PHP domain protein [Lactobacillus iners LactinV 09V1-c]
Protein Classification
PolC-type DNA polymerase III family protein( domain architecture ID 1000821)
PolC-type DNA polymerase III family protein similar to Leptotrichia shahii CRISPR-associated endoribonuclease C2c2, the effector of type VI CRISPR-Cas systems, which has two RNase activities-one for cutting its RNA target and the other for processing the CRISPR RNA (crRNA)
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||||||
| polC super family | cl35100 | DNA polymerase III PolC; Validated |
2-737 | 0e+00 | |||||||||||
DNA polymerase III PolC; Validated The actual alignment was detected with superfamily member PRK00448: Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 828.71 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | |||||||||||
| polC | PRK00448 | DNA polymerase III PolC; Validated |
2-737 | 0e+00 | |||||||||||
DNA polymerase III PolC; Validated Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 828.71 E-value: 0e+00
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| PHP_PolIIIA_POLC | cd07435 | Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ... |
316-743 | 1.73e-74 | |||||||||||
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: 242.38 E-value: 1.73e-74
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| PolC | COG2176 | DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
397-569 | 7.31e-72 | |||||||||||
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 231.96 E-value: 7.31e-72
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| dnaq | TIGR00573 | exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
403-615 | 6.18e-35 | |||||||||||
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA] Pssm-ID: 129663 [Multi-domain] Cd Length: 217 Bit Score: 132.19 E-value: 6.18e-35
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| EXOIII | smart00479 | exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
402-564 | 1.46e-34 | |||||||||||
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases; Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 129.34 E-value: 1.46e-34
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| RNase_T | pfam00929 | Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
404-559 | 4.89e-30 | |||||||||||
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.; Pssm-ID: 395743 [Multi-domain] Cd Length: 164 Bit Score: 116.30 E-value: 4.89e-30
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| CehA_McbA_metalo | NF038032 | CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ... |
316-379 | 2.52e-03 | |||||||||||
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: 40.77 E-value: 2.52e-03
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| Name | Accession | Description | Interval | E-value | |||||||||||
| polC | PRK00448 | DNA polymerase III PolC; Validated |
2-737 | 0e+00 | |||||||||||
DNA polymerase III PolC; Validated Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 828.71 E-value: 0e+00
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| PHP_PolIIIA_POLC | cd07435 | Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ... |
316-743 | 1.73e-74 | |||||||||||
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: 242.38 E-value: 1.73e-74
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| PolC | COG2176 | DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
397-569 | 7.31e-72 | |||||||||||
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 231.96 E-value: 7.31e-72
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| DnaQ | COG0847 | DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
402-564 | 2.65e-55 | |||||||||||
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair]; Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 186.92 E-value: 2.65e-55
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| DEDDh | cd06127 | DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
404-560 | 3.07e-51 | |||||||||||
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others. Pssm-ID: 176648 [Multi-domain] Cd Length: 159 Bit Score: 175.95 E-value: 3.07e-51
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| PRK07883 | PRK07883 | DEDD exonuclease domain-containing protein; |
403-555 | 3.01e-35 | |||||||||||
DEDD exonuclease domain-containing protein; Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 141.21 E-value: 3.01e-35
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| dnaq | TIGR00573 | exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
403-615 | 6.18e-35 | |||||||||||
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA] Pssm-ID: 129663 [Multi-domain] Cd Length: 217 Bit Score: 132.19 E-value: 6.18e-35
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| EXOIII | smart00479 | exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
402-564 | 1.46e-34 | |||||||||||
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases; Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 129.34 E-value: 1.46e-34
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| PRK08074 | PRK08074 | bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
401-564 | 6.53e-33 | |||||||||||
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 136.62 E-value: 6.53e-33
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| dinG_rel | TIGR01407 | DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ... |
403-566 | 4.84e-31 | |||||||||||
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli. [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273602 [Multi-domain] Cd Length: 850 Bit Score: 130.31 E-value: 4.84e-31
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| RNase_T | pfam00929 | Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
404-559 | 4.89e-30 | |||||||||||
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.; Pssm-ID: 395743 [Multi-domain] Cd Length: 164 Bit Score: 116.30 E-value: 4.89e-30
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| PRK07740 | PRK07740 | hypothetical protein; Provisional |
402-569 | 4.64e-29 | |||||||||||
hypothetical protein; Provisional Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 116.31 E-value: 4.64e-29
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| DNA_pol_III_epsilon_like | cd06130 | an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
403-554 | 8.81e-29 | |||||||||||
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III; This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex. Pssm-ID: 99834 [Multi-domain] Cd Length: 156 Bit Score: 112.60 E-value: 8.81e-29
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| PHP_PolIIIA_DnaE3 | cd12113 | Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
589-751 | 1.21e-27 | |||||||||||
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: 113.30 E-value: 1.21e-27
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| PRK08517 | PRK08517 | 3'-5' exonuclease; |
368-559 | 1.99e-26 | |||||||||||
3'-5' exonuclease; Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 108.96 E-value: 1.99e-26
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| DNA_pol_III_epsilon_Ecoli_like | cd06131 | DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
403-553 | 5.79e-26 | |||||||||||
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex. Pssm-ID: 99835 [Multi-domain] Cd Length: 167 Bit Score: 104.92 E-value: 5.79e-26
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| dnaE | PRK06826 | DNA polymerase III DnaE; Reviewed |
592-746 | 8.28e-26 | |||||||||||
DNA polymerase III DnaE; Reviewed Pssm-ID: 235868 [Multi-domain] Cd Length: 1151 Bit Score: 114.22 E-value: 8.28e-26
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| PRK06807 | PRK06807 | 3'-5' exonuclease; |
402-641 | 1.27e-24 | |||||||||||
3'-5' exonuclease; Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 105.28 E-value: 1.27e-24
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| polC_OBF | cd04484 | polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding ... |
219-301 | 1.27e-23 | |||||||||||
polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis. Pssm-ID: 239930 [Multi-domain] Cd Length: 82 Bit Score: 94.97 E-value: 1.27e-23
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| PRK07246 | PRK07246 | bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
396-564 | 1.00e-22 | |||||||||||
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 104.00 E-value: 1.00e-22
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| dnaE | PRK05673 | DNA polymerase III subunit alpha; Validated |
587-734 | 1.90e-21 | |||||||||||
DNA polymerase III subunit alpha; Validated Pssm-ID: 235554 [Multi-domain] Cd Length: 1135 Bit Score: 100.18 E-value: 1.90e-21
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| PRK05711 | PRK05711 | DNA polymerase III subunit epsilon; Provisional |
404-553 | 6.37e-20 | |||||||||||
DNA polymerase III subunit epsilon; Provisional Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 89.53 E-value: 6.37e-20
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| polc | TIGR00594 | DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are ... |
594-751 | 1.10e-19 | |||||||||||
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: 94.37 E-value: 1.10e-19
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| DnaE | COG0587 | DNA polymerase III, alpha subunit [Replication, recombination and repair]; |
590-727 | 1.64e-19 | |||||||||||
DNA polymerase III, alpha subunit [Replication, recombination and repair]; Pssm-ID: 440352 [Multi-domain] Cd Length: 1050 Bit Score: 93.98 E-value: 1.64e-19
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| PRK06310 | PRK06310 | DNA polymerase III subunit epsilon; Validated |
401-553 | 3.30e-19 | |||||||||||
DNA polymerase III subunit epsilon; Validated Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 87.96 E-value: 3.30e-19
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| POLIIIAc | smart00481 | DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ... |
318-381 | 1.08e-18 | |||||||||||
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: 80.39 E-value: 1.08e-18
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| PHP | pfam02811 | PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ... |
318-385 | 1.56e-18 | |||||||||||
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain. Pssm-ID: 460705 [Multi-domain] Cd Length: 171 Bit Score: 83.75 E-value: 1.56e-18
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| PRK09145 | PRK09145 | 3'-5' exonuclease; |
397-560 | 1.17e-17 | |||||||||||
3'-5' exonuclease; Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 81.87 E-value: 1.17e-17
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| ERI-1_3'hExo_like | cd06133 | DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
403-563 | 3.40e-15 | |||||||||||
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo. Pssm-ID: 99836 [Multi-domain] Cd Length: 176 Bit Score: 74.18 E-value: 3.40e-15
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| dnaE | PRK07374 | DNA polymerase III subunit alpha; Validated |
589-726 | 1.36e-14 | |||||||||||
DNA polymerase III subunit alpha; Validated Pssm-ID: 168927 [Multi-domain] Cd Length: 1170 Bit Score: 78.23 E-value: 1.36e-14
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| KapD | COG5018 | 3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
396-564 | 1.91e-14 | |||||||||||
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms]; Pssm-ID: 444042 [Multi-domain] Cd Length: 181 Bit Score: 72.20 E-value: 1.91e-14
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| DNA_pol3_a_NII | pfam11490 | DNA polymerase III polC-type N-terminus II; This is the second N-terminal domain, NII domain, ... |
93-198 | 4.01e-13 | |||||||||||
DNA polymerase III polC-type N-terminus II; This is the second N-terminal domain, NII domain, of the DNA polymerase III polC subunit A that is found only in Firmicutes. DNA polymerase polC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria. Purine asymmetry is a characteriztic of organizms with a heterodimeric DNA polymerase III alpha-subunit constituted by polC which probably plays a direct role in the maintenance of strand-biased gene distribution; since, among prokaryotic genomes, the distribution of genes on the leading and lagging strands of the replication fork is known to be biased. It has been predicted that the N-terminus of polC folds into two globular domains, NI and NII. A predicted hydrophobic surface patch suggests this domain may be involved in protein binding. This domain is associated with DNA_pol3_alpha pfam07733 and DNA_pol3_a_NI pfam14480. Pssm-ID: 431908 Cd Length: 117 Bit Score: 66.22 E-value: 4.01e-13
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| PRK06309 | PRK06309 | DNA polymerase III subunit epsilon; Validated |
404-551 | 6.02e-13 | |||||||||||
DNA polymerase III subunit epsilon; Validated Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 69.07 E-value: 6.02e-13
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| PHP | cd07309 | Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2 ... |
317-382 | 1.52e-12 | |||||||||||
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: 63.99 E-value: 1.52e-12
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| PRK09532 | PRK09532 | DNA polymerase III subunit alpha; Reviewed |
589-739 | 4.82e-11 | |||||||||||
DNA polymerase III subunit alpha; Reviewed Pssm-ID: 181933 [Multi-domain] Cd Length: 874 Bit Score: 66.30 E-value: 4.82e-11
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| PRK06063 | PRK06063 | DEDDh family exonuclease; |
400-553 | 7.02e-11 | |||||||||||
DEDDh family exonuclease; Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 63.95 E-value: 7.02e-11
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| PHP_HisPPase | cd07432 | Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ... |
317-379 | 2.81e-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: 58.79 E-value: 2.81e-10
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| PHP_PolIIIA | cd07431 | Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ... |
317-382 | 3.75e-10 | |||||||||||
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: 59.52 E-value: 3.75e-10
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| PHP | pfam02811 | PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ... |
590-675 | 6.21e-10 | |||||||||||
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain. Pssm-ID: 460705 [Multi-domain] Cd Length: 171 Bit Score: 58.71 E-value: 6.21e-10
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| PRK09182 | PRK09182 | DNA polymerase III subunit epsilon; Validated |
404-498 | 8.87e-10 | |||||||||||
DNA polymerase III subunit epsilon; Validated Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 60.37 E-value: 8.87e-10
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| PHP_PolIIIA_DnaE1 | cd07433 | Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
590-726 | 5.22e-09 | |||||||||||
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: 57.87 E-value: 5.22e-09
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| PHP_HisPPase_AMP | cd07438 | Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ... |
317-375 | 5.73e-09 | |||||||||||
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: 55.48 E-value: 5.73e-09
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| DNA_pol3_a_NI | pfam14480 | DNA polymerase III polC-type N-terminus I; This is the first N-terminal domain, NI domain, of ... |
7-78 | 5.94e-09 | |||||||||||
DNA polymerase III polC-type N-terminus I; This is the first N-terminal domain, NI domain, of the DNA polymerase III polC subunit A that is found only in Firmicutes. DNA polymerase polC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria. Purine asymmetry is a characteriztic of organizms with a heterodimeric DNA polymerase III alpha-subunit constituted by polC which probably plays a direct role in the maintenance of strand-biased gene distribution; since, among prokaryotic genomes, the distribution of genes on the leading and lagging strands of the replication fork is known to be biased. It has been predicted that the N-terminus of polC folds into two globular domains, NI and NII. A predicted patch of elecrostatic potential at the surface of this domain suggests a possible involvement in nucleic acid binding. This domain is associated with DNA_pol3_alpha pfam07733 and DNA_pol3_a_NI pfam11490. Pssm-ID: 433981 Cd Length: 72 Bit Score: 52.93 E-value: 5.94e-09
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| PRK07247 | PRK07247 | 3'-5' exonuclease; |
401-490 | 1.92e-08 | |||||||||||
3'-5' exonuclease; Pssm-ID: 180906 [Multi-domain] Cd Length: 195 Bit Score: 55.17 E-value: 1.92e-08
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| YciV | COG0613 | 5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ... |
316-379 | 3.01e-08 | |||||||||||
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism]; Pssm-ID: 440378 [Multi-domain] Cd Length: 188 Bit Score: 54.15 E-value: 3.01e-08
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| PRK09146 | PRK09146 | DNA polymerase III subunit epsilon; Validated |
402-558 | 6.99e-08 | |||||||||||
DNA polymerase III subunit epsilon; Validated Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 54.16 E-value: 6.99e-08
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| PRK06195 | PRK06195 | DNA polymerase III subunit epsilon; Validated |
403-554 | 2.53e-07 | |||||||||||
DNA polymerase III subunit epsilon; Validated Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 53.25 E-value: 2.53e-07
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| dnaE2 | PRK05672 | error-prone DNA polymerase; Validated |
318-379 | 2.87e-07 | |||||||||||
error-prone DNA polymerase; Validated Pssm-ID: 235553 [Multi-domain] Cd Length: 1046 Bit Score: 54.09 E-value: 2.87e-07
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| PRK07942 | PRK07942 | DNA polymerase III subunit epsilon; Provisional |
406-572 | 1.97e-06 | |||||||||||
DNA polymerase III subunit epsilon; Provisional Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 49.59 E-value: 1.97e-06
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| DNA_polA_I_Ecoli_like_exo | cd06139 | DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial ... |
401-538 | 2.43e-06 | |||||||||||
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair. Pssm-ID: 176651 [Multi-domain] Cd Length: 193 Bit Score: 48.67 E-value: 2.43e-06
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| RNaseT | cd06134 | DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ... |
398-504 | 2.53e-06 | |||||||||||
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site. Pssm-ID: 99837 [Multi-domain] Cd Length: 189 Bit Score: 48.44 E-value: 2.53e-06
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| HIS2 | COG1387 | Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and ... |
316-385 | 3.73e-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: 48.61 E-value: 3.73e-06
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| dnaE | PRK06920 | DNA polymerase III subunit alpha; |
596-737 | 4.39e-06 | |||||||||||
DNA polymerase III subunit alpha; Pssm-ID: 180749 [Multi-domain] Cd Length: 1107 Bit Score: 50.57 E-value: 4.39e-06
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| UvrD_C | pfam13361 | UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
370-480 | 6.06e-06 | |||||||||||
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold. Pssm-ID: 433145 [Multi-domain] Cd Length: 377 Bit Score: 49.33 E-value: 6.06e-06
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| PolA | COG0749 | DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ... |
401-538 | 1.47e-05 | |||||||||||
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and repair]; Pssm-ID: 440512 [Multi-domain] Cd Length: 575 Bit Score: 48.51 E-value: 1.47e-05
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| PHP_PolIIIA_DnaE1 | cd07433 | Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ... |
317-377 | 1.98e-05 | |||||||||||
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: 47.09 E-value: 1.98e-05
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| PHP_PolIIIA | cd07431 | Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ... |
595-737 | 2.10e-04 | |||||||||||
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: 42.96 E-value: 2.10e-04
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| ExoI_N | cd06138 | N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar ... |
404-555 | 4.68e-04 | |||||||||||
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site. Pssm-ID: 99841 [Multi-domain] Cd Length: 183 Bit Score: 41.87 E-value: 4.68e-04
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| PHP_HisPPase_Ycdx_like | cd07437 | Polymerase and Histidinol Phosphatase domain of Ycdx like; PHP Ycdx-like is a stand alone PHP ... |
317-398 | 1.27e-03 | |||||||||||
Polymerase and Histidinol Phosphatase domain of Ycdx like; PHP Ycdx-like is a stand alone PHP domain similar to Ycdx E. coli protein with an unknown physiological role. 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. 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. YcdX may be involved in swarming. Pssm-ID: 213992 [Multi-domain] Cd Length: 233 Bit Score: 41.27 E-value: 1.27e-03
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| dnaE | PRK07374 | DNA polymerase III subunit alpha; Validated |
317-384 | 1.71e-03 | |||||||||||
DNA polymerase III subunit alpha; Validated Pssm-ID: 168927 [Multi-domain] Cd Length: 1170 Bit Score: 42.02 E-value: 1.71e-03
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| PRK09532 | PRK09532 | DNA polymerase III subunit alpha; Reviewed |
317-384 | 2.35e-03 | |||||||||||
DNA polymerase III subunit alpha; Reviewed Pssm-ID: 181933 [Multi-domain] Cd Length: 874 Bit Score: 41.27 E-value: 2.35e-03
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| CehA_McbA_metalo | NF038032 | CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ... |
316-379 | 2.52e-03 | |||||||||||
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: 40.77 E-value: 2.52e-03
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| tRNA_anti-codon | pfam01336 | OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ... |
222-301 | 2.64e-03 | |||||||||||
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain. Pssm-ID: 460164 [Multi-domain] Cd Length: 75 Bit Score: 37.21 E-value: 2.64e-03
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| PRK07748 | PRK07748 | 3'-5' exonuclease KapD; |
420-482 | 3.56e-03 | |||||||||||
3'-5' exonuclease KapD; Pssm-ID: 236087 Cd Length: 207 Bit Score: 39.67 E-value: 3.56e-03
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| PHP_PolX | cd07436 | Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal ... |
319-374 | 7.40e-03 | |||||||||||
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: 38.94 E-value: 7.40e-03
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