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Conserved domains on  [gi|502068595|ref|WP_012705080|]
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PHP domain-containing protein [Clostridium botulinum]

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

CATH:  3.20.20.140
Gene Ontology:  GO:0046872
PubMed:  9685491
SCOP:  4000443

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YciV COG0613
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ...
 1-167 1.56e-44

5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism];


:

Pssm-ID: 440378 [Multi-domain]  Cd Length: 188  Bit Score: 147.36  E-value: 1.56e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595   1 MIIDTHIHeSKYSlDSEISLEEIVKRGKEIGLDGVCITDHESSDIMDEAHAYSKATGFLILVGAEILTY----EGDILVF 76
Cdd:COG0613    2 MKIDLHVH-TTAS-DGSLSPEELVARAKAAGLDVLAITDHDTVAGYEEAAEAAKELGLLVIPGVEISTRwegrEVHILGY 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595  77 GLKD----------IP-----KNKMHAKDLLKIVYENNGVAISAHPYRNN-NRGMGDYIREAKMLGLSGVEAFNGSTEPH 140
Cdd:COG0613   80 GIDPedpaleallgIPvekaeREWLSLEEAIDLIREAGGVAVLAHPFRYKrGRWLDDLLEELADAGLDGIEVYNGRHSPE 159

                        170       180
                 ....*....|....*....|....*..
gi 502068595 141 QNLLAYSLATELNLPCIGSSDAHVIEK 167
Cdd:COG0613  160 DNERAAELAEEYGLLATGGSDAHGPEK 186
 
Name Accession Description Interval E-value
YciV COG0613
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ...
 1-167 1.56e-44

5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism];


Pssm-ID: 440378 [Multi-domain]  Cd Length: 188  Bit Score: 147.36  E-value: 1.56e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595   1 MIIDTHIHeSKYSlDSEISLEEIVKRGKEIGLDGVCITDHESSDIMDEAHAYSKATGFLILVGAEILTY----EGDILVF 76
Cdd:COG0613    2 MKIDLHVH-TTAS-DGSLSPEELVARAKAAGLDVLAITDHDTVAGYEEAAEAAKELGLLVIPGVEISTRwegrEVHILGY 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595  77 GLKD----------IP-----KNKMHAKDLLKIVYENNGVAISAHPYRNN-NRGMGDYIREAKMLGLSGVEAFNGSTEPH 140
Cdd:COG0613   80 GIDPedpaleallgIPvekaeREWLSLEEAIDLIREAGGVAVLAHPFRYKrGRWLDDLLEELADAGLDGIEVYNGRHSPE 159

                        170       180
                 ....*....|....*....|....*..
gi 502068595 141 QNLLAYSLATELNLPCIGSSDAHVIEK 167
Cdd:COG0613  160 DNERAAELAEEYGLLATGGSDAHGPEK 186
PHP_HisPPase cd07432
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ...
 3-164 2.03e-33

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: 116.96  E-value: 2.03e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595   3 IDTHIHeSKYSLDSEISLEEIVKRGKEIGLDGVCITDHESSDIMDEAHAYSKATGFLILVGAEIltyegdilvfglkdip 82
Cdd:cd07432    1 ADLHIH-SVFSPDSDMTPEEIVERAIELGLDGIAITDHNTIDGAEEALKEAYKDGLLVIPGVEV---------------- 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595  83 knkmhakdllkivyennGVAISAHPYRNNNRGMGDYIREAKMLGLSGVEAFNGST-EPHQNLLAYSLATELNLPCIGSSD 161
Cdd:cd07432   64 -----------------TLVVLAHPDRPSRYGLSDLILKPLIKNGDAIEVNNSRLrYGLNNLAAKRYAELGGLPITGGSD 126


                 ...
gi 502068595 162 AHV 164
Cdd:cd07432  127 AHT 129
PHP_C pfam13263
PHP-associated; This is a subunit, probably the alpha, of bacterial and eukaryotic DNA ...
 139-194 2.29e-19

PHP-associated; This is a subunit, probably the alpha, of bacterial and eukaryotic DNA polymerase III, associated with the PHP domain, pfam02811.


Pssm-ID: 433069 [Multi-domain]  Cd Length: 56  Bit Score: 78.38  E-value: 2.29e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 502068595  139 PHQNLLAYSLATELNLPCIGSSDAHVIEKVGKYATVFPNGIRDEKDLIQAIKENNV 194
Cdd:pfam13263   1 GEANRKARRLAEKLGLPGTGGSDAHVLEEVGRAYTEFEEDIRTEEDLLEAIRKGRT 56
CehA_McbA_metalo NF038032
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ...
 4-195 4.69e-15

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: 72.36  E-value: 4.69e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595   4 DTHIHeSKYSlDSEISLEEIVKRGKEIGLDGVCITDHESS---DIMDEAHAYSkaTGFLILVGAEILTYEGDILVFGLKD 80
Cdd:NF038032   6 DLHIH-TNHS-DGPTTPEELARAALAEGLDVIALTDHNTIsgrAYFAELLASE--RGLLVIPGMEVTTFWGHMNLLGLDL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595  81 IP--------KNKMHAKDLLKIVYENNGVAISAHPYRnnnrgMGDYIR-----EAKMLGLSGV---EAFNGSTEPHQNLL 144
Cdd:NF038032  82 DPyidwrntdPGSPDIDEVIDEAHRQGGLVGIAHPFS-----PGGPLCtgcgwEALIDDLGKVdaiEVWNTPDPAPTNER 156

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 502068595 145 AYSLATEL-----NLPCIGSSDAHVI--EKVGKYATVF-PNGIRDEKDLIQAIKENNVC 195
Cdd:NF038032 157 ALALWYHLlnegfRITATGGSDAHDDfdERPGLPRTYVyVDGELSYEAILAALKAGRTY 215
POLIIIAc smart00481
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ...
 4-66 4.66e-10

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: 53.81  E-value: 4.66e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 502068595     4 DTHIHeSKYS-LDSEISLEEIVKRGKEIGLDGVCITDHESSDIMDEAHAYSKATGFLILVGAEI 66
Cdd:smart00481   1 DLHVH-SDYSlLDGALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYKAAKKAGIKPIIGLEA 63
polC PRK00448
DNA polymerase III PolC; Validated
 6-80 6.71e-04

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 40.21  E-value: 6.71e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 502068595    6 HIHESKYSLDSEISLEEIVKRGKEIGLDGVCITDHESSDIMDEAHAYSKATGFLILVGAEILTYEGDI-LVFGLKD 80
Cdd:PRK00448  338 HLHTKMSTMDAIPSVSELVKRAAKWGHKAIAITDHGVVQAFPEAYNAAKKAGIKVIYGVEANLVDDGVpIVYNEVD 413
polc TIGR00594
DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are ...
 6-40 5.22e-03

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: 37.75  E-value: 5.22e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 502068595     6 HIHeSKYS-LDSEISLEEIVKRGKEIGLDGVCITDH 40
Cdd:TIGR00594    5 HVH-SDYSlLDGAAKIKPLVKKAKELGMPALALTDH 39
 
Name Accession Description Interval E-value
YciV COG0613
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ...
 1-167 1.56e-44

5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism];


Pssm-ID: 440378 [Multi-domain]  Cd Length: 188  Bit Score: 147.36  E-value: 1.56e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595   1 MIIDTHIHeSKYSlDSEISLEEIVKRGKEIGLDGVCITDHESSDIMDEAHAYSKATGFLILVGAEILTY----EGDILVF 76
Cdd:COG0613    2 MKIDLHVH-TTAS-DGSLSPEELVARAKAAGLDVLAITDHDTVAGYEEAAEAAKELGLLVIPGVEISTRwegrEVHILGY 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595  77 GLKD----------IP-----KNKMHAKDLLKIVYENNGVAISAHPYRNN-NRGMGDYIREAKMLGLSGVEAFNGSTEPH 140
Cdd:COG0613   80 GIDPedpaleallgIPvekaeREWLSLEEAIDLIREAGGVAVLAHPFRYKrGRWLDDLLEELADAGLDGIEVYNGRHSPE 159

                        170       180
                 ....*....|....*....|....*..
gi 502068595 141 QNLLAYSLATELNLPCIGSSDAHVIEK 167
Cdd:COG0613  160 DNERAAELAEEYGLLATGGSDAHGPEK 186
PHP_HisPPase cd07432
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ...
 3-164 2.03e-33

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: 116.96  E-value: 2.03e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595   3 IDTHIHeSKYSLDSEISLEEIVKRGKEIGLDGVCITDHESSDIMDEAHAYSKATGFLILVGAEIltyegdilvfglkdip 82
Cdd:cd07432    1 ADLHIH-SVFSPDSDMTPEEIVERAIELGLDGIAITDHNTIDGAEEALKEAYKDGLLVIPGVEV---------------- 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595  83 knkmhakdllkivyennGVAISAHPYRNNNRGMGDYIREAKMLGLSGVEAFNGST-EPHQNLLAYSLATELNLPCIGSSD 161
Cdd:cd07432   64 -----------------TLVVLAHPDRPSRYGLSDLILKPLIKNGDAIEVNNSRLrYGLNNLAAKRYAELGGLPITGGSD 126


                 ...
gi 502068595 162 AHV 164
Cdd:cd07432  127 AHT 129
PHP_HisPPase_AMP cd07438
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ...
 3-163 1.80e-22

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: 89.37  E-value: 1.80e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595   3 IDTHIHeSKYSLDSEiSLEEIVKRGKEIGLDGVCITDHESSDIMDEAHAYSKATGFLILVGAEILTYEGDILVfglkdip 82
Cdd:cd07438    1 IDLHTH-STASDGTL-SPEELVELAKEAGLKVLAITDHDTVAGLEEALAAAKELGIELIPGVEISTEYEGREV------- 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595  83 knkmH----AKDLLKIVYENNGVAISAHP--YRNNNRGMGDYIREAKMLGLSGVEAFNGSTEPHQNLLAYSLATELNLPC 156
Cdd:cd07438   72 ----HilgsPEEAIELIHAAGGVAVLAHPglYKLSRKKLEELIEELKEAGLDGIEVYHPYHSPEDRERLLELAKEYGLLV 147


                 ....*..
gi 502068595 157 IGSSDAH 163
Cdd:cd07438  148 TGGSDFH 154
PHP_C pfam13263
PHP-associated; This is a subunit, probably the alpha, of bacterial and eukaryotic DNA ...
 139-194 2.29e-19

PHP-associated; This is a subunit, probably the alpha, of bacterial and eukaryotic DNA polymerase III, associated with the PHP domain, pfam02811.


Pssm-ID: 433069 [Multi-domain]  Cd Length: 56  Bit Score: 78.38  E-value: 2.29e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 502068595  139 PHQNLLAYSLATELNLPCIGSSDAHVIEKVGKYATVFPNGIRDEKDLIQAIKENNV 194
Cdd:pfam13263   1 GEANRKARRLAEKLGLPGTGGSDAHVLEEVGRAYTEFEEDIRTEEDLLEAIRKGRT 56
CehA_McbA_metalo NF038032
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ...
 4-195 4.69e-15

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: 72.36  E-value: 4.69e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595   4 DTHIHeSKYSlDSEISLEEIVKRGKEIGLDGVCITDHESS---DIMDEAHAYSkaTGFLILVGAEILTYEGDILVFGLKD 80
Cdd:NF038032   6 DLHIH-TNHS-DGPTTPEELARAALAEGLDVIALTDHNTIsgrAYFAELLASE--RGLLVIPGMEVTTFWGHMNLLGLDL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595  81 IP--------KNKMHAKDLLKIVYENNGVAISAHPYRnnnrgMGDYIR-----EAKMLGLSGV---EAFNGSTEPHQNLL 144
Cdd:NF038032  82 DPyidwrntdPGSPDIDEVIDEAHRQGGLVGIAHPFS-----PGGPLCtgcgwEALIDDLGKVdaiEVWNTPDPAPTNER 156

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 502068595 145 AYSLATEL-----NLPCIGSSDAHVI--EKVGKYATVF-PNGIRDEKDLIQAIKENNVC 195
Cdd:NF038032 157 ALALWYHLlnegfRITATGGSDAHDDfdERPGLPRTYVyVDGELSYEAILAALKAGRTY 215
POLIIIAc smart00481
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ...
 4-66 4.66e-10

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: 53.81  E-value: 4.66e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 502068595     4 DTHIHeSKYS-LDSEISLEEIVKRGKEIGLDGVCITDHESSDIMDEAHAYSKATGFLILVGAEI 66
Cdd:smart00481   1 DLHVH-SDYSlLDGALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYKAAKKAGIKPIIGLEA 63
HIS2 COG1387
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and ...
 1-172 5.21e-10

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: 57.47  E-value: 5.21e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595   1 MIIDTHIHeSKYSlDSEISLEEIVKRGKEIGLDGVCITDHESSDIM------DEAHAY--------SKATGFLILVGAEI 66
Cdd:COG1387    1 MRGDLHTH-TTYS-DGEGTIEEMVEAAIELGLEYIAITDHSPSLFVanglseERLLEYleeieelnEKYPDIKILKGIEV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595  67 ltyegDILVFGLKDIPKNK----------MH----------AKDLLKIVyENNGVAISAHP---YRNNNRGMGDYIRE-- 121
Cdd:COG1387   79 -----DILPDGSLDYPDELlapldyvigsVHsileedyeeyTERLLKAI-ENPLVDILGHPdgrLLGGRPGYEVDIEEvl 152

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 502068595 122 --AKMLGLsGVE--AFNGSTEPHQNLLAysLATELNLPCIGSSDAHVIEKVGKYA 172
Cdd:COG1387  153 eaAAENGV-ALEinTRPLRLDPSDELLK--LAKELGVKITIGSDAHSPEDLGDLE 204
PHP pfam02811
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ...
 4-66 1.58e-08

PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain.


Pssm-ID: 460705 [Multi-domain]  Cd Length: 171  Bit Score: 52.16  E-value: 1.58e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 502068595    4 DTHIHeSKYSL-DSEISLEEIVKRGKEIGLDGVCITDHESSDIMDEAHAYSKATGFLILVGAEI 66
Cdd:pfam02811   1 HLHVH-SEYSLlDGAARIEELVKRAKELGMPAIAITDHGNLFGAVEFYKAAKKAGIKPIIGCEV 63
PHP_HisPPase_Thermotoga_like cd12111
Polymerase and Histidinol Phosphatase domain of Thermotoga like; The PHP (also called ...
 4-191 8.08e-08

Polymerase and Histidinol Phosphatase domain of Thermotoga 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. Thermotoga PHP is an uncharacterized protein. HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to give 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: 213995 [Multi-domain]  Cd Length: 226  Bit Score: 50.88  E-value: 8.08e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595   4 DTHIHeSKYSlDSEISLEEIVKRGKEIGLDGVCITDH----------------------ESSDIMDE-----AHAYSKaT 56
Cdd:cd12111    5 DFHIH-TTYS-DGALSLSEVVDLYGQHGFDVIAITDHvvdrasligkfpqgthpgvteaNFEDYMEAlkveaKRAWEK-Y 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595  57 GFLILVGAEIL--TYEGDILVFGLKDIPKNKMHAKDLLKIVYENNGVAISAHPYRNNNrgmgDYIREAKMLGLSG---VE 131
Cdd:cd12111   82 EMIVIPGVELTnnTDSYHILGIDVKEYIDPCLSVEEIIAEIHKQGGIAVAAHPHRKNL----DGEHNSLYLWNNReryKH 157

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595 132 AFNGSTEPHQNLLaYSLATELNLPCIGSSDAHVIEKVGKYATVfpngIRDEKDlIQAIKE 191
Cdd:cd12111  158 LFDAWEIANRDDL-FNVVGLKKLPYIANSDFHKPKHLYSWKTL----LKCEKN-IEAIKE 211
DnaE COG0587
DNA polymerase III, alpha subunit [Replication, recombination and repair];
6-66 1.53e-04

DNA polymerase III, alpha subunit [Replication, recombination and repair];


Pssm-ID: 440352 [Multi-domain]  Cd Length: 1050  Bit Score: 42.36  E-value: 1.53e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 502068595    6 HIHeSKYS-LDSEISLEEIVKRGKEIGLDGVCITDHES-SDIMdEAHAYSKATGFLILVGAEI 66
Cdd:COG0587     9 HVH-SEYSlLDGASRPEELVARAAELGMPALAITDHGNlFGAV-RFYKAAKKAGIKPIIGCEL 69
PHP_HisPPase_Chlorobi_like cd12112
Polymerase and Histidinol Phosphatase domain of Chlorobi like; The PHP (also called histidinol ...
 4-163 2.08e-04

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: 41.16  E-value: 2.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595   4 DTHIHeSKYSlDSEISLEEIVKRGKEIGLDGVCITDH-----ESSDIM--DEAHAYSKA------TGFLILVGAEIlTYE 70
Cdd:cd12112   16 DFHTH-TVFS-DGHVWPEIRVREAWREGLDAIAITEHieyrpHKEDIPhpDRNRSYKIAkeaaesKGLLIIPGAEI-TRE 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595  71 ---GDILVFGLKDIpkNKMHAKDLLKIVyeNNGVAISA-----HP--YRNNNRGMGDYIREAKMLG---LSGVEAFNGST 137
Cdd:cd12112   93 kppGHLNALFLTDA--NALLVPDPLDAI--RAAKKQGAfvfwnHPgwPDQSPDGIALPPFHEKLIEeglIHGIEVMNGTE 168

                        170       180
                 ....*....|....*....|....*.
gi 502068595 138 EPHQnllAYSLATELNLPCIGSSDAH 163
Cdd:cd12112  169 YYPE---AIQWALEYNLTVMGTSDIH 191
PHP_PolIIIA_POLC cd07435
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ...
 6-95 3.37e-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: 40.53  E-value: 3.37e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595   6 HIHeSKYS-LDSEISLEEIVKRGKEIGLDGVCITDHESSDIMDEAHAYSKATGFLILVGAE---ILTYEGDILVfglkdi 81
Cdd:cd07435    5 HAH-TKMSaMDGVTSVKELVKRAAEWGHKAIAITDHGVVQAFPEAYEAAKKNGIKVIYGVEaylVDPYHITILV------ 77

                         90
                 ....*....|....
gi 502068595  82 pKNKMHAKDLLKIV 95
Cdd:cd07435   78 -KNQTGLKNLYKLV 90
polC PRK00448
DNA polymerase III PolC; Validated
 6-80 6.71e-04

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 40.21  E-value: 6.71e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 502068595    6 HIHESKYSLDSEISLEEIVKRGKEIGLDGVCITDHESSDIMDEAHAYSKATGFLILVGAEILTYEGDI-LVFGLKD 80
Cdd:PRK00448  338 HLHTKMSTMDAIPSVSELVKRAAKWGHKAIAITDHGVVQAFPEAYNAAKKAGIKVIYGVEANLVDDGVpIVYNEVD 413
PHP_PolIIIA cd07431
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ...
 6-40 6.88e-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: 39.11  E-value: 6.88e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 502068595   6 HIHeSKYS-LDSEISLEEIVKRGKEIGLDGVCITDH 40
Cdd:cd07431    4 HVH-SSYSlLDSAIRPEDLVARAKELGYSALALTDR 38
PHP_HisPPase_Ycdx_like cd07437
Polymerase and Histidinol Phosphatase domain of Ycdx like; PHP Ycdx-like is a stand alone PHP ...
 2-73 1.75e-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: 38.19  E-value: 1.75e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502068595   2 IIDTHIH----ESKYSldseiSLEEIVKRGKEIGLDGVCITDHeSSDIMDEAHAY---------SKATGFLILVGAE--I 66
Cdd:cd07437    2 LADLHTHtiasGHAYS-----TIEEMARAAAEKGLKLLGITDH-GPAMPGAPHPWyfgnlkvipREIYGVRILRGVEanI 75


                 ....*..
gi 502068595  67 LTYEGDI 73
Cdd:cd07437   76 IDYDGNL 82
dnaE PRK06826
DNA polymerase III DnaE; Reviewed
 6-40 4.12e-03

DNA polymerase III DnaE; Reviewed


Pssm-ID: 235868 [Multi-domain]  Cd Length: 1151  Bit Score: 37.95  E-value: 4.12e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 502068595    6 HIHeSKYSL-DSEISLEEIVKRGKEIGLDGVCITDH 40
Cdd:PRK06826    9 HVH-TEYSLlDGSARIKDLIKRAKELGMDSIAITDH 43
PHP_PolIIIA_DnaE3 cd12113
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ...
 6-40 4.16e-03

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: 37.42  E-value: 4.16e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 502068595   6 HIHeSKYS-LDSEISLEEIVKRGKEIGLDGVCITDH 40
Cdd:cd12113    6 HVH-TEYSlLDGAIRIKDLVKRAKELGMPALAITDH 40
polc TIGR00594
DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are ...
 6-40 5.22e-03

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: 37.75  E-value: 5.22e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 502068595     6 HIHeSKYS-LDSEISLEEIVKRGKEIGLDGVCITDH 40
Cdd:TIGR00594    5 HVH-SDYSlLDGAAKIKPLVKKAKELGMPALALTDH 39
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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