELDPEDmCRMATEQpqtLATYSVSDAVATYYLYM 471
Cdd:cd05783 153 KYreyTLDAVAKALLGEGKVELEKNI-SELNLYE---LAEYNYRDAELTLELTT 202
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
790-1136 |
1.85e-08 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 59.87 E-value: 1.85e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 790 EVKRCKNMEvlydsLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGrpLEL---DTDGIwc 866
Cdd:PRK05762 480 EAKREMNKP-----LSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQG--YQViygDTDST-- 550
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 867 vlpnsfpenFVfkTTNVKKPKVTISYPGAMLNIMVKEGFTNDQYQELAEPSSLTyvtrsensIFFEVDgpYLAMILPASK 946
Cdd:PRK05762 551 ---------FV--WLGGAHDEEDAAKIGRALVQEINQWWQEHLQQEFGLESALE--------LEFEKH--YRRFFMPTIR 609
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 947 EEGKKLKKRYA--VFNEDGSLaEL--KGFEVKRRGELQLIKIFQSSVFEAFLKGStleevygsvaKVADYWLDVLYS-KA 1021
Cdd:PRK05762 610 GAEEGSKKRYAglIQEGDGDG-RIvfKGLETVRTDWTPLAKEFQQELYERIFRGE----------PYVDYVREVIDKlRA 678
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1022 ANMPDselfELISENRsMSRKLEDYgeQKSTS--ISTAKRLAEFLGDQMVKDA---GLSCRYIISRK-PEgsPVTERAIP 1095
Cdd:PRK05762 679 GELDE----KLVYRKR-LRRPLDEY--QRNVPphVRAARLADEMGYKVGRPLQyqnGGKIGYVITVNgPE--PLEYRKSP 749
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 62198237 1096 laifqaeptvrkhflrkwlkssslqdfdiraiLDWDYYIER 1136
Cdd:PRK05762 750 --------------------------------IDYDYYIEK 758
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
789-1046 |
1.06e-07 |
|
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: 56.85 E-value: 1.06e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 789 AEVKRCKN--MEVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGRP-LEL---DTD 862
Cdd:pfam00136 137 KLLKEETDpfERAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYnFRViygDTD 216
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 863 GIwcvlpnsfpenFV-FKTTNVKKpkvtisypgamlniMVKEGFtndqyqELAEpssltYVTRS--ENSIFFEVDGPYLA 939
Cdd:pfam00136 217 SV-----------FIeFGGKDVEE--------------AMKIGD------ELAE-----HVNQDlfKSPIKLEFEKVYKP 260
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 940 MILPAskeegkklKKRYA----VFNEDGSLAELKGFEVKRRGELQLIKIFQSSVFEAFLKGSTLEEVygsVAKVADYWLD 1015
Cdd:pfam00136 261 LLLIS--------KKKYAglkyTAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSDRGLPVG---LEFVISILND 329
|
250 260 270
....*....|....*....|....*....|.
gi 62198237 1016 VLYSKAANMPDSELFELiseNRSMSRKLEDY 1046
Cdd:pfam00136 330 ARSDLRNNKVPLEKFVI---SKELSKPPDNY 357
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
267-381 |
1.87e-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: 1.87e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 267 PDPVVLAFDIETTKlPLKFPDAETDQIMMISYMIDGqGYLitnREIVSEDIedfeftpkpeyegpfcvfnepDEAHLIQR 346
Cdd:cd05781 1 PDLKTLAFDIEVYS-KYGTPNPRRDPIIVISLATSN-GDV---EFILAEGL---------------------DDRKIIRE 54
|
90 100 110
....*....|....*....|....*....|....*
gi 62198237 347 WFEHVQETKPTIMVTYNGDFFDWPFVEARAAVHGL 381
Cdd:cd05781 55 FVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGV 89
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
271-394 |
2.16e-06 |
|
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: 51.04 E-value: 2.16e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 271 VLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGylitnreiVSEDIEDFEFTPKPeyegpfC-------VFNEPDEAHL 343
Cdd:cd05777 9 ILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQG--------EGEPFIRNIFTLKT------CapivgaqVFSFETEEEL 74
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 62198237 344 IQRWFEHVQETKPTIMVTYNGDFFDWPFVEARAAVHGLSMQQEIGFQKDSQ 394
Cdd:cd05777 75 LLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIK 125
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
771-1017 |
2.25e-06 |
|
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: 52.10 E-value: 2.25e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 771 LHKVWKKKLSAAVEVGDAAEVKRcknmEVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANII-TQAREL 849
Cdd:cd05538 51 LKYLVELRLAAKESARAAARPAE----RDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLkLMIRWL 126
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 850 IEQIGRPLELDTDGIWCVLPNSFPenfvfkttnvkkpkvtisypgamlnimvkegfTNDQYQEL-AEPSSLTyvtrsENS 928
Cdd:cd05538 127 RRRGATPVEVDTDGIYFIPPNGVD--------------------------------TEDEEEELvRELSSTL-----PKG 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 929 IFFEVDGPYLAMILpaskeegkKLKKRYAVFNEDGSLAeLKGFEVKRRGELQLIKIFQSSVFEAFLKgstleevyGSVAK 1008
Cdd:cd05538 170 ITVEFDGRYRAMFS--------YKIKNYALLDYDGKLI-VKGSAFRSRGIEPFLREFLREAVRLLLQ--------GDGAG 232
|
....*....
gi 62198237 1009 VADYWLDVL 1017
Cdd:cd05538 233 VHDLYEDYL 241
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
272-466 |
5.34e-06 |
|
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Pssm-ID: 99828 [Multi-domain] Cd Length: 207 Bit Score: 49.72 E-value: 5.34e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 272 LAFDIETTKLPLKF---PDAETDQIMMISyMIDGQGYLITnreIVSEDIedfeftpkpeyegpfcvfnepDEAHLIQRWF 348
Cdd:cd05785 12 LQLDIETYSLPGFFfsnPDRGDDRIIIVA-LRDNRGWEEV---LHAEDA---------------------AEKELLEELV 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 349 EHVQETKPTIMVTYNGDFFDWPFVEARAAVHGLSMQqeIGfqKDSQGEYKAPQCIH-----MDCLRWV--KR---DSYLP 418
Cdd:cd05785 67 AIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGVPLA--IG--RDGSIPRQRPSRFRfaerlIDYPRYDipGRhviDTYFL 142
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 419 V----------GSHNLKAAAK--AKLGYDPVELDPEDMCRMATEQPQTLATYSVSDAVAT 466
Cdd:cd05785 143 VqlfdvssrdlPSYGLKAVAKhfGLASPDRTYIDGRQIAEVWRSDPARLLAYALDDVRET 202
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
804-1096 |
1.97e-05 |
|
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: 49.19 E-value: 1.97e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 804 LQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGRP-LELDTDGIWCVLPNSFPENfvfkttn 882
Cdd:cd05537 92 LSQAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQvIYGDTDSTFVWLGEELDAA------- 164
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 883 vkkpkvTISYPGAMLnimvkEGFTNDQYQE-LAEpsslTYVTRSENSIFFEVDgpYLAMILPA--SKEEGKklKKRYA-- 957
Cdd:cd05537 165 ------EAQAIGKEL-----ASQINQWWAQkLKE----EFGLESFLEIEFETH--YSRFFMPTirGSDEGS--KKRYAgl 225
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 958 VFNEDGSLAELKGFEVKRRGELQLIKIFQSSVFEAFLKGSTLEEVygsvakVADYwLDVLYskaANMPDSelfELISENR 1037
Cdd:cd05537 226 KSTDGGDELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGF------IKET-VEELL---AGELDE---LLVYRKR 292
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 1038 sMSRKLEDYGEQKSTSISTAKRLAEFLGDQMVKDAGLSCRYIISRK-PEgsPVTERAIPL 1096
Cdd:cd05537 293 -LRRPLSEYTKNVPPHVQAARLADQINRELGRPRQYQWIEYVITVNgPE--PLEYRTSPL 349
|
|
| RNase_H_2 |
pfam13482 |
RNase_H superfamily; |
272-435 |
6.85e-05 |
|
RNase_H superfamily;
Pssm-ID: 433246 [Multi-domain] Cd Length: 163 Bit Score: 45.28 E-value: 6.85e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 272 LAFDIETTKLplkFPDAETDqimmisYMIdgqGYLITNREivseDIEDFEFTPKPEyegpfcvfnePDEAHLIQRWFEHV 351
Cdd:pfam13482 1 LFFDIETTGL---SPGKNTI------YLI---GVYDVDGD----KVRTFVQYLAEG----------PTEEAAILQLFELL 54
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 352 QetKPTIMVTYNGDFFDWPFVEARAAVHGLSMQQeigfqkdsqgeykapqcIHMDCLRWVKRDSYlpvgSHNLKAAAKaK 431
Cdd:pfam13482 55 A--DYPLLVTFNGKSFDVPFIKRRFKRYDLDELF-----------------RHIDLLHPLRKLGL----ESGLKSVER-E 110
|
....
gi 62198237 432 LGYD 435
Cdd:pfam13482 111 LGIE 114
|
|
| DNA_pol_B_exo2 |
pfam10108 |
Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; This domain is found in ... |
335-475 |
7.83e-05 |
|
Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; This domain is found in various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Pssm-ID: 462958 [Multi-domain] Cd Length: 210 Bit Score: 46.07 E-value: 7.83e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 335 FNEPD--EAHLIQRWFEHVQETKPTImVTYNGDFFDWPFVEARAAVHGLS------MQQEIGFQKDSQGEYKAPQCIHMD 406
Cdd:pfam10108 30 LGEPEdsEKELIQRFFDGVEKYTPQL-VSFNGRGFDLPVLHYRALKHGVSaprywdTGDGDFKWNNYFNRYHTRHLDLMD 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 407 CLrwvkrdsylpvGSHNLKAAAK-----------AKLGydpveLDPEDMCRM-ATEQPQTLATYSVSDAVATYYLYMKYV 474
Cdd:pfam10108 109 LL-----------AGYGGRANAPldevakllgfpGKMG-----MDGSKVWELyQAGRLDEIRDYCETDVLNTYLVYLRFQ 172
|
.
gi 62198237 475 H 475
Cdd:pfam10108 173 L 173
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
271-378 |
3.10e-04 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 46.17 E-value: 3.10e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 271 VLAFDIETTKLP-LKFPDAETDQIMMISYMIDGQGYLItnreivsEDIEDFEFTPKPEYEGPFC-VFNEPDEAHLIQRWF 348
Cdd:PTZ00166 266 ILSFDIECIKLKgLGFPEAENDPVIQISSVVTNQGDEE-------EPLTKFIFTLKECASIAGAnVLSFETEKELLLAWA 338
|
90 100 110
....*....|....*....|....*....|
gi 62198237 349 EHVQETKPTIMVTYNGDFFDWPFVEARAAV 378
Cdd:PTZ00166 339 EFVIAVDPDFLTGYNIINFDLPYLLNRAKA 368
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
310-1063 |
3.06e-03 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 42.75 E-value: 3.06e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 310 REIVSEDIEDFEF-TPKP-------EYEGPFC-VFNEPDEAHLIQRWFEHVQETKPtiMVTYNGDFFDWPFVEARAAVHG 380
Cdd:PRK05761 171 RKLAEDWLPIFEApIPKIkriaidiEVYTPAKgRIPDDSEKELLAELFDIILEYPP--VVTFNGDNFDLPYLYNRALKLG 248
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 381 LSmQQEIGFQKDSQGEykapqciHMDCLRW---VKRDSYLPVG--SH---NLKAAAKAKLGYDPVELDPEDMCRMATEqp 452
Cdd:PRK05761 249 IP-KEEIPIEPGRAGI-------HIDLYKFfqnKAVRSYAFYGkyRHreaRLDAVGRALLGISKVELETNISELDLEE-- 318
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 453 qtLATYSVSDAVATYYLYMKY---VHPFIFALCTIIPMEPDEVLRKGSGTLCEALLMVQAFHANIIFPNKQEQEfnkltd 529
Cdd:PRK05761 319 --LAEYNFRDAEITLKLTFFNnelVLKLILLLSRISKLPIEELSRATISTWISNLEYWEHRKRGWLIPWKEDIL------ 390
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 530 dghVLDSET----------YVGGHVEALESGVFrsdipcrfrmnpaaFDfllqrvektlrhaleeeekvpveqvtnfeev 599
Cdd:PRK05761 391 ---RLDHEVykkaiikgkkYRGGLVFQPPPGIF--------------FN------------------------------- 422
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 600 cdeiksklaslkdvpsriecplIYHLDVGAMYPNIILTnrlqpsamvdeatcaacdfnkpgancqrkmawqwrgefmpas 679
Cdd:PRK05761 423 ----------------------VYVLDFASLYPSIIVK------------------------------------------ 438
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 680 rseyhriqhqlesekfpplfpegparafHELSreeqakYEKRRlADYCRKAYkkihITKVEERLTTICQRENSF---YVD 756
Cdd:PRK05761 439 ----------------------------WNLS------PETVR-IPECKCHY----DDEVPELGHSVCDDRPGLtsvLVG 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 757 TVRAFRDRRYefkglhkvwKKKlsaavevgdAAEVKRCKNMEVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVC 836
Cdd:PRK05761 480 LLRDFRVKIY---------KKK---------AKDPNLDEERRAWYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESIT 541
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 837 FTGANIITQARELIEQIG-RPLELDTDGIWcvlpnsfpenfvfkttnvkkpkVTisypgamlnimvkeGFTNDQYQELAE 915
Cdd:PRK05761 542 ALGREILLSTKKKAEELGlKVLYGDTDSLF----------------------VW--------------GPTKESLEELIK 585
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 916 pssltYVTRsENSIFFEVDGPYLAMILpaskeegKKLKKRYAVFNEDGSLaELKGFEVKRRGELQLIKIFQSSVFEAFLK 995
Cdd:PRK05761 586 -----EIEE-RTGIDLEVDKTYDWVAF-------SGLKKNYFGVLKDGKV-KIKGIVAKKRNTPEFVKELQREVLEVLKS 651
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 996 GSTLEEVYGSVAKVADYwLDVLYSK--AANMPDSELfeliSENRSMSRKLEDYGEQKSTSISTAKRLAEF 1063
Cdd:PRK05761 652 IRSPEDVEKVKDEIEDV-LKRYYEKlrAKDYPLDEL----AIRVRLSKPLDEYTKNTPQHVKAALQLRDY 716
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
728-832 |
5.93e-03 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 41.98 E-value: 5.93e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62198237 728 RKAYKKIHITkvEERLTTICQRENSFYVDTVRAFRD--RRYEFKGLHKVWKKKLSAAVEvgdAAEVKRCKNMEVLYDSLQ 805
Cdd:PHA02528 468 RKIYKKKMLA--AERNAELIKTILEDLNDSVDTPIDvdYYFDFSDEFKAELKTLTKSSL---KALLEECEKEIALCNTIQ 542
|
90 100
....*....|....*....|....*..
gi 62198237 806 LAHKCILNSFYGYVMRKGARWYSMEMA 832
Cdd:PHA02528 543 MARKILINSLYGALGNEHFRYYDLRNA 569
|
|
| |
