DNA-directed DNA polymerase gamma MIP1 [Saccharomyces cerevisiae S288C]
Protein Classification
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 ... |
581-960 | 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: 718.33 E-value: 0e+00
|
||||||||||
| DNApol_Exo | pfam18136 | DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ... |
95-362 | 8.92e-130 | ||||||
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: 399.33 E-value: 8.92e-130
|
||||||||||
| 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 ... |
581-960 | 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: 718.33 E-value: 0e+00
|
||||||||||
| DNApol_Exo | pfam18136 | DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ... |
95-362 | 8.92e-130 | ||||||
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: 399.33 E-value: 8.92e-130
|
||||||||||
| POLAc | smart00482 | DNA polymerase A domain; |
674-902 | 5.78e-64 | ||||||
DNA polymerase A domain; Pssm-ID: 214687 Cd Length: 207 Bit Score: 215.95 E-value: 5.78e-64
|
||||||||||
| DNA_pol_A | pfam00476 | DNA polymerase family A; |
682-920 | 3.61e-23 | ||||||
DNA polymerase family A; Pssm-ID: 459825 Cd Length: 368 Bit Score: 102.90 E-value: 3.61e-23
|
||||||||||
| PRK14975 | PRK14975 | bifunctional 3'-5' exonuclease/DNA polymerase; Provisional |
645-769 | 8.23e-08 | ||||||
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional Pssm-ID: 237876 [Multi-domain] Cd Length: 553 Bit Score: 56.53 E-value: 8.23e-08
|
||||||||||
| 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 ... |
581-960 | 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: 718.33 E-value: 0e+00
|
||||||||||
| DNApol_Exo | pfam18136 | DNA mitochondrial polymerase exonuclease domain; This domain belongs to human mitochondrial ... |
95-362 | 8.92e-130 | ||||||
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: 399.33 E-value: 8.92e-130
|
||||||||||
| POLAc | smart00482 | DNA polymerase A domain; |
674-902 | 5.78e-64 | ||||||
DNA polymerase A domain; Pssm-ID: 214687 Cd Length: 207 Bit Score: 215.95 E-value: 5.78e-64
|
||||||||||
| DNA_pol_A | cd06444 | Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ... |
605-945 | 2.04e-31 | ||||||
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: 126.76 E-value: 2.04e-31
|
||||||||||
| DNA_pol_A | pfam00476 | DNA polymerase family A; |
682-920 | 3.61e-23 | ||||||
DNA polymerase family A; Pssm-ID: 459825 Cd Length: 368 Bit Score: 102.90 E-value: 3.61e-23
|
||||||||||
| DNA_pol_A_Aquificae_like | cd08639 | Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences; ... |
682-920 | 4.34e-09 | ||||||
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: 59.60 E-value: 4.34e-09
|
||||||||||
| PRK14975 | PRK14975 | bifunctional 3'-5' exonuclease/DNA polymerase; Provisional |
645-769 | 8.23e-08 | ||||||
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional Pssm-ID: 237876 [Multi-domain] Cd Length: 553 Bit Score: 56.53 E-value: 8.23e-08
|
||||||||||
| DNA_pol_A_pol_I_B | cd08643 | Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ... |
647-803 | 5.68e-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: 53.59 E-value: 5.68e-07
|
||||||||||
| DNA_pol_A_pol_I_C | cd08637 | Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ... |
683-767 | 2.27e-03 | ||||||
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: 42.02 E-value: 2.27e-03
|
||||||||||
| Blast search parameters | ||||
|
