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Conserved domains on  [gi|87080815|ref|NP_059490|]
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DNA polymerase subunit gamma-1 isoform 1 [Mus musculus]

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 ...
 763-1181 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: 768.41  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  763 GASGPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRVVTRHPSFDEEGHYGAILPQVVTAGTITRRAVEPTWLTASN 842
Cdd:cd08641   44 DPQAKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSRHPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASN 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  843 ARPDRVGSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTAATVGISRE 922
Cdd:cd08641  124 AKKNRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRD 203

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  923 HAKIFNYGRIYGAGQSFAERLLMQFNHRLTRQEAAEKAQQMYAVTKGLRryrlsadgewlvkqlnlpvdrtedgwvslqd 1002
Cdd:cd08641  204 HAKVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIR------------------------------- 252

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815 1003 lRMIRREasrksrWKKWEVASERAWTGGTESEMFNKLESIAMSDTPRTPVLGCCISRAL-EPSVVQGEFITSRVNWVVQS 1081
Cdd:cd08641  253 -IAIQRS------TKGKRLFKRPFWSGGSESIMFNKLEEIAAQSQPRTPVLGACITSALlEPNLVKNEFMTSRINWVVQS 325

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815 1082 SAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAV 1161
Cdd:cd08641  326 SAVDYLHLMLVSMRWLIEKYDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTRAMFAQKLGINDLPQSVAFFSAV 405

                        410       420
                 ....*....|....*....|
gi 87080815 1162 DIDQCLRKEVTMDCKTPSNP 1181
Cdd:cd08641  406 DIDTVLRKEVDMDCVTPSNP 425
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 104-396 5.77e-138

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: 420.13  E-value: 5.77e-138
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815    104 PDVELRLPRLFGGNLDQHFRLLAQKQSLPYLEAAASLLEAQLPPEPKSWAWAEGWTRYGPEGEAEPVAIPEERALVFDVE 183
Cdd:pfam18136    1 PDIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASADLPPKPKKWAFKPGWTRYDPDGSPESVDYPLEDALVFDVE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815    184 VCLAEGTCPTLAVAISPSAWYSWCSRRLVEERYSWTsQLSPADLIPLGgstsassstkQDGQEQLVVGHNVSFDRAHIRE 263
Cdd:pfam18136   81 VCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT-DLTPKHLIPMG----------SPNKPRLIVGHNVSYDRARIKE 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815    264 QYLIQDSRMRFLDTMSMHMAISGLSSFQRSLWMGAKQGKHKTQQSTK-RGQKSPRKANGPAISSWDWMDISSANNLADVH 342
Cdd:pfam18136  150 EYNLEGTKTRFLDTMSLHIAVSGLTSRQRPLWMKYRKGKKKSDNSLAeHDELLEKKLSSSAVEDDDWVDVSSLNSLADVA 229

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 87080815    343 NLYVGGpPLEKEPRELFVKGSMRDIRENFQDLMQYCARDVWATFEVFQQQLPLF 396
Cdd:pfam18136  230 KLYCGI-ELDKELRDLFVKGTLEDIRDNFQDLMTYCARDVEATHEVFQKLFPLF 282
DNA_pol_A super family cl02626
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ...
 413-455 1.60e-14

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: 77.36  E-value: 1.60e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 87080815  413 GVSYLPVNQNWERYLTEAQNTYEELQREMKKSLMDLANDACQL 455
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 ...
 763-1181 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: 768.41  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  763 GASGPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRVVTRHPSFDEEGHYGAILPQVVTAGTITRRAVEPTWLTASN 842
Cdd:cd08641   44 DPQAKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSRHPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASN 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  843 ARPDRVGSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTAATVGISRE 922
Cdd:cd08641  124 AKKNRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRD 203

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  923 HAKIFNYGRIYGAGQSFAERLLMQFNHRLTRQEAAEKAQQMYAVTKGLRryrlsadgewlvkqlnlpvdrtedgwvslqd 1002
Cdd:cd08641  204 HAKVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIR------------------------------- 252

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815 1003 lRMIRREasrksrWKKWEVASERAWTGGTESEMFNKLESIAMSDTPRTPVLGCCISRAL-EPSVVQGEFITSRVNWVVQS 1081
Cdd:cd08641  253 -IAIQRS------TKGKRLFKRPFWSGGSESIMFNKLEEIAAQSQPRTPVLGACITSALlEPNLVKNEFMTSRINWVVQS 325

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815 1082 SAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAV 1161
Cdd:cd08641  326 SAVDYLHLMLVSMRWLIEKYDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTRAMFAQKLGINDLPQSVAFFSAV 405

                        410       420
                 ....*....|....*....|
gi 87080815 1162 DIDQCLRKEVTMDCKTPSNP 1181
Cdd:cd08641  406 DIDTVLRKEVDMDCVTPSNP 425
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 104-396 5.77e-138

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: 420.13  E-value: 5.77e-138
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815    104 PDVELRLPRLFGGNLDQHFRLLAQKQSLPYLEAAASLLEAQLPPEPKSWAWAEGWTRYGPEGEAEPVAIPEERALVFDVE 183
Cdd:pfam18136    1 PDIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASADLPPKPKKWAFKPGWTRYDPDGSPESVDYPLEDALVFDVE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815    184 VCLAEGTCPTLAVAISPSAWYSWCSRRLVEERYSWTsQLSPADLIPLGgstsassstkQDGQEQLVVGHNVSFDRAHIRE 263
Cdd:pfam18136   81 VCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT-DLTPKHLIPMG----------SPNKPRLIVGHNVSYDRARIKE 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815    264 QYLIQDSRMRFLDTMSMHMAISGLSSFQRSLWMGAKQGKHKTQQSTK-RGQKSPRKANGPAISSWDWMDISSANNLADVH 342
Cdd:pfam18136  150 EYNLEGTKTRFLDTMSLHIAVSGLTSRQRPLWMKYRKGKKKSDNSLAeHDELLEKKLSSSAVEDDDWVDVSSLNSLADVA 229

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 87080815    343 NLYVGGpPLEKEPRELFVKGSMRDIRENFQDLMQYCARDVWATFEVFQQQLPLF 396
Cdd:pfam18136  230 KLYCGI-ELDKELRDLFVKGTLEDIRDNFQDLMTYCARDVEATHEVFQKLFPLF 282
POLAc smart00482
DNA polymerase A domain;
849-1123 5.68e-66

DNA polymerase A domain;


Pssm-ID: 214687  Cd Length: 207  Bit Score: 221.73  E-value: 5.68e-66
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815     849 GSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAhfagmhgctafgwMTLQGRKSRGTDLHSKTAATV---------GI 919
Cdd:smart00482    1 GREIRRAFIAPPGYVLVSADYSQIELRILAHLSGD-------------ENLIEAFNNGGDIHTKTAAQVfgvpeeevtPE 67

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815     920 SREHAKIFNYGRIYGAGqsfAERLLMQFNhrLTRQEAAEKAQQMYAVTKGLRRYRlsadgewlvkqlnlpvdrtedgwvs 999
Cdd:smart00482   68 LRRAAKAINFGIIYGMG---AKGLAEQLG--ISEAEAKELIKKYFARFPGVRRYI------------------------- 117

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815    1000 lqdlrmirreasrkSRWKkwevasERAWTGGTESEMFNKLESIAMSDtPRTPVLGCCISRAlepsvvqgefitsRVNWVV 1079
Cdd:smart00482  118 --------------DRTL------EEARRKGYVTTLFGRRRYIPDID-SRNPVLRAAAERA-------------AVNTPI 163

                           250       260       270       280
                    ....*....|....*....|....*....|....*....|....
gi 87080815    1080 QSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREED 1123
Cdd:smart00482  164 QGSAADILKLAMIKMDEALKEFGLRARLLLQVHDELVFEVPEEE 207
DNA_pol_A pfam00476
DNA polymerase family A;
849-1155 9.97e-19

DNA polymerase family A;


Pssm-ID: 459825  Cd Length: 368  Bit Score: 89.42  E-value: 9.97e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815    849 GSELKAMVQAPPGYVLVGADVDSQELWIAAVL-GDAHFagmhgCTAFgwmtlqgrkSRGTDLHSKTAATV-GIS------ 920
Cdd:pfam00476  126 GRRIRKAFVAEPGWVLLSADYSQIELRILAHLsGDENL-----IEAF---------RNGEDIHTATASEVfGVPleevtp 191

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815    921 --REHAKIFNYGRIYGAG-QSFAERLlmqfnhRLTRQEAAEKAQQMYAVTKGLRRYrlsadgewlvkqlnlpVDRTedgw 997
Cdd:pfam00476  192 eqRRRAKAINFGIIYGMSaFGLAQQL------GISRKEAKEYIDRYFERYPGVKEY----------------MEET---- 245

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815    998 vslqdlrmiRREASRKsrwkkwevaserawtGGTESeMFNK---LESIAMSDTPRtpvlgccisRAlepsvvQGEfiTSR 1074
Cdd:pfam00476  246 ---------VEEAREK---------------GYVET-LLGRrryLPDINSSNRNL---------RS------FAE--RAA 283

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815   1075 VNWVVQSSAVDYLHLMLVAM-KWLFEEFaIDGRFCISIHDEVRYLVREEDRYRAAlalqitNLLTRCM-FAYKLGLnDLP 1152
Cdd:pfam00476  284 INAPIQGSAADIIKLAMIRVdEALKEEG-LKARLLLQVHDELVFEVPEEEVEEVA------ALVKEEMeNENAVKL-SVP 355


                   ...
gi 87080815   1153 QSV 1155
Cdd:pfam00476  356 LKV 358
DNA_pol_gammaA cd08641
Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in ...
 413-455 1.60e-14

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: 77.36  E-value: 1.60e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 87080815  413 GVSYLPVNQNWERYLTEAQNTYEELQREMKKSLMDLANDACQL 455
Cdd:cd08641    1 GSAYLPVNSNWERYLNTAEETYQELQQEVKESLMQLAEDACQL 43
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 851-936 4.68e-07

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


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 53.84  E-value: 4.68e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815   851 ELKAMVQAPPGYVLVGADVDSQELWIAAVL-GDAHFAgmhgcTAFGwmtlqgrksRGTDLHSKTAATV-------GISRE 922
Cdd:PRK14975  314 DIRSAFVADPGWKLVVADASQIELRVLAAYsGDERMI-----EAFR---------TGGDLHRLTASVGfgkpeeeKEERA 379

                          90
                  ....*....|....
gi 87080815   923 HAKIFNYGRIYGAG 936
Cdd:PRK14975  380 LAKAANFGAIYGAT 393
PolA COG0749
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ...
 858-958 1.00e-06

DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and repair];


Pssm-ID: 440512 [Multi-domain]  Cd Length: 575  Bit Score: 53.13  E-value: 1.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  858 APPGYVLVGADVdSQ-ELWIAavlgdAHFAG---MhgCTAFgwmtlqgrkSRGTDLHSKTAATV-GIS--------REHA 924
Cdd:COG0749  342 APEGYVLLSADY-SQiELRIL-----AHLSGdegL--IEAF---------REGEDIHAATAAEVfGVPleevtseqRRRA 404

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 87080815  925 KIFNYGRIYGAG-QSFAERLlmqfnhRLTRQEAAE 958
Cdd:COG0749  405 KAINFGIIYGMSaFGLARQL------GISRKEAKE 433
 
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 ...
 763-1181 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: 768.41  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  763 GASGPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRVVTRHPSFDEEGHYGAILPQVVTAGTITRRAVEPTWLTASN 842
Cdd:cd08641   44 DPQAKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSRHPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASN 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  843 ARPDRVGSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTAATVGISRE 922
Cdd:cd08641  124 AKKNRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRD 203

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  923 HAKIFNYGRIYGAGQSFAERLLMQFNHRLTRQEAAEKAQQMYAVTKGLRryrlsadgewlvkqlnlpvdrtedgwvslqd 1002
Cdd:cd08641  204 HAKVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIR------------------------------- 252

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815 1003 lRMIRREasrksrWKKWEVASERAWTGGTESEMFNKLESIAMSDTPRTPVLGCCISRAL-EPSVVQGEFITSRVNWVVQS 1081
Cdd:cd08641  253 -IAIQRS------TKGKRLFKRPFWSGGSESIMFNKLEEIAAQSQPRTPVLGACITSALlEPNLVKNEFMTSRINWVVQS 325

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815 1082 SAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAV 1161
Cdd:cd08641  326 SAVDYLHLMLVSMRWLIEKYDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTRAMFAQKLGINDLPQSVAFFSAV 405

                        410       420
                 ....*....|....*....|
gi 87080815 1162 DIDQCLRKEVTMDCKTPSNP 1181
Cdd:cd08641  406 DIDTVLRKEVDMDCVTPSNP 425
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 104-396 5.77e-138

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: 420.13  E-value: 5.77e-138
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815    104 PDVELRLPRLFGGNLDQHFRLLAQKQSLPYLEAAASLLEAQLPPEPKSWAWAEGWTRYGPEGEAEPVAIPEERALVFDVE 183
Cdd:pfam18136    1 PDIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASADLPPKPKKWAFKPGWTRYDPDGSPESVDYPLEDALVFDVE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815    184 VCLAEGTCPTLAVAISPSAWYSWCSRRLVEERYSWTsQLSPADLIPLGgstsassstkQDGQEQLVVGHNVSFDRAHIRE 263
Cdd:pfam18136   81 VCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT-DLTPKHLIPMG----------SPNKPRLIVGHNVSYDRARIKE 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815    264 QYLIQDSRMRFLDTMSMHMAISGLSSFQRSLWMGAKQGKHKTQQSTK-RGQKSPRKANGPAISSWDWMDISSANNLADVH 342
Cdd:pfam18136  150 EYNLEGTKTRFLDTMSLHIAVSGLTSRQRPLWMKYRKGKKKSDNSLAeHDELLEKKLSSSAVEDDDWVDVSSLNSLADVA 229

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 87080815    343 NLYVGGpPLEKEPRELFVKGSMRDIRENFQDLMQYCARDVWATFEVFQQQLPLF 396
Cdd:pfam18136  230 KLYCGI-ELDKELRDLFVKGTLEDIRDNFQDLMTYCARDVEATHEVFQKLFPLF 282
DNA_pol_A cd06444
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ...
 762-1168 1.44e-77

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: 259.66  E-value: 1.44e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  762 GGASGPRALEINKMISFWRNAHKRISSQMVvwlprsalprvvtrhpsfdeegHYGAILPQVVTAGTITRRAVEPTWLTAS 841
Cdd:cd06444   25 AHPAVPLLLEYKKLAKLWSANGWPWLDQWV----------------------RDGRFHPEYVPGGTVTGRWASRGGNAQQ 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  842 NARPDRVGSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAHFAGMHgctaFGwmtlqgrksRGTDLHSKTAATV---- 917
Cdd:cd06444   83 IPRRDPLGRDIRQAFVADPGWTLVVADASQLELRVLAALSGDEALAEA----FG---------RGGDLYTATASAMfgvp 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  918 --GISREHAKIFNYGRIYGAGQSFAERLLMQFNHRLTRQEAAEkaqqmyavtKGLRRYRLSADGEWLVKQLNLPVD---- 991
Cdd:cd06444  150 vgGGERQHAKIANLGAMYGATSGISARLLAQLRRISTKEAAAL---------IELFFSRFPAFPKAMEYVEDAARRgerg 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  992 RTEDGWVSLQDLRMIRREASRKSRwkkwevaserawtggtesemfnklesiamsdtprtpvlgccISRALEPSVVQGEFI 1071
Cdd:cd06444  221 GYVRTLLGRRSPPPDIRWTEVVSD-----------------------------------------PAAASRARRVRRAAG 259

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815 1072 TSRVNWVVQSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMfayklglndL 1151
Cdd:cd06444  260 RFARNFVVQGTAADWAKLAMVALRRRLEELALDARLVFFVHDEVVLHCPKEEAEAVAAIVREAAEQAVRL---------L 330

                        410
                 ....*....|....*..
gi 87080815 1152 PQSVAFFSAVDIDQCLR 1168
Cdd:cd06444  331 FGSVPVRFPVKIGVVWR 347
POLAc smart00482
DNA polymerase A domain;
849-1123 5.68e-66

DNA polymerase A domain;


Pssm-ID: 214687  Cd Length: 207  Bit Score: 221.73  E-value: 5.68e-66
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815     849 GSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAhfagmhgctafgwMTLQGRKSRGTDLHSKTAATV---------GI 919
Cdd:smart00482    1 GREIRRAFIAPPGYVLVSADYSQIELRILAHLSGD-------------ENLIEAFNNGGDIHTKTAAQVfgvpeeevtPE 67

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815     920 SREHAKIFNYGRIYGAGqsfAERLLMQFNhrLTRQEAAEKAQQMYAVTKGLRRYRlsadgewlvkqlnlpvdrtedgwvs 999
Cdd:smart00482   68 LRRAAKAINFGIIYGMG---AKGLAEQLG--ISEAEAKELIKKYFARFPGVRRYI------------------------- 117

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815    1000 lqdlrmirreasrkSRWKkwevasERAWTGGTESEMFNKLESIAMSDtPRTPVLGCCISRAlepsvvqgefitsRVNWVV 1079
Cdd:smart00482  118 --------------DRTL------EEARRKGYVTTLFGRRRYIPDID-SRNPVLRAAAERA-------------AVNTPI 163

                           250       260       270       280
                    ....*....|....*....|....*....|....*....|....
gi 87080815    1080 QSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREED 1123
Cdd:smart00482  164 QGSAADILKLAMIKMDEALKEFGLRARLLLQVHDELVFEVPEEE 207
DNA_pol_A pfam00476
DNA polymerase family A;
849-1155 9.97e-19

DNA polymerase family A;


Pssm-ID: 459825  Cd Length: 368  Bit Score: 89.42  E-value: 9.97e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815    849 GSELKAMVQAPPGYVLVGADVDSQELWIAAVL-GDAHFagmhgCTAFgwmtlqgrkSRGTDLHSKTAATV-GIS------ 920
Cdd:pfam00476  126 GRRIRKAFVAEPGWVLLSADYSQIELRILAHLsGDENL-----IEAF---------RNGEDIHTATASEVfGVPleevtp 191

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815    921 --REHAKIFNYGRIYGAG-QSFAERLlmqfnhRLTRQEAAEKAQQMYAVTKGLRRYrlsadgewlvkqlnlpVDRTedgw 997
Cdd:pfam00476  192 eqRRRAKAINFGIIYGMSaFGLAQQL------GISRKEAKEYIDRYFERYPGVKEY----------------MEET---- 245

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815    998 vslqdlrmiRREASRKsrwkkwevaserawtGGTESeMFNK---LESIAMSDTPRtpvlgccisRAlepsvvQGEfiTSR 1074
Cdd:pfam00476  246 ---------VEEAREK---------------GYVET-LLGRrryLPDINSSNRNL---------RS------FAE--RAA 283

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815   1075 VNWVVQSSAVDYLHLMLVAM-KWLFEEFaIDGRFCISIHDEVRYLVREEDRYRAAlalqitNLLTRCM-FAYKLGLnDLP 1152
Cdd:pfam00476  284 INAPIQGSAADIIKLAMIRVdEALKEEG-LKARLLLQVHDELVFEVPEEEVEEVA------ALVKEEMeNENAVKL-SVP 355


                   ...
gi 87080815   1153 QSV 1155
Cdd:pfam00476  356 LKV 358
DNA_pol_gammaA cd08641
Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in ...
 413-455 1.60e-14

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: 77.36  E-value: 1.60e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 87080815  413 GVSYLPVNQNWERYLTEAQNTYEELQREMKKSLMDLANDACQL 455
Cdd:cd08641    1 GSAYLPVNSNWERYLNTAEETYQELQQEVKESLMQLAEDACQL 43
DNA_pol_A_Aquificae_like cd08639
Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences; ...
 850-1152 2.76e-07

Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences; 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 for phylogenetic anaylsis of bacteria. Species of the phylum Aquificae grow in extreme thermophilic environments. The Aquificae are non-spore-forming, Gram-negative rods and strictly thermophilic. Phylum Aquificae Pol A is different from E. coli Pol I by three signature sequences consisting of a 2 amino acids (aa) insert, a 5-6 aa insert and a 6 aa deletion. These signature sequences may provide a molecular marker for the family Aquificaceae and related species.


Pssm-ID: 176476  Cd Length: 324  Bit Score: 53.82  E-value: 2.76e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  850 SELKAMVQAPPGYVLVGADVDSQELWIAA-VLGDAHFAgmhgcTAFgwmtlqgrkSRGTDLHSKTAATV-GIS------- 920
Cdd:cd08639   91 REFRRCFVAPEGNKLIIADYSQIELRIAAeISGDERMI-----SAY---------QKGEDLHRLTASLItGKPieeitke 156

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  921 -REHAKIFNYGRIYGAG-QSFAERLLMQFNHRLTRQEaaekAQQMYAVTKGLRRYRLSAdgewlvkqlnlpvdrtedgWV 998
Cdd:cd08639  157 eRQLAKAVNFGLIYGMSaKGLREYARTNYGVEMSLEE----AEKFRESFFFFYKGILRW-------------------HH 213

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  999 SLQDLR--MIRREASRKSrwkKWEVASerawtggtesemfnklesiamsdtprtpvlgccisralepsvvqgefITSRVN 1076
Cdd:cd08639  214 RLKAKGpiEVRTLLGRRR---VFEYFT-----------------------------------------------FTEALN 243

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 87080815 1077 WVVQSSAVDYLHLmlvAMKWLFEEFA-IDGRFCISIHDEVRYLVREEDRYRAAlalqitNLLTRCMF-AYKLGLNDLP 1152
Cdd:cd08639  244 YPIQGTGADILKL---ALALLVDRLKdLDAKIVLCVHDEIVLEVPEDEAEEAK------KILESSMEeAGKRILKKVP 312
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 851-936 4.68e-07

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


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 53.84  E-value: 4.68e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815   851 ELKAMVQAPPGYVLVGADVDSQELWIAAVL-GDAHFAgmhgcTAFGwmtlqgrksRGTDLHSKTAATV-------GISRE 922
Cdd:PRK14975  314 DIRSAFVADPGWKLVVADASQIELRVLAAYsGDERMI-----EAFR---------TGGDLHRLTASVGfgkpeeeKEERA 379

                          90
                  ....*....|....
gi 87080815   923 HAKIFNYGRIYGAG 936
Cdd:PRK14975  380 LAKAANFGAIYGAT 393
DNA_pol_A_pol_I_C cd08637
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ...
 849-958 6.24e-07

Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Family A polymerase (polymerase I) 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 (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. 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: 176474  Cd Length: 377  Bit Score: 53.19  E-value: 6.24e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  849 GSELKAMVQAPPGYVLVGADVdSQ-ELWIAAvlgdaHFAG---MhgCTAFgwmtlqgrkSRGTDLHSKTAATV-GIS--- 920
Cdd:cd08637  138 GREIRKAFVAEEGWVLLSADY-SQiELRILA-----HLSGdeaL--IEAF---------KNGEDIHTRTAAEVfGVPpee 200

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 87080815  921 -----REHAKIFNYGRIYGAGQ-SFAERLlmqfnhRLTRQEAAE 958
Cdd:cd08637  201 vtpemRRIAKAVNFGIIYGISAfGLSQQL------GISRKEAKE 238
DNA_pol_A_pol_I_B cd08643
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ...
 822-936 7.62e-07

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: 53.21  E-value: 7.62e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  822 VVTAGTITRRAvepTWLTASNARPDRVGS----ELKAMVQAPPGYVLVGADVDSQELwiaAVLgdAHFAGMHGCTAFgwm 897
Cdd:cd08643  146 VNTNGAVTGRA---THFSPNMAQVPAVGSpygkECRELFGVPPGWSLVGADASGLEL---RCL--AHYLARYDGGAY--- 214

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 87080815  898 tlqGRKSRGTDLHSKTAATVGI-SREHAKIFNYGRIYGAG 936
Cdd:cd08643  215 ---TRKVLGGDIHWANAQAMGLlSRDGAKTFIYAFLYGAG 251
PolA COG0749
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ...
 858-958 1.00e-06

DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and repair];


Pssm-ID: 440512 [Multi-domain]  Cd Length: 575  Bit Score: 53.13  E-value: 1.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  858 APPGYVLVGADVdSQ-ELWIAavlgdAHFAG---MhgCTAFgwmtlqgrkSRGTDLHSKTAATV-GIS--------REHA 924
Cdd:COG0749  342 APEGYVLLSADY-SQiELRIL-----AHLSGdegL--IEAF---------REGEDIHAATAAEVfGVPleevtseqRRRA 404

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 87080815  925 KIFNYGRIYGAG-QSFAERLlmqfnhRLTRQEAAE 958
Cdd:COG0749  405 KAINFGIIYGMSaFGLARQL------GISRKEAKE 433
PRK05755 PRK05755
DNA polymerase I; Provisional
 853-958 1.82e-06

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 52.40  E-value: 1.82e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815   853 KAMVqAPPGYVLVGADVdSQ-ELWIAavlgdAHFAGMHG-CTAFgwmtlqgrkSRGTDLHSKTAATV-GISRE------- 922
Cdd:PRK05755  643 KAFV-APEGYKLLSADY-SQiELRIL-----AHLSGDEGlIEAF---------AEGEDIHTATASEVfGVPLEevtseqr 706

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 87080815   923 -HAKIFNYGRIYGAG-QSFAERLlmqfnhRLTRQEAAE 958
Cdd:PRK05755  707 rRAKAINFGIIYGMSaFGLAQQL------GISRKEAKE 738
DNA_pol_A_theta cd08638
DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis and ...
 858-973 1.93e-03

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: 41.83  E-value: 1.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 87080815  858 APPGYVLVGADVdSQ-ELWIAAvlgdaHFAGMHG-CTAFgwmtlqgrkSRGTDLHSKTAATV-GIS--------REHAKI 926
Cdd:cd08638  136 PPPGRVLLSADY-SQlELRILA-----HLSGDPAlIELL---------NSGGDVFKMIAAQWlGKPveevtdeeRQQAKQ 200

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 87080815  927 FNYGRIYGAG-QSFAERLlmqfnhRLTRQEAAEKAQQMYAVTKGLRRY 973
Cdd:cd08638  201 LVYGILYGMGaKSLAEQL------GVSEEEAKQFIESFKNAYPGVRRF 242
 
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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