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Conserved domains on  [gi|489494884|ref|WP_003399801|]
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MULTISPECIES: PHP domain-containing protein [Mycobacterium]

Protein Classification

PHP domain-containing protein( domain architecture ID 11482977)

PHP (polymerase and histidinol phosphatase) domain-containing protein with an N-terminal helix-hairpin-helix domain and a C-terminal PHP domain

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK07945 PRK07945
PHP domain-containing protein;
1-335 0e+00

PHP domain-containing protein;


:

Pssm-ID: 236135 [Multi-domain]  Cd Length: 335  Bit Score: 654.36  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884   1 MDPVTALRQIAYYKDRNRHDPRRVMAYRNAADIIEGLDDAARQRHGQANSWQSLAGIGPKTAKVIAQAWSGREPDLLAEL 80
Cdd:PRK07945   1 MDPVAALRRIAFLLERARADTYRVRAFRRAADVVEALDAAERARRARAGSLTSLPGIGPKTAKVIAQALAGRVPDYLAEL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  81 RADAEDLGGGAIRAALRGDLHLHSNWSDGSAPIEEMMATAAALGHQYCALTDHSPRLTIANGLSPDRLRKQLDVIDELRE 160
Cdd:PRK07945  81 RADAEPLGGGALRAALRGDLHTHSDWSDGGSPIEEMARTAAALGHEYCALTDHSPRLTVANGLSAERLRKQLDVVAELNE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 161 KFAPLRILTGIEVDILEDGSLDQEPEMLDRLDIVVASVHSKLSMDSAAMTRRMVRAVANGHTDVLGHCTGRLIAGNRGIR 240
Cdd:PRK07945 161 ELAPFRILTGIEVDILDDGSLDQEPELLDRLDVVVASVHSKLRMDAAAMTRRMLAAVANPHTDVLGHCTGRLVTGNRGTR 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 241 PESKFDAEAVFTACREHGTAVEINSRPERRDPPTRLLHLARDIGCVFSIDTDAHAPGQLDFLGYGAQRALDAEVPADRIV 320
Cdd:PRK07945 241 PESKFDAEAVFAACREHGTAVEINSRPERRDPPTRLLRLALDAGCLFSIDTDAHAPGQLDWLGYGCERAEEAGVPADRIV 320

                        330
                 ....*....|....*
gi 489494884 321 NTWPADTLLAWTGSH 335
Cdd:PRK07945 321 NTWPADRLLAWTGSR 335
 
Name Accession Description Interval E-value
PRK07945 PRK07945
PHP domain-containing protein;
1-335 0e+00

PHP domain-containing protein;


Pssm-ID: 236135 [Multi-domain]  Cd Length: 335  Bit Score: 654.36  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884   1 MDPVTALRQIAYYKDRNRHDPRRVMAYRNAADIIEGLDDAARQRHGQANSWQSLAGIGPKTAKVIAQAWSGREPDLLAEL 80
Cdd:PRK07945   1 MDPVAALRRIAFLLERARADTYRVRAFRRAADVVEALDAAERARRARAGSLTSLPGIGPKTAKVIAQALAGRVPDYLAEL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  81 RADAEDLGGGAIRAALRGDLHLHSNWSDGSAPIEEMMATAAALGHQYCALTDHSPRLTIANGLSPDRLRKQLDVIDELRE 160
Cdd:PRK07945  81 RADAEPLGGGALRAALRGDLHTHSDWSDGGSPIEEMARTAAALGHEYCALTDHSPRLTVANGLSAERLRKQLDVVAELNE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 161 KFAPLRILTGIEVDILEDGSLDQEPEMLDRLDIVVASVHSKLSMDSAAMTRRMVRAVANGHTDVLGHCTGRLIAGNRGIR 240
Cdd:PRK07945 161 ELAPFRILTGIEVDILDDGSLDQEPELLDRLDVVVASVHSKLRMDAAAMTRRMLAAVANPHTDVLGHCTGRLVTGNRGTR 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 241 PESKFDAEAVFTACREHGTAVEINSRPERRDPPTRLLHLARDIGCVFSIDTDAHAPGQLDFLGYGAQRALDAEVPADRIV 320
Cdd:PRK07945 241 PESKFDAEAVFAACREHGTAVEINSRPERRDPPTRLLRLALDAGCLFSIDTDAHAPGQLDWLGYGCERAEEAGVPADRIV 320

                        330
                 ....*....|....*
gi 489494884 321 NTWPADTLLAWTGSH 335
Cdd:PRK07945 321 NTWPADRLLAWTGSR 335
PHP_PolX cd07436
Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal ...
 96-331 3.80e-119

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: 342.86  E-value: 3.80e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  96 LRGDLHLHSNWSDGSAPIEEMMATAAALGHQYCALTDHSPRLTIANGLSPDRLRKQLDVIDELREKFAPLRILTGIEVDI 175
Cdd:cd07436    5 IRGDLHVHTTWSDGRNSIEEMAEAARALGYEYIAITDHSKSLRVANGLSEERLREQIEEIDALNEKLPGIRILKGIEVDI 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 176 LEDGSLDQEPEMLDRLDIVVASVHSKLSMDSAAMTRRMVRAVANGHTDVLGHCTGRLIagnrGIRPESKFDAEAVFTACR 255
Cdd:cd07436   85 LPDGSLDYPDEVLAELDVVVASVHSGFNQSEEEMTERLLKAIENPHVDILGHPTGRLL----GRREGYEVDMERVIEAAA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489494884 256 EHGTAVEINSRPERRDPPTRLLHLARDIGCVFSIDTDAHAPGQLDFLGYGAQRALDAEVPADRIVNTWPADTLLAW 331
Cdd:cd07436  161 ETGTALEINANPDRLDLDDRHARRAKEAGVKIAINTDAHSTDGLDNMRYGVGTARRGWLEKEDVLNTLPLEELLKF 236
HIS2 COG1387
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and ...
 96-331 3.37e-107

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: 312.47  E-value: 3.37e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  96 LRGDLHLHSNWSDGSAPIEEMMATAAALGHQYCALTDHSPRLTIANGLSPDRLRKQLDVIDELREKFAPLRILTGIEVDI 175
Cdd:COG1387    1 MRGDLHTHTTYSDGEGTIEEMVEAAIELGLEYIAITDHSPSLFVANGLSEERLLEYLEEIEELNEKYPDIKILKGIEVDI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 176 LEDGSLDQEPEMLDRLDIVVASVHSKLSMDSAAMTRRMVRAVANGHTDVLGHCTGRLIagnrGIRPESKFDAEAVFTACR 255
Cdd:COG1387   81 LPDGSLDYPDELLAPLDYVIGSVHSILEEDYEEYTERLLKAIENPLVDILGHPDGRLL----GGRPGYEVDIEEVLEAAA 156

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489494884 256 EHGTAVEINSRPERRDPPTRLLHLARDIGCVFSIDTDAHAPGQLDFLGYGAQRALDAEVPADRIVNTWPADTLLAW 331
Cdd:COG1387  157 ENGVALEINTRPLRLDPSDELLKLAKELGVKITIGSDAHSPEDLGDLEYGVALARRAGLTKEDVFNTLRKEELLKL 232
PHP pfam02811
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ...
 99-199 8.61e-14

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


Pssm-ID: 460705 [Multi-domain]  Cd Length: 171  Bit Score: 68.34  E-value: 8.61e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884   99 DLHLHSNWS--DGSAPIEEMMATAAALGHQYCALTDHSPRLTIanglspdrlrkqLDVIDELREkfAPLRILTGIEVDIL 176
Cdd:pfam02811   1 HLHVHSEYSllDGAARIEELVKRAKELGMPAIAITDHGNLFGA------------VEFYKAAKK--AGIKPIIGCEVYVA 66

                          90       100
                  ....*....|....*....|...
gi 489494884  177 EDGSLDQEPEMLDRLDIVVASVH 199
Cdd:pfam02811  67 PGSREETEKLLAKYFDLVLLAVH 89
POLIIIAc smart00481
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ...
 99-177 1.19e-11

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: 59.59  E-value: 1.19e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884    99 DLHLHSNWS--DGSAPIEEMMATAAALGHQYCALTDHSprltiaNGLSPDRLRKqldvidelREKFAPLRILTGIEVDIL 176
Cdd:smart00481   1 DLHVHSDYSllDGALSPEELVKRAKELGLKAIAITDHG------NLFGAVEFYK--------AAKKAGIKPIIGLEANIV 66


                   .
gi 489494884   177 E 177
Cdd:smart00481  67 D 67
hisJ_fam TIGR01856
histidinol phosphate phosphatase, HisJ family; This model represents the histidinol phosphate ...
 99-298 4.15e-11

histidinol phosphate phosphatase, HisJ family; This model represents the histidinol phosphate phosphatase HisJ of Bacillus subtilis, and related proteins from a number of species within a larger family of phosphatases in the PHP hydrolase family. HisJ catalyzes the penultimate step of histidine biosynthesis but shows no homology to the functionally equivalent sequence in E. coli, a domain of the bifunctional HisB protein. Note, however, that many species have two members and that Clostridium perfringens, predicted not to make histidine, has five members of this family; this family is designated subfamily rather than equivalog to indicate that members may not all act as HisJ.


Pssm-ID: 273837 [Multi-domain]  Cd Length: 253  Bit Score: 62.41  E-value: 4.15e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884   99 DLHLHSNWS-DGSAPIEEMMATAAALG-HQYCaLTDHSPRLTIANG---LSPDRLRKQLDV----IDELREKFA-PLRIL 168
Cdd:TIGR01856   2 DSHSHSPFCaHGTDTLREVVQEAIQLGfEEIC-FTEHAPRPFYYPEedfLKKEMLFLSLPEyfqeINQLKQEYAdKIKIL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  169 TGIEVDILEdGSLDQEPEMLDR--LDIVVASVH-------------------------SKLSMDSAAMTRRMVRAVANgh 221
Cdd:TIGR01856  81 IGLEVDYIP-GFEEEIKDFLDSynLDFVIGSVHhlggipidfdieefdetlfsfqknlEQAQRDYFESQYDSIQNLFK-- 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  222 TDVLGHCTgrLIA-----GNRGIRPESKFDA-EAVFTACREHGTAVEINSRPERRD-----PPTRLLHLARDIGCVFSID 290
Cdd:TIGR01856 158 PLVIGHLD--LVKkfgplTDVSSKSDEVRELlQRILKAVASYGKALEINTSGFRKPleeayPSKELLNLAKELGIPLVLG 235


                  ....*...
gi 489494884  291 TDAHAPGQ 298
Cdd:TIGR01856 236 SDAHGPGQ 243
CehA_McbA_metalo NF038032
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ...
 96-173 4.34e-09

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: 56.95  E-value: 4.34e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489494884  96 LRGDLHLHSNWSDGSAPIEEMMATAAALGHQYCALTDHSprlTIAnglspdrlrkQLDVIDELREKFAPLRILTGIEV 173
Cdd:NF038032   3 YSGDLHIHTNHSDGPTTPEELARAALAEGLDVIALTDHN---TIS----------GRAYFAELLASERGLLVIPGMEV 67
nside_bi_sphtase NF041577
3',5'-nucleoside bisphosphate phosphatase;
99-133 3.27e-05

3',5'-nucleoside bisphosphate phosphatase;


Pssm-ID: 469462 [Multi-domain]  Cd Length: 276  Bit Score: 44.90  E-value: 3.27e-05
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 489494884  99 DLHLHSNWSDGSAPIEEMMATAAALGHQYCALTDH 133
Cdd:NF041577   5 DLHCHSTVSDGLLSPAEVVRRAAARGVELLALTDH 39
 
Name Accession Description Interval E-value
PRK07945 PRK07945
PHP domain-containing protein;
1-335 0e+00

PHP domain-containing protein;


Pssm-ID: 236135 [Multi-domain]  Cd Length: 335  Bit Score: 654.36  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884   1 MDPVTALRQIAYYKDRNRHDPRRVMAYRNAADIIEGLDDAARQRHGQANSWQSLAGIGPKTAKVIAQAWSGREPDLLAEL 80
Cdd:PRK07945   1 MDPVAALRRIAFLLERARADTYRVRAFRRAADVVEALDAAERARRARAGSLTSLPGIGPKTAKVIAQALAGRVPDYLAEL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  81 RADAEDLGGGAIRAALRGDLHLHSNWSDGSAPIEEMMATAAALGHQYCALTDHSPRLTIANGLSPDRLRKQLDVIDELRE 160
Cdd:PRK07945  81 RADAEPLGGGALRAALRGDLHTHSDWSDGGSPIEEMARTAAALGHEYCALTDHSPRLTVANGLSAERLRKQLDVVAELNE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 161 KFAPLRILTGIEVDILEDGSLDQEPEMLDRLDIVVASVHSKLSMDSAAMTRRMVRAVANGHTDVLGHCTGRLIAGNRGIR 240
Cdd:PRK07945 161 ELAPFRILTGIEVDILDDGSLDQEPELLDRLDVVVASVHSKLRMDAAAMTRRMLAAVANPHTDVLGHCTGRLVTGNRGTR 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 241 PESKFDAEAVFTACREHGTAVEINSRPERRDPPTRLLHLARDIGCVFSIDTDAHAPGQLDFLGYGAQRALDAEVPADRIV 320
Cdd:PRK07945 241 PESKFDAEAVFAACREHGTAVEINSRPERRDPPTRLLRLALDAGCLFSIDTDAHAPGQLDWLGYGCERAEEAGVPADRIV 320

                        330
                 ....*....|....*
gi 489494884 321 NTWPADTLLAWTGSH 335
Cdd:PRK07945 321 NTWPADRLLAWTGSR 335
PHP_PolX cd07436
Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal ...
 96-331 3.80e-119

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: 342.86  E-value: 3.80e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  96 LRGDLHLHSNWSDGSAPIEEMMATAAALGHQYCALTDHSPRLTIANGLSPDRLRKQLDVIDELREKFAPLRILTGIEVDI 175
Cdd:cd07436    5 IRGDLHVHTTWSDGRNSIEEMAEAARALGYEYIAITDHSKSLRVANGLSEERLREQIEEIDALNEKLPGIRILKGIEVDI 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 176 LEDGSLDQEPEMLDRLDIVVASVHSKLSMDSAAMTRRMVRAVANGHTDVLGHCTGRLIagnrGIRPESKFDAEAVFTACR 255
Cdd:cd07436   85 LPDGSLDYPDEVLAELDVVVASVHSGFNQSEEEMTERLLKAIENPHVDILGHPTGRLL----GRREGYEVDMERVIEAAA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489494884 256 EHGTAVEINSRPERRDPPTRLLHLARDIGCVFSIDTDAHAPGQLDFLGYGAQRALDAEVPADRIVNTWPADTLLAW 331
Cdd:cd07436  161 ETGTALEINANPDRLDLDDRHARRAKEAGVKIAINTDAHSTDGLDNMRYGVGTARRGWLEKEDVLNTLPLEELLKF 236
HIS2 COG1387
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and ...
 96-331 3.37e-107

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: 312.47  E-value: 3.37e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  96 LRGDLHLHSNWSDGSAPIEEMMATAAALGHQYCALTDHSPRLTIANGLSPDRLRKQLDVIDELREKFAPLRILTGIEVDI 175
Cdd:COG1387    1 MRGDLHTHTTYSDGEGTIEEMVEAAIELGLEYIAITDHSPSLFVANGLSEERLLEYLEEIEELNEKYPDIKILKGIEVDI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 176 LEDGSLDQEPEMLDRLDIVVASVHSKLSMDSAAMTRRMVRAVANGHTDVLGHCTGRLIagnrGIRPESKFDAEAVFTACR 255
Cdd:COG1387   81 LPDGSLDYPDELLAPLDYVIGSVHSILEEDYEEYTERLLKAIENPLVDILGHPDGRLL----GGRPGYEVDIEEVLEAAA 156

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489494884 256 EHGTAVEINSRPERRDPPTRLLHLARDIGCVFSIDTDAHAPGQLDFLGYGAQRALDAEVPADRIVNTWPADTLLAW 331
Cdd:COG1387  157 ENGVALEINTRPLRLDPSDELLKLAKELGVKITIGSDAHSPEDLGDLEYGVALARRAGLTKEDVFNTLRKEELLKL 232
PRK08609 PRK08609
DNA polymerase/3'-5' exonuclease PolX;
97-331 3.58e-68

DNA polymerase/3'-5' exonuclease PolX;


Pssm-ID: 236311 [Multi-domain]  Cd Length: 570  Bit Score: 223.29  E-value: 3.58e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  97 RGDLHLHSNWSDGSAPIEEMMATAAALGHQYCALTDHSPRLTIANGLSPDRLRKQLDVIDELREKFAPLRILTGIEVDIL 176
Cdd:PRK08609 335 QGDLHMHTTWSDGAFSIEEMVEACIAKGYEYMAITDHSQYLKVANGLTEERLLEQAEEIKALNEKYPEIDILSGIEMDIL 414

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 177 EDGSLDQEPEMLDRLDIVVASVHSKLSMDSAAMTRRMVRAVANGHTDVLGHCTGRLIagnrGIRPESKFDAEAVFTACRE 256
Cdd:PRK08609 415 PDGSLDYDDEVLAELDYVIAAIHSSFSQSEEEIMKRLENACRNPYVRLIAHPTGRLI----GRRDGYDVNIDQLIELAKE 490

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489494884 257 HGTAVEINSRPERRDPPTRLLHLARDIGCVFSIDTDAHAPGQLDFLGYGAQRALDAEVPADRIVNTWPADTLLAW 331
Cdd:PRK08609 491 TNTALELNANPNRLDLSAEHLKKAQEAGVKLAINTDAHHTEMLDDMKYGVATARKGWIQKDRVINTWSREEFKDF 565
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
79-331 2.71e-56

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


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 191.94  E-value: 2.71e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  79 ELRadaEDlgGGAIRAAL-------------RGDLHLHSNWSDGSAPIEEMMATAAALGHQYCALTDHSPRLTIANGLSP 145
Cdd:COG1796  311 ELR---ED--RGEIEAAEegrlpelvelddiRGDLHHHTTWSDGGASIEEMAAAAAARGYYYIAITDHSSSLVVAGGLDE 385

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 146 DRLRKQLDVIDELREKFAPLRILTGIEVDILEDGSLDQEPEMLDRLDIVVASVHSKLSMDSAAMTRRMVRAVANGHTDVL 225
Cdd:COG1796  386 ERLLQQEEEIDALNERLDGIILLLGGEEDILDDGGLDDDDDLLLEDDDVVAAVHHSFLLQDEEMTRRRLAAANEPVVVII 465

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 226 GHCTGRLIagnrGIRPESKFDAEAVFTACREHGTAVEINSRPERRDPPTRLLHLARDIGCVFSIDTDAHAPGQLDFLGYG 305
Cdd:COG1796  466 HHPTGRLL----LRRRPYYVDDEAIIAAAAAAGALEEENNAPRRLLLLDDLARAAAEGGVVIIIIDDAHHTDLLLDLMGG 541

                        250       260
                 ....*....|....*....|....*.
gi 489494884 306 AQRALDAEVPADRIVNTWPADTLLAW 331
Cdd:COG1796  542 GVAARRRWWLEKDVNNNTLLLELLLL 567
PHP_HisPPase_Ycdx_like cd07437
Polymerase and Histidinol Phosphatase domain of Ycdx like; PHP Ycdx-like is a stand alone PHP ...
 99-335 5.42e-34

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: 124.86  E-value: 5.42e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  99 DLHLHSNWSdGSA--PIEEMMATAAALGHQYCALTDHSPRLtianglsPDRLRKQ----LDVIDelREKFApLRILTGIE 172
Cdd:cd07437    4 DLHTHTIAS-GHAysTIEEMARAAAEKGLKLLGITDHGPAM-------PGAPHPWyfgnLKVIP--REIYG-VRILRGVE 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 173 VDIL-EDGSLDQEPEMLDRLDIVVASVHSK--LSMDSAAMTRRMVRAVANGHTDVLGHCtgrliaGNrgirPESKFDAEA 249
Cdd:cd07437   73 ANIIdYDGNLDLPERVLKRLDYVIASLHEPcfAPGTKEENTRAYINAMENPYVDIIGHP------GN----PRYPIDYEA 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 250 VFTACREHGTAVEIN------SRPERRDPPTRLLHLARDIGCVFSIDTDAHAP---GQLDFlgygAQRALD-AEVPADRI 319
Cdd:cd07437  143 VVKAAKEYNVLLEINnsslspSRKGSRENCREIAELCKKYGVPVIVGSDAHIAydiGNFDE----ALELLEeIGFPEELI 218

                        250
                 ....*....|....*.
gi 489494884 320 VNTWPaDTLLAWTGSH 335
Cdd:cd07437  219 LNTSP-ERLLDFLKLR 233
PRK09248 PRK09248
putative hydrolase; Validated
 99-324 9.29e-25

putative hydrolase; Validated


Pssm-ID: 236429 [Multi-domain]  Cd Length: 246  Bit Score: 100.30  E-value: 9.29e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  99 DLHLHSNWSdGSA--PIEEMMATAAALGHQYCALTDHSPrlTIANGlsPDR-----LRKQLDVIDELRekfaplrILTGI 171
Cdd:PRK09248   6 DTHTHTIAS-GHAysTLHENAAEAKQKGLKLFAITDHGP--DMPGA--PHYwhfgnLRVLPRKVDGVG-------ILRGI 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 172 EVDIL-EDGSLDQEPEMLDRLDIVVASVHSKL--SMDSAAMTRRMVRAVANGHTDVLGHctgrliAGNrgirPESKFDAE 248
Cdd:PRK09248  74 EANIKnYDGEIDLPGDMLKKLDIVIAGFHEPVfaPGDKETNTQALINAIKNGRVDIIGH------PGN----PKYPIDIE 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 249 AVFTACREHGTAVEIN------SRPERRDPPTRLLHLARDIGCVFSIDTDAH---APGQLDFlgygAQRALD-AEVPADR 318
Cdd:PRK09248 144 AVVKAAKEHNVALEINnssfghSRKGSEDNCRAIAALCKKAGVWVALGSDAHiafDIGNFEE----ALKILDeVGFPEER 219


                 ....*.
gi 489494884 319 IVNTWP 324
Cdd:PRK09248 220 ILNVSP 225
PHP_HisPPase_Hisj_like cd12110
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase of Hisj like; ...
 99-301 5.16e-19

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: 84.54  E-value: 5.16e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  99 DLHLHSNWSD-GSAPIEEMMATAAALG-HQYCaLTDHSPR-----LTIANGLSPDRLRKQLDVIDELREKFA-PLRILTG 170
Cdd:cd12110    2 DYHTHTPRCDhASGTLEEYVEAAIELGfTEIG-FSEHAPLpfefdDYPESRMAEEELEDYVEEIRRLKEKYAdQIEIKLG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 171 IEVDILEdGSLDQEPEML--DRLDIVVASVH---------------SKLSMDSAAMTRR----MVRAVANGHTDVLGHCT 229
Cdd:cd12110   81 LEVDYFP-GYEEELRELLygYPLDYVIGSVHflggwgfdfpedgiaEYFEGDIDELYERyfdlVEKAIESGLFDIIGHPD 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 230 grLIAGNRGIRPESKFD---AEAVFTACREHGTAVEINSRPERRD-----PPTRLLHLARDIGCVFSIDTDAHAPGQLDF 301
Cdd:cd12110  160 --LIKKFGKNDEPDEDYeelIERILRAIAEAGVALEINTAGLRKPvgepyPSPEFLELAKELGIPVTLGSDAHSPEDVGQ 237
PRK08392 PRK08392
hypothetical protein; Provisional
 99-296 5.51e-15

hypothetical protein; Provisional


Pssm-ID: 169423 [Multi-domain]  Cd Length: 215  Bit Score: 72.89  E-value: 5.51e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  99 DLHLHSNWSDGSAPIEEMMATAAALGHQYCALTDHSPRLTianglsPDRLRKQLDVIDELREKfAPLRILTGIEVDILED 178
Cdd:PRK08392   2 DLHTHTVYSDGIGSVRDNIAEAERKGLRLVGISDHIHYFT------PSKFNAYINEIRQWGEE-SEIVVLAGIEANITPN 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 179 GsLDQEPEMLDRLDIVVASVHSKLSMDSAAMTRRMVR-AVANGHTDVLGHctgrliAGNR----GIRPESKFDaeAVFTA 253
Cdd:PRK08392  75 G-VDITDDFAKKLDYVIASVHEWFGRPEHHEYIELVKlALMDENVDIIGH------FGNSfpyiGYPSEEELK--EILDL 145

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 489494884 254 CREHGTAVEINSRpeRRDPPTRLLHLARDIGCVFSIDTDAHAP 296
Cdd:PRK08392 146 AEAYGKAFEISSR--YRVPDLEFIRECIKRGIKLTFASDAHRP 186
PHP pfam02811
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ...
 99-199 8.61e-14

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


Pssm-ID: 460705 [Multi-domain]  Cd Length: 171  Bit Score: 68.34  E-value: 8.61e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884   99 DLHLHSNWS--DGSAPIEEMMATAAALGHQYCALTDHSPRLTIanglspdrlrkqLDVIDELREkfAPLRILTGIEVDIL 176
Cdd:pfam02811   1 HLHVHSEYSllDGAARIEELVKRAKELGMPAIAITDHGNLFGA------------VEFYKAAKK--AGIKPIIGCEVYVA 66

                          90       100
                  ....*....|....*....|...
gi 489494884  177 EDGSLDQEPEMLDRLDIVVASVH 199
Cdd:pfam02811  67 PGSREETEKLLAKYFDLVLLAVH 89
POLIIIAc smart00481
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ...
 99-177 1.19e-11

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: 59.59  E-value: 1.19e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884    99 DLHLHSNWS--DGSAPIEEMMATAAALGHQYCALTDHSprltiaNGLSPDRLRKqldvidelREKFAPLRILTGIEVDIL 176
Cdd:smart00481   1 DLHVHSDYSllDGALSPEELVKRAKELGLKAIAITDHG------NLFGAVEFYK--------AAKKAGIKPIIGLEANIV 66


                   .
gi 489494884   177 E 177
Cdd:smart00481  67 D 67
YciV COG0613
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ...
 95-298 2.50e-11

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


Pssm-ID: 440378 [Multi-domain]  Cd Length: 188  Bit Score: 61.85  E-value: 2.50e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  95 ALRGDLHLHSNWSDGSAPIEEMMATAAALGHQYCALTDHsprltianglspDRLRKQLDVIDELREKfaPLRILTGIEVD 174
Cdd:COG0613    1 WMKIDLHVHTTASDGSLSPEELVARAKAAGLDVLAITDH------------DTVAGYEEAAEAAKEL--GLLVIPGVEIS 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 175 ILEDGS--------LDQE-PEMLDRLDIVV-ASVHSKLSMDSAAmtrRMVRAvANGHTdVLGHctgrLIAGNRGIRPESK 244
Cdd:COG0613   67 TRWEGRevhilgygIDPEdPALEALLGIPVeKAEREWLSLEEAI---DLIRE-AGGVA-VLAH----PFRYKRGRWLDDL 137

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 489494884 245 FDAeavftACREHGTAVEINSRPERRDPPTRLLHLARDIGCVFSIDTDAHAPGQ 298
Cdd:COG0613  138 LEE-----LADAGLDGIEVYNGRHSPEDNERAAELAEEYGLLATGGSDAHGPEK 186
HHH_8 pfam14716
Helix-hairpin-helix domain;
6-67 3.91e-11

Helix-hairpin-helix domain;


Pssm-ID: 434152 [Multi-domain]  Cd Length: 67  Bit Score: 57.90  E-value: 3.91e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489494884    6 ALRQIAYYKDRNRHDPRRVMAYRNAADIIEGLDDAARQRHGqansWQSLAGIGPKTAKVIAQ 67
Cdd:pfam14716   7 ALEELADLLELKGEDPFRVRAYRRAARALEALPEEITSLEE----LTKLPGIGKKIAAKIEE 64
hisJ_fam TIGR01856
histidinol phosphate phosphatase, HisJ family; This model represents the histidinol phosphate ...
 99-298 4.15e-11

histidinol phosphate phosphatase, HisJ family; This model represents the histidinol phosphate phosphatase HisJ of Bacillus subtilis, and related proteins from a number of species within a larger family of phosphatases in the PHP hydrolase family. HisJ catalyzes the penultimate step of histidine biosynthesis but shows no homology to the functionally equivalent sequence in E. coli, a domain of the bifunctional HisB protein. Note, however, that many species have two members and that Clostridium perfringens, predicted not to make histidine, has five members of this family; this family is designated subfamily rather than equivalog to indicate that members may not all act as HisJ.


Pssm-ID: 273837 [Multi-domain]  Cd Length: 253  Bit Score: 62.41  E-value: 4.15e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884   99 DLHLHSNWS-DGSAPIEEMMATAAALG-HQYCaLTDHSPRLTIANG---LSPDRLRKQLDV----IDELREKFA-PLRIL 168
Cdd:TIGR01856   2 DSHSHSPFCaHGTDTLREVVQEAIQLGfEEIC-FTEHAPRPFYYPEedfLKKEMLFLSLPEyfqeINQLKQEYAdKIKIL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  169 TGIEVDILEdGSLDQEPEMLDR--LDIVVASVH-------------------------SKLSMDSAAMTRRMVRAVANgh 221
Cdd:TIGR01856  81 IGLEVDYIP-GFEEEIKDFLDSynLDFVIGSVHhlggipidfdieefdetlfsfqknlEQAQRDYFESQYDSIQNLFK-- 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  222 TDVLGHCTgrLIA-----GNRGIRPESKFDA-EAVFTACREHGTAVEINSRPERRD-----PPTRLLHLARDIGCVFSID 290
Cdd:TIGR01856 158 PLVIGHLD--LVKkfgplTDVSSKSDEVRELlQRILKAVASYGKALEINTSGFRKPleeayPSKELLNLAKELGIPLVLG 235


                  ....*...
gi 489494884  291 TDAHAPGQ 298
Cdd:TIGR01856 236 SDAHGPGQ 243
CehA_McbA_metalo NF038032
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ...
 96-173 4.34e-09

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: 56.95  E-value: 4.34e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489494884  96 LRGDLHLHSNWSDGSAPIEEMMATAAALGHQYCALTDHSprlTIAnglspdrlrkQLDVIDELREKFAPLRILTGIEV 173
Cdd:NF038032   3 YSGDLHIHTNHSDGPTTPEELARAALAEGLDVIALTDHN---TIS----------GRAYFAELLASERGLLVIPGMEV 67
PHP_HisPPase cd07432
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ...
 99-294 9.75e-09

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: 53.01  E-value: 9.75e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  99 DLHLHSNWSDGSA-PIEEMMATAAALGHQYCALTDHsprLTIANglsPDRLRKQldvidelrEKFAPLRILTGIEVDIle 177
Cdd:cd07432    2 DLHIHSVFSPDSDmTPEEIVERAIELGLDGIAITDH---NTIDG---AEEALKE--------AYKDGLLVIPGVEVTL-- 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 178 dgsldqepemldrldivvasvhsklsmdsaamtrrmvravanghtDVLGHCTgrliagnrgiRPESKFDAEAVFTACREH 257
Cdd:cd07432   66 ---------------------------------------------VVLAHPD----------RPSRYGLSDLILKPLIKN 90

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 489494884 258 GTAVEI-NSRPERRDPPTRLLHLARDIGCVFSIDTDAH 294
Cdd:cd07432   91 GDAIEVnNSRLRYGLNNLAAKRYAELGGLPITGGSDAH 128
PHP cd07309
Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2 ...
 98-175 3.66e-07

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: 47.42  E-value: 3.66e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489494884  98 GDLHLHSNWSDG-SAPIEEMMATAAALGHQYCALTDHSPrltiANGLSPDRLRKQLDVIDELREkfAPLRILTGIEVDI 175
Cdd:cd07309    1 VDLHTHTVFSDGdHAKLTELVDKAKELGPDALAITDHGN----LRGLAEFNTAGK*NHIKAAEA--AGIKIIIGSEVNL 73
PRK06361 PRK06361
histidinol phosphate phosphatase domain-containing protein;
103-299 3.84e-07

histidinol phosphate phosphatase domain-containing protein;


Pssm-ID: 180543 [Multi-domain]  Cd Length: 212  Bit Score: 49.96  E-value: 3.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 103 HSNWSDGSAPIEEMMATAAALGHQYCALTDHSPRLTIanglsPDRLRKQLDVIDELrEKFAPLRILTGIEVDILEDGSLD 182
Cdd:PRK06361   2 HTIFSDGELIPSELVRRARVLGYRAIAITDHADASNL-----EEILEKLVRAAEEL-ELYWDIEVIPGVELTHVPPKLIP 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884 183 QEPEMLDRL--DIVVasVHSKlSMDSAAMTRRMVRAVANGHTDVLGHctGRLIagnrgirpeSKFDAEAVftacREHGTA 260
Cdd:PRK06361  76 KLAKKARDLgaEIVV--VHGE-TIVEPVEEGTNLAAIECEDVDILAH--PGLI---------TEEEAELA----AENGVF 137

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 489494884 261 VEINSRPERRDPPTRLLHLARDIGCVFSIDTDAHAPGQL 299
Cdd:PRK06361 138 LEITARKGHSLTNGHVARIAREAGAPLVINTDTHAPSDL 176
PHP_HisPPase_AMP cd07438
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ...
 99-179 8.85e-07

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: 47.77  E-value: 8.85e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884  99 DLHLHSNWSDGSAPIEEMMATAAALGHQYCALTDHSprlTIANglspdrlrkqldvIDELRE--KFAPLRILTGIEVDIL 176
Cdd:cd07438    2 DLHTHSTASDGTLSPEELVELAKEAGLKVLAITDHD---TVAG-------------LEEALAaaKELGIELIPGVEISTE 65


                 ...
gi 489494884 177 EDG 179
Cdd:cd07438   66 YEG 68
DnaE COG0587
DNA polymerase III, alpha subunit [Replication, recombination and repair];
100-133 3.61e-06

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


Pssm-ID: 440352 [Multi-domain]  Cd Length: 1050  Bit Score: 48.53  E-value: 3.61e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 489494884  100 LHLHSNWS--DGSAPIEEMMATAAALGHQYCALTDH 133
Cdd:COG0587     8 LHVHSEYSllDGASRPEELVARAAELGMPALAITDH 43
PHP_PolIIIA_DnaE3 cd12113
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ...
 100-133 4.34e-06

Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that is responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. The PolIIIA PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination, and like other PHP structures, the PolIIIA PHP exhibits a distorted (beta/alpha) 7 barrel and coordinates up to 3 metals. Initially, it was proposed that PHP region might be involved in pyrophosphate hydrolysis, but such an activity has not been found. It has been shown that the PHP of PolIIIA has a trinuclear metal complex and is capable of proofreading activity. Bacterial genome replication and DNA repair mechanisms is related to the GC content of its genomes. There is a correlation between GC content variations and the dimeric combinations of PolIIIA subunits. Eubacteria can be grouped into different GC variable groups: the full-spectrum or dnaE1 group, the high-GC or dnaE2-dnaE1 group, and the low GC or polC-dnaE3 group.


Pssm-ID: 213997 [Multi-domain]  Cd Length: 283  Bit Score: 47.43  E-value: 4.34e-06
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 489494884 100 LHLHSNWS--DGSAPIEEMMATAAALGHQYCALTDH 133
Cdd:cd12113    5 LHVHTEYSllDGAIRIKDLVKRAKELGMPALAITDH 40
nside_bi_sphtase NF041577
3',5'-nucleoside bisphosphate phosphatase;
99-133 3.27e-05

3',5'-nucleoside bisphosphate phosphatase;


Pssm-ID: 469462 [Multi-domain]  Cd Length: 276  Bit Score: 44.90  E-value: 3.27e-05
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 489494884  99 DLHLHSNWSDGSAPIEEMMATAAALGHQYCALTDH 133
Cdd:NF041577   5 DLHCHSTVSDGLLSPAEVVRRAAARGVELLALTDH 39
polc TIGR00594
DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are ...
 100-133 1.04e-04

DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are known are DNA polymerases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273161 [Multi-domain]  Cd Length: 1022  Bit Score: 44.29  E-value: 1.04e-04
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 489494884   100 LHLHSNWS--DGSAPIEEMMATAAALGHQYCALTDH 133
Cdd:TIGR00594    4 LHVHSDYSllDGAAKIKPLVKKAKELGMPALALTDH 39
PHP_PolIIIA_POLC cd07435
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ...
 100-133 1.27e-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: 1.27e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 489494884 100 LHLHSNWS--DGSAPIEEMMATAAALGHQYCALTDH 133
Cdd:cd07435    4 LHAHTKMSamDGVTSVKELVKRAAEWGHKAIAITDH 39
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
 6-85 2.49e-04

Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.


Pssm-ID: 143386 [Multi-domain]  Cd Length: 307  Bit Score: 42.18  E-value: 2.49e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489494884   6 ALRQIAYYKDRNRHDPRRVMAYRNAADIIEGLD---DAARQRHGqanswqsLAGIGPKTAKVIAQAWSGREPDLLAELRA 82
Cdd:cd00141    6 ILEELADLLELLGGNPFRVRAYRKAARALESLPepiESLEEAKK-------LPGIGKKIAEKIEEILETGKLRKLEELRE 78


                 ...
gi 489494884  83 DAE 85
Cdd:cd00141   79 DVP 81
PHP_PolIIIA cd07431
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ...
 100-133 1.01e-03

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: 39.49  E-value: 1.01e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 489494884 100 LHLHSNWS--DGSAPIEEMMATAAALGHQYCALTDH 133
Cdd:cd07431    3 LHVHSSYSllDSAIRPEDLVARAKELGYSALALTDR 38
dnaE PRK05673
DNA polymerase III subunit alpha; Validated
 100-133 1.08e-03

DNA polymerase III subunit alpha; Validated


Pssm-ID: 235554 [Multi-domain]  Cd Length: 1135  Bit Score: 40.86  E-value: 1.08e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 489494884  100 LHLHSNWS--DGSAPIEEMMATAAALGHQYCALTDH 133
Cdd:PRK05673    5 LHVHSEYSllDGAAKIKPLVKKAAELGMPAVALTDH 40
dnaE PRK06826
DNA polymerase III DnaE; Reviewed
 100-133 1.22e-03

DNA polymerase III DnaE; Reviewed


Pssm-ID: 235868 [Multi-domain]  Cd Length: 1151  Bit Score: 40.64  E-value: 1.22e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 489494884  100 LHLHSNWS--DGSAPIEEMMATAAALGHQYCALTDH 133
Cdd:PRK06826    8 LHVHTEYSllDGSARIKDLIKRAKELGMDSIAITDH 43
PHP_HisPPase_Thermotoga_like cd12111
Polymerase and Histidinol Phosphatase domain of Thermotoga like; The PHP (also called ...
 99-163 1.28e-03

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: 39.71  E-value: 1.28e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489494884  99 DLHLHSNWSDGSAPIEEMMATAAALGHQYCALTDHsprltIANGLSPDRLRKQLDVIDELREKFA 163
Cdd:cd12111    5 DFHIHTTYSDGALSLSEVVDLYGQHGFDVIAITDH-----VVDRASLIGKFPQGTHPGVTEANFE 64
polC PRK00448
DNA polymerase III PolC; Validated
 97-133 1.70e-03

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 40.21  E-value: 1.70e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 489494884   97 RGDLHLHSNWS--DGSAPIEEMMATAAALGHQYCALTDH 133
Cdd:PRK00448  334 RVELHLHTKMStmDAIPSVSELVKRAAKWGHKAIAITDH 372
 
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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