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Conserved domains on  [gi|187171277|ref|NP_001119603|]
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DNA polymerase subunit gamma-1 [Homo sapiens]

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 ...
 785-1203 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: 781.50  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  785 GASGPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRAVIRHPDYDEEGLYGAILPQVVTAGTITRRAVEPTWLTASN 864
Cdd:cd08641    44 DPQAKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSRHPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASN 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  865 ARPDRVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTATTVGISRE 944
Cdd:cd08641   124 AKKNRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRD 203

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  945 HAKIFNYGRIYGAGQPFAERLLMQFNHRLTQQEAAEKAQQMYAATKGLRWyrlsdegewlvrelnlpvdrteggwislqd 1024
Cdd:cd08641   204 HAKVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIRI------------------------------ 253

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277 1025 lrkvqretARKSQWKKWEVVAERAWKGGTESEMFNKLESIATSDIPRTPVLGCCISRAL-EPSAVQEEFMTSRVNWVVQS 1103
Cdd:cd08641   254 --------AIQRSTKGKRLFKRPFWSGGSESIMFNKLEEIAAQSQPRTPVLGACITSALlEPNLVKNEFMTSRINWVVQS 325

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277 1104 SAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAV 1183
Cdd:cd08641   326 SAVDYLHLMLVSMRWLIEKYDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTRAMFAQKLGINDLPQSVAFFSAV 405

                         410       420
                  ....*....|....*....|
gi 187171277 1184 DIDRCLRKEVTMDCKTPSNP 1203
Cdd:cd08641   406 DIDTVLRKEVDMDCVTPSNP 425
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 121-414 1.67e-142

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: 432.46  E-value: 1.67e-142
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277   121 PDVELRLPPLYGDNLDQHFRLLAQKQSLPYLEAANLLLQAQLPPKPPAWAWAEGWTRYGPEGEAVPVAIPEERALVFDVE 200
Cdd:pfam18136    1 PDIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASADLPPKPKKWAFKPGWTRYDPDGSPESVDYPLEDALVFDVE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277   201 VCLAEGTCPTLAVAISPSAWYSWCSQRLVEERYSWTsQLSPADLIPLEVPTgassptqrdwQEQLVVGHNVSFDRAHIRE 280
Cdd:pfam18136   81 VCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT-DLTPKHLIPMGSPN----------KPRLIVGHNVSYDRARIKE 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277   281 QYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWIAAKQGKHKVQPPTKQGQKSQRKARRGPAISSWDWLDISSVNSLAEVH 360
Cdd:pfam18136  150 EYNLEGTKTRFLDTMSLHIAVSGLTSRQRPLWMKYRKGKKKSDNSLAEHDELLEKKLSSSAVEDDDWVDVSSLNSLADVA 229

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 187171277   361 RLYVGGpPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDVWATHEVFQQQLPLF 414
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 ...
 431-473 1.71e-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: 1.71e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 187171277  431 GVSYLPVNQNWERYLAEAQGTYEELQREMKKSLMDLANDACQL 473
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 ...
 785-1203 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: 781.50  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  785 GASGPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRAVIRHPDYDEEGLYGAILPQVVTAGTITRRAVEPTWLTASN 864
Cdd:cd08641    44 DPQAKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSRHPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASN 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  865 ARPDRVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTATTVGISRE 944
Cdd:cd08641   124 AKKNRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRD 203

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  945 HAKIFNYGRIYGAGQPFAERLLMQFNHRLTQQEAAEKAQQMYAATKGLRWyrlsdegewlvrelnlpvdrteggwislqd 1024
Cdd:cd08641   204 HAKVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIRI------------------------------ 253

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277 1025 lrkvqretARKSQWKKWEVVAERAWKGGTESEMFNKLESIATSDIPRTPVLGCCISRAL-EPSAVQEEFMTSRVNWVVQS 1103
Cdd:cd08641   254 --------AIQRSTKGKRLFKRPFWSGGSESIMFNKLEEIAAQSQPRTPVLGACITSALlEPNLVKNEFMTSRINWVVQS 325

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277 1104 SAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAV 1183
Cdd:cd08641   326 SAVDYLHLMLVSMRWLIEKYDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTRAMFAQKLGINDLPQSVAFFSAV 405

                         410       420
                  ....*....|....*....|
gi 187171277 1184 DIDRCLRKEVTMDCKTPSNP 1203
Cdd:cd08641   406 DIDTVLRKEVDMDCVTPSNP 425
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 121-414 1.67e-142

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: 432.46  E-value: 1.67e-142
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277   121 PDVELRLPPLYGDNLDQHFRLLAQKQSLPYLEAANLLLQAQLPPKPPAWAWAEGWTRYGPEGEAVPVAIPEERALVFDVE 200
Cdd:pfam18136    1 PDIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASADLPPKPKKWAFKPGWTRYDPDGSPESVDYPLEDALVFDVE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277   201 VCLAEGTCPTLAVAISPSAWYSWCSQRLVEERYSWTsQLSPADLIPLEVPTgassptqrdwQEQLVVGHNVSFDRAHIRE 280
Cdd:pfam18136   81 VCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT-DLTPKHLIPMGSPN----------KPRLIVGHNVSYDRARIKE 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277   281 QYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWIAAKQGKHKVQPPTKQGQKSQRKARRGPAISSWDWLDISSVNSLAEVH 360
Cdd:pfam18136  150 EYNLEGTKTRFLDTMSLHIAVSGLTSRQRPLWMKYRKGKKKSDNSLAEHDELLEKKLSSSAVEDDDWVDVSSLNSLADVA 229

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 187171277   361 RLYVGGpPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDVWATHEVFQQQLPLF 414
Cdd:pfam18136  230 KLYCGI-ELDKELRDLFVKGTLEDIRDNFQDLMTYCARDVEATHEVFQKLFPLF 282
POLAc smart00482
DNA polymerase A domain;
871-1145 2.39e-65

DNA polymerase A domain;


Pssm-ID: 214687  Cd Length: 207  Bit Score: 219.80  E-value: 2.39e-65
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277    871 GSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAhfagmhgctafgwMTLQGRKSRGTDLHSKTATTV---------GI 941
Cdd:smart00482    1 GREIRRAFIAPPGYVLVSADYSQIELRILAHLSGD-------------ENLIEAFNNGGDIHTKTAAQVfgvpeeevtPE 67

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277    942 SREHAKIFNYGRIYGAGqpfAERLLMQFNhrLTQQEAAEKAQQMYAATKGLRWYRlsdegewlvrelnlpvDRTeggwis 1021
Cdd:smart00482   68 LRRAAKAINFGIIYGMG---AKGLAEQLG--ISEAEAKELIKKYFARFPGVRRYI----------------DRT------ 120

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277   1022 lqdlrkvqretarksqwkkwevvAERAWKGGTESEMFNKLESIATSDiPRTPVLGCCISRAlepsavqeefmtsRVNWVV 1101
Cdd:smart00482  121 -----------------------LEEARRKGYVTTLFGRRRYIPDID-SRNPVLRAAAERA-------------AVNTPI 163

                           250       260       270       280
                    ....*....|....*....|....*....|....*....|....
gi 187171277   1102 QSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREED 1145
Cdd:smart00482  164 QGSAADILKLAMIKMDEALKEFGLRARLLLQVHDELVFEVPEEE 207
DNA_pol_A pfam00476
DNA polymerase family A;
871-1177 2.72e-17

DNA polymerase family A;


Pssm-ID: 459825  Cd Length: 368  Bit Score: 85.18  E-value: 2.72e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277   871 GSELKAMVQAPPGYTLVGADVDSQELWIAAVL-GDAHFagmhgCTAFgwmtlqgrkSRGTDLHSKTATTV-GIS------ 942
Cdd:pfam00476  126 GRRIRKAFVAEPGWVLLSADYSQIELRILAHLsGDENL-----IEAF---------RNGEDIHTATASEVfGVPleevtp 191

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277   943 --REHAKIFNYGRIYGAGqPF--AERLlmqfnhRLTQQEAAEKAQQMYAATKGLRwyrlsdegEWLvrelnlpvDRTegg 1018
Cdd:pfam00476  192 eqRRRAKAINFGIIYGMS-AFglAQQL------GISRKEAKEYIDRYFERYPGVK--------EYM--------EET--- 245

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  1019 wislqdlrkvqRETARKsqwkkwevvaerawKGGTESeMFNK---LESIATSDiprtpvlgccisralepSAVQEEFMTS 1095
Cdd:pfam00476  246 -----------VEEARE--------------KGYVET-LLGRrryLPDINSSN-----------------RNLRSFAERA 282

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  1096 RVNWVVQSSAVDYLHLMLVAM-KWLFEEFaIDGRFCISIHDEVRYLVREEDRYRAAlalqitNLLTRCM-FAYKLGLnDL 1173
Cdd:pfam00476  283 AINAPIQGSAADIIKLAMIRVdEALKEEG-LKARLLLQVHDELVFEVPEEEVEEVA------ALVKEEMeNENAVKL-SV 354


                   ....
gi 187171277  1174 PQSV 1177
Cdd:pfam00476  355 PLKV 358
DNA_pol_gammaA cd08641
Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in ...
 431-473 1.71e-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: 1.71e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 187171277  431 GVSYLPVNQNWERYLAEAQGTYEELQREMKKSLMDLANDACQL 473
Cdd:cd08641     1 GSAYLPVNSNWERYLNTAEETYQELQQEVKESLMQLAEDACQL 43
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 873-1012 2.13e-06

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


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 51.91  E-value: 2.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  873 ELKAMVQAPPGYTLVGADVDSQELWIAAVL-GDAHFAgmhgcTAFGwmtlqgrksRGTDLHSKTATTV-------GISRE 944
Cdd:PRK14975  314 DIRSAFVADPGWKLVVADASQIELRVLAAYsGDERMI-----EAFR---------TGGDLHRLTASVGfgkpeeeKEERA 379

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  945 HAKIFNYGRIYGAGQPF----------AERLLMQFN------HRLTQQEAAEKAQQMYAAT--------KGLRWYRLSDE 1000
Cdd:PRK14975  380 LAKAANFGAIYGATSKGlqeyaknygeAARLLERLRraypraVGWVERAAREGERGGVVRTllgrtsppPGFAWRARRRA 459

                         170
                  ....*....|..
gi 187171277 1001 GEWLVRELNLPV 1012
Cdd:PRK14975  460 RSRGRFTRNFPV 471
PolA COG0749
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ...
 880-980 1.75e-04

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


Pssm-ID: 440512 [Multi-domain]  Cd Length: 575  Bit Score: 45.81  E-value: 1.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  880 APPGYTLVGADVdSQ-ELWIAAvlgdaHFAG---MhgCTAFgwmtlqgrkSRGTDLHSKTATTV-GIS--------REHA 946
Cdd:COG0749   342 APEGYVLLSADY-SQiELRILA-----HLSGdegL--IEAF---------REGEDIHAATAAEVfGVPleevtseqRRRA 404

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 187171277  947 KIFNYGRIYGAGqPF--AERLlmqfnhRLTQQEAAE 980
Cdd:COG0749   405 KAINFGIIYGMS-AFglARQL------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 ...
 785-1203 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: 781.50  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  785 GASGPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRAVIRHPDYDEEGLYGAILPQVVTAGTITRRAVEPTWLTASN 864
Cdd:cd08641    44 DPQAKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSRHPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASN 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  865 ARPDRVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTATTVGISRE 944
Cdd:cd08641   124 AKKNRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRD 203

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  945 HAKIFNYGRIYGAGQPFAERLLMQFNHRLTQQEAAEKAQQMYAATKGLRWyrlsdegewlvrelnlpvdrteggwislqd 1024
Cdd:cd08641   204 HAKVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIRI------------------------------ 253

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277 1025 lrkvqretARKSQWKKWEVVAERAWKGGTESEMFNKLESIATSDIPRTPVLGCCISRAL-EPSAVQEEFMTSRVNWVVQS 1103
Cdd:cd08641   254 --------AIQRSTKGKRLFKRPFWSGGSESIMFNKLEEIAAQSQPRTPVLGACITSALlEPNLVKNEFMTSRINWVVQS 325

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277 1104 SAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAV 1183
Cdd:cd08641   326 SAVDYLHLMLVSMRWLIEKYDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTRAMFAQKLGINDLPQSVAFFSAV 405

                         410       420
                  ....*....|....*....|
gi 187171277 1184 DIDRCLRKEVTMDCKTPSNP 1203
Cdd:cd08641   406 DIDTVLRKEVDMDCVTPSNP 425
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 121-414 1.67e-142

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: 432.46  E-value: 1.67e-142
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277   121 PDVELRLPPLYGDNLDQHFRLLAQKQSLPYLEAANLLLQAQLPPKPPAWAWAEGWTRYGPEGEAVPVAIPEERALVFDVE 200
Cdd:pfam18136    1 PDIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASADLPPKPKKWAFKPGWTRYDPDGSPESVDYPLEDALVFDVE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277   201 VCLAEGTCPTLAVAISPSAWYSWCSQRLVEERYSWTsQLSPADLIPLEVPTgassptqrdwQEQLVVGHNVSFDRAHIRE 280
Cdd:pfam18136   81 VCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT-DLTPKHLIPMGSPN----------KPRLIVGHNVSYDRARIKE 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277   281 QYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWIAAKQGKHKVQPPTKQGQKSQRKARRGPAISSWDWLDISSVNSLAEVH 360
Cdd:pfam18136  150 EYNLEGTKTRFLDTMSLHIAVSGLTSRQRPLWMKYRKGKKKSDNSLAEHDELLEKKLSSSAVEDDDWVDVSSLNSLADVA 229

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 187171277   361 RLYVGGpPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDVWATHEVFQQQLPLF 414
Cdd:pfam18136  230 KLYCGI-ELDKELRDLFVKGTLEDIRDNFQDLMTYCARDVEATHEVFQKLFPLF 282
DNA_pol_A cd06444
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ...
 784-1190 5.75e-86

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: 283.54  E-value: 5.75e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  784 GGASGPRALEINKMISFWRNAHKRISSQMVvwlprsalpravirhpdydeegLYGAILPQVVTAGTITRRAVEPTWLTAS 863
Cdd:cd06444    25 AHPAVPLLLEYKKLAKLWSANGWPWLDQWV----------------------RDGRFHPEYVPGGTVTGRWASRGGNAQQ 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  864 NARPDRVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAHFAGMHgctafgwmtlQGRKSRGTDLHSKTATTV---G 940
Cdd:cd06444    83 IPRRDPLGRDIRQAFVADPGWTLVVADASQLELRVLAALSGDEALAEA----------FGRGGDLYTATASAMFGVpvgG 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  941 ISREHAKIFNYGRIYGAGQPFAERLLMQFNHRLTQQEAAEkaqqmyaatKGLRWYRLSDEGEWLVRELNLPVDRTEGG-- 1018
Cdd:cd06444   153 GERQHAKIANLGAMYGATSGISARLLAQLRRISTKEAAAL---------IELFFSRFPAFPKAMEYVEDAARRGERGGyv 223

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277 1019 --WISLQDLRKVQRETARKSQwkkwevvaerawkggtesemfnklesiatsdiprtpvlgccISRALEPSAVQEEFMTSR 1096
Cdd:cd06444   224 rtLLGRRSPPPDIRWTEVVSD-----------------------------------------PAAASRARRVRRAAGRFA 262

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277 1097 VNWVVQSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMfayklglndLPQS 1176
Cdd:cd06444   263 RNFVVQGTAADWAKLAMVALRRRLEELALDARLVFFVHDEVVLHCPKEEAEAVAAIVREAAEQAVRL---------LFGS 333

                         410
                  ....*....|....
gi 187171277 1177 VAFFSAVDIDRCLR 1190
Cdd:cd06444   334 VPVRFPVKIGVVWR 347
POLAc smart00482
DNA polymerase A domain;
871-1145 2.39e-65

DNA polymerase A domain;


Pssm-ID: 214687  Cd Length: 207  Bit Score: 219.80  E-value: 2.39e-65
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277    871 GSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAhfagmhgctafgwMTLQGRKSRGTDLHSKTATTV---------GI 941
Cdd:smart00482    1 GREIRRAFIAPPGYVLVSADYSQIELRILAHLSGD-------------ENLIEAFNNGGDIHTKTAAQVfgvpeeevtPE 67

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277    942 SREHAKIFNYGRIYGAGqpfAERLLMQFNhrLTQQEAAEKAQQMYAATKGLRWYRlsdegewlvrelnlpvDRTeggwis 1021
Cdd:smart00482   68 LRRAAKAINFGIIYGMG---AKGLAEQLG--ISEAEAKELIKKYFARFPGVRRYI----------------DRT------ 120

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277   1022 lqdlrkvqretarksqwkkwevvAERAWKGGTESEMFNKLESIATSDiPRTPVLGCCISRAlepsavqeefmtsRVNWVV 1101
Cdd:smart00482  121 -----------------------LEEARRKGYVTTLFGRRRYIPDID-SRNPVLRAAAERA-------------AVNTPI 163

                           250       260       270       280
                    ....*....|....*....|....*....|....*....|....
gi 187171277   1102 QSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREED 1145
Cdd:smart00482  164 QGSAADILKLAMIKMDEALKEFGLRARLLLQVHDELVFEVPEEE 207
DNA_pol_A pfam00476
DNA polymerase family A;
871-1177 2.72e-17

DNA polymerase family A;


Pssm-ID: 459825  Cd Length: 368  Bit Score: 85.18  E-value: 2.72e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277   871 GSELKAMVQAPPGYTLVGADVDSQELWIAAVL-GDAHFagmhgCTAFgwmtlqgrkSRGTDLHSKTATTV-GIS------ 942
Cdd:pfam00476  126 GRRIRKAFVAEPGWVLLSADYSQIELRILAHLsGDENL-----IEAF---------RNGEDIHTATASEVfGVPleevtp 191

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277   943 --REHAKIFNYGRIYGAGqPF--AERLlmqfnhRLTQQEAAEKAQQMYAATKGLRwyrlsdegEWLvrelnlpvDRTegg 1018
Cdd:pfam00476  192 eqRRRAKAINFGIIYGMS-AFglAQQL------GISRKEAKEYIDRYFERYPGVK--------EYM--------EET--- 245

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  1019 wislqdlrkvqRETARKsqwkkwevvaerawKGGTESeMFNK---LESIATSDiprtpvlgccisralepSAVQEEFMTS 1095
Cdd:pfam00476  246 -----------VEEARE--------------KGYVET-LLGRrryLPDINSSN-----------------RNLRSFAERA 282

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  1096 RVNWVVQSSAVDYLHLMLVAM-KWLFEEFaIDGRFCISIHDEVRYLVREEDRYRAAlalqitNLLTRCM-FAYKLGLnDL 1173
Cdd:pfam00476  283 AINAPIQGSAADIIKLAMIRVdEALKEEG-LKARLLLQVHDELVFEVPEEEVEEVA------ALVKEEMeNENAVKL-SV 354


                   ....
gi 187171277  1174 PQSV 1177
Cdd:pfam00476  355 PLKV 358
DNA_pol_gammaA cd08641
Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in ...
 431-473 1.71e-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: 1.71e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 187171277  431 GVSYLPVNQNWERYLAEAQGTYEELQREMKKSLMDLANDACQL 473
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; ...
 872-1008 4.28e-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: 53.44  E-value: 4.28e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  872 SELKAMVQAPPGYTLVGADVDSQELWIAA-VLGDAHFAgmhgcTAFgwmtlqgrkSRGTDLHSKTATTV-GIS------- 942
Cdd:cd08639    91 REFRRCFVAPEGNKLIIADYSQIELRIAAeISGDERMI-----SAY---------QKGEDLHRLTASLItGKPieeitke 156

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 187171277  943 -REHAKIFNYGRIYGAGqpfAERLLMQ----FNHRLTQQEAAEKAQQMYAATKG-LRWY-RLSDEGEWLVREL 1008
Cdd:cd08639   157 eRQLAKAVNFGLIYGMS---AKGLREYartnYGVEMSLEEAEKFRESFFFFYKGiLRWHhRLKAKGPIEVRTL 226
DNA_pol_A_pol_I_B cd08643
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ...
 844-960 1.76e-06

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: 52.05  E-value: 1.76e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  844 VVTAGTITRRAvepTWLTASNARPDRVGS----ELKAMVQAPPGYTLVGADVDSQELwiaAVLgdAHFAGMHGCTAFgwm 919
Cdd:cd08643   146 VNTNGAVTGRA---THFSPNMAQVPAVGSpygkECRELFGVPPGWSLVGADASGLEL---RCL--AHYLARYDGGAY--- 214

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 187171277  920 tlqGRKSRGTDLHSKTATTVGI-SREHAKIFNYGRIYGAGQP 960
Cdd:cd08643   215 ---TRKVLGGDIHWANAQAMGLlSRDGAKTFIYAFLYGAGDE 253
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 873-1012 2.13e-06

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


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 51.91  E-value: 2.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  873 ELKAMVQAPPGYTLVGADVDSQELWIAAVL-GDAHFAgmhgcTAFGwmtlqgrksRGTDLHSKTATTV-------GISRE 944
Cdd:PRK14975  314 DIRSAFVADPGWKLVVADASQIELRVLAAYsGDERMI-----EAFR---------TGGDLHRLTASVGfgkpeeeKEERA 379

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  945 HAKIFNYGRIYGAGQPF----------AERLLMQFN------HRLTQQEAAEKAQQMYAAT--------KGLRWYRLSDE 1000
Cdd:PRK14975  380 LAKAANFGAIYGATSKGlqeyaknygeAARLLERLRraypraVGWVERAAREGERGGVVRTllgrtsppPGFAWRARRRA 459

                         170
                  ....*....|..
gi 187171277 1001 GEWLVRELNLPV 1012
Cdd:PRK14975  460 RSRGRFTRNFPV 471
DNA_pol_A_pol_I_C cd08637
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ...
 871-980 2.11e-05

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: 48.19  E-value: 2.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  871 GSELKAMVQAPPGYTLVGADVdSQ-ELWIAAvlgdaHFAG---MhgCTAFgwmtlqgrkSRGTDLHSKTATTV-GIS--- 942
Cdd:cd08637   138 GREIRKAFVAEEGWVLLSADY-SQiELRILA-----HLSGdeaL--IEAF---------KNGEDIHTRTAAEVfGVPpee 200

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 187171277  943 -----REHAKIFNYGRIYGAGqPF--AERLlmqfnhRLTQQEAAE 980
Cdd:cd08637   201 vtpemRRIAKAVNFGIIYGIS-AFglSQQL------GISRKEAKE 238
PolA COG0749
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ...
 880-980 1.75e-04

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


Pssm-ID: 440512 [Multi-domain]  Cd Length: 575  Bit Score: 45.81  E-value: 1.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  880 APPGYTLVGADVdSQ-ELWIAAvlgdaHFAG---MhgCTAFgwmtlqgrkSRGTDLHSKTATTV-GIS--------REHA 946
Cdd:COG0749   342 APEGYVLLSADY-SQiELRILA-----HLSGdegL--IEAF---------REGEDIHAATAAEVfGVPleevtseqRRRA 404

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 187171277  947 KIFNYGRIYGAGqPF--AERLlmqfnhRLTQQEAAE 980
Cdd:COG0749   405 KAINFGIIYGMS-AFglARQL------GISRKEAKE 433
PRK05755 PRK05755
DNA polymerase I; Provisional
 875-980 1.15e-03

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 43.16  E-value: 1.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187171277  875 KAMVqAPPGYTLVGADVdSQ-ELWIAavlgdAHFAGMHG-CTAFgwmtlqgrkSRGTDLHSKTATTV-GISRE------- 944
Cdd:PRK05755  643 KAFV-APEGYKLLSADY-SQiELRIL-----AHLSGDEGlIEAF---------AEGEDIHTATASEVfGVPLEevtseqr 706

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 187171277  945 -HAKIFNYGRIYGAGqPF--AERLlmqfnhRLTQQEAAE 980
Cdd:PRK05755  707 rRAKAINFGIIYGMS-AFglAQQL------GISRKEAKE 738
 
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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