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Conserved domains on  [gi|1622930091|ref|XP_028702868|]
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DNA polymerase zeta catalytic subunit isoform X2 [Macaca mulatta]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
POLBc_zeta cd05534
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ...
2581-3029 0e+00

DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.


:

Pssm-ID: 99917  Cd Length: 451  Bit Score: 865.37  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2581 GSQYRVESMMLRIAKPMNYIPVTPSVQQRSQMRAPQCVPLIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHV 2660
Cdd:cd05534      1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2661 ENLGKYDEFKFGCTSLRVPPD--LLYQVRHDITVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSR 2738
Cdd:cd05534     81 EELNGGGKFGFLGVKLYLPPPplDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDDKKLQR 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2739 MLDARQLGLKLIANVTFGYTAANFSGRMPCIEVGDSIVHKARETLERAIKLVNDTKKWGARVVYGDTDSMFVLLKGATKE 2818
Cdd:cd05534    161 ILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLFVLLPGRTKE 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2819 QSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPVFDAKGIETVRRDSCPAVSKILERSLK 2898
Cdd:cd05534    241 EAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAVQKILEKSLR 320
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2899 LLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYRGSfSYKPGACVPALELT-RKMLTYDRRSEPQVGERVPYVII 2977
Cdd:cd05534    321 ILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLG-TYKEGATLPAGAIVaLRRMEKDPRAEPQYGERVPYVVV 399
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1622930091 2978 YGTPGVPLIQLVRRPVEVLQDPTLRLNATYYITKQILPPLARIFSLIGIDVF 3029
Cdd:cd05534    400 RGEPGSRLIDLVVSPEEFLADPSLRLDAEYYITKQIIPALDRLFNLVGVDVQ 451
DUF4683 pfam15735
Domain of unknown function (DUF4683); This domain family is found in eukaryotes, and is ...
753-1133 0e+00

Domain of unknown function (DUF4683); This domain family is found in eukaryotes, and is typically between 384 and 400 amino acids in length.


:

Pssm-ID: 464832  Cd Length: 391  Bit Score: 579.52  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  753 NRTMVHSLNSTADESGLNKLKIRYEEFQEHKTEKPSLSQQAAHYMFFPSVVLSNCLTR---PQKLSPVTYKLQPG-NKPS 828
Cdd:pfam15735    1 VRNYVFDDDQSTDESDVGKLKIRYESFQENKAEKTSLSQQEAHYKFFPSVVLSNCLSRrsaLKKLGPVTYKLQQFkSRQS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  829 RLKLNKKK--LAGHQETFTKSSETGSTKDNS-IQNNPCNSN-PEKDSAFASDlTKTSRGAFENKTPTD--GFIDCHFGDG 902
Cdd:pfam15735   81 RLKLGKKKlnLDGKQEPEKKTHDKASTKEKCnLQGNALNKNiPETEVELDSD-VQVAHSAFKNKMSIDpaNSDSCHFSDD 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  903 TLETEQSFGLYGNKYTLRAKRKVNYETEDSESSFVTHNSKISLPHPMEIGESLDGTLKSRKRRKMSKKLPPVIIKYIIIN 982
Cdd:pfam15735  160 SEESYDASSLCGSKYTLRAKRKVNYETEDSESSEKIHNSKESLPQGSKEEDDDDGSPKSQKRRKVSKKEPPVIIKYIIIN 239
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  983 RFRGRKNMLVKLGKIDAKEKQVILTEEKMELYKKLAPLKDFWPKVPDSPATKYPIYPLTPKKSHRRKSKHKSAKKKTG-K 1061
Cdd:pfam15735  240 RFKGRKNMLVKLGKVDSSETTVTLTEEKLEKYKKLAPLKDFWPKVPDSPATKYPVYPLTPKKSPKRKAKCKSTNKKRIqR 319
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622930091 1062 QQRTNNENIKRTLSFRKKRSHALLSPPSPSYNAETEDCDLNYSDVMSKLGFLSERSTSPINSSPPRCWSPTD 1133
Cdd:pfam15735  320 LPNTESSNIKRTLSFKRKRSHASLSPPQPSYNAETEDCDLNYSDVMSKLGFLSERSLSPTASTPPRCWSPTD 391
DNA_polB_zeta_exo cd05778
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ...
2291-2555 1.07e-95

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: 309.17  E-value: 1.07e-95
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2291 IQNLTLISVELHARTRRDLEPDPEFDPICALFYCISSDAPLPDTEKTElTGVIVIDKDKTVFSQDiryqtplLIRSGITG 2370
Cdd:cd05778      1 HQHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANK-VGVIIVDELKSNASNG-------RIRSGLSG 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2371 LEVTYAADEKALFHEIAHIIKRgchqhvrcfqyphffyfckqlrkrnmYDPDILLGYEIQMHSWGYLLQRAAALSVDLC- 2449
Cdd:cd05778     73 IPVEVVESELELFEELIDLVRR--------------------------FDPDILSGYEIQRSSWGYLIERAAALGIDDLl 126
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2450 QMISRVPDDKiENRFAAERDEYGSYTMSEINIVGRITLNLWRIMRNEVALTNYTFENVSFHVLHQRFPLFTFRVLSDWFD 2529
Cdd:cd05778    127 DEISRVPSDS-NGKFGDRDDEWGYTHTSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYK 205
                          250       260
                   ....*....|....*....|....*.
gi 1622930091 2530 NKTDLYRWKMVDHYVSRVRGNLQMLE 2555
Cdd:cd05778    206 SGSASERWRVLEYYLKRVRLNLEILD 231
zf-C4pol pfam14260
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ...
3065-3132 2.02e-17

C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1.


:

Pssm-ID: 464119  Cd Length: 68  Bit Score: 78.95  E-value: 2.02e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622930091 3065 CPVCDDLTQhGICSKCRSQPQHVAVILNQEIRELERKQEQLVKICKNCTGCFDRHIPCVSLNCPVLFK 3132
Cdd:pfam14260    1 CLGCGAPEE-PLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYM 67
PTZ00166 super family cl36522
DNA polymerase delta catalytic subunit; Provisional
6-182 1.79e-14

DNA polymerase delta catalytic subunit; Provisional


The actual alignment was detected with superfamily member PTZ00166:

Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 80.46  E-value: 1.79e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091    6 IVTADYYMASplqglDTCQ-SPLTQAPVKK---VPVVRIFGATPAGQKTCLHLHGIFPYLYVPydgygqQPESYLSQMAF 81
Cdd:PTZ00166    46 QLDADYTEKD-----DKSQgNPHNTVSGVRhveVPIIRLYGVTKEGHSVLVNVHNFFPYFYIE------APPNFLPEDSQ 114
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091   82 SIDRALNVALGNPSS---TAQHVFKVSLVSGMPFYGYHEK-ERHFMKIYLYNPAVVKRICELLQSGAIMN-------KFY 150
Cdd:PTZ00166   115 KLKRELNAQLSEQSQfkkYQNTVLDIEIVKKESLMYYKGNgEKDFLKITVQLPKMVPRLRSLIESGVVVCgggwdgiRLF 194
                          170       180       190
                   ....*....|....*....|....*....|..
gi 1622930091  151 QPHEAHIPYLLQLFIDYNLYGMNLINLAAVKF 182
Cdd:PTZ00166   195 QTYESNVPFVLRFLIDNNITGGSWLTLPKGKY 226
REV3L_RBD cd22287
REV7 binding domain found in protein reversionless 3-like (REV3L) and similar proteins; REV3L, ...
1872-1894 9.22e-09

REV7 binding domain found in protein reversionless 3-like (REV3L) and similar proteins; REV3L, also called REV3-like, or REV3, or DNA polymerase zeta catalytic subunit (POLZ), is the catalytic subunit of the DNA polymerase zeta complex, an error-prone polymerase specialized in translesion DNA synthesis (TLS). REV3L lacks an intrinsic 3'-5' exonuclease activity and thus has no proofreading function. The model corresponds to a conserved region that is responsible for the binding of REV7.


:

Pssm-ID: 412083  Cd Length: 23  Bit Score: 52.95  E-value: 9.22e-09
                           10        20
                   ....*....|....*....|...
gi 1622930091 1872 RTAHILKPLMSPPSREEIMATLL 1894
Cdd:cd22287      1 RTAHILKPLMSPPSREEIMATLL 23
 
Name Accession Description Interval E-value
POLBc_zeta cd05534
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ...
2581-3029 0e+00

DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.


Pssm-ID: 99917  Cd Length: 451  Bit Score: 865.37  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2581 GSQYRVESMMLRIAKPMNYIPVTPSVQQRSQMRAPQCVPLIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHV 2660
Cdd:cd05534      1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2661 ENLGKYDEFKFGCTSLRVPPD--LLYQVRHDITVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSR 2738
Cdd:cd05534     81 EELNGGGKFGFLGVKLYLPPPplDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDDKKLQR 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2739 MLDARQLGLKLIANVTFGYTAANFSGRMPCIEVGDSIVHKARETLERAIKLVNDTKKWGARVVYGDTDSMFVLLKGATKE 2818
Cdd:cd05534    161 ILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLFVLLPGRTKE 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2819 QSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPVFDAKGIETVRRDSCPAVSKILERSLK 2898
Cdd:cd05534    241 EAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAVQKILEKSLR 320
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2899 LLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYRGSfSYKPGACVPALELT-RKMLTYDRRSEPQVGERVPYVII 2977
Cdd:cd05534    321 ILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLG-TYKEGATLPAGAIVaLRRMEKDPRAEPQYGERVPYVVV 399
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1622930091 2978 YGTPGVPLIQLVRRPVEVLQDPTLRLNATYYITKQILPPLARIFSLIGIDVF 3029
Cdd:cd05534    400 RGEPGSRLIDLVVSPEEFLADPSLRLDAEYYITKQIIPALDRLFNLVGVDVQ 451
DUF4683 pfam15735
Domain of unknown function (DUF4683); This domain family is found in eukaryotes, and is ...
753-1133 0e+00

Domain of unknown function (DUF4683); This domain family is found in eukaryotes, and is typically between 384 and 400 amino acids in length.


Pssm-ID: 464832  Cd Length: 391  Bit Score: 579.52  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  753 NRTMVHSLNSTADESGLNKLKIRYEEFQEHKTEKPSLSQQAAHYMFFPSVVLSNCLTR---PQKLSPVTYKLQPG-NKPS 828
Cdd:pfam15735    1 VRNYVFDDDQSTDESDVGKLKIRYESFQENKAEKTSLSQQEAHYKFFPSVVLSNCLSRrsaLKKLGPVTYKLQQFkSRQS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  829 RLKLNKKK--LAGHQETFTKSSETGSTKDNS-IQNNPCNSN-PEKDSAFASDlTKTSRGAFENKTPTD--GFIDCHFGDG 902
Cdd:pfam15735   81 RLKLGKKKlnLDGKQEPEKKTHDKASTKEKCnLQGNALNKNiPETEVELDSD-VQVAHSAFKNKMSIDpaNSDSCHFSDD 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  903 TLETEQSFGLYGNKYTLRAKRKVNYETEDSESSFVTHNSKISLPHPMEIGESLDGTLKSRKRRKMSKKLPPVIIKYIIIN 982
Cdd:pfam15735  160 SEESYDASSLCGSKYTLRAKRKVNYETEDSESSEKIHNSKESLPQGSKEEDDDDGSPKSQKRRKVSKKEPPVIIKYIIIN 239
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  983 RFRGRKNMLVKLGKIDAKEKQVILTEEKMELYKKLAPLKDFWPKVPDSPATKYPIYPLTPKKSHRRKSKHKSAKKKTG-K 1061
Cdd:pfam15735  240 RFKGRKNMLVKLGKVDSSETTVTLTEEKLEKYKKLAPLKDFWPKVPDSPATKYPVYPLTPKKSPKRKAKCKSTNKKRIqR 319
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622930091 1062 QQRTNNENIKRTLSFRKKRSHALLSPPSPSYNAETEDCDLNYSDVMSKLGFLSERSTSPINSSPPRCWSPTD 1133
Cdd:pfam15735  320 LPNTESSNIKRTLSFKRKRSHASLSPPQPSYNAETEDCDLNYSDVMSKLGFLSERSLSPTASTPPRCWSPTD 391
DNA_pol_B pfam00136
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
2577-3024 2.73e-114

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: 371.56  E-value: 2.73e-114
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2577 VLTRGSQYRVESMMLRIAKPMNYIpVTPSVQQRSQMRAPQCVpLIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTC 2656
Cdd:pfam00136    6 VLEGGQQIRVESCLLRLALEEGFI-LPDRPSAKGDEDGYQGA-TVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCYTTL 83
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2657 LGHVENlgkydefkfgctSLRVPPDLLYQvrhDITVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKqDRAL 2736
Cdd:pfam00136   84 VRSVDE------------ANNLPPEDNLI---TVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEET-DPFE 147
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2737 SRMLDARQLGLKLIANVTFGYTAANfSGRMPCIEVGDSIVHKARETLERAIKLVNDTKKWGARVVYGDTDSMFVLLKGAT 2816
Cdd:pfam00136  148 RAILDKQQLALKITANSVYGFTGFA-NGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYNFRVIYGDTDSVFIEFGGKD 226
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2817 KEQSFKIGQEIAEAVT-ATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPvFDAKGIETVRRDSCPAVSKILER 2895
Cdd:pfam00136  227 VEEAMKIGDELAEHVNqDLFKSPIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFNK-LDMKGVDLVRRDNCPLVKEVIKK 305
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2896 SLKLLFETRDISLIKQYVQRQCM----KLLEGKASIQDFIFAKEYRGSFSYKPGACVPALELTRKMLTYDRRsEPQVGER 2971
Cdd:pfam00136  306 VLDLLLSDRGLPVGLEFVISILNdarsDLRNNKVPLEKFVISKELSKPPDNYKSKNLPHVEVALRMNKRNGE-APEVGDR 384
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622930091 2972 VPYVII---YGTPGVPLIQLVRRPVEVLQDpTLRLNATYYITKQILPPLARIFSLI 3024
Cdd:pfam00136  385 IPYVIVkaaKGLKNLLIYERAEDPEYVLEN-NLPIDYEYYFSNQLIPPVARLLEPI 439
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
2420-3153 5.15e-113

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 388.23  E-value: 5.15e-113
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2420 DPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKI---ENRFAAErdEYGSYTMSEINIVGRITLNLWRIMRNE 2496
Cdd:PTZ00166   345 DPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSvikDSKFSSK--QMGTRESKEINIEGRIQFDVMDLIRRD 422
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2497 VALTNYTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYRWKMV----DHYVSrvrgnLQMLEQLDLIGKTSEMARLFGI 2572
Cdd:PTZ00166   423 YKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVyclkDAILP-----LRLLDKLLLIYNYVEMARVTGT 497
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2573 QFLHVLTRGSQYRVESMMLRIAKPMNY-IPVTPSVQQRSQMRAPQCVplIMEPESRFYSNSVLVLDFQSLYPSIVIAYNY 2651
Cdd:PTZ00166   498 PIGWLLTRGQQIKVTSQLLRKCKKLNYvIPTVKYSGGGSEEKYEGAT--VLEPKKGFYDEPIATLDFASLYPSIMIAHNL 575
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2652 CFSTclghvenLGKYDEFKfgctslRVPPDLLyqvrhdiTVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYK 2731
Cdd:PTZ00166   576 CYST-------LVPPNDAN------NYPEDTY-------VTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEK 635
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2732 qDRALSRMLDARQLGLKLIANVTFGYTAANFSGRMPCIEVGDSIVHKARETLERAIKLVND--TKKWG----ARVVYGDT 2805
Cdd:PTZ00166   636 -DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKhyTKANGykhdATVIYGDT 714
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2806 DSmfVLLKGATK--EQSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPVfDAKGIETVRR 2883
Cdd:PTZ00166   715 DS--VMVKFGTDdiQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAGLLYTNPEKYDKI-DCKGIETVRR 791
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2884 DSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYrGSFSYKpgACVPALELTRKMLTYDRR 2963
Cdd:PTZ00166   792 DNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRIDISLLVITKSL-GKDDYE--GRLAHVELAKKLRQRDPG 868
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2964 SEPQVGERVPYVIIYGTPGVPLIQLVRRPVEVLqDPTLRLNATYYItKQILPPLARIFSLIGIDVFSWYHELPRIHKATN 3043
Cdd:PTZ00166   869 SAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVL-ENNIPIDTQYYL-DQIKNPLLRIFEGVMDNPDSLFSGEHTRHITIS 946
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 3044 SSrsepegRKGTISQYFT-TLHCPVCDDLTQHG-ICSKCRS--QPQHVAVILNqEIRELERKQEQLVKICKNCTGCFDRH 3119
Cdd:PTZ00166   947 SS------SKGGLSKFVKkQLQCLGCKSVIKEGaLCDNCNQnkEPSIYGKKLA-KRRHKEAEYSQLWTQCQRCQGSLHQE 1019
                          730       740       750
                   ....*....|....*....|....*....|....
gi 1622930091 3120 IPCVSLNCPVLFKVSRVNRELSKapyLRQLLDQF 3153
Cdd:PTZ00166  1020 VICTNRDCPIFYRRKKVQKDLAE---LQELLSRF 1050
DNA_polB_zeta_exo cd05778
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ...
2291-2555 1.07e-95

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: 309.17  E-value: 1.07e-95
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2291 IQNLTLISVELHARTRRDLEPDPEFDPICALFYCISSDAPLPDTEKTElTGVIVIDKDKTVFSQDiryqtplLIRSGITG 2370
Cdd:cd05778      1 HQHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANK-VGVIIVDELKSNASNG-------RIRSGLSG 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2371 LEVTYAADEKALFHEIAHIIKRgchqhvrcfqyphffyfckqlrkrnmYDPDILLGYEIQMHSWGYLLQRAAALSVDLC- 2449
Cdd:cd05778     73 IPVEVVESELELFEELIDLVRR--------------------------FDPDILSGYEIQRSSWGYLIERAAALGIDDLl 126
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2450 QMISRVPDDKiENRFAAERDEYGSYTMSEINIVGRITLNLWRIMRNEVALTNYTFENVSFHVLHQRFPLFTFRVLSDWFD 2529
Cdd:cd05778    127 DEISRVPSDS-NGKFGDRDDEWGYTHTSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYK 205
                          250       260
                   ....*....|....*....|....*.
gi 1622930091 2530 NKTDLYRWKMVDHYVSRVRGNLQMLE 2555
Cdd:cd05778    206 SGSASERWRVLEYYLKRVRLNLEILD 231
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
2313-2814 2.85e-91

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: 306.38  E-value: 2.85e-91
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  2313 PEFDPICALFYCISSDAPLPDTEKTELtgvIVIDKDKTVFSQDIRYQT-----PLLIRSGITGLEVTYAADEKALFHEia 2387
Cdd:smart00486    1 PPLKILSFDIETYTDGGNFPDAEIFDD---EIIQISLVINDGDKKGANrrilfTLGTCKEIDGIEVYEFNNEKELLLA-- 75
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  2388 hiikrgchqhvrcfqyphFFYFCKQlrkrnmYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPD-DKIENRFAA 2466
Cdd:smart00486   76 ------------------FFEFIKK------YDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIgLRIPNKKPL 131
                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  2467 ERDEYGSYTMSEINIVGRITLNLWRIMRNEVALTNYTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYRWkMVDHYVSR 2546
Cdd:smart00486  132 FGSKSFGLSDIKVYIKGRLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDE-LLRYCIQD 210
                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  2547 VRGNLQMLEQLDLIGKTSEMARLFGIQFLHVLTRGSQYRVESMMLRIAKPMNYIPVTPSVQQRSQMRAPQCVP------L 2620
Cdd:smart00486  211 AVLTLKLFNKLNVIPLIIELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEPDLKKKvkyeggK 290
                           330       340       350       360       370       380       390       400
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  2621 IMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHVENLGKYDEFKFgctslrvppdllYQVRHDITVSPNGVAFV 2700
Cdd:smart00486  291 VLEPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKGDLIIP------------EDLLTIKYEKGNKYRFV 358
                           410       420       430       440       450       460       470       480
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  2701 KPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSR-MLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKA 2779
Cdd:smart00486  359 KKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESEELKkLLDSRQLALKLTANSVYGYLGFTNS-RLPCKPLAASVTALG 437
                           490       500       510
                    ....*....|....*....|....*....|....*..
gi 1622930091  2780 RETLERAIKLVND--TKKWGARVVYGDTDSMFVLLKG 2814
Cdd:smart00486  438 REILEKTKELIEEngYPKPGFKVIYGDTDSIFVTKPG 474
PolB COG0417
DNA polymerase B elongation subunit [Replication, recombination and repair];
2342-3027 4.13e-84

DNA polymerase B elongation subunit [Replication, recombination and repair];


Pssm-ID: 440186 [Multi-domain]  Cd Length: 794  Bit Score: 295.97  E-value: 4.13e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2342 VIVIdkdkTVFSQDIRYQTPLLIRSGItGLEVTYAADEKALFHEIAHIIKRgchqhvrcfqyphffyfckqlrkrnmYDP 2421
Cdd:COG0417    184 IISI----GLAGSDGEKKVLMLGREGV-DFEVEYFDDEKALLEAFFEIIRE--------------------------YDP 232
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2422 DILLGYEIQMHSWGYLLQRAAALSVDLcqMISRvpddkieNRFAAERDEYGSYTMseINIVGRITLNLWRIMRN-EVALT 2500
Cdd:COG0417    233 DIIIGWNVDNFDLPYLQKRAERLGIPL--DLGR-------DGSEPSWREHGGQGF--ASIPGRVVIDLYDALKSaTYKFK 301
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2501 NYTFENVSFHVLHqrfplftfrvlsdwfDNKTDLYRWKMVDHYVSR----VRGNLQ-------MLEQLDLIGKTSEMARL 2569
Cdd:COG0417    302 SYSLDAVAEELLG---------------EGKLIVDGGEIERLWDDDkpalAEYNLRdaeltlrIFEKTLLLPFLIELSRI 366
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2570 FGIQFLHVLTRGSQYRVESMMLRIAKPMNY-IPVTPSVQQRSQMRApqcvpLIMEPESRFYSNsVLVLDFQSLYPSIVIA 2648
Cdd:COG0417    367 TGLPLDDVGRAGSSAAFENLLLPEAHRRGYlAPNKGEIKGEAYPGG-----YVLDPKPGLYEN-VLVLDFKSLYPSIIRT 440
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2649 YNYCFST-CLGHVENLGKYDefkfgctslrvppdllyqvrhditVSPN-GVAFVKPsvRKGVLPRMLEEILKTRFMVKQS 2726
Cdd:COG0417    441 FNISPETlVEGGEEPCGDED------------------------VAPGfGHRFCRE--PKGILPSILEELWDERDEAKKK 494
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2727 MKAYKQDRALSRMLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKARETLERAIKLVndtKKWGARVVYGDTD 2806
Cdd:COG0417    495 MKKAKPDSEEYRLYDALQQALKILMNSFYGVLGSEGC-RFYDPELAESITARGREIIKQTIEKA---EELGYKVIYGDTD 570
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2807 SMFVLLKGATKEQSFKIGQEIAEAVTATNPKPVKLKFEKVYLPcVLQT--KKRYVGYmyetldQKDPVFDAKGIETVRRD 2884
Cdd:COG0417    571 SLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRR-FFFPgsKKRYAGL------TEDGKIDIKGLEAVRSD 643
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2885 SCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYRGSFS-YKpgACVPA-LELTRKMLTYDR 2962
Cdd:COG0417    644 WTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSeYE--KNVPPhVRAARKLDERGR 721
                          650       660       670       680       690       700
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622930091 2963 rsEPQVGERVPYVIIYGTPGVpliqlvrRPVEVLQDPTLRLNATYYITKQILPPLARIFSLIGID 3027
Cdd:COG0417    722 --PYQRGDKISYVITKGGGRV-------EPVELAKERESEIDYDYYIEKQLKPTADRILEAFGVS 777
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
2409-3021 3.68e-50

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: 196.82  E-value: 3.68e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2409 FCKQLRKRnmyDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKIENRFAAERdeygsytmseinIVGRITLN 2488
Cdd:TIGR00592  591 FMAKVKKI---DPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGER------------TCGRMICD 655
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2489 LWRIMRNEVALTNYTFENVSFHVLH-QRFPLFTFRVLSDWFDNKTDLYrwkMVDHYVSRVRGNLQMLEQLDLIGKTSEMA 2567
Cdd:TIGR00592  656 VEISAKELIRCKSYDLSELVQQILKtERKVIPIDNINNMYSESSSLTY---LLEHTWKDAMFILQIMCELNVLPLALQIT 732
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2568 RLFGIQFLHVLTRGSQYRVESMMLRIAKPMNYI-PVTPSVQQRSQMR--------------APQCVPLIMEPESRFYSNS 2632
Cdd:TIGR00592  733 NIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIvPDKQIFRKQQKLGdedeeidgykkgkkAAYAGGLVLEPKVGLYDKY 812
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2633 VLVLDFQSLYPSIVIAYNYCFSTclghVENLGKYDEfkfgctsLRVPPDllyqvrhditvspngvafvkPSVRKGVLPRM 2712
Cdd:TIGR00592  813 VLLMDFNSLYPSIIQEFNICFTT----VQQKVDEDE-------LPELPD--------------------SELEMGILPRE 861
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2713 LEEILKTRFMVKQSMKAyKQDRALSRMLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKARETLERAIKLVnd 2792
Cdd:TIGR00592  862 LRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKS-RFYAKPLAALVTAKGREILEHTRQLV-- 937
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2793 tKKWGARVVYGDTDSMFVLLKGATKEQSFKIGQEIAEAVTATNpKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPV 2872
Cdd:TIGR00592  938 -EEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLY-KLLELDIDGVFKRLLLLKKKKYAAIKVEGDSDGNYT 1015
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2873 F--DAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKL----LEGKASIQDFIFAKEY-RGSFSYKPG 2945
Cdd:TIGR00592 1016 TkqEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIgknvLNGEVPLEKFVINKQLtRDPKDYPDG 1095
                          570       580       590       600       610       620       630
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1622930091 2946 ACVPALELTRKMLTYDRRSEPQvGERVPYVIIYGTPGVPLIQLVRRPVEVL-QDPTLRLNATYYITKQILPPLARIF 3021
Cdd:TIGR00592 1096 ASLPHVHVALRINARGGRKVKA-GDVVSYVICKDGGNLSARQRAYALEELQrKHNNLIYDTQYYLEHQIHPVVLRIL 1171
zf-C4pol pfam14260
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ...
3065-3132 2.02e-17

C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1.


Pssm-ID: 464119  Cd Length: 68  Bit Score: 78.95  E-value: 2.02e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622930091 3065 CPVCDDLTQhGICSKCRSQPQHVAVILNQEIRELERKQEQLVKICKNCTGCFDRHIPCVSLNCPVLFK 3132
Cdd:pfam14260    1 CLGCGAPEE-PLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYM 67
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
6-182 1.79e-14

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 80.46  E-value: 1.79e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091    6 IVTADYYMASplqglDTCQ-SPLTQAPVKK---VPVVRIFGATPAGQKTCLHLHGIFPYLYVPydgygqQPESYLSQMAF 81
Cdd:PTZ00166    46 QLDADYTEKD-----DKSQgNPHNTVSGVRhveVPIIRLYGVTKEGHSVLVNVHNFFPYFYIE------APPNFLPEDSQ 114
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091   82 SIDRALNVALGNPSS---TAQHVFKVSLVSGMPFYGYHEK-ERHFMKIYLYNPAVVKRICELLQSGAIMN-------KFY 150
Cdd:PTZ00166   115 KLKRELNAQLSEQSQfkkYQNTVLDIEIVKKESLMYYKGNgEKDFLKITVQLPKMVPRLRSLIESGVVVCgggwdgiRLF 194
                          170       180       190
                   ....*....|....*....|....*....|..
gi 1622930091  151 QPHEAHIPYLLQLFIDYNLYGMNLINLAAVKF 182
Cdd:PTZ00166   195 QTYESNVPFVLRFLIDNNITGGSWLTLPKGKY 226
REV3L_RBD cd22287
REV7 binding domain found in protein reversionless 3-like (REV3L) and similar proteins; REV3L, ...
1872-1894 9.22e-09

REV7 binding domain found in protein reversionless 3-like (REV3L) and similar proteins; REV3L, also called REV3-like, or REV3, or DNA polymerase zeta catalytic subunit (POLZ), is the catalytic subunit of the DNA polymerase zeta complex, an error-prone polymerase specialized in translesion DNA synthesis (TLS). REV3L lacks an intrinsic 3'-5' exonuclease activity and thus has no proofreading function. The model corresponds to a conserved region that is responsible for the binding of REV7.


Pssm-ID: 412083  Cd Length: 23  Bit Score: 52.95  E-value: 9.22e-09
                           10        20
                   ....*....|....*....|...
gi 1622930091 1872 RTAHILKPLMSPPSREEIMATLL 1894
Cdd:cd22287      1 RTAHILKPLMSPPSREEIMATLL 23
DNA_pol_B_exo1 pfam03104
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ...
2311-2507 4.00e-07

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: 55.12  E-value: 4.00e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2311 PDPEF--DP---ICALFYCISSDAPLPdtekteltgvIVIDKDKTVFSQDIrYQTPLLIRSGITGLEVTYAADEKALFHe 2385
Cdd:pfam03104  172 PDAENvkDPiiqISCMLDGQGEPEPEP----------RFLFTLRECDSEDI-EDFEYTPKPIYPGVKVFEFPSEKELLR- 239
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2386 iahiikrgchqhvrcfqypHFFYFCKQlrkrnmYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDkieNRFA 2465
Cdd:pfam03104  240 -------------------RFFEFIRQ------YDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNRG---GRSK 291
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1622930091 2466 AERDEYGSYTMSEINIVGRITLNLWRIMRNEVALTNYTFENV 2507
Cdd:pfam03104  292 VREIGFGTRSYEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
DNA_pol_B_exo1 pfam03104
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ...
51-191 5.80e-07

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: 54.35  E-value: 5.80e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091   51 CLHLHGIFPYLYVPYDGYGQQPE--SYLSQMAFSIDRalnvalgnpsstaqhVFKVSLVSGMPFYGYHEKERHFMKIYLY 128
Cdd:pfam03104    9 CVNVFGFKPYFYCLAPDGKELEEviEEIKELYEGLDK---------------IEKIELKLKKSLYGYEEDPVPYLKVSFA 73
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1622930091  129 NPAVVKRICELLQSGAIMNKFyqphEAHIPYLLQLFIDYNLYGMNLINLAAVKFRKARRKSNT 191
Cdd:pfam03104   74 NPRPLLKIRKYLSPENISDVY----EYDVDYLERFLIDNDIVGFGWYKVKVYPFRAEGRISNC 132
 
Name Accession Description Interval E-value
POLBc_zeta cd05534
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ...
2581-3029 0e+00

DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.


Pssm-ID: 99917  Cd Length: 451  Bit Score: 865.37  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2581 GSQYRVESMMLRIAKPMNYIPVTPSVQQRSQMRAPQCVPLIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHV 2660
Cdd:cd05534      1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2661 ENLGKYDEFKFGCTSLRVPPD--LLYQVRHDITVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSR 2738
Cdd:cd05534     81 EELNGGGKFGFLGVKLYLPPPplDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDDKKLQR 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2739 MLDARQLGLKLIANVTFGYTAANFSGRMPCIEVGDSIVHKARETLERAIKLVNDTKKWGARVVYGDTDSMFVLLKGATKE 2818
Cdd:cd05534    161 ILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLFVLLPGRTKE 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2819 QSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPVFDAKGIETVRRDSCPAVSKILERSLK 2898
Cdd:cd05534    241 EAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAVQKILEKSLR 320
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2899 LLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYRGSfSYKPGACVPALELT-RKMLTYDRRSEPQVGERVPYVII 2977
Cdd:cd05534    321 ILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLG-TYKEGATLPAGAIVaLRRMEKDPRAEPQYGERVPYVVV 399
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1622930091 2978 YGTPGVPLIQLVRRPVEVLQDPTLRLNATYYITKQILPPLARIFSLIGIDVF 3029
Cdd:cd05534    400 RGEPGSRLIDLVVSPEEFLADPSLRLDAEYYITKQIIPALDRLFNLVGVDVQ 451
DUF4683 pfam15735
Domain of unknown function (DUF4683); This domain family is found in eukaryotes, and is ...
753-1133 0e+00

Domain of unknown function (DUF4683); This domain family is found in eukaryotes, and is typically between 384 and 400 amino acids in length.


Pssm-ID: 464832  Cd Length: 391  Bit Score: 579.52  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  753 NRTMVHSLNSTADESGLNKLKIRYEEFQEHKTEKPSLSQQAAHYMFFPSVVLSNCLTR---PQKLSPVTYKLQPG-NKPS 828
Cdd:pfam15735    1 VRNYVFDDDQSTDESDVGKLKIRYESFQENKAEKTSLSQQEAHYKFFPSVVLSNCLSRrsaLKKLGPVTYKLQQFkSRQS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  829 RLKLNKKK--LAGHQETFTKSSETGSTKDNS-IQNNPCNSN-PEKDSAFASDlTKTSRGAFENKTPTD--GFIDCHFGDG 902
Cdd:pfam15735   81 RLKLGKKKlnLDGKQEPEKKTHDKASTKEKCnLQGNALNKNiPETEVELDSD-VQVAHSAFKNKMSIDpaNSDSCHFSDD 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  903 TLETEQSFGLYGNKYTLRAKRKVNYETEDSESSFVTHNSKISLPHPMEIGESLDGTLKSRKRRKMSKKLPPVIIKYIIIN 982
Cdd:pfam15735  160 SEESYDASSLCGSKYTLRAKRKVNYETEDSESSEKIHNSKESLPQGSKEEDDDDGSPKSQKRRKVSKKEPPVIIKYIIIN 239
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  983 RFRGRKNMLVKLGKIDAKEKQVILTEEKMELYKKLAPLKDFWPKVPDSPATKYPIYPLTPKKSHRRKSKHKSAKKKTG-K 1061
Cdd:pfam15735  240 RFKGRKNMLVKLGKVDSSETTVTLTEEKLEKYKKLAPLKDFWPKVPDSPATKYPVYPLTPKKSPKRKAKCKSTNKKRIqR 319
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622930091 1062 QQRTNNENIKRTLSFRKKRSHALLSPPSPSYNAETEDCDLNYSDVMSKLGFLSERSTSPINSSPPRCWSPTD 1133
Cdd:pfam15735  320 LPNTESSNIKRTLSFKRKRSHASLSPPQPSYNAETEDCDLNYSDVMSKLGFLSERSLSPTASTPPRCWSPTD 391
DNA_pol_B pfam00136
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
2577-3024 2.73e-114

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: 371.56  E-value: 2.73e-114
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2577 VLTRGSQYRVESMMLRIAKPMNYIpVTPSVQQRSQMRAPQCVpLIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTC 2656
Cdd:pfam00136    6 VLEGGQQIRVESCLLRLALEEGFI-LPDRPSAKGDEDGYQGA-TVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCYTTL 83
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2657 LGHVENlgkydefkfgctSLRVPPDLLYQvrhDITVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKqDRAL 2736
Cdd:pfam00136   84 VRSVDE------------ANNLPPEDNLI---TVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEET-DPFE 147
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2737 SRMLDARQLGLKLIANVTFGYTAANfSGRMPCIEVGDSIVHKARETLERAIKLVNDTKKWGARVVYGDTDSMFVLLKGAT 2816
Cdd:pfam00136  148 RAILDKQQLALKITANSVYGFTGFA-NGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYNFRVIYGDTDSVFIEFGGKD 226
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2817 KEQSFKIGQEIAEAVT-ATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPvFDAKGIETVRRDSCPAVSKILER 2895
Cdd:pfam00136  227 VEEAMKIGDELAEHVNqDLFKSPIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFNK-LDMKGVDLVRRDNCPLVKEVIKK 305
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2896 SLKLLFETRDISLIKQYVQRQCM----KLLEGKASIQDFIFAKEYRGSFSYKPGACVPALELTRKMLTYDRRsEPQVGER 2971
Cdd:pfam00136  306 VLDLLLSDRGLPVGLEFVISILNdarsDLRNNKVPLEKFVISKELSKPPDNYKSKNLPHVEVALRMNKRNGE-APEVGDR 384
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622930091 2972 VPYVII---YGTPGVPLIQLVRRPVEVLQDpTLRLNATYYITKQILPPLARIFSLI 3024
Cdd:pfam00136  385 IPYVIVkaaKGLKNLLIYERAEDPEYVLEN-NLPIDYEYYFSNQLIPPVARLLEPI 439
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
2420-3153 5.15e-113

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 388.23  E-value: 5.15e-113
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2420 DPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKI---ENRFAAErdEYGSYTMSEINIVGRITLNLWRIMRNE 2496
Cdd:PTZ00166   345 DPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSvikDSKFSSK--QMGTRESKEINIEGRIQFDVMDLIRRD 422
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2497 VALTNYTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYRWKMV----DHYVSrvrgnLQMLEQLDLIGKTSEMARLFGI 2572
Cdd:PTZ00166   423 YKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVyclkDAILP-----LRLLDKLLLIYNYVEMARVTGT 497
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2573 QFLHVLTRGSQYRVESMMLRIAKPMNY-IPVTPSVQQRSQMRAPQCVplIMEPESRFYSNSVLVLDFQSLYPSIVIAYNY 2651
Cdd:PTZ00166   498 PIGWLLTRGQQIKVTSQLLRKCKKLNYvIPTVKYSGGGSEEKYEGAT--VLEPKKGFYDEPIATLDFASLYPSIMIAHNL 575
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2652 CFSTclghvenLGKYDEFKfgctslRVPPDLLyqvrhdiTVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYK 2731
Cdd:PTZ00166   576 CYST-------LVPPNDAN------NYPEDTY-------VTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEK 635
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2732 qDRALSRMLDARQLGLKLIANVTFGYTAANFSGRMPCIEVGDSIVHKARETLERAIKLVND--TKKWG----ARVVYGDT 2805
Cdd:PTZ00166   636 -DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKhyTKANGykhdATVIYGDT 714
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2806 DSmfVLLKGATK--EQSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPVfDAKGIETVRR 2883
Cdd:PTZ00166   715 DS--VMVKFGTDdiQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAGLLYTNPEKYDKI-DCKGIETVRR 791
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2884 DSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYrGSFSYKpgACVPALELTRKMLTYDRR 2963
Cdd:PTZ00166   792 DNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRIDISLLVITKSL-GKDDYE--GRLAHVELAKKLRQRDPG 868
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2964 SEPQVGERVPYVIIYGTPGVPLIQLVRRPVEVLqDPTLRLNATYYItKQILPPLARIFSLIGIDVFSWYHELPRIHKATN 3043
Cdd:PTZ00166   869 SAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVL-ENNIPIDTQYYL-DQIKNPLLRIFEGVMDNPDSLFSGEHTRHITIS 946
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 3044 SSrsepegRKGTISQYFT-TLHCPVCDDLTQHG-ICSKCRS--QPQHVAVILNqEIRELERKQEQLVKICKNCTGCFDRH 3119
Cdd:PTZ00166   947 SS------SKGGLSKFVKkQLQCLGCKSVIKEGaLCDNCNQnkEPSIYGKKLA-KRRHKEAEYSQLWTQCQRCQGSLHQE 1019
                          730       740       750
                   ....*....|....*....|....*....|....
gi 1622930091 3120 IPCVSLNCPVLFKVSRVNRELSKapyLRQLLDQF 3153
Cdd:PTZ00166  1020 VICTNRDCPIFYRRKKVQKDLAE---LQELLSRF 1050
POLBc cd00145
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ...
2614-3022 7.71e-108

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: 348.21  E-value: 7.71e-108
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2614 APQCVPLIMEPEsRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHVENLGKYDEFkfgctslrvppdllyqvrhditvs 2693
Cdd:cd00145      1 EPYEGGYVFDPI-PGLYENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYI------------------------ 55
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2694 pnGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSRMLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGD 2773
Cdd:cd00145     56 --GVGFRSPKDRKGLLPRILEELLNFRDEAKKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFF-RFYDPEVAA 132
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2774 SIVHKARETLERAIKLVNDTkkwGARVVYGDTDSMFVLLKG-ATKEQSFKIGQEIAEAVtaTNPKPVKLKFEKVYLPCVL 2852
Cdd:cd00145    133 SITSFGREIIQDTIALVEEH---GARVIYGDTDSIFVSLPKmGTKEDAIKEGREILQEL--ADEHLLELEFEKVYLPFFL 207
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2853 QTKKRYVGYMYETlDQKDPVFDAKGIETVRRDSCPAVSKILERSLKLLFETRDisliKQYVQRQCMKLLegkasiqdfif 2932
Cdd:cd00145    208 GKKKRYAGLDIWK-GQDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEER----KVEAVKEYIDEL----------- 271
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2933 akeyrgsfsykpgacvpaleltrkmltydrrsepqvgERVPYVIIYGTPGVPLIQLVrRPVEVLQDPTLRLNATYYITKQ 3012
Cdd:cd00145    272 -------------------------------------DKVKYVVTRGGKGVPDYERA-DPPLEDLDKRHRIDYEYYLERL 313
                          410
                   ....*....|
gi 1622930091 3013 ILPPLARIFS 3022
Cdd:cd00145    314 LQPPLERIFE 323
DNA_polB_zeta_exo cd05778
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ...
2291-2555 1.07e-95

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: 309.17  E-value: 1.07e-95
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2291 IQNLTLISVELHARTRRDLEPDPEFDPICALFYCISSDAPLPDTEKTElTGVIVIDKDKTVFSQDiryqtplLIRSGITG 2370
Cdd:cd05778      1 HQHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANK-VGVIIVDELKSNASNG-------RIRSGLSG 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2371 LEVTYAADEKALFHEIAHIIKRgchqhvrcfqyphffyfckqlrkrnmYDPDILLGYEIQMHSWGYLLQRAAALSVDLC- 2449
Cdd:cd05778     73 IPVEVVESELELFEELIDLVRR--------------------------FDPDILSGYEIQRSSWGYLIERAAALGIDDLl 126
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2450 QMISRVPDDKiENRFAAERDEYGSYTMSEINIVGRITLNLWRIMRNEVALTNYTFENVSFHVLHQRFPLFTFRVLSDWFD 2529
Cdd:cd05778    127 DEISRVPSDS-NGKFGDRDDEWGYTHTSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYK 205
                          250       260
                   ....*....|....*....|....*.
gi 1622930091 2530 NKTDLYRWKMVDHYVSRVRGNLQMLE 2555
Cdd:cd05778    206 SGSASERWRVLEYYLKRVRLNLEILD 231
POLBc_delta cd05533
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
2621-3024 1.08e-94

DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.


Pssm-ID: 99916  Cd Length: 393  Bit Score: 313.05  E-value: 1.08e-94
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2621 IMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLghvenlgKYDEFKfgctslRVPPDllyqvrhDITVSPNGVAFV 2700
Cdd:cd05533      8 VIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLL-------NKNTAK------KLPPE-------DYIKTPNGDYFV 67
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2701 KPSVRKGVLPRMLEEILKTRFMVKQSMKAYKqDRALSRMLDARQLGLKLIANVTFGYTAANfSGRMPCIEVGDSIVHKAR 2780
Cdd:cd05533     68 KSSVRKGLLPEILEELLAARKRAKKDLKEET-DPFKKAVLDGRQLALKISANSVYGFTGAT-VGKLPCLEISSSVTSFGR 145
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2781 ETLERAIKLVND--TKK----WGARVVYGDTDSMFVLLKGATKEQSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQT 2854
Cdd:cd05533    146 QMIEKTKKLVEEkyTKAngysHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLIN 225
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2855 KKRYVGYMYETLDQKDPVfDAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAK 2934
Cdd:cd05533    226 KKRYAGLLWTNPDKHDKM-DTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLLQNKIDISLLVITK 304
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2935 EY-RGSFSYKpgACVPALELTRKMLTYDRRSEPQVGERVPYVIIYGTPGVPLIQLVRRPVEVLQDpTLRLNATYYITKQI 3013
Cdd:cd05533    305 ALtKTADDYA--GKQAHVELAERMRKRDPGSAPNVGDRVPYVIIKGAKGAKAYEKAEDPIYVLEN-NIPIDTQYYLENQL 381
                          410
                   ....*....|.
gi 1622930091 3014 LPPLARIFSLI 3024
Cdd:cd05533    382 SKPLLRIFEPI 392
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
2313-2814 2.85e-91

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: 306.38  E-value: 2.85e-91
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  2313 PEFDPICALFYCISSDAPLPDTEKTELtgvIVIDKDKTVFSQDIRYQT-----PLLIRSGITGLEVTYAADEKALFHEia 2387
Cdd:smart00486    1 PPLKILSFDIETYTDGGNFPDAEIFDD---EIIQISLVINDGDKKGANrrilfTLGTCKEIDGIEVYEFNNEKELLLA-- 75
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  2388 hiikrgchqhvrcfqyphFFYFCKQlrkrnmYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPD-DKIENRFAA 2466
Cdd:smart00486   76 ------------------FFEFIKK------YDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIgLRIPNKKPL 131
                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  2467 ERDEYGSYTMSEINIVGRITLNLWRIMRNEVALTNYTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYRWkMVDHYVSR 2546
Cdd:smart00486  132 FGSKSFGLSDIKVYIKGRLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDE-LLRYCIQD 210
                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  2547 VRGNLQMLEQLDLIGKTSEMARLFGIQFLHVLTRGSQYRVESMMLRIAKPMNYIPVTPSVQQRSQMRAPQCVP------L 2620
Cdd:smart00486  211 AVLTLKLFNKLNVIPLIIELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEPDLKKKvkyeggK 290
                           330       340       350       360       370       380       390       400
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  2621 IMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHVENLGKYDEFKFgctslrvppdllYQVRHDITVSPNGVAFV 2700
Cdd:smart00486  291 VLEPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKGDLIIP------------EDLLTIKYEKGNKYRFV 358
                           410       420       430       440       450       460       470       480
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091  2701 KPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSR-MLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKA 2779
Cdd:smart00486  359 KKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESEELKkLLDSRQLALKLTANSVYGYLGFTNS-RLPCKPLAASVTALG 437
                           490       500       510
                    ....*....|....*....|....*....|....*..
gi 1622930091  2780 RETLERAIKLVND--TKKWGARVVYGDTDSMFVLLKG 2814
Cdd:smart00486  438 REILEKTKELIEEngYPKPGFKVIYGDTDSIFVTKPG 474
PolB COG0417
DNA polymerase B elongation subunit [Replication, recombination and repair];
2342-3027 4.13e-84

DNA polymerase B elongation subunit [Replication, recombination and repair];


Pssm-ID: 440186 [Multi-domain]  Cd Length: 794  Bit Score: 295.97  E-value: 4.13e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2342 VIVIdkdkTVFSQDIRYQTPLLIRSGItGLEVTYAADEKALFHEIAHIIKRgchqhvrcfqyphffyfckqlrkrnmYDP 2421
Cdd:COG0417    184 IISI----GLAGSDGEKKVLMLGREGV-DFEVEYFDDEKALLEAFFEIIRE--------------------------YDP 232
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2422 DILLGYEIQMHSWGYLLQRAAALSVDLcqMISRvpddkieNRFAAERDEYGSYTMseINIVGRITLNLWRIMRN-EVALT 2500
Cdd:COG0417    233 DIIIGWNVDNFDLPYLQKRAERLGIPL--DLGR-------DGSEPSWREHGGQGF--ASIPGRVVIDLYDALKSaTYKFK 301
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2501 NYTFENVSFHVLHqrfplftfrvlsdwfDNKTDLYRWKMVDHYVSR----VRGNLQ-------MLEQLDLIGKTSEMARL 2569
Cdd:COG0417    302 SYSLDAVAEELLG---------------EGKLIVDGGEIERLWDDDkpalAEYNLRdaeltlrIFEKTLLLPFLIELSRI 366
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2570 FGIQFLHVLTRGSQYRVESMMLRIAKPMNY-IPVTPSVQQRSQMRApqcvpLIMEPESRFYSNsVLVLDFQSLYPSIVIA 2648
Cdd:COG0417    367 TGLPLDDVGRAGSSAAFENLLLPEAHRRGYlAPNKGEIKGEAYPGG-----YVLDPKPGLYEN-VLVLDFKSLYPSIIRT 440
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2649 YNYCFST-CLGHVENLGKYDefkfgctslrvppdllyqvrhditVSPN-GVAFVKPsvRKGVLPRMLEEILKTRFMVKQS 2726
Cdd:COG0417    441 FNISPETlVEGGEEPCGDED------------------------VAPGfGHRFCRE--PKGILPSILEELWDERDEAKKK 494
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2727 MKAYKQDRALSRMLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKARETLERAIKLVndtKKWGARVVYGDTD 2806
Cdd:COG0417    495 MKKAKPDSEEYRLYDALQQALKILMNSFYGVLGSEGC-RFYDPELAESITARGREIIKQTIEKA---EELGYKVIYGDTD 570
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2807 SMFVLLKGATKEQSFKIGQEIAEAVTATNPKPVKLKFEKVYLPcVLQT--KKRYVGYmyetldQKDPVFDAKGIETVRRD 2884
Cdd:COG0417    571 SLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRR-FFFPgsKKRYAGL------TEDGKIDIKGLEAVRSD 643
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2885 SCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYRGSFS-YKpgACVPA-LELTRKMLTYDR 2962
Cdd:COG0417    644 WTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSeYE--KNVPPhVRAARKLDERGR 721
                          650       660       670       680       690       700
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622930091 2963 rsEPQVGERVPYVIIYGTPGVpliqlvrRPVEVLQDPTLRLNATYYITKQILPPLARIFSLIGID 3027
Cdd:COG0417    722 --PYQRGDKISYVITKGGGRV-------EPVELAKERESEIDYDYYIEKQLKPTADRILEAFGVS 777
PRK05762 PRK05762
DNA polymerase II; Reviewed
2419-3027 4.27e-57

DNA polymerase II; Reviewed


Pssm-ID: 235595 [Multi-domain]  Cd Length: 786  Bit Score: 214.72  E-value: 4.27e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2419 YDPDILLGYEIQMHSWGYLLQRAAALSVDLcqMISRVpDDKIENRFAAERDEYGSYTmseinIVGRITLNLWRIMRnevA 2498
Cdd:PRK05762   217 HDPDVIIGWNVVQFDLRLLQERAERYGIPL--RLGRD-GSELEWREHPFRSGYGFAS-----VPGRLVLDGIDALK---S 285
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2499 LTN----YTFENVSFHVL---------HQRFPLFTFRvlsdWFDNKTDLYRWKMVDhyvsrVRGNLQMLEQLDLIGKTSE 2565
Cdd:PRK05762   286 ATWvfdsFSLEYVSQRLLgegkaiddpYDRMDEIDRR----FAEDKPALARYNLKD-----CELVTRIFEKTKLLPFLLE 356
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2566 MARLFGIQflhvLTR--GSQYRVESMMLRIAKPMNYipVTPSVQQRsqmrAPQCVP--LIMEPESRFYSNsVLVLDFQSL 2641
Cdd:PRK05762   357 RATVTGLP----LDRvgGSVAAFEHLYLPRAHRAGY--VAPNLGER----PGEASPggYVMDSKPGLYDS-VLVLDFKSL 425
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2642 YPSIVIAYNYCFstcLGHVENLGKYDEfkfgctslrvppdllyqvrhDITVSPNGVAFVKPsvrKGVLPRMLEEILKTRF 2721
Cdd:PRK05762   426 YPSIIRTFNIDP---DGLVEGLAQPPE--------------------ESVAGFLGARFSRE---KHFLPEIVERLWEGRD 479
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2722 MVKQSMKAykqdralsrmldARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKARETLERAIKLVndtKKWGARVV 2801
Cdd:PRK05762   480 EAKREMNK------------PLSQAIKIIMNAFYGVLGSSGC-RFFDPRLASSITMRGHEIMKQTRELI---EAQGYQVI 543
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2802 YGDTDSMFVLLKGA-TKEQSFKIGQEIAEAVTATNPKPVK----------LKFEKVYLPCVLQT--------KKRYVGYM 2862
Cdd:PRK05762   544 YGDTDSTFVWLGGAhDEEDAAKIGRALVQEINQWWQEHLQqefglesaleLEFEKHYRRFFMPTirgaeegsKKRYAGLI 623
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2863 YETLDQKDPVFdaKGIETVRRDSCPAVSKILERSLKLLFETRD-ISLIKQYVqrqcMKLLEGKASiQDFIFAKEYRGSFS 2941
Cdd:PRK05762   624 QEGDGDGRIVF--KGLETVRTDWTPLAKEFQQELYERIFRGEPyVDYVREVI----DKLRAGELD-EKLVYRKRLRRPLD 696
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2942 -YKPGacVP-----ALELTRKMLTYDRRSEPQVGERVPYVIIYGTPGvpliqlvrrPVEVLQDPtlrLNATYYITKQILP 3015
Cdd:PRK05762   697 eYQRN--VPphvraARLADEMGYKVGRPLQYQNGGKIGYVITVNGPE---------PLEYRKSP---IDYDYYIEKQLQP 762
                          650
                   ....*....|..
gi 1622930091 3016 PLARIFSLIGID 3027
Cdd:PRK05762   763 VADRILPFFGDD 774
POLBc_alpha cd05532
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
2620-3027 1.24e-51

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: 188.94  E-value: 1.24e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2620 LIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHVENLGKYDEFKfgctslrVPPdllyqvrhditvspngvaf 2699
Cdd:cd05532     12 LVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEDDEEPP-------LPP------------------- 65
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2700 vkPSVRKGVLPRMLEEILKTRFMVKQSMKAyKQDRALSRMLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKA 2779
Cdd:cd05532     66 --SDQEKGILPRIIRKLVERRRQVKKLMKS-EKDPDKKAQLDIRQLALKLTANSMYGCLGFSYS-RFYAKPLAALITSKG 141
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2780 RETLERAIKLVNdtkKWGARVVYGDTDSMFVLLKGATKEQSFKIGQEIAEAVTAtNPKPVKLKFEKVYLPCVLQTKKRYV 2859
Cdd:cd05532    142 REILQKTKDLVE---KMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNK-SYKKLEIDIDGVFKRLLLLKKKKYA 217
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2860 GYMYETLDQKDPVFDAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKL----LEGKASIQDFIFAK- 2934
Cdd:cd05532    218 ALKVVDDDKGKLKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRKInedlRNGKIPLEKFIITKq 297
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2935 ------EYRGSFSYkPGACVpALELTRKMLTYdrrsepQVGERVPYVIIYGTPGVPLIQLVRRPVEVLQDPTLRLNATYY 3008
Cdd:cd05532    298 ltknpeEYPDKKSL-PHVQV-ALRMNKRGRKV------KAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYY 369
                          410       420
                   ....*....|....*....|
gi 1622930091 3009 ITKQILPPLARIFSLI-GID 3027
Cdd:cd05532    370 LSQQILPPISRLCEPIeGTD 389
POLBc_B3 cd05536
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ...
2620-3026 1.17e-50

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: 185.22  E-value: 1.17e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2620 LIMEPESRFYSNsVLVLDFQSLYPSIVIAYNycfstclghvenlgkydefkfgctslrVPPD-LLYQVRHDITVSPN-GV 2697
Cdd:cd05536      8 IVLEPEKGLHEN-IVVLDFSSLYPSIMIKYN---------------------------ISPDtLVREGCEDCDVEPQvGH 59
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2698 AFVKPsvRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSRMLDARQLGLKLIANVTFGYTAANfSGRMPCIEVGDSIVH 2777
Cdd:cd05536     60 KFRKD--PPGFIPSVLEDLLEERRRIKEKMKKLDPESEEYKLLDERQRAIKILANSFYGYMGWA-NARWYCKECAEAVTA 136
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2778 KARETLERAIKLVndtKKWGARVVYGDTDSMFVLLKGATkeqsfKIGQEIAEAVTATNPK-PVKLKFEKVYLPCVLQTKK 2856
Cdd:cd05536    137 WGREYIKTTIKIA---EEKGFKVIYGDTDSLFVKIDGAD-----AVKKKVKKLLKYINEElPLELEIEKFYKRGFFVTKK 208
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2857 RYVGYmyeTLDQKdpvFDAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEY 2936
Cdd:cd05536    209 RYAGL---TEDGK---IDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVIEKLKRGEVPPEKLVIWKQL 282
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2937 RGSFS-YKpgACVPALELTRKMLtyDRRSEPQVGERVPYVIIYGtPGvpliQLVRR--PVEVLQDPTlRLNATYYITKQI 3013
Cdd:cd05536    283 TKDLSeYK--ATGPHVAAAKKLA--KRGYKVRPGTKIGYVIVKG-SG----KISDRayPYDMVDEKH-KYDAEYYIDNQV 352
                          410
                   ....*....|...
gi 1622930091 3014 LPPLARIFSLIGI 3026
Cdd:cd05536    353 LPAVLRILEAFGY 365
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
2409-3021 3.68e-50

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: 196.82  E-value: 3.68e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2409 FCKQLRKRnmyDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKIENRFAAERdeygsytmseinIVGRITLN 2488
Cdd:TIGR00592  591 FMAKVKKI---DPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGER------------TCGRMICD 655
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2489 LWRIMRNEVALTNYTFENVSFHVLH-QRFPLFTFRVLSDWFDNKTDLYrwkMVDHYVSRVRGNLQMLEQLDLIGKTSEMA 2567
Cdd:TIGR00592  656 VEISAKELIRCKSYDLSELVQQILKtERKVIPIDNINNMYSESSSLTY---LLEHTWKDAMFILQIMCELNVLPLALQIT 732
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2568 RLFGIQFLHVLTRGSQYRVESMMLRIAKPMNYI-PVTPSVQQRSQMR--------------APQCVPLIMEPESRFYSNS 2632
Cdd:TIGR00592  733 NIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIvPDKQIFRKQQKLGdedeeidgykkgkkAAYAGGLVLEPKVGLYDKY 812
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2633 VLVLDFQSLYPSIVIAYNYCFSTclghVENLGKYDEfkfgctsLRVPPDllyqvrhditvspngvafvkPSVRKGVLPRM 2712
Cdd:TIGR00592  813 VLLMDFNSLYPSIIQEFNICFTT----VQQKVDEDE-------LPELPD--------------------SELEMGILPRE 861
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2713 LEEILKTRFMVKQSMKAyKQDRALSRMLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKARETLERAIKLVnd 2792
Cdd:TIGR00592  862 LRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKS-RFYAKPLAALVTAKGREILEHTRQLV-- 937
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2793 tKKWGARVVYGDTDSMFVLLKGATKEQSFKIGQEIAEAVTATNpKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPV 2872
Cdd:TIGR00592  938 -EEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLY-KLLELDIDGVFKRLLLLKKKKYAAIKVEGDSDGNYT 1015
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2873 F--DAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKL----LEGKASIQDFIFAKEY-RGSFSYKPG 2945
Cdd:TIGR00592 1016 TkqEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIgknvLNGEVPLEKFVINKQLtRDPKDYPDG 1095
                          570       580       590       600       610       620       630
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1622930091 2946 ACVPALELTRKMLTYDRRSEPQvGERVPYVIIYGTPGVPLIQLVRRPVEVL-QDPTLRLNATYYITKQILPPLARIF 3021
Cdd:TIGR00592 1096 ASLPHVHVALRINARGGRKVKA-GDVVSYVICKDGGNLSARQRAYALEELQrKHNNLIYDTQYYLEHQIHPVVLRIL 1171
DEDDy_DNA_polB_exo cd05160
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ...
2305-2555 2.31e-48

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: 172.15  E-value: 2.31e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2305 TRRDLEPDPEFDPICALFYCISSDaplpdtekteltGVIVIDKDKTVFSQDIRYqtpllirsGITGLEVTYAADEKALFH 2384
Cdd:cd05160      9 TPPVGGPEPDRDPIICITYADSFD------------GVKVVFLLKTSTVGDDIE--------FIDGIEVEYFADEKELLK 68
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2385 EIAHIIKRgchqhvrcfqyphffyfckqlrkrnmYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKIEnrf 2464
Cdd:cd05160     69 RFFDIIRE--------------------------YDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKS--- 119
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2465 aaerdeygSYTMSEINIVGRITLNLWRIMRNEVALTNYTFENVSFHVLHQRFPLFTFRvlsDWFDNKTDLYRWKMVDHYV 2544
Cdd:cd05160    120 --------SGSTERIAVKGRVVFDLLAAYKRDFKLKSYTLDAVAEELLGEGKEKVDGE---IIEDAEWEEDPERLIEYNL 188
                          250
                   ....*....|.
gi 1622930091 2545 SRVRGNLQMLE 2555
Cdd:cd05160    189 KDAELTLQILE 199
POLBc_Pol_II cd05537
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ...
2620-3025 9.37e-29

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: 120.83  E-value: 9.37e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2620 LIMEPESRFYSNsVLVLDFQSLYPSIVIAYNYcfsTCLGHVENLGKYDEfkfgctslrvppdllyqvrHDITVSPNGVAF 2699
Cdd:cd05537      7 YVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLI---DPLGLIEGLKAPDP-------------------EDLIPGFLGARF 63
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2700 vkpSVRKGVLPRMLEEILKTRFMVKQSmkaykQDRALSRmldarqlGLKLIANVTFGYTAAN----FSGRMPC--IEVGD 2773
Cdd:cd05537     64 ---SREKHILPDLIARLWAARDEAKRE-----KNAPLSQ-------AIKIIMNSFYGVLGSTgcrfFDPRLASsiTLRGH 128
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2774 SIVHKARETLERAiklvndtkkwGARVVYGDTDSMFVLLKGA-TKEQSFKIGQEIAEAVTATNPKPVK----------LK 2842
Cdd:cd05537    129 EIMKQTRAWIEQQ----------GYQVIYGDTDSTFVWLGEElDAAEAQAIGKELASQINQWWAQKLKeefglesfleIE 198
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2843 FEKVYLPCVLQT--------KKRYVGyMYETLDQKDPVFdaKGIETVRRDSCPAVSKILERSLKLLFETRDI-SLIKQYV 2913
Cdd:cd05537    199 FETHYSRFFMPTirgsdegsKKRYAG-LKSTDGGDELVF--KGLETVRSDWTPLARQFQKELYERVFNDEPYeGFIKETV 275
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2914 QrqcmKLLEGKASIQdFIFAKeyrgsfsykpgacvpalELTRKMLTYDRRSEPQV-GERVPYViIYGTPGVPLIQLVRRP 2992
Cdd:cd05537    276 E----ELLAGELDEL-LVYRK-----------------RLRRPLSEYTKNVPPHVqAARLADQ-INRELGRPRQYQWIEY 332
                          410       420       430
                   ....*....|....*....|....*....|....*....
gi 1622930091 2993 V------EVLQDPTLRLNATYYITKQILPPLARIFSLIG 3025
Cdd:cd05537    333 VitvngpEPLEYRTSPLDYQHYIDKQLKPIADSILPFLG 371
PRK05761 PRK05761
DNA-directed DNA polymerase I;
2620-3017 2.40e-27

DNA-directed DNA polymerase I;


Pssm-ID: 235594 [Multi-domain]  Cd Length: 787  Bit Score: 121.72  E-value: 2.40e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2620 LIMEPESRFYSNsVLVLDFQSLYPSIVIAYNYCFSTcLGHVENLGKYDefkfgctslRVPPDLLYQVRHDitvspngvaf 2699
Cdd:PRK05761   411 LVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPET-VRIPECKCHYD---------DEVPELGHSVCDD---------- 469
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2700 vkpsvrKGVLPRMLEEILKT-RFMVKQSMKAYKQDRALSRM-LDARQLGLKLIANVTFGYTAA-NFsgRMPCIEVGDSIV 2776
Cdd:PRK05761   470 ------RPGLTSVLVGLLRDfRVKIYKKKAKDPNLDEERRAwYDVVQRALKVFLNASYGVFGAeNF--KLYRIEVAESIT 541
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2777 HKARETLERAIKLvndTKKWGARVVYGDTDSMFVllKGATKEQSFKIGQEIAEAVTatnpkpVKLKFEKVYLPCVLQ-TK 2855
Cdd:PRK05761   542 ALGREILLSTKKK---AEELGLKVLYGDTDSLFV--WGPTKESLEELIKEIEERTG------IDLEVDKTYDWVAFSgLK 610
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2856 KRYVGYMyetldqKDPVFDAKGIETVRRDSCPAVSKILERSLKLLFETRDIS-------LIKQYVQRQCMKLLEGKASIQ 2928
Cdd:PRK05761   611 KNYFGVL------KDGKVKIKGIVAKKRNTPEFVKELQREVLEVLKSIRSPEdvekvkdEIEDVLKRYYEKLRAKDYPLD 684
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2929 DFIFAK-------EYrgsfSYKPGACVPALELTRKMltydrRSEPQVGERVPYVIIYGTPGVPLIQLVRrpvevLQDptl 3001
Cdd:PRK05761   685 ELAIRVrlskpldEY----TKNTPQHVKAALQLRDY-----GVEVSPGDIISYVKVDDKRGVKPVQLAK-----LSE--- 747
                          410       420
                   ....*....|....*....|..
gi 1622930091 3002 rLNATYYIT------KQILPPL 3017
Cdd:PRK05761   748 -IDVEKYIEllrsalEQILSAL 768
POLBc_B2 cd05531
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ...
2620-2977 5.02e-21

DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.


Pssm-ID: 99914  Cd Length: 352  Bit Score: 97.80  E-value: 5.02e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2620 LIMEPESRFYSNsVLVLDFQSLYPSIVIAYNycFSTclghvENLGKydefkfGCTSLRVPPDLLYQVRHDitvspngvaf 2699
Cdd:cd05531      9 LVFQPEPGLYEN-VAQIDFSSMYPSIIVKYN--ISP-----ETINC------RCCECRDHVYLGHRICLK---------- 64
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2700 vkpsvRKGVLPRMLEEILKTRfmvkqsmKAYKQDRALSRMLDARQLGLKLIANVTFGYTA---ANFsGRmpcIEVGDSIV 2776
Cdd:cd05531     65 -----RRGFLPEVLEPLLERR-------LEYKRLKKEEDPYAGRQKALKWILVTSFGYLGyknAKF-GR---IEVHEAIT 128
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2777 HKARETLERAIKLVNDTkkwGARVVYGDTDSMFVllKGATKEQSFKigQEIAEAVTatnpkpVKLKFEKVY-----LPCV 2851
Cdd:cd05531    129 AYGRKILLRAKEIAEEM---GFRVLHGIVDSLWI--QGRGDIEELA--REIEERTG------IPLKLEGHYdwivfLPER 195
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2852 --LQTKKRYVGYMyetldqKDPVFDAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIK-------QYVQRQCMKLLE 2922
Cdd:cd05531    196 dgLGAPNRYFGRL------SDGEMKVRGIELRRRDTPPFVKKFQEEALDILASAKTPEELLklreealDLFRRYLQRLRE 269
                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622930091 2923 GKasIQDFIFAKE-YRGSFSYKPGACVPALELTRKMLTYdrrsepQVGERVPYVII 2977
Cdd:cd05531    270 GD--LEDLIIEKKiSKRSSEYKVLASTALKALRAKGVSV------VPGMKIEYIVR 317
zf-C4pol pfam14260
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ...
3065-3132 2.02e-17

C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1.


Pssm-ID: 464119  Cd Length: 68  Bit Score: 78.95  E-value: 2.02e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622930091 3065 CPVCDDLTQhGICSKCRSQPQHVAVILNQEIRELERKQEQLVKICKNCTGCFDRHIPCVSLNCPVLFK 3132
Cdd:pfam14260    1 CLGCGAPEE-PLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYM 67
PHA03036 PHA03036
DNA polymerase; Provisional
2621-2908 1.25e-16

DNA polymerase; Provisional


Pssm-ID: 222962 [Multi-domain]  Cd Length: 1004  Bit Score: 87.38  E-value: 1.25e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2621 IMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHVENLGKYDEFKFGCTSLRV--PPDLLYQvrHDITVSPNGVA 2698
Cdd:PHA03036   535 VFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVNDNRLEAEINKQELRRKypYPRYIYV--HCEPRSPDLVS 612
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2699 --FVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQ--DRALsrmLDARQLGLKLIANVTFG----YTAANFS------- 2763
Cdd:PHA03036   613 eiAVFDRRIEGIIPKLLKTFLEERARYKKLLKEATSsvEKAI---YDSMQYTYKIVANSVYGlmgfRNSALYSyasaksc 689
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2764 ---GRMpCIEVGDSIVHKA-----RETL-----------ERAIKL-----VNDTKKWGARVVYGDTDSMFVLLKGATKEQ 2819
Cdd:PHA03036   690 taiGRN-MIKYLNSVLNGSklingKLILancpinpffkdDRSIDTnydtnLPVEYNFTFRSVYGDTDSVFLEINTKDVDK 768
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2820 SFKIGQEIAEAV-TATNPKPVKLKFEKVYLPCVLQTKKRYVGYMY--ETLDQKDPVFDAKGIETVRRDSCP----AVSKI 2892
Cdd:PHA03036   769 SIKIAKELERIInEKVLFDNFKIEFEAVYKNLIMQSKKKYTTLKYiaSSTDGSVPERVNKGTSETRRDVSKfhkyMIKIY 848
                          330
                   ....*....|....*.
gi 1622930091 2893 LERSLKLLFETRDISL 2908
Cdd:PHA03036   849 KTRLLDMLSEGNMNSN 864
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
6-182 1.79e-14

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 80.46  E-value: 1.79e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091    6 IVTADYYMASplqglDTCQ-SPLTQAPVKK---VPVVRIFGATPAGQKTCLHLHGIFPYLYVPydgygqQPESYLSQMAF 81
Cdd:PTZ00166    46 QLDADYTEKD-----DKSQgNPHNTVSGVRhveVPIIRLYGVTKEGHSVLVNVHNFFPYFYIE------APPNFLPEDSQ 114
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091   82 SIDRALNVALGNPSS---TAQHVFKVSLVSGMPFYGYHEK-ERHFMKIYLYNPAVVKRICELLQSGAIMN-------KFY 150
Cdd:PTZ00166   115 KLKRELNAQLSEQSQfkkYQNTVLDIEIVKKESLMYYKGNgEKDFLKITVQLPKMVPRLRSLIESGVVVCgggwdgiRLF 194
                          170       180       190
                   ....*....|....*....|....*....|..
gi 1622930091  151 QPHEAHIPYLLQLFIDYNLYGMNLINLAAVKF 182
Cdd:PTZ00166   195 QTYESNVPFVLRFLIDNNITGGSWLTLPKGKY 226
POLBc_B1 cd05530
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ...
2620-2992 2.38e-14

DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.


Pssm-ID: 99913  Cd Length: 372  Bit Score: 77.78  E-value: 2.38e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2620 LIMEPESRFYSNsVLVLDFQSLYPSIVIAYNYCFST--CLgHVENlgKYDEFkfgctslrvpPDLLYQVRHDitvspngv 2697
Cdd:cd05530     17 IVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYETvnCP-HCEC--KTNEV----------PEVGHWVCKK-------- 74
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2698 afvkpsvRKGVLPRMLEEILKTRFMV-KQSMKAYKQDRALSRMLDARQLGLKLIANVTFG-YTAANFSgrMPCIEVGDSI 2775
Cdd:cd05530     75 -------RPGITSQIIGLLRDLRVKIyKKKAKDKSLDEEMRQWYDVVQSAMKVFINASYGvFGAENFP--LYCPPVAEST 145
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2776 VHKARETLERAIKlvnDTKKWGARVVYGDTDSMFvlLKGATKEQSFKIgQEIAEavtatNPKPVKLKFEKVYLPCVLQT- 2854
Cdd:cd05530    146 TALGRYIITSTIK---KARELGLKVLYGDTDSLF--LWNPPQEQLEDL-VEWVE-----KELGLDLELDKEYRYVVFSGl 214
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2855 KKRYVGYMyetldqKDPVFDAKGIETVRRDSCPAVSKILERSLKLLFETR---DIS----LIKQYVQRQCMKLLEGKASI 2927
Cdd:cd05530    215 KKNYLGVT------KDGSVDIKGLLGKKRNTPEFVKELFYEVIEILSAVNspeDFEkareKIRDIVKGVYKRLKKKEYTL 288
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622930091 2928 QDFIF-------AKEYRGSfsyKPgacvPALELTRKMLTYDRRSEPqvGERVPYVIIYGTPGVPLIQLVRRP 2992
Cdd:cd05530    289 DQLAFkvmlskpPEEYTKN---TP----QHVKAARQLEKYGRNVEA--GDIISYVKVKGKEGVKPVQLARLD 351
43 PHA02528
DNA polymerase; Provisional
2421-2937 6.19e-13

DNA polymerase; Provisional


Pssm-ID: 177369 [Multi-domain]  Cd Length: 881  Bit Score: 75.11  E-value: 6.19e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2421 PDILLGYEIQMHSWGYLLQRaaalsvdlcqmISRVPDDKIENRF-----AAER---DEYGS----YTMSEINIVGRITLn 2488
Cdd:PHA02528   194 PVIFTGWNVELFDVPYIINR-----------IKNILGEKTAKRLspwgkVKERtieNMYGReeiaYDISGISILDYLDL- 261
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2489 lwrimRNEVALTN---YTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYrwkmVDHYVSRVRGNLQMLEQLDLIGKTSE 2565
Cdd:PHA02528   262 -----YKKFTFTNqpsYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKY----IEYNIIDVELVDRLDDKRKLIELVLS 332
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2566 MARLFGIQFLHVLtrgSQYRVESMMLRIAKPMNYIpVTPsvQQRSQMRAPQCVPLIMEPESRFYsNSVLVLDFQSLYPSI 2645
Cdd:PHA02528   333 MAYYAKINFEDVF---SPIKTWDAIIFNSLKEEKI-VIP--ENKSHKKQKYAGAFVKEPVPGAY-RWVVSFDLTSLYPSI 405
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2646 VIAYNYCFSTCLG--HVENLGKYDEfkfgcTSLRVPPDllyqvrhDITVSPNGVAFVKPsvRKGVLPRMLEEILKTRFMV 2723
Cdd:PHA02528   406 IRQVNISPETIAGtfHVAPVHEYIN-----KTAPRPSD-------EYSCSPNGWMYRKD--IRGVIPTEIKKVFDQRKIY 471
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2724 KQSMKAYKQDRALSRMLdARQLGLKLIANVTFGYTAANFSGRMPCI-EVGDSIVHKARETLERAIKLVNDTK-------- 2794
Cdd:PHA02528   472 KKKMLAAERNAELIKTI-LEDLNDSVDTPIDVDYYFDFSDEFKAELkTLTKSSLKALLEECEKEIALCNTIQmarkilin 550
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2795 ------------------------------KWGAR-----------------VVYGDTDSMFVLLK------GATKEQ-- 2819
Cdd:PHA02528   551 slygalgnehfryydlrnaeaitlfgqlaiQWIERkmneylnklcktededyVIYGDTDSIYVNLDplvekvGEDKFKdt 630
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2820 ----SF--KIG------------QEIAEAVTATNPKpVKLKFEKVYLPCVLQTKKRYVGYMY--ETLDQKDPVFDAKGIE 2879
Cdd:PHA02528   631 nhwvDFldKFCkermepyidssyRELCEYMNNYEHL-MFMDREAIAGPGFWTAKKRYALNVWdsEGTRYAEPKLKIMGIE 709
                          570       580       590       600       610       620
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2880 TVRRDSCPAVSKILERSLKLLfetrdislikqyvqrqcmkLLEGKASIQDFI--FAKEYR 2937
Cdd:PHA02528   710 TQRSSTPKAVQKALKEAIRRI-------------------LQEGEESLQEYIkeFEKEFR 750
DNA_polB_delta_exo cd05777
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ...
2420-2512 1.07e-11

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: 67.22  E-value: 1.07e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2420 DPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKI---ENRFAAERdeYGSYTMSEINIVGRITLNLWRIMRNE 2496
Cdd:cd05777     86 DPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKStikDTTFSSKQ--MGTRETKEINIEGRIQFDLLQVIQRD 163
                           90
                   ....*....|....*.
gi 1622930091 2497 VALTNYTFENVSFHVL 2512
Cdd:cd05777    164 YKLRSYSLNSVSAHFL 179
REV3L_RBD cd22287
REV7 binding domain found in protein reversionless 3-like (REV3L) and similar proteins; REV3L, ...
1872-1894 9.22e-09

REV7 binding domain found in protein reversionless 3-like (REV3L) and similar proteins; REV3L, also called REV3-like, or REV3, or DNA polymerase zeta catalytic subunit (POLZ), is the catalytic subunit of the DNA polymerase zeta complex, an error-prone polymerase specialized in translesion DNA synthesis (TLS). REV3L lacks an intrinsic 3'-5' exonuclease activity and thus has no proofreading function. The model corresponds to a conserved region that is responsible for the binding of REV7.


Pssm-ID: 412083  Cd Length: 23  Bit Score: 52.95  E-value: 9.22e-09
                           10        20
                   ....*....|....*....|...
gi 1622930091 1872 RTAHILKPLMSPPSREEIMATLL 1894
Cdd:cd22287      1 RTAHILKPLMSPPSREEIMATLL 23
DNA_pol_B_exo1 pfam03104
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ...
2311-2507 4.00e-07

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: 55.12  E-value: 4.00e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2311 PDPEF--DP---ICALFYCISSDAPLPdtekteltgvIVIDKDKTVFSQDIrYQTPLLIRSGITGLEVTYAADEKALFHe 2385
Cdd:pfam03104  172 PDAENvkDPiiqISCMLDGQGEPEPEP----------RFLFTLRECDSEDI-EDFEYTPKPIYPGVKVFEFPSEKELLR- 239
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2386 iahiikrgchqhvrcfqypHFFYFCKQlrkrnmYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDkieNRFA 2465
Cdd:pfam03104  240 -------------------RFFEFIRQ------YDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNRG---GRSK 291
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1622930091 2466 AERDEYGSYTMSEINIVGRITLNLWRIMRNEVALTNYTFENV 2507
Cdd:pfam03104  292 VREIGFGTRSYEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
DNA_pol_B_exo1 pfam03104
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ...
51-191 5.80e-07

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: 54.35  E-value: 5.80e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091   51 CLHLHGIFPYLYVPYDGYGQQPE--SYLSQMAFSIDRalnvalgnpsstaqhVFKVSLVSGMPFYGYHEKERHFMKIYLY 128
Cdd:pfam03104    9 CVNVFGFKPYFYCLAPDGKELEEviEEIKELYEGLDK---------------IEKIELKLKKSLYGYEEDPVPYLKVSFA 73
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1622930091  129 NPAVVKRICELLQSGAIMNKFyqphEAHIPYLLQLFIDYNLYGMNLINLAAVKFRKARRKSNT 191
Cdd:pfam03104   74 NPRPLLKIRKYLSPENISDVY----EYDVDYLERFLIDNDIVGFGWYKVKVYPFRAEGRISNC 132
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
2420-2763 6.93e-05

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: 48.90  E-value: 6.93e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2420 DPDIllgyEIQMHSWGYLLQRAAalSVDLCQMISRVPDDKIEN---RFAAERDEYGSYTMSEIN----------IVGRIT 2486
Cdd:TIGR00592  285 DTDV----EITVNGDNFDLVYLA--DRQVFQFYWDAYEDPAEKlgvVLLFGRDVDHVSPCVQVKginrdlfflpREGKID 358
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2487 LNLWRIMRNEVALTNYTFENVSFHVLhqRFPLFTFRVLSdwfdnKTDLYRWKMVDHYVSRVRGNLQMLeqLDLIGKTSEM 2566
Cdd:TIGR00592  359 FDLGKVTRRTINLPDYYLEFVSELAL--GYKKEKFRAKP-----IAKKYEFEAPDIDAPYSSEYLEVT--YELGKEFAPM 429
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2567 ----ARLFGIQFLHVLTRGSQYRVESMMLRIAKPMNYIPVTpSVQQRSQMRAPQCV-------PLIMEPESRFYSNSVLV 2635
Cdd:TIGR00592  430 ealpSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVK-GPDELEYPRRSWCKyeggyvkPPNVEKGLDKTPPPLVV 508
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2636 LDF--QSLYPSIVIAYNYCFSTCLGHVENLGKydefKFGCTSLRVPPDLLYqvRHDITVSPNGVAFVKPsvrkGVLPRML 2713
Cdd:TIGR00592  509 LDFsmKSLNPSIIRNEIVSIPDTLHREFALDK----PPPEPPYDVHPCVGT--RPKDCSFPLDLKGEFP----GKKPSLV 578
                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1622930091 2714 EEILKTRFMVKQSMKAYKQ-DRALSRMLDARQLGLKLIANVTFGYTAANFS 2763
Cdd:TIGR00592  579 EDLATERALIKKFMAKVKKiDPDEIVGHDYQQRALKVLANRINDLKIPTWS 629
POLBc_Pol_II_B cd05538
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ...
2705-2900 1.16e-04

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: 47.10  E-value: 1.16e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2705 RKGVLPRMLEEILKTRFMVKQSMKAYKqDRALSRMLDARQLGLKLIANVTFGYTAA---NFSGrmpcIEVGDSIVHKARE 2781
Cdd:cd05538     43 SLGIFLALLKYLVELRLAAKESARAAA-RPAERDAFKAKQAAFKVLINSFYGYLGTglhAFSD----PEAAAEVTRLGRE 117
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2782 TLEraiKLVNDTKKWGARVVYGDTDSMFVL----LKGATKEqsfkigQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKR 2857
Cdd:cd05538    118 LLK---LMIRWLRRRGATPVEVDTDGIYFIppngVDTEDEE------EELVRELSSTLPKGITVEFDGRYRAMFSYKIKN 188
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|...
gi 1622930091 2858 YVgymyeTLDQKDPVFdAKGIETVRRDSCPAVSKILERSLKLL 2900
Cdd:cd05538    189 YA-----LLDYDGKLI-VKGSAFRSRGIEPFLREFLREAVRLL 225
PHA03334 PHA03334
putative DNA polymerase catalytic subunit; Provisional
2619-2809 2.31e-04

putative DNA polymerase catalytic subunit; Provisional


Pssm-ID: 223049 [Multi-domain]  Cd Length: 1545  Bit Score: 47.16  E-value: 2.31e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2619 PLIMEPESRFYSNSVLVLDFQSLYPSiviayNYC----------FSTCLGHVENLGKYD----EFKFGCTSlrvppdLLY 2684
Cdd:PHA03334   641 PLTGLTFAGPYQGTELTLDFASLYPS-----NMCdanispeaivDPDCTARVRGWVVFDwkkiDRGFGKAT------LMY 709
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2685 QVRHDITVSPNGVAFvkPSVRKGVLPRMleeiLKTRFMVKQSMKAYKqDRALSRMLDARQLGLKLIANVTFGytaanfsg 2764
Cdd:PHA03334   710 TILRTKPEEPSWRRF--TTYTTSSLNHY----LSMRTEYKGAMKQAK-DPKLKSYHNQLQNEMKICANSHYG-------- 774
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1622930091 2765 rmpcieVGDSIVHKARETLER-AIKLVNDTKKWGA--RVVYGDTDS-MF 2809
Cdd:PHA03334   775 ------VAPHACQHLITTLGRhKIKLVEEFIKKEPgmTVNYGDTDSvMF 817
DNA_polB_B3_exo cd05781
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ...
2419-2508 4.77e-04

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: 43.85  E-value: 4.77e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930091 2419 YDPDILLGYEIQMHSWGYLLQRAAALSV--DLCQMISRVPddkienrfaaERDEYGSYTmseinIVGRITLNLWRIMRNE 2496
Cdd:cd05781     62 YDPDIIVGYNSNAFDWPYLVERARVLGVklDVGRRGGSEP----------STGVYGHYS-----ITGRLNVDLYDFAEEI 126
                           90
                   ....*....|..
gi 1622930091 2497 VALTNYTFENVS 2508
Cdd:cd05781    127 PEVKVKTLENVA 138
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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