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Conserved domains on  [gi|159146215|gb|ABW90571|]
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DNA polymerase, partial [Bacteriophage APSE-2]

Protein Classification

DNA polymerase family A protein( domain architecture ID 2074)

DNA polymerase A family protein functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication

EC:  2.7.7.7
Gene Ontology:  GO:0003887|GO:0006260|GO:0003677

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_pol_A super family cl02626
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ...
 24-360 3.73e-64

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 cd08642:

Pssm-ID: 470638 [Multi-domain]  Cd Length: 378  Bit Score: 208.63  E-value: 3.73e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215  24 LAKSALTAVENEQKRLSTVTQQLTdnAVQNATQRDALLQHIASAFGITLPDMQASTLQrrINDPDIPPALRELLSVRLQS 103
Cdd:cd08642    1 LVNAAIACDDQYKEELLEEAKELT--GLDNPNSPAQLKDWLNEQGGEVDSLLKKDVVA--LLLKTAPGDVKRVLELRQEL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 104 CTTSTSKYKALLKSVSADGRLRGTKQFCGASRTGRWAGRVFQPDNLPRPTLDpnTIDNGIEALKAGCA---ELICDDIMQ 180
Cdd:cd08642   77 SKTSVKKYEAMERAVCSDGRVRGLLQFYGANRTGRWAGRLVQVQNLPRNYLK--DLDLARELVKSGDFdalELLYGSVPD 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 181 LTSSALRGCIIAPPGKKLVISDLSNIEGRMLAWLAGENWKVNAFSefdngKGDDLYKLAYARAFNLLPEDVTKDQ--RQI 258
Cdd:cd08642  155 VLSQLIRTAFIPSEGHRFIVSDFSAIEARVIAWLAGEQWRLDVFA-----THGKIYEASASQMFGVPVEKIGKNShlRQK 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 259 GKVMELGLGYGGGVAAFLTF-ALAYGLDLDELAeaalpnippgvkreamrwyqksvetdktyglsekifvtcdSLKRMWR 337
Cdd:cd08642  230 GKVAELALGYGGSVGALKAMgALEMGLTEDELP----------------------------------------GIVDAWR 269

                        330       340
                 ....*....|....*....|...
gi 159146215 338 NAHPQTVSFWYDIEDAVKQAIQS 360
Cdd:cd08642  270 NANPNIVKLWWDVDKAAKKAVKE 292
 
Name Accession Description Interval E-value
DNA_pol_A_pol_I_A cd08642
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ...
 24-360 3.73e-64

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 ,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: 176479 [Multi-domain]  Cd Length: 378  Bit Score: 208.63  E-value: 3.73e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215  24 LAKSALTAVENEQKRLSTVTQQLTdnAVQNATQRDALLQHIASAFGITLPDMQASTLQrrINDPDIPPALRELLSVRLQS 103
Cdd:cd08642    1 LVNAAIACDDQYKEELLEEAKELT--GLDNPNSPAQLKDWLNEQGGEVDSLLKKDVVA--LLLKTAPGDVKRVLELRQEL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 104 CTTSTSKYKALLKSVSADGRLRGTKQFCGASRTGRWAGRVFQPDNLPRPTLDpnTIDNGIEALKAGCA---ELICDDIMQ 180
Cdd:cd08642   77 SKTSVKKYEAMERAVCSDGRVRGLLQFYGANRTGRWAGRLVQVQNLPRNYLK--DLDLARELVKSGDFdalELLYGSVPD 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 181 LTSSALRGCIIAPPGKKLVISDLSNIEGRMLAWLAGENWKVNAFSefdngKGDDLYKLAYARAFNLLPEDVTKDQ--RQI 258
Cdd:cd08642  155 VLSQLIRTAFIPSEGHRFIVSDFSAIEARVIAWLAGEQWRLDVFA-----THGKIYEASASQMFGVPVEKIGKNShlRQK 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 259 GKVMELGLGYGGGVAAFLTF-ALAYGLDLDELAeaalpnippgvkreamrwyqksvetdktyglsekifvtcdSLKRMWR 337
Cdd:cd08642  230 GKVAELALGYGGSVGALKAMgALEMGLTEDELP----------------------------------------GIVDAWR 269

                        330       340
                 ....*....|....*....|...
gi 159146215 338 NAHPQTVSFWYDIEDAVKQAIQS 360
Cdd:cd08642  270 NANPNIVKLWWDVDKAAKKAVKE 292
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 12-311 5.36e-21

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


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 94.28  E-value: 5.36e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215  12 KINRRGMCMDVELAKSALTAVENEQKRLSTVTQQLTDNAVQnatQRDALLQHIASAF------------GITLPDMQAST 79
Cdd:PRK14975 172 EMELAGLPWDTDVHEALLAELLGPRPAAGGRPARLAELAAE---IREALGRPRLNPDspqqvlralrraGIELPSTRKWE 248

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215  80 LqRRINDPDIPPAL--RELlsVRLQScttstsKYK-ALLKSVSADGRLRGTKQFCGASrTGRWAGRvfQPD--NLPRPtl 154
Cdd:PRK14975 249 L-REIDHPAVEPLLeyRKL--SKLLS------ANGwAWLDYWVRDGRFHPEYVPGGVV-TGRWASR--GPNaqQIPRD-- 314

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 155 dpntidngiealkagcaelicddimqltssaLRGCIIAPPGKKLVISDLSNIEGRMLAWLAGENWKVNAFsefdnGKGDD 234
Cdd:PRK14975 315 -------------------------------IRSAFVADPGWKLVVADASQIELRVLAAYSGDERMIEAF-----RTGGD 358

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 159146215 235 LYKLAYARAFNLLPEDvtKDQRQIGKVMELGLGYGGGVAAFLTFALAYGldldElAEAALPNIPPGVKReAMRWYQK 311
Cdd:PRK14975 359 LHRLTASVGFGKPEEE--KEERALAKAANFGAIYGATSKGLQEYAKNYG----E-AARLLERLRRAYPR-AVGWVER 427
POLAc smart00482
DNA polymerase A domain;
183-326 4.75e-19

DNA polymerase A domain;


Pssm-ID: 214687  Cd Length: 207  Bit Score: 84.21  E-value: 4.75e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215   183 SSALRGCIIAPPGKKLVISDLSNIEGRMLAWLAGENWKVNAFSEfdngkGDDLYKLAYARAFNLLPEDVTKDQRQIGKVM 262
Cdd:smart00482   1 GREIRRAFIAPPGYVLVSADYSQIELRILAHLSGDENLIEAFNN-----GGDIHTKTAAQVFGVPEEEVTPELRRAAKAI 75

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 159146215   263 ELGLGYGGGvaafltfalAYGL---------DLDELAEAALPNIpPGVKreamRWYQKSVETDKTYGLSEKIF 326
Cdd:smart00482  76 NFGIIYGMG---------AKGLaeqlgiseaEAKELIKKYFARF-PGVR----RYIDRTLEEARRKGYVTTLF 134
DNA_pol_A pfam00476
DNA polymerase family A;
186-281 3.84e-12

DNA polymerase family A;


Pssm-ID: 459825  Cd Length: 368  Bit Score: 66.69  E-value: 3.84e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215  186 LRGCIIAPPGKKLVISDLSNIEGRMLAWLAGENWKVNAFSEfdngkGDDLYKLAYARAFNLLPEDVTKDQRQIGKVMELG 265
Cdd:pfam00476 129 IRKAFVAEPGWVLLSADYSQIELRILAHLSGDENLIEAFRN-----GEDIHTATASEVFGVPLEEVTPEQRRRAKAINFG 203

                          90
                  ....*....|....*.
gi 159146215  266 LGYGGGVaafltFALA 281
Cdd:pfam00476 204 IIYGMSA-----FGLA 214
PolA COG0749
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ...
 187-269 3.08e-08

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


Pssm-ID: 440512 [Multi-domain]  Cd Length: 575  Bit Score: 55.44  E-value: 3.08e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 187 RGCIIAPPGKKLVISDLSNIEGRMLAWLAGENWKVNAFSEfdngkGDDLYKLAYARAFNLLPEDVTKDQRQIGKVMELGL 266
Cdd:COG0749  337 RKAFVAPEGYVLLSADYSQIELRILAHLSGDEGLIEAFRE-----GEDIHAATAAEVFGVPLEEVTSEQRRRAKAINFGI 411


                 ...
gi 159146215 267 GYG 269
Cdd:COG0749  412 IYG 414
 
Name Accession Description Interval E-value
DNA_pol_A_pol_I_A cd08642
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ...
 24-360 3.73e-64

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 ,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: 176479 [Multi-domain]  Cd Length: 378  Bit Score: 208.63  E-value: 3.73e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215  24 LAKSALTAVENEQKRLSTVTQQLTdnAVQNATQRDALLQHIASAFGITLPDMQASTLQrrINDPDIPPALRELLSVRLQS 103
Cdd:cd08642    1 LVNAAIACDDQYKEELLEEAKELT--GLDNPNSPAQLKDWLNEQGGEVDSLLKKDVVA--LLLKTAPGDVKRVLELRQEL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 104 CTTSTSKYKALLKSVSADGRLRGTKQFCGASRTGRWAGRVFQPDNLPRPTLDpnTIDNGIEALKAGCA---ELICDDIMQ 180
Cdd:cd08642   77 SKTSVKKYEAMERAVCSDGRVRGLLQFYGANRTGRWAGRLVQVQNLPRNYLK--DLDLARELVKSGDFdalELLYGSVPD 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 181 LTSSALRGCIIAPPGKKLVISDLSNIEGRMLAWLAGENWKVNAFSefdngKGDDLYKLAYARAFNLLPEDVTKDQ--RQI 258
Cdd:cd08642  155 VLSQLIRTAFIPSEGHRFIVSDFSAIEARVIAWLAGEQWRLDVFA-----THGKIYEASASQMFGVPVEKIGKNShlRQK 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 259 GKVMELGLGYGGGVAAFLTF-ALAYGLDLDELAeaalpnippgvkreamrwyqksvetdktyglsekifvtcdSLKRMWR 337
Cdd:cd08642  230 GKVAELALGYGGSVGALKAMgALEMGLTEDELP----------------------------------------GIVDAWR 269

                        330       340
                 ....*....|....*....|...
gi 159146215 338 NAHPQTVSFWYDIEDAVKQAIQS 360
Cdd:cd08642  270 NANPNIVKLWWDVDKAAKKAVKE 292
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 12-311 5.36e-21

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


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 94.28  E-value: 5.36e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215  12 KINRRGMCMDVELAKSALTAVENEQKRLSTVTQQLTDNAVQnatQRDALLQHIASAF------------GITLPDMQAST 79
Cdd:PRK14975 172 EMELAGLPWDTDVHEALLAELLGPRPAAGGRPARLAELAAE---IREALGRPRLNPDspqqvlralrraGIELPSTRKWE 248

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215  80 LqRRINDPDIPPAL--RELlsVRLQScttstsKYK-ALLKSVSADGRLRGTKQFCGASrTGRWAGRvfQPD--NLPRPtl 154
Cdd:PRK14975 249 L-REIDHPAVEPLLeyRKL--SKLLS------ANGwAWLDYWVRDGRFHPEYVPGGVV-TGRWASR--GPNaqQIPRD-- 314

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 155 dpntidngiealkagcaelicddimqltssaLRGCIIAPPGKKLVISDLSNIEGRMLAWLAGENWKVNAFsefdnGKGDD 234
Cdd:PRK14975 315 -------------------------------IRSAFVADPGWKLVVADASQIELRVLAAYSGDERMIEAF-----RTGGD 358

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 159146215 235 LYKLAYARAFNLLPEDvtKDQRQIGKVMELGLGYGGGVAAFLTFALAYGldldElAEAALPNIPPGVKReAMRWYQK 311
Cdd:PRK14975 359 LHRLTASVGFGKPEEE--KEERALAKAANFGAIYGATSKGLQEYAKNYG----E-AARLLERLRRAYPR-AVGWVER 427
POLAc smart00482
DNA polymerase A domain;
183-326 4.75e-19

DNA polymerase A domain;


Pssm-ID: 214687  Cd Length: 207  Bit Score: 84.21  E-value: 4.75e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215   183 SSALRGCIIAPPGKKLVISDLSNIEGRMLAWLAGENWKVNAFSEfdngkGDDLYKLAYARAFNLLPEDVTKDQRQIGKVM 262
Cdd:smart00482   1 GREIRRAFIAPPGYVLVSADYSQIELRILAHLSGDENLIEAFNN-----GGDIHTKTAAQVFGVPEEEVTPELRRAAKAI 75

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 159146215   263 ELGLGYGGGvaafltfalAYGL---------DLDELAEAALPNIpPGVKreamRWYQKSVETDKTYGLSEKIF 326
Cdd:smart00482  76 NFGIIYGMG---------AKGLaeqlgiseaEAKELIKKYFARF-PGVR----RYIDRTLEEARRKGYVTTLF 134
DNA_pol_A_Aquificae_like cd08639
Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences; ...
 91-292 1.79e-17

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: 82.33  E-value: 1.79e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215  91 PALRELLSVRlqSCTTSTSKYKALLKS--VSADGRLRGTKQFCGAsRTGRwagrvFQPDNlprptldPNtidngiealka 168
Cdd:cd08639   30 PAVRLLLEYR--KLNKLISTFGEKLPKhiHPVTGRIHPSFNQIGA-ASGR-----MSCSN-------PN----------- 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 169 gcaelicddIMQL-TSSALRGCIIAPPGKKLVISDLSNIEGRMLAWLAGENWKVNAFSefdngKGDDLYKLAYARAFNLL 247
Cdd:cd08639   84 ---------LQQIpREREFRRCFVAPEGNKLIIADYSQIELRIAAEISGDERMISAYQ-----KGEDLHRLTASLITGKP 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 159146215 248 PEDVTKDQRQIGKVMELGLGYGGGVAAFLTFA-LAYGLDLdELAEA 292
Cdd:cd08639  150 IEEITKEERQLAKAVNFGLIYGMSAKGLREYArTNYGVEM-SLEEA 194
DNA_pol_A cd06444
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ...
 87-271 1.26e-15

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: 77.07  E-value: 1.26e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215  87 PDIPPALRELLSVRLQScttstsKY-KALLKSVSADGRLRGtkQFC-GASRTGRWAGRVFQPDNLPRPTLDpntidngie 164
Cdd:cd06444   27 PAVPLLLEYKKLAKLWS------ANgWPWLDQWVRDGRFHP--EYVpGGTVTGRWASRGGNAQQIPRRDPL--------- 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 165 alkagcaelicddimqltSSALRGCIIAPPGKKLVISDLSNIEGRMLAWLAGENWKVNAFsefdnGKGDDLYKLAYARAF 244
Cdd:cd06444   90 ------------------GRDIRQAFVADPGWTLVVADASQLELRVLAALSGDEALAEAF-----GRGGDLYTATASAMF 146

                        170       180
                 ....*....|....*....|....*..
gi 159146215 245 nllPEDVTKDQRQIGKVMELGLGYGGG 271
Cdd:cd06444  147 ---GVPVGGGERQHAKIANLGAMYGAT 170
DNA_pol_A pfam00476
DNA polymerase family A;
186-281 3.84e-12

DNA polymerase family A;


Pssm-ID: 459825  Cd Length: 368  Bit Score: 66.69  E-value: 3.84e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215  186 LRGCIIAPPGKKLVISDLSNIEGRMLAWLAGENWKVNAFSEfdngkGDDLYKLAYARAFNLLPEDVTKDQRQIGKVMELG 265
Cdd:pfam00476 129 IRKAFVAEPGWVLLSADYSQIELRILAHLSGDENLIEAFRN-----GEDIHTATASEVFGVPLEEVTPEQRRRAKAINFG 203

                          90
                  ....*....|....*.
gi 159146215  266 LGYGGGVaafltFALA 281
Cdd:pfam00476 204 IIYGMSA-----FGLA 214
DNA_pol_A_pol_I_C cd08637
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ...
 186-269 1.15e-09

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: 59.36  E-value: 1.15e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 186 LRGCIIAPPGKKLVISDLSNIEGRMLAWLAGENWKVNAFSEfdngkGDDLYKLAYARAFNLLPEDVTKDQRQIGKVMELG 265
Cdd:cd08637  141 IRKAFVAEEGWVLLSADYSQIELRILAHLSGDEALIEAFKN-----GEDIHTRTAAEVFGVPPEEVTPEMRRIAKAVNFG 215


                 ....
gi 159146215 266 LGYG 269
Cdd:cd08637  216 IIYG 219
PRK05755 PRK05755
DNA polymerase I; Provisional
 187-269 7.15e-09

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 57.41  E-value: 7.15e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 187 RGCIIAPPGKKLVISDLSNIEGRMLAWLAGENWKVNAFSEfdngkGDDLYKLAYARAFNLLPEDVTKDQRQIGKVMELGL 266
Cdd:PRK05755 642 RKAFVAPEGYKLLSADYSQIELRILAHLSGDEGLIEAFAE-----GEDIHTATASEVFGVPLEEVTSEQRRRAKAINFGI 716


                 ...
gi 159146215 267 GYG 269
Cdd:PRK05755 717 IYG 719
PolA COG0749
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ...
 187-269 3.08e-08

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


Pssm-ID: 440512 [Multi-domain]  Cd Length: 575  Bit Score: 55.44  E-value: 3.08e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 187 RGCIIAPPGKKLVISDLSNIEGRMLAWLAGENWKVNAFSEfdngkGDDLYKLAYARAFNLLPEDVTKDQRQIGKVMELGL 266
Cdd:COG0749  337 RKAFVAPEGYVLLSADYSQIELRILAHLSGDEGLIEAFRE-----GEDIHAATAAEVFGVPLEEVTSEQRRRAKAINFGI 411


                 ...
gi 159146215 267 GYG 269
Cdd:COG0749  412 IYG 414
DNA_pol_A_plastid_like cd08640
DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in ...
 186-325 6.69e-07

DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication; DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during 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). The three-dimensional structure of plastid DNA polymerase has substantial similarity to Pol I. The structure of Pol I 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: 176477  Cd Length: 371  Bit Score: 50.86  E-value: 6.69e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 186 LRGCIIAPPGKKLVISDLSNIEGRMLAWLAGENWKVNAFsefdNGKGD-------DLYKL---AYARAFNLLP------- 248
Cdd:cd08640  109 IRKAFIASPGNTLIVADYSQLELRLLAHMTRCKSMIEAF----NAGGDfhsrtasGMYPHvaeAVANGEVLLEwksegkp 184

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159146215 249 -----EDVTKDQRQIGKVMELGLGYGGgvAAFlTFALAYGLDLDElAEAALPNIPPGvKREAMRWYQKSVETDKTYGLSE 323
Cdd:cd08640  185 papllKDKFKSERRKAKVLNFSIAYGK--TAH-GLAKDWKVKLKE-AERTVDAWYSD-RPEVEQWQKKTKKEARERGYTR 259


                 ..
gi 159146215 324 KI 325
Cdd:cd08640  260 TL 261
 
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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