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Conserved domains on  [gi|1622930112|ref|XP_028702874|]
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DNA polymerase zeta catalytic subunit isoform X7 [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 ...
2460-2908 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: 865.76  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2460 GSQYRVESMMLRIAKPMNYIPVTPSVQQRSQMRAPQCVPLIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHV 2539
Cdd:cd05534      1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2540 ENLGKYDEFKFGCTSLRVPPD--LLYQVRHDITVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSR 2617
Cdd:cd05534     81 EELNGGGKFGFLGVKLYLPPPplDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDDKKLQR 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2618 MLDARQLGLKLIANVTFGYTAANFSGRMPCIEVGDSIVHKARETLERAIKLVNDTKKWGARVVYGDTDSMFVLLKGATKE 2697
Cdd:cd05534    161 ILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLFVLLPGRTKE 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2698 QSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPVFDAKGIETVRRDSCPAVSKILERSLK 2777
Cdd:cd05534    241 EAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAVQKILEKSLR 320
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2778 LLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYRGSfSYKPGACVPALELT-RKMLTYDRRSEPQVGERVPYVII 2856
Cdd:cd05534    321 ILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLG-TYKEGATLPAGAIVaLRRMEKDPRAEPQYGERVPYVVV 399
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1622930112 2857 YGTPGVPLIQLVRRPVEVLQDPTLRLNATYYITKQILPPLARIFSLIGIDVF 2908
Cdd:cd05534    400 RGEPGSRLIDLVVSPEEFLADPSLRLDAEYYITKQIIPALDRLFNLVGVDVQ 451
DUF4683 pfam15735
Domain of unknown function (DUF4683); This domain family is found in eukaryotes, and is ...
632-1012 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: 576.43  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  632 NRTMVHSLNSTADESGLNKLKIRYEEFQEHKTEKPSLSQQAAHYMFFPSVVLSNCLTR---PQKLSPVTYKLQPG-NKPS 707
Cdd:pfam15735    1 VRNYVFDDDQSTDESDVGKLKIRYESFQENKAEKTSLSQQEAHYKFFPSVVLSNCLSRrsaLKKLGPVTYKLQQFkSRQS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  708 RLKLNKKK--LAGHQETFTKSSETGSTKDNS-IQNNPCNSN-PEKDSAFASDlTKTSRGAFENKTPTD--GFIDCHFGDG 781
Cdd:pfam15735   81 RLKLGKKKlnLDGKQEPEKKTHDKASTKEKCnLQGNALNKNiPETEVELDSD-VQVAHSAFKNKMSIDpaNSDSCHFSDD 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  782 TLETEQSFGLYGNKYTLRAKRKVNYETEDSESSFVTHNSKISLPHPMEIGESLDGTLKSRKRRKMSKKLPPVIIKYIIIN 861
Cdd:pfam15735  160 SEESYDASSLCGSKYTLRAKRKVNYETEDSESSEKIHNSKESLPQGSKEEDDDDGSPKSQKRRKVSKKEPPVIIKYIIIN 239
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  862 RFRGRKNMLVKLGKIDAKEKQVILTEEKMELYKKLAPLKDFWPKVPDSPATKYPIYPLTPKKSHRRKSKHKSAKKKTG-K 940
Cdd:pfam15735  240 RFKGRKNMLVKLGKVDSSETTVTLTEEKLEKYKKLAPLKDFWPKVPDSPATKYPVYPLTPKKSPKRKAKCKSTNKKRIqR 319
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622930112  941 QQRTNNENIKRTLSFRKKRSHALLSPPSPSYNAETEDCDLNYSDVMSKLGFLSERSTSPINSSPPRCWSPTD 1012
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 ...
2170-2434 1.37e-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: 308.78  E-value: 1.37e-95
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2170 IQNLTLISVELHARTRRDLEPDPEFDPICALFYCISSDAPLPDTEKTElTGVIVIDKDKTVFSQDiryqtplLIRSGITG 2249
Cdd:cd05778      1 HQHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANK-VGVIIVDELKSNASNG-------RIRSGLSG 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2250 LEVTYAADEKALFHEIAHIIKRgchqhvrcfqyphffyfckqlrkrnmYDPDILLGYEIQMHSWGYLLQRAAALSVDLC- 2328
Cdd:cd05778     73 IPVEVVESELELFEELIDLVRR--------------------------FDPDILSGYEIQRSSWGYLIERAAALGIDDLl 126
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2329 QMISRVPDDKiENRFAAERDEYGSYTMSEINIVGRITLNLWRIMRNEVALTNYTFENVSFHVLHQRFPLFTFRVLSDWFD 2408
Cdd:cd05778    127 DEISRVPSDS-NGKFGDRDDEWGYTHTSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYK 205
                          250       260
                   ....*....|....*....|....*.
gi 1622930112 2409 NKTDLYRWKMVDHYVSRVRGNLQMLE 2434
Cdd:cd05778    206 SGSASERWRVLEYYLKRVRLNLEILD 231
zf-C4pol pfam14260
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ...
2944-3011 2.36e-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: 78.57  E-value: 2.36e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622930112 2944 CPVCDDLTQhGICSKCRSQPQHVAVILNQEIRELERKQEQLVKICKNCTGCFDRHIPCVSLNCPVLFK 3011
Cdd:pfam14260    1 CLGCGAPEE-PLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYM 67
REV3L_RBD cd22287
REV7 binding domain found in protein reversionless 3-like (REV3L) and similar proteins; REV3L, ...
1751-1773 8.87e-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: 8.87e-09
                           10        20
                   ....*....|....*....|...
gi 1622930112 1751 RTAHILKPLMSPPSREEIMATLL 1773
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 ...
2460-2908 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: 865.76  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2460 GSQYRVESMMLRIAKPMNYIPVTPSVQQRSQMRAPQCVPLIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHV 2539
Cdd:cd05534      1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2540 ENLGKYDEFKFGCTSLRVPPD--LLYQVRHDITVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSR 2617
Cdd:cd05534     81 EELNGGGKFGFLGVKLYLPPPplDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDDKKLQR 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2618 MLDARQLGLKLIANVTFGYTAANFSGRMPCIEVGDSIVHKARETLERAIKLVNDTKKWGARVVYGDTDSMFVLLKGATKE 2697
Cdd:cd05534    161 ILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLFVLLPGRTKE 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2698 QSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPVFDAKGIETVRRDSCPAVSKILERSLK 2777
Cdd:cd05534    241 EAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAVQKILEKSLR 320
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2778 LLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYRGSfSYKPGACVPALELT-RKMLTYDRRSEPQVGERVPYVII 2856
Cdd:cd05534    321 ILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLG-TYKEGATLPAGAIVaLRRMEKDPRAEPQYGERVPYVVV 399
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1622930112 2857 YGTPGVPLIQLVRRPVEVLQDPTLRLNATYYITKQILPPLARIFSLIGIDVF 2908
Cdd:cd05534    400 RGEPGSRLIDLVVSPEEFLADPSLRLDAEYYITKQIIPALDRLFNLVGVDVQ 451
DUF4683 pfam15735
Domain of unknown function (DUF4683); This domain family is found in eukaryotes, and is ...
632-1012 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: 576.43  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  632 NRTMVHSLNSTADESGLNKLKIRYEEFQEHKTEKPSLSQQAAHYMFFPSVVLSNCLTR---PQKLSPVTYKLQPG-NKPS 707
Cdd:pfam15735    1 VRNYVFDDDQSTDESDVGKLKIRYESFQENKAEKTSLSQQEAHYKFFPSVVLSNCLSRrsaLKKLGPVTYKLQQFkSRQS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  708 RLKLNKKK--LAGHQETFTKSSETGSTKDNS-IQNNPCNSN-PEKDSAFASDlTKTSRGAFENKTPTD--GFIDCHFGDG 781
Cdd:pfam15735   81 RLKLGKKKlnLDGKQEPEKKTHDKASTKEKCnLQGNALNKNiPETEVELDSD-VQVAHSAFKNKMSIDpaNSDSCHFSDD 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  782 TLETEQSFGLYGNKYTLRAKRKVNYETEDSESSFVTHNSKISLPHPMEIGESLDGTLKSRKRRKMSKKLPPVIIKYIIIN 861
Cdd:pfam15735  160 SEESYDASSLCGSKYTLRAKRKVNYETEDSESSEKIHNSKESLPQGSKEEDDDDGSPKSQKRRKVSKKEPPVIIKYIIIN 239
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  862 RFRGRKNMLVKLGKIDAKEKQVILTEEKMELYKKLAPLKDFWPKVPDSPATKYPIYPLTPKKSHRRKSKHKSAKKKTG-K 940
Cdd:pfam15735  240 RFKGRKNMLVKLGKVDSSETTVTLTEEKLEKYKKLAPLKDFWPKVPDSPATKYPVYPLTPKKSPKRKAKCKSTNKKRIqR 319
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622930112  941 QQRTNNENIKRTLSFRKKRSHALLSPPSPSYNAETEDCDLNYSDVMSKLGFLSERSTSPINSSPPRCWSPTD 1012
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 ...
2456-2903 2.77e-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: 371.17  E-value: 2.77e-114
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2456 VLTRGSQYRVESMMLRIAKPMNYIpVTPSVQQRSQMRAPQCVpLIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTC 2535
Cdd:pfam00136    6 VLEGGQQIRVESCLLRLALEEGFI-LPDRPSAKGDEDGYQGA-TVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCYTTL 83
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2536 LGHVENlgkydefkfgctSLRVPPDLLYQvrhDITVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKqDRAL 2615
Cdd:pfam00136   84 VRSVDE------------ANNLPPEDNLI---TVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEET-DPFE 147
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2616 SRMLDARQLGLKLIANVTFGYTAANfSGRMPCIEVGDSIVHKARETLERAIKLVNDTKKWGARVVYGDTDSMFVLLKGAT 2695
Cdd:pfam00136  148 RAILDKQQLALKITANSVYGFTGFA-NGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYNFRVIYGDTDSVFIEFGGKD 226
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2696 KEQSFKIGQEIAEAVT-ATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPvFDAKGIETVRRDSCPAVSKILER 2774
Cdd:pfam00136  227 VEEAMKIGDELAEHVNqDLFKSPIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFNK-LDMKGVDLVRRDNCPLVKEVIKK 305
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2775 SLKLLFETRDISLIKQYVQRQCM----KLLEGKASIQDFIFAKEYRGSFSYKPGACVPALELTRKMLTYDRRsEPQVGER 2850
Cdd:pfam00136  306 VLDLLLSDRGLPVGLEFVISILNdarsDLRNNKVPLEKFVISKELSKPPDNYKSKNLPHVEVALRMNKRNGE-APEVGDR 384
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622930112 2851 VPYVII---YGTPGVPLIQLVRRPVEVLQDpTLRLNATYYITKQILPPLARIFSLI 2903
Cdd:pfam00136  385 IPYVIVkaaKGLKNLLIYERAEDPEYVLEN-NLPIDYEYYFSNQLIPPVARLLEPI 439
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
2299-3032 8.45e-113

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 387.85  E-value: 8.45e-113
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2299 DPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKI---ENRFAAErdEYGSYTMSEINIVGRITLNLWRIMRNE 2375
Cdd:PTZ00166   345 DPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSvikDSKFSSK--QMGTRESKEINIEGRIQFDVMDLIRRD 422
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2376 VALTNYTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYRWKMV----DHYVSrvrgnLQMLEQLDLIGKTSEMARLFGI 2451
Cdd:PTZ00166   423 YKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVyclkDAILP-----LRLLDKLLLIYNYVEMARVTGT 497
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2452 QFLHVLTRGSQYRVESMMLRIAKPMNY-IPVTPSVQQRSQMRAPQCVplIMEPESRFYSNSVLVLDFQSLYPSIVIAYNY 2530
Cdd:PTZ00166   498 PIGWLLTRGQQIKVTSQLLRKCKKLNYvIPTVKYSGGGSEEKYEGAT--VLEPKKGFYDEPIATLDFASLYPSIMIAHNL 575
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2531 CFSTclghvenLGKYDEFKfgctslRVPPDLLyqvrhdiTVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYK 2610
Cdd:PTZ00166   576 CYST-------LVPPNDAN------NYPEDTY-------VTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEK 635
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2611 qDRALSRMLDARQLGLKLIANVTFGYTAANFSGRMPCIEVGDSIVHKARETLERAIKLVND--TKKWG----ARVVYGDT 2684
Cdd:PTZ00166   636 -DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKhyTKANGykhdATVIYGDT 714
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2685 DSmfVLLKGATK--EQSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPVfDAKGIETVRR 2762
Cdd:PTZ00166   715 DS--VMVKFGTDdiQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAGLLYTNPEKYDKI-DCKGIETVRR 791
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2763 DSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYrGSFSYKpgACVPALELTRKMLTYDRR 2842
Cdd:PTZ00166   792 DNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRIDISLLVITKSL-GKDDYE--GRLAHVELAKKLRQRDPG 868
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2843 SEPQVGERVPYVIIYGTPGVPLIQLVRRPVEVLqDPTLRLNATYYItKQILPPLARIFSLIGIDVFSWYHELPRIHKATN 2922
Cdd:PTZ00166   869 SAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVL-ENNIPIDTQYYL-DQIKNPLLRIFEGVMDNPDSLFSGEHTRHITIS 946
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2923 SSrsepegRKGTISQYFT-TLHCPVCDDLTQHG-ICSKCRS--QPQHVAVILNqEIRELERKQEQLVKICKNCTGCFDRH 2998
Cdd:PTZ00166   947 SS------SKGGLSKFVKkQLQCLGCKSVIKEGaLCDNCNQnkEPSIYGKKLA-KRRHKEAEYSQLWTQCQRCQGSLHQE 1019
                          730       740       750
                   ....*....|....*....|....*....|....
gi 1622930112 2999 IPCVSLNCPVLFKVSRVNRELSKapyLRQLLDQF 3032
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 ...
2170-2434 1.37e-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: 308.78  E-value: 1.37e-95
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2170 IQNLTLISVELHARTRRDLEPDPEFDPICALFYCISSDAPLPDTEKTElTGVIVIDKDKTVFSQDiryqtplLIRSGITG 2249
Cdd:cd05778      1 HQHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANK-VGVIIVDELKSNASNG-------RIRSGLSG 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2250 LEVTYAADEKALFHEIAHIIKRgchqhvrcfqyphffyfckqlrkrnmYDPDILLGYEIQMHSWGYLLQRAAALSVDLC- 2328
Cdd:cd05778     73 IPVEVVESELELFEELIDLVRR--------------------------FDPDILSGYEIQRSSWGYLIERAAALGIDDLl 126
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2329 QMISRVPDDKiENRFAAERDEYGSYTMSEINIVGRITLNLWRIMRNEVALTNYTFENVSFHVLHQRFPLFTFRVLSDWFD 2408
Cdd:cd05778    127 DEISRVPSDS-NGKFGDRDDEWGYTHTSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYK 205
                          250       260
                   ....*....|....*....|....*.
gi 1622930112 2409 NKTDLYRWKMVDHYVSRVRGNLQMLE 2434
Cdd:cd05778    206 SGSASERWRVLEYYLKRVRLNLEILD 231
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
2192-2693 2.97e-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: 2.97e-91
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  2192 PEFDPICALFYCISSDAPLPDTEKTELtgvIVIDKDKTVFSQDIRYQT-----PLLIRSGITGLEVTYAADEKALFHEia 2266
Cdd:smart00486    1 PPLKILSFDIETYTDGGNFPDAEIFDD---EIIQISLVINDGDKKGANrrilfTLGTCKEIDGIEVYEFNNEKELLLA-- 75
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  2267 hiikrgchqhvrcfqyphFFYFCKQlrkrnmYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPD-DKIENRFAA 2345
Cdd:smart00486   76 ------------------FFEFIKK------YDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIgLRIPNKKPL 131
                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  2346 ERDEYGSYTMSEINIVGRITLNLWRIMRNEVALTNYTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYRWkMVDHYVSR 2425
Cdd:smart00486  132 FGSKSFGLSDIKVYIKGRLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDE-LLRYCIQD 210
                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  2426 VRGNLQMLEQLDLIGKTSEMARLFGIQFLHVLTRGSQYRVESMMLRIAKPMNYIPVTPSVQQRSQMRAPQCVP------L 2499
Cdd:smart00486  211 AVLTLKLFNKLNVIPLIIELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEPDLKKKvkyeggK 290
                           330       340       350       360       370       380       390       400
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  2500 IMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHVENLGKYDEFKFgctslrvppdllYQVRHDITVSPNGVAFV 2579
Cdd:smart00486  291 VLEPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKGDLIIP------------EDLLTIKYEKGNKYRFV 358
                           410       420       430       440       450       460       470       480
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  2580 KPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSR-MLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKA 2658
Cdd:smart00486  359 KKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESEELKkLLDSRQLALKLTANSVYGYLGFTNS-RLPCKPLAASVTALG 437
                           490       500       510
                    ....*....|....*....|....*....|....*..
gi 1622930112  2659 RETLERAIKLVND--TKKWGARVVYGDTDSMFVLLKG 2693
Cdd:smart00486  438 REILEKTKELIEEngYPKPGFKVIYGDTDSIFVTKPG 474
PolB COG0417
DNA polymerase B elongation subunit [Replication, recombination and repair];
2221-2906 3.93e-84

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


Pssm-ID: 440186 [Multi-domain]  Cd Length: 794  Bit Score: 295.97  E-value: 3.93e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2221 VIVIdkdkTVFSQDIRYQTPLLIRSGItGLEVTYAADEKALFHEIAHIIKRgchqhvrcfqyphffyfckqlrkrnmYDP 2300
Cdd:COG0417    184 IISI----GLAGSDGEKKVLMLGREGV-DFEVEYFDDEKALLEAFFEIIRE--------------------------YDP 232
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2301 DILLGYEIQMHSWGYLLQRAAALSVDLcqMISRvpddkieNRFAAERDEYGSYTMseINIVGRITLNLWRIMRN-EVALT 2379
Cdd:COG0417    233 DIIIGWNVDNFDLPYLQKRAERLGIPL--DLGR-------DGSEPSWREHGGQGF--ASIPGRVVIDLYDALKSaTYKFK 301
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2380 NYTFENVSFHVLHqrfplftfrvlsdwfDNKTDLYRWKMVDHYVSR----VRGNLQ-------MLEQLDLIGKTSEMARL 2448
Cdd:COG0417    302 SYSLDAVAEELLG---------------EGKLIVDGGEIERLWDDDkpalAEYNLRdaeltlrIFEKTLLLPFLIELSRI 366
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2449 FGIQFLHVLTRGSQYRVESMMLRIAKPMNY-IPVTPSVQQRSQMRApqcvpLIMEPESRFYSNsVLVLDFQSLYPSIVIA 2527
Cdd:COG0417    367 TGLPLDDVGRAGSSAAFENLLLPEAHRRGYlAPNKGEIKGEAYPGG-----YVLDPKPGLYEN-VLVLDFKSLYPSIIRT 440
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2528 YNYCFST-CLGHVENLGKYDefkfgctslrvppdllyqvrhditVSPN-GVAFVKPsvRKGVLPRMLEEILKTRFMVKQS 2605
Cdd:COG0417    441 FNISPETlVEGGEEPCGDED------------------------VAPGfGHRFCRE--PKGILPSILEELWDERDEAKKK 494
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2606 MKAYKQDRALSRMLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKARETLERAIKLVndtKKWGARVVYGDTD 2685
Cdd:COG0417    495 MKKAKPDSEEYRLYDALQQALKILMNSFYGVLGSEGC-RFYDPELAESITARGREIIKQTIEKA---EELGYKVIYGDTD 570
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2686 SMFVLLKGATKEQSFKIGQEIAEAVTATNPKPVKLKFEKVYLPcVLQT--KKRYVGYmyetldQKDPVFDAKGIETVRRD 2763
Cdd:COG0417    571 SLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRR-FFFPgsKKRYAGL------TEDGKIDIKGLEAVRSD 643
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2764 SCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYRGSFS-YKpgACVPA-LELTRKMLTYDR 2841
Cdd:COG0417    644 WTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSeYE--KNVPPhVRAARKLDERGR 721
                          650       660       670       680       690       700
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622930112 2842 rsEPQVGERVPYVIIYGTPGVpliqlvrRPVEVLQDPTLRLNATYYITKQILPPLARIFSLIGID 2906
Cdd:COG0417    722 --PYQRGDKISYVITKGGGRV-------EPVELAKERESEIDYDYYIEKQLKPTADRILEAFGVS 777
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
2288-2900 6.10e-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: 196.05  E-value: 6.10e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2288 FCKQLRKRnmyDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKIENRFAAERdeygsytmseinIVGRITLN 2367
Cdd:TIGR00592  591 FMAKVKKI---DPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGER------------TCGRMICD 655
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2368 LWRIMRNEVALTNYTFENVSFHVLH-QRFPLFTFRVLSDWFDNKTDLYrwkMVDHYVSRVRGNLQMLEQLDLIGKTSEMA 2446
Cdd:TIGR00592  656 VEISAKELIRCKSYDLSELVQQILKtERKVIPIDNINNMYSESSSLTY---LLEHTWKDAMFILQIMCELNVLPLALQIT 732
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2447 RLFGIQFLHVLTRGSQYRVESMMLRIAKPMNYI-PVTPSVQQRSQMR--------------APQCVPLIMEPESRFYSNS 2511
Cdd:TIGR00592  733 NIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIvPDKQIFRKQQKLGdedeeidgykkgkkAAYAGGLVLEPKVGLYDKY 812
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2512 VLVLDFQSLYPSIVIAYNYCFSTclghVENLGKYDEfkfgctsLRVPPDllyqvrhditvspngvafvkPSVRKGVLPRM 2591
Cdd:TIGR00592  813 VLLMDFNSLYPSIIQEFNICFTT----VQQKVDEDE-------LPELPD--------------------SELEMGILPRE 861
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2592 LEEILKTRFMVKQSMKAyKQDRALSRMLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKARETLERAIKLVnd 2671
Cdd:TIGR00592  862 LRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKS-RFYAKPLAALVTAKGREILEHTRQLV-- 937
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2672 tKKWGARVVYGDTDSMFVLLKGATKEQSFKIGQEIAEAVTATNpKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPV 2751
Cdd:TIGR00592  938 -EEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLY-KLLELDIDGVFKRLLLLKKKKYAAIKVEGDSDGNYT 1015
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2752 F--DAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKL----LEGKASIQDFIFAKEY-RGSFSYKPG 2824
Cdd:TIGR00592 1016 TkqEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIgknvLNGEVPLEKFVINKQLtRDPKDYPDG 1095
                          570       580       590       600       610       620       630
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1622930112 2825 ACVPALELTRKMLTYDRRSEPQvGERVPYVIIYGTPGVPLIQLVRRPVEVL-QDPTLRLNATYYITKQILPPLARIF 2900
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 ...
2944-3011 2.36e-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: 78.57  E-value: 2.36e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622930112 2944 CPVCDDLTQhGICSKCRSQPQHVAVILNQEIRELERKQEQLVKICKNCTGCFDRHIPCVSLNCPVLFK 3011
Cdd:pfam14260    1 CLGCGAPEE-PLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYM 67
REV3L_RBD cd22287
REV7 binding domain found in protein reversionless 3-like (REV3L) and similar proteins; REV3L, ...
1751-1773 8.87e-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: 8.87e-09
                           10        20
                   ....*....|....*....|...
gi 1622930112 1751 RTAHILKPLMSPPSREEIMATLL 1773
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 ...
2190-2386 4.12e-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: 54.73  E-value: 4.12e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2190 PDPEF--DP---ICALFYCISSDAPLPdtekteltgvIVIDKDKTVFSQDIrYQTPLLIRSGITGLEVTYAADEKALFHe 2264
Cdd:pfam03104  172 PDAENvkDPiiqISCMLDGQGEPEPEP----------RFLFTLRECDSEDI-EDFEYTPKPIYPGVKVFEFPSEKELLR- 239
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2265 iahiikrgchqhvrcfqypHFFYFCKQlrkrnmYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDkieNRFA 2344
Cdd:pfam03104  240 -------------------RFFEFIRQ------YDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNRG---GRSK 291
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1622930112 2345 AERDEYGSYTMSEINIVGRITLNLWRIMRNEVALTNYTFENV 2386
Cdd:pfam03104  292 VREIGFGTRSYEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
 
Name Accession Description Interval E-value
POLBc_zeta cd05534
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ...
2460-2908 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: 865.76  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2460 GSQYRVESMMLRIAKPMNYIPVTPSVQQRSQMRAPQCVPLIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHV 2539
Cdd:cd05534      1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2540 ENLGKYDEFKFGCTSLRVPPD--LLYQVRHDITVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSR 2617
Cdd:cd05534     81 EELNGGGKFGFLGVKLYLPPPplDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDDKKLQR 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2618 MLDARQLGLKLIANVTFGYTAANFSGRMPCIEVGDSIVHKARETLERAIKLVNDTKKWGARVVYGDTDSMFVLLKGATKE 2697
Cdd:cd05534    161 ILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLFVLLPGRTKE 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2698 QSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPVFDAKGIETVRRDSCPAVSKILERSLK 2777
Cdd:cd05534    241 EAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAVQKILEKSLR 320
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2778 LLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYRGSfSYKPGACVPALELT-RKMLTYDRRSEPQVGERVPYVII 2856
Cdd:cd05534    321 ILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLG-TYKEGATLPAGAIVaLRRMEKDPRAEPQYGERVPYVVV 399
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1622930112 2857 YGTPGVPLIQLVRRPVEVLQDPTLRLNATYYITKQILPPLARIFSLIGIDVF 2908
Cdd:cd05534    400 RGEPGSRLIDLVVSPEEFLADPSLRLDAEYYITKQIIPALDRLFNLVGVDVQ 451
DUF4683 pfam15735
Domain of unknown function (DUF4683); This domain family is found in eukaryotes, and is ...
632-1012 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: 576.43  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  632 NRTMVHSLNSTADESGLNKLKIRYEEFQEHKTEKPSLSQQAAHYMFFPSVVLSNCLTR---PQKLSPVTYKLQPG-NKPS 707
Cdd:pfam15735    1 VRNYVFDDDQSTDESDVGKLKIRYESFQENKAEKTSLSQQEAHYKFFPSVVLSNCLSRrsaLKKLGPVTYKLQQFkSRQS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  708 RLKLNKKK--LAGHQETFTKSSETGSTKDNS-IQNNPCNSN-PEKDSAFASDlTKTSRGAFENKTPTD--GFIDCHFGDG 781
Cdd:pfam15735   81 RLKLGKKKlnLDGKQEPEKKTHDKASTKEKCnLQGNALNKNiPETEVELDSD-VQVAHSAFKNKMSIDpaNSDSCHFSDD 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  782 TLETEQSFGLYGNKYTLRAKRKVNYETEDSESSFVTHNSKISLPHPMEIGESLDGTLKSRKRRKMSKKLPPVIIKYIIIN 861
Cdd:pfam15735  160 SEESYDASSLCGSKYTLRAKRKVNYETEDSESSEKIHNSKESLPQGSKEEDDDDGSPKSQKRRKVSKKEPPVIIKYIIIN 239
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  862 RFRGRKNMLVKLGKIDAKEKQVILTEEKMELYKKLAPLKDFWPKVPDSPATKYPIYPLTPKKSHRRKSKHKSAKKKTG-K 940
Cdd:pfam15735  240 RFKGRKNMLVKLGKVDSSETTVTLTEEKLEKYKKLAPLKDFWPKVPDSPATKYPVYPLTPKKSPKRKAKCKSTNKKRIqR 319
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622930112  941 QQRTNNENIKRTLSFRKKRSHALLSPPSPSYNAETEDCDLNYSDVMSKLGFLSERSTSPINSSPPRCWSPTD 1012
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 ...
2456-2903 2.77e-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: 371.17  E-value: 2.77e-114
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2456 VLTRGSQYRVESMMLRIAKPMNYIpVTPSVQQRSQMRAPQCVpLIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTC 2535
Cdd:pfam00136    6 VLEGGQQIRVESCLLRLALEEGFI-LPDRPSAKGDEDGYQGA-TVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCYTTL 83
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2536 LGHVENlgkydefkfgctSLRVPPDLLYQvrhDITVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKqDRAL 2615
Cdd:pfam00136   84 VRSVDE------------ANNLPPEDNLI---TVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEET-DPFE 147
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2616 SRMLDARQLGLKLIANVTFGYTAANfSGRMPCIEVGDSIVHKARETLERAIKLVNDTKKWGARVVYGDTDSMFVLLKGAT 2695
Cdd:pfam00136  148 RAILDKQQLALKITANSVYGFTGFA-NGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYNFRVIYGDTDSVFIEFGGKD 226
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2696 KEQSFKIGQEIAEAVT-ATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPvFDAKGIETVRRDSCPAVSKILER 2774
Cdd:pfam00136  227 VEEAMKIGDELAEHVNqDLFKSPIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFNK-LDMKGVDLVRRDNCPLVKEVIKK 305
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2775 SLKLLFETRDISLIKQYVQRQCM----KLLEGKASIQDFIFAKEYRGSFSYKPGACVPALELTRKMLTYDRRsEPQVGER 2850
Cdd:pfam00136  306 VLDLLLSDRGLPVGLEFVISILNdarsDLRNNKVPLEKFVISKELSKPPDNYKSKNLPHVEVALRMNKRNGE-APEVGDR 384
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622930112 2851 VPYVII---YGTPGVPLIQLVRRPVEVLQDpTLRLNATYYITKQILPPLARIFSLI 2903
Cdd:pfam00136  385 IPYVIVkaaKGLKNLLIYERAEDPEYVLEN-NLPIDYEYYFSNQLIPPVARLLEPI 439
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
2299-3032 8.45e-113

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 387.85  E-value: 8.45e-113
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2299 DPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKI---ENRFAAErdEYGSYTMSEINIVGRITLNLWRIMRNE 2375
Cdd:PTZ00166   345 DPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSvikDSKFSSK--QMGTRESKEINIEGRIQFDVMDLIRRD 422
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2376 VALTNYTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYRWKMV----DHYVSrvrgnLQMLEQLDLIGKTSEMARLFGI 2451
Cdd:PTZ00166   423 YKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVyclkDAILP-----LRLLDKLLLIYNYVEMARVTGT 497
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2452 QFLHVLTRGSQYRVESMMLRIAKPMNY-IPVTPSVQQRSQMRAPQCVplIMEPESRFYSNSVLVLDFQSLYPSIVIAYNY 2530
Cdd:PTZ00166   498 PIGWLLTRGQQIKVTSQLLRKCKKLNYvIPTVKYSGGGSEEKYEGAT--VLEPKKGFYDEPIATLDFASLYPSIMIAHNL 575
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2531 CFSTclghvenLGKYDEFKfgctslRVPPDLLyqvrhdiTVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYK 2610
Cdd:PTZ00166   576 CYST-------LVPPNDAN------NYPEDTY-------VTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEK 635
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2611 qDRALSRMLDARQLGLKLIANVTFGYTAANFSGRMPCIEVGDSIVHKARETLERAIKLVND--TKKWG----ARVVYGDT 2684
Cdd:PTZ00166   636 -DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKhyTKANGykhdATVIYGDT 714
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2685 DSmfVLLKGATK--EQSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPVfDAKGIETVRR 2762
Cdd:PTZ00166   715 DS--VMVKFGTDdiQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAGLLYTNPEKYDKI-DCKGIETVRR 791
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2763 DSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYrGSFSYKpgACVPALELTRKMLTYDRR 2842
Cdd:PTZ00166   792 DNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRIDISLLVITKSL-GKDDYE--GRLAHVELAKKLRQRDPG 868
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2843 SEPQVGERVPYVIIYGTPGVPLIQLVRRPVEVLqDPTLRLNATYYItKQILPPLARIFSLIGIDVFSWYHELPRIHKATN 2922
Cdd:PTZ00166   869 SAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVL-ENNIPIDTQYYL-DQIKNPLLRIFEGVMDNPDSLFSGEHTRHITIS 946
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2923 SSrsepegRKGTISQYFT-TLHCPVCDDLTQHG-ICSKCRS--QPQHVAVILNqEIRELERKQEQLVKICKNCTGCFDRH 2998
Cdd:PTZ00166   947 SS------SKGGLSKFVKkQLQCLGCKSVIKEGaLCDNCNQnkEPSIYGKKLA-KRRHKEAEYSQLWTQCQRCQGSLHQE 1019
                          730       740       750
                   ....*....|....*....|....*....|....
gi 1622930112 2999 IPCVSLNCPVLFKVSRVNRELSKapyLRQLLDQF 3032
Cdd:PTZ00166  1020 VICTNRDCPIFYRRKKVQKDLAE---LQELLSRF 1050
POLBc cd00145
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ...
2493-2901 7.39e-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: 7.39e-108
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2493 APQCVPLIMEPEsRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHVENLGKYDEFkfgctslrvppdllyqvrhditvs 2572
Cdd:cd00145      1 EPYEGGYVFDPI-PGLYENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYI------------------------ 55
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2573 pnGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSRMLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGD 2652
Cdd:cd00145     56 --GVGFRSPKDRKGLLPRILEELLNFRDEAKKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFF-RFYDPEVAA 132
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2653 SIVHKARETLERAIKLVNDTkkwGARVVYGDTDSMFVLLKG-ATKEQSFKIGQEIAEAVtaTNPKPVKLKFEKVYLPCVL 2731
Cdd:cd00145    133 SITSFGREIIQDTIALVEEH---GARVIYGDTDSIFVSLPKmGTKEDAIKEGREILQEL--ADEHLLELEFEKVYLPFFL 207
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2732 QTKKRYVGYMYETlDQKDPVFDAKGIETVRRDSCPAVSKILERSLKLLFETRDisliKQYVQRQCMKLLegkasiqdfif 2811
Cdd:cd00145    208 GKKKRYAGLDIWK-GQDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEER----KVEAVKEYIDEL----------- 271
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2812 akeyrgsfsykpgacvpaleltrkmltydrrsepqvgERVPYVIIYGTPGVPLIQLVrRPVEVLQDPTLRLNATYYITKQ 2891
Cdd:cd00145    272 -------------------------------------DKVKYVVTRGGKGVPDYERA-DPPLEDLDKRHRIDYEYYLERL 313
                          410
                   ....*....|
gi 1622930112 2892 ILPPLARIFS 2901
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 ...
2170-2434 1.37e-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: 308.78  E-value: 1.37e-95
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2170 IQNLTLISVELHARTRRDLEPDPEFDPICALFYCISSDAPLPDTEKTElTGVIVIDKDKTVFSQDiryqtplLIRSGITG 2249
Cdd:cd05778      1 HQHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANK-VGVIIVDELKSNASNG-------RIRSGLSG 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2250 LEVTYAADEKALFHEIAHIIKRgchqhvrcfqyphffyfckqlrkrnmYDPDILLGYEIQMHSWGYLLQRAAALSVDLC- 2328
Cdd:cd05778     73 IPVEVVESELELFEELIDLVRR--------------------------FDPDILSGYEIQRSSWGYLIERAAALGIDDLl 126
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2329 QMISRVPDDKiENRFAAERDEYGSYTMSEINIVGRITLNLWRIMRNEVALTNYTFENVSFHVLHQRFPLFTFRVLSDWFD 2408
Cdd:cd05778    127 DEISRVPSDS-NGKFGDRDDEWGYTHTSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYK 205
                          250       260
                   ....*....|....*....|....*.
gi 1622930112 2409 NKTDLYRWKMVDHYVSRVRGNLQMLE 2434
Cdd:cd05778    206 SGSASERWRVLEYYLKRVRLNLEILD 231
POLBc_delta cd05533
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
2500-2903 1.32e-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: 312.66  E-value: 1.32e-94
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2500 IMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLghvenlgKYDEFKfgctslRVPPDllyqvrhDITVSPNGVAFV 2579
Cdd:cd05533      8 VIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLL-------NKNTAK------KLPPE-------DYIKTPNGDYFV 67
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2580 KPSVRKGVLPRMLEEILKTRFMVKQSMKAYKqDRALSRMLDARQLGLKLIANVTFGYTAANfSGRMPCIEVGDSIVHKAR 2659
Cdd:cd05533     68 KSSVRKGLLPEILEELLAARKRAKKDLKEET-DPFKKAVLDGRQLALKISANSVYGFTGAT-VGKLPCLEISSSVTSFGR 145
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2660 ETLERAIKLVND--TKK----WGARVVYGDTDSMFVLLKGATKEQSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQT 2733
Cdd:cd05533    146 QMIEKTKKLVEEkyTKAngysHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLIN 225
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2734 KKRYVGYMYETLDQKDPVfDAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAK 2813
Cdd:cd05533    226 KKRYAGLLWTNPDKHDKM-DTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLLQNKIDISLLVITK 304
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2814 EY-RGSFSYKpgACVPALELTRKMLTYDRRSEPQVGERVPYVIIYGTPGVPLIQLVRRPVEVLQDpTLRLNATYYITKQI 2892
Cdd:cd05533    305 ALtKTADDYA--GKQAHVELAERMRKRDPGSAPNVGDRVPYVIIKGAKGAKAYEKAEDPIYVLEN-NIPIDTQYYLENQL 381
                          410
                   ....*....|.
gi 1622930112 2893 LPPLARIFSLI 2903
Cdd:cd05533    382 SKPLLRIFEPI 392
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
2192-2693 2.97e-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: 2.97e-91
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  2192 PEFDPICALFYCISSDAPLPDTEKTELtgvIVIDKDKTVFSQDIRYQT-----PLLIRSGITGLEVTYAADEKALFHEia 2266
Cdd:smart00486    1 PPLKILSFDIETYTDGGNFPDAEIFDD---EIIQISLVINDGDKKGANrrilfTLGTCKEIDGIEVYEFNNEKELLLA-- 75
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  2267 hiikrgchqhvrcfqyphFFYFCKQlrkrnmYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPD-DKIENRFAA 2345
Cdd:smart00486   76 ------------------FFEFIKK------YDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIgLRIPNKKPL 131
                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  2346 ERDEYGSYTMSEINIVGRITLNLWRIMRNEVALTNYTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYRWkMVDHYVSR 2425
Cdd:smart00486  132 FGSKSFGLSDIKVYIKGRLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDE-LLRYCIQD 210
                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  2426 VRGNLQMLEQLDLIGKTSEMARLFGIQFLHVLTRGSQYRVESMMLRIAKPMNYIPVTPSVQQRSQMRAPQCVP------L 2499
Cdd:smart00486  211 AVLTLKLFNKLNVIPLIIELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEPDLKKKvkyeggK 290
                           330       340       350       360       370       380       390       400
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  2500 IMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHVENLGKYDEFKFgctslrvppdllYQVRHDITVSPNGVAFV 2579
Cdd:smart00486  291 VLEPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKGDLIIP------------EDLLTIKYEKGNKYRFV 358
                           410       420       430       440       450       460       470       480
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112  2580 KPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSR-MLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKA 2658
Cdd:smart00486  359 KKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESEELKkLLDSRQLALKLTANSVYGYLGFTNS-RLPCKPLAASVTALG 437
                           490       500       510
                    ....*....|....*....|....*....|....*..
gi 1622930112  2659 RETLERAIKLVND--TKKWGARVVYGDTDSMFVLLKG 2693
Cdd:smart00486  438 REILEKTKELIEEngYPKPGFKVIYGDTDSIFVTKPG 474
PolB COG0417
DNA polymerase B elongation subunit [Replication, recombination and repair];
2221-2906 3.93e-84

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


Pssm-ID: 440186 [Multi-domain]  Cd Length: 794  Bit Score: 295.97  E-value: 3.93e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2221 VIVIdkdkTVFSQDIRYQTPLLIRSGItGLEVTYAADEKALFHEIAHIIKRgchqhvrcfqyphffyfckqlrkrnmYDP 2300
Cdd:COG0417    184 IISI----GLAGSDGEKKVLMLGREGV-DFEVEYFDDEKALLEAFFEIIRE--------------------------YDP 232
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2301 DILLGYEIQMHSWGYLLQRAAALSVDLcqMISRvpddkieNRFAAERDEYGSYTMseINIVGRITLNLWRIMRN-EVALT 2379
Cdd:COG0417    233 DIIIGWNVDNFDLPYLQKRAERLGIPL--DLGR-------DGSEPSWREHGGQGF--ASIPGRVVIDLYDALKSaTYKFK 301
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2380 NYTFENVSFHVLHqrfplftfrvlsdwfDNKTDLYRWKMVDHYVSR----VRGNLQ-------MLEQLDLIGKTSEMARL 2448
Cdd:COG0417    302 SYSLDAVAEELLG---------------EGKLIVDGGEIERLWDDDkpalAEYNLRdaeltlrIFEKTLLLPFLIELSRI 366
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2449 FGIQFLHVLTRGSQYRVESMMLRIAKPMNY-IPVTPSVQQRSQMRApqcvpLIMEPESRFYSNsVLVLDFQSLYPSIVIA 2527
Cdd:COG0417    367 TGLPLDDVGRAGSSAAFENLLLPEAHRRGYlAPNKGEIKGEAYPGG-----YVLDPKPGLYEN-VLVLDFKSLYPSIIRT 440
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2528 YNYCFST-CLGHVENLGKYDefkfgctslrvppdllyqvrhditVSPN-GVAFVKPsvRKGVLPRMLEEILKTRFMVKQS 2605
Cdd:COG0417    441 FNISPETlVEGGEEPCGDED------------------------VAPGfGHRFCRE--PKGILPSILEELWDERDEAKKK 494
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2606 MKAYKQDRALSRMLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKARETLERAIKLVndtKKWGARVVYGDTD 2685
Cdd:COG0417    495 MKKAKPDSEEYRLYDALQQALKILMNSFYGVLGSEGC-RFYDPELAESITARGREIIKQTIEKA---EELGYKVIYGDTD 570
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2686 SMFVLLKGATKEQSFKIGQEIAEAVTATNPKPVKLKFEKVYLPcVLQT--KKRYVGYmyetldQKDPVFDAKGIETVRRD 2763
Cdd:COG0417    571 SLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRR-FFFPgsKKRYAGL------TEDGKIDIKGLEAVRSD 643
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2764 SCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYRGSFS-YKpgACVPA-LELTRKMLTYDR 2841
Cdd:COG0417    644 WTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSeYE--KNVPPhVRAARKLDERGR 721
                          650       660       670       680       690       700
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622930112 2842 rsEPQVGERVPYVIIYGTPGVpliqlvrRPVEVLQDPTLRLNATYYITKQILPPLARIFSLIGID 2906
Cdd:COG0417    722 --PYQRGDKISYVITKGGGRV-------EPVELAKERESEIDYDYYIEKQLKPTADRILEAFGVS 777
PRK05762 PRK05762
DNA polymerase II; Reviewed
2298-2906 4.06e-57

DNA polymerase II; Reviewed


Pssm-ID: 235595 [Multi-domain]  Cd Length: 786  Bit Score: 214.72  E-value: 4.06e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2298 YDPDILLGYEIQMHSWGYLLQRAAALSVDLcqMISRVpDDKIENRFAAERDEYGSYTmseinIVGRITLNLWRIMRnevA 2377
Cdd:PRK05762   217 HDPDVIIGWNVVQFDLRLLQERAERYGIPL--RLGRD-GSELEWREHPFRSGYGFAS-----VPGRLVLDGIDALK---S 285
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2378 LTN----YTFENVSFHVL---------HQRFPLFTFRvlsdWFDNKTDLYRWKMVDhyvsrVRGNLQMLEQLDLIGKTSE 2444
Cdd:PRK05762   286 ATWvfdsFSLEYVSQRLLgegkaiddpYDRMDEIDRR----FAEDKPALARYNLKD-----CELVTRIFEKTKLLPFLLE 356
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2445 MARLFGIQflhvLTR--GSQYRVESMMLRIAKPMNYipVTPSVQQRsqmrAPQCVP--LIMEPESRFYSNsVLVLDFQSL 2520
Cdd:PRK05762   357 RATVTGLP----LDRvgGSVAAFEHLYLPRAHRAGY--VAPNLGER----PGEASPggYVMDSKPGLYDS-VLVLDFKSL 425
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2521 YPSIVIAYNYCFstcLGHVENLGKYDEfkfgctslrvppdllyqvrhDITVSPNGVAFVKPsvrKGVLPRMLEEILKTRF 2600
Cdd:PRK05762   426 YPSIIRTFNIDP---DGLVEGLAQPPE--------------------ESVAGFLGARFSRE---KHFLPEIVERLWEGRD 479
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2601 MVKQSMKAykqdralsrmldARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKARETLERAIKLVndtKKWGARVV 2680
Cdd:PRK05762   480 EAKREMNK------------PLSQAIKIIMNAFYGVLGSSGC-RFFDPRLASSITMRGHEIMKQTRELI---EAQGYQVI 543
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2681 YGDTDSMFVLLKGA-TKEQSFKIGQEIAEAVTATNPKPVK----------LKFEKVYLPCVLQT--------KKRYVGYM 2741
Cdd:PRK05762   544 YGDTDSTFVWLGGAhDEEDAAKIGRALVQEINQWWQEHLQqefglesaleLEFEKHYRRFFMPTirgaeegsKKRYAGLI 623
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2742 YETLDQKDPVFdaKGIETVRRDSCPAVSKILERSLKLLFETRD-ISLIKQYVqrqcMKLLEGKASiQDFIFAKEYRGSFS 2820
Cdd:PRK05762   624 QEGDGDGRIVF--KGLETVRTDWTPLAKEFQQELYERIFRGEPyVDYVREVI----DKLRAGELD-EKLVYRKRLRRPLD 696
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2821 -YKPGacVP-----ALELTRKMLTYDRRSEPQVGERVPYVIIYGTPGvpliqlvrrPVEVLQDPtlrLNATYYITKQILP 2894
Cdd:PRK05762   697 eYQRN--VPphvraARLADEMGYKVGRPLQYQNGGKIGYVITVNGPE---------PLEYRKSP---IDYDYYIEKQLQP 762
                          650
                   ....*....|..
gi 1622930112 2895 PLARIFSLIGID 2906
Cdd:PRK05762   763 VADRILPFFGDD 774
POLBc_alpha cd05532
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
2499-2906 1.34e-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: 188.56  E-value: 1.34e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2499 LIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHVENLGKYDEFKfgctslrVPPdllyqvrhditvspngvaf 2578
Cdd:cd05532     12 LVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEDDEEPP-------LPP------------------- 65
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2579 vkPSVRKGVLPRMLEEILKTRFMVKQSMKAyKQDRALSRMLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKA 2658
Cdd:cd05532     66 --SDQEKGILPRIIRKLVERRRQVKKLMKS-EKDPDKKAQLDIRQLALKLTANSMYGCLGFSYS-RFYAKPLAALITSKG 141
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2659 RETLERAIKLVNdtkKWGARVVYGDTDSMFVLLKGATKEQSFKIGQEIAEAVTAtNPKPVKLKFEKVYLPCVLQTKKRYV 2738
Cdd:cd05532    142 REILQKTKDLVE---KMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNK-SYKKLEIDIDGVFKRLLLLKKKKYA 217
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2739 GYMYETLDQKDPVFDAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKL----LEGKASIQDFIFAK- 2813
Cdd:cd05532    218 ALKVVDDDKGKLKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRKInedlRNGKIPLEKFIITKq 297
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2814 ------EYRGSFSYkPGACVpALELTRKMLTYdrrsepQVGERVPYVIIYGTPGVPLIQLVRRPVEVLQDPTLRLNATYY 2887
Cdd:cd05532    298 ltknpeEYPDKKSL-PHVQV-ALRMNKRGRKV------KAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYY 369
                          410       420
                   ....*....|....*....|
gi 1622930112 2888 ITKQILPPLARIFSLI-GID 2906
Cdd:cd05532    370 LSQQILPPISRLCEPIeGTD 389
POLBc_B3 cd05536
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ...
2499-2905 1.12e-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: 1.12e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2499 LIMEPESRFYSNsVLVLDFQSLYPSIVIAYNycfstclghvenlgkydefkfgctslrVPPD-LLYQVRHDITVSPN-GV 2576
Cdd:cd05536      8 IVLEPEKGLHEN-IVVLDFSSLYPSIMIKYN---------------------------ISPDtLVREGCEDCDVEPQvGH 59
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2577 AFVKPsvRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSRMLDARQLGLKLIANVTFGYTAANfSGRMPCIEVGDSIVH 2656
Cdd:cd05536     60 KFRKD--PPGFIPSVLEDLLEERRRIKEKMKKLDPESEEYKLLDERQRAIKILANSFYGYMGWA-NARWYCKECAEAVTA 136
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2657 KARETLERAIKLVndtKKWGARVVYGDTDSMFVLLKGATkeqsfKIGQEIAEAVTATNPK-PVKLKFEKVYLPCVLQTKK 2735
Cdd:cd05536    137 WGREYIKTTIKIA---EEKGFKVIYGDTDSLFVKIDGAD-----AVKKKVKKLLKYINEElPLELEIEKFYKRGFFVTKK 208
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2736 RYVGYmyeTLDQKdpvFDAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEY 2815
Cdd:cd05536    209 RYAGL---TEDGK---IDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVIEKLKRGEVPPEKLVIWKQL 282
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2816 RGSFS-YKpgACVPALELTRKMLtyDRRSEPQVGERVPYVIIYGtPGvpliQLVRR--PVEVLQDPTlRLNATYYITKQI 2892
Cdd:cd05536    283 TKDLSeYK--ATGPHVAAAKKLA--KRGYKVRPGTKIGYVIVKG-SG----KISDRayPYDMVDEKH-KYDAEYYIDNQV 352
                          410
                   ....*....|...
gi 1622930112 2893 LPPLARIFSLIGI 2905
Cdd:cd05536    353 LPAVLRILEAFGY 365
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
2288-2900 6.10e-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: 196.05  E-value: 6.10e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2288 FCKQLRKRnmyDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKIENRFAAERdeygsytmseinIVGRITLN 2367
Cdd:TIGR00592  591 FMAKVKKI---DPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGER------------TCGRMICD 655
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2368 LWRIMRNEVALTNYTFENVSFHVLH-QRFPLFTFRVLSDWFDNKTDLYrwkMVDHYVSRVRGNLQMLEQLDLIGKTSEMA 2446
Cdd:TIGR00592  656 VEISAKELIRCKSYDLSELVQQILKtERKVIPIDNINNMYSESSSLTY---LLEHTWKDAMFILQIMCELNVLPLALQIT 732
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2447 RLFGIQFLHVLTRGSQYRVESMMLRIAKPMNYI-PVTPSVQQRSQMR--------------APQCVPLIMEPESRFYSNS 2511
Cdd:TIGR00592  733 NIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIvPDKQIFRKQQKLGdedeeidgykkgkkAAYAGGLVLEPKVGLYDKY 812
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2512 VLVLDFQSLYPSIVIAYNYCFSTclghVENLGKYDEfkfgctsLRVPPDllyqvrhditvspngvafvkPSVRKGVLPRM 2591
Cdd:TIGR00592  813 VLLMDFNSLYPSIIQEFNICFTT----VQQKVDEDE-------LPELPD--------------------SELEMGILPRE 861
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2592 LEEILKTRFMVKQSMKAyKQDRALSRMLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKARETLERAIKLVnd 2671
Cdd:TIGR00592  862 LRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKS-RFYAKPLAALVTAKGREILEHTRQLV-- 937
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2672 tKKWGARVVYGDTDSMFVLLKGATKEQSFKIGQEIAEAVTATNpKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPV 2751
Cdd:TIGR00592  938 -EEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLY-KLLELDIDGVFKRLLLLKKKKYAAIKVEGDSDGNYT 1015
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2752 F--DAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKL----LEGKASIQDFIFAKEY-RGSFSYKPG 2824
Cdd:TIGR00592 1016 TkqEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIgknvLNGEVPLEKFVINKQLtRDPKDYPDG 1095
                          570       580       590       600       610       620       630
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1622930112 2825 ACVPALELTRKMLTYDRRSEPQvGERVPYVIIYGTPGVPLIQLVRRPVEVL-QDPTLRLNATYYITKQILPPLARIF 2900
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 ...
2184-2434 2.22e-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: 2.22e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2184 TRRDLEPDPEFDPICALFYCISSDaplpdtekteltGVIVIDKDKTVFSQDIRYqtpllirsGITGLEVTYAADEKALFH 2263
Cdd:cd05160      9 TPPVGGPEPDRDPIICITYADSFD------------GVKVVFLLKTSTVGDDIE--------FIDGIEVEYFADEKELLK 68
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2264 EIAHIIKRgchqhvrcfqyphffyfckqlrkrnmYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKIEnrf 2343
Cdd:cd05160     69 RFFDIIRE--------------------------YDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKS--- 119
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2344 aaerdeygSYTMSEINIVGRITLNLWRIMRNEVALTNYTFENVSFHVLHQRFPLFTFRvlsDWFDNKTDLYRWKMVDHYV 2423
Cdd:cd05160    120 --------SGSTERIAVKGRVVFDLLAAYKRDFKLKSYTLDAVAEELLGEGKEKVDGE---IIEDAEWEEDPERLIEYNL 188
                          250
                   ....*....|.
gi 1622930112 2424 SRVRGNLQMLE 2434
Cdd:cd05160    189 KDAELTLQILE 199
POLBc_Pol_II cd05537
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ...
2499-2904 8.97e-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: 8.97e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2499 LIMEPESRFYSNsVLVLDFQSLYPSIVIAYNYcfsTCLGHVENLGKYDEfkfgctslrvppdllyqvrHDITVSPNGVAF 2578
Cdd:cd05537      7 YVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLI---DPLGLIEGLKAPDP-------------------EDLIPGFLGARF 63
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2579 vkpSVRKGVLPRMLEEILKTRFMVKQSmkaykQDRALSRmldarqlGLKLIANVTFGYTAAN----FSGRMPC--IEVGD 2652
Cdd:cd05537     64 ---SREKHILPDLIARLWAARDEAKRE-----KNAPLSQ-------AIKIIMNSFYGVLGSTgcrfFDPRLASsiTLRGH 128
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2653 SIVHKARETLERAiklvndtkkwGARVVYGDTDSMFVLLKGA-TKEQSFKIGQEIAEAVTATNPKPVK----------LK 2721
Cdd:cd05537    129 EIMKQTRAWIEQQ----------GYQVIYGDTDSTFVWLGEElDAAEAQAIGKELASQINQWWAQKLKeefglesfleIE 198
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2722 FEKVYLPCVLQT--------KKRYVGyMYETLDQKDPVFdaKGIETVRRDSCPAVSKILERSLKLLFETRDI-SLIKQYV 2792
Cdd:cd05537    199 FETHYSRFFMPTirgsdegsKKRYAG-LKSTDGGDELVF--KGLETVRSDWTPLARQFQKELYERVFNDEPYeGFIKETV 275
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2793 QrqcmKLLEGKASIQdFIFAKeyrgsfsykpgacvpalELTRKMLTYDRRSEPQV-GERVPYViIYGTPGVPLIQLVRRP 2871
Cdd:cd05537    276 E----ELLAGELDEL-LVYRK-----------------RLRRPLSEYTKNVPPHVqAARLADQ-INRELGRPRQYQWIEY 332
                          410       420       430
                   ....*....|....*....|....*....|....*....
gi 1622930112 2872 V------EVLQDPTLRLNATYYITKQILPPLARIFSLIG 2904
Cdd:cd05537    333 VitvngpEPLEYRTSPLDYQHYIDKQLKPIADSILPFLG 371
PRK05761 PRK05761
DNA-directed DNA polymerase I;
2499-2896 2.29e-27

DNA-directed DNA polymerase I;


Pssm-ID: 235594 [Multi-domain]  Cd Length: 787  Bit Score: 121.72  E-value: 2.29e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2499 LIMEPESRFYSNsVLVLDFQSLYPSIVIAYNYCFSTcLGHVENLGKYDefkfgctslRVPPDLLYQVRHDitvspngvaf 2578
Cdd:PRK05761   411 LVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPET-VRIPECKCHYD---------DEVPELGHSVCDD---------- 469
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2579 vkpsvrKGVLPRMLEEILKT-RFMVKQSMKAYKQDRALSRM-LDARQLGLKLIANVTFGYTAA-NFsgRMPCIEVGDSIV 2655
Cdd:PRK05761   470 ------RPGLTSVLVGLLRDfRVKIYKKKAKDPNLDEERRAwYDVVQRALKVFLNASYGVFGAeNF--KLYRIEVAESIT 541
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2656 HKARETLERAIKLvndTKKWGARVVYGDTDSMFVllKGATKEQSFKIGQEIAEAVTatnpkpVKLKFEKVYLPCVLQ-TK 2734
Cdd:PRK05761   542 ALGREILLSTKKK---AEELGLKVLYGDTDSLFV--WGPTKESLEELIKEIEERTG------IDLEVDKTYDWVAFSgLK 610
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2735 KRYVGYMyetldqKDPVFDAKGIETVRRDSCPAVSKILERSLKLLFETRDIS-------LIKQYVQRQCMKLLEGKASIQ 2807
Cdd:PRK05761   611 KNYFGVL------KDGKVKIKGIVAKKRNTPEFVKELQREVLEVLKSIRSPEdvekvkdEIEDVLKRYYEKLRAKDYPLD 684
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2808 DFIFAK-------EYrgsfSYKPGACVPALELTRKMltydrRSEPQVGERVPYVIIYGTPGVPLIQLVRrpvevLQDptl 2880
Cdd:PRK05761   685 ELAIRVrlskpldEY----TKNTPQHVKAALQLRDY-----GVEVSPGDIISYVKVDDKRGVKPVQLAK-----LSE--- 747
                          410       420
                   ....*....|....*....|..
gi 1622930112 2881 rLNATYYIT------KQILPPL 2896
Cdd:PRK05761   748 -IDVEKYIEllrsalEQILSAL 768
POLBc_B2 cd05531
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ...
2499-2856 4.81e-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: 4.81e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2499 LIMEPESRFYSNsVLVLDFQSLYPSIVIAYNycFSTclghvENLGKydefkfGCTSLRVPPDLLYQVRHDitvspngvaf 2578
Cdd:cd05531      9 LVFQPEPGLYEN-VAQIDFSSMYPSIIVKYN--ISP-----ETINC------RCCECRDHVYLGHRICLK---------- 64
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2579 vkpsvRKGVLPRMLEEILKTRfmvkqsmKAYKQDRALSRMLDARQLGLKLIANVTFGYTA---ANFsGRmpcIEVGDSIV 2655
Cdd:cd05531     65 -----RRGFLPEVLEPLLERR-------LEYKRLKKEEDPYAGRQKALKWILVTSFGYLGyknAKF-GR---IEVHEAIT 128
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2656 HKARETLERAIKLVNDTkkwGARVVYGDTDSMFVllKGATKEQSFKigQEIAEAVTatnpkpVKLKFEKVY-----LPCV 2730
Cdd:cd05531    129 AYGRKILLRAKEIAEEM---GFRVLHGIVDSLWI--QGRGDIEELA--REIEERTG------IPLKLEGHYdwivfLPER 195
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2731 --LQTKKRYVGYMyetldqKDPVFDAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIK-------QYVQRQCMKLLE 2801
Cdd:cd05531    196 dgLGAPNRYFGRL------SDGEMKVRGIELRRRDTPPFVKKFQEEALDILASAKTPEELLklreealDLFRRYLQRLRE 269
                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622930112 2802 GKasIQDFIFAKE-YRGSFSYKPGACVPALELTRKMLTYdrrsepQVGERVPYVII 2856
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 ...
2944-3011 2.36e-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: 78.57  E-value: 2.36e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622930112 2944 CPVCDDLTQhGICSKCRSQPQHVAVILNQEIRELERKQEQLVKICKNCTGCFDRHIPCVSLNCPVLFK 3011
Cdd:pfam14260    1 CLGCGAPEE-PLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYM 67
PHA03036 PHA03036
DNA polymerase; Provisional
2500-2787 1.45e-16

DNA polymerase; Provisional


Pssm-ID: 222962 [Multi-domain]  Cd Length: 1004  Bit Score: 87.00  E-value: 1.45e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2500 IMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHVENLGKYDEFKFGCTSLRV--PPDLLYQvrHDITVSPNGVA 2577
Cdd:PHA03036   535 VFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVNDNRLEAEINKQELRRKypYPRYIYV--HCEPRSPDLVS 612
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2578 --FVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQ--DRALsrmLDARQLGLKLIANVTFG----YTAANFS------- 2642
Cdd:PHA03036   613 eiAVFDRRIEGIIPKLLKTFLEERARYKKLLKEATSsvEKAI---YDSMQYTYKIVANSVYGlmgfRNSALYSyasaksc 689
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2643 ---GRMpCIEVGDSIVHKA-----RETL-----------ERAIKL-----VNDTKKWGARVVYGDTDSMFVLLKGATKEQ 2698
Cdd:PHA03036   690 taiGRN-MIKYLNSVLNGSklingKLILancpinpffkdDRSIDTnydtnLPVEYNFTFRSVYGDTDSVFLEINTKDVDK 768
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2699 SFKIGQEIAEAV-TATNPKPVKLKFEKVYLPCVLQTKKRYVGYMY--ETLDQKDPVFDAKGIETVRRDSCP----AVSKI 2771
Cdd:PHA03036   769 SIKIAKELERIInEKVLFDNFKIEFEAVYKNLIMQSKKKYTTLKYiaSSTDGSVPERVNKGTSETRRDVSKfhkyMIKIY 848
                          330
                   ....*....|....*.
gi 1622930112 2772 LERSLKLLFETRDISL 2787
Cdd:PHA03036   849 KTRLLDMLSEGNMNSN 864
POLBc_B1 cd05530
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ...
2499-2871 2.64e-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: 77.39  E-value: 2.64e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2499 LIMEPESRFYSNsVLVLDFQSLYPSIVIAYNYCFST--CLgHVENlgKYDEFkfgctslrvpPDLLYQVRHDitvspngv 2576
Cdd:cd05530     17 IVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYETvnCP-HCEC--KTNEV----------PEVGHWVCKK-------- 74
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2577 afvkpsvRKGVLPRMLEEILKTRFMV-KQSMKAYKQDRALSRMLDARQLGLKLIANVTFG-YTAANFSgrMPCIEVGDSI 2654
Cdd:cd05530     75 -------RPGITSQIIGLLRDLRVKIyKKKAKDKSLDEEMRQWYDVVQSAMKVFINASYGvFGAENFP--LYCPPVAEST 145
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2655 VHKARETLERAIKlvnDTKKWGARVVYGDTDSMFvlLKGATKEQSFKIgQEIAEavtatNPKPVKLKFEKVYLPCVLQT- 2733
Cdd:cd05530    146 TALGRYIITSTIK---KARELGLKVLYGDTDSLF--LWNPPQEQLEDL-VEWVE-----KELGLDLELDKEYRYVVFSGl 214
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2734 KKRYVGYMyetldqKDPVFDAKGIETVRRDSCPAVSKILERSLKLLFETR---DIS----LIKQYVQRQCMKLLEGKASI 2806
Cdd:cd05530    215 KKNYLGVT------KDGSVDIKGLLGKKRNTPEFVKELFYEVIEILSAVNspeDFEkareKIRDIVKGVYKRLKKKEYTL 288
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622930112 2807 QDFIF-------AKEYRGSfsyKPgacvPALELTRKMLTYDRRSEPqvGERVPYVIIYGTPGVPLIQLVRRP 2871
Cdd:cd05530    289 DQLAFkvmlskpPEEYTKN---TP----QHVKAARQLEKYGRNVEA--GDIISYVKVKGKEGVKPVQLARLD 351
43 PHA02528
DNA polymerase; Provisional
2300-2816 7.84e-13

DNA polymerase; Provisional


Pssm-ID: 177369 [Multi-domain]  Cd Length: 881  Bit Score: 74.73  E-value: 7.84e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2300 PDILLGYEIQMHSWGYLLQRaaalsvdlcqmISRVPDDKIENRF-----AAER---DEYGS----YTMSEINIVGriTLN 2367
Cdd:PHA02528   194 PVIFTGWNVELFDVPYIINR-----------IKNILGEKTAKRLspwgkVKERtieNMYGReeiaYDISGISILD--YLD 260
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2368 LWRimrnEVALTN---YTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYrwkmVDHYVSRVRGNLQMLEQLDLIGKTSE 2444
Cdd:PHA02528   261 LYK----KFTFTNqpsYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKY----IEYNIIDVELVDRLDDKRKLIELVLS 332
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2445 MARLFGIQFLHVLtrgSQYRVESMMLRIAKPMNYIpVTPsvQQRSQMRAPQCVPLIMEPESRFYsNSVLVLDFQSLYPSI 2524
Cdd:PHA02528   333 MAYYAKINFEDVF---SPIKTWDAIIFNSLKEEKI-VIP--ENKSHKKQKYAGAFVKEPVPGAY-RWVVSFDLTSLYPSI 405
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2525 VIAYNYCFSTCLG--HVENLGKYDEfkfgcTSLRVPPDllyqvrhDITVSPNGVAFVKPsvRKGVLPRMLEEILKTRFMV 2602
Cdd:PHA02528   406 IRQVNISPETIAGtfHVAPVHEYIN-----KTAPRPSD-------EYSCSPNGWMYRKD--IRGVIPTEIKKVFDQRKIY 471
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2603 KQSMKAYKQDRALSRMLdARQLGLKLIANVTFGYTAANFSGRMPCI-EVGDSIVHKARETLERAIKLVNDTK-------- 2673
Cdd:PHA02528   472 KKKMLAAERNAELIKTI-LEDLNDSVDTPIDVDYYFDFSDEFKAELkTLTKSSLKALLEECEKEIALCNTIQmarkilin 550
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2674 ------------------------------KWGAR-----------------VVYGDTDSMFVLLK------GATKEQ-- 2698
Cdd:PHA02528   551 slygalgnehfryydlrnaeaitlfgqlaiQWIERkmneylnklcktededyVIYGDTDSIYVNLDplvekvGEDKFKdt 630
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2699 ----SF--KIG------------QEIAEAVTATNPKpVKLKFEKVYLPCVLQTKKRYVGYMY--ETLDQKDPVFDAKGIE 2758
Cdd:PHA02528   631 nhwvDFldKFCkermepyidssyRELCEYMNNYEHL-MFMDREAIAGPGFWTAKKRYALNVWdsEGTRYAEPKLKIMGIE 709
                          570       580       590       600       610       620
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2759 TVRRDSCPAVSKILERSLKLLfetrdislikqyvqrqcmkLLEGKASIQDFI--FAKEYR 2816
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; ...
2299-2391 1.05e-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: 1.05e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2299 DPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKI---ENRFAAERdeYGSYTMSEINIVGRITLNLWRIMRNE 2375
Cdd:cd05777     86 DPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKStikDTTFSSKQ--MGTRETKEINIEGRIQFDLLQVIQRD 163
                           90
                   ....*....|....*.
gi 1622930112 2376 VALTNYTFENVSFHVL 2391
Cdd:cd05777    164 YKLRSYSLNSVSAHFL 179
REV3L_RBD cd22287
REV7 binding domain found in protein reversionless 3-like (REV3L) and similar proteins; REV3L, ...
1751-1773 8.87e-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: 8.87e-09
                           10        20
                   ....*....|....*....|...
gi 1622930112 1751 RTAHILKPLMSPPSREEIMATLL 1773
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 ...
2190-2386 4.12e-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: 54.73  E-value: 4.12e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2190 PDPEF--DP---ICALFYCISSDAPLPdtekteltgvIVIDKDKTVFSQDIrYQTPLLIRSGITGLEVTYAADEKALFHe 2264
Cdd:pfam03104  172 PDAENvkDPiiqISCMLDGQGEPEPEP----------RFLFTLRECDSEDI-EDFEYTPKPIYPGVKVFEFPSEKELLR- 239
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2265 iahiikrgchqhvrcfqypHFFYFCKQlrkrnmYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDkieNRFA 2344
Cdd:pfam03104  240 -------------------RFFEFIRQ------YDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNRG---GRSK 291
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1622930112 2345 AERDEYGSYTMSEINIVGRITLNLWRIMRNEVALTNYTFENV 2386
Cdd:pfam03104  292 VREIGFGTRSYEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
2299-2642 8.93e-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: 48.51  E-value: 8.93e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2299 DPDIllgyEIQMHSWGYLLQRAAalSVDLCQMISRVPDDKIEN---RFAAERDEYGSYTMSEIN----------IVGRIT 2365
Cdd:TIGR00592  285 DTDV----EITVNGDNFDLVYLA--DRQVFQFYWDAYEDPAEKlgvVLLFGRDVDHVSPCVQVKginrdlfflpREGKID 358
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2366 LNLWRIMRNEVALTNYTFENVSFHVLhqRFPLFTFRVLSdwfdnKTDLYRWKMVDHYVSRVRGNLQMLeqLDLIGKTSEM 2445
Cdd:TIGR00592  359 FDLGKVTRRTINLPDYYLEFVSELAL--GYKKEKFRAKP-----IAKKYEFEAPDIDAPYSSEYLEVT--YELGKEFAPM 429
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2446 ----ARLFGIQFLHVLTRGSQYRVESMMLRIAKPMNYIPVTpSVQQRSQMRAPQCV-------PLIMEPESRFYSNSVLV 2514
Cdd:TIGR00592  430 ealpSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVK-GPDELEYPRRSWCKyeggyvkPPNVEKGLDKTPPPLVV 508
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2515 LDF--QSLYPSIVIAYNYCFSTCLGHVENLGKydefKFGCTSLRVPPDLLYqvRHDITVSPNGVAFVKPsvrkGVLPRML 2592
Cdd:TIGR00592  509 LDFsmKSLNPSIIRNEIVSIPDTLHREFALDK----PPPEPPYDVHPCVGT--RPKDCSFPLDLKGEFP----GKKPSLV 578
                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1622930112 2593 EEILKTRFMVKQSMKAYKQ-DRALSRMLDARQLGLKLIANVTFGYTAANFS 2642
Cdd:TIGR00592  579 EDLATERALIKKFMAKVKKiDPDEIVGHDYQQRALKVLANRINDLKIPTWS 629
POLBc_Pol_II_B cd05538
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ...
2584-2779 1.11e-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: 1.11e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2584 RKGVLPRMLEEILKTRFMVKQSMKAYKqDRALSRMLDARQLGLKLIANVTFGYTAA---NFSGrmpcIEVGDSIVHKARE 2660
Cdd:cd05538     43 SLGIFLALLKYLVELRLAAKESARAAA-RPAERDAFKAKQAAFKVLINSFYGYLGTglhAFSD----PEAAAEVTRLGRE 117
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2661 TLEraiKLVNDTKKWGARVVYGDTDSMFVL----LKGATKEqsfkigQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKR 2736
Cdd:cd05538    118 LLK---LMIRWLRRRGATPVEVDTDGIYFIppngVDTEDEE------EELVRELSSTLPKGITVEFDGRYRAMFSYKIKN 188
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|...
gi 1622930112 2737 YVgymyeTLDQKDPVFdAKGIETVRRDSCPAVSKILERSLKLL 2779
Cdd:cd05538    189 YA-----LLDYDGKLI-VKGSAFRSRGIEPFLREFLREAVRLL 225
PHA03334 PHA03334
putative DNA polymerase catalytic subunit; Provisional
2498-2688 2.23e-04

putative DNA polymerase catalytic subunit; Provisional


Pssm-ID: 223049 [Multi-domain]  Cd Length: 1545  Bit Score: 47.16  E-value: 2.23e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2498 PLIMEPESRFYSNSVLVLDFQSLYPSiviayNYC----------FSTCLGHVENLGKYD----EFKFGCTSlrvppdLLY 2563
Cdd:PHA03334   641 PLTGLTFAGPYQGTELTLDFASLYPS-----NMCdanispeaivDPDCTARVRGWVVFDwkkiDRGFGKAT------LMY 709
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2564 QVRHDITVSPNGVAFvkPSVRKGVLPRMleeiLKTRFMVKQSMKAYKqDRALSRMLDARQLGLKLIANVTFGytaanfsg 2643
Cdd:PHA03334   710 TILRTKPEEPSWRRF--TTYTTSSLNHY----LSMRTEYKGAMKQAK-DPKLKSYHNQLQNEMKICANSHYG-------- 774
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1622930112 2644 rmpcieVGDSIVHKARETLER-AIKLVNDTKKWGA--RVVYGDTDS-MF 2688
Cdd:PHA03334   775 ------VAPHACQHLITTLGRhKIKLVEEFIKKEPgmTVNYGDTDSvMF 817
DNA_polB_B3_exo cd05781
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ...
2298-2387 4.58e-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: 4.58e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930112 2298 YDPDILLGYEIQMHSWGYLLQRAAALSV--DLCQMISRVPddkienrfaaERDEYGSYTmseinIVGRITLNLWRIMRNE 2375
Cdd:cd05781     62 YDPDIIVGYNSNAFDWPYLVERARVLGVklDVGRRGGSEP----------STGVYGHYS-----ITGRLNVDLYDFAEEI 126
                           90
                   ....*....|..
gi 1622930112 2376 VALTNYTFENVS 2387
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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