|
Name |
Accession |
Description |
Interval |
E-value |
| POLBc_epsilon |
cd05535 |
DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
525-1147 |
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: 1335.39 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 525 GHVLDSETYVGGHVEALESGVFRSDIPCRFKMNPAAFDYLVQNVEKTLRHAIEEEERLPLDQVTNFQEVCDEIKVKLNSL 604
Cdd:cd05535 1 GHLLESETYVGGHVEALESGVFRSDIPCRFKLDPDAIQELLQNVDETLRFAIEVEGKIPLDQVENFEEVREEILEKLQSL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 605 KDVPNRIECPLIYHLDVGAMYPNIILTNRLQPSAMVDEATCAACDFNKPGANCQRRMTWQWRGEFMPASRSEYHRIQQQL 684
Cdd:cd05535 81 RDNPKRSEKPLIYHLDVAAMYPNIILTNRLQPDAIVDEDVCAACDFNKPGKTCQRRMEWAWRGEYFPASRGEYERIKQQL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 685 ESEKFPPLYPDGAPRAFHELSREEQAKYEKKRLADYCRKAYKKIHVTKVEERVTTICQRENSFYVDTVRAFRDRRYEFKG 764
Cdd:cd05535 161 ESEKFPPLFPGGPPKSFHELSPEEQAEELKKRLKDYSRKVYKKTHVTKEEERSTTICQRENPFYVDTVRAFRDRRYEYKG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 765 LHKVWKKKLSAAMETGDASEVKRCKNMEILYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELI 844
Cdd:cd05535 241 LHKVWKKKLEAAKAAGDAAEIKEAKKMVVLYDSLQLAHKCILNSFYGYVMRKGSRWYSMEMAGIVCYTGANIIQMARELV 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 845 EQIGRPLELDTDGIWCVLPNSFPENFVIKSTNakKPKVTISYPGAMLNILVKEGFTNDQYQELQDPASLTYVTRSENSIF 924
Cdd:cd05535 321 EQIGRPLELDTDGIWCILPKSFPENFTFKTKN--GKKVTISYPCVMLNHLVHKKFTNDQYQELVDPSTGTYETRSENSIF 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 925 FEVDGPYLAMILPASKEEGKKLKKRYAVFNEDGSLAELKGFEVKRRGELQLVKIFQSSVFEAFLKGTTLEEVYASVAKVA 1004
Cdd:cd05535 399 FEVDGPYKAMILPASKEEGKLLKKRYAVFNEDGSLAELKGFEVKRRGELQLIKIFQSEVFDAFLKGSTLEECYAAVAAVA 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1005 DYWLDVLYSKAANMPDSELFELISENRSMSRKLEDYGEQKSTSISTAKRLAEFLGDQMVKDAGLSCRFIISKKPEGSPVT 1084
Cdd:cd05535 479 NYWLDVLDSKGENLDDEELFELISENRSMSKKLEEYGNQKSTSITTAKRLAEFLGDQMVKDKGLSCKYIISKKPEGSPVT 558
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2024358764 1085 ERAIPLAIFQAEPSVRKHYLRKWLKSPSLQDFNIRAILDWDYYIERLGSTIQKIITIPAALQQ 1147
Cdd:cd05535 559 ERAIPVAIFQAEPEVRKHYLRKWLKDPSDEDLDIRDIIDWDYYIERLGSTIQKIITIPAALQG 621
|
|
| DUF1744 |
pfam08490 |
Domain of unknown function (DUF1744); This domain is found at the C-terminal of the epsilon ... |
1522-1921 |
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: 599.15 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1522 LTTMFSAERSALLERVGEE---LLPPDKHTFEVRAETDPKAICRAIQRLLLGYKDERRGPTLIAVQSNWELKRLASGIPI 1598
Cdd:pfam08490 1 LEKLYKELRAKKLDKLEKWsgaFEYPEDMTFEVTYFTDERKAYKALSRALSKYKEEKSGPTLLVLQSPKDLSYLLSKIPI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1599 LDEFPLVPIRVTD-DISYSVLDWQRHAARRMIRHYLNLDTCLSQAFEMSRYYHIPIGNLPDDISTFGSDLFFSRHLRRHN 1677
Cdd:pfam08490 81 LNEFPVVSIPSNDaDSSLPALGWQSVVAKRMVNHYLSLGSWLSHLIELARYFDIPLCNLESDDPLFLIDIFYARRLKKNN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1678 HLLWLSPTARPDLGGKEADDNRLVMEFDERA-SVEINNPGCYSTVCLELDIQSLAVNTVLQSHHVNDMEGcSSMSISFDV 1756
Cdd:pfam08490 161 IVLWWSPSPLPDLGGREKDDNPNTLGLMEELdSPEINNPGAYSNVCLELDIRNLAVNTILQSALINELEG-SDLSTAFDA 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1757 iqqASLEDMVTGNQAANIPASYDETALCSNTFRILKSMVVSWVKEITQyHNIYADNQVIHFYRWLRSPSSLLYDPALHRT 1836
Cdd:pfam08490 240 ---ASHTLDEYSKGDVNSSSTYDEDAFSSAAFRVLRSMVKSWWDDALK-GNVFADLLVDHFVRWVQSPDSLLYDPALHRH 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1837 LHNMMKKLFLQLVAEFRRLGSSVVYANFNRIILCTKKRRIEDAISYMEYIINSIHSKEIFHSLTISFSRCWEFLLWMDPA 1916
Cdd:pfam08490 316 VHNLMKKAFLQLLAEFKRLGSTVVYADFNRILLQTSKPSVENAYAYSQYIVKAIRSKPLFHFLDLKIVRYWDYLLWMDEA 395
|
....*
gi 2024358764 1917 NYGGI 1921
Cdd:pfam08490 396 NYGGV 400
|
|
| DNA_polB_epsilon_exo |
cd05779 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ... |
262-465 |
3.14e-151 |
|
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: 465.97 E-value: 3.14e-151
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 262 DPVVLAFDIETTKLPLKFPDPETDQIMMISYMIDGQGYLITNREIVSEDIEDFEFTPKPEYEGPFCVFNEPDESHLIQRW 341
Cdd:cd05779 1 DPRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNREIVSEDIEDFEYTPKPEYEGPFKVFNEPDEKALLQRF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 342 FEHVQETKPTIIVTYNGDFFDWPFVEARAAAHGINMYQEIGFQKDSQGEYKASQCIHMDCLRWVKRDSYLPVGSHNLKAA 421
Cdd:cd05779 81 FEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQGLKAV 160
|
170 180 190 200
....*....|....*....|....*....|....*....|....
gi 2024358764 422 AKAKLGYDPVELDPEEMCRMATEEPQTLATYSVSDAVATYYMYM 465
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 ... |
80-420 |
1.17e-84 |
|
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: 281.23 E-value: 1.17e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 80 FIQEDGSRFKVALPYRPYFYVATQQGCE-REVSSFLAKKFQGKIakleTVPKEDLDLPNHLVGLKRH---YLKLSFSTVD 155
Cdd:pfam03104 1 KTDEGVSVCVNVFGFKPYFYCLAPDGKElEEVIEEIKELYEGLD----KIEKIELKLKKSLYGYEEDpvpYLKVSFANPR 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 156 ELVKVRKEISPAvrknrerdqandvytsmlssalaggslttseegaskkvtnqmdNIVDMREYDVPYHMRLSIDLKIHVA 235
Cdd:pfam03104 77 PLLKIRKYLSPE-------------------------------------------NISDVYEYDVDYLERFLIDNDIVGF 113
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 236 HWYNVRY-------RGSTFPPEITRRDDLVER-------PDPVVLAFDIETTKLPLKFPDPE--TDQIMMISYMIDGQG- 298
Cdd:pfam03104 114 GWYKVKVypfraegRISNCDVEIDCDSPDLISvpfekewPPLRVLSFDIECTSLPGKFPDAEnvKDPIIQISCMLDGQGe 193
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 299 ------YLITNREIVSEDIEDFEFTPKPEYEGPfCVFNEPDESHLIQRWFEHVQETKPTIIVTYNGDFFDWPFVEARAAA 372
Cdd:pfam03104 194 pepeprFLFTLRECDSEDIEDFEYTPKPIYPGV-KVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKE 272
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2024358764 373 --------------HGINMYQEIGFQKDSQGEYKASQCIHMDCLRWVKRDSYLPvgSHNLKA 420
Cdd:pfam03104 273 lyivklssigrlnrGGRSKVREIGFGTRSYEKVKISGRLHLDLYRVIKRDYKLP--SYKLNA 332
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
261-864 |
1.06e-71 |
|
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: 249.37 E-value: 1.06e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 261 PDPVVLAFDIETTKLPLKFPDPE--TDQIMMISYMIDGQGYLITNReivsedIEDFEFTPKPEYEGPFCVFNEpDESHLI 338
Cdd:smart00486 1 PPLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANR------RILFTLGTCKEIDGIEVYEFN-NEKELL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 339 QRWFEHVQETKPTIIVTYNGDFFDWPFVEARAAAHGINMYQEIGFQKDSQG------------------EYKASQCIHMD 400
Cdd:smart00486 74 LAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGLRipnkkplfgsksfglsdiKVYIKGRLVID 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 401 CLRWVKRDSYLPvgSHNLKAAAKAKLGYDPVELDPEEMCRM---ATEEPQTLATYSVSDAVATYYMYMKY-VHPFIFALC 476
Cdd:smart00486 154 LYRLYKNKLKLP--SYKLDTVAEYLLGKEKDDLPYKDIPELyngNYEERDELLRYCIQDAVLTLKLFNKLnVIPLIIELA 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 477 TIIPMEPDEVLRKGSGTLCEALLMVQAYHANIIFPNKQEQEFNKLTEDGHVLDSetYVGGHVEALESGVFRSDipcrfkm 556
Cdd:smart00486 232 RIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEPDLKKKVK--YEGGKVLEPKKGFYDNP------- 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 557 npaafdylvqnvektlrhaieeeerlpldqvtnfqevcdeikvklnslkdvpnriecplIYHLDVGAMYPNIILTNRLQP 636
Cdd:smart00486 303 -----------------------------------------------------------VLVLDFNSLYPSIIIAHNLCY 323
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 637 SAMVDEATCAACDFNKpgancqrrmtwqwrgefmpasrseyhriqqqlesekfpplypdgaprafhelsreeqakyekkr 716
Cdd:smart00486 324 STLVGVGEVVIKGDLI---------------------------------------------------------------- 339
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 717 ladyCRKAYKKIHVTKVEERVTTICQRENSFYVDTVRAFRDRRYEFKGLHKVWKkklsaametgdasevKRCKNMEILYD 796
Cdd:smart00486 340 ----IPEDLLTIKYEKGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEK---------------DESEELKKLLD 400
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2024358764 797 SLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGRP------LELDTDGIWCVLPN 864
Cdd:smart00486 401 SRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGYPkpgfkvIYGDTDSIFVTKPG 474
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
67-1146 |
2.62e-57 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 215.08 E-value: 2.62e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 67 DEDRRAVsaVDYYFIQEDGSRFKVALP-YRPYFYVATQQgcEREVSSFLAKkfQGKIAKLETVPKEDLDlpnhlvGLKRH 145
Cdd:COG0417 14 DEDGKPV--IELWGRTEDGPSVLLDVTgFRPYFYVPLPD--EEKLEELLRD--IKEITEVEPVKLKSFF------GEPVP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 146 YLKLSFSTVDELVKVRKEISPAVRknrerdqanDVYtsmlssalaggslttseegaskkvtnqmdnivdmrEYDVPYHMR 225
Cdd:COG0417 82 VLKIYTRDPRDVRELRDRLKEGGI---------DVY-----------------------------------EADIRFHDR 117
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 226 LSIDLKIHVAHWYNVRYRGSTFPPEITRRDDLVERPDPV-----VLAFDIETTkLPLKFPDPETD-QIMMISYMiDGQGY 299
Cdd:COG0417 118 YLIDRFLTPGVWYEGEVEEDGGKLDYEVKENPRLKPEDYrpklkVLSFDIEVS-TPRGFPDPERDgPIISIGLA-GSDGE 195
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 300 ---LITNREIVSEDIEDFEftpkpeyegpfcvfnepDESHLIQRWFEHVQETKPTIIVTYNGDFFDWPFVEARAAAHGIN 376
Cdd:COG0417 196 kkvLMLGREGVDFEVEYFD-----------------DEKALLEAFFEIIREYDPDIIIGWNVDNFDLPYLQKRAERLGIP 258
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 377 M-----YQEIGFQKD-SQGEYKASQCIHMDCLRWVKRDSY-LPvgSHNLKAAAKAKLGYDPVELDPEEMCRMATEEPQTL 449
Cdd:COG0417 259 LdlgrdGSEPSWREHgGQGFASIPGRVVIDLYDALKSATYkFK--SYSLDAVAEELLGEGKLIVDGGEIERLWDDDKPAL 336
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 450 ATYSVSDAVATYYMYMK-YVHPFIFALCTIIPMEPDEVLRKGSGTLCEALLMVQAYHANIIFPNKQEQEfnkltedghvl 528
Cdd:COG0417 337 AEYNLRDAELTLRIFEKtLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGYLAPNKGEIK----------- 405
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 529 dSETYVGGHVeaLES--GVFrsdipcrfkmnpaaFDYLVqnvektlrhaieeeerlpldqvtnfqevcdeikvklnslkd 606
Cdd:COG0417 406 -GEAYPGGYV--LDPkpGLY--------------ENVLV----------------------------------------- 427
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 607 vpnriecpliyhLDVGAMYPNIILTNRLQPSAMVDEATCAACDFNKpgancqrrmtwqwrgefmpasrseyhriqqqles 686
Cdd:COG0417 428 ------------LDFKSLYPSIIRTFNISPETLVEGGEEPCGDEDV---------------------------------- 461
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 687 ekfpplypdgAPRAFHELSREEQakyekkrladycrkaykkiHVTKveervtTIcqrensfyVDTVRAFRDRryefkglh 766
Cdd:COG0417 462 ----------APGFGHRFCREPK-------------------GILP------SI--------LEELWDERDE-------- 490
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 767 kvWKKKLSaamETGDASEVKRcknmeiLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQ 846
Cdd:COG0417 491 --AKKKMK---KAKPDSEEYR------LYDALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEE 559
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 847 IG-RPLELDTDGIwcvlpnsfpenFVikstnaKKPKVTISYPGAMLNILVKEgfTNdqyQELQDPASLtyvtrsensiff 925
Cdd:COG0417 560 LGyKVIYGDTDSL-----------FV------WLPKASLEEAIEIGKELAEE--IN---AWWPSGLEL------------ 605
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 926 EVDGPYLAMILPASkeegkklKKRYAVFNEDGSLaELKGFEVKRRGELQLVKIFQSSVFEAFLKGTTLEEVyasVAKVAD 1005
Cdd:COG0417 606 EFEKHYRRFFFPGS-------KKRYAGLTEDGKI-DIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKA---VEYVRD 674
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1006 YWLDVlysKAANMPDSELfeLISenRSMSRKLEDYgeQKSTS--ISTAKRLAEflgdqmvkdaglscrfiiskkpEGSPV 1083
Cdd:COG0417 675 VIEKL---RAGEVDLDDL--VIR--KRLRKPLSEY--EKNVPphVRAARKLDE----------------------RGRPY 723
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2024358764 1084 TERAIP-----LAIFQAEPsvrkhylrkwlksPSLQDFNIRAIlDWDYYIERlgsTIqkiitIPAALQ 1146
Cdd:COG0417 724 QRGDKIsyvitKGGGRVEP-------------VELAKERESEI-DYDYYIEK---QL-----KPTADR 769
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
795-1129 |
1.30e-13 |
|
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: 77.02 E-value: 1.30e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 795 YDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGrpLEL---DTDGIWCVLPNSFPENfV 871
Cdd:TIGR00592 888 YDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEMN--LEViygDTDSIMINTPGTKYEE-V 964
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 872 IKSTNAKKPKVTISYPgaMLNIlvkegftndqyqelqdpasltyvtrsensiffEVDGPYLAMILPAskeegkklKKRYA 951
Cdd:TIGR00592 965 FKIGKEFKSEVNKLYK--LLEL--------------------------------DIDGVFKRLLLLK--------KKKYA 1002
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 952 VFNEDGSLA-------ELKGFEVKRRGELQLVKIFQSSVFEAFLKGTTLEEVyasVAKVADYWLDVLYSKAANMPDSELF 1024
Cdd:TIGR00592 1003 AIKVEGDSDgnyttkqEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEA---VEEVQEVLEKIGKNVLNGEVPLEKF 1079
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1025 ELiseNRSMSRKLEDYGEQKS-TSISTAKRLAEfLGDQMVKdAGLSCRFIISKkpEGSPVTERAiplAIFQAEPSVRKHy 1103
Cdd:TIGR00592 1080 VI---NKQLTRDPKDYPDGASlPHVHVALRINA-RGGRKVK-AGDVVSYVICK--DGGNLSARQ---RAYALEELQRKH- 1148
|
330 340
....*....|....*....|....*.
gi 2024358764 1104 lrKWLkspslqdfniraILDWDYYIE 1129
Cdd:TIGR00592 1149 --NNL------------IYDTQYYLE 1160
|
|
| YprB |
COG3359 |
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function ... |
255-466 |
1.98e-11 |
|
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function prediction only];
Pssm-ID: 442587 [Multi-domain] Cd Length: 198 Bit Score: 65.35 E-value: 1.98e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 255 DDLVERPDPVVlaFDIETTKLplkfpDPETDQIMMISYMIDGQGYLITnREIVSEDIEDfeftpkpeyegpfcvfnepdE 334
Cdd:COG3359 9 AELLPSEDLLF--FDIETTGL-----SGGGTVIFLIGLADGEGDGFVV-RQYFGEDPGE--------------------E 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 335 SHLIQRWFEHVQETKptIIVTYNGDFFDWPFVEARAAAHGInmyqeigfqkdsqgEYKASQCIHMDCLRWVKRDSYLPVG 414
Cdd:COG3359 61 AALLEAFLEWLADYK--LLVTYNGKSFDLPFLKTRFTLHRL--------------PPPLPEFPHLDLLHPARRLWKNRLP 124
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 2024358764 415 SHNLKAAAKaKLGYDPVEldpeemcrmateepqtlaTYSVSDAVATYYMYMK 466
Cdd:COG3359 125 SGGLKTVEE-LLGIERED------------------DLPGYEAPRLYRRYLR 157
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
65-1130 |
1.54e-10 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 66.80 E-value: 1.54e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 65 VLD---EDRRAVSAVDYYFIQEDGSRfKVALP--YRPYFYVATQQgceREVSSFLAKKFQGKIAKLETVPKEDldlpnhl 139
Cdd:PRK05762 8 ILTrhyRDTPGGPEVELWLATDEGPR-VVLLDpqFRPYFIPAEQD---ERAESLLAGEIGVRLSPLALKDFHR------- 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 140 vglkRHYLKLSFSTVDELVKVRKeispavrknRERDQANDVYtsmlssalaggslttseegaskkvtnqmdnivdmrEYD 219
Cdd:PRK05762 77 ----RPVLGLYCRQHRQLTRLPK---------RLREGGVDVY-----------------------------------EAD 108
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 220 VPYHMRLSIDLKIHVAHWYNVRYRGSTFPPEItRRDDLveRPDPV------VLAFDIETTklplkfpdpetdqimmISYM 293
Cdd:PRK05762 109 IRFPERYLMERFITPCVWFSGEVEQYTTDGVL-RNARL--KPAPDyrpplkVVSLDIETS----------------NKGE 169
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 294 IDGQGYLITNREIVsediedFEFTPKPEYEGPFcVFNEPDESHLIQRWFEHVQETKPTIIVTYNGDFFDWPFVEARAAAH 373
Cdd:PRK05762 170 LYSIGLEGCGQRPV------IMLGPPNGEALDF-LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERY 242
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 374 GINM----------YQEIGFQKDsQGEYKASQCIHMDCLRWVKR-----DSYlpvgshNLKAAAKAKLG----YDPVELD 434
Cdd:PRK05762 243 GIPLrlgrdgseleWREHPFRSG-YGFASVPGRLVLDGIDALKSatwvfDSF------SLEYVSQRLLGegkaIDDPYDR 315
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 435 PEEMCRMATEEPQTLATYSVSDAVATYYMYMKY-VHPFIFALCTIIPMEPDEVlrKGSGTLCEALLMVQAYHANIIFPNK 513
Cdd:PRK05762 316 MDEIDRRFAEDKPALARYNLKDCELVTRIFEKTkLLPFLLERATVTGLPLDRV--GGSVAAFEHLYLPRAHRAGYVAPNL 393
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 514 QEQEfnkltedghvldSETYVGGHVeaLES--GVFRSdipcrfkmnpaafdylvqnvektlrhaieeeerlpldqvtnfq 591
Cdd:PRK05762 394 GERP------------GEASPGGYV--MDSkpGLYDS------------------------------------------- 416
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 592 evcdeikvklnslkdvpnriecplIYHLDVGAMYPNIILTNRLQPSAMVDEatcaacdfnkpgancqrrmtwqwrgefmp 671
Cdd:PRK05762 417 ------------------------VLVLDFKSLYPSIIRTFNIDPDGLVEG----------------------------- 443
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 672 asrseyhriQQQLESEKFPPlyPDGAprAFHelsreeqakyekkrladycrkaykkihvtkveervtticqRENSFYVDT 751
Cdd:PRK05762 444 ---------LAQPPEESVAG--FLGA--RFS----------------------------------------REKHFLPEI 470
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 752 VrafrdrryefkglhkvwkKKLSAAMEtgdasEVKRCKNMEilydsLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCF 831
Cdd:PRK05762 471 V------------------ERLWEGRD-----EAKREMNKP-----LSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITM 522
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 832 TGANIITQARELIEQIGrpLEL---DTDGIWCVLPNSFPENFVIKSTNAKKPKVtisypGAMLNILVKEGFTNDQYQELQ 908
Cdd:PRK05762 523 RGHEIMKQTRELIEAQG--YQViygDTDSTFVWLGGAHDEEDAAKIGRALVQEI-----NQWWQEHLQQEFGLESALELE 595
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 909 dpasltyvtrsensifFEVDgpYLAMILPASKEEGKKLKKRYA--VFNEDGSLaEL--KGFEVKRRGELQLVKIFQSSVF 984
Cdd:PRK05762 596 ----------------FEKH--YRRFFMPTIRGAEEGSKKRYAglIQEGDGDG-RIvfKGLETVRTDWTPLAKEFQQELY 656
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 985 EAFLKGTtleevyasvaKVADYWLDVLYS-KAANMPDselfELISENRsMSRKLEDYgeQKSTS--ISTAKRLAEFLGDQ 1061
Cdd:PRK05762 657 ERIFRGE----------PYVDYVREVIDKlRAGELDE----KLVYRKR-LRRPLDEY--QRNVPphVRAARLADEMGYKV 719
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2024358764 1062 MVKDA---GLSCRFIIS-KKPEgsPVTERaiplaifqaepsvrkhylrkwlKSPslqdfniraiLDWDYYIER 1130
Cdd:PRK05762 720 GRPLQyqnGGKIGYVITvNGPE--PLEYR----------------------KSP----------IDYDYYIEK 758
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
794-1040 |
1.01e-05 |
|
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: 50.30 E-value: 1.01e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 794 LYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGRP-LEL---DTDGIwcvlpnsfpen 869
Cdd:pfam00136 150 ILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYnFRViygDTDSV----------- 218
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 870 FVIKSTNAKKPKVTIsypGAMLNILVkegfTNDQYQelqdpasltyvtrseNSIFFEVDGPYLAMILPAskeegkklKKR 949
Cdd:pfam00136 219 FIEFGGKDVEEAMKI---GDELAEHV----NQDLFK---------------SPIKLEFEKVYKPLLLIS--------KKK 268
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 950 YA----VFNEDGSLAELKGFEVKRRGELQLVKIFQSSVFEAFLKGTTLEEVYASVAKVadywLDVLYSKAANMP-DSELF 1024
Cdd:pfam00136 269 YAglkyTAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSDRGLPVGLEFVISI----LNDARSDLRNNKvPLEKF 344
|
250
....*....|....*.
gi 2024358764 1025 ELiseNRSMSRKLEDY 1040
Cdd:pfam00136 345 VI---SKELSKPPDNY 357
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
217-385 |
1.07e-05 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 50.80 E-value: 1.07e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 217 EYDVPYHMRLSIDLKIHVAHW----------YNVRYRGSTFPPEI-TRRDDLVERPD--------PV-VLAFDIETTKLP 276
Cdd:PTZ00166 198 ESNVPFVLRFLIDNNITGGSWltlpkgkykiRPPKKKTSTCQIEVdCSYEDLIPLPPegeyltiaPLrILSFDIECIKLK 277
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 277 -LKFPDPETDQIMMISYMIDGQGYLItnreivsEDIEDFEFTPKPEYEGPFC-VFNEPDESHLIQRWFEHVQETKPTIIV 354
Cdd:PTZ00166 278 gLGFPEAENDPVIQISSVVTNQGDEE-------EPLTKFIFTLKECASIAGAnVLSFETEKELLLAWAEFVIAVDPDFLT 350
|
170 180 190
....*....|....*....|....*....|.
gi 2024358764 355 TYNGDFFDWPFVEARAAAHGINMYQEIGFQK 385
Cdd:PTZ00166 351 GYNIINFDLPYLLNRAKALKLNDFKYLGRIK 381
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| POLBc_epsilon |
cd05535 |
DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
525-1147 |
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: 1335.39 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 525 GHVLDSETYVGGHVEALESGVFRSDIPCRFKMNPAAFDYLVQNVEKTLRHAIEEEERLPLDQVTNFQEVCDEIKVKLNSL 604
Cdd:cd05535 1 GHLLESETYVGGHVEALESGVFRSDIPCRFKLDPDAIQELLQNVDETLRFAIEVEGKIPLDQVENFEEVREEILEKLQSL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 605 KDVPNRIECPLIYHLDVGAMYPNIILTNRLQPSAMVDEATCAACDFNKPGANCQRRMTWQWRGEFMPASRSEYHRIQQQL 684
Cdd:cd05535 81 RDNPKRSEKPLIYHLDVAAMYPNIILTNRLQPDAIVDEDVCAACDFNKPGKTCQRRMEWAWRGEYFPASRGEYERIKQQL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 685 ESEKFPPLYPDGAPRAFHELSREEQAKYEKKRLADYCRKAYKKIHVTKVEERVTTICQRENSFYVDTVRAFRDRRYEFKG 764
Cdd:cd05535 161 ESEKFPPLFPGGPPKSFHELSPEEQAEELKKRLKDYSRKVYKKTHVTKEEERSTTICQRENPFYVDTVRAFRDRRYEYKG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 765 LHKVWKKKLSAAMETGDASEVKRCKNMEILYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELI 844
Cdd:cd05535 241 LHKVWKKKLEAAKAAGDAAEIKEAKKMVVLYDSLQLAHKCILNSFYGYVMRKGSRWYSMEMAGIVCYTGANIIQMARELV 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 845 EQIGRPLELDTDGIWCVLPNSFPENFVIKSTNakKPKVTISYPGAMLNILVKEGFTNDQYQELQDPASLTYVTRSENSIF 924
Cdd:cd05535 321 EQIGRPLELDTDGIWCILPKSFPENFTFKTKN--GKKVTISYPCVMLNHLVHKKFTNDQYQELVDPSTGTYETRSENSIF 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 925 FEVDGPYLAMILPASKEEGKKLKKRYAVFNEDGSLAELKGFEVKRRGELQLVKIFQSSVFEAFLKGTTLEEVYASVAKVA 1004
Cdd:cd05535 399 FEVDGPYKAMILPASKEEGKLLKKRYAVFNEDGSLAELKGFEVKRRGELQLIKIFQSEVFDAFLKGSTLEECYAAVAAVA 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1005 DYWLDVLYSKAANMPDSELFELISENRSMSRKLEDYGEQKSTSISTAKRLAEFLGDQMVKDAGLSCRFIISKKPEGSPVT 1084
Cdd:cd05535 479 NYWLDVLDSKGENLDDEELFELISENRSMSKKLEEYGNQKSTSITTAKRLAEFLGDQMVKDKGLSCKYIISKKPEGSPVT 558
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2024358764 1085 ERAIPLAIFQAEPSVRKHYLRKWLKSPSLQDFNIRAILDWDYYIERLGSTIQKIITIPAALQQ 1147
Cdd:cd05535 559 ERAIPVAIFQAEPEVRKHYLRKWLKDPSDEDLDIRDIIDWDYYIERLGSTIQKIITIPAALQG 621
|
|
| DUF1744 |
pfam08490 |
Domain of unknown function (DUF1744); This domain is found at the C-terminal of the epsilon ... |
1522-1921 |
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: 599.15 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1522 LTTMFSAERSALLERVGEE---LLPPDKHTFEVRAETDPKAICRAIQRLLLGYKDERRGPTLIAVQSNWELKRLASGIPI 1598
Cdd:pfam08490 1 LEKLYKELRAKKLDKLEKWsgaFEYPEDMTFEVTYFTDERKAYKALSRALSKYKEEKSGPTLLVLQSPKDLSYLLSKIPI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1599 LDEFPLVPIRVTD-DISYSVLDWQRHAARRMIRHYLNLDTCLSQAFEMSRYYHIPIGNLPDDISTFGSDLFFSRHLRRHN 1677
Cdd:pfam08490 81 LNEFPVVSIPSNDaDSSLPALGWQSVVAKRMVNHYLSLGSWLSHLIELARYFDIPLCNLESDDPLFLIDIFYARRLKKNN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1678 HLLWLSPTARPDLGGKEADDNRLVMEFDERA-SVEINNPGCYSTVCLELDIQSLAVNTVLQSHHVNDMEGcSSMSISFDV 1756
Cdd:pfam08490 161 IVLWWSPSPLPDLGGREKDDNPNTLGLMEELdSPEINNPGAYSNVCLELDIRNLAVNTILQSALINELEG-SDLSTAFDA 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1757 iqqASLEDMVTGNQAANIPASYDETALCSNTFRILKSMVVSWVKEITQyHNIYADNQVIHFYRWLRSPSSLLYDPALHRT 1836
Cdd:pfam08490 240 ---ASHTLDEYSKGDVNSSSTYDEDAFSSAAFRVLRSMVKSWWDDALK-GNVFADLLVDHFVRWVQSPDSLLYDPALHRH 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1837 LHNMMKKLFLQLVAEFRRLGSSVVYANFNRIILCTKKRRIEDAISYMEYIINSIHSKEIFHSLTISFSRCWEFLLWMDPA 1916
Cdd:pfam08490 316 VHNLMKKAFLQLLAEFKRLGSTVVYADFNRILLQTSKPSVENAYAYSQYIVKAIRSKPLFHFLDLKIVRYWDYLLWMDEA 395
|
....*
gi 2024358764 1917 NYGGI 1921
Cdd:pfam08490 396 NYGGV 400
|
|
| DNA_polB_epsilon_exo |
cd05779 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ... |
262-465 |
3.14e-151 |
|
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: 465.97 E-value: 3.14e-151
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 262 DPVVLAFDIETTKLPLKFPDPETDQIMMISYMIDGQGYLITNREIVSEDIEDFEFTPKPEYEGPFCVFNEPDESHLIQRW 341
Cdd:cd05779 1 DPRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNREIVSEDIEDFEYTPKPEYEGPFKVFNEPDEKALLQRF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 342 FEHVQETKPTIIVTYNGDFFDWPFVEARAAAHGINMYQEIGFQKDSQGEYKASQCIHMDCLRWVKRDSYLPVGSHNLKAA 421
Cdd:cd05779 81 FEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQGLKAV 160
|
170 180 190 200
....*....|....*....|....*....|....*....|....
gi 2024358764 422 AKAKLGYDPVELDPEEMCRMATEEPQTLATYSVSDAVATYYMYM 465
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 ... |
80-420 |
1.17e-84 |
|
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: 281.23 E-value: 1.17e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 80 FIQEDGSRFKVALPYRPYFYVATQQGCE-REVSSFLAKKFQGKIakleTVPKEDLDLPNHLVGLKRH---YLKLSFSTVD 155
Cdd:pfam03104 1 KTDEGVSVCVNVFGFKPYFYCLAPDGKElEEVIEEIKELYEGLD----KIEKIELKLKKSLYGYEEDpvpYLKVSFANPR 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 156 ELVKVRKEISPAvrknrerdqandvytsmlssalaggslttseegaskkvtnqmdNIVDMREYDVPYHMRLSIDLKIHVA 235
Cdd:pfam03104 77 PLLKIRKYLSPE-------------------------------------------NISDVYEYDVDYLERFLIDNDIVGF 113
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 236 HWYNVRY-------RGSTFPPEITRRDDLVER-------PDPVVLAFDIETTKLPLKFPDPE--TDQIMMISYMIDGQG- 298
Cdd:pfam03104 114 GWYKVKVypfraegRISNCDVEIDCDSPDLISvpfekewPPLRVLSFDIECTSLPGKFPDAEnvKDPIIQISCMLDGQGe 193
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 299 ------YLITNREIVSEDIEDFEFTPKPEYEGPfCVFNEPDESHLIQRWFEHVQETKPTIIVTYNGDFFDWPFVEARAAA 372
Cdd:pfam03104 194 pepeprFLFTLRECDSEDIEDFEYTPKPIYPGV-KVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKE 272
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2024358764 373 --------------HGINMYQEIGFQKDSQGEYKASQCIHMDCLRWVKRDSYLPvgSHNLKA 420
Cdd:pfam03104 273 lyivklssigrlnrGGRSKVREIGFGTRSYEKVKISGRLHLDLYRVIKRDYKLP--SYKLNA 332
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
261-864 |
1.06e-71 |
|
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: 249.37 E-value: 1.06e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 261 PDPVVLAFDIETTKLPLKFPDPE--TDQIMMISYMIDGQGYLITNReivsedIEDFEFTPKPEYEGPFCVFNEpDESHLI 338
Cdd:smart00486 1 PPLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANR------RILFTLGTCKEIDGIEVYEFN-NEKELL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 339 QRWFEHVQETKPTIIVTYNGDFFDWPFVEARAAAHGINMYQEIGFQKDSQG------------------EYKASQCIHMD 400
Cdd:smart00486 74 LAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGLRipnkkplfgsksfglsdiKVYIKGRLVID 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 401 CLRWVKRDSYLPvgSHNLKAAAKAKLGYDPVELDPEEMCRM---ATEEPQTLATYSVSDAVATYYMYMKY-VHPFIFALC 476
Cdd:smart00486 154 LYRLYKNKLKLP--SYKLDTVAEYLLGKEKDDLPYKDIPELyngNYEERDELLRYCIQDAVLTLKLFNKLnVIPLIIELA 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 477 TIIPMEPDEVLRKGSGTLCEALLMVQAYHANIIFPNKQEQEFNKLTEDGHVLDSetYVGGHVEALESGVFRSDipcrfkm 556
Cdd:smart00486 232 RIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEPDLKKKVK--YEGGKVLEPKKGFYDNP------- 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 557 npaafdylvqnvektlrhaieeeerlpldqvtnfqevcdeikvklnslkdvpnriecplIYHLDVGAMYPNIILTNRLQP 636
Cdd:smart00486 303 -----------------------------------------------------------VLVLDFNSLYPSIIIAHNLCY 323
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 637 SAMVDEATCAACDFNKpgancqrrmtwqwrgefmpasrseyhriqqqlesekfpplypdgaprafhelsreeqakyekkr 716
Cdd:smart00486 324 STLVGVGEVVIKGDLI---------------------------------------------------------------- 339
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 717 ladyCRKAYKKIHVTKVEERVTTICQRENSFYVDTVRAFRDRRYEFKGLHKVWKkklsaametgdasevKRCKNMEILYD 796
Cdd:smart00486 340 ----IPEDLLTIKYEKGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEK---------------DESEELKKLLD 400
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2024358764 797 SLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGRP------LELDTDGIWCVLPN 864
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 ... |
265-465 |
2.30e-58 |
|
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: 200.27 E-value: 2.30e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 265 VLAFDIETTKLPlKFPDPETDQIMMISYMIDGQGYLITNREIVSEDIEDFEFtpkpeyEGPFCVFNEPDESHLIQRWFEH 344
Cdd:cd05160 1 VLSFDIETTPPV-GGPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDDIEF------IDGIEVEYFADEKELLKRFFDI 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 345 VQETKPTIIVTYNGDFFDWPFVEARAAAHGI----NMYQEIGFQK--DSQGEYKASQCIHMDCLRWVKRDSYLPvgSHNL 418
Cdd:cd05160 74 IREYDPDILTGYNIDDFDLPYLLKRAEALGIkltdGIYRRSGGEKssGSTERIAVKGRVVFDLLAAYKRDFKLK--SYTL 151
|
170 180 190 200
....*....|....*....|....*....|....*....|....*...
gi 2024358764 419 KAAAKAKLGYDPVELDPEEMCR-MATEEPQTLATYSVSDAVATYYMYM 465
Cdd:cd05160 152 DAVAEELLGEGKEKVDGEIIEDaEWEEDPERLIEYNLKDAELTLQILE 199
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
67-1146 |
2.62e-57 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 215.08 E-value: 2.62e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 67 DEDRRAVsaVDYYFIQEDGSRFKVALP-YRPYFYVATQQgcEREVSSFLAKkfQGKIAKLETVPKEDLDlpnhlvGLKRH 145
Cdd:COG0417 14 DEDGKPV--IELWGRTEDGPSVLLDVTgFRPYFYVPLPD--EEKLEELLRD--IKEITEVEPVKLKSFF------GEPVP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 146 YLKLSFSTVDELVKVRKEISPAVRknrerdqanDVYtsmlssalaggslttseegaskkvtnqmdnivdmrEYDVPYHMR 225
Cdd:COG0417 82 VLKIYTRDPRDVRELRDRLKEGGI---------DVY-----------------------------------EADIRFHDR 117
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 226 LSIDLKIHVAHWYNVRYRGSTFPPEITRRDDLVERPDPV-----VLAFDIETTkLPLKFPDPETD-QIMMISYMiDGQGY 299
Cdd:COG0417 118 YLIDRFLTPGVWYEGEVEEDGGKLDYEVKENPRLKPEDYrpklkVLSFDIEVS-TPRGFPDPERDgPIISIGLA-GSDGE 195
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 300 ---LITNREIVSEDIEDFEftpkpeyegpfcvfnepDESHLIQRWFEHVQETKPTIIVTYNGDFFDWPFVEARAAAHGIN 376
Cdd:COG0417 196 kkvLMLGREGVDFEVEYFD-----------------DEKALLEAFFEIIREYDPDIIIGWNVDNFDLPYLQKRAERLGIP 258
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 377 M-----YQEIGFQKD-SQGEYKASQCIHMDCLRWVKRDSY-LPvgSHNLKAAAKAKLGYDPVELDPEEMCRMATEEPQTL 449
Cdd:COG0417 259 LdlgrdGSEPSWREHgGQGFASIPGRVVIDLYDALKSATYkFK--SYSLDAVAEELLGEGKLIVDGGEIERLWDDDKPAL 336
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 450 ATYSVSDAVATYYMYMK-YVHPFIFALCTIIPMEPDEVLRKGSGTLCEALLMVQAYHANIIFPNKQEQEfnkltedghvl 528
Cdd:COG0417 337 AEYNLRDAELTLRIFEKtLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGYLAPNKGEIK----------- 405
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 529 dSETYVGGHVeaLES--GVFrsdipcrfkmnpaaFDYLVqnvektlrhaieeeerlpldqvtnfqevcdeikvklnslkd 606
Cdd:COG0417 406 -GEAYPGGYV--LDPkpGLY--------------ENVLV----------------------------------------- 427
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 607 vpnriecpliyhLDVGAMYPNIILTNRLQPSAMVDEATCAACDFNKpgancqrrmtwqwrgefmpasrseyhriqqqles 686
Cdd:COG0417 428 ------------LDFKSLYPSIIRTFNISPETLVEGGEEPCGDEDV---------------------------------- 461
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 687 ekfpplypdgAPRAFHELSREEQakyekkrladycrkaykkiHVTKveervtTIcqrensfyVDTVRAFRDRryefkglh 766
Cdd:COG0417 462 ----------APGFGHRFCREPK-------------------GILP------SI--------LEELWDERDE-------- 490
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 767 kvWKKKLSaamETGDASEVKRcknmeiLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQ 846
Cdd:COG0417 491 --AKKKMK---KAKPDSEEYR------LYDALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEE 559
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 847 IG-RPLELDTDGIwcvlpnsfpenFVikstnaKKPKVTISYPGAMLNILVKEgfTNdqyQELQDPASLtyvtrsensiff 925
Cdd:COG0417 560 LGyKVIYGDTDSL-----------FV------WLPKASLEEAIEIGKELAEE--IN---AWWPSGLEL------------ 605
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 926 EVDGPYLAMILPASkeegkklKKRYAVFNEDGSLaELKGFEVKRRGELQLVKIFQSSVFEAFLKGTTLEEVyasVAKVAD 1005
Cdd:COG0417 606 EFEKHYRRFFFPGS-------KKRYAGLTEDGKI-DIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKA---VEYVRD 674
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1006 YWLDVlysKAANMPDSELfeLISenRSMSRKLEDYgeQKSTS--ISTAKRLAEflgdqmvkdaglscrfiiskkpEGSPV 1083
Cdd:COG0417 675 VIEKL---RAGEVDLDDL--VIR--KRLRKPLSEY--EKNVPphVRAARKLDE----------------------RGRPY 723
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2024358764 1084 TERAIP-----LAIFQAEPsvrkhylrkwlksPSLQDFNIRAIlDWDYYIERlgsTIqkiitIPAALQ 1146
Cdd:COG0417 724 QRGDKIsyvitKGGGRVEP-------------VELAKERESEI-DYDYYIEK---QL-----KPTADR 769
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
614-1141 |
5.52e-46 |
|
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis.
Pssm-ID: 99912 [Multi-domain] Cd Length: 323 Bit Score: 169.47 E-value: 5.52e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 614 PLIYHLDVGAMYPNIILTNRLQPSAMVDEATCAACDFNKPgancqrrmtwqwrgefmpasrseyhriqqqlesekfpply 693
Cdd:cd00145 17 ENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYIG---------------------------------------- 56
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 694 pdgaprafhelsreeqakyekkrladycrkaykkihvtkVEERVTTICQRENSFYVDTVRAFRDRRYEFKGLHKvwkkkl 773
Cdd:cd00145 57 ---------------------------------------VGFRSPKDRKGLLPRILEELLNFRDEAKKRMKAAK------ 91
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 774 saametgdasevkRCKNMEILYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIG-RPLE 852
Cdd:cd00145 92 -------------LAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGaRVIY 158
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 853 LDTDGIWCVLPNSFPENFVIKstnakkpkvtisypgamlnilvkegFTNDQYQELqdpasltyvtRSENSIFFEVDGPYL 932
Cdd:cd00145 159 GDTDSIFVSLPKMGTKEDAIK-------------------------EGREILQEL----------ADEHLLELEFEKVYL 203
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 933 AMILPAskeegkklKKRYAVFNE----DGSLAELKGFEVKRRGELQLVKIFQSSVFEAFLK-GTTLEEVYASVAKVadyw 1007
Cdd:cd00145 204 PFFLGK--------KKRYAGLDIwkgqDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEeERKVEAVKEYIDEL---- 271
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1008 ldvlyskaanmpdselfelisenrsmsrkledygeqkstsistakrlaeflgdQMVKdaglscrFIISKKPEGSPVTERA 1087
Cdd:cd00145 272 -----------------------------------------------------DKVK-------YVVTRGGKGVPDYERA 291
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....
gi 2024358764 1088 IplaifqaepsvrkhylrkwlksPSLQDFNIRAILDWDYYIERLGSTIQKIITI 1141
Cdd:cd00145 292 D----------------------PPLEDLDKRHRIDYEYYLERLLQPPLERIFE 323
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
261-461 |
2.13e-21 |
|
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show similarity to eukaryotic DNA polymerases involved in DNA replication. Some archaea possess multiple family-B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family-B DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.
Pssm-ID: 99823 [Multi-domain] Cd Length: 195 Bit Score: 94.34 E-value: 2.13e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 261 PDPVVLAFDIETtKLPLKFPDPETDQIMMISYMIDGQGYLITNREIVSEDIEDFEftpkpeyegpfcvfnepDESHLIQR 340
Cdd:cd05780 1 EDLKILSFDIEV-LNHEGEPNPEKDPIIMISFADEGGNKVITWKKFDLPFVEVVK-----------------TEKEMIKR 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 341 WFEHVQETKPTIIVTYNGDFFDWPFVEARAAAHGINM-----YQEIGFQKdsQGEYKASQC---IHMDCLRWVKRdsYLP 412
Cdd:cd05780 63 FIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELdlgrdGSEIKIQR--GGFNNASEIkgrIHVDLYPVARR--TLN 138
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|.
gi 2024358764 413 VGSHNLKAAAKAKLGYDPVELDPEEMCRM--ATEEPQTLATYSVSDAVATY 461
Cdd:cd05780 139 LTRYTLERVYEELFGIEKEDVPGEEIAEAwdSGENLERLFRYSMEDAKYTY 189
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
769-1145 |
2.28e-18 |
|
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: 89.31 E-value: 2.28e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 769 WKKKLSAAMETGDASEVKRcknmeILYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIG 848
Cdd:cd05536 79 ERRRIKEKMKKLDPESEEY-----KLLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAEEKG 153
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 849 -RPLELDTDGIwcvlpnsfpenFVIKstnakkpkvtisyPGAMLNILVKEGFTNDQYQELqdpasltyvtrsenSIFFEV 927
Cdd:cd05536 154 fKVIYGDTDSL-----------FVKI-------------DGADAVKKKVKKLLKYINEEL--------------PLELEI 195
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 928 DGPYLAMILPAskeegkklKKRYAVFNEDGSLaELKGFEVKRRGELQLVKIFQSSVFEAFLKgttleevYASVAKVADYW 1007
Cdd:cd05536 196 EKFYKRGFFVT--------KKRYAGLTEDGKI-DVVGLEVVRRDWSEIAKETQARVLEAILK-------EGDVEEAVKIV 259
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1008 LDVLYS-KAANMPDSELfeLISEnrSMSRKLEDYgEQKSTSISTAKRLAEfLGDQMVKdaGLSCRFIISKKPegSPVTER 1086
Cdd:cd05536 260 KEVIEKlKRGEVPPEKL--VIWK--QLTKDLSEY-KATGPHVAAAKKLAK-RGYKVRP--GTKIGYVIVKGS--GKISDR 329
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*....
gi 2024358764 1087 AIPLAIFQAEPSVrkhylrkwlkspslqdfnirailDWDYYIERlgstiQkiiTIPAAL 1145
Cdd:cd05536 330 AYPYDMVDEKHKY-----------------------DAEYYIDN-----Q---VLPAVL 357
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
795-1129 |
1.30e-13 |
|
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: 77.02 E-value: 1.30e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 795 YDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGrpLEL---DTDGIWCVLPNSFPENfV 871
Cdd:TIGR00592 888 YDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEMN--LEViygDTDSIMINTPGTKYEE-V 964
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 872 IKSTNAKKPKVTISYPgaMLNIlvkegftndqyqelqdpasltyvtrsensiffEVDGPYLAMILPAskeegkklKKRYA 951
Cdd:TIGR00592 965 FKIGKEFKSEVNKLYK--LLEL--------------------------------DIDGVFKRLLLLK--------KKKYA 1002
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 952 VFNEDGSLA-------ELKGFEVKRRGELQLVKIFQSSVFEAFLKGTTLEEVyasVAKVADYWLDVLYSKAANMPDSELF 1024
Cdd:TIGR00592 1003 AIKVEGDSDgnyttkqEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEA---VEEVQEVLEKIGKNVLNGEVPLEKF 1079
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1025 ELiseNRSMSRKLEDYGEQKS-TSISTAKRLAEfLGDQMVKdAGLSCRFIISKkpEGSPVTERAiplAIFQAEPSVRKHy 1103
Cdd:TIGR00592 1080 VI---NKQLTRDPKDYPDGASlPHVHVALRINA-RGGRKVK-AGDVVSYVICK--DGGNLSARQ---RAYALEELQRKH- 1148
|
330 340
....*....|....*....|....*.
gi 2024358764 1104 lrKWLkspslqdfniraILDWDYYIE 1129
Cdd:TIGR00592 1149 --NNL------------IYDTQYYLE 1160
|
|
| YprB |
COG3359 |
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function ... |
255-466 |
1.98e-11 |
|
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function prediction only];
Pssm-ID: 442587 [Multi-domain] Cd Length: 198 Bit Score: 65.35 E-value: 1.98e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 255 DDLVERPDPVVlaFDIETTKLplkfpDPETDQIMMISYMIDGQGYLITnREIVSEDIEDfeftpkpeyegpfcvfnepdE 334
Cdd:COG3359 9 AELLPSEDLLF--FDIETTGL-----SGGGTVIFLIGLADGEGDGFVV-RQYFGEDPGE--------------------E 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 335 SHLIQRWFEHVQETKptIIVTYNGDFFDWPFVEARAAAHGInmyqeigfqkdsqgEYKASQCIHMDCLRWVKRDSYLPVG 414
Cdd:COG3359 61 AALLEAFLEWLADYK--LLVTYNGKSFDLPFLKTRFTLHRL--------------PPPLPEFPHLDLLHPARRLWKNRLP 124
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 2024358764 415 SHNLKAAAKaKLGYDPVEldpeemcrmateepqtlaTYSVSDAVATYYMYMK 466
Cdd:COG3359 125 SGGLKTVEE-LLGIERED------------------DLPGYEAPRLYRRYLR 157
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
65-1130 |
1.54e-10 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 66.80 E-value: 1.54e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 65 VLD---EDRRAVSAVDYYFIQEDGSRfKVALP--YRPYFYVATQQgceREVSSFLAKKFQGKIAKLETVPKEDldlpnhl 139
Cdd:PRK05762 8 ILTrhyRDTPGGPEVELWLATDEGPR-VVLLDpqFRPYFIPAEQD---ERAESLLAGEIGVRLSPLALKDFHR------- 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 140 vglkRHYLKLSFSTVDELVKVRKeispavrknRERDQANDVYtsmlssalaggslttseegaskkvtnqmdnivdmrEYD 219
Cdd:PRK05762 77 ----RPVLGLYCRQHRQLTRLPK---------RLREGGVDVY-----------------------------------EAD 108
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 220 VPYHMRLSIDLKIHVAHWYNVRYRGSTFPPEItRRDDLveRPDPV------VLAFDIETTklplkfpdpetdqimmISYM 293
Cdd:PRK05762 109 IRFPERYLMERFITPCVWFSGEVEQYTTDGVL-RNARL--KPAPDyrpplkVVSLDIETS----------------NKGE 169
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 294 IDGQGYLITNREIVsediedFEFTPKPEYEGPFcVFNEPDESHLIQRWFEHVQETKPTIIVTYNGDFFDWPFVEARAAAH 373
Cdd:PRK05762 170 LYSIGLEGCGQRPV------IMLGPPNGEALDF-LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERY 242
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 374 GINM----------YQEIGFQKDsQGEYKASQCIHMDCLRWVKR-----DSYlpvgshNLKAAAKAKLG----YDPVELD 434
Cdd:PRK05762 243 GIPLrlgrdgseleWREHPFRSG-YGFASVPGRLVLDGIDALKSatwvfDSF------SLEYVSQRLLGegkaIDDPYDR 315
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 435 PEEMCRMATEEPQTLATYSVSDAVATYYMYMKY-VHPFIFALCTIIPMEPDEVlrKGSGTLCEALLMVQAYHANIIFPNK 513
Cdd:PRK05762 316 MDEIDRRFAEDKPALARYNLKDCELVTRIFEKTkLLPFLLERATVTGLPLDRV--GGSVAAFEHLYLPRAHRAGYVAPNL 393
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 514 QEQEfnkltedghvldSETYVGGHVeaLES--GVFRSdipcrfkmnpaafdylvqnvektlrhaieeeerlpldqvtnfq 591
Cdd:PRK05762 394 GERP------------GEASPGGYV--MDSkpGLYDS------------------------------------------- 416
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 592 evcdeikvklnslkdvpnriecplIYHLDVGAMYPNIILTNRLQPSAMVDEatcaacdfnkpgancqrrmtwqwrgefmp 671
Cdd:PRK05762 417 ------------------------VLVLDFKSLYPSIIRTFNIDPDGLVEG----------------------------- 443
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 672 asrseyhriQQQLESEKFPPlyPDGAprAFHelsreeqakyekkrladycrkaykkihvtkveervtticqRENSFYVDT 751
Cdd:PRK05762 444 ---------LAQPPEESVAG--FLGA--RFS----------------------------------------REKHFLPEI 470
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 752 VrafrdrryefkglhkvwkKKLSAAMEtgdasEVKRCKNMEilydsLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCF 831
Cdd:PRK05762 471 V------------------ERLWEGRD-----EAKREMNKP-----LSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITM 522
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 832 TGANIITQARELIEQIGrpLEL---DTDGIWCVLPNSFPENFVIKSTNAKKPKVtisypGAMLNILVKEGFTNDQYQELQ 908
Cdd:PRK05762 523 RGHEIMKQTRELIEAQG--YQViygDTDSTFVWLGGAHDEEDAAKIGRALVQEI-----NQWWQEHLQQEFGLESALELE 595
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 909 dpasltyvtrsensifFEVDgpYLAMILPASKEEGKKLKKRYA--VFNEDGSLaEL--KGFEVKRRGELQLVKIFQSSVF 984
Cdd:PRK05762 596 ----------------FEKH--YRRFFMPTIRGAEEGSKKRYAglIQEGDGDG-RIvfKGLETVRTDWTPLAKEFQQELY 656
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 985 EAFLKGTtleevyasvaKVADYWLDVLYS-KAANMPDselfELISENRsMSRKLEDYgeQKSTS--ISTAKRLAEFLGDQ 1061
Cdd:PRK05762 657 ERIFRGE----------PYVDYVREVIDKlRAGELDE----KLVYRKR-LRRPLDEY--QRNVPphVRAARLADEMGYKV 719
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2024358764 1062 MVKDA---GLSCRFIIS-KKPEgsPVTERaiplaifqaepsvrkhylrkwlKSPslqdfniraiLDWDYYIER 1130
Cdd:PRK05762 720 GRPLQyqnGGKIGYVITvNGPE--PLEYR----------------------KSP----------IDYDYYIEK 758
|
|
| DNA_polB_B1_exo |
cd05783 |
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ... |
261-465 |
4.43e-10 |
|
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: 61.57 E-value: 4.43e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 261 PDPVVLAFDIET-TKLPLKFPDPETDQIMMISY-MIDGQGYlitnREIVSEDIEDFEFTPKPEYEGPFCVFNEpDESHLI 338
Cdd:cd05783 3 PKLKRIAIDIEVyTPIKGRIPDPKTAEYPVISVaLAGSDGL----KRVLVLKREGVEGLEGLLPEGAEVEFFD-SEKELI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 339 QRWFEHVQETkPtIIVTYNGDFFDWPFVEARAAAHGI-NMYQEIGFQKDSqGEYKASqcIHMDCLRWVKRDS---YLPVG 414
Cdd:cd05783 78 REAFKIISEY-P-IVLTFNGDNFDLPYLYNRALKLGIpKEEIPIYLKRDY-ATLKHG--IHIDLYKFFSNRAiqvYAFGN 152
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 2024358764 415 SH---NLKAAAKAKLGYDPVELDpEEMCRMATEEpqtLATYSVSDAVATYYMYM 465
Cdd:cd05783 153 KYreyTLDAVAKALLGEGKVELE-KNISELNLYE---LAEYNYRDAELTLELTT 202
|
|
| DNA_polB_like1_exo |
cd05782 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
265-466 |
1.17e-09 |
|
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: 60.33 E-value: 1.17e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 265 VLAFDIETTklplkfPDPETDQIMMISYMIDGQGYLITNREIVSEDIEDfEFTPKP-------------EYEGPFCVFNE 331
Cdd:cd05782 1 ILVFDIETV------PDVDLGRRLYLLLELDDLEVLEKRFAQRLEKSGS-DFLPLPfhkvvsisalyrdDDGGFLKVRTL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 332 P--DESHLIQRWFEHVQETKPTIiVTYNGDFFDWPFVEARAAAHGINM--YQEIGfQKDSQGEYKASQcIHMDCLRWVKr 407
Cdd:cd05782 74 DgaDEKELLEDFFQLIEKKNPRL-VSFNGRGFDLPVLHLRALIHGVSApaYFDLG-NKDWNYRNRYSE-RHLDLMDLLA- 149
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2024358764 408 dSYLPVGSHNLKAAAKAkLGYdPVELDPE-----EMcrMATEEPQTLATYSVSDAVATYYMYMK 466
Cdd:cd05782 150 -FYGARARASLDLLAKL-LGI-PGKMDVDgsqvwEL--YAEGKLDEIAEYCETDVLNTYLLYLR 208
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
261-375 |
2.44e-09 |
|
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarchaea. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B-DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.
Pssm-ID: 99824 [Multi-domain] Cd Length: 188 Bit Score: 58.88 E-value: 2.44e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 261 PDPVVLAFDIETTKlPLKFPDPETDQIMMISYMIDGqGYLitnREIVSEDIedfeftpkpeyegpfcvfnepDESHLIQR 340
Cdd:cd05781 1 PDLKTLAFDIEVYS-KYGTPNPRRDPIIVISLATSN-GDV---EFILAEGL---------------------DDRKIIRE 54
|
90 100 110
....*....|....*....|....*....|....*
gi 2024358764 341 WFEHVQETKPTIIVTYNGDFFDWPFVEARAAAHGI 375
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; ... |
265-394 |
4.12e-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: 59.13 E-value: 4.12e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 265 VLAFDIETTKLPLKFPDPETDQIMMISYMIDGQGylitnreiVSEDIEDFEFTPKPeyegpfC-------VFNEPDESHL 337
Cdd:cd05777 9 ILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQG--------EGEPFIRNIFTLKT------CapivgaqVFSFETEEEL 74
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 2024358764 338 IQRWFEHVQETKPTIIVTYNGDFFDWPFVEARAAAHGINMYQEIGFQKDSQGEYKAS 394
Cdd:cd05777 75 LLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDT 131
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
795-1090 |
1.19e-08 |
|
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: 59.51 E-value: 1.19e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 795 YDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGrpLEL---DTDGIWcVLPNSFPENFV 871
Cdd:cd05532 103 LDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKMN--LEViygDTDSIM-INTGTTDYEEA 179
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 872 IKSTNAKKPKVtisypgamlnilvkegftNDQYQELQdpasltyvtrsensifFEVDGPYLAMILPAskeegkklKKRYA 951
Cdd:cd05532 180 KKLGNKIKKEV------------------NKSYKKLE----------------IDIDGVFKRLLLLK--------KKKYA 217
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 952 ----VFNEDGSLA-ELKGFEVKRRGELQLVKIFQSSVFEAFLKGTTLEEVyasVAKVADYWLDVLYSKAANMPDSELFEL 1026
Cdd:cd05532 218 alkvVDDDKGKLKkEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDI---VENIHEYLRKINEDLRNGKIPLEKFII 294
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 1027 iseNRSMSRKLEDYGEQKST-SISTAKRL----AEFL-GDQMvkdaglscRFIISKKPEGSPVTERAIPL 1090
Cdd:cd05532 295 ---TKQLTKNPEEYPDKKSLpHVQVALRMnkrgRKVKaGDTI--------PYIICKDGSSKSLADRAYHP 353
|
|
| RNase_H_2 |
pfam13482 |
RNase_H superfamily; |
266-429 |
7.26e-07 |
|
RNase_H superfamily;
Pssm-ID: 433246 [Multi-domain] Cd Length: 163 Bit Score: 51.06 E-value: 7.26e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 266 LAFDIETTKLplkfpDPETDQImmisYMIdgqGYLITNREivseDIEDFEFTPKPEyegpfcvfnePDESHLIQRWFEHV 345
Cdd:pfam13482 1 LFFDIETTGL-----SPGKNTI----YLI---GVYDVDGD----KVRTFVQYLAEG----------PTEEAAILQLFELL 54
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 346 QetKPTIIVTYNGDFFDWPFVEARAAAHGINMYQeigfqkdsqgeykasqcIHMDCLRWVKRDSYlpvgSHNLKAAAKaK 425
Cdd:pfam13482 55 A--DYPLLVTFNGKSFDVPFIKRRFKRYDLDELF-----------------RHIDLLHPLRKLGL----ESGLKSVER-E 110
|
....
gi 2024358764 426 LGYD 429
Cdd:pfam13482 111 LGIE 114
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
266-460 |
3.34e-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: 50.10 E-value: 3.34e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 266 LAFDIETTKLPLKF---PDPETDQIMMISyMIDGQGYLITnreIVSEDIedfeftpkpeyegpfcvfnepDESHLIQRWF 342
Cdd:cd05785 12 LQLDIETYSLPGFFfsnPDRGDDRIIIVA-LRDNRGWEEV---LHAEDA---------------------AEKELLEELV 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 343 EHVQETKPTIIVTYNGDFFDWPFVEARAAAHGINM----YQEIGFQKDSQGEYkASQCIhmDCLRWV--KR---DSYLPV 413
Cdd:cd05785 67 AIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGVPLaigrDGSIPRQRPSRFRF-AERLI--DYPRYDipGRhviDTYFLV 143
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*....
gi 2024358764 414 ----------GSHNLKAAAK--AKLGYDPVELDPEEMCRMATEEPQTLATYSVSDAVAT 460
Cdd:cd05785 144 qlfdvssrdlPSYGLKAVAKhfGLASPDRTYIDGRQIAEVWRSDPARLLAYALDDVRET 202
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
794-1040 |
1.01e-05 |
|
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: 50.30 E-value: 1.01e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 794 LYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGRP-LEL---DTDGIwcvlpnsfpen 869
Cdd:pfam00136 150 ILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYnFRViygDTDSV----------- 218
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 870 FVIKSTNAKKPKVTIsypGAMLNILVkegfTNDQYQelqdpasltyvtrseNSIFFEVDGPYLAMILPAskeegkklKKR 949
Cdd:pfam00136 219 FIEFGGKDVEEAMKI---GDELAEHV----NQDLFK---------------SPIKLEFEKVYKPLLLIS--------KKK 268
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 950 YA----VFNEDGSLAELKGFEVKRRGELQLVKIFQSSVFEAFLKGTTLEEVYASVAKVadywLDVLYSKAANMP-DSELF 1024
Cdd:pfam00136 269 YAglkyTAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSDRGLPVGLEFVISI----LNDARSDLRNNKvPLEKF 344
|
250
....*....|....*.
gi 2024358764 1025 ELiseNRSMSRKLEDY 1040
Cdd:pfam00136 345 VI---SKELSKPPDNY 357
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
798-1109 |
1.04e-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: 50.34 E-value: 1.04e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 798 LQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELIEQIGRP-LELDTDGIWCVLPNSFPEnfviksTN 876
Cdd:cd05537 92 LSQAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQvIYGDTDSTFVWLGEELDA------AE 165
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 877 AKK-PKVTISYPGAMLNILVKEGFTNDQYQELQdpasltyvtrsensifFEVDgpYLAMILPA--SKEEGKklKKRYA-- 951
Cdd:cd05537 166 AQAiGKELASQINQWWAQKLKEEFGLESFLEIE----------------FETH--YSRFFMPTirGSDEGS--KKRYAgl 225
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 952 VFNEDGSLAELKGFEVKRRGELQLVKIFQSSVFEAFLKGTTLEEVYASVakvadywLDVLYskaANMPDSelfELISENR 1031
Cdd:cd05537 226 KSTDGGDELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGFIKET-------VEELL---AGELDE---LLVYRKR 292
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2024358764 1032 sMSRKLEDYGEQKSTSISTAKRLAEFLGDQMVKDAGLSCRFIISKK-PEgsPVTERAIPLAiFQaepsvrkHYLRKWLK 1109
Cdd:cd05537 293 -LRRPLSEYTKNVPPHVQAARLADQINRELGRPRQYQWIEYVITVNgPE--PLEYRTSPLD-YQ-------HYIDKQLK 360
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
217-385 |
1.07e-05 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 50.80 E-value: 1.07e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 217 EYDVPYHMRLSIDLKIHVAHW----------YNVRYRGSTFPPEI-TRRDDLVERPD--------PV-VLAFDIETTKLP 276
Cdd:PTZ00166 198 ESNVPFVLRFLIDNNITGGSWltlpkgkykiRPPKKKTSTCQIEVdCSYEDLIPLPPegeyltiaPLrILSFDIECIKLK 277
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 277 -LKFPDPETDQIMMISYMIDGQGYLItnreivsEDIEDFEFTPKPEYEGPFC-VFNEPDESHLIQRWFEHVQETKPTIIV 354
Cdd:PTZ00166 278 gLGFPEAENDPVIQISSVVTNQGDEE-------EPLTKFIFTLKECASIAGAnVLSFETEKELLLAWAEFVIAVDPDFLT 350
|
170 180 190
....*....|....*....|....*....|.
gi 2024358764 355 TYNGDFFDWPFVEARAAAHGINMYQEIGFQK 385
Cdd:PTZ00166 351 GYNIINFDLPYLLNRAKALKLNDFKYLGRIK 381
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
795-1011 |
1.29e-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: 49.79 E-value: 1.29e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 795 YDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANII-TQARELIEQIGRPLELDTDGIWCVLPNSFpenfvik 873
Cdd:cd05538 77 FKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLkLMIRWLRRRGATPVEVDTDGIYFIPPNGV------- 149
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 874 sTNAKKPKVTISypgaMLNILVKEGftndqyqelqdpasltyvtrsensIFFEVDGPYLAMILpaskeegkKLKKRYAVF 953
Cdd:cd05538 150 -DTEDEEEELVR----ELSSTLPKG------------------------ITVEFDGRYRAMFS--------YKIKNYALL 192
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*...
gi 2024358764 954 NEDGSLAeLKGFEVKRRGELQLVKIFQSSVFEAFLKGttleevyaSVAKVADYWLDVL 1011
Cdd:cd05538 193 DYDGKLI-VKGSAFRSRGIEPFLREFLREAVRLLLQG--------DGAGVHDLYEDYL 241
|
|
| DNA_pol_B_exo2 |
pfam10108 |
Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; This domain is found in ... |
329-375 |
8.17e-04 |
|
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: 42.99 E-value: 8.17e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 2024358764 329 FNEPD--ESHLIQRWFEHVQETKPTIiVTYNGDFFDWPFVEARAAAHGI 375
Cdd:pfam10108 30 LGEPEdsEKELIQRFFDGVEKYTPQL-VSFNGRGFDLPVLHYRALKHGV 77
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
304-1057 |
8.94e-04 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 44.68 E-value: 8.94e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 304 REIVSEDIEDFEF-TPKP-------EYEGPFC-VFNEPDESHLIQRWFEHVQETKPtiIVTYNGDFFDWPFVEARAAAHG 374
Cdd:PRK05761 171 RKLAEDWLPIFEApIPKIkriaidiEVYTPAKgRIPDDSEKELLAELFDIILEYPP--VVTFNGDNFDLPYLYNRALKLG 248
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 375 InmyqeigfQKDSQGEYKASQCIHMDCLRW---VKRDSYLPVG--SH---NLKAAAKAKLGYDPVELDpEEMCRMATEEp 446
Cdd:PRK05761 249 I--------PKEEIPIEPGRAGIHIDLYKFfqnKAVRSYAFYGkyRHreaRLDAVGRALLGISKVELE-TNISELDLEE- 318
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 447 qtLATYSVSDAVATYYMYMKY---VHPFIFALCTIIPMEPDEVLRKGSGTLCEALLMVQAYHANIIFPNKqeqefnkltE 523
Cdd:PRK05761 319 --LAEYNFRDAEITLKLTFFNnelVLKLILLLSRISKLPIEELSRATISTWISNLEYWEHRKRGWLIPWK---------E 387
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 524 DGHVLDSET----------YVGGHVEALESGVFrsdipcrfkmnpaaFDylvqnvektlrhaieeeerlpldqvtnfqev 593
Cdd:PRK05761 388 DILRLDHEVykkaiikgkkYRGGLVFQPPPGIF--------------FN------------------------------- 422
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 594 cdeikvklnslkdvpnriecplIYHLDVGAMYPNIILTnrlqpsamvdeatcaacdfnkpgancqrrmtwqwrgefmpas 673
Cdd:PRK05761 423 ----------------------VYVLDFASLYPSIIVK------------------------------------------ 438
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 674 rseyhriqqqlesekfpplypdgaprafHELSreeqakYEKKRladyCRKAYKKIHVtKVEERVTTICQRENSF---YVD 750
Cdd:PRK05761 439 ----------------------------WNLS------PETVR----IPECKCHYDD-EVPELGHSVCDDRPGLtsvLVG 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 751 TVRAFRDRRYefkglhkvwKKKlsaametgdASEVKRCKNMEILYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVC 830
Cdd:PRK05761 480 LLRDFRVKIY---------KKK---------AKDPNLDEERRAWYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESIT 541
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 831 FTGANIITQARELIEQIG-RPLELDTDGIWcvlpnsfpenfvikstnakkpkVTisypgamlnilvkeGFTNDQYQELQd 909
Cdd:PRK05761 542 ALGREILLSTKKKAEELGlKVLYGDTDSLF----------------------VW--------------GPTKESLEELI- 584
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 910 paslTYVTRsENSIFFEVDGPYLAMILpaskeegKKLKKRYAVFNEDGSLaELKGFEVKRRGELQLVKIFQSSVFEAFLK 989
Cdd:PRK05761 585 ----KEIEE-RTGIDLEVDKTYDWVAF-------SGLKKNYFGVLKDGKV-KIKGIVAKKRNTPEFVKELQREVLEVLKS 651
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 990 GTTLEEVYASVAKVADYwLDVLYSK--AANMPDSELfeliSENRSMSRKLEDYGEQKSTSISTAKRLAEF 1057
Cdd:PRK05761 652 IRSPEDVEKVKDEIEDV-LKRYYEKlrAKDYPLDEL----AIRVRLSKPLDEYTKNTPQHVKAALQLRDY 716
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
265-382 |
6.18e-03 |
|
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: 40.68 E-value: 6.18e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 265 VLAFDIETTKLPLKFPDPETDQIMMISYMIDGQGYLITNRE------IVSEDIEDFEFTPKPEYEG--PFCVFNepDESH 336
Cdd:cd05778 6 ILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDAnkvgviIVDELKSNASNGRIRSGLSgiPVEVVE--SELE 83
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 2024358764 337 LIQRWFEHVQETKPTIIVTYNGDFFDWPFVEARAAA-HGINMYQEIG 382
Cdd:cd05778 84 LFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAAlGIDDLLDEIS 130
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
722-826 |
9.56e-03 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 41.21 E-value: 9.56e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358764 722 RKAYKKIHVTkvEERVTTICQRENSFYVDTVRAFR--DRRYEFKGLHKVWKKKLSAAMETGdasEVKRCKNMEILYDSLQ 799
Cdd:PHA02528 468 RKIYKKKMLA--AERNAELIKTILEDLNDSVDTPIdvDYYFDFSDEFKAELKTLTKSSLKA---LLEECEKEIALCNTIQ 542
|
90 100
....*....|....*....|....*..
gi 2024358764 800 LAHKCILNSFYGYVMRKGARWYSMEMA 826
Cdd:PHA02528 543 MARKILINSLYGALGNEHFRYYDLRNA 569
|
|
| |
