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Conserved domains on  [gi|1958650263|ref|XP_038948876|]
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DNA polymerase subunit gamma-1 isoform X3 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_pol_A super family cl02626
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ...
 772-1145 0e+00

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: 665.17  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  772 GPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRAVTRHPSFDEESHYGAILPQVVTAGTITRRAVEPTWLTASNARP 851
Cdd:cd08641     47 AKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSRHPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASNAKK 126

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  852 DRVGSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTAATVGISREHAK 931
Cdd:cd08641    127 NRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRDHAK 206

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  932 VFNYGRIYGAGQSFAERLLMQFNHRLSRQEAADKAQQMYAVTKGLRryrlsddgewlvkqlnvpvdrtedgwvslqdlRK 1011
Cdd:cd08641    207 VFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIR--------------------------------IA 254

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263 1012 IRREasrksrWKKWEVVTERAWTGGTESEMFNKLESIAMSDTPRTPVLGCCISRAL-EPSVVQGEFMTSRVNWVVQSSAV 1090
Cdd:cd08641    255 IQRS------TKGKRLFKRPFWSGGSESIMFNKLEEIAAQSQPRTPVLGACITSALlEPNLVKNEFMTSRINWVVQSSAV 328

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1958650263 1091 DYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTR 1145
Cdd:cd08641    329 DYLHLMLVSMRWLIEKYDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTR 383
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 104-396 5.00e-139

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: 421.29  E-value: 5.00e-139
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  104 PDVQLRLPRLFGGNLDQHFRLLAQKQSLPYLEAAASLSEAQLPPQPRKWVWAEGWTRYGPEGEAEPVAIPEERALVFDVE 183
Cdd:pfam18136    1 PDIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASADLPPKPKKWAFKPGWTRYDPDGSPESVDYPLEDALVFDVE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  184 VCLAEGTCPTLAVAISPSAWYSWCSRRLVEERYSWTsQLSPADLIPLGVSAsassstqqdwQEQLVVGHNVSFDRAHIRE 263
Cdd:pfam18136   81 VCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT-DLTPKHLIPMGSPN----------KPRLIVGHNVSYDRARIKE 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  264 QYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWMGAKQGKHKTQH-PTKRGQKSQKNANGPAISSWDWMDISSANNLADVH 342
Cdd:pfam18136  150 EYNLEGTKTRFLDTMSLHIAVSGLTSRQRPLWMKYRKGKKKSDNsLAEHDELLEKKLSSSAVEDDDWVDVSSLNSLADVA 229

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958650263  343 NLYVGGPrLAKEPRELFVKGSMRDIRENFQDLMEYCARDVWATFEVFQQQLPLF 396
Cdd:pfam18136  230 KLYCGIE-LDKELRDLFVKGTLEDIRDNFQDLMTYCARDVEATHEVFQKLFPLF 282
DNA_pol_A super family cl02626
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ...
 413-455 1.24e-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: 77.74  E-value: 1.24e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1958650263  413 GVSYLPVNQNWERYLTEAQSTYEELQREMKKSLMELANDACQL 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 ...
 772-1145 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: 665.17  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  772 GPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRAVTRHPSFDEESHYGAILPQVVTAGTITRRAVEPTWLTASNARP 851
Cdd:cd08641     47 AKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSRHPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASNAKK 126

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  852 DRVGSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTAATVGISREHAK 931
Cdd:cd08641    127 NRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRDHAK 206

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  932 VFNYGRIYGAGQSFAERLLMQFNHRLSRQEAADKAQQMYAVTKGLRryrlsddgewlvkqlnvpvdrtedgwvslqdlRK 1011
Cdd:cd08641    207 VFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIR--------------------------------IA 254

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263 1012 IRREasrksrWKKWEVVTERAWTGGTESEMFNKLESIAMSDTPRTPVLGCCISRAL-EPSVVQGEFMTSRVNWVVQSSAV 1090
Cdd:cd08641    255 IQRS------TKGKRLFKRPFWSGGSESIMFNKLEEIAAQSQPRTPVLGACITSALlEPNLVKNEFMTSRINWVVQSSAV 328

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1958650263 1091 DYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTR 1145
Cdd:cd08641    329 DYLHLMLVSMRWLIEKYDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTR 383
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 104-396 5.00e-139

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: 421.29  E-value: 5.00e-139
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  104 PDVQLRLPRLFGGNLDQHFRLLAQKQSLPYLEAAASLSEAQLPPQPRKWVWAEGWTRYGPEGEAEPVAIPEERALVFDVE 183
Cdd:pfam18136    1 PDIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASADLPPKPKKWAFKPGWTRYDPDGSPESVDYPLEDALVFDVE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  184 VCLAEGTCPTLAVAISPSAWYSWCSRRLVEERYSWTsQLSPADLIPLGVSAsassstqqdwQEQLVVGHNVSFDRAHIRE 263
Cdd:pfam18136   81 VCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT-DLTPKHLIPMGSPN----------KPRLIVGHNVSYDRARIKE 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  264 QYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWMGAKQGKHKTQH-PTKRGQKSQKNANGPAISSWDWMDISSANNLADVH 342
Cdd:pfam18136  150 EYNLEGTKTRFLDTMSLHIAVSGLTSRQRPLWMKYRKGKKKSDNsLAEHDELLEKKLSSSAVEDDDWVDVSSLNSLADVA 229

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958650263  343 NLYVGGPrLAKEPRELFVKGSMRDIRENFQDLMEYCARDVWATFEVFQQQLPLF 396
Cdd:pfam18136  230 KLYCGIE-LDKELRDLFVKGTLEDIRDNFQDLMTYCARDVEATHEVFQKLFPLF 282
POLAc smart00482
DNA polymerase A domain;
855-1129 1.40e-65

DNA polymerase A domain;


Pssm-ID: 214687  Cd Length: 207  Bit Score: 220.19  E-value: 1.40e-65
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263   855 GSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAhfagmhgctafgwMTLQGRKSRGTDLHSKTAATV---------GI 925
Cdd:smart00482    1 GREIRRAFIAPPGYVLVSADYSQIELRILAHLSGD-------------ENLIEAFNNGGDIHTKTAAQVfgvpeeevtPE 67

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263   926 SREHAKVFNYGRIYGAGqsfAERLLMQFNhrLSRQEAADKAQQMYAVTKGLRRYRlsddgewlvkqlnvpvdrtedgwvs 1005
Cdd:smart00482   68 LRRAAKAINFGIIYGMG---AKGLAEQLG--ISEAEAKELIKKYFARFPGVRRYI------------------------- 117

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  1006 lqdlrkirreasrkSRWKkwevvtERAWTGGTESEMFNKLESIAMSDtPRTPVLGCCISRAlepsvvqgefmtsRVNWVV 1085
Cdd:smart00482  118 --------------DRTL------EEARRKGYVTTLFGRRRYIPDID-SRNPVLRAAAERA-------------AVNTPI 163

                           250       260       270       280
                    ....*....|....*....|....*....|....*....|....
gi 1958650263  1086 QSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREED 1129
Cdd:smart00482  164 QGSAADILKLAMIKMDEALKEFGLRARLLLQVHDELVFEVPEEE 207
DNA_pol_A pfam00476
DNA polymerase family A;
855-1134 1.82e-18

DNA polymerase family A;


Pssm-ID: 459825  Cd Length: 368  Bit Score: 88.65  E-value: 1.82e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  855 GSELKAMVQAPPGYVLVGADVDSQELWIAAVL-GDAHFagmhgCTAFgwmtlqgrkSRGTDLHSKTAATV-GIS------ 926
Cdd:pfam00476  126 GRRIRKAFVAEPGWVLLSADYSQIELRILAHLsGDENL-----IEAF---------RNGEDIHTATASEVfGVPleevtp 191

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  927 --REHAKVFNYGRIYGAG-QSFAERLlmqfnhRLSRQEAADKAQQMYAVTKGLRRYrlsddgewlvkqlnvpvdrtedgw 1003
Cdd:pfam00476  192 eqRRRAKAINFGIIYGMSaFGLAQQL------GISRKEAKEYIDRYFERYPGVKEY------------------------ 241

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263 1004 vslqdLRKIRREASRKsrwkkwevvterawtGGTESeMFNK---LESIAMSDTPRtpvlgccisRAlepsvvQGEfmTSR 1080
Cdd:pfam00476  242 -----MEETVEEAREK---------------GYVET-LLGRrryLPDINSSNRNL---------RS------FAE--RAA 283

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1958650263 1081 VNWVVQSSAVDYLHLMLVAM-KWLFEEFaIDGRFCISIHDEVRYLVREEDRYRAA 1134
Cdd:pfam00476  284 INAPIQGSAADIIKLAMIRVdEALKEEG-LKARLLLQVHDELVFEVPEEEVEEVA 337
DNA_pol_gammaA cd08641
Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in ...
 413-455 1.24e-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: 77.74  E-value: 1.24e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1958650263  413 GVSYLPVNQNWERYLTEAQSTYEELQREMKKSLMELANDACQL 455
Cdd:cd08641      1 GSAYLPVNSNWERYLNTAEETYQELQQEVKESLMQLAEDACQL 43
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 857-942 3.66e-07

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


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 54.22  E-value: 3.66e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  857 ELKAMVQAPPGYVLVGADVDSQELWIAAVL-GDAHFAgmhgcTAFGwmtlqgrksRGTDLHSKTAATV-------GISRE 928
Cdd:PRK14975   314 DIRSAFVADPGWKLVVADASQIELRVLAAYsGDERMI-----EAFR---------TGGDLHRLTASVGfgkpeeeKEERA 379

                           90
                   ....*....|....
gi 1958650263  929 HAKVFNYGRIYGAG 942
Cdd:PRK14975   380 LAKAANFGAIYGAT 393
PolA COG0749
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ...
 864-964 4.64e-07

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


Pssm-ID: 440512 [Multi-domain]  Cd Length: 575  Bit Score: 53.90  E-value: 4.64e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  864 APPGYVLVGADVdSQ-ELWIAAvlgdaHFAG---MhgCTAFgwmtlqgrkSRGTDLHSKTAATV-GIS--------REHA 930
Cdd:COG0749    342 APEGYVLLSADY-SQiELRILA-----HLSGdegL--IEAF---------REGEDIHAATAAEVfGVPleevtseqRRRA 404

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1958650263  931 KVFNYGRIYGAG-QSFAERLlmqfnhRLSRQEAAD 964
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 ...
 772-1145 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: 665.17  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  772 GPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRAVTRHPSFDEESHYGAILPQVVTAGTITRRAVEPTWLTASNARP 851
Cdd:cd08641     47 AKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSRHPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASNAKK 126

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  852 DRVGSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTAATVGISREHAK 931
Cdd:cd08641    127 NRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRDHAK 206

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  932 VFNYGRIYGAGQSFAERLLMQFNHRLSRQEAADKAQQMYAVTKGLRryrlsddgewlvkqlnvpvdrtedgwvslqdlRK 1011
Cdd:cd08641    207 VFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIR--------------------------------IA 254

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263 1012 IRREasrksrWKKWEVVTERAWTGGTESEMFNKLESIAMSDTPRTPVLGCCISRAL-EPSVVQGEFMTSRVNWVVQSSAV 1090
Cdd:cd08641    255 IQRS------TKGKRLFKRPFWSGGSESIMFNKLEEIAAQSQPRTPVLGACITSALlEPNLVKNEFMTSRINWVVQSSAV 328

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1958650263 1091 DYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTR 1145
Cdd:cd08641    329 DYLHLMLVSMRWLIEKYDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTR 383
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 104-396 5.00e-139

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: 421.29  E-value: 5.00e-139
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  104 PDVQLRLPRLFGGNLDQHFRLLAQKQSLPYLEAAASLSEAQLPPQPRKWVWAEGWTRYGPEGEAEPVAIPEERALVFDVE 183
Cdd:pfam18136    1 PDIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASADLPPKPKKWAFKPGWTRYDPDGSPESVDYPLEDALVFDVE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  184 VCLAEGTCPTLAVAISPSAWYSWCSRRLVEERYSWTsQLSPADLIPLGVSAsassstqqdwQEQLVVGHNVSFDRAHIRE 263
Cdd:pfam18136   81 VCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT-DLTPKHLIPMGSPN----------KPRLIVGHNVSYDRARIKE 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  264 QYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWMGAKQGKHKTQH-PTKRGQKSQKNANGPAISSWDWMDISSANNLADVH 342
Cdd:pfam18136  150 EYNLEGTKTRFLDTMSLHIAVSGLTSRQRPLWMKYRKGKKKSDNsLAEHDELLEKKLSSSAVEDDDWVDVSSLNSLADVA 229

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958650263  343 NLYVGGPrLAKEPRELFVKGSMRDIRENFQDLMEYCARDVWATFEVFQQQLPLF 396
Cdd:pfam18136  230 KLYCGIE-LDKELRDLFVKGTLEDIRDNFQDLMTYCARDVEATHEVFQKLFPLF 282
DNA_pol_A cd06444
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ...
 768-1145 1.43e-73

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: 248.10  E-value: 1.43e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  768 GGARGPRALEINKMISFWRNAHKRISSQMVvwlprsalpravtrhpsfdeesHYGAILPQVVTAGTITRRAVEPTWLTAS 847
Cdd:cd06444     25 AHPAVPLLLEYKKLAKLWSANGWPWLDQWV----------------------RDGRFHPEYVPGGTVTGRWASRGGNAQQ 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  848 NARPDRVGSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAHFAGMHgctaFGwmtlqgrksRGTDLHSKTAATV---- 923
Cdd:cd06444     83 IPRRDPLGRDIRQAFVADPGWTLVVADASQLELRVLAALSGDEALAEA----FG---------RGGDLYTATASAMfgvp 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  924 --GISREHAKVFNYGRIYGAGQSFAERLLMQFNHRLSRQEAAdkaqqmyavTKGLRRYRLSDDGEWLVKQLNVPVD---- 997
Cdd:cd06444    150 vgGGERQHAKIANLGAMYGATSGISARLLAQLRRISTKEAAA---------LIELFFSRFPAFPKAMEYVEDAARRgerg 220

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  998 RTEDGWVSLQDLRKIRREASRKSRwkkwevvterawtggtesemfnklesiamsdtprtpvlgccISRALEPSVVQGEFM 1077
Cdd:cd06444    221 GYVRTLLGRRSPPPDIRWTEVVSD-----------------------------------------PAAASRARRVRRAAG 259

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958650263 1078 TSRVNWVVQSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTR 1145
Cdd:cd06444    260 RFARNFVVQGTAADWAKLAMVALRRRLEELALDARLVFFVHDEVVLHCPKEEAEAVAAIVREAAEQAV 327
POLAc smart00482
DNA polymerase A domain;
855-1129 1.40e-65

DNA polymerase A domain;


Pssm-ID: 214687  Cd Length: 207  Bit Score: 220.19  E-value: 1.40e-65
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263   855 GSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAhfagmhgctafgwMTLQGRKSRGTDLHSKTAATV---------GI 925
Cdd:smart00482    1 GREIRRAFIAPPGYVLVSADYSQIELRILAHLSGD-------------ENLIEAFNNGGDIHTKTAAQVfgvpeeevtPE 67

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263   926 SREHAKVFNYGRIYGAGqsfAERLLMQFNhrLSRQEAADKAQQMYAVTKGLRRYRlsddgewlvkqlnvpvdrtedgwvs 1005
Cdd:smart00482   68 LRRAAKAINFGIIYGMG---AKGLAEQLG--ISEAEAKELIKKYFARFPGVRRYI------------------------- 117

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  1006 lqdlrkirreasrkSRWKkwevvtERAWTGGTESEMFNKLESIAMSDtPRTPVLGCCISRAlepsvvqgefmtsRVNWVV 1085
Cdd:smart00482  118 --------------DRTL------EEARRKGYVTTLFGRRRYIPDID-SRNPVLRAAAERA-------------AVNTPI 163

                           250       260       270       280
                    ....*....|....*....|....*....|....*....|....
gi 1958650263  1086 QSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREED 1129
Cdd:smart00482  164 QGSAADILKLAMIKMDEALKEFGLRARLLLQVHDELVFEVPEEE 207
DNA_pol_A pfam00476
DNA polymerase family A;
855-1134 1.82e-18

DNA polymerase family A;


Pssm-ID: 459825  Cd Length: 368  Bit Score: 88.65  E-value: 1.82e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  855 GSELKAMVQAPPGYVLVGADVDSQELWIAAVL-GDAHFagmhgCTAFgwmtlqgrkSRGTDLHSKTAATV-GIS------ 926
Cdd:pfam00476  126 GRRIRKAFVAEPGWVLLSADYSQIELRILAHLsGDENL-----IEAF---------RNGEDIHTATASEVfGVPleevtp 191

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  927 --REHAKVFNYGRIYGAG-QSFAERLlmqfnhRLSRQEAADKAQQMYAVTKGLRRYrlsddgewlvkqlnvpvdrtedgw 1003
Cdd:pfam00476  192 eqRRRAKAINFGIIYGMSaFGLAQQL------GISRKEAKEYIDRYFERYPGVKEY------------------------ 241

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263 1004 vslqdLRKIRREASRKsrwkkwevvterawtGGTESeMFNK---LESIAMSDTPRtpvlgccisRAlepsvvQGEfmTSR 1080
Cdd:pfam00476  242 -----MEETVEEAREK---------------GYVET-LLGRrryLPDINSSNRNL---------RS------FAE--RAA 283

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1958650263 1081 VNWVVQSSAVDYLHLMLVAM-KWLFEEFaIDGRFCISIHDEVRYLVREEDRYRAA 1134
Cdd:pfam00476  284 INAPIQGSAADIIKLAMIRVdEALKEEG-LKARLLLQVHDELVFEVPEEEVEEVA 337
DNA_pol_gammaA cd08641
Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in ...
 413-455 1.24e-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: 77.74  E-value: 1.24e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1958650263  413 GVSYLPVNQNWERYLTEAQSTYEELQREMKKSLMELANDACQL 455
Cdd:cd08641      1 GSAYLPVNSNWERYLNTAEETYQELQQEVKESLMQLAEDACQL 43
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 857-942 3.66e-07

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


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 54.22  E-value: 3.66e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  857 ELKAMVQAPPGYVLVGADVDSQELWIAAVL-GDAHFAgmhgcTAFGwmtlqgrksRGTDLHSKTAATV-------GISRE 928
Cdd:PRK14975   314 DIRSAFVADPGWKLVVADASQIELRVLAAYsGDERMI-----EAFR---------TGGDLHRLTASVGfgkpeeeKEERA 379

                           90
                   ....*....|....
gi 1958650263  929 HAKVFNYGRIYGAG 942
Cdd:PRK14975   380 LAKAANFGAIYGAT 393
DNA_pol_A_pol_I_B cd08643
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ...
 828-942 3.79e-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: 53.98  E-value: 3.79e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  828 VVTAGTITRRAvepTWLTASNARPDRVGS----ELKAMVQAPPGYVLVGADVDSQELwiaAVLgdAHFAGMHGCTAFgwm 903
Cdd:cd08643    146 VNTNGAVTGRA---THFSPNMAQVPAVGSpygkECRELFGVPPGWSLVGADASGLEL---RCL--AHYLARYDGGAY--- 214

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1958650263  904 tlqGRKSRGTDLHSKTAATVGI-SREHAKVFNYGRIYGAG 942
Cdd:cd08643    215 ---TRKVLGGDIHWANAQAMGLlSRDGAKTFIYAFLYGAG 251
DNA_pol_A_pol_I_C cd08637
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ...
 855-964 3.91e-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: 53.58  E-value: 3.91e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  855 GSELKAMVQAPPGYVLVGADVdSQ-ELWIAAvlgdaHFAG---MhgCTAFgwmtlqgrkSRGTDLHSKTAATV-GIS--- 926
Cdd:cd08637    138 GREIRKAFVAEEGWVLLSADY-SQiELRILA-----HLSGdeaL--IEAF---------KNGEDIHTRTAAEVfGVPpee 200

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1958650263  927 -----REHAKVFNYGRIYGAGQ-SFAERLlmqfnhRLSRQEAAD 964
Cdd:cd08637    201 vtpemRRIAKAVNFGIIYGISAfGLSQQL------GISRKEAKE 238
DNA_pol_A_Aquificae_like cd08639
Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences; ...
 856-964 4.54e-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: 53.05  E-value: 4.54e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  856 SELKAMVQAPPGYVLVGADVDSQELWIAA-VLGDAHFAgmhgcTAFgwmtlqgrkSRGTDLHSKTAATV-GIS------- 926
Cdd:cd08639     91 REFRRCFVAPEGNKLIIADYSQIELRIAAeISGDERMI-----SAY---------QKGEDLHRLTASLItGKPieeitke 156

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1958650263  927 -REHAKVFNYGRIYGAG-QSFAERLLMQFNHRLSRQEAAD 964
Cdd:cd08639    157 eRQLAKAVNFGLIYGMSaKGLREYARTNYGVEMSLEEAEK 196
PolA COG0749
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ...
 864-964 4.64e-07

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


Pssm-ID: 440512 [Multi-domain]  Cd Length: 575  Bit Score: 53.90  E-value: 4.64e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  864 APPGYVLVGADVdSQ-ELWIAAvlgdaHFAG---MhgCTAFgwmtlqgrkSRGTDLHSKTAATV-GIS--------REHA 930
Cdd:COG0749    342 APEGYVLLSADY-SQiELRILA-----HLSGdegL--IEAF---------REGEDIHAATAAEVfGVPleevtseqRRRA 404

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1958650263  931 KVFNYGRIYGAG-QSFAERLlmqfnhRLSRQEAAD 964
Cdd:COG0749    405 KAINFGIIYGMSaFGLARQL------GISRKEAKE 433
PRK05755 PRK05755
DNA polymerase I; Provisional
 859-964 1.21e-06

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 52.79  E-value: 1.21e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  859 KAMVqAPPGYVLVGADVdSQ-ELWIAavlgdAHFAGMHG-CTAFgwmtlqgrkSRGTDLHSKTAATV-GISRE------- 928
Cdd:PRK05755   643 KAFV-APEGYKLLSADY-SQiELRIL-----AHLSGDEGlIEAF---------AEGEDIHTATASEVfGVPLEevtseqr 706

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1958650263  929 -HAKVFNYGRIYGAG-QSFAERLlmqfnhRLSRQEAAD 964
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 ...
 864-979 2.28e-04

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: 44.91  E-value: 2.28e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650263  864 APPGYVLVGADVdSQ-ELWIAAvlgdaHFAGMHG-CTAFgwmtlqgrkSRGTDLHSKTAATV-GIS--------REHAKV 932
Cdd:cd08638    136 PPPGRVLLSADY-SQlELRILA-----HLSGDPAlIELL---------NSGGDVFKMIAAQWlGKPveevtdeeRQQAKQ 200

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1958650263  933 FNYGRIYGAG-QSFAERLlmqfnhRLSRQEAADKAQQMYAVTKGLRRY 979
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.
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