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Conserved domains on  [gi|497915560|ref|WP_010229716|]
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MULTISPECIES: PHP domain-containing protein [unclassified Pseudonocardia]

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 ...
 1-261 5.67e-56

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


:

Pssm-ID: 440378 [Multi-domain]  Cd Length: 188  Bit Score: 178.56  E-value: 5.67e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560   1 MPVIDLHAHSTASDGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDAV-AALPAGLSLVRGAEFSCLsptgrpgEPRCS 79
Cdd:COG0613    1 WMKIDLHVHTTASDGSLSPEELVARAKAAGLDVLAITDHDTVAGYEEAAeAAKELGLLVIPGVEISTR-------WEGRE 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560  80 VHLLGYLFDPRHDAIVAEQdrlreervqrlhtmigrmaadGYPVDVDTvfahlpeggsagrphlaralvaagvvgsvdea 159
Cdd:COG0613   74 VHILGYGIDPEDPALEALL---------------------GIPVEKAE-------------------------------- 100

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560 160 faellhndspyyvpRADTAVETAVEMIVAAGGIAVFAHPLARRRGTVIEPsVLVDLVGYGLGGVEVDHPNHLPADRELLR 239
Cdd:COG0613  101 --------------REWLSLEEAIDLIREAGGVAVLAHPFRYKRGRWLDD-LLEELADAGLDGIEVYNGRHSPEDNERAA 165

                        250       260
                 ....*....|....*....|..
gi 497915560 240 GLAAEHGLLATGSSDYHGTNKT 261
Cdd:COG0613  166 ELAEEYGLLATGGSDAHGPEKP 187
 
Name Accession Description Interval E-value
YciV COG0613
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ...
 1-261 5.67e-56

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


Pssm-ID: 440378 [Multi-domain]  Cd Length: 188  Bit Score: 178.56  E-value: 5.67e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560   1 MPVIDLHAHSTASDGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDAV-AALPAGLSLVRGAEFSCLsptgrpgEPRCS 79
Cdd:COG0613    1 WMKIDLHVHTTASDGSLSPEELVARAKAAGLDVLAITDHDTVAGYEEAAeAAKELGLLVIPGVEISTR-------WEGRE 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560  80 VHLLGYLFDPRHDAIVAEQdrlreervqrlhtmigrmaadGYPVDVDTvfahlpeggsagrphlaralvaagvvgsvdea 159
Cdd:COG0613   74 VHILGYGIDPEDPALEALL---------------------GIPVEKAE-------------------------------- 100

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560 160 faellhndspyyvpRADTAVETAVEMIVAAGGIAVFAHPLARRRGTVIEPsVLVDLVGYGLGGVEVDHPNHLPADRELLR 239
Cdd:COG0613  101 --------------REWLSLEEAIDLIREAGGVAVLAHPFRYKRGRWLDD-LLEELADAGLDGIEVYNGRHSPEDNERAA 165

                        250       260
                 ....*....|....*....|..
gi 497915560 240 GLAAEHGLLATGSSDYHGTNKT 261
Cdd:COG0613  166 ELAEEYGLLATGGSDAHGPEKP 187
PHP_HisPPase_AMP cd07438
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ...
 4-257 1.29e-50

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: 163.72  E-value: 1.29e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560   4 IDLHAHSTASDGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDAVAALPA-GLSLVRGAEFSCLsptgrpgEPRCSVHL 82
Cdd:cd07438    1 IDLHTHSTASDGTLSPEELVELAKEAGLKVLAITDHDTVAGLEEALAAAKElGIELIPGVEISTE-------YEGREVHI 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560  83 LGylfdprhdaivaeqdrlreervqrlhtmigrmaadgypvdvdtvfahlpeggsagrphlaralvaagvvgsvdeafae 162
Cdd:cd07438   74 LG------------------------------------------------------------------------------ 75

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560 163 llhndspyyvpradtAVETAVEMIVAAGGIAVFAHPLARRRGTVIEPSVLVDLVGYGLGGVEVDHPNHLPADRELLRGLA 242
Cdd:cd07438   76 ---------------SPEEAIELIHAAGGVAVLAHPGLYKLSRKKLEELIEELKEAGLDGIEVYHPYHSPEDRERLLELA 140

                        250
                 ....*....|....*
gi 497915560 243 AEHGLLATGSSDYHG 257
Cdd:cd07438  141 KEYGLLVTGGSDFHG 155
nside_bi_sphtase NF041577
3',5'-nucleoside bisphosphate phosphatase;
1-258 2.94e-48

3',5'-nucleoside bisphosphate phosphatase;


Pssm-ID: 469462 [Multi-domain]  Cd Length: 276  Bit Score: 162.00  E-value: 2.94e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560   1 MPVIDLHAHSTASDGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDA-VAALPAGLSLVRGAEFScLSPTGRpgeprcS 79
Cdd:NF041577   1 MLNVDLHCHSTVSDGLLSPAEVVRRAAARGVELLALTDHDDVGGLAEArAAAAELGLRFVNGVEIS-VTWGGH------T 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560  80 VHLLGYLFDPRHDAIVAEQDRLREERVQRLHTMIGRMAADGYPVDVDTVFAHLPEGGSAGRPHLARALVAAGVVGSVDEA 159
Cdd:NF041577  74 VHIVGLGIDPAHPALVAGLASIRAGRIERARRMAASLAKVGIEGAFEGAMRYADNPEMISRTHFARFLVETGVAKDVRSV 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560 160 FAELLHNDSPYYVPRADTAVETAVEMIVAAGGIAVFAHPLARRRGTVIEPSVLVDLVGYGLGGVEVDHPNHLPADRELLR 239
Cdd:NF041577 154 FKKYLVKGKPGYVEHEWASLADAVGWIRAAGGVAVIAHPGRYDLGRTTLERLLTEFKALGGEAIEVVSGSHSADDVGRFA 233

                        250
                 ....*....|....*....
gi 497915560 240 GLAAEHGLLATGSSDYHGT 258
Cdd:NF041577 234 RLAREFGLLASRGSDFHGP 252
CehA_McbA_metalo NF038032
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ...
 5-65 2.97e-11

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: 62.73  E-value: 2.97e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 497915560   5 DLHAHSTASDGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDAVAALPA--GLSLVRGAEFS 65
Cdd:NF038032   6 DLHIHTNHSDGPTTPEELARAALAEGLDVIALTDHNTISGRAYFAELLASerGLLVIPGMEVT 68
POLIIIAc smart00481
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ...
 5-65 3.29e-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: 54.96  E-value: 3.29e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 497915560     5 DLHAHSTAS--DGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDAV-AALPAGLSLVRGAEFS 65
Cdd:smart00481   1 DLHVHSDYSllDGALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYkAAKKAGIKPIIGLEAN 64
PHP pfam02811
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ...
 5-85 2.33e-09

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


Pssm-ID: 460705 [Multi-domain]  Cd Length: 171  Bit Score: 55.24  E-value: 2.33e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560    5 DLHAHSTAS--DGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDAV-AALPAGLSLVRGAEFScLSPTGRPGEPR---- 77
Cdd:pfam02811   1 HLHVHSEYSllDGAARIEELVKRAKELGMPAIAITDHGNLFGAVEFYkAAKKAGIKPIIGCEVY-VAPGSREETEKllak 79

                          90
                  ....*....|....
gi 497915560   78 ------CSVHLLGY 85
Cdd:pfam02811  80 yfdlvlLAVHEVGY 93
dnaE2 PRK05672
error-prone DNA polymerase; Validated
 6-77 2.02e-07

error-prone DNA polymerase; Validated


Pssm-ID: 235553 [Multi-domain]  Cd Length: 1046  Bit Score: 52.17  E-value: 2.02e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 497915560    6 LHAHSTAS--DGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDA-VAALPAGLSLVRGAEFScLSPTGRPGEPR 77
Cdd:PRK05672    8 LHCHSNFSflDGASHPEELVERAARLGLRALAITDECGLAGVVRAaEAAKELGLRLVIGAELS-LGPDPDPGGPH 81
 
Name Accession Description Interval E-value
YciV COG0613
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ...
 1-261 5.67e-56

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


Pssm-ID: 440378 [Multi-domain]  Cd Length: 188  Bit Score: 178.56  E-value: 5.67e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560   1 MPVIDLHAHSTASDGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDAV-AALPAGLSLVRGAEFSCLsptgrpgEPRCS 79
Cdd:COG0613    1 WMKIDLHVHTTASDGSLSPEELVARAKAAGLDVLAITDHDTVAGYEEAAeAAKELGLLVIPGVEISTR-------WEGRE 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560  80 VHLLGYLFDPRHDAIVAEQdrlreervqrlhtmigrmaadGYPVDVDTvfahlpeggsagrphlaralvaagvvgsvdea 159
Cdd:COG0613   74 VHILGYGIDPEDPALEALL---------------------GIPVEKAE-------------------------------- 100

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560 160 faellhndspyyvpRADTAVETAVEMIVAAGGIAVFAHPLARRRGTVIEPsVLVDLVGYGLGGVEVDHPNHLPADRELLR 239
Cdd:COG0613  101 --------------REWLSLEEAIDLIREAGGVAVLAHPFRYKRGRWLDD-LLEELADAGLDGIEVYNGRHSPEDNERAA 165

                        250       260
                 ....*....|....*....|..
gi 497915560 240 GLAAEHGLLATGSSDYHGTNKT 261
Cdd:COG0613  166 ELAEEYGLLATGGSDAHGPEKP 187
PHP_HisPPase_AMP cd07438
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ...
 4-257 1.29e-50

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: 163.72  E-value: 1.29e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560   4 IDLHAHSTASDGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDAVAALPA-GLSLVRGAEFSCLsptgrpgEPRCSVHL 82
Cdd:cd07438    1 IDLHTHSTASDGTLSPEELVELAKEAGLKVLAITDHDTVAGLEEALAAAKElGIELIPGVEISTE-------YEGREVHI 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560  83 LGylfdprhdaivaeqdrlreervqrlhtmigrmaadgypvdvdtvfahlpeggsagrphlaralvaagvvgsvdeafae 162
Cdd:cd07438   74 LG------------------------------------------------------------------------------ 75

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560 163 llhndspyyvpradtAVETAVEMIVAAGGIAVFAHPLARRRGTVIEPSVLVDLVGYGLGGVEVDHPNHLPADRELLRGLA 242
Cdd:cd07438   76 ---------------SPEEAIELIHAAGGVAVLAHPGLYKLSRKKLEELIEELKEAGLDGIEVYHPYHSPEDRERLLELA 140

                        250
                 ....*....|....*
gi 497915560 243 AEHGLLATGSSDYHG 257
Cdd:cd07438  141 KEYGLLVTGGSDFHG 155
nside_bi_sphtase NF041577
3',5'-nucleoside bisphosphate phosphatase;
1-258 2.94e-48

3',5'-nucleoside bisphosphate phosphatase;


Pssm-ID: 469462 [Multi-domain]  Cd Length: 276  Bit Score: 162.00  E-value: 2.94e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560   1 MPVIDLHAHSTASDGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDA-VAALPAGLSLVRGAEFScLSPTGRpgeprcS 79
Cdd:NF041577   1 MLNVDLHCHSTVSDGLLSPAEVVRRAAARGVELLALTDHDDVGGLAEArAAAAELGLRFVNGVEIS-VTWGGH------T 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560  80 VHLLGYLFDPRHDAIVAEQDRLREERVQRLHTMIGRMAADGYPVDVDTVFAHLPEGGSAGRPHLARALVAAGVVGSVDEA 159
Cdd:NF041577  74 VHIVGLGIDPAHPALVAGLASIRAGRIERARRMAASLAKVGIEGAFEGAMRYADNPEMISRTHFARFLVETGVAKDVRSV 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560 160 FAELLHNDSPYYVPRADTAVETAVEMIVAAGGIAVFAHPLARRRGTVIEPSVLVDLVGYGLGGVEVDHPNHLPADRELLR 239
Cdd:NF041577 154 FKKYLVKGKPGYVEHEWASLADAVGWIRAAGGVAVIAHPGRYDLGRTTLERLLTEFKALGGEAIEVVSGSHSADDVGRFA 233

                        250
                 ....*....|....*....
gi 497915560 240 GLAAEHGLLATGSSDYHGT 258
Cdd:NF041577 234 RLAREFGLLASRGSDFHGP 252
PHP_HisPPase cd07432
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ...
 4-65 1.82e-13

Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to produce histidinol. HisPPase can be classified into two types: the bifunctional HisPPase found in proteobacteria that belongs to the DDDD superfamily and the monofunctional Bacillus subtilis type that is a member of the PHP family. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. The PHP domain of HisPPase is structurally homologous to other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel.


Pssm-ID: 213987 [Multi-domain]  Cd Length: 129  Bit Score: 65.72  E-value: 1.82e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 497915560   4 IDLHAHSTAS-DGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDAVA-ALPAGLSLVRGAEFS 65
Cdd:cd07432    1 ADLHIHSVFSpDSDMTPEEIVERAIELGLDGIAITDHNTIDGAEEALKeAYKDGLLVIPGVEVT 64
CehA_McbA_metalo NF038032
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ...
 5-65 2.97e-11

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: 62.73  E-value: 2.97e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 497915560   5 DLHAHSTASDGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDAVAALPA--GLSLVRGAEFS 65
Cdd:NF038032   6 DLHIHTNHSDGPTTPEELARAALAEGLDVIALTDHNTISGRAYFAELLASerGLLVIPGMEVT 68
HIS2 COG1387
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and ...
 4-39 1.93e-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: 59.40  E-value: 1.93e-10
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 497915560   4 IDLHAHSTASDGTDTPAELVRAAGAAGLDVVAITDH 39
Cdd:COG1387    3 GDLHTHTTYSDGEGTIEEMVEAAIELGLEYIAITDH 38
POLIIIAc smart00481
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ...
 5-65 3.29e-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: 54.96  E-value: 3.29e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 497915560     5 DLHAHSTAS--DGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDAV-AALPAGLSLVRGAEFS 65
Cdd:smart00481   1 DLHVHSDYSllDGALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYkAAKKAGIKPIIGLEAN 64
PHP pfam02811
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ...
 5-85 2.33e-09

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


Pssm-ID: 460705 [Multi-domain]  Cd Length: 171  Bit Score: 55.24  E-value: 2.33e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560    5 DLHAHSTAS--DGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDAV-AALPAGLSLVRGAEFScLSPTGRPGEPR---- 77
Cdd:pfam02811   1 HLHVHSEYSllDGAARIEELVKRAKELGMPAIAITDHGNLFGAVEFYkAAKKAGIKPIIGCEVY-VAPGSREETEKllak 79

                          90
                  ....*....|....
gi 497915560   78 ------CSVHLLGY 85
Cdd:pfam02811  80 yfdlvlLAVHEVGY 93
DnaE COG0587
DNA polymerase III, alpha subunit [Replication, recombination and repair];
6-85 2.94e-08

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


Pssm-ID: 440352 [Multi-domain]  Cd Length: 1050  Bit Score: 54.69  E-value: 2.94e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560    6 LHAHSTAS--DGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDAV-AALPAGLSLVRGAEFScLSPTGRPGEPRcsvHL 82
Cdd:COG0587     8 LHVHSEYSllDGASRPEELVARAAELGMPALAITDHGNLFGAVRFYkAAKKAGIKPIIGCELY-VAPGSRDDAGY---HL 83


                  ...
gi 497915560   83 LGY 85
Cdd:COG0587    84 VLL 86
PHP_PolX cd07436
Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal ...
 5-39 3.63e-08

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: 52.81  E-value: 3.63e-08
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 497915560   5 DLHAHSTASDGTDTPAELVRAAGAAGLDVVAITDH 39
Cdd:cd07436    8 DLHVHTTWSDGRNSIEEMAEAARALGYEYIAITDH 42
dnaE2 PRK05672
error-prone DNA polymerase; Validated
 6-77 2.02e-07

error-prone DNA polymerase; Validated


Pssm-ID: 235553 [Multi-domain]  Cd Length: 1046  Bit Score: 52.17  E-value: 2.02e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 497915560    6 LHAHSTAS--DGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDA-VAALPAGLSLVRGAEFScLSPTGRPGEPR 77
Cdd:PRK05672    8 LHCHSNFSflDGASHPEELVERAARLGLRALAITDECGLAGVVRAaEAAKELGLRLVIGAELS-LGPDPDPGGPH 81
PHP_HisPPase_Chlorobi_like cd12112
Polymerase and Histidinol Phosphatase domain of Chlorobi like; The PHP (also called histidinol ...
 5-71 2.45e-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: 47.71  E-value: 2.45e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560   5 DLHAHSTASDGTDTPAELVRAAGAAGLDVVAITDH--------DTTHG-----WDDAV-AALPAGLSLVRGAEFSCLSPT 70
Cdd:cd12112   16 DFHTHTVFSDGHVWPEIRVREAWREGLDAIAITEHieyrphkeDIPHPdrnrsYKIAKeAAESKGLLIIPGAEITREKPP 95


                 .
gi 497915560  71 G 71
Cdd:cd12112   96 G 96
PHP_PolIIIA cd07431
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ...
 6-65 3.60e-06

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: 46.43  E-value: 3.60e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 497915560   6 LHAHSTAS--DGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDD-AVAALPAGLSLVRGAEFS 65
Cdd:cd07431    3 LHVHSSYSllDSAIRPEDLVARAKELGYSALALTDRNVLYGAVRfYKACKKAGIKPIIGLELT 65
PHP cd07309
Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2 ...
 4-65 6.95e-06

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: 43.57  E-value: 6.95e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 497915560   4 IDLHAHSTASDG-TDTPAELVRAAGAAGLDVVAITDH--------DTTHGWDDAVAAL-PAGLSLVRGAEFS 65
Cdd:cd07309    1 VDLHTHTVFSDGdHAKLTELVDKAKELGPDALAITDHgnlrglaeFNTAGK*NHIKAAeAAGIKIIIGSEVN 72
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
5-39 1.56e-05

DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 45.95  E-value: 1.56e-05
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 497915560   5 DLHAHSTASDGTDTPAELVRAAGAAGLDVVAITDH 39
Cdd:COG1796  339 DLHHHTTWSDGGASIEEMAAAAAARGYYYIAITDH 373
PHP_HisPPase_Thermotoga_like cd12111
Polymerase and Histidinol Phosphatase domain of Thermotoga like; The PHP (also called ...
 5-39 3.51e-05

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: 43.95  E-value: 3.51e-05
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 497915560   5 DLHAHSTASDGTDTPAELVRAAGAAGLDVVAITDH 39
Cdd:cd12111    5 DFHIHTTYSDGALSLSEVVDLYGQHGFDVIAITDH 39
PRK08609 PRK08609
DNA polymerase/3'-5' exonuclease PolX;
5-39 5.88e-05

DNA polymerase/3'-5' exonuclease PolX;


Pssm-ID: 236311 [Multi-domain]  Cd Length: 570  Bit Score: 44.18  E-value: 5.88e-05
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 497915560   5 DLHAHSTASDGTDTPAELVRAAGAAGLDVVAITDH 39
Cdd:PRK08609 337 DLHMHTTWSDGAFSIEEMVEACIAKGYEYMAITDH 371
polC PRK00448
DNA polymerase III PolC; Validated
 4-65 6.20e-05

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 44.44  E-value: 6.20e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 497915560    4 IDLHAHSTAS--DGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDAV-AALPAGLSLVRGAEFS 65
Cdd:PRK00448  335 VELHLHTKMStmDAIPSVSELVKRAAKWGHKAIAITDHGVVQAFPEAYnAAKKAGIKVIYGVEAN 399
PHP_HisPPase_Ycdx_like cd07437
Polymerase and Histidinol Phosphatase domain of Ycdx like; PHP Ycdx-like is a stand alone PHP ...
 3-45 1.09e-04

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: 42.43  E-value: 1.09e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 497915560   3 VIDLHAHSTASD-GTDTPAELVRAAGAAGLDVVAITDH-----DTTHGW 45
Cdd:cd07437    2 LADLHTHTIASGhAYSTIEEMARAAAEKGLKLLGITDHgpampGAPHPW 50
PHP_PolIIIA_POLC cd07435
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ...
 4-91 1.21e-04

Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at PolC gene; DNA polymerase III alphas (PolIIIAs) that contain a PHP domain have been classified into four basic groups based on phylogenetic and domain structural analyses: polC, dnaE1, dnaE2, and dnaE3. The PolC group is distinct from the other three and is clustered together. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. PolC PHP is located in different location compare to dnaE1, 2, and 3. The PHP domain has four conserved sequence motifs and and contains an invariant histidine that is involved in metal ion coordination.The PHP domain of PolC is structurally homologous to other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. PHP domains found in dnaEs of thermophilic origin exhibit 3'-5' exonuclease activity. In contrast, PolC PHP lacks detectable nuclease activity.


Pssm-ID: 213990 [Multi-domain]  Cd Length: 268  Bit Score: 42.85  E-value: 1.21e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497915560   4 IDLHAHSTAS--DGTDTPAELVRAAGAAGLDVVAITDHDTTHGWDDAVAAL-PAGLSLVRGAEfsclsptgrpgeprcsv 80
Cdd:cd07435    2 VELHAHTKMSamDGVTSVKELVKRAAEWGHKAIAITDHGVVQAFPEAYEAAkKNGIKVIYGVE----------------- 64

                         90
                 ....*....|.
gi 497915560  81 hllGYLFDPRH 91
Cdd:cd07435   65 ---AYLVDPYH 72
PRK06361 PRK06361
histidinol phosphate phosphatase domain-containing protein;
8-39 2.19e-04

histidinol phosphate phosphatase domain-containing protein;


Pssm-ID: 180543 [Multi-domain]  Cd Length: 212  Bit Score: 41.48  E-value: 2.19e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 497915560   8 AHSTASDGTDTPAELVRAAGAAGLDVVAITDH 39
Cdd:PRK06361   1 THTIFSDGELIPSELVRRARVLGYRAIAITDH 32
PRK07945 PRK07945
PHP domain-containing protein;
5-39 2.19e-03

PHP domain-containing protein;


Pssm-ID: 236135 [Multi-domain]  Cd Length: 335  Bit Score: 39.19  E-value: 2.19e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 497915560   5 DLHAHSTASDGTDTPAELVRAAGAAGLDVVAITDH 39
Cdd:PRK07945  99 DLHTHSDWSDGGSPIEEMARTAAALGHEYCALTDH 133
PRK08392 PRK08392
hypothetical protein; Provisional
 4-39 2.94e-03

hypothetical protein; Provisional


Pssm-ID: 169423 [Multi-domain]  Cd Length: 215  Bit Score: 38.23  E-value: 2.94e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 497915560   4 IDLHAHSTASDGTDTPAELVRAAGAAGLDVVAITDH 39
Cdd:PRK08392   1 MDLHTHTVYSDGIGSVRDNIAEAERKGLRLVGISDH 36
 
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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