MULTISPECIES: RNase AM [Enterobacter]
Protein Classification
PHP domain-containing protein( domain architecture ID 11427581)
PHP (Polymerase and Histidinol Phosphatase) domain-containing protein has an invariant histidine that is involved in metal ion coordination, similar to Bifidobacterium adolescentis metal-dependent phosphoesterase
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| nside_bi_sphtase super family | cl49536 | 3',5'-nucleoside bisphosphate phosphatase; |
10-282 | 1.45e-108 | |||||
3',5'-nucleoside bisphosphate phosphatase; The actual alignment was detected with superfamily member NF041577: Pssm-ID: 469462 [Multi-domain] Cd Length: 276 Bit Score: 316.08 E-value: 1.45e-108
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| Name | Accession | Description | Interval | E-value | |||||
| nside_bi_sphtase | NF041577 | 3',5'-nucleoside bisphosphate phosphatase; |
10-282 | 1.45e-108 | |||||
3',5'-nucleoside bisphosphate phosphatase; Pssm-ID: 469462 [Multi-domain] Cd Length: 276 Bit Score: 316.08 E-value: 1.45e-108
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| YciV | COG0613 | 5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ... |
7-263 | 1.22e-62 | |||||
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism]; Pssm-ID: 440378 [Multi-domain] Cd Length: 188 Bit Score: 195.90 E-value: 1.22e-62
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| PHP_HisPPase_AMP | cd07438 | Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ... |
10-257 | 1.81e-56 | |||||
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: 179.13 E-value: 1.81e-56
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| POLIIIAc | smart00481 | DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ... |
11-77 | 2.33e-12 | |||||
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: 61.13 E-value: 2.33e-12
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| CehA_McbA_metalo | NF038032 | CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ... |
11-92 | 1.98e-08 | |||||
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: 54.64 E-value: 1.98e-08
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| PHP | pfam02811 | PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ... |
11-73 | 2.23e-06 | |||||
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain. Pssm-ID: 460705 [Multi-domain] Cd Length: 171 Bit Score: 46.77 E-value: 2.23e-06
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| dnaE2 | PRK05672 | error-prone DNA polymerase; Validated |
6-74 | 1.23e-05 | |||||
error-prone DNA polymerase; Validated Pssm-ID: 235553 [Multi-domain] Cd Length: 1046 Bit Score: 46.77 E-value: 1.23e-05
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| Name | Accession | Description | Interval | E-value | |||||
| nside_bi_sphtase | NF041577 | 3',5'-nucleoside bisphosphate phosphatase; |
10-282 | 1.45e-108 | |||||
3',5'-nucleoside bisphosphate phosphatase; Pssm-ID: 469462 [Multi-domain] Cd Length: 276 Bit Score: 316.08 E-value: 1.45e-108
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| YciV | COG0613 | 5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ... |
7-263 | 1.22e-62 | |||||
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism]; Pssm-ID: 440378 [Multi-domain] Cd Length: 188 Bit Score: 195.90 E-value: 1.22e-62
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| PHP_HisPPase_AMP | cd07438 | Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ... |
10-257 | 1.81e-56 | |||||
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: 179.13 E-value: 1.81e-56
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| PHP_HisPPase | cd07432 | Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ... |
10-74 | 3.11e-13 | |||||
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: 65.34 E-value: 3.11e-13
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| POLIIIAc | smart00481 | DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ... |
11-77 | 2.33e-12 | |||||
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: 61.13 E-value: 2.33e-12
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| CehA_McbA_metalo | NF038032 | CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ... |
11-92 | 1.98e-08 | |||||
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: 54.64 E-value: 1.98e-08
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| HIS2 | COG1387 | Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and ... |
8-73 | 3.65e-08 | |||||
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: 52.85 E-value: 3.65e-08
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| PHP | pfam02811 | PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ... |
11-73 | 2.23e-06 | |||||
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain. Pssm-ID: 460705 [Multi-domain] Cd Length: 171 Bit Score: 46.77 E-value: 2.23e-06
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| DnaE | COG0587 | DNA polymerase III, alpha subunit [Replication, recombination and repair]; |
12-56 | 3.63e-06 | |||||
DNA polymerase III, alpha subunit [Replication, recombination and repair]; Pssm-ID: 440352 [Multi-domain] Cd Length: 1050 Bit Score: 48.14 E-value: 3.63e-06
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| dnaE2 | PRK05672 | error-prone DNA polymerase; Validated |
6-74 | 1.23e-05 | |||||
error-prone DNA polymerase; Validated Pssm-ID: 235553 [Multi-domain] Cd Length: 1046 Bit Score: 46.77 E-value: 1.23e-05
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| polC | PRK00448 | DNA polymerase III PolC; Validated |
12-73 | 2.08e-05 | |||||
DNA polymerase III PolC; Validated Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 45.98 E-value: 2.08e-05
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| PHP_PolIIIA_POLC | cd07435 | Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ... |
12-80 | 1.49e-04 | |||||
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: 42.46 E-value: 1.49e-04
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| PRK06361 | PRK06361 | histidinol phosphate phosphatase domain-containing protein; |
15-76 | 1.92e-04 | |||||
histidinol phosphate phosphatase domain-containing protein; Pssm-ID: 180543 [Multi-domain] Cd Length: 212 Bit Score: 41.87 E-value: 1.92e-04
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| PHP_PolX | cd07436 | Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal ... |
11-45 | 3.03e-04 | |||||
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: 41.25 E-value: 3.03e-04
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| PHP_PolIIIA_DnaE3 | cd12113 | Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
12-45 | 4.03e-04 | |||||
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: 41.27 E-value: 4.03e-04
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| PHP_PolIIIA_DnaE1 | cd07433 | Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
12-45 | 1.65e-03 | |||||
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: 39.38 E-value: 1.65e-03
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| PHP | cd07309 | Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2 ... |
11-91 | 1.97e-03 | |||||
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: 36.64 E-value: 1.97e-03
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| PHP_HisPPase_Chlorobi_like | cd12112 | Polymerase and Histidinol Phosphatase domain of Chlorobi like; The PHP (also called histidinol ... |
11-45 | 2.65e-03 | |||||
Polymerase and Histidinol Phosphatase domain of Chlorobi like; 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. Chlorobi PHP is uncharacterized protein. HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to produce histidinol. The 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 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: 213996 [Multi-domain] Cd Length: 235 Bit Score: 38.46 E-value: 2.65e-03
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| PHP_PolIIIA | cd07431 | Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ... |
12-85 | 5.36e-03 | |||||
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: 37.18 E-value: 5.36e-03
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