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Conserved domains on  [gi|493475497|ref|WP_006430488|]
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PHP domain-containing protein [Natrinema versiforme]

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 ...
 1-164 1.41e-35

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


:

Pssm-ID: 440378 [Multi-domain]  Cd Length: 188  Bit Score: 124.64  E-value: 1.41e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497   1 MYAVDLHAHTRFFHGRRSLGDrfdplgvrlLAEAADRRGLDGVATTNHDYYTAFDP------SPDIETLPGIEITTDRG- 73
Cdd:COG0613    1 WMKIDLHVHTTASDGSLSPEE---------LVARAKAAGLDVLAITDHDTVAGYEEaaeaakELGLLVIPGVEISTRWEg 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497  74 ---HVLVVGPDPP------------AATKPGALSPEEAVALAHDRDCAAIVAHPFRNS-------TVRELEAVPFDAIEV 131
Cdd:COG0613   72 revHILGYGIDPEdpaleallgipvEKAEREWLSLEEAIDLIREAGGVAVLAHPFRYKrgrwlddLLEELADAGLDGIEV 151

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 493475497 132 -NGKH-PRSRPLVEQLAEERDLPLVGGSDAHYPFE 164
Cdd:COG0613  152 yNGRHsPEDNERAAELAEEYGLLATGGSDAHGPEK 186
PfuEndoQ-like super family cl40582
lesion-specific endonuclease similar to Pyrococcus furiosus EndoQ; Pyrococcus furiosus EndoQ ...
 143-201 2.98e-03

lesion-specific endonuclease similar to Pyrococcus furiosus EndoQ; Pyrococcus furiosus EndoQ is a lesion-specific endonuclease which is assumed to be involved in DNA repair pathways in Thermococcales. It recognizes a deaminated base and hydrolyzes the phosphodiester bond 5' to the site of the lesion. Initially identified as a hypoxanthine-specific endonuclease, it has now been shown that EndoQ also recognizes uracil, xanthine, and apurinic/apyrimidinic (AP) sites in DNA, and that a homolog in Bacillus pumilus shares functional properties of the archaeal EndoQs.


The actual alignment was detected with superfamily member cd19067:

Pssm-ID: 410989 [Multi-domain]  Cd Length: 395  Bit Score: 38.16  E-value: 2.98e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 493475497 143 EQLAEERDLPLVGGSDAHYPFEVGRAYTVVEADRLTPASIVAAIRDG---RVSATVsrsGFD 201
Cdd:cd19067  191 WRISELDRYTFLSNSDAHSPPKIGREANVFELEEPSYKEIKKALKRKdgrKILATI---EFF 249
 
Name Accession Description Interval E-value
YciV COG0613
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ...
 1-164 1.41e-35

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


Pssm-ID: 440378 [Multi-domain]  Cd Length: 188  Bit Score: 124.64  E-value: 1.41e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497   1 MYAVDLHAHTRFFHGRRSLGDrfdplgvrlLAEAADRRGLDGVATTNHDYYTAFDP------SPDIETLPGIEITTDRG- 73
Cdd:COG0613    1 WMKIDLHVHTTASDGSLSPEE---------LVARAKAAGLDVLAITDHDTVAGYEEaaeaakELGLLVIPGVEISTRWEg 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497  74 ---HVLVVGPDPP------------AATKPGALSPEEAVALAHDRDCAAIVAHPFRNS-------TVRELEAVPFDAIEV 131
Cdd:COG0613   72 revHILGYGIDPEdpaleallgipvEKAEREWLSLEEAIDLIREAGGVAVLAHPFRYKrgrwlddLLEELADAGLDGIEV 151

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 493475497 132 -NGKH-PRSRPLVEQLAEERDLPLVGGSDAHYPFE 164
Cdd:COG0613  152 yNGRHsPEDNERAAELAEEYGLLATGGSDAHGPEK 186
CehA_McbA_metalo NF038032
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ...
 2-194 5.25e-27

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: 105.48  E-value: 5.25e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497   2 YAVDLHAHTRFFHGRRSLGDrfdplgvrlLAEAADRRGLDGVATTNHD------YYTAFDPS-PDIETLPGIEITTDRGH 74
Cdd:NF038032   3 YSGDLHIHTNHSDGPTTPEE---------LARAALAEGLDVIALTDHNtisgraYFAELLASeRGLLVIPGMEVTTFWGH 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497  75 VLVVGPDPPAA-----TKPGALSPEEAVALAHDRDCAAIVAHPFR----NSTVRELEAVP-----FDAIEV-NGKHPRSR 139
Cdd:NF038032  74 MNLLGLDLDPYidwrnTDPGSPDIDEVIDEAHRQGGLVGIAHPFSpggpLCTGCGWEALIddlgkVDAIEVwNTPDPAPT 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493475497 140 PLV------EQLAEERDLPLVGGSDAHYPFE--VGRAYTVVEADR-LTPASIVAAIRDGRVSAT 194
Cdd:NF038032 154 NERalalwyHLLNEGFRITATGGSDAHDDFDerPGLPRTYVYVDGeLSYEAILAALKAGRTYVT 217
PHP_HisPPase cd07432
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ...
 4-161 2.37e-19

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: 80.75  E-value: 2.37e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497   4 VDLHAHTRFFHGRRslgdrfdpLGVRLLAEAADRRGLDGVATTNHDYYTAFD------PSPDIETLPGIEITtdrghvlv 77
Cdd:cd07432    1 ADLHIHSVFSPDSD--------MTPEEIVERAIELGLDGIAITDHNTIDGAEealkeaYKDGLLVIPGVEVT-------- 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497  78 vgpdppaatkpgalspeeavalahdrdcAAIVAHPFRNST------VRELEAVPFDAIEVN---GKHPRSRPLVEQLAEE 148
Cdd:cd07432   65 ----------------------------LVVLAHPDRPSRyglsdlILKPLIKNGDAIEVNnsrLRYGLNNLAAKRYAEL 116

                        170
                 ....*....|...
gi 493475497 149 RDLPLVGGSDAHY 161
Cdd:cd07432  117 GGLPITGGSDAHT 129
PHP_C pfam13263
PHP-associated; This is a subunit, probably the alpha, of bacterial and eukaryotic DNA ...
 136-191 1.67e-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: 71.06  E-value: 1.67e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 493475497  136 PRSRPLVEQLAEERDLPLVGGSDAHYPFEVGRAYTVVEADRLTPASIVAAIRDGRV 191
Cdd:pfam13263   1 GEANRKARRLAEKLGLPGTGGSDAHVLEEVGRAYTEFEEDIRTEEDLLEAIRKGRT 56
POLIIIAc smart00481
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ...
 5-70 3.24e-04

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: 38.02  E-value: 3.24e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493475497     5 DLHAHTRFfhgrrSLGDRFdpLGVRLLAEAADRRGLDGVATTNHDyyTAFDPSP--------DIETLPGIEITT 70
Cdd:smart00481   1 DLHVHSDY-----SLLDGA--LSPEELVKRAKELGLKAIAITDHG--NLFGAVEfykaakkaGIKPIIGLEANI 65
PRK08392 PRK08392
hypothetical protein; Provisional
 5-167 4.55e-04

hypothetical protein; Provisional


Pssm-ID: 169423 [Multi-domain]  Cd Length: 215  Bit Score: 40.15  E-value: 4.55e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497   5 DLHAHTRFFHGrrsLGDRFDPLGvrllaeAADRRGLDGVATTNHDYYtaFDPS---------------PDIETLPGIEit 69
Cdd:PRK08392   2 DLHTHTVYSDG---IGSVRDNIA------EAERKGLRLVGISDHIHY--FTPSkfnayineirqwgeeSEIVVLAGIE-- 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497  70 tdrGHVLVVGPDPPA----------------ATKPGALSPEEAVALAHDRDCAAIVAHpFRNS-------TVRELEAVpF 126
Cdd:PRK08392  69 ---ANITPNGVDITDdfakkldyviasvhewFGRPEHHEYIELVKLALMDENVDIIGH-FGNSfpyigypSEEELKEI-L 143

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 493475497 127 DAIEVNGK----HPRSR-PLVEQLAE--ERDLPLVGGSDAHYPFEVGR 167
Cdd:PRK08392 144 DLAEAYGKafeiSSRYRvPDLEFIREciKRGIKLTFASDAHRPEDVGN 191
PfuEndoQ-like cd19067
lesion-specific endonuclease similar to Pyrococcus furiosus EndoQ; Pyrococcus furiosus EndoQ ...
 143-201 2.98e-03

lesion-specific endonuclease similar to Pyrococcus furiosus EndoQ; Pyrococcus furiosus EndoQ is a lesion-specific endonuclease which is assumed to be involved in DNA repair pathways in Thermococcales. It recognizes a deaminated base and hydrolyzes the phosphodiester bond 5' to the site of the lesion. Initially identified as a hypoxanthine-specific endonuclease, it has now been shown that EndoQ also recognizes uracil, xanthine, and apurinic/apyrimidinic (AP) sites in DNA, and that a homolog in Bacillus pumilus shares functional properties of the archaeal EndoQs.


Pssm-ID: 410989 [Multi-domain]  Cd Length: 395  Bit Score: 38.16  E-value: 2.98e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 493475497 143 EQLAEERDLPLVGGSDAHYPFEVGRAYTVVEADRLTPASIVAAIRDG---RVSATVsrsGFD 201
Cdd:cd19067  191 WRISELDRYTFLSNSDAHSPPKIGREANVFELEEPSYKEIKKALKRKdgrKILATI---EFF 249
 
Name Accession Description Interval E-value
YciV COG0613
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ...
 1-164 1.41e-35

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


Pssm-ID: 440378 [Multi-domain]  Cd Length: 188  Bit Score: 124.64  E-value: 1.41e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497   1 MYAVDLHAHTRFFHGRRSLGDrfdplgvrlLAEAADRRGLDGVATTNHDYYTAFDP------SPDIETLPGIEITTDRG- 73
Cdd:COG0613    1 WMKIDLHVHTTASDGSLSPEE---------LVARAKAAGLDVLAITDHDTVAGYEEaaeaakELGLLVIPGVEISTRWEg 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497  74 ---HVLVVGPDPP------------AATKPGALSPEEAVALAHDRDCAAIVAHPFRNS-------TVRELEAVPFDAIEV 131
Cdd:COG0613   72 revHILGYGIDPEdpaleallgipvEKAEREWLSLEEAIDLIREAGGVAVLAHPFRYKrgrwlddLLEELADAGLDGIEV 151

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 493475497 132 -NGKH-PRSRPLVEQLAEERDLPLVGGSDAHYPFE 164
Cdd:COG0613  152 yNGRHsPEDNERAAELAEEYGLLATGGSDAHGPEK 186
CehA_McbA_metalo NF038032
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ...
 2-194 5.25e-27

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: 105.48  E-value: 5.25e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497   2 YAVDLHAHTRFFHGRRSLGDrfdplgvrlLAEAADRRGLDGVATTNHD------YYTAFDPS-PDIETLPGIEITTDRGH 74
Cdd:NF038032   3 YSGDLHIHTNHSDGPTTPEE---------LARAALAEGLDVIALTDHNtisgraYFAELLASeRGLLVIPGMEVTTFWGH 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497  75 VLVVGPDPPAA-----TKPGALSPEEAVALAHDRDCAAIVAHPFR----NSTVRELEAVP-----FDAIEV-NGKHPRSR 139
Cdd:NF038032  74 MNLLGLDLDPYidwrnTDPGSPDIDEVIDEAHRQGGLVGIAHPFSpggpLCTGCGWEALIddlgkVDAIEVwNTPDPAPT 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493475497 140 PLV------EQLAEERDLPLVGGSDAHYPFE--VGRAYTVVEADR-LTPASIVAAIRDGRVSAT 194
Cdd:NF038032 154 NERalalwyHLLNEGFRITATGGSDAHDDFDerPGLPRTYVYVDGeLSYEAILAALKAGRTYVT 217
PHP_HisPPase cd07432
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ...
 4-161 2.37e-19

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: 80.75  E-value: 2.37e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497   4 VDLHAHTRFFHGRRslgdrfdpLGVRLLAEAADRRGLDGVATTNHDYYTAFD------PSPDIETLPGIEITtdrghvlv 77
Cdd:cd07432    1 ADLHIHSVFSPDSD--------MTPEEIVERAIELGLDGIAITDHNTIDGAEealkeaYKDGLLVIPGVEVT-------- 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497  78 vgpdppaatkpgalspeeavalahdrdcAAIVAHPFRNST------VRELEAVPFDAIEVN---GKHPRSRPLVEQLAEE 148
Cdd:cd07432   65 ----------------------------LVVLAHPDRPSRyglsdlILKPLIKNGDAIEVNnsrLRYGLNNLAAKRYAEL 116

                        170
                 ....*....|...
gi 493475497 149 RDLPLVGGSDAHY 161
Cdd:cd07432  117 GGLPITGGSDAHT 129
PHP_C pfam13263
PHP-associated; This is a subunit, probably the alpha, of bacterial and eukaryotic DNA ...
 136-191 1.67e-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: 71.06  E-value: 1.67e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 493475497  136 PRSRPLVEQLAEERDLPLVGGSDAHYPFEVGRAYTVVEADRLTPASIVAAIRDGRV 191
Cdd:pfam13263   1 GEANRKARRLAEKLGLPGTGGSDAHVLEEVGRAYTEFEEDIRTEEDLLEAIRKGRT 56
PHP_HisPPase_AMP cd07438
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ...
 4-160 2.34e-14

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: 68.19  E-value: 2.34e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497   4 VDLHAHTRFfhgrrSLGdRFDPlgvRLLAEAADRRGLDGVATTNHDyyT--------AFDPSPDIETLPGIEITTD--RG 73
Cdd:cd07438    1 IDLHTHSTA-----SDG-TLSP---EELVELAKEAGLKVLAITDHD--TvagleealAAAKELGIELIPGVEISTEyeGR 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497  74 HVLVVGpdppaatkpgalSPEEAVALAHDRDCAAIVAHPFRN--------STVRELEAVPFDAIEV-NGKH-PRSRPLVE 143
Cdd:cd07438   70 EVHILG------------SPEEAIELIHAAGGVAVLAHPGLYklsrkkleELIEELKEAGLDGIEVyHPYHsPEDRERLL 137

                        170
                 ....*....|....*..
gi 493475497 144 QLAEERDLPLVGGSDAH 160
Cdd:cd07438  138 ELAKEYGLLVTGGSDFH 154
HIS2 COG1387
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and ...
 4-166 2.72e-06

Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and metabolism, General function prediction only]; Histidinol phosphatase or related hydrolase of the PHP family is part of the Pathway/BioSystem: Histidine biosynthesis


Pssm-ID: 440997 [Multi-domain]  Cd Length: 232  Bit Score: 46.69  E-value: 2.72e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497   4 VDLHAHTRFFHGRRSLGDrfdplgvrlLAEAADRRGLDGVATTNHDYYTAFDPS--------------------PDIETL 63
Cdd:COG1387    3 GDLHTHTTYSDGEGTIEE---------MVEAAIELGLEYIAITDHSPSLFVANGlseerlleyleeieelnekyPDIKIL 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497  64 PGIEIttdrGHVLVVGPDPPAATkpgaLSP------------EEAVALAHDRDCAA-------IVAHP------FRNSTV 118
Cdd:COG1387   74 KGIEV----DILPDGSLDYPDEL----LAPldyvigsvhsilEEDYEEYTERLLKAienplvdILGHPdgrllgGRPGYE 145

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 493475497 119 RELEAVpFDA-------IEVNGKHPRSRPLVE--QLAEERDLPLVGGSDAHYPFEVG 166
Cdd:COG1387  146 VDIEEV-LEAaaengvaLEINTRPLRLDPSDEllKLAKELGVKITIGSDAHSPEDLG 201
POLIIIAc smart00481
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ...
 5-70 3.24e-04

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: 38.02  E-value: 3.24e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493475497     5 DLHAHTRFfhgrrSLGDRFdpLGVRLLAEAADRRGLDGVATTNHDyyTAFDPSP--------DIETLPGIEITT 70
Cdd:smart00481   1 DLHVHSDY-----SLLDGA--LSPEELVKRAKELGLKAIAITDHG--NLFGAVEfykaakkaGIKPIIGLEANI 65
PRK08392 PRK08392
hypothetical protein; Provisional
 5-167 4.55e-04

hypothetical protein; Provisional


Pssm-ID: 169423 [Multi-domain]  Cd Length: 215  Bit Score: 40.15  E-value: 4.55e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497   5 DLHAHTRFFHGrrsLGDRFDPLGvrllaeAADRRGLDGVATTNHDYYtaFDPS---------------PDIETLPGIEit 69
Cdd:PRK08392   2 DLHTHTVYSDG---IGSVRDNIA------EAERKGLRLVGISDHIHY--FTPSkfnayineirqwgeeSEIVVLAGIE-- 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493475497  70 tdrGHVLVVGPDPPA----------------ATKPGALSPEEAVALAHDRDCAAIVAHpFRNS-------TVRELEAVpF 126
Cdd:PRK08392  69 ---ANITPNGVDITDdfakkldyviasvhewFGRPEHHEYIELVKLALMDENVDIIGH-FGNSfpyigypSEEELKEI-L 143

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 493475497 127 DAIEVNGK----HPRSR-PLVEQLAE--ERDLPLVGGSDAHYPFEVGR 167
Cdd:PRK08392 144 DLAEAYGKafeiSSRYRvPDLEFIREciKRGIKLTFASDAHRPEDVGN 191
PfuEndoQ-like cd19067
lesion-specific endonuclease similar to Pyrococcus furiosus EndoQ; Pyrococcus furiosus EndoQ ...
 143-201 2.98e-03

lesion-specific endonuclease similar to Pyrococcus furiosus EndoQ; Pyrococcus furiosus EndoQ is a lesion-specific endonuclease which is assumed to be involved in DNA repair pathways in Thermococcales. It recognizes a deaminated base and hydrolyzes the phosphodiester bond 5' to the site of the lesion. Initially identified as a hypoxanthine-specific endonuclease, it has now been shown that EndoQ also recognizes uracil, xanthine, and apurinic/apyrimidinic (AP) sites in DNA, and that a homolog in Bacillus pumilus shares functional properties of the archaeal EndoQs.


Pssm-ID: 410989 [Multi-domain]  Cd Length: 395  Bit Score: 38.16  E-value: 2.98e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 493475497 143 EQLAEERDLPLVGGSDAHYPFEVGRAYTVVEADRLTPASIVAAIRDG---RVSATVsrsGFD 201
Cdd:cd19067  191 WRISELDRYTFLSNSDAHSPPKIGREANVFELEEPSYKEIKKALKRKdgrKILATI---EFF 249
PRK08123 PRK08123
histidinol-phosphatase HisJ;
144-173 3.02e-03

histidinol-phosphatase HisJ;


Pssm-ID: 236155 [Multi-domain]  Cd Length: 270  Bit Score: 37.96  E-value: 3.02e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 493475497 144 QLAEERDLPLVGGSDAHYPFEVGRAYTVVE 173
Cdd:PRK08123 236 TLAKKLGIPLVYGSDAHSAADVGRGYDTIE 265
PHP_HisPPase_Hisj_like cd12110
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase of Hisj like; ...
 128-169 6.46e-03

Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase of Hisj like; Bacillus subtilis YtvP HisJ has strong histidinol phosphate phosphatase (HisPPase) 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. HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to produce 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 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: 213994 [Multi-domain]  Cd Length: 244  Bit Score: 36.77  E-value: 6.46e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 493475497 128 AIEVNG----KHPR----SRPLVEqLAEERDLPLVGGSDAHYPFEVGRAY 169
Cdd:cd12110  191 ALEINTaglrKPVGepypSPEFLE-LAKELGIPVTLGSDAHSPEDVGQGY 239
 
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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