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Conserved domains on  [gi|966953351|ref|XP_014998464|]
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DNA polymerase subunit gamma-1 isoform X1 [Macaca mulatta]

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 ...
 774-1192 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: 779.58  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  774 GASGPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRAVIRHPDYDEEGLYGAILPQVVTAGTITRRAVEPTWLTASN 853
Cdd:cd08641    44 DPQAKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSRHPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASN 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  854 ARPDRVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTATTVGISRE 933
Cdd:cd08641   124 AKKNRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRD 203

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  934 HAKVFNYGRIYGAGQPFAERLLMQFNHRLTQQEAAEKAQQMYAITKGLRWyrlsdegewlvrelhlpvdrteggwislqd 1013
Cdd:cd08641   204 HAKVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIRI------------------------------ 253

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351 1014 lrKVQREaarkshRKKWEVIAERAWKGGTESEMFNKLESIATSDIPRTPVLG-CRISRALEPSAVQGEFMTSRVNWVVQS 1092
Cdd:cd08641   254 --AIQRS------TKGKRLFKRPFWSGGSESIMFNKLEEIAAQSQPRTPVLGaCITSALLEPNLVKNEFMTSRINWVVQS 325

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351 1093 SAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAV 1172
Cdd:cd08641   326 SAVDYLHLMLVSMRWLIEKYDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTRAMFAQKLGINDLPQSVAFFSAV 405

                         410       420
                  ....*....|....*....|
gi 966953351 1173 DIDRCLRKEVTMDCKTPSNP 1192
Cdd:cd08641   406 DIDTVLRKEVDMDCVTPSNP 425
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 111-403 1.68e-141

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: 429.76  E-value: 1.68e-141
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351   111 PDVELRLPPLYGDNLDQHFRLLAQKQSLPYLEAANSLLQAQLPPQPTGWAWAEGWTRYGPEGEAVPVAIPEERALVFDVE 190
Cdd:pfam18136    1 PDIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASADLPPKPKKWAFKPGWTRYDPDGSPESVDYPLEDALVFDVE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351   191 VCLAEGICPTLAVAISPSAWYSWCSRRLVEERYSWTsQLSPADLIPLEVPAgasptqrdwQEQLVVGHNVSFDRAHIREQ 270
Cdd:pfam18136   81 VCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT-DLTPKHLIPMGSPN---------KPRLIVGHNVSYDRARIKEE 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351   271 YLIQGSHMRFLDTMSMHMAISGLSSFQRSLWIAAKQGKHKVQGSTKQGQKSQRKARRGPAISSWDWLDISSVNSLAEVHR 350
Cdd:pfam18136  151 YNLEGTKTRFLDTMSLHIAVSGLTSRQRPLWMKYRKGKKKSDNSLAEHDELLEKKLSSSAVEDDDWVDVSSLNSLADVAK 230

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|...
gi 966953351   351 LYVGGpPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDVWATHEVFQQQLPLF 403
Cdd:pfam18136  231 LYCGI-ELDKELRDLFVKGTLEDIRDNFQDLMTYCARDVEATHEVFQKLFPLF 282
DNA_pol_A super family cl02626
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ...
 420-462 1.62e-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: 1.62e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 966953351  420 GVSYLPVNQNWERYLAEAQGTYEELQREMKKSLMDLANDACQL 462
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 ...
 774-1192 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: 779.58  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  774 GASGPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRAVIRHPDYDEEGLYGAILPQVVTAGTITRRAVEPTWLTASN 853
Cdd:cd08641    44 DPQAKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSRHPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASN 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  854 ARPDRVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTATTVGISRE 933
Cdd:cd08641   124 AKKNRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRD 203

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  934 HAKVFNYGRIYGAGQPFAERLLMQFNHRLTQQEAAEKAQQMYAITKGLRWyrlsdegewlvrelhlpvdrteggwislqd 1013
Cdd:cd08641   204 HAKVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIRI------------------------------ 253

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351 1014 lrKVQREaarkshRKKWEVIAERAWKGGTESEMFNKLESIATSDIPRTPVLG-CRISRALEPSAVQGEFMTSRVNWVVQS 1092
Cdd:cd08641   254 --AIQRS------TKGKRLFKRPFWSGGSESIMFNKLEEIAAQSQPRTPVLGaCITSALLEPNLVKNEFMTSRINWVVQS 325

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351 1093 SAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAV 1172
Cdd:cd08641   326 SAVDYLHLMLVSMRWLIEKYDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTRAMFAQKLGINDLPQSVAFFSAV 405

                         410       420
                  ....*....|....*....|
gi 966953351 1173 DIDRCLRKEVTMDCKTPSNP 1192
Cdd:cd08641   406 DIDTVLRKEVDMDCVTPSNP 425
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 111-403 1.68e-141

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: 429.76  E-value: 1.68e-141
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351   111 PDVELRLPPLYGDNLDQHFRLLAQKQSLPYLEAANSLLQAQLPPQPTGWAWAEGWTRYGPEGEAVPVAIPEERALVFDVE 190
Cdd:pfam18136    1 PDIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASADLPPKPKKWAFKPGWTRYDPDGSPESVDYPLEDALVFDVE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351   191 VCLAEGICPTLAVAISPSAWYSWCSRRLVEERYSWTsQLSPADLIPLEVPAgasptqrdwQEQLVVGHNVSFDRAHIREQ 270
Cdd:pfam18136   81 VCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT-DLTPKHLIPMGSPN---------KPRLIVGHNVSYDRARIKEE 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351   271 YLIQGSHMRFLDTMSMHMAISGLSSFQRSLWIAAKQGKHKVQGSTKQGQKSQRKARRGPAISSWDWLDISSVNSLAEVHR 350
Cdd:pfam18136  151 YNLEGTKTRFLDTMSLHIAVSGLTSRQRPLWMKYRKGKKKSDNSLAEHDELLEKKLSSSAVEDDDWVDVSSLNSLADVAK 230

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|...
gi 966953351   351 LYVGGpPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDVWATHEVFQQQLPLF 403
Cdd:pfam18136  231 LYCGI-ELDKELRDLFVKGTLEDIRDNFQDLMTYCARDVEATHEVFQKLFPLF 282
POLAc smart00482
DNA polymerase A domain;
860-1134 1.29e-65

DNA polymerase A domain;


Pssm-ID: 214687  Cd Length: 207  Bit Score: 220.57  E-value: 1.29e-65
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351    860 GSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAhfagmhgctafgwMTLQGRKSRGTDLHSKTATTV---------GI 930
Cdd:smart00482    1 GREIRRAFIAPPGYVLVSADYSQIELRILAHLSGD-------------ENLIEAFNNGGDIHTKTAAQVfgvpeeevtPE 67

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351    931 SREHAKVFNYGRIYGAGqpfAERLLMQFNhrLTQQEAAEKAQQMYAITKGLRWYRlsdegewlvrelhlpvDRTeggwis 1010
Cdd:smart00482   68 LRRAAKAINFGIIYGMG---AKGLAEQLG--ISEAEAKELIKKYFARFPGVRRYI----------------DRT------ 120

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351   1011 lqdlrkvqreaarkshrkkweviAERAWKGGTESEMFNKLESIATSDiPRTPVLGCRISRAlepsavqgefmtsRVNWVV 1090
Cdd:smart00482  121 -----------------------LEEARRKGYVTTLFGRRRYIPDID-SRNPVLRAAAERA-------------AVNTPI 163

                           250       260       270       280
                    ....*....|....*....|....*....|....*....|....
gi 966953351   1091 QSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREED 1134
Cdd:smart00482  164 QGSAADILKLAMIKMDEALKEFGLRARLLLQVHDELVFEVPEEE 207
DNA_pol_A pfam00476
DNA polymerase family A;
860-1166 7.61e-17

DNA polymerase family A;


Pssm-ID: 459825  Cd Length: 368  Bit Score: 83.64  E-value: 7.61e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351   860 GSELKAMVQAPPGYTLVGADVDSQELWIAAVL-GDAHFagmhgCTAFgwmtlqgrkSRGTDLHSKTATTV-GIS------ 931
Cdd:pfam00476  126 GRRIRKAFVAEPGWVLLSADYSQIELRILAHLsGDENL-----IEAF---------RNGEDIHTATASEVfGVPleevtp 191

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351   932 --REHAKVFNYGRIYGAGqPF--AERLlmqfnhRLTQQEAAEKAQQMYAITKGLRwyrlsdegEWLvrelhlpvDRTegg 1007
Cdd:pfam00476  192 eqRRRAKAINFGIIYGMS-AFglAQQL------GISRKEAKEYIDRYFERYPGVK--------EYM--------EET--- 245

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  1008 wislqdlrkvqREAARKshrkkweviaerawKGGTESeMFNK---LESIATSDiprtpvlgcRISRAlepsavQGEfmTS 1084
Cdd:pfam00476  246 -----------VEEARE--------------KGYVET-LLGRrryLPDINSSN---------RNLRS------FAE--RA 282

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  1085 RVNWVVQSSAVDYLHLMLVAM-KWLFEEFaIDGRFCISIHDEVRYLVREEDRYRAAlalqitNLLTRCM-FAYKLGLnDL 1162
Cdd:pfam00476  283 AINAPIQGSAADIIKLAMIRVdEALKEEG-LKARLLLQVHDELVFEVPEEEVEEVA------ALVKEEMeNENAVKL-SV 354


                   ....
gi 966953351  1163 PQSV 1166
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 ...
 420-462 1.62e-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: 1.62e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 966953351  420 GVSYLPVNQNWERYLAEAQGTYEELQREMKKSLMDLANDACQL 462
Cdd:cd08641     1 GSAYLPVNSNWERYLNTAEETYQELQQEVKESLMQLAEDACQL 43
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 862-947 2.46e-06

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


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 51.53  E-value: 2.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  862 ELKAMVQAPPGYTLVGADVDSQELWIAAVL-GDAHFAgmhgcTAFGwmtlqgrksRGTDLHSKTATTV-------GISRE 933
Cdd:PRK14975  314 DIRSAFVADPGWKLVVADASQIELRVLAAYsGDERMI-----EAFR---------TGGDLHRLTASVGfgkpeeeKEERA 379

                          90
                  ....*....|....
gi 966953351  934 HAKVFNYGRIYGAG 947
Cdd:PRK14975  380 LAKAANFGAIYGAT 393
PolA COG0749
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ...
 869-969 9.84e-05

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


Pssm-ID: 440512 [Multi-domain]  Cd Length: 575  Bit Score: 46.58  E-value: 9.84e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  869 APPGYTLVGADVdSQ-ELWIAAvlgdaHFAG---MhgCTAFgwmtlqgrkSRGTDLHSKTATTV-GIS--------REHA 935
Cdd:COG0749   342 APEGYVLLSADY-SQiELRILA-----HLSGdegL--IEAF---------REGEDIHAATAAEVfGVPleevtseqRRRA 404

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 966953351  936 KVFNYGRIYGAGqPF--AERLlmqfnhRLTQQEAAE 969
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 ...
 774-1192 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: 779.58  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  774 GASGPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRAVIRHPDYDEEGLYGAILPQVVTAGTITRRAVEPTWLTASN 853
Cdd:cd08641    44 DPQAKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSRHPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASN 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  854 ARPDRVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTATTVGISRE 933
Cdd:cd08641   124 AKKNRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRD 203

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  934 HAKVFNYGRIYGAGQPFAERLLMQFNHRLTQQEAAEKAQQMYAITKGLRWyrlsdegewlvrelhlpvdrteggwislqd 1013
Cdd:cd08641   204 HAKVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIRI------------------------------ 253

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351 1014 lrKVQREaarkshRKKWEVIAERAWKGGTESEMFNKLESIATSDIPRTPVLG-CRISRALEPSAVQGEFMTSRVNWVVQS 1092
Cdd:cd08641   254 --AIQRS------TKGKRLFKRPFWSGGSESIMFNKLEEIAAQSQPRTPVLGaCITSALLEPNLVKNEFMTSRINWVVQS 325

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351 1093 SAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAV 1172
Cdd:cd08641   326 SAVDYLHLMLVSMRWLIEKYDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTRAMFAQKLGINDLPQSVAFFSAV 405

                         410       420
                  ....*....|....*....|
gi 966953351 1173 DIDRCLRKEVTMDCKTPSNP 1192
Cdd:cd08641   406 DIDTVLRKEVDMDCVTPSNP 425
DNApol_Exo pfam18136
DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ...
 111-403 1.68e-141

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: 429.76  E-value: 1.68e-141
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351   111 PDVELRLPPLYGDNLDQHFRLLAQKQSLPYLEAANSLLQAQLPPQPTGWAWAEGWTRYGPEGEAVPVAIPEERALVFDVE 190
Cdd:pfam18136    1 PDIDFKLPPLQGSNIDEHFRRIGEEQAEPYLSLAEELASADLPPKPKKWAFKPGWTRYDPDGSPESVDYPLEDALVFDVE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351   191 VCLAEGICPTLAVAISPSAWYSWCSRRLVEERYSWTsQLSPADLIPLEVPAgasptqrdwQEQLVVGHNVSFDRAHIREQ 270
Cdd:pfam18136   81 VCVKDGPYPTMATAVSPTAWYSWVSPRLLGETDVPT-DLTPKHLIPMGSPN---------KPRLIVGHNVSYDRARIKEE 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351   271 YLIQGSHMRFLDTMSMHMAISGLSSFQRSLWIAAKQGKHKVQGSTKQGQKSQRKARRGPAISSWDWLDISSVNSLAEVHR 350
Cdd:pfam18136  151 YNLEGTKTRFLDTMSLHIAVSGLTSRQRPLWMKYRKGKKKSDNSLAEHDELLEKKLSSSAVEDDDWVDVSSLNSLADVAK 230

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|...
gi 966953351   351 LYVGGpPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDVWATHEVFQQQLPLF 403
Cdd:pfam18136  231 LYCGI-ELDKELRDLFVKGTLEDIRDNFQDLMTYCARDVEATHEVFQKLFPLF 282
DNA_pol_A cd06444
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ...
 773-1179 4.44e-84

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: 278.15  E-value: 4.44e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  773 GGASGPRALEINKMISFWRNAHKRISSQMVvwlprsalpravirhpdydeegLYGAILPQVVTAGTITRRAVEPTWLTAS 852
Cdd:cd06444    25 AHPAVPLLLEYKKLAKLWSANGWPWLDQWV----------------------RDGRFHPEYVPGGTVTGRWASRGGNAQQ 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  853 NARPDRVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAHFAGMHgctafgwmtlQGRKSRGTDLHSKTATTV---G 929
Cdd:cd06444    83 IPRRDPLGRDIRQAFVADPGWTLVVADASQLELRVLAALSGDEALAEA----------FGRGGDLYTATASAMFGVpvgG 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  930 ISREHAKVFNYGRIYGAGQPFAERLLMQFNHRLTQQEAAEkaqqmyaitKGLRWYRLSDEGEWLVRELHLPVDRTEGG-- 1007
Cdd:cd06444   153 GERQHAKIANLGAMYGATSGISARLLAQLRRISTKEAAAL---------IELFFSRFPAFPKAMEYVEDAARRGERGGyv 223

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351 1008 --WISLQDLRKVQREAARKShrkkweviaerawkggtesemfnklesiatsdiprtpvlgcRISRALEPSAVQGEFMTSR 1085
Cdd:cd06444   224 rtLLGRRSPPPDIRWTEVVS-----------------------------------------DPAAASRARRVRRAAGRFA 262

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351 1086 VNWVVQSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMfayklglndLPQS 1165
Cdd:cd06444   263 RNFVVQGTAADWAKLAMVALRRRLEELALDARLVFFVHDEVVLHCPKEEAEAVAAIVREAAEQAVRL---------LFGS 333

                         410
                  ....*....|....
gi 966953351 1166 VAFFSAVDIDRCLR 1179
Cdd:cd06444   334 VPVRFPVKIGVVWR 347
POLAc smart00482
DNA polymerase A domain;
860-1134 1.29e-65

DNA polymerase A domain;


Pssm-ID: 214687  Cd Length: 207  Bit Score: 220.57  E-value: 1.29e-65
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351    860 GSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAhfagmhgctafgwMTLQGRKSRGTDLHSKTATTV---------GI 930
Cdd:smart00482    1 GREIRRAFIAPPGYVLVSADYSQIELRILAHLSGD-------------ENLIEAFNNGGDIHTKTAAQVfgvpeeevtPE 67

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351    931 SREHAKVFNYGRIYGAGqpfAERLLMQFNhrLTQQEAAEKAQQMYAITKGLRWYRlsdegewlvrelhlpvDRTeggwis 1010
Cdd:smart00482   68 LRRAAKAINFGIIYGMG---AKGLAEQLG--ISEAEAKELIKKYFARFPGVRRYI----------------DRT------ 120

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351   1011 lqdlrkvqreaarkshrkkweviAERAWKGGTESEMFNKLESIATSDiPRTPVLGCRISRAlepsavqgefmtsRVNWVV 1090
Cdd:smart00482  121 -----------------------LEEARRKGYVTTLFGRRRYIPDID-SRNPVLRAAAERA-------------AVNTPI 163

                           250       260       270       280
                    ....*....|....*....|....*....|....*....|....
gi 966953351   1091 QSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREED 1134
Cdd:smart00482  164 QGSAADILKLAMIKMDEALKEFGLRARLLLQVHDELVFEVPEEE 207
DNA_pol_A pfam00476
DNA polymerase family A;
860-1166 7.61e-17

DNA polymerase family A;


Pssm-ID: 459825  Cd Length: 368  Bit Score: 83.64  E-value: 7.61e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351   860 GSELKAMVQAPPGYTLVGADVDSQELWIAAVL-GDAHFagmhgCTAFgwmtlqgrkSRGTDLHSKTATTV-GIS------ 931
Cdd:pfam00476  126 GRRIRKAFVAEPGWVLLSADYSQIELRILAHLsGDENL-----IEAF---------RNGEDIHTATASEVfGVPleevtp 191

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351   932 --REHAKVFNYGRIYGAGqPF--AERLlmqfnhRLTQQEAAEKAQQMYAITKGLRwyrlsdegEWLvrelhlpvDRTegg 1007
Cdd:pfam00476  192 eqRRRAKAINFGIIYGMS-AFglAQQL------GISRKEAKEYIDRYFERYPGVK--------EYM--------EET--- 245

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  1008 wislqdlrkvqREAARKshrkkweviaerawKGGTESeMFNK---LESIATSDiprtpvlgcRISRAlepsavQGEfmTS 1084
Cdd:pfam00476  246 -----------VEEARE--------------KGYVET-LLGRrryLPDINSSN---------RNLRS------FAE--RA 282

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  1085 RVNWVVQSSAVDYLHLMLVAM-KWLFEEFaIDGRFCISIHDEVRYLVREEDRYRAAlalqitNLLTRCM-FAYKLGLnDL 1162
Cdd:pfam00476  283 AINAPIQGSAADIIKLAMIRVdEALKEEG-LKARLLLQVHDELVFEVPEEEVEEVA------ALVKEEMeNENAVKL-SV 354


                   ....
gi 966953351  1163 PQSV 1166
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 ...
 420-462 1.62e-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: 1.62e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 966953351  420 GVSYLPVNQNWERYLAEAQGTYEELQREMKKSLMDLANDACQL 462
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; ...
 861-1163 2.60e-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: 54.21  E-value: 2.60e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  861 SELKAMVQAPPGYTLVGADVDSQELWIAA-VLGDAHFAgmhgcTAFgwmtlqgrkSRGTDLHSKTATTV-GIS------- 931
Cdd:cd08639    91 REFRRCFVAPEGNKLIIADYSQIELRIAAeISGDERMI-----SAY---------QKGEDLHRLTASLItGKPieeitke 156

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  932 -REHAKVFNYGRIYGAGqpfaerllmqfnhrltqqeaaekaqqmyaiTKGLRWYRLSDEGewlvrelhlpVDrteggwIS 1010
Cdd:cd08639   157 eRQLAKAVNFGLIYGMS------------------------------AKGLREYARTNYG----------VE------MS 190

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351 1011 LQDLRKVqREAARKshRKKWEviaERAWkggtesemfnklESIATSDIPRTPVLGCRISRALEPSavqgefMTSRVNWVV 1090
Cdd:cd08639   191 LEEAEKF-RESFFF--FYKGI---LRWH------------HRLKAKGPIEVRTLLGRRRVFEYFT------FTEALNYPI 246

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 966953351 1091 QSSAVDYLHLmlvAMKWLFEEFA-IDGRFCISIHDEVRYLVREEDRYRAAlalqitNLLTRCMF-AYKLGLNDLP 1163
Cdd:cd08639   247 QGTGADILKL---ALALLVDRLKdLDAKIVLCVHDEIVLEVPEDEAEEAK------KILESSMEeAGKRILKKVP 312
DNA_pol_A_pol_I_B cd08643
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ...
 833-949 9.65e-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: 9.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  833 VVTAGTITRRAvepTWLTASNARPDRVGS----ELKAMVQAPPGYTLVGADVDSQELwiaAVLgdAHFAGMHGCTAFgwm 908
Cdd:cd08643   146 VNTNGAVTGRA---THFSPNMAQVPAVGSpygkECRELFGVPPGWSLVGADASGLEL---RCL--AHYLARYDGGAY--- 214

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 966953351  909 tlqGRKSRGTDLHSKTATTVGI-SREHAKVFNYGRIYGAGQP 949
Cdd:cd08643   215 ---TRKVLGGDIHWANAQAMGLlSRDGAKTFIYAFLYGAGDE 253
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 862-947 2.46e-06

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


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 51.53  E-value: 2.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  862 ELKAMVQAPPGYTLVGADVDSQELWIAAVL-GDAHFAgmhgcTAFGwmtlqgrksRGTDLHSKTATTV-------GISRE 933
Cdd:PRK14975  314 DIRSAFVADPGWKLVVADASQIELRVLAAYsGDERMI-----EAFR---------TGGDLHRLTASVGfgkpeeeKEERA 379

                          90
                  ....*....|....
gi 966953351  934 HAKVFNYGRIYGAG 947
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 ...
 860-969 1.19e-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: 48.96  E-value: 1.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  860 GSELKAMVQAPPGYTLVGADVdSQ-ELWIAAvlgdaHFAG---MhgCTAFgwmtlqgrkSRGTDLHSKTATTV-GIS--- 931
Cdd:cd08637   138 GREIRKAFVAEEGWVLLSADY-SQiELRILA-----HLSGdeaL--IEAF---------KNGEDIHTRTAAEVfGVPpee 200

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 966953351  932 -----REHAKVFNYGRIYGAGqPF--AERLlmqfnhRLTQQEAAE 969
Cdd:cd08637   201 vtpemRRIAKAVNFGIIYGIS-AFglSQQL------GISRKEAKE 238
PolA COG0749
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ...
 869-969 9.84e-05

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


Pssm-ID: 440512 [Multi-domain]  Cd Length: 575  Bit Score: 46.58  E-value: 9.84e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  869 APPGYTLVGADVdSQ-ELWIAAvlgdaHFAG---MhgCTAFgwmtlqgrkSRGTDLHSKTATTV-GIS--------REHA 935
Cdd:COG0749   342 APEGYVLLSADY-SQiELRILA-----HLSGdegL--IEAF---------REGEDIHAATAAEVfGVPleevtseqRRRA 404

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 966953351  936 KVFNYGRIYGAGqPF--AERLlmqfnhRLTQQEAAE 969
Cdd:COG0749   405 KAINFGIIYGMS-AFglARQL------GISRKEAKE 433
PRK05755 PRK05755
DNA polymerase I; Provisional
 864-969 5.76e-04

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 44.31  E-value: 5.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966953351  864 KAMVqAPPGYTLVGADVdSQ-ELWIAAvlgdaHFAGMHG-CTAFgwmtlqgrkSRGTDLHSKTATTV-GISRE------- 933
Cdd:PRK05755  643 KAFV-APEGYKLLSADY-SQiELRILA-----HLSGDEGlIEAF---------AEGEDIHTATASEVfGVPLEevtseqr 706

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 966953351  934 -HAKVFNYGRIYGAGqPF--AERLlmqfnhRLTQQEAAE 969
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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