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Conserved domains on  [gi|873896210|ref|WP_048602658|]
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PHP domain-containing protein [Rubeoparvulum massiliense]

Protein Classification

PHP_HisPPase and PHP_C domain-containing protein( domain architecture ID 11427627)

PHP_HisPPase and PHP_C domain-containing protein

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 ...
 1-161 2.99e-39

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


:

Pssm-ID: 440378 [Multi-domain]  Cd Length: 188  Bit Score: 133.11  E-value: 2.99e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210   1 MLIDTHMHEkTYSgDSHQALEEIVKTARERGLDAVCITDHESNRLWDEAHRYAKENGFPIFVGTEILT----KEGDLVVF 76
Cdd:COG0613    2 MKIDLHVHT-TAS-DGSLSPEELVARAKAAGLDVLAITDHDTVAGYEEAAEAAKELGLLVIPGVEISTrwegREVHILGY 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210  77 GLT----DLPEEM-----------LHAQDLIRLVDQAGGVCISAHPYRTNNRGLGNHLRD---VEGLAGVEAFNGNTPPH 138
Cdd:COG0613   80 GIDpedpALEALLgipvekaerewLSLEEAIDLIREAGGVAVLAHPFRYKRGRWLDDLLEelaDAGLDGIEVYNGRHSPE 159

                        170       180
                 ....*....|....*....|...
gi 873896210 139 HNLMAYAVATELGLPMFGASDAH 161
Cdd:COG0613  160 DNERAAELAEEYGLLATGGSDAH 182
PHP_C pfam13263
PHP-associated; This is a subunit, probably the alpha, of bacterial and eukaryotic DNA ...
 137-192 2.00e-16

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: 70.29  E-value: 2.00e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 873896210  137 PHHNLMAYAVATELGLPMFGASDAHWAHQVGKYATIFPDGIRDEQDLIAAIRSKEV 192
Cdd:pfam13263   1 GEANRKARRLAEKLGLPGTGGSDAHVLEEVGRAYTEFEEDIRTEEDLLEAIRKGRT 56
 
Name Accession Description Interval E-value
YciV COG0613
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ...
 1-161 2.99e-39

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


Pssm-ID: 440378 [Multi-domain]  Cd Length: 188  Bit Score: 133.11  E-value: 2.99e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210   1 MLIDTHMHEkTYSgDSHQALEEIVKTARERGLDAVCITDHESNRLWDEAHRYAKENGFPIFVGTEILT----KEGDLVVF 76
Cdd:COG0613    2 MKIDLHVHT-TAS-DGSLSPEELVARAKAAGLDVLAITDHDTVAGYEEAAEAAKELGLLVIPGVEISTrwegREVHILGY 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210  77 GLT----DLPEEM-----------LHAQDLIRLVDQAGGVCISAHPYRTNNRGLGNHLRD---VEGLAGVEAFNGNTPPH 138
Cdd:COG0613   80 GIDpedpALEALLgipvekaerewLSLEEAIDLIREAGGVAVLAHPFRYKRGRWLDDLLEelaDAGLDGIEVYNGRHSPE 159

                        170       180
                 ....*....|....*....|...
gi 873896210 139 HNLMAYAVATELGLPMFGASDAH 161
Cdd:COG0613  160 DNERAAELAEEYGLLATGGSDAH 182
PHP_HisPPase cd07432
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ...
 3-162 6.25e-28

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: 102.32  E-value: 6.25e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210   3 IDTHMHEkTYSGDSHQALEEIVKTARERGLDAVCITDHESNRLWDEAHRYAKENGFPIFVGTEIltkegdlvvfgltdlp 82
Cdd:cd07432    1 ADLHIHS-VFSPDSDMTPEEIVERAIELGLDGIAITDHNTIDGAEEALKEAYKDGLLVIPGVEV---------------- 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210  83 eemlhaqdlirlvdqagGVCISAHPYRTNNRGLGN--HLRDVEGLAGVEAFNGNTPPHHN-LMAYAVATELGLPMFGASD 159
Cdd:cd07432   64 -----------------TLVVLAHPDRPSRYGLSDliLKPLIKNGDAIEVNNSRLRYGLNnLAAKRYAELGGLPITGGSD 126


                 ...
gi 873896210 160 AHW 162
Cdd:cd07432  127 AHT 129
PHP_C pfam13263
PHP-associated; This is a subunit, probably the alpha, of bacterial and eukaryotic DNA ...
 137-192 2.00e-16

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: 70.29  E-value: 2.00e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 873896210  137 PHHNLMAYAVATELGLPMFGASDAHWAHQVGKYATIFPDGIRDEQDLIAAIRSKEV 192
Cdd:pfam13263   1 GEANRKARRLAEKLGLPGTGGSDAHVLEEVGRAYTEFEEDIRTEEDLLEAIRKGRT 56
CehA_McbA_metalo NF038032
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ...
 4-189 7.13e-14

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: 68.89  E-value: 7.13e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210   4 DTHMHekTYSGDSHQALEEIVKTARERGLDAVCITDHesNRLW---DEAHRYAKENGFPIFVGTEILTKEGDLVVFGLTD 80
Cdd:NF038032   6 DLHIH--TNHSDGPTTPEELARAALAEGLDVIALTDH--NTISgraYFAELLASERGLLVIPGMEVTTFWGHMNLLGLDL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210  81 LPE--------EMLHAQDLIRLVDQAGGVCISAHPYRT---NNRGLGN--HLRDVEGLAGVEAFNGNTPPHHNLMAYAVA 147
Cdd:NF038032  82 DPYidwrntdpGSPDIDEVIDEAHRQGGLVGIAHPFSPggpLCTGCGWeaLIDDLGKVDAIEVWNTPDPAPTNERALALW 161

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 873896210 148 TEL---G--LPMFGASDAH--WAHQVGKYAT-IFPDGIRDEQDLIAAIRS 189
Cdd:NF038032 162 YHLlneGfrITATGGSDAHddFDERPGLPRTyVYVDGELSYEAILAALKA 211
POLIIIAc smart00481
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ...
 4-66 2.83e-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: 54.19  E-value: 2.83e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 873896210     4 DTHMHEKtYSG-DSHQALEEIVKTARERGLDAVCITDHESNRLWDEAHRYAKENGFPIFVGTEI 66
Cdd:smart00481   1 DLHVHSD-YSLlDGALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYKAAKKAGIKPIIGLEA 63
PRK09248 PRK09248
putative hydrolase; Validated
 2-92 5.86e-08

putative hydrolase; Validated


Pssm-ID: 236429 [Multi-domain]  Cd Length: 246  Bit Score: 51.38  E-value: 5.86e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210   2 LIDTHMHekTY-SGDSHQALEEIVKTARERGLDAVCITDHESNrLWDEAHRY---------AKENGFPIFVGTE--ILTK 69
Cdd:PRK09248   4 PVDTHTH--TIaSGHAYSTLHENAAEAKQKGLKLFAITDHGPD-MPGAPHYWhfgnlrvlpRKVDGVGILRGIEanIKNY 80

                         90       100
                 ....*....|....*....|...
gi 873896210  70 EGDLvvfgltDLPEEMLHAQDLI 92
Cdd:PRK09248  81 DGEI------DLPGDMLKKLDIV 97
PHP pfam02811
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ...
 4-66 5.21e-07

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


Pssm-ID: 460705 [Multi-domain]  Cd Length: 171  Bit Score: 47.92  E-value: 5.21e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 873896210    4 DTHMHekT-YS-GDSHQALEEIVKTARERGLDAVCITDHeSNRL-WDEAHRYAKENGFPIFVGTEI 66
Cdd:pfam02811   1 HLHVH--SeYSlLDGAARIEELVKRAKELGMPAIAITDH-GNLFgAVEFYKAAKKAGIKPIIGCEV 63
 
Name Accession Description Interval E-value
YciV COG0613
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ...
 1-161 2.99e-39

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


Pssm-ID: 440378 [Multi-domain]  Cd Length: 188  Bit Score: 133.11  E-value: 2.99e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210   1 MLIDTHMHEkTYSgDSHQALEEIVKTARERGLDAVCITDHESNRLWDEAHRYAKENGFPIFVGTEILT----KEGDLVVF 76
Cdd:COG0613    2 MKIDLHVHT-TAS-DGSLSPEELVARAKAAGLDVLAITDHDTVAGYEEAAEAAKELGLLVIPGVEISTrwegREVHILGY 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210  77 GLT----DLPEEM-----------LHAQDLIRLVDQAGGVCISAHPYRTNNRGLGNHLRD---VEGLAGVEAFNGNTPPH 138
Cdd:COG0613   80 GIDpedpALEALLgipvekaerewLSLEEAIDLIREAGGVAVLAHPFRYKRGRWLDDLLEelaDAGLDGIEVYNGRHSPE 159

                        170       180
                 ....*....|....*....|...
gi 873896210 139 HNLMAYAVATELGLPMFGASDAH 161
Cdd:COG0613  160 DNERAAELAEEYGLLATGGSDAH 182
PHP_HisPPase cd07432
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ...
 3-162 6.25e-28

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: 102.32  E-value: 6.25e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210   3 IDTHMHEkTYSGDSHQALEEIVKTARERGLDAVCITDHESNRLWDEAHRYAKENGFPIFVGTEIltkegdlvvfgltdlp 82
Cdd:cd07432    1 ADLHIHS-VFSPDSDMTPEEIVERAIELGLDGIAITDHNTIDGAEEALKEAYKDGLLVIPGVEV---------------- 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210  83 eemlhaqdlirlvdqagGVCISAHPYRTNNRGLGN--HLRDVEGLAGVEAFNGNTPPHHN-LMAYAVATELGLPMFGASD 159
Cdd:cd07432   64 -----------------TLVVLAHPDRPSRYGLSDliLKPLIKNGDAIEVNNSRLRYGLNnLAAKRYAELGGLPITGGSD 126


                 ...
gi 873896210 160 AHW 162
Cdd:cd07432  127 AHT 129
PHP_HisPPase_AMP cd07438
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ...
 3-161 9.45e-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: 87.06  E-value: 9.45e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210   3 IDTHMHeKTYSGDSHQAlEEIVKTARERGLDAVCITDHESNRLWDEAHRYAKENGFPIFVGTEIltkegdlvvfgLTDLP 82
Cdd:cd07438    1 IDLHTH-STASDGTLSP-EELVELAKEAGLKVLAITDHDTVAGLEEALAAAKELGIELIPGVEI-----------STEYE 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210  83 EEMLH----AQDLIRLVDQAGGVCISAHP--YRTNNRGLGNHLRDV--EGLAGVEAFNGNTPPHHNLMAYAVATELGLPM 154
Cdd:cd07438   68 GREVHilgsPEEAIELIHAAGGVAVLAHPglYKLSRKKLEELIEELkeAGLDGIEVYHPYHSPEDRERLLELAKEYGLLV 147


                 ....*..
gi 873896210 155 FGASDAH 161
Cdd:cd07438  148 TGGSDFH 154
PHP_C pfam13263
PHP-associated; This is a subunit, probably the alpha, of bacterial and eukaryotic DNA ...
 137-192 2.00e-16

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: 70.29  E-value: 2.00e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 873896210  137 PHHNLMAYAVATELGLPMFGASDAHWAHQVGKYATIFPDGIRDEQDLIAAIRSKEV 192
Cdd:pfam13263   1 GEANRKARRLAEKLGLPGTGGSDAHVLEEVGRAYTEFEEDIRTEEDLLEAIRKGRT 56
CehA_McbA_metalo NF038032
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ...
 4-189 7.13e-14

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: 68.89  E-value: 7.13e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210   4 DTHMHekTYSGDSHQALEEIVKTARERGLDAVCITDHesNRLW---DEAHRYAKENGFPIFVGTEILTKEGDLVVFGLTD 80
Cdd:NF038032   6 DLHIH--TNHSDGPTTPEELARAALAEGLDVIALTDH--NTISgraYFAELLASERGLLVIPGMEVTTFWGHMNLLGLDL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210  81 LPE--------EMLHAQDLIRLVDQAGGVCISAHPYRT---NNRGLGN--HLRDVEGLAGVEAFNGNTPPHHNLMAYAVA 147
Cdd:NF038032  82 DPYidwrntdpGSPDIDEVIDEAHRQGGLVGIAHPFSPggpLCTGCGWeaLIDDLGKVDAIEVWNTPDPAPTNERALALW 161

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 873896210 148 TEL---G--LPMFGASDAH--WAHQVGKYAT-IFPDGIRDEQDLIAAIRS 189
Cdd:NF038032 162 YHLlneGfrITATGGSDAHddFDERPGLPRTyVYVDGELSYEAILAALKA 211
HIS2 COG1387
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and ...
 1-170 3.03e-13

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: 65.95  E-value: 3.03e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210   1 MLIDTHMHekTYSGDSHQALEEIVKTARERGLDAVCITDH-----ESNRL--------WDEAHRYAKE-NGFPIFVGTEI 66
Cdd:COG1387    1 MRGDLHTH--TTYSDGEGTIEEMVEAAIELGLEYIAITDHspslfVANGLseerlleyLEEIEELNEKyPDIKILKGIEV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210  67 ltkegDLVVFGLTDLPEEML----------H----------AQDLIRLVDQaGGVCISAHP-YRTNNRGLGnHLRDVEGL 125
Cdd:COG1387   79 -----DILPDGSLDYPDELLapldyvigsvHsileedyeeyTERLLKAIEN-PLVDILGHPdGRLLGGRPG-YEVDIEEV 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 873896210 126 AGVEAFNG-----NTPPHHNLMAYAV---ATELGLPM-FGaSDAHWAHQVGKYA 170
Cdd:COG1387  152 LEAAAENGvaleiNTRPLRLDPSDELlklAKELGVKItIG-SDAHSPEDLGDLE 204
POLIIIAc smart00481
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ...
 4-66 2.83e-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: 54.19  E-value: 2.83e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 873896210     4 DTHMHEKtYSG-DSHQALEEIVKTARERGLDAVCITDHESNRLWDEAHRYAKENGFPIFVGTEI 66
Cdd:smart00481   1 DLHVHSD-YSLlDGALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYKAAKKAGIKPIIGLEA 63
PHP_HisPPase_Thermotoga_like cd12111
Polymerase and Histidinol Phosphatase domain of Thermotoga like; The PHP (also called ...
 1-114 1.63e-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: 52.81  E-value: 1.63e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210   1 MLIDTHMHeKTYSgDSHQALEEIVKTARERGLDAVCITDHESNR--------------------------LWDEAHRYAK 54
Cdd:cd12111    2 LLCDFHIH-TTYS-DGALSLSEVVDLYGQHGFDVIAITDHVVDRasligkfpqgthpgvteanfedymeaLKVEAKRAWE 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 873896210  55 ENGFPIFVGTEIlTKEGD---LVVFGLTDLPEEMLHAQDLIRLVDQAGGVCISAHPYRTNNRG 114
Cdd:cd12111   80 KYEMIVIPGVEL-TNNTDsyhILGIDVKEYIDPCLSVEEIIAEIHKQGGIAVAAHPHRKNLDG 141
PRK09248 PRK09248
putative hydrolase; Validated
 2-92 5.86e-08

putative hydrolase; Validated


Pssm-ID: 236429 [Multi-domain]  Cd Length: 246  Bit Score: 51.38  E-value: 5.86e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210   2 LIDTHMHekTY-SGDSHQALEEIVKTARERGLDAVCITDHESNrLWDEAHRY---------AKENGFPIFVGTE--ILTK 69
Cdd:PRK09248   4 PVDTHTH--TIaSGHAYSTLHENAAEAKQKGLKLFAITDHGPD-MPGAPHYWhfgnlrvlpRKVDGVGILRGIEanIKNY 80

                         90       100
                 ....*....|....*....|...
gi 873896210  70 EGDLvvfgltDLPEEMLHAQDLI 92
Cdd:PRK09248  81 DGEI------DLPGDMLKKLDIV 97
PHP_PolX cd07436
Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal ...
 4-86 1.00e-07

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: 50.50  E-value: 1.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210   4 DTHMHeKTYSgDSHQALEEIVKTARERGLDAVCITDHeSNRL--------------WDEAHRYAKEN-GFPIFVGTE--I 66
Cdd:cd07436    8 DLHVH-TTWS-DGRNSIEEMAEAARALGYEYIAITDH-SKSLrvanglseerlreqIEEIDALNEKLpGIRILKGIEvdI 84

                         90       100
                 ....*....|....*....|
gi 873896210  67 LtKEGDLvvfgltDLPEEML 86
Cdd:cd07436   85 L-PDGSL------DYPDEVL 97
PHP_HisPPase_Ycdx_like cd07437
Polymerase and Histidinol Phosphatase domain of Ycdx like; PHP Ycdx-like is a stand alone PHP ...
 2-92 3.15e-07

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: 49.36  E-value: 3.15e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210   2 LIDTHMHekT-YSGDSHQALEEIVKTARERGLDAVCITDHESNRLwDEAHRY---------AKENGFPIFVGTE--ILTK 69
Cdd:cd07437    2 LADLHTH--TiASGHAYSTIEEMARAAAEKGLKLLGITDHGPAMP-GAPHPWyfgnlkvipREIYGVRILRGVEanIIDY 78

                         90       100
                 ....*....|....*....|...
gi 873896210  70 EGDLvvfgltDLPEEMLHAQDLI 92
Cdd:cd07437   79 DGNL------DLPERVLKRLDYV 95
PHP pfam02811
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ...
 4-66 5.21e-07

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


Pssm-ID: 460705 [Multi-domain]  Cd Length: 171  Bit Score: 47.92  E-value: 5.21e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 873896210    4 DTHMHekT-YS-GDSHQALEEIVKTARERGLDAVCITDHeSNRL-WDEAHRYAKENGFPIFVGTEI 66
Cdd:pfam02811   1 HLHVH--SeYSlLDGAARIEELVKRAKELGMPAIAITDH-GNLFgAVEFYKAAKKAGIKPIIGCEV 63
PHP_HisPPase_Chlorobi_like cd12112
Polymerase and Histidinol Phosphatase domain of Chlorobi like; The PHP (also called histidinol ...
 4-168 2.02e-06

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: 46.94  E-value: 2.02e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210   4 DTHMHekTYSGDSHQALEEIVKTARERGLDAVCITDH-------------ESNRLWDEAHRYAKENGFPIFVGTEIlTKE 70
Cdd:cd12112   16 DFHTH--TVFSDGHVWPEIRVREAWREGLDAIAITEHieyrphkediphpDRNRSYKIAKEAAESKGLLIIPGAEI-TRE 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210  71 ---GDLVVFGLTD----LPEEmlhAQDLIRLVDQAGGVCISAHPYRTNNRGLGNHLRDV------EGLA-GVEAFNGNTP 136
Cdd:cd12112   93 kppGHLNALFLTDanalLVPD---PLDAIRAAKKQGAFVFWNHPGWPDQSPDGIALPPFheklieEGLIhGIEVMNGTEY 169

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 873896210 137 PHHnlmAYAVATELGLPMFGASDAH----WAHQVGK 168
Cdd:cd12112  170 YPE---AIQWALEYNLTVMGTSDIHglidWTYDLKG 202
polC PRK00448
DNA polymerase III PolC; Validated
 6-65 3.38e-04

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 40.98  E-value: 3.38e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 873896210    6 HMHEKTYSGDSHQALEEIVKTARERGLDAVCITDHESNRLWDEAHRYAKENGF-PIFvGTE 65
Cdd:PRK00448  338 HLHTKMSTMDAIPSVSELVKRAAKWGHKAIAITDHGVVQAFPEAYNAAKKAGIkVIY-GVE 397
PHP_PolIIIA cd07431
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ...
 20-81 3.60e-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: 39.88  E-value: 3.60e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 873896210  20 LEEIVKTARERGLDAVCITDHesNRL--WDEAHRYAKENGF-PIFvGTEiLTKEGDLVVFGLTDL 81
Cdd:cd07431   18 PEDLVARAKELGYSALALTDR--NVLygAVRFYKACKKAGIkPII-GLE-LTVEGDGEPYPLLLL 78
PHP_PolIIIA_DnaE2 cd07434
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ...
 21-75 7.69e-04

Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; PolIIIA DnaE2 plays a role in SOS mutagenesis/translesion synthesis and has dominant effects in determining GC variability in the bacterial genome. PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. PolIIIA core enzyme catalyzes the reaction for polymerizing both DNA strands. PolC PHP is located in a different location compared to dnaE1, 2, and 3. dnaE1 is the longest compared to dnaE2 and dnaE3. A unique motif was also identified in dnaE1 and dnaE3 genes. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PHP domains found in DnaEs of thermophilic origin exhibit 3'-5' exonuclease activity.


Pssm-ID: 213989 [Multi-domain]  Cd Length: 260  Bit Score: 39.36  E-value: 7.69e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210  21 EEIVKTARERGLDAVCITDHES----NRlwdeAHRYAKENGFPIFVGTEILTKEG-DLVV 75
Cdd:cd07434   20 EELVARAAELGYRALAITDECSlagvVR----AHAAAKELGLKLIVGSELVLADGtRLVL 75
DnaE COG0587
DNA polymerase III, alpha subunit [Replication, recombination and repair];
5-66 1.05e-03

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


Pssm-ID: 440352 [Multi-domain]  Cd Length: 1050  Bit Score: 39.67  E-value: 1.05e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 873896210    5 THMHEKT-YS---GDSHqaLEEIVKTARERGLDAVCITDHesNRLWD--EAHRYAKENGF-PIfVGTEI 66
Cdd:COG0587     6 VHLHVHSeYSlldGASR--PEELVARAAELGMPALAITDH--GNLFGavRFYKAAKKAGIkPI-IGCEL 69
dnaE2 PRK05672
error-prone DNA polymerase; Validated
 14-190 1.20e-03

error-prone DNA polymerase; Validated


Pssm-ID: 235553 [Multi-domain]  Cd Length: 1046  Bit Score: 39.45  E-value: 1.20e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210   14 GDSHQalEEIVKTARERGLDAVCITDHESNRLWDEAHRYAKENGFPIFVGTEI-LTKEGD-----LVVF-----GLTDLP 82
Cdd:PRK05672   19 GASHP--EELVERAARLGLRALAITDECGLAGVVRAAEAAKELGLRLVIGAELsLGPDPDpggphLLVLardreGYGRLS 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873896210   83 EEMLHAQ----------DLIRLVDQAGGVC-----------ISAHPYRTNNRGLGNHLRDVEGLAGVEAFNGNTPPH--- 138
Cdd:PRK05672   97 RLITRARlragkgeyrlDLDDLAEPAGGHWailtgcrkgfvILALPYGGDAAALAALAALLDAFFADRVWLELTLHGrpd 176

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 873896210  139 ---HNLMAYAVATELGLPMFGASDAHWAHQvgkyatifpdGIRDEQDLIAAIRSK 190
Cdd:PRK05672  177 ddrRNARLAALAARAGVPLVATGDVHMHHR----------SRRRLQDAMTAIRAR 221
PRK07328 PRK07328
histidinol-phosphatase; Provisional
 1-40 1.96e-03

histidinol-phosphatase; Provisional


Pssm-ID: 235992 [Multi-domain]  Cd Length: 269  Bit Score: 38.08  E-value: 1.96e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 873896210   1 MLIDTHMHekTY-SGDSHQALEEIVKTARERGLDAVCITDH 40
Cdd:PRK07328   2 MLVDYHMH--TPlCGHAVGTPEEYVQAARRAGLKEIGFTDH 40
PHP_PolIIIA_POLC cd07435
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ...
 6-66 4.78e-03

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: 37.07  E-value: 4.78e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 873896210   6 HMHEKTYSGDSHQALEEIVKTARERGLDAVCITDHESNRLWDEAHRYAKENGF-PIFvGTEI 66
Cdd:cd07435    5 HAHTKMSAMDGVTSVKELVKRAAEWGHKAIAITDHGVVQAFPEAYEAAKKNGIkVIY-GVEA 65
 
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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