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Conserved domains on  [gi|460081495|gb|AGH06279|]
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DNA polymerase, partial [Synechococcus phage S-RIP2]

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 ...
 2-171 8.25e-55

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 cd08643:

Pssm-ID: 470638  Cd Length: 429  Bit Score: 178.78  E-value: 8.25e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495   2 DHDFRKLFMPTPGQIMVGADLAGIELRMLAHYLARYDQGRYADILLNGDIHQVNADKIGISRRDV-KTVTYAFLYGAGDA 80
Cdd:cd08643  174 GKECRELFGVPPGWSLVGADASGLELRCLAHYLARYDGGAYTRKVLGGDIHWANAQAMGLLSRDGaKTFIYAFLYGAGDE 253

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495  81 KIGH----SFDSSLN--------------DSAAKRKGKEIRSAFVDAIDGLAELLEAIKT-ASEKGFVRSVDGRKIHVDS 141
Cdd:cd08643  254 KLGQivgdDLRTAKNlnaewpqtkkgtikKIADKAKGRVVRANFLKGLPALGKLIKKVKEaAKKRGHLVGLDGRRIRVRS 333

                        170       180       190
                 ....*....|....*....|....*....|
gi 460081495 142 PHKSLNYLLQSGAGVLAKRWMVINHQNTQE 171
Cdd:cd08643  334 AHAALNTLLQSAGAILMKKWLVLLDDELTA 363
 
Name Accession Description Interval E-value
DNA_pol_A_pol_I_B cd08643
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ...
 2-171 8.25e-55

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: 178.78  E-value: 8.25e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495   2 DHDFRKLFMPTPGQIMVGADLAGIELRMLAHYLARYDQGRYADILLNGDIHQVNADKIGISRRDV-KTVTYAFLYGAGDA 80
Cdd:cd08643  174 GKECRELFGVPPGWSLVGADASGLELRCLAHYLARYDGGAYTRKVLGGDIHWANAQAMGLLSRDGaKTFIYAFLYGAGDE 253

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495  81 KIGH----SFDSSLN--------------DSAAKRKGKEIRSAFVDAIDGLAELLEAIKT-ASEKGFVRSVDGRKIHVDS 141
Cdd:cd08643  254 KLGQivgdDLRTAKNlnaewpqtkkgtikKIADKAKGRVVRANFLKGLPALGKLIKKVKEaAKKRGHLVGLDGRRIRVRS 333

                        170       180       190
                 ....*....|....*....|....*....|
gi 460081495 142 PHKSLNYLLQSGAGVLAKRWMVINHQNTQE 171
Cdd:cd08643  334 AHAALNTLLQSAGAILMKKWLVLLDDELTA 363
POLAc smart00482
DNA polymerase A domain;
6-163 3.67e-19

DNA polymerase A domain;


Pssm-ID: 214687  Cd Length: 207  Bit Score: 80.75  E-value: 3.67e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495     6 RKLFMPTPGQIMVGADLAGIELRMLAHYLAryDQGRYADILLNGDIHQVNADKI---------GISRRDVKTVTYAFLYG 76
Cdd:smart00482   5 RRAFIAPPGYVLVSADYSQIELRILAHLSG--DENLIEAFNNGGDIHTKTAAQVfgvpeeevtPELRRAAKAINFGIIYG 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495    77 AGDAKIGHSFDSSLNDsaakrkGKEIRSAFVDAIDGLAELLEAIKT-ASEKGFVRSVDGRKIHVD------------SPH 143
Cdd:smart00482  83 MGAKGLAEQLGISEAE------AKELIKKYFARFPGVRRYIDRTLEeARRKGYVTTLFGRRRYIPdidsrnpvlraaAER 156

                          170       180
                   ....*....|....*....|
gi 460081495   144 KSLNYLLQSGAGVLAKRWMV 163
Cdd:smart00482 157 AAVNTPIQGSAADILKLAMI 176
DNA_pol_A pfam00476
DNA polymerase family A;
6-163 8.96e-14

DNA polymerase family A;


Pssm-ID: 459825  Cd Length: 368  Bit Score: 67.85  E-value: 8.96e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495    6 RKLFMPTPGQIMVGADLAGIELRMLAHY------LARYDQGRyadillngDIHQVNADKI-GIS--------RRDVKTVT 70
Cdd:pfam00476 130 RKAFVAEPGWVLLSADYSQIELRILAHLsgdenlIEAFRNGE--------DIHTATASEVfGVPleevtpeqRRRAKAIN 201

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495   71 YAFLYGAGDakigHSFDSSLNDSaaKRKGKEIRSAFVDAIDGLAELLEAIK-TASEKGFVRSVDGRKIHVDSPHKS---- 145
Cdd:pfam00476 202 FGIIYGMSA----FGLAQQLGIS--RKEAKEYIDRYFERYPGVKEYMEETVeEAREKGYVETLLGRRRYLPDINSSnrnl 275

                         170       180
                  ....*....|....*....|....*.
gi 460081495  146 --------LNYLLQSGAGVLAKRWMV 163
Cdd:pfam00476 276 rsfaeraaINAPIQGSAADIIKLAMI 301
phage_DpoZ_1 NF038380
aminoadenine-incorporating DNA polymerase DpoZ;
6-166 1.09e-07

aminoadenine-incorporating DNA polymerase DpoZ;


Pssm-ID: 468497 [Multi-domain]  Cd Length: 604  Bit Score: 50.43  E-value: 1.09e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495   6 RKLFMPTPGQIMVGADLAGIELRMLAHYLARYDQGR-YADIlLNGDIHQVNADKIGISRR-------DVKTVTYAFLYGA 77
Cdd:NF038380 356 RPIFLPDEGQVWLCSDLAQFEFRIFAHLVNNPSIIAaYAED-PELDFHQIVADMTGLPRNatysgqaNAKQINLGMIFNM 434

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495  78 GDAKIG---------HSFDSSLNDSAAKRKGKE---IRSAFVDAIDGLAELLE-AIKTASEKGFVRSVDGRKI---HVDS 141
Cdd:NF038380 435 GNGKLAdkmgmpyewEEFTFGKEVRRYKKAGPEamaVIENYHRKLPGVKELADrAKAVAKERGYVRTAMGRRLrfpGGMK 514

                        170       180
                 ....*....|....*....|....*.
gi 460081495 142 PHKSLNYLLQSGAGVLAKR-WMVINH 166
Cdd:NF038380 515 TYKASGLLIQATAADLNKEnLLEIDE 540
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 3-136 3.93e-06

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


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 45.75  E-value: 3.93e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495   3 HDFRKLFMPTPGQIMVGADLAGIELRMLAHY------LARYDQGryadillnGDIHQVNADKI-------GISRRDVKTV 69
Cdd:PRK14975 313 RDIRSAFVADPGWKLVVADASQIELRVLAAYsgdermIEAFRTG--------GDLHRLTASVGfgkpeeeKEERALAKAA 384

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 460081495  70 TYAFLYGAGdAKIGHSFDSSLNDSAAkrkgkeIRSAFVDAIDGLAELLEAIKTASEKG-FVRSVDGRK 136
Cdd:PRK14975 385 NFGAIYGAT-SKGLQEYAKNYGEAAR------LLERLRRAYPRAVGWVERAAREGERGgVVRTLLGRT 445
PolA COG0749
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ...
 6-138 2.76e-05

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


Pssm-ID: 440512 [Multi-domain]  Cd Length: 575  Bit Score: 43.50  E-value: 2.76e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495   6 RKLFMPTPGQIMVGADLAGIELRMLAHyLARyDQGryadiLL-----NGDIHQVNADKI-GIS--------RRDVKTVTY 71
Cdd:COG0749  337 RKAFVAPEGYVLLSADYSQIELRILAH-LSG-DEG-----LIeafreGEDIHAATAAEVfGVPleevtseqRRRAKAINF 409

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 460081495  72 AFLYG------AGDAKIGhsfdsslndsaakRK-GKEIRSAFVDAIDGLAELLEAIK-TASEKGFVRSVDGRKIH 138
Cdd:COG0749  410 GIIYGmsafglARQLGIS-------------RKeAKEYIDRYFERYPGVKDYMEETVeEAREKGYVETLFGRRRY 471
 
Name Accession Description Interval E-value
DNA_pol_A_pol_I_B cd08643
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ...
 2-171 8.25e-55

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: 178.78  E-value: 8.25e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495   2 DHDFRKLFMPTPGQIMVGADLAGIELRMLAHYLARYDQGRYADILLNGDIHQVNADKIGISRRDV-KTVTYAFLYGAGDA 80
Cdd:cd08643  174 GKECRELFGVPPGWSLVGADASGLELRCLAHYLARYDGGAYTRKVLGGDIHWANAQAMGLLSRDGaKTFIYAFLYGAGDE 253

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495  81 KIGH----SFDSSLN--------------DSAAKRKGKEIRSAFVDAIDGLAELLEAIKT-ASEKGFVRSVDGRKIHVDS 141
Cdd:cd08643  254 KLGQivgdDLRTAKNlnaewpqtkkgtikKIADKAKGRVVRANFLKGLPALGKLIKKVKEaAKKRGHLVGLDGRRIRVRS 333

                        170       180       190
                 ....*....|....*....|....*....|
gi 460081495 142 PHKSLNYLLQSGAGVLAKRWMVINHQNTQE 171
Cdd:cd08643  334 AHAALNTLLQSAGAILMKKWLVLLDDELTA 363
POLAc smart00482
DNA polymerase A domain;
6-163 3.67e-19

DNA polymerase A domain;


Pssm-ID: 214687  Cd Length: 207  Bit Score: 80.75  E-value: 3.67e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495     6 RKLFMPTPGQIMVGADLAGIELRMLAHYLAryDQGRYADILLNGDIHQVNADKI---------GISRRDVKTVTYAFLYG 76
Cdd:smart00482   5 RRAFIAPPGYVLVSADYSQIELRILAHLSG--DENLIEAFNNGGDIHTKTAAQVfgvpeeevtPELRRAAKAINFGIIYG 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495    77 AGDAKIGHSFDSSLNDsaakrkGKEIRSAFVDAIDGLAELLEAIKT-ASEKGFVRSVDGRKIHVD------------SPH 143
Cdd:smart00482  83 MGAKGLAEQLGISEAE------AKELIKKYFARFPGVRRYIDRTLEeARRKGYVTTLFGRRRYIPdidsrnpvlraaAER 156

                          170       180
                   ....*....|....*....|
gi 460081495   144 KSLNYLLQSGAGVLAKRWMV 163
Cdd:smart00482 157 AAVNTPIQGSAADILKLAMI 176
DNA_pol_A cd06444
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ...
 3-163 1.04e-17

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: 79.00  E-value: 1.04e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495   3 HDFRKLFMPTPGQIMVGADLAGIELRMLAHYLARYDQGRYAdiLLNGDIHQVNA------DKIGISRRDVKTVTYAFLYG 76
Cdd:cd06444   91 RDIRQAFVADPGWTLVVADASQLELRVLAALSGDEALAEAF--GRGGDLYTATAsamfgvPVGGGERQHAKIANLGAMYG 168

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495  77 AGDAKIGHS-----FDSSLNDSAAKRKGKEIRSAFVDAIDglaELLEAIKTASEKGFVRSVDGRKIHVDSP--------- 142
Cdd:cd06444  169 ATSGISARLlaqlrRISTKEAAALIELFFSRFPAFPKAME---YVEDAARRGERGGYVRTLLGRRSPPPDIrwtevvsdp 245

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 460081495 143 --------------HKSLNYLLQSGAGVLAKRWMV 163
Cdd:cd06444  246 aaasrarrvrraagRFARNFVVQGTAADWAKLAMV 280
DNA_pol_A_theta cd08638
DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis and ...
 6-163 2.51e-14

DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis and in somatic hypermutation; DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis (TLS) and in somatic hypermutation (SHM). DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Pol theta is an exception among family A polymerases and generates processive single base substitutions. Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. Polymerase theta mostly has amino-terminal helicase domain, a carboxy-terminal polymerase domain and an intervening space region.


Pssm-ID: 176475  Cd Length: 373  Bit Score: 69.56  E-value: 2.51e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495   6 RKLFMPTPGQIMVGADLAGIELRMLAHYLAryDQgRYADILLNG-DIHQVNADKI-GIS--------RRDVKTVTYAFLY 75
Cdd:cd08638  131 RHAFIPPPGRVLLSADYSQLELRILAHLSG--DP-ALIELLNSGgDVFKMIAAQWlGKPveevtdeeRQQAKQLVYGILY 207

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495  76 GAGdakiGHSFDSSLNDSAAkrKGKEIRSAFVDAIDGLAELL-EAIKTASEKGFVRSVDGRK-----IHVDSPH------ 143
Cdd:cd08638  208 GMG----AKSLAEQLGVSEE--EAKQFIESFKNAYPGVRRFIrETIERARRNGFVETLTGRRrylpeINSGNSSeraqae 281

                        170       180
                 ....*....|....*....|.
gi 460081495 144 -KSLNYLLQSGAGVLAKRWMV 163
Cdd:cd08638  282 rQAVNTVIQGSAADIMKIAMI 302
DNA_pol_A pfam00476
DNA polymerase family A;
6-163 8.96e-14

DNA polymerase family A;


Pssm-ID: 459825  Cd Length: 368  Bit Score: 67.85  E-value: 8.96e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495    6 RKLFMPTPGQIMVGADLAGIELRMLAHY------LARYDQGRyadillngDIHQVNADKI-GIS--------RRDVKTVT 70
Cdd:pfam00476 130 RKAFVAEPGWVLLSADYSQIELRILAHLsgdenlIEAFRNGE--------DIHTATASEVfGVPleevtpeqRRRAKAIN 201

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495   71 YAFLYGAGDakigHSFDSSLNDSaaKRKGKEIRSAFVDAIDGLAELLEAIK-TASEKGFVRSVDGRKIHVDSPHKS---- 145
Cdd:pfam00476 202 FGIIYGMSA----FGLAQQLGIS--RKEAKEYIDRYFERYPGVKEYMEETVeEAREKGYVETLLGRRRYLPDINSSnrnl 275

                         170       180
                  ....*....|....*....|....*.
gi 460081495  146 --------LNYLLQSGAGVLAKRWMV 163
Cdd:pfam00476 276 rsfaeraaINAPIQGSAADIIKLAMI 301
DNA_pol_A_plastid_like cd08640
DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in ...
 6-168 1.40e-08

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: 52.78  E-value: 1.40e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495   6 RKLFMPTPGQIMVGADLAGIELRMLAHY------LARYDQGryadillnGDIHQ-------------------------- 53
Cdd:cd08640  110 RKAFIASPGNTLIVADYSQLELRLLAHMtrcksmIEAFNAG--------GDFHSrtasgmyphvaeavangevllewkse 181

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495  54 ------VNADKIGISRRDVKTVTYAFLYGagdaKIGHSFDSSLndsaaKRKGKEIRSAFVDAIDGLAELL----EAIKTA 123
Cdd:cd08640  182 gkppapLLKDKFKSERRKAKVLNFSIAYG----KTAHGLAKDW-----KVKLKEAERTVDAWYSDRPEVEqwqkKTKKEA 252

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 460081495 124 SEKGFVRSVDGRKIHV-DSPHK-----------SLNYLLQSGAGVLAKRWMVINHQN 168
Cdd:cd08640  253 RERGYTRTLLGRYRYLpDIKSRnrkkrghaeraAINTPIQGSAADIAMKAMLRIYRN 309
DNA_pol_A_pol_I_C cd08637
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ...
 6-140 2.01e-08

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: 52.42  E-value: 2.01e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495   6 RKLFMPTPGQIMVGADLAGIELRMLAHyLARyDQGRYADILLNGDIHQVNADKI-GIS--------RRDVKTVTYAFLYG 76
Cdd:cd08637  142 RKAFVAEEGWVLLSADYSQIELRILAH-LSG-DEALIEAFKNGEDIHTRTAAEVfGVPpeevtpemRRIAKAVNFGIIYG 219

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 460081495  77 AGD---AK-IGHSfdsslndsaaKRKGKEIRSAFVDAIDGLAELLEAIK-TASEKGFVRSVDGRKIHVD 140
Cdd:cd08637  220 ISAfglSQqLGIS----------RKEAKEYIDRYFARYPGVKEYMEETVeEAREKGYVETLFGRRRYIP 278
DNA_pol_A_Aquificae_like cd08639
Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences; ...
 2-172 8.55e-08

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: 50.74  E-value: 8.55e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495   2 DHDFRKLFMPTPGQIMVGADLAGIELRMLAHY------LARYDQGR-----YADILLNGDIHQVNADKigisRRDVKTVT 70
Cdd:cd08639   90 EREFRRCFVAPEGNKLIIADYSQIELRIAAEIsgdermISAYQKGEdlhrlTASLITGKPIEEITKEE----RQLAKAVN 165

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495  71 YAFLYGAGD------AKIGHSFDSSLNDSaakrkgKEIRSAFVDAIDGLAELLEAIKTASEKgFVRSVDGRKIHVDSP-- 142
Cdd:cd08639  166 FGLIYGMSAkglreyARTNYGVEMSLEEA------EKFRESFFFFYKGILRWHHRLKAKGPI-EVRTLLGRRRVFEYFtf 238

                        170       180       190
                 ....*....|....*....|....*....|.
gi 460081495 143 HKSLNYLLQ-SGAGVLaKRWMVINHQNTQEL 172
Cdd:cd08639  239 TEALNYPIQgTGADIL-KLALALLVDRLKDL 268
phage_DpoZ_1 NF038380
aminoadenine-incorporating DNA polymerase DpoZ;
6-166 1.09e-07

aminoadenine-incorporating DNA polymerase DpoZ;


Pssm-ID: 468497 [Multi-domain]  Cd Length: 604  Bit Score: 50.43  E-value: 1.09e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495   6 RKLFMPTPGQIMVGADLAGIELRMLAHYLARYDQGR-YADIlLNGDIHQVNADKIGISRR-------DVKTVTYAFLYGA 77
Cdd:NF038380 356 RPIFLPDEGQVWLCSDLAQFEFRIFAHLVNNPSIIAaYAED-PELDFHQIVADMTGLPRNatysgqaNAKQINLGMIFNM 434

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495  78 GDAKIG---------HSFDSSLNDSAAKRKGKE---IRSAFVDAIDGLAELLE-AIKTASEKGFVRSVDGRKI---HVDS 141
Cdd:NF038380 435 GNGKLAdkmgmpyewEEFTFGKEVRRYKKAGPEamaVIENYHRKLPGVKELADrAKAVAKERGYVRTAMGRRLrfpGGMK 514

                        170       180
                 ....*....|....*....|....*.
gi 460081495 142 PHKSLNYLLQSGAGVLAKR-WMVINH 166
Cdd:NF038380 515 TYKASGLLIQATAADLNKEnLLEIDE 540
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 3-136 3.93e-06

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


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 45.75  E-value: 3.93e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495   3 HDFRKLFMPTPGQIMVGADLAGIELRMLAHY------LARYDQGryadillnGDIHQVNADKI-------GISRRDVKTV 69
Cdd:PRK14975 313 RDIRSAFVADPGWKLVVADASQIELRVLAAYsgdermIEAFRTG--------GDLHRLTASVGfgkpeeeKEERALAKAA 384

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 460081495  70 TYAFLYGAGdAKIGHSFDSSLNDSAAkrkgkeIRSAFVDAIDGLAELLEAIKTASEKG-FVRSVDGRK 136
Cdd:PRK14975 385 NFGAIYGAT-SKGLQEYAKNYGEAAR------LLERLRRAYPRAVGWVERAAREGERGgVVRTLLGRT 445
PRK05755 PRK05755
DNA polymerase I; Provisional
 6-139 1.32e-05

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 44.31  E-value: 1.32e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495   6 RKLFMPTPGQIMVGADLAGIELRMLAHY------LARYDQGryADI-------LLNGDIHQVNADKigisRRDVKTVTYA 72
Cdd:PRK05755 642 RKAFVAPEGYKLLSADYSQIELRILAHLsgdeglIEAFAEG--EDIhtataseVFGVPLEEVTSEQ----RRRAKAINFG 715

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 460081495  73 FLYGAGDakigHSFDSSLNDSaakRK-GKEIrsafvdaID-------GLAELLEAIK-TASEKGFVRSVDGRKIHV 139
Cdd:PRK05755 716 IIYGMSA----FGLAQQLGIS---RKeAKEY-------IDryferypGVKEYMERTVeQAREKGYVETLFGRRRYL 777
PolA COG0749
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ...
 6-138 2.76e-05

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


Pssm-ID: 440512 [Multi-domain]  Cd Length: 575  Bit Score: 43.50  E-value: 2.76e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460081495   6 RKLFMPTPGQIMVGADLAGIELRMLAHyLARyDQGryadiLL-----NGDIHQVNADKI-GIS--------RRDVKTVTY 71
Cdd:COG0749  337 RKAFVAPEGYVLLSADYSQIELRILAH-LSG-DEG-----LIeafreGEDIHAATAAEVfGVPleevtseqRRRAKAINF 409

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 460081495  72 AFLYG------AGDAKIGhsfdsslndsaakRK-GKEIRSAFVDAIDGLAELLEAIK-TASEKGFVRSVDGRKIH 138
Cdd:COG0749  410 GIIYGmsafglARQLGIS-------------RKeAKEYIDRYFERYPGVKDYMEETVeEAREKGYVETLFGRRRY 471
DNA_pol_gammaA cd08641
Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in ...
 50-100 1.60e-03

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: 38.07  E-value: 1.60e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 460081495  50 DIHQVNADKIGISRRDVKTVTYAFLYGAGDA---KIGHSFDSSLNDSAAKRKGK 100
Cdd:cd08641  189 DLHSKTASILGISRDHAKVFNYGRIYGAGQPfaeRLLMQFNPRLTPAEATEKAK 242
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • 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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