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Conserved domains on  [gi|765684951|sp|P54099|]
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RecName: Full=DNA polymerase subunit gamma-1; AltName: Full=3'-5' exodeoxyribonuclease; AltName: Full=5'-deoxyribose-phosphate lyase; AltName: Full=Mitochondrial DNA polymerase catalytic subunit; AltName: Full=PolG-alpha; Short=PolgA

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 ...
 764-1182 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: 768.79  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  764 GASGPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRVVTRHPAFDEEGHYGAILPQVVTAGTITRRAVEPTWLTASN 843
Cdd:cd08641    44 DPQAKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSRHPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASN 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  844 ARPDRVGSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTAATVGISRE 923
Cdd:cd08641   124 AKKNRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRD 203

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  924 HAKIFNYGRIYGAGQSFAERLLMQFNHRLTRQEAAEKAQQMYAVTKGLRryrlsadgewlvkqlnlpvdrtedgwvslqd 1003
Cdd:cd08641   204 HAKVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIR------------------------------- 252

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951 1004 lRMIRREASRKSRWKKwevaaeRAWTGGTESEMFNKLESIAMSDTPRTPVLGCCISRAL-EPSVVQGEFITSRVNWVVQS 1082
Cdd:cd08641   253 -IAIQRSTKGKRLFKR------PFWSGGSESIMFNKLEEIAAQSQPRTPVLGACITSALlEPNLVKNEFMTSRINWVVQS 325

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951 1083 SAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAV 1162
Cdd:cd08641   326 SAVDYLHLMLVSMRWLIEKYDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTRAMFAQKLGINDLPQSVAFFSAV 405

                         410       420
                  ....*....|....*....|
gi 765684951 1163 DIDQCLRKEVTMDCKTPSNP 1182
Cdd:cd08641   406 DIDTVLRKEVDMDCVTPSNP 425
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 104-397 2.94e-133

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: 407.80  E-value: 2.94e-133
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951   104 PDVELRLPRLFGGNLDQHFRLLAQKQSLPYLEAAASLLEAQLPPEPKSWAWAEGWTRYGPEGEAEPVAIPEERALVFDVE 183
Cdd:pfam18136    1 PDIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASADLPPKPKKWAFKPGWTRYDPDGSPESVDYPLEDALVFDVE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951   184 VCLAEGTCPTLAVAISPSAWYSWCSRRLVEERYSWTsQLSPADLIPLGgstsassstkQDGQEQLVVGHNVSFDRAHIRE 263
Cdd:pfam18136   81 VCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT-DLTPKHLIPMG----------SPNKPRLIVGHNVSYDRARIKE 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951   264 QYLIQDSRMRFLDTMSMHMAISGLSSFQRSLWMGAKQGKHKNPAAHKARAEVPEESQWSSESSSWDWMDISSANNLADVH 343
Cdd:pfam18136  150 EYNLEGTKTRFLDTMSLHIAVSGLTSRQRPLWMKYRKGKKKSDNSLAEHDELLEKKLSSSAVEDDDWVDVSSLNSLADVA 229

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 765684951   344 NLYVGGpPLEKEPRELFVKGSMRDIRENFQDLMQYCARDVWATFEVFQQQLPLF 397
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 ...
 414-456 1.56e-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: 1.56e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 765684951  414 GVSYLPVNQNWERYLTEAQNTYEELQREMKKSLMDLANDACQL 456
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 ...
 764-1182 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: 768.79  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  764 GASGPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRVVTRHPAFDEEGHYGAILPQVVTAGTITRRAVEPTWLTASN 843
Cdd:cd08641    44 DPQAKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSRHPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASN 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  844 ARPDRVGSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTAATVGISRE 923
Cdd:cd08641   124 AKKNRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRD 203

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  924 HAKIFNYGRIYGAGQSFAERLLMQFNHRLTRQEAAEKAQQMYAVTKGLRryrlsadgewlvkqlnlpvdrtedgwvslqd 1003
Cdd:cd08641   204 HAKVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIR------------------------------- 252

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951 1004 lRMIRREASRKSRWKKwevaaeRAWTGGTESEMFNKLESIAMSDTPRTPVLGCCISRAL-EPSVVQGEFITSRVNWVVQS 1082
Cdd:cd08641   253 -IAIQRSTKGKRLFKR------PFWSGGSESIMFNKLEEIAAQSQPRTPVLGACITSALlEPNLVKNEFMTSRINWVVQS 325

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951 1083 SAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAV 1162
Cdd:cd08641   326 SAVDYLHLMLVSMRWLIEKYDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTRAMFAQKLGINDLPQSVAFFSAV 405

                         410       420
                  ....*....|....*....|
gi 765684951 1163 DIDQCLRKEVTMDCKTPSNP 1182
Cdd:cd08641   406 DIDTVLRKEVDMDCVTPSNP 425
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 104-397 2.94e-133

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: 407.80  E-value: 2.94e-133
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951   104 PDVELRLPRLFGGNLDQHFRLLAQKQSLPYLEAAASLLEAQLPPEPKSWAWAEGWTRYGPEGEAEPVAIPEERALVFDVE 183
Cdd:pfam18136    1 PDIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASADLPPKPKKWAFKPGWTRYDPDGSPESVDYPLEDALVFDVE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951   184 VCLAEGTCPTLAVAISPSAWYSWCSRRLVEERYSWTsQLSPADLIPLGgstsassstkQDGQEQLVVGHNVSFDRAHIRE 263
Cdd:pfam18136   81 VCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT-DLTPKHLIPMG----------SPNKPRLIVGHNVSYDRARIKE 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951   264 QYLIQDSRMRFLDTMSMHMAISGLSSFQRSLWMGAKQGKHKNPAAHKARAEVPEESQWSSESSSWDWMDISSANNLADVH 343
Cdd:pfam18136  150 EYNLEGTKTRFLDTMSLHIAVSGLTSRQRPLWMKYRKGKKKSDNSLAEHDELLEKKLSSSAVEDDDWVDVSSLNSLADVA 229

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 765684951   344 NLYVGGpPLEKEPRELFVKGSMRDIRENFQDLMQYCARDVWATFEVFQQQLPLF 397
Cdd:pfam18136  230 KLYCGI-ELDKELRDLFVKGTLEDIRDNFQDLMTYCARDVEATHEVFQKLFPLF 282
POLAc smart00482
DNA polymerase A domain;
850-1124 4.54e-66

DNA polymerase A domain;


Pssm-ID: 214687  Cd Length: 207  Bit Score: 221.73  E-value: 4.54e-66
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951    850 GSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAhfagmhgctafgwMTLQGRKSRGTDLHSKTAATV---------GI 920
Cdd:smart00482    1 GREIRRAFIAPPGYVLVSADYSQIELRILAHLSGD-------------ENLIEAFNNGGDIHTKTAAQVfgvpeeevtPE 67

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951    921 SREHAKIFNYGRIYGAGqsfAERLLMQFNhrLTRQEAAEKAQQMYAVTKGLRRYRlsadgewlvkqlnlpvDRTedgwvs 1000
Cdd:smart00482   68 LRRAAKAINFGIIYGMG---AKGLAEQLG--ISEAEAKELIKKYFARFPGVRRYI----------------DRT------ 120

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951   1001 lqdlrmirreasrksrwkkwevaAERAWTGGTESEMFNKLESIAMSDtPRTPVLGCCISRAlepsvvqgefitsRVNWVV 1080
Cdd:smart00482  121 -----------------------LEEARRKGYVTTLFGRRRYIPDID-SRNPVLRAAAERA-------------AVNTPI 163

                           250       260       270       280
                    ....*....|....*....|....*....|....*....|....
gi 765684951   1081 QSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREED 1124
Cdd:smart00482  164 QGSAADILKLAMIKMDEALKEFGLRARLLLQVHDELVFEVPEEE 207
DNA_pol_A pfam00476
DNA polymerase family A;
850-1156 9.28e-19

DNA polymerase family A;


Pssm-ID: 459825  Cd Length: 368  Bit Score: 89.81  E-value: 9.28e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951   850 GSELKAMVQAPPGYVLVGADVDSQELWIAAVL-GDAHFagmhgCTAFgwmtlqgrkSRGTDLHSKTAATV-GIS------ 921
Cdd:pfam00476  126 GRRIRKAFVAEPGWVLLSADYSQIELRILAHLsGDENL-----IEAF---------RNGEDIHTATASEVfGVPleevtp 191

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951   922 --REHAKIFNYGRIYGAG-QSFAERLlmqfnhRLTRQEAAEKAQQMYAVTKGLRRYrlsadgewlvkqlnlpVDRT---- 994
Cdd:pfam00476  192 eqRRRAKAINFGIIYGMSaFGLAQQL------GISRKEAKEYIDRYFERYPGVKEY----------------MEETveea 249

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951   995 -EDGWVS--------LQDLRmiRREASRKSrwkkwevAAERAwtggtesemfnklesiamsdtprtpvlgccisraleps 1065
Cdd:pfam00476  250 rEKGYVEtllgrrryLPDIN--SSNRNLRS-------FAERA-------------------------------------- 282

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  1066 vvqgefitsRVNWVVQSSAVDYLHLMLVAM-KWLFEEFaIDGRFCISIHDEVRYLVREEDRYRAAlalqitNLLTRCM-F 1143
Cdd:pfam00476  283 ---------AINAPIQGSAADIIKLAMIRVdEALKEEG-LKARLLLQVHDELVFEVPEEEVEEVA------ALVKEEMeN 346

                          330
                   ....*....|...
gi 765684951  1144 AYKLGLnDLPQSV 1156
Cdd:pfam00476  347 ENAVKL-SVPLKV 358
DNA_pol_gammaA cd08641
Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in ...
 414-456 1.56e-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: 1.56e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 765684951  414 GVSYLPVNQNWERYLTEAQNTYEELQREMKKSLMDLANDACQL 456
Cdd:cd08641     1 GSAYLPVNSNWERYLNTAEETYQELQQEVKESLMQLAEDACQL 43
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 852-937 5.96e-07

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


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 53.84  E-value: 5.96e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  852 ELKAMVQAPPGYVLVGADVDSQELWIAAVL-GDAHFAgmhgcTAFGwmtlqgrksRGTDLHSKTAATV-------GISRE 923
Cdd:PRK14975  314 DIRSAFVADPGWKLVVADASQIELRVLAAYsGDERMI-----EAFR---------TGGDLHRLTASVGfgkpeeeKEERA 379

                          90
                  ....*....|....
gi 765684951  924 HAKIFNYGRIYGAG 937
Cdd:PRK14975  380 LAKAANFGAIYGAT 393
PolA COG0749
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ...
 859-959 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 765684951  859 APPGYVLVGADVdSQ-ELWIAavlgdAHFAG---MhgCTAFgwmtlqgrkSRGTDLHSKTAATV-GIS--------REHA 925
Cdd:COG0749   342 APEGYVLLSADY-SQiELRIL-----AHLSGdegL--IEAF---------REGEDIHAATAAEVfGVPleevtseqRRRA 404

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 765684951  926 KIFNYGRIYGAG-QSFAERLlmqfnhRLTRQEAAE 959
Cdd:COG0749   405 KAINFGIIYGMSaFGLARQL------GISRKEAKE 433
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 248-313 6.00e-03

DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.


Pssm-ID: 176648 [Multi-domain]  Cd Length: 159  Bit Score: 38.82  E-value: 6.00e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 765684951  248 LVVGHNVSFDRAHIR---EQYLIQDSRMRFLDTMSMHMAISGLSSFQRSLWMGAKQGKHKNPAAHKARA 313
Cdd:cd06127    81 VLVAHNASFDLRFLNrelRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLEGAHRALA 149
 
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 ...
 764-1182 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: 768.79  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  764 GASGPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRVVTRHPAFDEEGHYGAILPQVVTAGTITRRAVEPTWLTASN 843
Cdd:cd08641    44 DPQAKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSRHPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASN 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  844 ARPDRVGSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTAATVGISRE 923
Cdd:cd08641   124 AKKNRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRD 203

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  924 HAKIFNYGRIYGAGQSFAERLLMQFNHRLTRQEAAEKAQQMYAVTKGLRryrlsadgewlvkqlnlpvdrtedgwvslqd 1003
Cdd:cd08641   204 HAKVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIR------------------------------- 252

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951 1004 lRMIRREASRKSRWKKwevaaeRAWTGGTESEMFNKLESIAMSDTPRTPVLGCCISRAL-EPSVVQGEFITSRVNWVVQS 1082
Cdd:cd08641   253 -IAIQRSTKGKRLFKR------PFWSGGSESIMFNKLEEIAAQSQPRTPVLGACITSALlEPNLVKNEFMTSRINWVVQS 325

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951 1083 SAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAV 1162
Cdd:cd08641   326 SAVDYLHLMLVSMRWLIEKYDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTRAMFAQKLGINDLPQSVAFFSAV 405

                         410       420
                  ....*....|....*....|
gi 765684951 1163 DIDQCLRKEVTMDCKTPSNP 1182
Cdd:cd08641   406 DIDTVLRKEVDMDCVTPSNP 425
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 104-397 2.94e-133

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: 407.80  E-value: 2.94e-133
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951   104 PDVELRLPRLFGGNLDQHFRLLAQKQSLPYLEAAASLLEAQLPPEPKSWAWAEGWTRYGPEGEAEPVAIPEERALVFDVE 183
Cdd:pfam18136    1 PDIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASADLPPKPKKWAFKPGWTRYDPDGSPESVDYPLEDALVFDVE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951   184 VCLAEGTCPTLAVAISPSAWYSWCSRRLVEERYSWTsQLSPADLIPLGgstsassstkQDGQEQLVVGHNVSFDRAHIRE 263
Cdd:pfam18136   81 VCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT-DLTPKHLIPMG----------SPNKPRLIVGHNVSYDRARIKE 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951   264 QYLIQDSRMRFLDTMSMHMAISGLSSFQRSLWMGAKQGKHKNPAAHKARAEVPEESQWSSESSSWDWMDISSANNLADVH 343
Cdd:pfam18136  150 EYNLEGTKTRFLDTMSLHIAVSGLTSRQRPLWMKYRKGKKKSDNSLAEHDELLEKKLSSSAVEDDDWVDVSSLNSLADVA 229

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 765684951   344 NLYVGGpPLEKEPRELFVKGSMRDIRENFQDLMQYCARDVWATFEVFQQQLPLF 397
Cdd:pfam18136  230 KLYCGI-ELDKELRDLFVKGTLEDIRDNFQDLMTYCARDVEATHEVFQKLFPLF 282
DNA_pol_A cd06444
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ...
 763-1169 4.60e-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: 258.50  E-value: 4.60e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  763 GGASGPRALEINKMISFWRNAHKRISSQMVvwlprsalprvvtrhpafdeegHYGAILPQVVTAGTITRRAVEPTWLTAS 842
Cdd:cd06444    25 AHPAVPLLLEYKKLAKLWSANGWPWLDQWV----------------------RDGRFHPEYVPGGTVTGRWASRGGNAQQ 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  843 NARPDRVGSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAHFAGMHgctaFGwmtlqgrksRGTDLHSKTAATV---- 918
Cdd:cd06444    83 IPRRDPLGRDIRQAFVADPGWTLVVADASQLELRVLAALSGDEALAEA----FG---------RGGDLYTATASAMfgvp 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  919 --GISREHAKIFNYGRIYGAGQSFAERLLMQFNHRLTRQEAAEkaqqmyavtKGLRRYRLSADGEWLVKQLNLPVD---- 992
Cdd:cd06444   150 vgGGERQHAKIANLGAMYGATSGISARLLAQLRRISTKEAAAL---------IELFFSRFPAFPKAMEYVEDAARRgerg 220

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  993 RTEDGWVSLQDLRMIRREASRKSRwkkwevaaerawtggtesemfnklesiamsdtprtpvlgccISRALEPSVVQGEFI 1072
Cdd:cd06444   221 GYVRTLLGRRSPPPDIRWTEVVSD-----------------------------------------PAAASRARRVRRAAG 259

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951 1073 TSRVNWVVQSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMfayklglndL 1152
Cdd:cd06444   260 RFARNFVVQGTAADWAKLAMVALRRRLEELALDARLVFFVHDEVVLHCPKEEAEAVAAIVREAAEQAVRL---------L 330

                         410
                  ....*....|....*..
gi 765684951 1153 PQSVAFFSAVDIDQCLR 1169
Cdd:cd06444   331 FGSVPVRFPVKIGVVWR 347
POLAc smart00482
DNA polymerase A domain;
850-1124 4.54e-66

DNA polymerase A domain;


Pssm-ID: 214687  Cd Length: 207  Bit Score: 221.73  E-value: 4.54e-66
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951    850 GSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAhfagmhgctafgwMTLQGRKSRGTDLHSKTAATV---------GI 920
Cdd:smart00482    1 GREIRRAFIAPPGYVLVSADYSQIELRILAHLSGD-------------ENLIEAFNNGGDIHTKTAAQVfgvpeeevtPE 67

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951    921 SREHAKIFNYGRIYGAGqsfAERLLMQFNhrLTRQEAAEKAQQMYAVTKGLRRYRlsadgewlvkqlnlpvDRTedgwvs 1000
Cdd:smart00482   68 LRRAAKAINFGIIYGMG---AKGLAEQLG--ISEAEAKELIKKYFARFPGVRRYI----------------DRT------ 120

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951   1001 lqdlrmirreasrksrwkkwevaAERAWTGGTESEMFNKLESIAMSDtPRTPVLGCCISRAlepsvvqgefitsRVNWVV 1080
Cdd:smart00482  121 -----------------------LEEARRKGYVTTLFGRRRYIPDID-SRNPVLRAAAERA-------------AVNTPI 163

                           250       260       270       280
                    ....*....|....*....|....*....|....*....|....
gi 765684951   1081 QSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREED 1124
Cdd:smart00482  164 QGSAADILKLAMIKMDEALKEFGLRARLLLQVHDELVFEVPEEE 207
DNA_pol_A pfam00476
DNA polymerase family A;
850-1156 9.28e-19

DNA polymerase family A;


Pssm-ID: 459825  Cd Length: 368  Bit Score: 89.81  E-value: 9.28e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951   850 GSELKAMVQAPPGYVLVGADVDSQELWIAAVL-GDAHFagmhgCTAFgwmtlqgrkSRGTDLHSKTAATV-GIS------ 921
Cdd:pfam00476  126 GRRIRKAFVAEPGWVLLSADYSQIELRILAHLsGDENL-----IEAF---------RNGEDIHTATASEVfGVPleevtp 191

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951   922 --REHAKIFNYGRIYGAG-QSFAERLlmqfnhRLTRQEAAEKAQQMYAVTKGLRRYrlsadgewlvkqlnlpVDRT---- 994
Cdd:pfam00476  192 eqRRRAKAINFGIIYGMSaFGLAQQL------GISRKEAKEYIDRYFERYPGVKEY----------------MEETveea 249

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951   995 -EDGWVS--------LQDLRmiRREASRKSrwkkwevAAERAwtggtesemfnklesiamsdtprtpvlgccisraleps 1065
Cdd:pfam00476  250 rEKGYVEtllgrrryLPDIN--SSNRNLRS-------FAERA-------------------------------------- 282

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  1066 vvqgefitsRVNWVVQSSAVDYLHLMLVAM-KWLFEEFaIDGRFCISIHDEVRYLVREEDRYRAAlalqitNLLTRCM-F 1143
Cdd:pfam00476  283 ---------AINAPIQGSAADIIKLAMIRVdEALKEEG-LKARLLLQVHDELVFEVPEEEVEEVA------ALVKEEMeN 346

                          330
                   ....*....|...
gi 765684951  1144 AYKLGLnDLPQSV 1156
Cdd:pfam00476  347 ENAVKL-SVPLKV 358
DNA_pol_gammaA cd08641
Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in ...
 414-456 1.56e-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: 1.56e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 765684951  414 GVSYLPVNQNWERYLTEAQNTYEELQREMKKSLMDLANDACQL 456
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; ...
 851-1153 2.92e-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: 2.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  851 SELKAMVQAPPGYVLVGADVDSQELWIAA-VLGDAHFAgmhgcTAFgwmtlqgrkSRGTDLHSKTAATV-GIS------- 921
Cdd:cd08639    91 REFRRCFVAPEGNKLIIADYSQIELRIAAeISGDERMI-----SAY---------QKGEDLHRLTASLItGKPieeitke 156

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  922 -REHAKIFNYGRIYGAG-QSFAERLLMQFNHRLTRQEaaekAQQMYAVTKGLRRYRLSAdgewlvkqlnlpvdrtedgWV 999
Cdd:cd08639   157 eRQLAKAVNFGLIYGMSaKGLREYARTNYGVEMSLEE----AEKFRESFFFFYKGILRW-------------------HH 213

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951 1000 SLQDLR--MIRREASRKSRWkkwevaaerawtggtesemfnklesiamsDTPRtpvlgccisralepsvvqgefITSRVN 1077
Cdd:cd08639   214 RLKAKGpiEVRTLLGRRRVF-----------------------------EYFT---------------------FTEALN 243

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 765684951 1078 WVVQSSAVDYLHLmlvAMKWLFEEFA-IDGRFCISIHDEVRYLVREEDRYRAAlalqitNLLTRCMF-AYKLGLNDLP 1153
Cdd:cd08639   244 YPIQGTGADILKL---ALALLVDRLKdLDAKIVLCVHDEIVLEVPEDEAEEAK------KILESSMEeAGKRILKKVP 312
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 852-937 5.96e-07

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


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 53.84  E-value: 5.96e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  852 ELKAMVQAPPGYVLVGADVDSQELWIAAVL-GDAHFAgmhgcTAFGwmtlqgrksRGTDLHSKTAATV-------GISRE 923
Cdd:PRK14975  314 DIRSAFVADPGWKLVVADASQIELRVLAAYsGDERMI-----EAFR---------TGGDLHRLTASVGfgkpeeeKEERA 379

                          90
                  ....*....|....
gi 765684951  924 HAKIFNYGRIYGAG 937
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 ...
 850-959 6.25e-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: 6.25e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  850 GSELKAMVQAPPGYVLVGADVdSQ-ELWIAAvlgdaHFAG---MhgCTAFgwmtlqgrkSRGTDLHSKTAATV-GIS--- 921
Cdd:cd08637   138 GREIRKAFVAEEGWVLLSADY-SQiELRILA-----HLSGdeaL--IEAF---------KNGEDIHTRTAAEVfGVPpee 200

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 765684951  922 -----REHAKIFNYGRIYGAGQ-SFAERLlmqfnhRLTRQEAAE 959
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 ...
 823-937 8.39e-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: 52.82  E-value: 8.39e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  823 VVTAGTITRRAvepTWLTASNARPDRVGS----ELKAMVQAPPGYVLVGADVDSQELwiaAVLgdAHFAGMHGCTAFgwm 898
Cdd:cd08643   146 VNTNGAVTGRA---THFSPNMAQVPAVGSpygkECRELFGVPPGWSLVGADASGLEL---RCL--AHYLARYDGGAY--- 214

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 765684951  899 tlqGRKSRGTDLHSKTAATVGI-SREHAKIFNYGRIYGAG 937
Cdd:cd08643   215 ---TRKVLGGDIHWANAQAMGLlSRDGAKTFIYAFLYGAG 251
PolA COG0749
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ...
 859-959 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 765684951  859 APPGYVLVGADVdSQ-ELWIAavlgdAHFAG---MhgCTAFgwmtlqgrkSRGTDLHSKTAATV-GIS--------REHA 925
Cdd:COG0749   342 APEGYVLLSADY-SQiELRIL-----AHLSGdegL--IEAF---------REGEDIHAATAAEVfGVPleevtseqRRRA 404

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 765684951  926 KIFNYGRIYGAG-QSFAERLlmqfnhRLTRQEAAE 959
Cdd:COG0749   405 KAINFGIIYGMSaFGLARQL------GISRKEAKE 433
PRK05755 PRK05755
DNA polymerase I; Provisional
 854-959 1.83e-06

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 52.40  E-value: 1.83e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765684951  854 KAMVqAPPGYVLVGADVdSQ-ELWIAavlgdAHFAGMHG-CTAFgwmtlqgrkSRGTDLHSKTAATV-GISRE------- 923
Cdd:PRK05755  643 KAFV-APEGYKLLSADY-SQiELRIL-----AHLSGDEGlIEAF---------AEGEDIHTATASEVfGVPLEevtseqr 706

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 765684951  924 -HAKIFNYGRIYGAG-QSFAERLlmqfnhRLTRQEAAE 959
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 ...
 859-974 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 765684951  859 APPGYVLVGADVdSQ-ELWIAAvlgdaHFAGMHG-CTAFgwmtlqgrkSRGTDLHSKTAATV-GIS--------REHAKI 927
Cdd:cd08638   136 PPPGRVLLSADY-SQlELRILA-----HLSGDPAlIELL---------NSGGDVFKMIAAQWlGKPveevtdeeRQQAKQ 200

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 765684951  928 FNYGRIYGAG-QSFAERLlmqfnhRLTRQEAAEKAQQMYAVTKGLRRY 974
Cdd:cd08638   201 LVYGILYGMGaKSLAEQL------GVSEEEAKQFIESFKNAYPGVRRF 242
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 248-313 6.00e-03

DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.


Pssm-ID: 176648 [Multi-domain]  Cd Length: 159  Bit Score: 38.82  E-value: 6.00e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 765684951  248 LVVGHNVSFDRAHIR---EQYLIQDSRMRFLDTMSMHMAISGLSSFQRSLWMGAKQGKHKNPAAHKARA 313
Cdd:cd06127    81 VLVAHNASFDLRFLNrelRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLEGAHRALA 149
 
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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