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Conserved domains on  [gi|1622930109|ref|XP_028702873|]
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DNA polymerase zeta catalytic subunit isoform X6 [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 ...
2477-2925 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: 866.14  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2477 GSQYRVESMMLRIAKPMNYIPVTPSVQQRSQMRAPQCVPLIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHV 2556
Cdd:cd05534      1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2557 ENLGKYDEFKFGCTSLRVPPD--LLYQVRHDITVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSR 2634
Cdd:cd05534     81 EELNGGGKFGFLGVKLYLPPPplDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDDKKLQR 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2635 MLDARQLGLKLIANVTFGYTAANFSGRMPCIEVGDSIVHKARETLERAIKLVNDTKKWGARVVYGDTDSMFVLLKGATKE 2714
Cdd:cd05534    161 ILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLFVLLPGRTKE 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2715 QSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPVFDAKGIETVRRDSCPAVSKILERSLK 2794
Cdd:cd05534    241 EAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAVQKILEKSLR 320
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2795 LLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYRGSfSYKPGACVPALELT-RKMLTYDRRSEPQVGERVPYVII 2873
Cdd:cd05534    321 ILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLG-TYKEGATLPAGAIVaLRRMEKDPRAEPQYGERVPYVVV 399
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1622930109 2874 YGTPGVPLIQLVRRPVEVLQDPTLRLNATYYITKQILPPLARIFSLIGIDVF 2925
Cdd:cd05534    400 RGEPGSRLIDLVVSPEEFLADPSLRLDAEYYITKQIIPALDRLFNLVGVDVQ 451
DUF4683 pfam15735
Domain of unknown function (DUF4683); This domain family is found in eukaryotes, and is ...
675-1055 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: 577.20  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  675 NRTMVHSLNSTADESGLNKLKIRYEEFQEHKTEKPSLSQQAAHYMFFPSVVLSNCLTR---PQKLSPVTYKLQPG-NKPS 750
Cdd:pfam15735    1 VRNYVFDDDQSTDESDVGKLKIRYESFQENKAEKTSLSQQEAHYKFFPSVVLSNCLSRrsaLKKLGPVTYKLQQFkSRQS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  751 RLKLNKKK--LAGHQETFTKSSETGSTKDNS-IQNNPCNSN-PEKDSAFASDlTKTSRGAFENKTPTD--GFIDCHFGDG 824
Cdd:pfam15735   81 RLKLGKKKlnLDGKQEPEKKTHDKASTKEKCnLQGNALNKNiPETEVELDSD-VQVAHSAFKNKMSIDpaNSDSCHFSDD 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  825 TLETEQSFGLYGNKYTLRAKRKVNYETEDSESSFVTHNSKISLPHPMEIGESLDGTLKSRKRRKMSKKLPPVIIKYIIIN 904
Cdd:pfam15735  160 SEESYDASSLCGSKYTLRAKRKVNYETEDSESSEKIHNSKESLPQGSKEEDDDDGSPKSQKRRKVSKKEPPVIIKYIIIN 239
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  905 RFRGRKNMLVKLGKIDAKEKQVILTEEKMELYKKLAPLKDFWPKVPDSPATKYPIYPLTPKKSHRRKSKHKSAKKKTG-K 983
Cdd:pfam15735  240 RFKGRKNMLVKLGKVDSSETTVTLTEEKLEKYKKLAPLKDFWPKVPDSPATKYPVYPLTPKKSPKRKAKCKSTNKKRIqR 319
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622930109  984 QQRTNNENIKRTLSFRKKRSHALLSPPSPSYNAETEDCDLNYSDVMSKLGFLSERSTSPINSSPPRCWSPTD 1055
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 ...
2213-2451 1.36e-100

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: 323.03  E-value: 1.36e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2213 IQNLTLISVELHARTRRDLEPDPEFDPICALFYCISSDAPLPDTEKTElTGVIVIDKDKTVFSQDiryqtplLIRSGITG 2292
Cdd:cd05778      1 HQHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANK-VGVIIVDELKSNASNG-------RIRSGLSG 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2293 LEVTYAADEKALFHEIAHIIKRYDPDILLGYEIQMHSWGYLLQRAAALSVDLC-QMISRVPDDKiENRFAAERDEYGSYT 2371
Cdd:cd05778     73 IPVEVVESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLlDEISRVPSDS-NGKFGDRDDEWGYTH 151
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2372 MSEINIVGRITLNLWRIMRNEVALTNYTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYRWKMVDHYVSRVRGNLQMLE 2451
Cdd:cd05778    152 TSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEILD 231
zf-C4pol pfam14260
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ...
2961-3028 1.52e-17

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


:

Pssm-ID: 464119  Cd Length: 68  Bit Score: 78.95  E-value: 1.52e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622930109 2961 CPVCDDLTQhGICSKCRSQPQHVAVILNQEIRELERKQEQLVKICKNCTGCFDRHIPCVSLNCPVLFK 3028
Cdd:pfam14260    1 CLGCGAPEE-PLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYM 67
REV3L_RBD cd22287
REV7 binding domain found in protein reversionless 3-like (REV3L) and similar proteins; REV3L, ...
1794-1816 9.83e-09

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


:

Pssm-ID: 412083  Cd Length: 23  Bit Score: 52.95  E-value: 9.83e-09
                           10        20
                   ....*....|....*....|...
gi 1622930109 1794 RTAHILKPLMSPPSREEIMATLL 1816
Cdd:cd22287      1 RTAHILKPLMSPPSREEIMATLL 23
DNA_pol_B_exo1 super family cl27305
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ...
23-113 1.41e-05

DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold.


The actual alignment was detected with superfamily member pfam03104:

Pssm-ID: 397292  Cd Length: 333  Bit Score: 50.11  E-value: 1.41e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109   23 VFKVSLVSGMPFYGYHEKERHFMKIYLYNPAVVKRICELLQSGAIMNKFyqphEAHIPYLLQLFIDYNLYGMNLINLAAV 102
Cdd:pfam03104   46 IEKIELKLKKSLYGYEEDPVPYLKVSFANPRPLLKIRKYLSPENISDVY----EYDVDYLERFLIDNDIVGFGWYKVKVY 121
                           90
                   ....*....|.
gi 1622930109  103 KFRKARRKSNT 113
Cdd:pfam03104  122 PFRAEGRISNC 132
 
Name Accession Description Interval E-value
POLBc_zeta cd05534
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ...
2477-2925 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: 866.14  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2477 GSQYRVESMMLRIAKPMNYIPVTPSVQQRSQMRAPQCVPLIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHV 2556
Cdd:cd05534      1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2557 ENLGKYDEFKFGCTSLRVPPD--LLYQVRHDITVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSR 2634
Cdd:cd05534     81 EELNGGGKFGFLGVKLYLPPPplDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDDKKLQR 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2635 MLDARQLGLKLIANVTFGYTAANFSGRMPCIEVGDSIVHKARETLERAIKLVNDTKKWGARVVYGDTDSMFVLLKGATKE 2714
Cdd:cd05534    161 ILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLFVLLPGRTKE 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2715 QSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPVFDAKGIETVRRDSCPAVSKILERSLK 2794
Cdd:cd05534    241 EAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAVQKILEKSLR 320
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2795 LLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYRGSfSYKPGACVPALELT-RKMLTYDRRSEPQVGERVPYVII 2873
Cdd:cd05534    321 ILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLG-TYKEGATLPAGAIVaLRRMEKDPRAEPQYGERVPYVVV 399
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1622930109 2874 YGTPGVPLIQLVRRPVEVLQDPTLRLNATYYITKQILPPLARIFSLIGIDVF 2925
Cdd:cd05534    400 RGEPGSRLIDLVVSPEEFLADPSLRLDAEYYITKQIIPALDRLFNLVGVDVQ 451
DUF4683 pfam15735
Domain of unknown function (DUF4683); This domain family is found in eukaryotes, and is ...
675-1055 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: 577.20  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  675 NRTMVHSLNSTADESGLNKLKIRYEEFQEHKTEKPSLSQQAAHYMFFPSVVLSNCLTR---PQKLSPVTYKLQPG-NKPS 750
Cdd:pfam15735    1 VRNYVFDDDQSTDESDVGKLKIRYESFQENKAEKTSLSQQEAHYKFFPSVVLSNCLSRrsaLKKLGPVTYKLQQFkSRQS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  751 RLKLNKKK--LAGHQETFTKSSETGSTKDNS-IQNNPCNSN-PEKDSAFASDlTKTSRGAFENKTPTD--GFIDCHFGDG 824
Cdd:pfam15735   81 RLKLGKKKlnLDGKQEPEKKTHDKASTKEKCnLQGNALNKNiPETEVELDSD-VQVAHSAFKNKMSIDpaNSDSCHFSDD 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  825 TLETEQSFGLYGNKYTLRAKRKVNYETEDSESSFVTHNSKISLPHPMEIGESLDGTLKSRKRRKMSKKLPPVIIKYIIIN 904
Cdd:pfam15735  160 SEESYDASSLCGSKYTLRAKRKVNYETEDSESSEKIHNSKESLPQGSKEEDDDDGSPKSQKRRKVSKKEPPVIIKYIIIN 239
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  905 RFRGRKNMLVKLGKIDAKEKQVILTEEKMELYKKLAPLKDFWPKVPDSPATKYPIYPLTPKKSHRRKSKHKSAKKKTG-K 983
Cdd:pfam15735  240 RFKGRKNMLVKLGKVDSSETTVTLTEEKLEKYKKLAPLKDFWPKVPDSPATKYPVYPLTPKKSPKRKAKCKSTNKKRIqR 319
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622930109  984 QQRTNNENIKRTLSFRKKRSHALLSPPSPSYNAETEDCDLNYSDVMSKLGFLSERSTSPINSSPPRCWSPTD 1055
Cdd:pfam15735  320 LPNTESSNIKRTLSFKRKRSHASLSPPQPSYNAETEDCDLNYSDVMSKLGFLSERSLSPTASTPPRCWSPTD 391
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
2233-3049 1.64e-116

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 398.63  E-value: 1.64e-116
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2233 PDPEFDPICAlfycISSDAPLPDTEKTELTgvividkdKTVFSqdiryqtpLLIRSGITGLEVTYAADEKALFHEIAHII 2312
Cdd:PTZ00166   282 PEAENDPVIQ----ISSVVTNQGDEEEPLT--------KFIFT--------LKECASIAGANVLSFETEKELLLAWAEFV 341
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2313 KRYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKI---ENRFAAErdEYGSYTMSEINIVGRITLNLWRIM 2389
Cdd:PTZ00166   342 IAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSvikDSKFSSK--QMGTRESKEINIEGRIQFDVMDLI 419
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2390 RNEVALTNYTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYRWKMV----DHYVSrvrgnLQMLEQLDLIGKTSEMARL 2465
Cdd:PTZ00166   420 RRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVyclkDAILP-----LRLLDKLLLIYNYVEMARV 494
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2466 FGIQFLHVLTRGSQYRVESMMLRIAKPMNY-IPVTPSVQQRSQMRAPQCVplIMEPESRFYSNSVLVLDFQSLYPSIVIA 2544
Cdd:PTZ00166   495 TGTPIGWLLTRGQQIKVTSQLLRKCKKLNYvIPTVKYSGGGSEEKYEGAT--VLEPKKGFYDEPIATLDFASLYPSIMIA 572
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2545 YNYCFSTclghvenLGKYDEFKfgctslRVPPDLLyqvrhdiTVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMK 2624
Cdd:PTZ00166   573 HNLCYST-------LVPPNDAN------NYPEDTY-------VTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMK 632
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2625 AYKqDRALSRMLDARQLGLKLIANVTFGYTAANFSGRMPCIEVGDSIVHKARETLERAIKLVND--TKKWG----ARVVY 2698
Cdd:PTZ00166   633 DEK-DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKhyTKANGykhdATVIY 711
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2699 GDTDSmfVLLKGATK--EQSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPVfDAKGIET 2776
Cdd:PTZ00166   712 GDTDS--VMVKFGTDdiQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAGLLYTNPEKYDKI-DCKGIET 788
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2777 VRRDSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYrGSFSYKpgACVPALELTRKMLTY 2856
Cdd:PTZ00166   789 VRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRIDISLLVITKSL-GKDDYE--GRLAHVELAKKLRQR 865
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2857 DRRSEPQVGERVPYVIIYGTPGVPLIQLVRRPVEVLqDPTLRLNATYYItKQILPPLARIFSLIGIDVFSWYHELPRIHK 2936
Cdd:PTZ00166   866 DPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVL-ENNIPIDTQYYL-DQIKNPLLRIFEGVMDNPDSLFSGEHTRHI 943
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2937 ATNSSrsepegRKGTISQYFT-TLHCPVCDDLTQHG-ICSKCRS--QPQHVAVILNqEIRELERKQEQLVKICKNCTGCF 3012
Cdd:PTZ00166   944 TISSS------SKGGLSKFVKkQLQCLGCKSVIKEGaLCDNCNQnkEPSIYGKKLA-KRRHKEAEYSQLWTQCQRCQGSL 1016
                          810       820       830
                   ....*....|....*....|....*....|....*..
gi 1622930109 3013 DRHIPCVSLNCPVLFKVSRVNRELSKapyLRQLLDQF 3049
Cdd:PTZ00166  1017 HQEVICTNRDCPIFYRRKKVQKDLAE---LQELLSRF 1050
DNA_pol_B pfam00136
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
2473-2920 2.66e-114

DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.


Pssm-ID: 395085  Cd Length: 439  Bit Score: 371.56  E-value: 2.66e-114
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2473 VLTRGSQYRVESMMLRIAKPMNYIpVTPSVQQRSQMRAPQCVpLIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTC 2552
Cdd:pfam00136    6 VLEGGQQIRVESCLLRLALEEGFI-LPDRPSAKGDEDGYQGA-TVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCYTTL 83
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2553 LGHVENlgkydefkfgctSLRVPPDLLYQvrhDITVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKqDRAL 2632
Cdd:pfam00136   84 VRSVDE------------ANNLPPEDNLI---TVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEET-DPFE 147
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2633 SRMLDARQLGLKLIANVTFGYTAANfSGRMPCIEVGDSIVHKARETLERAIKLVNDTKKWGARVVYGDTDSMFVLLKGAT 2712
Cdd:pfam00136  148 RAILDKQQLALKITANSVYGFTGFA-NGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYNFRVIYGDTDSVFIEFGGKD 226
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2713 KEQSFKIGQEIAEAVT-ATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPvFDAKGIETVRRDSCPAVSKILER 2791
Cdd:pfam00136  227 VEEAMKIGDELAEHVNqDLFKSPIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFNK-LDMKGVDLVRRDNCPLVKEVIKK 305
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2792 SLKLLFETRDISLIKQYVQRQCM----KLLEGKASIQDFIFAKEYRGSFSYKPGACVPALELTRKMLTYDRRsEPQVGER 2867
Cdd:pfam00136  306 VLDLLLSDRGLPVGLEFVISILNdarsDLRNNKVPLEKFVISKELSKPPDNYKSKNLPHVEVALRMNKRNGE-APEVGDR 384
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622930109 2868 VPYVII---YGTPGVPLIQLVRRPVEVLQDpTLRLNATYYITKQILPPLARIFSLI 2920
Cdd:pfam00136  385 IPYVIVkaaKGLKNLLIYERAEDPEYVLEN-NLPIDYEYYFSNQLIPPVARLLEPI 439
DNA_polB_zeta_exo cd05778
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ...
2213-2451 1.36e-100

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: 323.03  E-value: 1.36e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2213 IQNLTLISVELHARTRRDLEPDPEFDPICALFYCISSDAPLPDTEKTElTGVIVIDKDKTVFSQDiryqtplLIRSGITG 2292
Cdd:cd05778      1 HQHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANK-VGVIIVDELKSNASNG-------RIRSGLSG 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2293 LEVTYAADEKALFHEIAHIIKRYDPDILLGYEIQMHSWGYLLQRAAALSVDLC-QMISRVPDDKiENRFAAERDEYGSYT 2371
Cdd:cd05778     73 IPVEVVESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLlDEISRVPSDS-NGKFGDRDDEWGYTH 151
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2372 MSEINIVGRITLNLWRIMRNEVALTNYTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYRWKMVDHYVSRVRGNLQMLE 2451
Cdd:cd05778    152 TSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEILD 231
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
2235-2710 3.47e-96

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: 320.63  E-value: 3.47e-96
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  2235 PEFDPICALFYCISSDAPLPDTEKTELtgvIVIDKDKTVFSQDIRYQT-----PLLIRSGITGLEVTYAADEKALFHEIA 2309
Cdd:smart00486    1 PPLKILSFDIETYTDGGNFPDAEIFDD---EIIQISLVINDGDKKGANrrilfTLGTCKEIDGIEVYEFNNEKELLLAFF 77
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  2310 HIIKRYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPD-DKIENRFAAERDEYGSYTMSEINIVGRITLNLWRI 2388
Cdd:smart00486   78 EFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIgLRIPNKKPLFGSKSFGLSDIKVYIKGRLVIDLYRL 157
                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  2389 MRNEVALTNYTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYRWkMVDHYVSRVRGNLQMLEQLDLIGKTSEMARLFGI 2468
Cdd:smart00486  158 YKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDE-LLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGI 236
                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  2469 QFLHVLTRGSQYRVESMMLRIAKPMNYIPVTPSVQQRSQMRAPQCVP------LIMEPESRFYSNSVLVLDFQSLYPSIV 2542
Cdd:smart00486  237 PLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEPDLKKKvkyeggKVLEPKKGFYDNPVLVLDFNSLYPSII 316
                           330       340       350       360       370       380       390       400
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  2543 IAYNYCFSTCLGHVENLGKYDEFKFgctslrvppdllYQVRHDITVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQS 2622
Cdd:smart00486  317 IAHNLCYSTLVGVGEVVIKGDLIIP------------EDLLTIKYEKGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKL 384
                           410       420       430       440       450       460       470       480
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  2623 MKAYKQDRALSR-MLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKARETLERAIKLVND--TKKWGARVVYG 2699
Cdd:smart00486  385 MKKEKDESEELKkLLDSRQLALKLTANSVYGYLGFTNS-RLPCKPLAASVTALGREILEKTKELIEEngYPKPGFKVIYG 463
                           490
                    ....*....|.
gi 1622930109  2700 DTDSMFVLLKG 2710
Cdd:smart00486  464 DTDSIFVTKPG 474
PolB COG0417
DNA polymerase B elongation subunit [Replication, recombination and repair];
2264-2923 5.99e-89

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


Pssm-ID: 440186 [Multi-domain]  Cd Length: 794  Bit Score: 310.22  E-value: 5.99e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2264 VIVIdkdkTVFSQDIRYQTPLLIRSGItGLEVTYAADEKALFHEIAHIIKRYDPDILLGYEIQMHSWGYLLQRAAALSVD 2343
Cdd:COG0417    184 IISI----GLAGSDGEKKVLMLGREGV-DFEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNFDLPYLQKRAERLGIP 258
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2344 LcqMISRvpddkieNRFAAERDEYGSYTMseINIVGRITLNLWRIMRN-EVALTNYTFENVSFHVLHqrfplftfrvlsd 2422
Cdd:COG0417    259 L--DLGR-------DGSEPSWREHGGQGF--ASIPGRVVIDLYDALKSaTYKFKSYSLDAVAEELLG------------- 314
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2423 wfDNKTDLYRWKMVDHYVSR----VRGNLQ-------MLEQLDLIGKTSEMARLFGIQFLHVLTRGSQYRVESMMLRIAK 2491
Cdd:COG0417    315 --EGKLIVDGGEIERLWDDDkpalAEYNLRdaeltlrIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAH 392
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2492 PMNY-IPVTPSVQQRSQMRApqcvpLIMEPESRFYSNsVLVLDFQSLYPSIVIAYNYCFST-CLGHVENLGKYDefkfgc 2569
Cdd:COG0417    393 RRGYlAPNKGEIKGEAYPGG-----YVLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPETlVEGGEEPCGDED------ 460
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2570 tslrvppdllyqvrhditVSPN-GVAFVKPsvRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSRMLDARQLGLKLIAN 2648
Cdd:COG0417    461 ------------------VAPGfGHRFCRE--PKGILPSILEELWDERDEAKKKMKKAKPDSEEYRLYDALQQALKILMN 520
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2649 VTFGYTAANFSgRMPCIEVGDSIVHKARETLERAIKLVndtKKWGARVVYGDTDSMFVLLKGATKEQSFKIGQEIAEAVT 2728
Cdd:COG0417    521 SFYGVLGSEGC-RFYDPELAESITARGREIIKQTIEKA---EELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEIN 596
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2729 ATNPKPVKLKFEKVYLPcVLQT--KKRYVGYmyetldQKDPVFDAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIK 2806
Cdd:COG0417    597 AWWPSGLELEFEKHYRR-FFFPgsKKRYAGL------TEDGKIDIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAV 669
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2807 QYVQRQCMKLLEGKASIQDFIFAKEYRGSFS-YKpgACVPA-LELTRKMLTYDRrsEPQVGERVPYVIIYGTPGVpliql 2884
Cdd:COG0417    670 EYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSeYE--KNVPPhVRAARKLDERGR--PYQRGDKISYVITKGGGRV----- 740
                          650       660       670
                   ....*....|....*....|....*....|....*....
gi 1622930109 2885 vrRPVEVLQDPTLRLNATYYITKQILPPLARIFSLIGID 2923
Cdd:COG0417    741 --EPVELAKERESEIDYDYYIEKQLKPTADRILEAFGVS 777
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
2298-2917 4.92e-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: 196.43  E-value: 4.92e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2298 AADEKALFHEIAHIIKRYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKIENRFAAERdeygsytmseinI 2377
Cdd:TIGR00592  581 LATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGER------------T 648
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2378 VGRITLNLWRIMRNEVALTNYTFENVSFHVLH-QRFPLFTFRVLSDWFDNKTDLYrwkMVDHYVSRVRGNLQMLEQLDLI 2456
Cdd:TIGR00592  649 CGRMICDVEISAKELIRCKSYDLSELVQQILKtERKVIPIDNINNMYSESSSLTY---LLEHTWKDAMFILQIMCELNVL 725
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2457 GKTSEMARLFGIQFLHVLTRGSQYRVESMMLRIAKPMNYI-PVTPSVQQRSQMR--------------APQCVPLIMEPE 2521
Cdd:TIGR00592  726 PLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIvPDKQIFRKQQKLGdedeeidgykkgkkAAYAGGLVLEPK 805
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2522 SRFYSNSVLVLDFQSLYPSIVIAYNYCFSTclghVENLGKYDEfkfgctsLRVPPDllyqvrhditvspngvafvkPSVR 2601
Cdd:TIGR00592  806 VGLYDKYVLLMDFNSLYPSIIQEFNICFTT----VQQKVDEDE-------LPELPD--------------------SELE 854
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2602 KGVLPRMLEEILKTRFMVKQSMKAyKQDRALSRMLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKARETLER 2681
Cdd:TIGR00592  855 MGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKS-RFYAKPLAALVTAKGREILEH 932
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2682 AIKLVndtKKWGARVVYGDTDSMFVLLKGATKEQSFKIGQEIAEAVTATNpKPVKLKFEKVYLPCVLQTKKRYVGYMYET 2761
Cdd:TIGR00592  933 TRQLV---EEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLY-KLLELDIDGVFKRLLLLKKKKYAAIKVEG 1008
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2762 LDQKDPVF--DAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKL----LEGKASIQDFIFAKEY-RG 2834
Cdd:TIGR00592 1009 DSDGNYTTkqEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIgknvLNGEVPLEKFVINKQLtRD 1088
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2835 SFSYKPGACVPALELTRKMLTYDRRSEPQvGERVPYVIIYGTPGVPLIQLVRRPVEVL-QDPTLRLNATYYITKQILPPL 2913
Cdd:TIGR00592 1089 PKDYPDGASLPHVHVALRINARGGRKVKA-GDVVSYVICKDGGNLSARQRAYALEELQrKHNNLIYDTQYYLEHQIHPVV 1167

                   ....
gi 1622930109 2914 ARIF 2917
Cdd:TIGR00592 1168 LRIL 1171
zf-C4pol pfam14260
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ...
2961-3028 1.52e-17

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


Pssm-ID: 464119  Cd Length: 68  Bit Score: 78.95  E-value: 1.52e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622930109 2961 CPVCDDLTQhGICSKCRSQPQHVAVILNQEIRELERKQEQLVKICKNCTGCFDRHIPCVSLNCPVLFK 3028
Cdd:pfam14260    1 CLGCGAPEE-PLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYM 67
DNA_pol_B_exo1 pfam03104
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ...
2233-2403 2.93e-11

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: 67.83  E-value: 2.93e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2233 PDPEF--DP---ICALFYCISSDAPLPdtekteltgvIVIDKDKTVFSQDIrYQTPLLIRSGITGLEVTYAADEKALFHE 2307
Cdd:pfam03104  172 PDAENvkDPiiqISCMLDGQGEPEPEP----------RFLFTLRECDSEDI-EDFEYTPKPIYPGVKVFEFPSEKELLRR 240
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2308 IAHIIKRYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDkieNRFAAERDEYGSYTMSEINIVGRITLNLWR 2387
Cdd:pfam03104  241 FFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNRG---GRSKVREIGFGTRSYEKVKISGRLHLDLYR 317
                          170
                   ....*....|....*.
gi 1622930109 2388 IMRNEVALTNYTFENV 2403
Cdd:pfam03104  318 VIKRDYKLPSYKLNAV 333
REV3L_RBD cd22287
REV7 binding domain found in protein reversionless 3-like (REV3L) and similar proteins; REV3L, ...
1794-1816 9.83e-09

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


Pssm-ID: 412083  Cd Length: 23  Bit Score: 52.95  E-value: 9.83e-09
                           10        20
                   ....*....|....*....|...
gi 1622930109 1794 RTAHILKPLMSPPSREEIMATLL 1816
Cdd:cd22287      1 RTAHILKPLMSPPSREEIMATLL 23
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
2220-2659 7.13e-07

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: 55.45  E-value: 7.13e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2220 SVELHARTRRDLEPDPEFDP----ICALFY----CISSDAPLPDTEKTELTGVIVIDKDKTVFSQDIRYQTPLLIRSGIT 2291
Cdd:TIGR00592  181 KRAEFAGGDVQMEGDPELKLasfdIETYFHdgkdFFPGDENPADEEIMISTTPVIAKQWDYESEPEARVVTWKKPDKPTT 260
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2292 GLEVTYAADEKALFHEIAHIIKRYDPDIllgyEIQMHSWGYLLQRAAalSVDLCQMISRVPDDKIEN---RFAAERDEYG 2368
Cdd:TIGR00592  261 GSYVESVSEEISMIKRFWDVIDQEDTDV----EITVNGDNFDLVYLA--DRQVFQFYWDAYEDPAEKlgvVLLFGRDVDH 334
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2369 SYTMSEIN----------IVGRITLNLWRIMRNEVALTNYTFENVSFHVLhqRFPLFTFRVLSdwfdnKTDLYRWKMVDH 2438
Cdd:TIGR00592  335 VSPCVQVKginrdlfflpREGKIDFDLGKVTRRTINLPDYYLEFVSELAL--GYKKEKFRAKP-----IAKKYEFEAPDI 407
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2439 YVSRVRGNLQMLeqLDLIGKTSEM----ARLFGIQFLHVLTRGSQYRVESMMLRIAKPMNYIPVTpSVQQRSQMRAPQCV 2514
Cdd:TIGR00592  408 DAPYSSEYLEVT--YELGKEFAPMealpSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVK-GPDELEYPRRSWCK 484
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2515 -------PLIMEPESRFYSNSVLVLDF--QSLYPSIVIAYNYCFSTCLGHVENLGKydefKFGCTSLRVPPDLLYqvRHD 2585
Cdd:TIGR00592  485 yeggyvkPPNVEKGLDKTPPPLVVLDFsmKSLNPSIIRNEIVSIPDTLHREFALDK----PPPEPPYDVHPCVGT--RPK 558
                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622930109 2586 ITVSPNGVAFVKPsvrkGVLPRMLEEILKTRFMVKQSMKAYKQ-DRALSRMLDARQLGLKLIANVTFGYTAANFS 2659
Cdd:TIGR00592  559 DCSFPLDLKGEFP----GKKPSLVEDLATERALIKKFMAKVKKiDPDEIVGHDYQQRALKVLANRINDLKIPTWS 629
DNA_pol_B_exo1 pfam03104
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ...
23-113 1.41e-05

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: 50.11  E-value: 1.41e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109   23 VFKVSLVSGMPFYGYHEKERHFMKIYLYNPAVVKRICELLQSGAIMNKFyqphEAHIPYLLQLFIDYNLYGMNLINLAAV 102
Cdd:pfam03104   46 IEKIELKLKKSLYGYEEDPVPYLKVSFANPRPLLKIRKYLSPENISDVY----EYDVDYLERFLIDNDIVGFGWYKVKVY 121
                           90
                   ....*....|.
gi 1622930109  103 KFRKARRKSNT 113
Cdd:pfam03104  122 PFRAEGRISNC 132
 
Name Accession Description Interval E-value
POLBc_zeta cd05534
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ...
2477-2925 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: 866.14  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2477 GSQYRVESMMLRIAKPMNYIPVTPSVQQRSQMRAPQCVPLIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHV 2556
Cdd:cd05534      1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2557 ENLGKYDEFKFGCTSLRVPPD--LLYQVRHDITVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSR 2634
Cdd:cd05534     81 EELNGGGKFGFLGVKLYLPPPplDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDDKKLQR 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2635 MLDARQLGLKLIANVTFGYTAANFSGRMPCIEVGDSIVHKARETLERAIKLVNDTKKWGARVVYGDTDSMFVLLKGATKE 2714
Cdd:cd05534    161 ILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLFVLLPGRTKE 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2715 QSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPVFDAKGIETVRRDSCPAVSKILERSLK 2794
Cdd:cd05534    241 EAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAVQKILEKSLR 320
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2795 LLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYRGSfSYKPGACVPALELT-RKMLTYDRRSEPQVGERVPYVII 2873
Cdd:cd05534    321 ILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLG-TYKEGATLPAGAIVaLRRMEKDPRAEPQYGERVPYVVV 399
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1622930109 2874 YGTPGVPLIQLVRRPVEVLQDPTLRLNATYYITKQILPPLARIFSLIGIDVF 2925
Cdd:cd05534    400 RGEPGSRLIDLVVSPEEFLADPSLRLDAEYYITKQIIPALDRLFNLVGVDVQ 451
DUF4683 pfam15735
Domain of unknown function (DUF4683); This domain family is found in eukaryotes, and is ...
675-1055 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: 577.20  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  675 NRTMVHSLNSTADESGLNKLKIRYEEFQEHKTEKPSLSQQAAHYMFFPSVVLSNCLTR---PQKLSPVTYKLQPG-NKPS 750
Cdd:pfam15735    1 VRNYVFDDDQSTDESDVGKLKIRYESFQENKAEKTSLSQQEAHYKFFPSVVLSNCLSRrsaLKKLGPVTYKLQQFkSRQS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  751 RLKLNKKK--LAGHQETFTKSSETGSTKDNS-IQNNPCNSN-PEKDSAFASDlTKTSRGAFENKTPTD--GFIDCHFGDG 824
Cdd:pfam15735   81 RLKLGKKKlnLDGKQEPEKKTHDKASTKEKCnLQGNALNKNiPETEVELDSD-VQVAHSAFKNKMSIDpaNSDSCHFSDD 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  825 TLETEQSFGLYGNKYTLRAKRKVNYETEDSESSFVTHNSKISLPHPMEIGESLDGTLKSRKRRKMSKKLPPVIIKYIIIN 904
Cdd:pfam15735  160 SEESYDASSLCGSKYTLRAKRKVNYETEDSESSEKIHNSKESLPQGSKEEDDDDGSPKSQKRRKVSKKEPPVIIKYIIIN 239
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  905 RFRGRKNMLVKLGKIDAKEKQVILTEEKMELYKKLAPLKDFWPKVPDSPATKYPIYPLTPKKSHRRKSKHKSAKKKTG-K 983
Cdd:pfam15735  240 RFKGRKNMLVKLGKVDSSETTVTLTEEKLEKYKKLAPLKDFWPKVPDSPATKYPVYPLTPKKSPKRKAKCKSTNKKRIqR 319
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622930109  984 QQRTNNENIKRTLSFRKKRSHALLSPPSPSYNAETEDCDLNYSDVMSKLGFLSERSTSPINSSPPRCWSPTD 1055
Cdd:pfam15735  320 LPNTESSNIKRTLSFKRKRSHASLSPPQPSYNAETEDCDLNYSDVMSKLGFLSERSLSPTASTPPRCWSPTD 391
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
2233-3049 1.64e-116

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 398.63  E-value: 1.64e-116
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2233 PDPEFDPICAlfycISSDAPLPDTEKTELTgvividkdKTVFSqdiryqtpLLIRSGITGLEVTYAADEKALFHEIAHII 2312
Cdd:PTZ00166   282 PEAENDPVIQ----ISSVVTNQGDEEEPLT--------KFIFT--------LKECASIAGANVLSFETEKELLLAWAEFV 341
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2313 KRYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKI---ENRFAAErdEYGSYTMSEINIVGRITLNLWRIM 2389
Cdd:PTZ00166   342 IAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSvikDSKFSSK--QMGTRESKEINIEGRIQFDVMDLI 419
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2390 RNEVALTNYTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYRWKMV----DHYVSrvrgnLQMLEQLDLIGKTSEMARL 2465
Cdd:PTZ00166   420 RRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVyclkDAILP-----LRLLDKLLLIYNYVEMARV 494
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2466 FGIQFLHVLTRGSQYRVESMMLRIAKPMNY-IPVTPSVQQRSQMRAPQCVplIMEPESRFYSNSVLVLDFQSLYPSIVIA 2544
Cdd:PTZ00166   495 TGTPIGWLLTRGQQIKVTSQLLRKCKKLNYvIPTVKYSGGGSEEKYEGAT--VLEPKKGFYDEPIATLDFASLYPSIMIA 572
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2545 YNYCFSTclghvenLGKYDEFKfgctslRVPPDLLyqvrhdiTVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMK 2624
Cdd:PTZ00166   573 HNLCYST-------LVPPNDAN------NYPEDTY-------VTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMK 632
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2625 AYKqDRALSRMLDARQLGLKLIANVTFGYTAANFSGRMPCIEVGDSIVHKARETLERAIKLVND--TKKWG----ARVVY 2698
Cdd:PTZ00166   633 DEK-DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKhyTKANGykhdATVIY 711
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2699 GDTDSmfVLLKGATK--EQSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPVfDAKGIET 2776
Cdd:PTZ00166   712 GDTDS--VMVKFGTDdiQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAGLLYTNPEKYDKI-DCKGIET 788
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2777 VRRDSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEYrGSFSYKpgACVPALELTRKMLTY 2856
Cdd:PTZ00166   789 VRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRIDISLLVITKSL-GKDDYE--GRLAHVELAKKLRQR 865
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2857 DRRSEPQVGERVPYVIIYGTPGVPLIQLVRRPVEVLqDPTLRLNATYYItKQILPPLARIFSLIGIDVFSWYHELPRIHK 2936
Cdd:PTZ00166   866 DPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVL-ENNIPIDTQYYL-DQIKNPLLRIFEGVMDNPDSLFSGEHTRHI 943
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2937 ATNSSrsepegRKGTISQYFT-TLHCPVCDDLTQHG-ICSKCRS--QPQHVAVILNqEIRELERKQEQLVKICKNCTGCF 3012
Cdd:PTZ00166   944 TISSS------SKGGLSKFVKkQLQCLGCKSVIKEGaLCDNCNQnkEPSIYGKKLA-KRRHKEAEYSQLWTQCQRCQGSL 1016
                          810       820       830
                   ....*....|....*....|....*....|....*..
gi 1622930109 3013 DRHIPCVSLNCPVLFKVSRVNRELSKapyLRQLLDQF 3049
Cdd:PTZ00166  1017 HQEVICTNRDCPIFYRRKKVQKDLAE---LQELLSRF 1050
DNA_pol_B pfam00136
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
2473-2920 2.66e-114

DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.


Pssm-ID: 395085  Cd Length: 439  Bit Score: 371.56  E-value: 2.66e-114
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2473 VLTRGSQYRVESMMLRIAKPMNYIpVTPSVQQRSQMRAPQCVpLIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTC 2552
Cdd:pfam00136    6 VLEGGQQIRVESCLLRLALEEGFI-LPDRPSAKGDEDGYQGA-TVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCYTTL 83
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2553 LGHVENlgkydefkfgctSLRVPPDLLYQvrhDITVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKqDRAL 2632
Cdd:pfam00136   84 VRSVDE------------ANNLPPEDNLI---TVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEET-DPFE 147
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2633 SRMLDARQLGLKLIANVTFGYTAANfSGRMPCIEVGDSIVHKARETLERAIKLVNDTKKWGARVVYGDTDSMFVLLKGAT 2712
Cdd:pfam00136  148 RAILDKQQLALKITANSVYGFTGFA-NGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYNFRVIYGDTDSVFIEFGGKD 226
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2713 KEQSFKIGQEIAEAVT-ATNPKPVKLKFEKVYLPCVLQTKKRYVGYMYETLDQKDPvFDAKGIETVRRDSCPAVSKILER 2791
Cdd:pfam00136  227 VEEAMKIGDELAEHVNqDLFKSPIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFNK-LDMKGVDLVRRDNCPLVKEVIKK 305
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2792 SLKLLFETRDISLIKQYVQRQCM----KLLEGKASIQDFIFAKEYRGSFSYKPGACVPALELTRKMLTYDRRsEPQVGER 2867
Cdd:pfam00136  306 VLDLLLSDRGLPVGLEFVISILNdarsDLRNNKVPLEKFVISKELSKPPDNYKSKNLPHVEVALRMNKRNGE-APEVGDR 384
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622930109 2868 VPYVII---YGTPGVPLIQLVRRPVEVLQDpTLRLNATYYITKQILPPLARIFSLI 2920
Cdd:pfam00136  385 IPYVIVkaaKGLKNLLIYERAEDPEYVLEN-NLPIDYEYYFSNQLIPPVARLLEPI 439
POLBc cd00145
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ...
2510-2918 7.44e-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: 7.44e-108
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2510 APQCVPLIMEPEsRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHVENLGKYDEFkfgctslrvppdllyqvrhditvs 2589
Cdd:cd00145      1 EPYEGGYVFDPI-PGLYENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYI------------------------ 55
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2590 pnGVAFVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSRMLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGD 2669
Cdd:cd00145     56 --GVGFRSPKDRKGLLPRILEELLNFRDEAKKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFF-RFYDPEVAA 132
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2670 SIVHKARETLERAIKLVNDTkkwGARVVYGDTDSMFVLLKG-ATKEQSFKIGQEIAEAVtaTNPKPVKLKFEKVYLPCVL 2748
Cdd:cd00145    133 SITSFGREIIQDTIALVEEH---GARVIYGDTDSIFVSLPKmGTKEDAIKEGREILQEL--ADEHLLELEFEKVYLPFFL 207
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2749 QTKKRYVGYMYETlDQKDPVFDAKGIETVRRDSCPAVSKILERSLKLLFETRDisliKQYVQRQCMKLLegkasiqdfif 2828
Cdd:cd00145    208 GKKKRYAGLDIWK-GQDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEER----KVEAVKEYIDEL----------- 271
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2829 akeyrgsfsykpgacvpaleltrkmltydrrsepqvgERVPYVIIYGTPGVPLIQLVrRPVEVLQDPTLRLNATYYITKQ 2908
Cdd:cd00145    272 -------------------------------------DKVKYVVTRGGKGVPDYERA-DPPLEDLDKRHRIDYEYYLERL 313
                          410
                   ....*....|
gi 1622930109 2909 ILPPLARIFS 2918
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 ...
2213-2451 1.36e-100

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: 323.03  E-value: 1.36e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2213 IQNLTLISVELHARTRRDLEPDPEFDPICALFYCISSDAPLPDTEKTElTGVIVIDKDKTVFSQDiryqtplLIRSGITG 2292
Cdd:cd05778      1 HQHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANK-VGVIIVDELKSNASNG-------RIRSGLSG 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2293 LEVTYAADEKALFHEIAHIIKRYDPDILLGYEIQMHSWGYLLQRAAALSVDLC-QMISRVPDDKiENRFAAERDEYGSYT 2371
Cdd:cd05778     73 IPVEVVESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLlDEISRVPSDS-NGKFGDRDDEWGYTH 151
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2372 MSEINIVGRITLNLWRIMRNEVALTNYTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYRWKMVDHYVSRVRGNLQMLE 2451
Cdd:cd05778    152 TSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEILD 231
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
2235-2710 3.47e-96

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: 320.63  E-value: 3.47e-96
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  2235 PEFDPICALFYCISSDAPLPDTEKTELtgvIVIDKDKTVFSQDIRYQT-----PLLIRSGITGLEVTYAADEKALFHEIA 2309
Cdd:smart00486    1 PPLKILSFDIETYTDGGNFPDAEIFDD---EIIQISLVINDGDKKGANrrilfTLGTCKEIDGIEVYEFNNEKELLLAFF 77
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  2310 HIIKRYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPD-DKIENRFAAERDEYGSYTMSEINIVGRITLNLWRI 2388
Cdd:smart00486   78 EFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIgLRIPNKKPLFGSKSFGLSDIKVYIKGRLVIDLYRL 157
                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  2389 MRNEVALTNYTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYRWkMVDHYVSRVRGNLQMLEQLDLIGKTSEMARLFGI 2468
Cdd:smart00486  158 YKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDE-LLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGI 236
                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  2469 QFLHVLTRGSQYRVESMMLRIAKPMNYIPVTPSVQQRSQMRAPQCVP------LIMEPESRFYSNSVLVLDFQSLYPSIV 2542
Cdd:smart00486  237 PLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEPDLKKKvkyeggKVLEPKKGFYDNPVLVLDFNSLYPSII 316
                           330       340       350       360       370       380       390       400
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  2543 IAYNYCFSTCLGHVENLGKYDEFKFgctslrvppdllYQVRHDITVSPNGVAFVKPSVRKGVLPRMLEEILKTRFMVKQS 2622
Cdd:smart00486  317 IAHNLCYSTLVGVGEVVIKGDLIIP------------EDLLTIKYEKGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKL 384
                           410       420       430       440       450       460       470       480
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109  2623 MKAYKQDRALSR-MLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKARETLERAIKLVND--TKKWGARVVYG 2699
Cdd:smart00486  385 MKKEKDESEELKkLLDSRQLALKLTANSVYGYLGFTNS-RLPCKPLAASVTALGREILEKTKELIEEngYPKPGFKVIYG 463
                           490
                    ....*....|.
gi 1622930109  2700 DTDSMFVLLKG 2710
Cdd:smart00486  464 DTDSIFVTKPG 474
POLBc_delta cd05533
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
2517-2920 1.34e-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: 1.34e-94
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2517 IMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLghvenlgKYDEFKfgctslRVPPDllyqvrhDITVSPNGVAFV 2596
Cdd:cd05533      8 VIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLL-------NKNTAK------KLPPE-------DYIKTPNGDYFV 67
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2597 KPSVRKGVLPRMLEEILKTRFMVKQSMKAYKqDRALSRMLDARQLGLKLIANVTFGYTAANfSGRMPCIEVGDSIVHKAR 2676
Cdd:cd05533     68 KSSVRKGLLPEILEELLAARKRAKKDLKEET-DPFKKAVLDGRQLALKISANSVYGFTGAT-VGKLPCLEISSSVTSFGR 145
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2677 ETLERAIKLVND--TKK----WGARVVYGDTDSMFVLLKGATKEQSFKIGQEIAEAVTATNPKPVKLKFEKVYLPCVLQT 2750
Cdd:cd05533    146 QMIEKTKKLVEEkyTKAngysHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLIN 225
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2751 KKRYVGYMYETLDQKDPVfDAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAK 2830
Cdd:cd05533    226 KKRYAGLLWTNPDKHDKM-DTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLLQNKIDISLLVITK 304
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2831 EY-RGSFSYKpgACVPALELTRKMLTYDRRSEPQVGERVPYVIIYGTPGVPLIQLVRRPVEVLQDpTLRLNATYYITKQI 2909
Cdd:cd05533    305 ALtKTADDYA--GKQAHVELAERMRKRDPGSAPNVGDRVPYVIIKGAKGAKAYEKAEDPIYVLEN-NIPIDTQYYLENQL 381
                          410
                   ....*....|.
gi 1622930109 2910 LPPLARIFSLI 2920
Cdd:cd05533    382 SKPLLRIFEPI 392
PolB COG0417
DNA polymerase B elongation subunit [Replication, recombination and repair];
2264-2923 5.99e-89

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


Pssm-ID: 440186 [Multi-domain]  Cd Length: 794  Bit Score: 310.22  E-value: 5.99e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2264 VIVIdkdkTVFSQDIRYQTPLLIRSGItGLEVTYAADEKALFHEIAHIIKRYDPDILLGYEIQMHSWGYLLQRAAALSVD 2343
Cdd:COG0417    184 IISI----GLAGSDGEKKVLMLGREGV-DFEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNFDLPYLQKRAERLGIP 258
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2344 LcqMISRvpddkieNRFAAERDEYGSYTMseINIVGRITLNLWRIMRN-EVALTNYTFENVSFHVLHqrfplftfrvlsd 2422
Cdd:COG0417    259 L--DLGR-------DGSEPSWREHGGQGF--ASIPGRVVIDLYDALKSaTYKFKSYSLDAVAEELLG------------- 314
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2423 wfDNKTDLYRWKMVDHYVSR----VRGNLQ-------MLEQLDLIGKTSEMARLFGIQFLHVLTRGSQYRVESMMLRIAK 2491
Cdd:COG0417    315 --EGKLIVDGGEIERLWDDDkpalAEYNLRdaeltlrIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAH 392
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2492 PMNY-IPVTPSVQQRSQMRApqcvpLIMEPESRFYSNsVLVLDFQSLYPSIVIAYNYCFST-CLGHVENLGKYDefkfgc 2569
Cdd:COG0417    393 RRGYlAPNKGEIKGEAYPGG-----YVLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPETlVEGGEEPCGDED------ 460
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2570 tslrvppdllyqvrhditVSPN-GVAFVKPsvRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSRMLDARQLGLKLIAN 2648
Cdd:COG0417    461 ------------------VAPGfGHRFCRE--PKGILPSILEELWDERDEAKKKMKKAKPDSEEYRLYDALQQALKILMN 520
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2649 VTFGYTAANFSgRMPCIEVGDSIVHKARETLERAIKLVndtKKWGARVVYGDTDSMFVLLKGATKEQSFKIGQEIAEAVT 2728
Cdd:COG0417    521 SFYGVLGSEGC-RFYDPELAESITARGREIIKQTIEKA---EELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEIN 596
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2729 ATNPKPVKLKFEKVYLPcVLQT--KKRYVGYmyetldQKDPVFDAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIK 2806
Cdd:COG0417    597 AWWPSGLELEFEKHYRR-FFFPgsKKRYAGL------TEDGKIDIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAV 669
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2807 QYVQRQCMKLLEGKASIQDFIFAKEYRGSFS-YKpgACVPA-LELTRKMLTYDRrsEPQVGERVPYVIIYGTPGVpliql 2884
Cdd:COG0417    670 EYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSeYE--KNVPPhVRAARKLDERGR--PYQRGDKISYVITKGGGRV----- 740
                          650       660       670
                   ....*....|....*....|....*....|....*....
gi 1622930109 2885 vrRPVEVLQDPTLRLNATYYITKQILPPLARIFSLIGID 2923
Cdd:COG0417    741 --EPVELAKERESEIDYDYYIEKQLKPTADRILEAFGVS 777
PRK05762 PRK05762
DNA polymerase II; Reviewed
2297-2923 3.18e-61

DNA polymerase II; Reviewed


Pssm-ID: 235595 [Multi-domain]  Cd Length: 786  Bit Score: 227.05  E-value: 3.18e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2297 YAADEKALFHEIAHIIKRYDPDILLGYEIQMHSWGYLLQRAAALSVDLcqMISRVpDDKIENRFAAERDEYGSYTmsein 2376
Cdd:PRK05762   199 YVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPL--RLGRD-GSELEWREHPFRSGYGFAS----- 270
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2377 IVGRITLNLWRIMRnevALTN----YTFENVSFHVL---------HQRFPLFTFRvlsdWFDNKTDLYRWKMVDhyvsrV 2443
Cdd:PRK05762   271 VPGRLVLDGIDALK---SATWvfdsFSLEYVSQRLLgegkaiddpYDRMDEIDRR----FAEDKPALARYNLKD-----C 338
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2444 RGNLQMLEQLDLIGKTSEMARLFGIQflhvLTR--GSQYRVESMMLRIAKPMNYipVTPSVQQRsqmrAPQCVP--LIME 2519
Cdd:PRK05762   339 ELVTRIFEKTKLLPFLLERATVTGLP----LDRvgGSVAAFEHLYLPRAHRAGY--VAPNLGER----PGEASPggYVMD 408
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2520 PESRFYSNsVLVLDFQSLYPSIVIAYNYCFstcLGHVENLGKYDEfkfgctslrvppdllyqvrhDITVSPNGVAFVKPs 2599
Cdd:PRK05762   409 SKPGLYDS-VLVLDFKSLYPSIIRTFNIDP---DGLVEGLAQPPE--------------------ESVAGFLGARFSRE- 463
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2600 vrKGVLPRMLEEILKTRFMVKQSMKAykqdralsrmldARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKARETL 2679
Cdd:PRK05762   464 --KHFLPEIVERLWEGRDEAKREMNK------------PLSQAIKIIMNAFYGVLGSSGC-RFFDPRLASSITMRGHEIM 528
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2680 ERAIKLVndtKKWGARVVYGDTDSMFVLLKGA-TKEQSFKIGQEIAEAVTATNPKPVK----------LKFEKVYLPCVL 2748
Cdd:PRK05762   529 KQTRELI---EAQGYQVIYGDTDSTFVWLGGAhDEEDAAKIGRALVQEINQWWQEHLQqefglesaleLEFEKHYRRFFM 605
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2749 QT--------KKRYVGYMYETLDQKDPVFdaKGIETVRRDSCPAVSKILERSLKLLFETRD-ISLIKQYVqrqcMKLLEG 2819
Cdd:PRK05762   606 PTirgaeegsKKRYAGLIQEGDGDGRIVF--KGLETVRTDWTPLAKEFQQELYERIFRGEPyVDYVREVI----DKLRAG 679
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2820 KASiQDFIFAKEYRGSFS-YKPGacVP-----ALELTRKMLTYDRRSEPQVGERVPYVIIYGTPGvpliqlvrrPVEVLQ 2893
Cdd:PRK05762   680 ELD-EKLVYRKRLRRPLDeYQRN--VPphvraARLADEMGYKVGRPLQYQNGGKIGYVITVNGPE---------PLEYRK 747
                          650       660       670
                   ....*....|....*....|....*....|
gi 1622930109 2894 DPtlrLNATYYITKQILPPLARIFSLIGID 2923
Cdd:PRK05762   748 SP---IDYDYYIEKQLQPVADRILPFFGDD 774
DEDDy_DNA_polB_exo cd05160
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ...
2227-2451 2.39e-53

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: 186.41  E-value: 2.39e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2227 TRRDLEPDPEFDPICALFYCISSDaplpdtekteltGVIVIDKDKTVFSQDIRYqtpllirsGITGLEVTYAADEKALFH 2306
Cdd:cd05160      9 TPPVGGPEPDRDPIICITYADSFD------------GVKVVFLLKTSTVGDDIE--------FIDGIEVEYFADEKELLK 68
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2307 EIAHIIKRYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKIEnrfaaerdeygSYTMSEINIVGRITLNLW 2386
Cdd:cd05160     69 RFFDIIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKS-----------SGSTERIAVKGRVVFDLL 137
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622930109 2387 RIMRNEVALTNYTFENVSFHVLHQRFPLFTFRvlsDWFDNKTDLYRWKMVDHYVSRVRGNLQMLE 2451
Cdd:cd05160    138 AAYKRDFKLKSYTLDAVAEELLGEGKEKVDGE---IIEDAEWEEDPERLIEYNLKDAELTLQILE 199
POLBc_alpha cd05532
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
2516-2923 1.35e-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: 1.35e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2516 LIMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHVENLGKYDEFKfgctslrVPPdllyqvrhditvspngvaf 2595
Cdd:cd05532     12 LVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEDDEEPP-------LPP------------------- 65
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2596 vkPSVRKGVLPRMLEEILKTRFMVKQSMKAyKQDRALSRMLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKA 2675
Cdd:cd05532     66 --SDQEKGILPRIIRKLVERRRQVKKLMKS-EKDPDKKAQLDIRQLALKLTANSMYGCLGFSYS-RFYAKPLAALITSKG 141
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2676 RETLERAIKLVNdtkKWGARVVYGDTDSMFVLLKGATKEQSFKIGQEIAEAVTAtNPKPVKLKFEKVYLPCVLQTKKRYV 2755
Cdd:cd05532    142 REILQKTKDLVE---KMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNK-SYKKLEIDIDGVFKRLLLLKKKKYA 217
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2756 GYMYETLDQKDPVFDAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKL----LEGKASIQDFIFAK- 2830
Cdd:cd05532    218 ALKVVDDDKGKLKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRKInedlRNGKIPLEKFIITKq 297
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2831 ------EYRGSFSYkPGACVpALELTRKMLTYdrrsepQVGERVPYVIIYGTPGVPLIQLVRRPVEVLQDPTLRLNATYY 2904
Cdd:cd05532    298 ltknpeEYPDKKSL-PHVQV-ALRMNKRGRKV------KAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYY 369
                          410       420
                   ....*....|....*....|
gi 1622930109 2905 ITKQILPPLARIFSLI-GID 2923
Cdd:cd05532    370 LSQQILPPISRLCEPIeGTD 389
POLBc_B3 cd05536
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ...
2516-2922 1.13e-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: 1.13e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2516 LIMEPESRFYSNsVLVLDFQSLYPSIVIAYNycfstclghvenlgkydefkfgctslrVPPD-LLYQVRHDITVSPN-GV 2593
Cdd:cd05536      8 IVLEPEKGLHEN-IVVLDFSSLYPSIMIKYN---------------------------ISPDtLVREGCEDCDVEPQvGH 59
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2594 AFVKPsvRKGVLPRMLEEILKTRFMVKQSMKAYKQDRALSRMLDARQLGLKLIANVTFGYTAANfSGRMPCIEVGDSIVH 2673
Cdd:cd05536     60 KFRKD--PPGFIPSVLEDLLEERRRIKEKMKKLDPESEEYKLLDERQRAIKILANSFYGYMGWA-NARWYCKECAEAVTA 136
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2674 KARETLERAIKLVndtKKWGARVVYGDTDSMFVLLKGATkeqsfKIGQEIAEAVTATNPK-PVKLKFEKVYLPCVLQTKK 2752
Cdd:cd05536    137 WGREYIKTTIKIA---EEKGFKVIYGDTDSLFVKIDGAD-----AVKKKVKKLLKYINEElPLELEIEKFYKRGFFVTKK 208
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2753 RYVGYmyeTLDQKdpvFDAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKLLEGKASIQDFIFAKEY 2832
Cdd:cd05536    209 RYAGL---TEDGK---IDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVIEKLKRGEVPPEKLVIWKQL 282
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2833 RGSFS-YKpgACVPALELTRKMLtyDRRSEPQVGERVPYVIIYGtPGvpliQLVRR--PVEVLQDPTlRLNATYYITKQI 2909
Cdd:cd05536    283 TKDLSeYK--ATGPHVAAAKKLA--KRGYKVRPGTKIGYVIVKG-SG----KISDRayPYDMVDEKH-KYDAEYYIDNQV 352
                          410
                   ....*....|...
gi 1622930109 2910 LPPLARIFSLIGI 2922
Cdd:cd05536    353 LPAVLRILEAFGY 365
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
2298-2917 4.92e-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: 196.43  E-value: 4.92e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2298 AADEKALFHEIAHIIKRYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKIENRFAAERdeygsytmseinI 2377
Cdd:TIGR00592  581 LATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGER------------T 648
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2378 VGRITLNLWRIMRNEVALTNYTFENVSFHVLH-QRFPLFTFRVLSDWFDNKTDLYrwkMVDHYVSRVRGNLQMLEQLDLI 2456
Cdd:TIGR00592  649 CGRMICDVEISAKELIRCKSYDLSELVQQILKtERKVIPIDNINNMYSESSSLTY---LLEHTWKDAMFILQIMCELNVL 725
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2457 GKTSEMARLFGIQFLHVLTRGSQYRVESMMLRIAKPMNYI-PVTPSVQQRSQMR--------------APQCVPLIMEPE 2521
Cdd:TIGR00592  726 PLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIvPDKQIFRKQQKLGdedeeidgykkgkkAAYAGGLVLEPK 805
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2522 SRFYSNSVLVLDFQSLYPSIVIAYNYCFSTclghVENLGKYDEfkfgctsLRVPPDllyqvrhditvspngvafvkPSVR 2601
Cdd:TIGR00592  806 VGLYDKYVLLMDFNSLYPSIIQEFNICFTT----VQQKVDEDE-------LPELPD--------------------SELE 854
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2602 KGVLPRMLEEILKTRFMVKQSMKAyKQDRALSRMLDARQLGLKLIANVTFGYTAANFSgRMPCIEVGDSIVHKARETLER 2681
Cdd:TIGR00592  855 MGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKS-RFYAKPLAALVTAKGREILEH 932
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2682 AIKLVndtKKWGARVVYGDTDSMFVLLKGATKEQSFKIGQEIAEAVTATNpKPVKLKFEKVYLPCVLQTKKRYVGYMYET 2761
Cdd:TIGR00592  933 TRQLV---EEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLY-KLLELDIDGVFKRLLLLKKKKYAAIKVEG 1008
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2762 LDQKDPVF--DAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIKQYVQRQCMKL----LEGKASIQDFIFAKEY-RG 2834
Cdd:TIGR00592 1009 DSDGNYTTkqEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIgknvLNGEVPLEKFVINKQLtRD 1088
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2835 SFSYKPGACVPALELTRKMLTYDRRSEPQvGERVPYVIIYGTPGVPLIQLVRRPVEVL-QDPTLRLNATYYITKQILPPL 2913
Cdd:TIGR00592 1089 PKDYPDGASLPHVHVALRINARGGRKVKA-GDVVSYVICKDGGNLSARQRAYALEELQrKHNNLIYDTQYYLEHQIHPVV 1167

                   ....
gi 1622930109 2914 ARIF 2917
Cdd:TIGR00592 1168 LRIL 1171
POLBc_Pol_II cd05537
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ...
2516-2921 9.03e-29

DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.


Pssm-ID: 99920  Cd Length: 371  Bit Score: 120.83  E-value: 9.03e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2516 LIMEPESRFYSNsVLVLDFQSLYPSIVIAYNYcfsTCLGHVENLGKYDEfkfgctslrvppdllyqvrHDITVSPNGVAF 2595
Cdd:cd05537      7 YVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLI---DPLGLIEGLKAPDP-------------------EDLIPGFLGARF 63
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2596 vkpSVRKGVLPRMLEEILKTRFMVKQSmkaykQDRALSRmldarqlGLKLIANVTFGYTAAN----FSGRMPC--IEVGD 2669
Cdd:cd05537     64 ---SREKHILPDLIARLWAARDEAKRE-----KNAPLSQ-------AIKIIMNSFYGVLGSTgcrfFDPRLASsiTLRGH 128
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2670 SIVHKARETLERAiklvndtkkwGARVVYGDTDSMFVLLKGA-TKEQSFKIGQEIAEAVTATNPKPVK----------LK 2738
Cdd:cd05537    129 EIMKQTRAWIEQQ----------GYQVIYGDTDSTFVWLGEElDAAEAQAIGKELASQINQWWAQKLKeefglesfleIE 198
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2739 FEKVYLPCVLQT--------KKRYVGyMYETLDQKDPVFdaKGIETVRRDSCPAVSKILERSLKLLFETRDI-SLIKQYV 2809
Cdd:cd05537    199 FETHYSRFFMPTirgsdegsKKRYAG-LKSTDGGDELVF--KGLETVRSDWTPLARQFQKELYERVFNDEPYeGFIKETV 275
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2810 QrqcmKLLEGKASIQdFIFAKeyrgsfsykpgacvpalELTRKMLTYDRRSEPQV-GERVPYViIYGTPGVPLIQLVRRP 2888
Cdd:cd05537    276 E----ELLAGELDEL-LVYRK-----------------RLRRPLSEYTKNVPPHVqAARLADQ-INRELGRPRQYQWIEY 332
                          410       420       430
                   ....*....|....*....|....*....|....*....
gi 1622930109 2889 V------EVLQDPTLRLNATYYITKQILPPLARIFSLIG 2921
Cdd:cd05537    333 VitvngpEPLEYRTSPLDYQHYIDKQLKPIADSILPFLG 371
PRK05761 PRK05761
DNA-directed DNA polymerase I;
2516-2913 2.31e-27

DNA-directed DNA polymerase I;


Pssm-ID: 235594 [Multi-domain]  Cd Length: 787  Bit Score: 121.72  E-value: 2.31e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2516 LIMEPESRFYSNsVLVLDFQSLYPSIVIAYNYCFSTcLGHVENLGKYDefkfgctslRVPPDLLYQVRHDitvspngvaf 2595
Cdd:PRK05761   411 LVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPET-VRIPECKCHYD---------DEVPELGHSVCDD---------- 469
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2596 vkpsvrKGVLPRMLEEILKT-RFMVKQSMKAYKQDRALSRM-LDARQLGLKLIANVTFGYTAA-NFsgRMPCIEVGDSIV 2672
Cdd:PRK05761   470 ------RPGLTSVLVGLLRDfRVKIYKKKAKDPNLDEERRAwYDVVQRALKVFLNASYGVFGAeNF--KLYRIEVAESIT 541
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2673 HKARETLERAIKLvndTKKWGARVVYGDTDSMFVllKGATKEQSFKIGQEIAEAVTatnpkpVKLKFEKVYLPCVLQ-TK 2751
Cdd:PRK05761   542 ALGREILLSTKKK---AEELGLKVLYGDTDSLFV--WGPTKESLEELIKEIEERTG------IDLEVDKTYDWVAFSgLK 610
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2752 KRYVGYMyetldqKDPVFDAKGIETVRRDSCPAVSKILERSLKLLFETRDIS-------LIKQYVQRQCMKLLEGKASIQ 2824
Cdd:PRK05761   611 KNYFGVL------KDGKVKIKGIVAKKRNTPEFVKELQREVLEVLKSIRSPEdvekvkdEIEDVLKRYYEKLRAKDYPLD 684
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2825 DFIFAK-------EYrgsfSYKPGACVPALELTRKMltydrRSEPQVGERVPYVIIYGTPGVPLIQLVRrpvevLQDptl 2897
Cdd:PRK05761   685 ELAIRVrlskpldEY----TKNTPQHVKAALQLRDY-----GVEVSPGDIISYVKVDDKRGVKPVQLAK-----LSE--- 747
                          410       420
                   ....*....|....*....|..
gi 1622930109 2898 rLNATYYIT------KQILPPL 2913
Cdd:PRK05761   748 -IDVEKYIEllrsalEQILSAL 768
POLBc_B2 cd05531
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ...
2516-2873 4.84e-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: 4.84e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2516 LIMEPESRFYSNsVLVLDFQSLYPSIVIAYNycFSTclghvENLGKydefkfGCTSLRVPPDLLYQVRHDitvspngvaf 2595
Cdd:cd05531      9 LVFQPEPGLYEN-VAQIDFSSMYPSIIVKYN--ISP-----ETINC------RCCECRDHVYLGHRICLK---------- 64
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2596 vkpsvRKGVLPRMLEEILKTRfmvkqsmKAYKQDRALSRMLDARQLGLKLIANVTFGYTA---ANFsGRmpcIEVGDSIV 2672
Cdd:cd05531     65 -----RRGFLPEVLEPLLERR-------LEYKRLKKEEDPYAGRQKALKWILVTSFGYLGyknAKF-GR---IEVHEAIT 128
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2673 HKARETLERAIKLVNDTkkwGARVVYGDTDSMFVllKGATKEQSFKigQEIAEAVTatnpkpVKLKFEKVY-----LPCV 2747
Cdd:cd05531    129 AYGRKILLRAKEIAEEM---GFRVLHGIVDSLWI--QGRGDIEELA--REIEERTG------IPLKLEGHYdwivfLPER 195
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2748 --LQTKKRYVGYMyetldqKDPVFDAKGIETVRRDSCPAVSKILERSLKLLFETRDISLIK-------QYVQRQCMKLLE 2818
Cdd:cd05531    196 dgLGAPNRYFGRL------SDGEMKVRGIELRRRDTPPFVKKFQEEALDILASAKTPEELLklreealDLFRRYLQRLRE 269
                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622930109 2819 GKasIQDFIFAKE-YRGSFSYKPGACVPALELTRKMLTYdrrsepQVGERVPYVII 2873
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 ...
2961-3028 1.52e-17

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


Pssm-ID: 464119  Cd Length: 68  Bit Score: 78.95  E-value: 1.52e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622930109 2961 CPVCDDLTQhGICSKCRSQPQHVAVILNQEIRELERKQEQLVKICKNCTGCFDRHIPCVSLNCPVLFK 3028
Cdd:pfam14260    1 CLGCGAPEE-PLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYM 67
PHA03036 PHA03036
DNA polymerase; Provisional
2517-2804 1.36e-16

DNA polymerase; Provisional


Pssm-ID: 222962 [Multi-domain]  Cd Length: 1004  Bit Score: 87.00  E-value: 1.36e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2517 IMEPESRFYSNSVLVLDFQSLYPSIVIAYNYCFSTCLGHVENLGKYDEFKFGCTSLRV--PPDLLYQvrHDITVSPNGVA 2594
Cdd:PHA03036   535 VFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVNDNRLEAEINKQELRRKypYPRYIYV--HCEPRSPDLVS 612
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2595 --FVKPSVRKGVLPRMLEEILKTRFMVKQSMKAYKQ--DRALsrmLDARQLGLKLIANVTFG----YTAANFS------- 2659
Cdd:PHA03036   613 eiAVFDRRIEGIIPKLLKTFLEERARYKKLLKEATSsvEKAI---YDSMQYTYKIVANSVYGlmgfRNSALYSyasaksc 689
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2660 ---GRMpCIEVGDSIVHKA-----RETL-----------ERAIKL-----VNDTKKWGARVVYGDTDSMFVLLKGATKEQ 2715
Cdd:PHA03036   690 taiGRN-MIKYLNSVLNGSklingKLILancpinpffkdDRSIDTnydtnLPVEYNFTFRSVYGDTDSVFLEINTKDVDK 768
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2716 SFKIGQEIAEAV-TATNPKPVKLKFEKVYLPCVLQTKKRYVGYMY--ETLDQKDPVFDAKGIETVRRDSCP----AVSKI 2788
Cdd:PHA03036   769 SIKIAKELERIInEKVLFDNFKIEFEAVYKNLIMQSKKKYTTLKYiaSSTDGSVPERVNKGTSETRRDVSKfhkyMIKIY 848
                          330
                   ....*....|....*.
gi 1622930109 2789 LERSLKLLFETRDISL 2804
Cdd:PHA03036   849 KTRLLDMLSEGNMNSN 864
DNA_polB_delta_exo cd05777
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ...
2233-2408 2.03e-14

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: 75.31  E-value: 2.03e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2233 PDPEFDPICAlfycISSdaplpdtekteltgVIVIDKDKTVFSQDIryqTPLLIRSGITGLEVTYAADEKALFHEIAHII 2312
Cdd:cd05777     24 PEPEKDPVIQ----IAN--------------VVTRQGEGEPFIRNI---FTLKTCAPIVGAQVFSFETEEELLLAWRDFV 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2313 KRYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDKI---ENRFAAERdeYGSYTMSEINIVGRITLNLWRIM 2389
Cdd:cd05777     83 QEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKStikDTTFSSKQ--MGTRETKEINIEGRIQFDLLQVI 160
                          170
                   ....*....|....*....
gi 1622930109 2390 RNEVALTNYTFENVSFHVL 2408
Cdd:cd05777    161 QRDYKLRSYSLNSVSAHFL 179
POLBc_B1 cd05530
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ...
2516-2888 2.88e-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: 2.88e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2516 LIMEPESRFYSNsVLVLDFQSLYPSIVIAYNYCFST--CLgHVENlgKYDEFkfgctslrvpPDLLYQVRHDitvspngv 2593
Cdd:cd05530     17 IVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYETvnCP-HCEC--KTNEV----------PEVGHWVCKK-------- 74
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2594 afvkpsvRKGVLPRMLEEILKTRFMV-KQSMKAYKQDRALSRMLDARQLGLKLIANVTFG-YTAANFSgrMPCIEVGDSI 2671
Cdd:cd05530     75 -------RPGITSQIIGLLRDLRVKIyKKKAKDKSLDEEMRQWYDVVQSAMKVFINASYGvFGAENFP--LYCPPVAEST 145
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2672 VHKARETLERAIKlvnDTKKWGARVVYGDTDSMFvlLKGATKEQSFKIgQEIAEavtatNPKPVKLKFEKVYLPCVLQT- 2750
Cdd:cd05530    146 TALGRYIITSTIK---KARELGLKVLYGDTDSLF--LWNPPQEQLEDL-VEWVE-----KELGLDLELDKEYRYVVFSGl 214
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2751 KKRYVGYMyetldqKDPVFDAKGIETVRRDSCPAVSKILERSLKLLFETR---DIS----LIKQYVQRQCMKLLEGKASI 2823
Cdd:cd05530    215 KKNYLGVT------KDGSVDIKGLLGKKRNTPEFVKELFYEVIEILSAVNspeDFEkareKIRDIVKGVYKRLKKKEYTL 288
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622930109 2824 QDFIF-------AKEYRGSfsyKPgacvPALELTRKMLTYDRRSEPqvGERVPYVIIYGTPGVPLIQLVRRP 2888
Cdd:cd05530    289 DQLAFkvmlskpPEEYTKN---TP----QHVKAARQLEKYGRNVEA--GDIISYVKVKGKEGVKPVQLARLD 351
43 PHA02528
DNA polymerase; Provisional
2301-2833 7.31e-13

DNA polymerase; Provisional


Pssm-ID: 177369 [Multi-domain]  Cd Length: 881  Bit Score: 74.73  E-value: 7.31e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2301 EKALFHEIAHIIKRYDPDILLGYEIQMHSWGYLLQRaaalsvdlcqmISRVPDDKIENRF-----AAER---DEYGS--- 2369
Cdd:PHA02528   178 EREMLLEYINFWEENTPVIFTGWNVELFDVPYIINR-----------IKNILGEKTAKRLspwgkVKERtieNMYGReei 246
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2370 -YTMSEINIVGriTLNLWRimrnEVALTN---YTFENVSFHVLHQRFPLFTFRVLSDWFDNKTDLYrwkmVDHYVSRVRG 2445
Cdd:PHA02528   247 aYDISGISILD--YLDLYK----KFTFTNqpsYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKY----IEYNIIDVEL 316
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2446 NLQMLEQLDLIGKTSEMARLFGIQFLHVLtrgSQYRVESMMLRIAKPMNYIpVTPsvQQRSQMRAPQCVPLIMEPESRFY 2525
Cdd:PHA02528   317 VDRLDDKRKLIELVLSMAYYAKINFEDVF---SPIKTWDAIIFNSLKEEKI-VIP--ENKSHKKQKYAGAFVKEPVPGAY 390
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2526 sNSVLVLDFQSLYPSIVIAYNYCFSTCLG--HVENLGKYDEfkfgcTSLRVPPDllyqvrhDITVSPNGVAFVKPsvRKG 2603
Cdd:PHA02528   391 -RWVVSFDLTSLYPSIIRQVNISPETIAGtfHVAPVHEYIN-----KTAPRPSD-------EYSCSPNGWMYRKD--IRG 455
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2604 VLPRMLEEILKTRFMVKQSMKAYKQDRALSRMLdARQLGLKLIANVTFGYTAANFSGRMPCI-EVGDSIVHKARETLERA 2682
Cdd:PHA02528   456 VIPTEIKKVFDQRKIYKKKMLAAERNAELIKTI-LEDLNDSVDTPIDVDYYFDFSDEFKAELkTLTKSSLKALLEECEKE 534
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2683 IKLVNDTK--------------------------------------KWGAR-----------------VVYGDTDSMFVL 2707
Cdd:PHA02528   535 IALCNTIQmarkilinslygalgnehfryydlrnaeaitlfgqlaiQWIERkmneylnklcktededyVIYGDTDSIYVN 614
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2708 LK------GATKEQ------SF--KIG------------QEIAEAVTATNPKpVKLKFEKVYLPCVLQTKKRYVGYMY-- 2759
Cdd:PHA02528   615 LDplvekvGEDKFKdtnhwvDFldKFCkermepyidssyRELCEYMNNYEHL-MFMDREAIAGPGFWTAKKRYALNVWds 693
                          570       580       590       600       610       620       630
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1622930109 2760 ETLDQKDPVFDAKGIETVRRDSCPAVSKILERSLKLLfetrdislikqyvqrqcmkLLEGKASIQDFI--FAKEYR 2833
Cdd:PHA02528   694 EGTRYAEPKLKIMGIETQRSSTPKAVQKALKEAIRRI-------------------LQEGEESLQEYIkeFEKEFR 750
DNA_pol_B_exo1 pfam03104
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ...
2233-2403 2.93e-11

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: 67.83  E-value: 2.93e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2233 PDPEF--DP---ICALFYCISSDAPLPdtekteltgvIVIDKDKTVFSQDIrYQTPLLIRSGITGLEVTYAADEKALFHE 2307
Cdd:pfam03104  172 PDAENvkDPiiqISCMLDGQGEPEPEP----------RFLFTLRECDSEDI-EDFEYTPKPIYPGVKVFEFPSEKELLRR 240
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2308 IAHIIKRYDPDILLGYEIQMHSWGYLLQRAAALSVDLCQMISRVPDDkieNRFAAERDEYGSYTMSEINIVGRITLNLWR 2387
Cdd:pfam03104  241 FFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNRG---GRSKVREIGFGTRSYEKVKISGRLHLDLYR 317
                          170
                   ....*....|....*.
gi 1622930109 2388 IMRNEVALTNYTFENV 2403
Cdd:pfam03104  318 VIKRDYKLPSYKLNAV 333
REV3L_RBD cd22287
REV7 binding domain found in protein reversionless 3-like (REV3L) and similar proteins; REV3L, ...
1794-1816 9.83e-09

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


Pssm-ID: 412083  Cd Length: 23  Bit Score: 52.95  E-value: 9.83e-09
                           10        20
                   ....*....|....*....|...
gi 1622930109 1794 RTAHILKPLMSPPSREEIMATLL 1816
Cdd:cd22287      1 RTAHILKPLMSPPSREEIMATLL 23
DNA_polB_Kod1_like_exo cd05780
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ...
2294-2408 1.17e-07

DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show similarity to eukaryotic DNA polymerases involved in DNA replication. Some archaea possess multiple family-B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family-B DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.


Pssm-ID: 99823 [Multi-domain]  Cd Length: 195  Bit Score: 54.67  E-value: 1.17e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2294 EVTYAADEKALFHEIAHIIKRYDPDILLGYEIQMHSWGYLLQRAAALSVDLcqmisRVPDDKIENRFAAERDEYGSYtms 2373
Cdd:cd05780     49 FVEVVKTEKEMIKRFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIEL-----DLGRDGSEIKIQRGGFNNASE--- 120
                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1622930109 2374 einIVGRITLNLWRIMRNEVALTNYTFENVSFHVL 2408
Cdd:cd05780    121 ---IKGRIHVDLYPVARRTLNLTRYTLERVYEELF 152
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
2220-2659 7.13e-07

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: 55.45  E-value: 7.13e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2220 SVELHARTRRDLEPDPEFDP----ICALFY----CISSDAPLPDTEKTELTGVIVIDKDKTVFSQDIRYQTPLLIRSGIT 2291
Cdd:TIGR00592  181 KRAEFAGGDVQMEGDPELKLasfdIETYFHdgkdFFPGDENPADEEIMISTTPVIAKQWDYESEPEARVVTWKKPDKPTT 260
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2292 GLEVTYAADEKALFHEIAHIIKRYDPDIllgyEIQMHSWGYLLQRAAalSVDLCQMISRVPDDKIEN---RFAAERDEYG 2368
Cdd:TIGR00592  261 GSYVESVSEEISMIKRFWDVIDQEDTDV----EITVNGDNFDLVYLA--DRQVFQFYWDAYEDPAEKlgvVLLFGRDVDH 334
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2369 SYTMSEIN----------IVGRITLNLWRIMRNEVALTNYTFENVSFHVLhqRFPLFTFRVLSdwfdnKTDLYRWKMVDH 2438
Cdd:TIGR00592  335 VSPCVQVKginrdlfflpREGKIDFDLGKVTRRTINLPDYYLEFVSELAL--GYKKEKFRAKP-----IAKKYEFEAPDI 407
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2439 YVSRVRGNLQMLeqLDLIGKTSEM----ARLFGIQFLHVLTRGSQYRVESMMLRIAKPMNYIPVTpSVQQRSQMRAPQCV 2514
Cdd:TIGR00592  408 DAPYSSEYLEVT--YELGKEFAPMealpSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVK-GPDELEYPRRSWCK 484
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2515 -------PLIMEPESRFYSNSVLVLDF--QSLYPSIVIAYNYCFSTCLGHVENLGKydefKFGCTSLRVPPDLLYqvRHD 2585
Cdd:TIGR00592  485 yeggyvkPPNVEKGLDKTPPPLVVLDFsmKSLNPSIIRNEIVSIPDTLHREFALDK----PPPEPPYDVHPCVGT--RPK 558
                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622930109 2586 ITVSPNGVAFVKPsvrkGVLPRMLEEILKTRFMVKQSMKAYKQ-DRALSRMLDARQLGLKLIANVTFGYTAANFS 2659
Cdd:TIGR00592  559 DCSFPLDLKGEFP----GKKPSLVEDLATERALIKKFMAKVKKiDPDEIVGHDYQQRALKVLANRINDLKIPTWS 629
DNA_polB_B3_exo cd05781
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ...
2300-2404 3.89e-06

DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarchaea. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B-DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.


Pssm-ID: 99824 [Multi-domain]  Cd Length: 188  Bit Score: 50.02  E-value: 3.89e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2300 DEKALFHEIAHIIKRYDPDILLGYEIQMHSWGYLLQRAAALSV--DLCQMISRVPddkienrfaaERDEYGSYTmseinI 2377
Cdd:cd05781     47 DDRKIIREFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVklDVGRRGGSEP----------STGVYGHYS-----I 111
                           90       100
                   ....*....|....*....|....*..
gi 1622930109 2378 VGRITLNLWRIMRNEVALTNYTFENVS 2404
Cdd:cd05781    112 TGRLNVDLYDFAEEIPEVKVKTLENVA 138
DNA_pol_B_exo1 pfam03104
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ...
23-113 1.41e-05

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: 50.11  E-value: 1.41e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109   23 VFKVSLVSGMPFYGYHEKERHFMKIYLYNPAVVKRICELLQSGAIMNKFyqphEAHIPYLLQLFIDYNLYGMNLINLAAV 102
Cdd:pfam03104   46 IEKIELKLKKSLYGYEEDPVPYLKVSFANPRPLLKIRKYLSPENISDVY----EYDVDYLERFLIDNDIVGFGWYKVKVY 121
                           90
                   ....*....|.
gi 1622930109  103 KFRKARRKSNT 113
Cdd:pfam03104  122 PFRAEGRISNC 132
POLBc_Pol_II_B cd05538
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ...
2601-2796 1.12e-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: 1.12e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2601 RKGVLPRMLEEILKTRFMVKQSMKAYKqDRALSRMLDARQLGLKLIANVTFGYTAA---NFSGrmpcIEVGDSIVHKARE 2677
Cdd:cd05538     43 SLGIFLALLKYLVELRLAAKESARAAA-RPAERDAFKAKQAAFKVLINSFYGYLGTglhAFSD----PEAAAEVTRLGRE 117
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2678 TLEraiKLVNDTKKWGARVVYGDTDSMFVL----LKGATKEqsfkigQEIAEAVTATNPKPVKLKFEKVYLPCVLQTKKR 2753
Cdd:cd05538    118 LLK---LMIRWLRRRGATPVEVDTDGIYFIppngVDTEDEE------EELVRELSSTLPKGITVEFDGRYRAMFSYKIKN 188
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|...
gi 1622930109 2754 YVgymyeTLDQKDPVFdAKGIETVRRDSCPAVSKILERSLKLL 2796
Cdd:cd05538    189 YA-----LLDYDGKLI-VKGSAFRSRGIEPFLREFLREAVRLL 225
PHA03334 PHA03334
putative DNA polymerase catalytic subunit; Provisional
2515-2705 2.13e-04

putative DNA polymerase catalytic subunit; Provisional


Pssm-ID: 223049 [Multi-domain]  Cd Length: 1545  Bit Score: 47.16  E-value: 2.13e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2515 PLIMEPESRFYSNSVLVLDFQSLYPSiviayNYC----------FSTCLGHVENLGKYD----EFKFGCTSlrvppdLLY 2580
Cdd:PHA03334   641 PLTGLTFAGPYQGTELTLDFASLYPS-----NMCdanispeaivDPDCTARVRGWVVFDwkkiDRGFGKAT------LMY 709
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2581 QVRHDITVSPNGVAFvkPSVRKGVLPRMleeiLKTRFMVKQSMKAYKqDRALSRMLDARQLGLKLIANVTFGytaanfsg 2660
Cdd:PHA03334   710 TILRTKPEEPSWRRF--TTYTTSSLNHY----LSMRTEYKGAMKQAK-DPKLKSYHNQLQNEMKICANSHYG-------- 774
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1622930109 2661 rmpcieVGDSIVHKARETLER-AIKLVNDTKKWGA--RVVYGDTDS-MF 2705
Cdd:PHA03334   775 ------VAPHACQHLITTLGRhKIKLVEEFIKKEPgmTVNYGDTDSvMF 817
DNA_polB_like2_exo cd05785
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ...
2299-2406 2.82e-03

Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.


Pssm-ID: 99828 [Multi-domain]  Cd Length: 207  Bit Score: 41.63  E-value: 2.82e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2299 ADEKALFHEIAHIIKRYDPDILLGYEIQMHSWGYLLQRAAALSVDLC----QMISRVPDDKIenRFAAERDEYGSYtmse 2374
Cdd:cd05785     56 AAEKELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGVPLAigrdGSIPRQRPSRF--RFAERLIDYPRY---- 129
                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1622930109 2375 iNIVGRITLNLW-RIMRNEVA---LTNYTFENVSFH 2406
Cdd:cd05785    130 -DIPGRHVIDTYfLVQLFDVSsrdLPSYGLKAVAKH 164
DNA_polB_alpha_exo cd05776
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ...
2241-2408 3.19e-03

inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis. This explains why in most organisms, that no specific repair role, other than check point control, has been assigned to this enzyme. The exonuclease domain may have a structural role.


Pssm-ID: 99819 [Multi-domain]  Cd Length: 234  Bit Score: 41.83  E-value: 3.19e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2241 CALFYCISSDAPLPDTEKTELTGVIVIDKDKTVFSQDIRYQtpllirSGITGLEVTYAADEKALFHEIAHIIKRYDPDIL 2320
Cdd:cd05776     28 MLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKN------AKKKKTKVRIFENERALLNFFLAKLQKIDPDVL 101
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622930109 2321 LGYEIQMHSWGYLLQRAAALSVDLCQMISR----VPDDKIENRFAAERDEygsytmseinIVGRITLNLWRIMRNEVALT 2396
Cdd:cd05776    102 VGHDLEGFDLDVLLSRIQELKVPHWSRIGRlkrsVWPKKKGGGKFGEREL----------TAGRLLCDTYLSAKELIRCK 171
                          170
                   ....*....|..
gi 1622930109 2397 NYTFENVSFHVL 2408
Cdd:cd05776    172 SYDLTELSQQVL 183
 
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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