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Conserved domains on  [gi|17136648|ref|NP_476821|]
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DNA polymerase gamma subunit 1 [Drosophila melanogaster]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_pol_gammaA cd08641
Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in ...
 705-1107 0e+00

Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria; DNA polymerase gamma (Pol gamma), 5'-3' polymerase domain (Pol gammaA). Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), 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 A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gammaA, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains. Pol gammaA has also the right hand configuration. Pol gammaA has both polymerase and proofreading exonuclease activities separated by a spacer. Pol gamma holoenzyme is a heterotrimer containing one Pol gammaA subunit and a dimeric Pol gammaB subunit. Pol gamma is important for mitochondria DNA maintenance and mutation of the catalytic subunit of Pol gamma is implicated in more than 30 human diseases.


:

Pssm-ID: 176478  Cd Length: 425  Bit Score: 698.69  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  705 CQAAARVIDIARMMSYWRNNRDRIMGQMVVWLDSQQLPNEFT--GEKCQPIAYGAICPQVVACGTLTRRAMEPTWMTASN 782
Cdd:cd08641   44 DPQAKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSrhPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASN 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  783 SRPDRLGSELRSMVQAPPGYRLVGADVDSQELWIASVLGDAYACGEHGATPLGWMTLSGSKSNGSDMHSITAKAVGISRD 862
Cdd:cd08641  124 AKKNRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRD 203

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  863 HAKVINYARIYGAGQLFAETLLRQFNPTFSASEAKAKAMKMFSITKGKRVyrlreefhdeledrayssyeasrlAIQRNR 942
Cdd:cd08641  204 HAKVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIRI------------------------AIQRST 259

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  943 TLAEVFHRPNWQGGTESAMFNRLEEIATGSQPRTPFLGGRLSRALEADTGPEQEqrFLPTRINWVVQSGAVDFLHLMLVS 1022
Cdd:cd08641  260 KGKRLFKRPFWSGGSESIMFNKLEEIAAQSQPRTPVLGACITSALLEPNLVKNE--FMTSRINWVVQSSAVDYLHLMLVS 337

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648 1023 MRWLM---GSHVRFCLSFHDELRYLVKEELSPKAALAMHITNLMTRSFCVSRIGLQDLPMSVAFFSSVEVDTVLRKECTM 1099
Cdd:cd08641  338 MRWLIekyDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTRAMFAQKLGINDLPQSVAFFSAVDIDTVLRKEVDM 417


                 ....*...
gi 17136648 1100 DCKTPSNP 1107
Cdd:cd08641  418 DCVTPSNP 425
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 107-381 2.82e-132

DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial DNA polymerase (Pol-gamma). Pol-gamma has a catalytic subunit, Pol gamma-A, which possesses both polymerase and proofreading exonuclease activities and an accessory subunit, Pol gamma-B, which accelerates polymerization rate and suppresses exonuclease activity. This domain is the exonuclease domain of the catalytic subunit, Pol gamma-A.


:

Pssm-ID: 465664  Cd Length: 282  Bit Score: 403.57  E-value: 2.82e-132
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648    107 DVQLKLPALRGANIEEHFHNIAKEQVQPYEELLLPLVQCEqLPKRPKRWAFHTGWTAYDPeDGTATPVDHPLEKGLVFDV 186
Cdd:pfam18136    2 DIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASAD-LPPKPKKWAFKPGWTRYDP-DGSPESVDYPLEDALVFDV 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648    187 EVCVSEGQAPVLATAVSTKRWYSWVSSKLTKHRLSVEklepldvdtdserpHYTTDELIPLGT-TGPGLVVGHNVSYDRA 265
Cdd:pfam18136   80 EVCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT--------------DLTPKHLIPMGSpNKPRLIVGHNVSYDRA 145

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648    266 RLKEQYLTEDTGTRFVDTMSLHMCVSGVTSYQRAM-LKSKK---------------------EPAAEDLGWLEQSSLNSL 323
Cdd:pfam18136  146 RIKEEYNLEGTKTRFLDTMSLHIAVSGLTSRQRPLwMKYRKgkkksdnslaehdellekklsSSAVEDDDWVDVSSLNSL 225

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 17136648    324 VEVHRLYCGGDtLSKEPRNIFVEGTLEQVRQSFQSLTNYCASDVEATHRILRVLYPLY 381
Cdd:pfam18136  226 ADVAKLYCGIE-LDKELRDLFVKGTLEDIRDNFQDLMTYCARDVEATHEVFQKLFPLF 282
DNA_pol_A super family cl02626
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ...
 398-440 5.79e-13

Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), 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 A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic polymerase I (pol I) has two functional domains located on the same polypeptide; a 5'-3' polymerase and a 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and the DNA polymerase activity to fill in the resulting gap. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains.


The actual alignment was detected with superfamily member cd08641:

Pssm-ID: 470638  Cd Length: 425  Bit Score: 72.35  E-value: 5.79e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 17136648  398 GSAYLPVNSNWERYIREAQLTYEDLSIEAKYHLGRRAEEACSL 440
Cdd:cd08641    1 GSAYLPVNSNWERYLNTAEETYQELQQEVKESLMQLAEDACQL 43
 
Name Accession Description Interval E-value
DNA_pol_gammaA cd08641
Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in ...
 705-1107 0e+00

Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria; DNA polymerase gamma (Pol gamma), 5'-3' polymerase domain (Pol gammaA). Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), 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 A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gammaA, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains. Pol gammaA has also the right hand configuration. Pol gammaA has both polymerase and proofreading exonuclease activities separated by a spacer. Pol gamma holoenzyme is a heterotrimer containing one Pol gammaA subunit and a dimeric Pol gammaB subunit. Pol gamma is important for mitochondria DNA maintenance and mutation of the catalytic subunit of Pol gamma is implicated in more than 30 human diseases.


Pssm-ID: 176478  Cd Length: 425  Bit Score: 698.69  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  705 CQAAARVIDIARMMSYWRNNRDRIMGQMVVWLDSQQLPNEFT--GEKCQPIAYGAICPQVVACGTLTRRAMEPTWMTASN 782
Cdd:cd08641   44 DPQAKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSrhPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASN 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  783 SRPDRLGSELRSMVQAPPGYRLVGADVDSQELWIASVLGDAYACGEHGATPLGWMTLSGSKSNGSDMHSITAKAVGISRD 862
Cdd:cd08641  124 AKKNRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRD 203

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  863 HAKVINYARIYGAGQLFAETLLRQFNPTFSASEAKAKAMKMFSITKGKRVyrlreefhdeledrayssyeasrlAIQRNR 942
Cdd:cd08641  204 HAKVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIRI------------------------AIQRST 259

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  943 TLAEVFHRPNWQGGTESAMFNRLEEIATGSQPRTPFLGGRLSRALEADTGPEQEqrFLPTRINWVVQSGAVDFLHLMLVS 1022
Cdd:cd08641  260 KGKRLFKRPFWSGGSESIMFNKLEEIAAQSQPRTPVLGACITSALLEPNLVKNE--FMTSRINWVVQSSAVDYLHLMLVS 337

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648 1023 MRWLM---GSHVRFCLSFHDELRYLVKEELSPKAALAMHITNLMTRSFCVSRIGLQDLPMSVAFFSSVEVDTVLRKECTM 1099
Cdd:cd08641  338 MRWLIekyDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTRAMFAQKLGINDLPQSVAFFSAVDIDTVLRKEVDM 417


                 ....*...
gi 17136648 1100 DCKTPSNP 1107
Cdd:cd08641  418 DCVTPSNP 425
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 107-381 2.82e-132

DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial DNA polymerase (Pol-gamma). Pol-gamma has a catalytic subunit, Pol gamma-A, which possesses both polymerase and proofreading exonuclease activities and an accessory subunit, Pol gamma-B, which accelerates polymerization rate and suppresses exonuclease activity. This domain is the exonuclease domain of the catalytic subunit, Pol gamma-A.


Pssm-ID: 465664  Cd Length: 282  Bit Score: 403.57  E-value: 2.82e-132
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648    107 DVQLKLPALRGANIEEHFHNIAKEQVQPYEELLLPLVQCEqLPKRPKRWAFHTGWTAYDPeDGTATPVDHPLEKGLVFDV 186
Cdd:pfam18136    2 DIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASAD-LPPKPKKWAFKPGWTRYDP-DGSPESVDYPLEDALVFDV 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648    187 EVCVSEGQAPVLATAVSTKRWYSWVSSKLTKHRLSVEklepldvdtdserpHYTTDELIPLGT-TGPGLVVGHNVSYDRA 265
Cdd:pfam18136   80 EVCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT--------------DLTPKHLIPMGSpNKPRLIVGHNVSYDRA 145

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648    266 RLKEQYLTEDTGTRFVDTMSLHMCVSGVTSYQRAM-LKSKK---------------------EPAAEDLGWLEQSSLNSL 323
Cdd:pfam18136  146 RIKEEYNLEGTKTRFLDTMSLHIAVSGLTSRQRPLwMKYRKgkkksdnslaehdellekklsSSAVEDDDWVDVSSLNSL 225

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 17136648    324 VEVHRLYCGGDtLSKEPRNIFVEGTLEQVRQSFQSLTNYCASDVEATHRILRVLYPLY 381
Cdd:pfam18136  226 ADVAKLYCGIE-LDKELRDLFVKGTLEDIRDNFQDLMTYCARDVEATHEVFQKLFPLF 282
POLAc smart00482
DNA polymerase A domain;
789-1048 3.89e-58

DNA polymerase A domain;


Pssm-ID: 214687  Cd Length: 207  Bit Score: 199.00  E-value: 3.89e-58
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648     789 GSELRSMVQAPPGYRLVGADVDSQELWIASVLGDAyacgehgatplgwMTLSGSKSNGSDMHSITAKAV---------GI 859
Cdd:smart00482    1 GREIRRAFIAPPGYVLVSADYSQIELRILAHLSGD-------------ENLIEAFNNGGDIHTKTAAQVfgvpeeevtPE 67

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648     860 SRDHAKVINYARIYGAGqlfAETLLRQFNptFSASEAKAKAMKMFSITKGKRVYrlreefhdeledrayssyeasrlaiq 939
Cdd:smart00482   68 LRRAAKAINFGIIYGMG---AKGLAEQLG--ISEAEAKELIKKYFARFPGVRRY-------------------------- 116

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648     940 RNRTLAEVfhrpnWQGGTESAMFNRLEEIATGSqPRTPFLGGRLSRAleadtgpeqeqrflptRINWVVQSGAVDFLHLM 1019
Cdd:smart00482  117 IDRTLEEA-----RRKGYVTTLFGRRRYIPDID-SRNPVLRAAAERA----------------AVNTPIQGSAADILKLA 174

                           250       260       270
                    ....*....|....*....|....*....|..
gi 17136648    1020 LVSMRWLMGSH---VRFCLSFHDELRYLVKEE 1048
Cdd:smart00482  175 MIKMDEALKEFglrARLLLQVHDELVFEVPEE 206
DNA_pol_gammaA cd08641
Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in ...
 398-440 5.79e-13

Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria; DNA polymerase gamma (Pol gamma), 5'-3' polymerase domain (Pol gammaA). Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), 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 A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gammaA, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains. Pol gammaA has also the right hand configuration. Pol gammaA has both polymerase and proofreading exonuclease activities separated by a spacer. Pol gamma holoenzyme is a heterotrimer containing one Pol gammaA subunit and a dimeric Pol gammaB subunit. Pol gamma is important for mitochondria DNA maintenance and mutation of the catalytic subunit of Pol gamma is implicated in more than 30 human diseases.


Pssm-ID: 176478  Cd Length: 425  Bit Score: 72.35  E-value: 5.79e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 17136648  398 GSAYLPVNSNWERYIREAQLTYEDLSIEAKYHLGRRAEEACSL 440
Cdd:cd08641    1 GSAYLPVNSNWERYLNTAEETYQELQQEVKESLMQLAEDACQL 43
DNA_pol_A pfam00476
DNA polymerase family A;
788-1063 2.96e-12

DNA polymerase family A;


Pssm-ID: 459825  Cd Length: 368  Bit Score: 69.77  E-value: 2.96e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648    788 LGSELRSMVQAPPGYRLVGADVDSQELWI-ASVLGD-----AYAcgehgatplgwmtlsgsksNGSDMHSITAKAV-GIS 860
Cdd:pfam00476  125 EGRRIRKAFVAEPGWVLLSADYSQIELRIlAHLSGDenlieAFR-------------------NGEDIHTATASEVfGVP 185

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648    861 --------RDHAKVINYARIYGAGqlfAETLLRQFNptFSASEAKAKAMKMFSITKGKRvyrlreEFHDELEDRAyssye 932
Cdd:pfam00476  186 leevtpeqRRRAKAINFGIIYGMS---AFGLAQQLG--ISRKEAKEYIDRYFERYPGVK------EYMEETVEEA----- 249

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648    933 asrlaiqrnRTlaevfhrpnwQGGTESaMFNR---LEEIATGSQPRtpflggrlsRAleadtgpeQEQRflpTRINWVVQ 1009
Cdd:pfam00476  250 ---------RE----------KGYVET-LLGRrryLPDINSSNRNL---------RS--------FAER---AAINAPIQ 289

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 17136648   1010 SGAVDFLHLMLVSM-RWL--MGSHVRFCLSFHDELRYLVKEELspKAALAMHITNLM 1063
Cdd:pfam00476  290 GSAADIIKLAMIRVdEALkeEGLKARLLLQVHDELVFEVPEEE--VEEVAALVKEEM 344
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 756-1054 2.70e-08

bifunctional 3'-5' exonuclease/DNA polymerase; Provisional


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 58.07  E-value: 2.70e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648   756 GAICPQVVACGTLTRRameptwMTASNSRPDRLGSELRSMVQAPPGYRLVGADVDSQELWIA------SVLGDAYACGEh 829
Cdd:PRK14975  285 GRFHPEYVPGGVVTGR------WASRGPNAQQIPRDIRSAFVADPGWKLVVADASQIELRVLaaysgdERMIEAFRTGG- 357

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648   830 gatplgwmtlsgsksngsDMHSITA-------KAVGISRDHAKVINYARIYGAGqlfAETLLRQFNptfSASEAKakamk 902
Cdd:PRK14975  358 ------------------DLHRLTAsvgfgkpEEEKEERALAKAANFGAIYGAT---SKGLQEYAK---NYGEAA----- 408

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648   903 mfsitkgkrvyRLREEFHdeledRAYssyeasrlaiqrnrtlaEVFHRpnWQggtESAMfNRLEEiatGSQPRTpfLGGR 982
Cdd:PRK14975  409 -----------RLLERLR-----RAY-----------------PRAVG--WV---ERAA-REGER---GGVVRT--LLGR 444

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17136648   983 LSRALEADTGPEQEQRFLP--TRiNWVVQSGAVDFLHLMLV----SMRWLMGSHVRFCLsfHDELRYLVKEELSPKAA 1054
Cdd:PRK14975  445 TSPPPGFAWRARRRARSRGrfTR-NFPVQGTAADWAKLALAllrrRLAEGLDAELVFFV--HDEVVVECPEEEAEEVA 519
 
Name Accession Description Interval E-value
DNA_pol_gammaA cd08641
Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in ...
 705-1107 0e+00

Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria; DNA polymerase gamma (Pol gamma), 5'-3' polymerase domain (Pol gammaA). Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), 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 A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gammaA, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains. Pol gammaA has also the right hand configuration. Pol gammaA has both polymerase and proofreading exonuclease activities separated by a spacer. Pol gamma holoenzyme is a heterotrimer containing one Pol gammaA subunit and a dimeric Pol gammaB subunit. Pol gamma is important for mitochondria DNA maintenance and mutation of the catalytic subunit of Pol gamma is implicated in more than 30 human diseases.


Pssm-ID: 176478  Cd Length: 425  Bit Score: 698.69  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  705 CQAAARVIDIARMMSYWRNNRDRIMGQMVVWLDSQQLPNEFT--GEKCQPIAYGAICPQVVACGTLTRRAMEPTWMTASN 782
Cdd:cd08641   44 DPQAKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSrhPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASN 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  783 SRPDRLGSELRSMVQAPPGYRLVGADVDSQELWIASVLGDAYACGEHGATPLGWMTLSGSKSNGSDMHSITAKAVGISRD 862
Cdd:cd08641  124 AKKNRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRD 203

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  863 HAKVINYARIYGAGQLFAETLLRQFNPTFSASEAKAKAMKMFSITKGKRVyrlreefhdeledrayssyeasrlAIQRNR 942
Cdd:cd08641  204 HAKVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIRI------------------------AIQRST 259

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  943 TLAEVFHRPNWQGGTESAMFNRLEEIATGSQPRTPFLGGRLSRALEADTGPEQEqrFLPTRINWVVQSGAVDFLHLMLVS 1022
Cdd:cd08641  260 KGKRLFKRPFWSGGSESIMFNKLEEIAAQSQPRTPVLGACITSALLEPNLVKNE--FMTSRINWVVQSSAVDYLHLMLVS 337

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648 1023 MRWLM---GSHVRFCLSFHDELRYLVKEELSPKAALAMHITNLMTRSFCVSRIGLQDLPMSVAFFSSVEVDTVLRKECTM 1099
Cdd:cd08641  338 MRWLIekyDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTRAMFAQKLGINDLPQSVAFFSAVDIDTVLRKEVDM 417


                 ....*...
gi 17136648 1100 DCKTPSNP 1107
Cdd:cd08641  418 DCVTPSNP 425
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 107-381 2.82e-132

DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial DNA polymerase (Pol-gamma). Pol-gamma has a catalytic subunit, Pol gamma-A, which possesses both polymerase and proofreading exonuclease activities and an accessory subunit, Pol gamma-B, which accelerates polymerization rate and suppresses exonuclease activity. This domain is the exonuclease domain of the catalytic subunit, Pol gamma-A.


Pssm-ID: 465664  Cd Length: 282  Bit Score: 403.57  E-value: 2.82e-132
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648    107 DVQLKLPALRGANIEEHFHNIAKEQVQPYEELLLPLVQCEqLPKRPKRWAFHTGWTAYDPeDGTATPVDHPLEKGLVFDV 186
Cdd:pfam18136    2 DIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASAD-LPPKPKKWAFKPGWTRYDP-DGSPESVDYPLEDALVFDV 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648    187 EVCVSEGQAPVLATAVSTKRWYSWVSSKLTKHRLSVEklepldvdtdserpHYTTDELIPLGT-TGPGLVVGHNVSYDRA 265
Cdd:pfam18136   80 EVCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT--------------DLTPKHLIPMGSpNKPRLIVGHNVSYDRA 145

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648    266 RLKEQYLTEDTGTRFVDTMSLHMCVSGVTSYQRAM-LKSKK---------------------EPAAEDLGWLEQSSLNSL 323
Cdd:pfam18136  146 RIKEEYNLEGTKTRFLDTMSLHIAVSGLTSRQRPLwMKYRKgkkksdnslaehdellekklsSSAVEDDDWVDVSSLNSL 225

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 17136648    324 VEVHRLYCGGDtLSKEPRNIFVEGTLEQVRQSFQSLTNYCASDVEATHRILRVLYPLY 381
Cdd:pfam18136  226 ADVAKLYCGIE-LDKELRDLFVKGTLEDIRDNFQDLMTYCARDVEATHEVFQKLFPLF 282
POLAc smart00482
DNA polymerase A domain;
789-1048 3.89e-58

DNA polymerase A domain;


Pssm-ID: 214687  Cd Length: 207  Bit Score: 199.00  E-value: 3.89e-58
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648     789 GSELRSMVQAPPGYRLVGADVDSQELWIASVLGDAyacgehgatplgwMTLSGSKSNGSDMHSITAKAV---------GI 859
Cdd:smart00482    1 GREIRRAFIAPPGYVLVSADYSQIELRILAHLSGD-------------ENLIEAFNNGGDIHTKTAAQVfgvpeeevtPE 67

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648     860 SRDHAKVINYARIYGAGqlfAETLLRQFNptFSASEAKAKAMKMFSITKGKRVYrlreefhdeledrayssyeasrlaiq 939
Cdd:smart00482   68 LRRAAKAINFGIIYGMG---AKGLAEQLG--ISEAEAKELIKKYFARFPGVRRY-------------------------- 116

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648     940 RNRTLAEVfhrpnWQGGTESAMFNRLEEIATGSqPRTPFLGGRLSRAleadtgpeqeqrflptRINWVVQSGAVDFLHLM 1019
Cdd:smart00482  117 IDRTLEEA-----RRKGYVTTLFGRRRYIPDID-SRNPVLRAAAERA----------------AVNTPIQGSAADILKLA 174

                           250       260       270
                    ....*....|....*....|....*....|..
gi 17136648    1020 LVSMRWLMGSH---VRFCLSFHDELRYLVKEE 1048
Cdd:smart00482  175 MIKMDEALKEFglrARLLLQVHDELVFEVPEE 206
DNA_pol_A cd06444
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ...
 705-1094 2.55e-41

Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), 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 A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic polymerase I (pol I) has two functional domains located on the same polypeptide; a 5'-3' polymerase and a 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and the DNA polymerase activity to fill in the resulting gap. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains.


Pssm-ID: 176473 [Multi-domain]  Cd Length: 347  Bit Score: 155.65  E-value: 2.55e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  705 CQAAARVIDIARMMSYWRNNRDRIMGQMVvwldsqqlpneftgekcqpiAYGAICPQVVACGTLTRRAMEPTWMTASNSR 784
Cdd:cd06444   26 HPAVPLLLEYKKLAKLWSANGWPWLDQWV--------------------RDGRFHPEYVPGGTVTGRWASRGGNAQQIPR 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  785 PDRLGSELRSMVQAPPGYRLVGADVDSQELWIASVLGDAYACGEHGATplgwmtlsgsksnGSDMHSITAKAV------G 858
Cdd:cd06444   86 RDPLGRDIRQAFVADPGWTLVVADASQLELRVLAALSGDEALAEAFGR-------------GGDLYTATASAMfgvpvgG 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  859 ISRDHAKVINYARIYGAGQLFAETLLRQFNPTFSASEAkakamkmfsitkgkrvyrlreefhdELEDRAYSSYEASRLAI 938
Cdd:cd06444  153 GERQHAKIANLGAMYGATSGISARLLAQLRRISTKEAA-------------------------ALIELFFSRFPAFPKAM 207

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  939 QRNRTLAevfhRPNWQGGTESAMFNRleeiaTGSQP--RTPFLGGRLSRALEADTGPEQEQRFlptRINWVVQSGAVDFL 1016
Cdd:cd06444  208 EYVEDAA----RRGERGGYVRTLLGR-----RSPPPdiRWTEVVSDPAAASRARRVRRAAGRF---ARNFVVQGTAADWA 275

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648 1017 HLMLVSMRWL---MGSHVRFCLSFHDELRYLVKEELSPKAALAmhITNLMTRSFCVsriglqdLPMSVAFFSSVEVDTVL 1093
Cdd:cd06444  276 KLAMVALRRRleeLALDARLVFFVHDEVVLHCPKEEAEAVAAI--VREAAEQAVRL-------LFGSVPVRFPVKIGVVW 346


                 .
gi 17136648 1094 R 1094
Cdd:cd06444  347 R 347
DNA_pol_gammaA cd08641
Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in ...
 398-440 5.79e-13

Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria; DNA polymerase gamma (Pol gamma), 5'-3' polymerase domain (Pol gammaA). Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), 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 A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gammaA, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains. Pol gammaA has also the right hand configuration. Pol gammaA has both polymerase and proofreading exonuclease activities separated by a spacer. Pol gamma holoenzyme is a heterotrimer containing one Pol gammaA subunit and a dimeric Pol gammaB subunit. Pol gamma is important for mitochondria DNA maintenance and mutation of the catalytic subunit of Pol gamma is implicated in more than 30 human diseases.


Pssm-ID: 176478  Cd Length: 425  Bit Score: 72.35  E-value: 5.79e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 17136648  398 GSAYLPVNSNWERYIREAQLTYEDLSIEAKYHLGRRAEEACSL 440
Cdd:cd08641    1 GSAYLPVNSNWERYLNTAEETYQELQQEVKESLMQLAEDACQL 43
DNA_pol_A pfam00476
DNA polymerase family A;
788-1063 2.96e-12

DNA polymerase family A;


Pssm-ID: 459825  Cd Length: 368  Bit Score: 69.77  E-value: 2.96e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648    788 LGSELRSMVQAPPGYRLVGADVDSQELWI-ASVLGD-----AYAcgehgatplgwmtlsgsksNGSDMHSITAKAV-GIS 860
Cdd:pfam00476  125 EGRRIRKAFVAEPGWVLLSADYSQIELRIlAHLSGDenlieAFR-------------------NGEDIHTATASEVfGVP 185

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648    861 --------RDHAKVINYARIYGAGqlfAETLLRQFNptFSASEAKAKAMKMFSITKGKRvyrlreEFHDELEDRAyssye 932
Cdd:pfam00476  186 leevtpeqRRRAKAINFGIIYGMS---AFGLAQQLG--ISRKEAKEYIDRYFERYPGVK------EYMEETVEEA----- 249

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648    933 asrlaiqrnRTlaevfhrpnwQGGTESaMFNR---LEEIATGSQPRtpflggrlsRAleadtgpeQEQRflpTRINWVVQ 1009
Cdd:pfam00476  250 ---------RE----------KGYVET-LLGRrryLPDINSSNRNL---------RS--------FAER---AAINAPIQ 289

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 17136648   1010 SGAVDFLHLMLVSM-RWL--MGSHVRFCLSFHDELRYLVKEELspKAALAMHITNLM 1063
Cdd:pfam00476  290 GSAADIIKLAMIRVdEALkeEGLKARLLLQVHDELVFEVPEEE--VEEVAALVKEEM 344
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 756-1054 2.70e-08

bifunctional 3'-5' exonuclease/DNA polymerase; Provisional


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 58.07  E-value: 2.70e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648   756 GAICPQVVACGTLTRRameptwMTASNSRPDRLGSELRSMVQAPPGYRLVGADVDSQELWIA------SVLGDAYACGEh 829
Cdd:PRK14975  285 GRFHPEYVPGGVVTGR------WASRGPNAQQIPRDIRSAFVADPGWKLVVADASQIELRVLaaysgdERMIEAFRTGG- 357

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648   830 gatplgwmtlsgsksngsDMHSITA-------KAVGISRDHAKVINYARIYGAGqlfAETLLRQFNptfSASEAKakamk 902
Cdd:PRK14975  358 ------------------DLHRLTAsvgfgkpEEEKEERALAKAANFGAIYGAT---SKGLQEYAK---NYGEAA----- 408

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648   903 mfsitkgkrvyRLREEFHdeledRAYssyeasrlaiqrnrtlaEVFHRpnWQggtESAMfNRLEEiatGSQPRTpfLGGR 982
Cdd:PRK14975  409 -----------RLLERLR-----RAY-----------------PRAVG--WV---ERAA-REGER---GGVVRT--LLGR 444

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17136648   983 LSRALEADTGPEQEQRFLP--TRiNWVVQSGAVDFLHLMLV----SMRWLMGSHVRFCLsfHDELRYLVKEELSPKAA 1054
Cdd:PRK14975  445 TSPPPGFAWRARRRARSRGrfTR-NFPVQGTAADWAKLALAllrrRLAEGLDAELVFFV--HDEVVVECPEEEAEEVA 519
DNA_pol_A_pol_I_B cd08643
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ...
 756-876 4.25e-08

Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. A combination of phylogenomic and signature sequence-based (or phonetic) approaches is used to understand the evolutionary relationships among bacteria. DNA polymerase I is one of the conserved proteins that is used to search for protein signatures. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains.


Pssm-ID: 176480  Cd Length: 429  Bit Score: 57.06  E-value: 4.25e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  756 GAICPQVVACGTLTRRAMEPTWMTA---SNSRPdrLGSELRSMVQAPPGYRLVGADVDSQEL-WIASVLGD----AYAcg 827
Cdd:cd08643  140 GRIHGAVNTNGAVTGRATHFSPNMAqvpAVGSP--YGKECRELFGVPPGWSLVGADASGLELrCLAHYLARydggAYT-- 215

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 17136648  828 ehgatplgwmtlsgSKSNGSDMHSITAKAVGI-SRDHAKVINYARIYGAG 876
Cdd:cd08643  216 --------------RKVLGGDIHWANAQAMGLlSRDGAKTFIYAFLYGAG 251
DNA_pol_A_theta cd08638
DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis and ...
 792-1065 2.87e-05

DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis and in somatic hypermutation; DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis (TLS) and in somatic hypermutation (SHM). DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Pol theta is an exception among family A polymerases and generates processive single base substitutions. Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. Polymerase theta mostly has amino-terminal helicase domain, a carboxy-terminal polymerase domain and an intervening space region.


Pssm-ID: 176475  Cd Length: 373  Bit Score: 47.61  E-value: 2.87e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  792 LRSMVQAPPGYRLVGADVdSQ-ELWI-ASVLGDAyacgehgatplgwmTLSGSKSNGSDMH-SITAKAVGIS-------- 860
Cdd:cd08638  130 LRHAFIPPPGRVLLSADY-SQlELRIlAHLSGDP--------------ALIELLNSGGDVFkMIAAQWLGKPveevtdee 194

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  861 RDHAKVINYARIYGAGqlfAETLLRQFNptfsASEAKAKAMKmfsitkgkrvyrlrEEFHdeledRAYSsyeasrlAIQR 940
Cdd:cd08638  195 RQQAKQLVYGILYGMG---AKSLAEQLG----VSEEEAKQFI--------------ESFK-----NAYP-------GVRR 241

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136648  941 --NRTLAEVFHrpnwqggtesamfnrleeiatgsQPRTPFLGGRlSRALEADTGPEQEQRFLPTR--INWVVQSGAVDFL 1016
Cdd:cd08638  242 fiRETIERARR-----------------------NGFVETLTGR-RRYLPEINSGNSSERAQAERqaVNTVIQGSAADIM 297

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 17136648 1017 HLMLV-------SMRWLMGS-HVRFCLSFHDELRYLVKEELSPKAALAmhITNLMTR 1065
Cdd:cd08638  298 KIAMIniheklhSLLPNLPAgRARLVLQIHDELLFEVPESDVDEVARI--IKRSMEN 352
 
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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