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putative DNA polymerase III DnaE superfamily protein [Methanobacterium virus PhiF1]
List of domain hits
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Name | Accession | Description | Interval | E-value | |||||
PHP super family | cl23724 | Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2 ... |
165-438 | 1.34e-93 | |||||
Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PHP in polymerases has trinuclear zinc/magnesium dependent proofreading activity. It has also been shown that the PHP domain functions in DNA repair. The PHP structures have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. The actual alignment was detected with superfamily member cd12113: Pssm-ID: 451507 [Multi-domain] Cd Length: 283 Bit Score: 283.95 E-value: 1.34e-93
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UDG-F4_TTUDGA_SPO1dp_like | cd10030 | Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA ... |
3-145 | 1.69e-40 | |||||
Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA polymerase, and similar proteins; Uracil DNA glycosylase family 4 includes Thermotoga maritima TTUDGA, a robust uracil DNA glycosylase that shares narrow substrate specificity and high catalytic efficiency with family 1, acting on double-stranded and single-stranded uracil-containing DNA. Members of this family possess four conserved cysteine residues required to coordinate the [4Fe-4S] iron-sulfur cluster. This family also includes the N-terminal domain of Bacillus phage SPO1 DNA polymerase. Bacteriophage SPO1 is one of a group of large, lytic, tailed bacteriophages of Bacillus subtilis, and contains hydroxymethyluracil (hmUra) in place of thymine in their DNA. It has been speculated that this UDG domain may help discriminate between hmUra containing SPO1 DNA and thymine-containing host DNA. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. : Pssm-ID: 381680 Cd Length: 165 Bit Score: 142.20 E-value: 1.69e-40
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Name | Accession | Description | Interval | E-value | |||||
PHP_PolIIIA_DnaE3 | cd12113 | Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
165-438 | 1.34e-93 | |||||
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that is responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. The PolIIIA PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination, and like other PHP structures, the PolIIIA PHP exhibits a distorted (beta/alpha) 7 barrel and coordinates up to 3 metals. Initially, it was proposed that PHP region might be involved in pyrophosphate hydrolysis, but such an activity has not been found. It has been shown that the PHP of PolIIIA has a trinuclear metal complex and is capable of proofreading activity. Bacterial genome replication and DNA repair mechanisms is related to the GC content of its genomes. There is a correlation between GC content variations and the dimeric combinations of PolIIIA subunits. Eubacteria can be grouped into different GC variable groups: the full-spectrum or dnaE1 group, the high-GC or dnaE2-dnaE1 group, and the low GC or polC-dnaE3 group. Pssm-ID: 213997 [Multi-domain] Cd Length: 283 Bit Score: 283.95 E-value: 1.34e-93
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DnaE | COG0587 | DNA polymerase III, alpha subunit [Replication, recombination and repair]; |
159-440 | 1.03e-82 | |||||
DNA polymerase III, alpha subunit [Replication, recombination and repair]; Pssm-ID: 440352 [Multi-domain] Cd Length: 1050 Bit Score: 274.64 E-value: 1.03e-82
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dnaE | PRK06826 | DNA polymerase III DnaE; Reviewed |
165-440 | 5.12e-75 | |||||
DNA polymerase III DnaE; Reviewed Pssm-ID: 235868 [Multi-domain] Cd Length: 1151 Bit Score: 254.43 E-value: 5.12e-75
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polc | TIGR00594 | DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are ... |
161-438 | 3.95e-73 | |||||
DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are known are DNA polymerases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273161 [Multi-domain] Cd Length: 1022 Bit Score: 248.06 E-value: 3.95e-73
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PHP | pfam02811 | PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ... |
165-328 | 1.55e-50 | |||||
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain. Pssm-ID: 460705 [Multi-domain] Cd Length: 171 Bit Score: 168.88 E-value: 1.55e-50
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UDG-F4_TTUDGA_SPO1dp_like | cd10030 | Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA ... |
3-145 | 1.69e-40 | |||||
Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA polymerase, and similar proteins; Uracil DNA glycosylase family 4 includes Thermotoga maritima TTUDGA, a robust uracil DNA glycosylase that shares narrow substrate specificity and high catalytic efficiency with family 1, acting on double-stranded and single-stranded uracil-containing DNA. Members of this family possess four conserved cysteine residues required to coordinate the [4Fe-4S] iron-sulfur cluster. This family also includes the N-terminal domain of Bacillus phage SPO1 DNA polymerase. Bacteriophage SPO1 is one of a group of large, lytic, tailed bacteriophages of Bacillus subtilis, and contains hydroxymethyluracil (hmUra) in place of thymine in their DNA. It has been speculated that this UDG domain may help discriminate between hmUra containing SPO1 DNA and thymine-containing host DNA. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. Pssm-ID: 381680 Cd Length: 165 Bit Score: 142.20 E-value: 1.69e-40
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Udg4 | COG1573 | Uracil-DNA glycosylase [Replication, recombination and repair]; |
2-145 | 3.03e-39 | |||||
Uracil-DNA glycosylase [Replication, recombination and repair]; Pssm-ID: 441181 Cd Length: 189 Bit Score: 139.95 E-value: 3.03e-39
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UDG_fam4 | TIGR00758 | uracil-DNA glycosylase, family 4; This well-conserved family of proteins is about 200 residues ... |
3-145 | 1.00e-30 | |||||
uracil-DNA glycosylase, family 4; This well-conserved family of proteins is about 200 residues in length and homologous to the N-terminus of the DNA polymerase of phage SPO1 of Bacillus subtilis. The member from Thermus thermophilus HB8 is known to act as uracil-DNA glycosylase, an enzyme of DNA base excision repair. Its appearance as a domain of phage DNA polymerases could be consistent with uracil-DNA glycosylase activity. [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 129841 Cd Length: 173 Bit Score: 116.36 E-value: 1.00e-30
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UDG | pfam03167 | Uracil DNA glycosylase superfamily; |
13-145 | 3.30e-30 | |||||
Uracil DNA glycosylase superfamily; Pssm-ID: 397331 Cd Length: 154 Bit Score: 114.37 E-value: 3.30e-30
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Arch_udg | NF040953 | type-4 uracil-DNA glycosylase; |
1-145 | 1.31e-22 | |||||
type-4 uracil-DNA glycosylase; Pssm-ID: 468884 Cd Length: 183 Bit Score: 94.56 E-value: 1.31e-22
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UDG | smart00986 | Uracil DNA glycosylase superfamily; |
14-150 | 4.30e-22 | |||||
Uracil DNA glycosylase superfamily; Pssm-ID: 214956 Cd Length: 156 Bit Score: 92.06 E-value: 4.30e-22
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POLIIIAc | smart00481 | DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ... |
165-229 | 1.78e-20 | |||||
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family of hypothetical proteins Pssm-ID: 197753 [Multi-domain] Cd Length: 67 Bit Score: 84.63 E-value: 1.78e-20
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CehA_McbA_metalo | NF038032 | CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ... |
165-209 | 1.07e-05 | |||||
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is found in several partially characterized metallohydrolases, including McbA and CehA. Both were studied as hydrolases of carbaryl, a xenobiotic compound that does not contain a phosphate group, suggesting that presuming members of this family to be phosphoesterases (like many PHP domain-containing proteins) may be incorrect. Pssm-ID: 468321 [Multi-domain] Cd Length: 315 Bit Score: 47.32 E-value: 1.07e-05
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Name | Accession | Description | Interval | E-value | |||||
PHP_PolIIIA_DnaE3 | cd12113 | Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
165-438 | 1.34e-93 | |||||
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that is responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. The PolIIIA PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination, and like other PHP structures, the PolIIIA PHP exhibits a distorted (beta/alpha) 7 barrel and coordinates up to 3 metals. Initially, it was proposed that PHP region might be involved in pyrophosphate hydrolysis, but such an activity has not been found. It has been shown that the PHP of PolIIIA has a trinuclear metal complex and is capable of proofreading activity. Bacterial genome replication and DNA repair mechanisms is related to the GC content of its genomes. There is a correlation between GC content variations and the dimeric combinations of PolIIIA subunits. Eubacteria can be grouped into different GC variable groups: the full-spectrum or dnaE1 group, the high-GC or dnaE2-dnaE1 group, and the low GC or polC-dnaE3 group. Pssm-ID: 213997 [Multi-domain] Cd Length: 283 Bit Score: 283.95 E-value: 1.34e-93
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DnaE | COG0587 | DNA polymerase III, alpha subunit [Replication, recombination and repair]; |
159-440 | 1.03e-82 | |||||
DNA polymerase III, alpha subunit [Replication, recombination and repair]; Pssm-ID: 440352 [Multi-domain] Cd Length: 1050 Bit Score: 274.64 E-value: 1.03e-82
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dnaE | PRK06826 | DNA polymerase III DnaE; Reviewed |
165-440 | 5.12e-75 | |||||
DNA polymerase III DnaE; Reviewed Pssm-ID: 235868 [Multi-domain] Cd Length: 1151 Bit Score: 254.43 E-value: 5.12e-75
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polc | TIGR00594 | DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are ... |
161-438 | 3.95e-73 | |||||
DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are known are DNA polymerases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273161 [Multi-domain] Cd Length: 1022 Bit Score: 248.06 E-value: 3.95e-73
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dnaE | PRK05673 | DNA polymerase III subunit alpha; Validated |
161-440 | 6.15e-69 | |||||
DNA polymerase III subunit alpha; Validated Pssm-ID: 235554 [Multi-domain] Cd Length: 1135 Bit Score: 237.31 E-value: 6.15e-69
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dnaE | PRK07374 | DNA polymerase III subunit alpha; Validated |
161-440 | 2.94e-54 | |||||
DNA polymerase III subunit alpha; Validated Pssm-ID: 168927 [Multi-domain] Cd Length: 1170 Bit Score: 195.33 E-value: 2.94e-54
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PHP_PolIIIA_DnaE1 | cd07433 | Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
156-440 | 2.09e-51 | |||||
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. PolIIIA core enzyme catalyzes the reaction for polymerizing both DNA strands. dnaE1 is the longest compared to dnaE2 and dnaE3. A unique motif was also identified in dnaE1 and dnaE3 genes. Pssm-ID: 213988 [Multi-domain] Cd Length: 277 Bit Score: 174.59 E-value: 2.09e-51
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PHP | pfam02811 | PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ... |
165-328 | 1.55e-50 | |||||
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain. Pssm-ID: 460705 [Multi-domain] Cd Length: 171 Bit Score: 168.88 E-value: 1.55e-50
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PHP_PolIIIA_POLC | cd07435 | Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ... |
165-373 | 6.31e-46 | |||||
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at PolC gene; DNA polymerase III alphas (PolIIIAs) that contain a PHP domain have been classified into four basic groups based on phylogenetic and domain structural analyses: polC, dnaE1, dnaE2, and dnaE3. The PolC group is distinct from the other three and is clustered together. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. PolC PHP is located in different location compare to dnaE1, 2, and 3. The PHP domain has four conserved sequence motifs and and contains an invariant histidine that is involved in metal ion coordination.The PHP domain of PolC is structurally homologous to other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. PHP domains found in dnaEs of thermophilic origin exhibit 3'-5' exonuclease activity. In contrast, PolC PHP lacks detectable nuclease activity. Pssm-ID: 213990 [Multi-domain] Cd Length: 268 Bit Score: 159.95 E-value: 6.31e-46
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PRK09532 | PRK09532 | DNA polymerase III subunit alpha; Reviewed |
160-431 | 3.30e-43 | |||||
DNA polymerase III subunit alpha; Reviewed Pssm-ID: 181933 [Multi-domain] Cd Length: 874 Bit Score: 162.60 E-value: 3.30e-43
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UDG-F4_TTUDGA_SPO1dp_like | cd10030 | Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA ... |
3-145 | 1.69e-40 | |||||
Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA polymerase, and similar proteins; Uracil DNA glycosylase family 4 includes Thermotoga maritima TTUDGA, a robust uracil DNA glycosylase that shares narrow substrate specificity and high catalytic efficiency with family 1, acting on double-stranded and single-stranded uracil-containing DNA. Members of this family possess four conserved cysteine residues required to coordinate the [4Fe-4S] iron-sulfur cluster. This family also includes the N-terminal domain of Bacillus phage SPO1 DNA polymerase. Bacteriophage SPO1 is one of a group of large, lytic, tailed bacteriophages of Bacillus subtilis, and contains hydroxymethyluracil (hmUra) in place of thymine in their DNA. It has been speculated that this UDG domain may help discriminate between hmUra containing SPO1 DNA and thymine-containing host DNA. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. Pssm-ID: 381680 Cd Length: 165 Bit Score: 142.20 E-value: 1.69e-40
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Udg4 | COG1573 | Uracil-DNA glycosylase [Replication, recombination and repair]; |
2-145 | 3.03e-39 | |||||
Uracil-DNA glycosylase [Replication, recombination and repair]; Pssm-ID: 441181 Cd Length: 189 Bit Score: 139.95 E-value: 3.03e-39
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dnaE | PRK06920 | DNA polymerase III subunit alpha; |
161-440 | 1.15e-34 | |||||
DNA polymerase III subunit alpha; Pssm-ID: 180749 [Multi-domain] Cd Length: 1107 Bit Score: 137.62 E-value: 1.15e-34
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PHP_PolIIIA | cd07431 | Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ... |
162-373 | 2.69e-33 | |||||
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that is responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. The PolIIIA PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination, and like other PHP structures, exhibits a distorted (beta/alpha) 7 barrel and coordinates up to 3 metals. Initially, it was proposed that PHP region might be involved in pyrophosphate hydrolysis, but such activity has not been found. It has been shown that the PHP domain of PolIIIA has a trinuclear metal complex and is capable of proofreading activity. Pssm-ID: 213986 [Multi-domain] Cd Length: 179 Bit Score: 123.47 E-value: 2.69e-33
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UDG_fam4 | TIGR00758 | uracil-DNA glycosylase, family 4; This well-conserved family of proteins is about 200 residues ... |
3-145 | 1.00e-30 | |||||
uracil-DNA glycosylase, family 4; This well-conserved family of proteins is about 200 residues in length and homologous to the N-terminus of the DNA polymerase of phage SPO1 of Bacillus subtilis. The member from Thermus thermophilus HB8 is known to act as uracil-DNA glycosylase, an enzyme of DNA base excision repair. Its appearance as a domain of phage DNA polymerases could be consistent with uracil-DNA glycosylase activity. [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 129841 Cd Length: 173 Bit Score: 116.36 E-value: 1.00e-30
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UDG | pfam03167 | Uracil DNA glycosylase superfamily; |
13-145 | 3.30e-30 | |||||
Uracil DNA glycosylase superfamily; Pssm-ID: 397331 Cd Length: 154 Bit Score: 114.37 E-value: 3.30e-30
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Arch_udg | NF040953 | type-4 uracil-DNA glycosylase; |
1-145 | 1.31e-22 | |||||
type-4 uracil-DNA glycosylase; Pssm-ID: 468884 Cd Length: 183 Bit Score: 94.56 E-value: 1.31e-22
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UDG | smart00986 | Uracil DNA glycosylase superfamily; |
14-150 | 4.30e-22 | |||||
Uracil DNA glycosylase superfamily; Pssm-ID: 214956 Cd Length: 156 Bit Score: 92.06 E-value: 4.30e-22
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POLIIIAc | smart00481 | DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ... |
165-229 | 1.78e-20 | |||||
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family of hypothetical proteins Pssm-ID: 197753 [Multi-domain] Cd Length: 67 Bit Score: 84.63 E-value: 1.78e-20
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dnaE2 | PRK05672 | error-prone DNA polymerase; Validated |
159-374 | 1.06e-18 | |||||
error-prone DNA polymerase; Validated Pssm-ID: 235553 [Multi-domain] Cd Length: 1046 Bit Score: 89.15 E-value: 1.06e-18
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polC | PRK00448 | DNA polymerase III PolC; Validated |
239-370 | 3.47e-18 | |||||
DNA polymerase III PolC; Validated Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 87.59 E-value: 3.47e-18
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UDG-like | cd09593 | uracil-DNA glycosylases (UDG) and related enzymes; Uracil-DNA glycosylases (UDGs) initiate ... |
22-142 | 2.05e-17 | |||||
uracil-DNA glycosylases (UDG) and related enzymes; Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil may arise from misincorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations; thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. UDG family 1 is the most efficient uracil-DNA glycosylase (UDG, also known as UNG) and shows a specificity for uracil in DNA. UDG family 2 includes thymine DNA glycosylase which removes uracil and thymine from G:U and G:T mismatches, and mismatch-specific uracil DNA glycosylase (MUG) which in Escherichia coli is highly specific to G:U mismatches, but also repairs G:T mismatches at high enzyme concentration. UDG family 3 includes Human SMUG1 which can remove uracil and its oxidized pyrimidine derivatives from, single-stranded DNA and double-stranded DNA with a preference for single-stranded DNA. Pedobacter heparinus SMUG2, which is UDG family 3 SMUG1-like, displays catalytic activities towards DNA containing uracil or hypoxanthine/xanthine. UDG family 4 includes Thermotoga maritima TTUDGA, a robust UDG which like family 1, acts on double-stranded and single-stranded uracil-containing DNA. UDG family 5 (UDGb) includes Thermus thermophilus HB8 TTUDGB which acts on double-stranded uracil-containing DNA; it is a hypoxanthine DNA glycosylase acting on double-stranded hypoxanthine-containing DNA except for the C/I base pair, as well as a xanthine DNA glycosylase which acts on both double-stranded and single-stranded xanthine-containing DNA. UDG family 6 hypoxanthine-DNA glycosylase lacks any detectable UDG activity; it excises hypoxanthine. Other UDG families include one represented by Bradyrhizobium diazoefficiens Blr0248 which prefers single-stranded DNA and removes uracil, 5-hydroxymethyl-uracil or xanthine from it. Pssm-ID: 381677 Cd Length: 125 Bit Score: 78.20 E-value: 2.05e-17
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polC | PRK00448 | DNA polymerase III PolC; Validated |
165-229 | 9.05e-15 | |||||
DNA polymerase III PolC; Validated Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 76.80 E-value: 9.05e-15
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YciV | COG0613 | 5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ... |
165-363 | 1.65e-14 | |||||
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism]; Pssm-ID: 440378 [Multi-domain] Cd Length: 188 Bit Score: 71.48 E-value: 1.65e-14
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dnaE | PRK07279 | DNA polymerase III DnaE; Reviewed |
168-283 | 2.88e-13 | |||||
DNA polymerase III DnaE; Reviewed Pssm-ID: 180917 [Multi-domain] Cd Length: 1034 Bit Score: 71.99 E-value: 2.88e-13
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dnaE | PRK07135 | DNA polymerase III DnaE; Validated |
164-266 | 4.18e-13 | |||||
DNA polymerase III DnaE; Validated Pssm-ID: 235944 [Multi-domain] Cd Length: 973 Bit Score: 71.64 E-value: 4.18e-13
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PHP_PolIIIA_DnaE2 | cd07434 | Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ... |
161-427 | 2.48e-10 | |||||
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; PolIIIA DnaE2 plays a role in SOS mutagenesis/translesion synthesis and has dominant effects in determining GC variability in the bacterial genome. PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. PolIIIA core enzyme catalyzes the reaction for polymerizing both DNA strands. PolC PHP is located in a different location compared to dnaE1, 2, and 3. dnaE1 is the longest compared to dnaE2 and dnaE3. A unique motif was also identified in dnaE1 and dnaE3 genes. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PHP domains found in DnaEs of thermophilic origin exhibit 3'-5' exonuclease activity. Pssm-ID: 213989 [Multi-domain] Cd Length: 260 Bit Score: 60.93 E-value: 2.48e-10
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PHP_HisPPase | cd07432 | Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ... |
165-265 | 6.20e-10 | |||||
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to produce histidinol. HisPPase can be classified into two types: the bifunctional HisPPase found in proteobacteria that belongs to the DDDD superfamily and the monofunctional Bacillus subtilis type that is a member of the PHP family. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. The PHP domain of HisPPase is structurally homologous to other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. Pssm-ID: 213987 [Multi-domain] Cd Length: 129 Bit Score: 56.86 E-value: 6.20e-10
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PHP_HisPPase_AMP | cd07438 | Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ... |
165-225 | 4.08e-08 | |||||
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; The PHP domain of this HisPPase family has an unknown function. It has a second domain inserted in the middle that binds adenosine 5-monophosphate (AMP). The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to give histidinol. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. The PHP domain of HisPPase is structurally homologous to the other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. Pssm-ID: 213993 [Multi-domain] Cd Length: 155 Bit Score: 52.40 E-value: 4.08e-08
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PHP | cd07309 | Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2 ... |
164-228 | 4.40e-08 | |||||
Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PHP in polymerases has trinuclear zinc/magnesium dependent proofreading activity. It has also been shown that the PHP domain functions in DNA repair. The PHP structures have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. Pssm-ID: 213985 [Multi-domain] Cd Length: 88 Bit Score: 50.50 E-value: 4.40e-08
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UDG-F2_TDG_MUG | cd10028 | Uracil DNA glycosylase family 2, includes thymine DNA glycosylase, mismatch-specific uracil ... |
22-141 | 3.40e-06 | |||||
Uracil DNA glycosylase family 2, includes thymine DNA glycosylase, mismatch-specific uracil DNA glycosylase and similar proteins; Uracil DNA glycosylase family 2 consists of thymine DNA glycosylase (TDG), which removes uracil and thymine from G:U and G:T mismatches in double-stranded DNA. It includes mismatch-specific uracil DNA glycosylase (MUG), the prokaryotic homolog of TDG. Escherichia coli MUG is highly specific to G:U mismatches but also repairs G:T mismatches at high enzyme concentration. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil in DNA can arise as a result of misincorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other.. Pssm-ID: 381679 Cd Length: 163 Bit Score: 47.09 E-value: 3.40e-06
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HIS2 | COG1387 | Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and ... |
165-200 | 4.46e-06 | |||||
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and metabolism, General function prediction only]; Histidinol phosphatase or related hydrolase of the PHP family is part of the Pathway/BioSystem: Histidine biosynthesis Pssm-ID: 440997 [Multi-domain] Cd Length: 232 Bit Score: 47.46 E-value: 4.46e-06
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PHP_PolX | cd07436 | Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal ... |
164-199 | 5.76e-06 | |||||
Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal X-family DNA polymerases (PolXs) have a PHP domain at their C-terminus. The bacterial/archaeal PolX core domain and PHP domain interact with each other and together are involved in metal dependent 3'-5' exonuclease activity. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PolX is found in all kingdoms, however bacterial PolXs have a completely different domain structure from eukaryotic PolXs. Bacterial PolX has an extended conformation in contrast to the common closed 'right hand' conformation for DNA polymerases. This extended conformation is stabilized by the PHP domain. The PHP domain of PolX is structurally homologous to other members of the PHP family that has a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. Pssm-ID: 213991 [Multi-domain] Cd Length: 237 Bit Score: 47.41 E-value: 5.76e-06
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CehA_McbA_metalo | NF038032 | CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ... |
165-209 | 1.07e-05 | |||||
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is found in several partially characterized metallohydrolases, including McbA and CehA. Both were studied as hydrolases of carbaryl, a xenobiotic compound that does not contain a phosphate group, suggesting that presuming members of this family to be phosphoesterases (like many PHP domain-containing proteins) may be incorrect. Pssm-ID: 468321 [Multi-domain] Cd Length: 315 Bit Score: 47.32 E-value: 1.07e-05
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dnaE | PRK05898 | DNA polymerase III subunit alpha; |
164-264 | 1.73e-05 | |||||
DNA polymerase III subunit alpha; Pssm-ID: 135648 [Multi-domain] Cd Length: 971 Bit Score: 47.14 E-value: 1.73e-05
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UDG-F5_TTUDGB_like | cd10031 | Uracil DNA glycosylase family 5, includes Thermotoga maritima TTUDGB and similar proteins; ... |
16-113 | 2.51e-04 | |||||
Uracil DNA glycosylase family 5, includes Thermotoga maritima TTUDGB and similar proteins; Uracil DNA glycosylase family 5 includes Thermus thermophilus HB8 TTUDGB (also called UDGb) which is not only a UDG acting on double-stranded uracil-containing DNA, but also a hypoxanthine DNA glycosylase acting on double-stranded hypoxanthine-containing DNA (except for the C/I base pair), as well as a xanthine DNA glycosylase acting on both, double-stranded and single-stranded xanthine-containing DNA. TTUDGB also excises thymine from G:T mismatched DNA, and removes analogs of uracil from DNA, including 5-hydroxymethyluracil (hmU) and 5-fluorouracil (fU). This subfamily also contains Bradyrhizobium diazoefficiens family 5 homolog Blr5068 (UdgB) which has been found to efficiently excise uracil from ssDNA and dsDNA. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Similar to family 4 UDGs, members of this family possess four conserved cysteine residues required to coordinate the [4Fe-4S] iron-sulfur cluster. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. Pssm-ID: 381681 Cd Length: 204 Bit Score: 42.07 E-value: 2.51e-04
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PRK07945 | PRK07945 | PHP domain-containing protein; |
165-199 | 2.50e-03 | |||||
PHP domain-containing protein; Pssm-ID: 236135 [Multi-domain] Cd Length: 335 Bit Score: 39.96 E-value: 2.50e-03
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