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Conserved domains on  [gi|1774765362|gb|QGH71214|]
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putative DNA polymerase III DnaE superfamily protein [Methanobacterium virus PhiF1]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PHP super family cl23724
Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2 ...
 165-438 1.34e-93

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.


The actual alignment was detected with superfamily member cd12113:

Pssm-ID: 451507 [Multi-domain]  Cd Length: 283  Bit Score: 283.95  E-value: 1.34e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 165 HVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVT------DTLNRENGDR 238
Cdd:cd12113     6 HVHTEYSLLDGAIRIKDLVKRAKELGMPALAITDHGNMFGAIEFYKAAKKAGIKPIIGCEVYVApgsrfdKKDKKGDKRY 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 239 YHLVLLAKDNIGLRNLFKLNHIAH-ENFYYKPRVTIDLISDYSEGLIASTACVGGVISRRIINGDFDIARDTLSDLKAIF 317
Cdd:cd12113    86 YHLVLLAKNEEGYRNLMKLVSLAYlEGFYYKPRIDKELLAKYSEGLIALSACLAGEIPQLLLNGDEEEAREAALEYRDIF 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 318 G-DDLYVEVQPHKFEEQVMVNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKAILFNKKVGESS---IEGDTYHLM 393
Cdd:cd12113   166 GkDNFYLELQDHGLPEQKKVNEGLIELAKELGIPLVATNDVHYLNKEDAEAHDVLLCIQTGKTLDDPNrmrFDTDEFYLK 245

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1774765362 394 RPDE---LFyagaeANIPpevmrRAMINTHRIARGCNAKIEFHSSVYP 438
Cdd:cd12113   246 SPEEmreLF-----PDVP-----EALENTLEIAERCNVELDFGKLHLP 283
UDG-F4_TTUDGA_SPO1dp_like cd10030
Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA ...
 3-145 1.69e-40

Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA polymerase, and similar proteins; Uracil DNA glycosylase family 4 includes Thermotoga maritima TTUDGA, a robust uracil DNA glycosylase that shares narrow substrate specificity and high catalytic efficiency with family 1, acting on double-stranded and single-stranded uracil-containing DNA. Members of this family possess four conserved cysteine residues required to coordinate the [4Fe-4S] iron-sulfur cluster. This family also includes the N-terminal domain of Bacillus phage SPO1 DNA polymerase. Bacteriophage SPO1 is one of a group of large, lytic, tailed bacteriophages of Bacillus subtilis, and contains hydroxymethyluracil (hmUra) in place of thymine in their DNA. It has been speculated that this UDG domain may help discriminate between hmUra containing SPO1 DNA and thymine-containing host DNA. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other.


:

Pssm-ID: 381680  Cd Length: 165  Bit Score: 142.20  E-value: 1.69e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362   3 CARCGNREK-VIGRGSLSPVILFIGLNPGVEEVRVGAPFVGPSGKLLDEWVKHWNLPNNAIAITNIVKCHTPNEAGVTGE 81
Cdd:cd10030     4 CPLSKTRTNvVFGEGNPDAKLMFIGEAPGAEEDRQGRPFVGRAGKLLDKMLAAIGLSREDVYITNVVKCRPPGNRTPTPE 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1774765362  82 MLQNCKEYLDRQIDYLKPDMIMSLGRLASEALKGSSVNITKDIG-PYEYK-GVPLYTLPHPSYYLR 145
Cdd:cd10030    84 EIAACRPFLDRQIELIKPKVIVTLGRTAAQALLGKDAPISKLRGkWHEYEkGIPVLPTYHPAALLR 149
 
Name Accession Description Interval E-value
PHP_PolIIIA_DnaE3 cd12113
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ...
 165-438 1.34e-93

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: 283.95  E-value: 1.34e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 165 HVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVT------DTLNRENGDR 238
Cdd:cd12113     6 HVHTEYSLLDGAIRIKDLVKRAKELGMPALAITDHGNMFGAIEFYKAAKKAGIKPIIGCEVYVApgsrfdKKDKKGDKRY 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 239 YHLVLLAKDNIGLRNLFKLNHIAH-ENFYYKPRVTIDLISDYSEGLIASTACVGGVISRRIINGDFDIARDTLSDLKAIF 317
Cdd:cd12113    86 YHLVLLAKNEEGYRNLMKLVSLAYlEGFYYKPRIDKELLAKYSEGLIALSACLAGEIPQLLLNGDEEEAREAALEYRDIF 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 318 G-DDLYVEVQPHKFEEQVMVNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKAILFNKKVGESS---IEGDTYHLM 393
Cdd:cd12113   166 GkDNFYLELQDHGLPEQKKVNEGLIELAKELGIPLVATNDVHYLNKEDAEAHDVLLCIQTGKTLDDPNrmrFDTDEFYLK 245

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1774765362 394 RPDE---LFyagaeANIPpevmrRAMINTHRIARGCNAKIEFHSSVYP 438
Cdd:cd12113   246 SPEEmreLF-----PDVP-----EALENTLEIAERCNVELDFGKLHLP 283
DnaE COG0587
DNA polymerase III, alpha subunit [Replication, recombination and repair];
159-440 1.03e-82

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


Pssm-ID: 440352 [Multi-domain]  Cd Length: 1050  Bit Score: 274.64  E-value: 1.03e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  159 PTYTPIHVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVTDTLNRENGdr 238
Cdd:COG0587      3 PSFVHLHVHSEYSLLDGASRPEELVARAAELGMPALAITDHGNLFGAVRFYKAAKKAGIKPIIGCELYVAPGSRDDAG-- 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  239 YHLVLLAKDNIGLRNLFKLNHIAH-ENFYY-KPRVTIDLISDYSEGLIASTACVGGVISRRIINGDFDIARDTLSDLKAI 316
Cdd:COG0587     81 YHLVLLAKNREGYRNLCRLLSRAYlEGFYKgKPRIDLEDLAEHSEGLIALSGCLAGEVGQALLAGQYDEAEAALARLKDI 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  317 FGDDLYVEVQPHKFEEQVMVNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKAILFNKKVGE---SSIEGDTYHLM 393
Cdd:COG0587    161 FGDRFYLELQRHGLPEDRRVNAALLELARELGLPLVATNDVHYLNPEDAEAHDVLLCIRTGKTLDDpgrRRFANAERYLK 240

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|
gi 1774765362  394 RPDE---LFyagaeANIPpevmrRAMINTHRIARGCNAKIEFHSSVYPRF 440
Cdd:COG0587    241 SPEEmaeLF-----ADLP-----EALANTLEIAERCNFSLDLGKYQLPKF 280
dnaE PRK06826
DNA polymerase III DnaE; Reviewed
 165-440 5.12e-75

DNA polymerase III DnaE; Reviewed


Pssm-ID: 235868 [Multi-domain]  Cd Length: 1151  Bit Score: 254.43  E-value: 5.12e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  165 HVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYV-----TDTLNRENGDRY 239
Cdd:PRK06826     9 HVHTEYSLLDGSARIKDLIKRAKELGMDSIAITDHGVMYGVVDFYKAAKKQGIKPIIGCEVYVaprsrFDKEPDIDNETY 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  240 HLVLLAKDNIGLRNLFKLNHIAH-ENFYYKPRVTIDLISDYSEGLIASTACVGGVISRRIINGDFDIARDTLSDLKAIFG 318
Cdd:PRK06826    89 HLVLLAKNETGYKNLMKIVSKAFtEGFYYKPRVDHELLKEHSEGLIALSACLAGEVPRYILKGNYEKAKEAALFYKDIFG 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  319 -DDLYVEVQPHKFEEQVMVNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKAILFNKKVGES---SIEGDTYHLMR 394
Cdd:PRK06826   169 kENFYLELQDHGIPEQRKVNEELIKLSKELGIPLVATNDVHYIRKEDAKAHDVLLCIQTGKTVDDEnrmRFPSDEFYLKS 248

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|
gi 1774765362  395 PDE---LF-YAgaeanipPEvmrrAMINTHRIARGCNAKIEFHSSVYPRF 440
Cdd:PRK06826   249 PEEmyeLFsYV-------PE----ALENTVKIAERCNVEFEFGKSKLPKF 287
polc TIGR00594
DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are ...
 161-438 3.95e-73

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: 248.06  E-value: 3.95e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  161 YTPIHVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVTDTLN------RE 234
Cdd:TIGR00594    1 FVHLHVHSDYSLLDGAAKIKPLVKKAKELGMPALALTDHGNMFGAVEFYKACKKAGIKPIIGCEAYVAPGSRfdkkriSK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  235 NGDRYHLVLLAKDNIGLRNLFKLNHIAH-ENFYYKPRVTIDLISDYSEGLIASTACVGGVISRRIINGDFDIARDTLSDL 313
Cdd:TIGR00594   81 GKEAYHLILLAKNNTGYRNLMKLSSLAYlEGFYYKPRIDKELLEEHSEGLIALSACLSGEVPYLLLLGEERLAEEAALKY 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  314 KAIFGDDLYVEVQPHKFEEQVMVNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKAILFNKKVGESS---IEGDTY 390
Cdd:TIGR00594  161 QEIFGDDYYLELQDHGIPEQRVVNEALLEISEELGIPLVATNDVHYINPEDAHAHEILLCIQTGKTLSDPKrlkFYSDEF 240

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1774765362  391 HLMRPDE---LFyagaeANIPpevmrRAMINTHRIARGCNAKIEFHSSVYP 438
Cdd:TIGR00594  241 YLKSPEEmaeLF-----ADIP-----EALANTVEIAERCNLVDVKLGPPRL 281
PHP pfam02811
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ...
 165-328 1.55e-50

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


Pssm-ID: 460705 [Multi-domain]  Cd Length: 171  Bit Score: 168.88  E-value: 1.55e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 165 HVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVT----DTLNRENGDRYH 240
Cdd:pfam02811   3 HVHSEYSLLDGAARIEELVKRAKELGMPAIAITDHGNLFGAVEFYKAAKKAGIKPIIGCEVYVApgsrEETEKLLAKYFD 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 241 LVLLAKDNIGLRNLFKLNHIAHENfYYKPRVTIDLISDYSEGLIASTACVGGVISRRI-INGDFDIARDTLSDLKAIFGD 319
Cdd:pfam02811  83 LVLLAVHEVGYKNLIKLSSRAYLE-GFKPRIDKELLEEYFEGLIALSGCVLGHLDLILlAPGDYEEAEELAEEYLEIFGE 161

                         170
                  ....*....|
gi 1774765362 320 D-LYVEVQPH 328
Cdd:pfam02811 162 DgFYLEINTH 171
UDG-F4_TTUDGA_SPO1dp_like cd10030
Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA ...
 3-145 1.69e-40

Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA polymerase, and similar proteins; Uracil DNA glycosylase family 4 includes Thermotoga maritima TTUDGA, a robust uracil DNA glycosylase that shares narrow substrate specificity and high catalytic efficiency with family 1, acting on double-stranded and single-stranded uracil-containing DNA. Members of this family possess four conserved cysteine residues required to coordinate the [4Fe-4S] iron-sulfur cluster. This family also includes the N-terminal domain of Bacillus phage SPO1 DNA polymerase. Bacteriophage SPO1 is one of a group of large, lytic, tailed bacteriophages of Bacillus subtilis, and contains hydroxymethyluracil (hmUra) in place of thymine in their DNA. It has been speculated that this UDG domain may help discriminate between hmUra containing SPO1 DNA and thymine-containing host DNA. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other.


Pssm-ID: 381680  Cd Length: 165  Bit Score: 142.20  E-value: 1.69e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362   3 CARCGNREK-VIGRGSLSPVILFIGLNPGVEEVRVGAPFVGPSGKLLDEWVKHWNLPNNAIAITNIVKCHTPNEAGVTGE 81
Cdd:cd10030     4 CPLSKTRTNvVFGEGNPDAKLMFIGEAPGAEEDRQGRPFVGRAGKLLDKMLAAIGLSREDVYITNVVKCRPPGNRTPTPE 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1774765362  82 MLQNCKEYLDRQIDYLKPDMIMSLGRLASEALKGSSVNITKDIG-PYEYK-GVPLYTLPHPSYYLR 145
Cdd:cd10030    84 EIAACRPFLDRQIELIKPKVIVTLGRTAAQALLGKDAPISKLRGkWHEYEkGIPVLPTYHPAALLR 149
Udg4 COG1573
Uracil-DNA glycosylase [Replication, recombination and repair];
2-145 3.03e-39

Uracil-DNA glycosylase [Replication, recombination and repair];


Pssm-ID: 441181  Cd Length: 189  Bit Score: 139.95  E-value: 3.03e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362   2 SCARCG---NREK-VIGRGSLSPVILFIGLNPGVEEVRVGAPFVGPSGKLLDEWVKHWNLPNNAIAITNIVKCHTPNEAG 77
Cdd:COG1573    19 ACRRCPlveTRTQpVFGEGDPDARLMIVGEAPGAGEDRTGRPFVGRAGQLLDKMLAAAGLAREDVYITNAVKCRPPGNRK 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  78 VTGEMLQNCKEYLDRQIDYLKPDMIMSLGRLASEALKGSSVNITKDIG-PYEYK-GVPLYTLPHPSYYLR 145
Cdd:COG1573    99 PTPEEIAACRPFLEREIALIRPKVIVALGATAAQALLGAGERITRLRGkWHELPgGIPLLPTYHPSYLLR 168
UDG_fam4 TIGR00758
uracil-DNA glycosylase, family 4; This well-conserved family of proteins is about 200 residues ...
 3-145 1.00e-30

uracil-DNA glycosylase, family 4; This well-conserved family of proteins is about 200 residues in length and homologous to the N-terminus of the DNA polymerase of phage SPO1 of Bacillus subtilis. The member from Thermus thermophilus HB8 is known to act as uracil-DNA glycosylase, an enzyme of DNA base excision repair. Its appearance as a domain of phage DNA polymerases could be consistent with uracil-DNA glycosylase activity. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129841  Cd Length: 173  Bit Score: 116.36  E-value: 1.00e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362   3 CARCGNREK----VIGRGSLSPVILFIGLNPGVEEVRVGAPFVGPSGKLLDEWVKHWNLPNNAIAITNIVKCHTPNEAGV 78
Cdd:TIGR00758   1 CRRCELHKTrtnaVPGDGNPDANIMFVGEAPGREEDRKGRPFVGRAGKLLDEMLAAIGLSRENVYITNVVKCRPPNNRDP 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1774765362  79 TGEMLQNCKEYLDRQIDYLKPDMIMSLGRLASEALKGSSVNITKDIG---PYEYKGVPLYTLP--HPSYYLR 145
Cdd:TIGR00758  81 TPEEVEACAPYLVKQIELIRPKVIICLGRTAAQSILGKNDGITKIRGrvfEYRYIGTKIKITAtyHPAALLR 152
UDG pfam03167
Uracil DNA glycosylase superfamily;
13-145 3.30e-30

Uracil DNA glycosylase superfamily;


Pssm-ID: 397331  Cd Length: 154  Bit Score: 114.37  E-value: 3.30e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  13 IGRGSLSPVILFIGLNPGVEEVRVGAPFVGPSGKLLDEWVKHWNLPNNA-----IAITNIVKCHTPNEAGVTGEMLQNCK 87
Cdd:pfam03167   1 PGFGPPNAKVLIVGEAPGADEDATGLPFVGRAGNLLWKLLNAAGLTRDLfspqgVYITNVVKCRPGNRRKPTSHEIDACW 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1774765362  88 EYLDRQIDYLKPDMIMSLGRLASEALKGSSVnITKDIG-PYEYKGVPLYTLPHPSYYLR 145
Cdd:pfam03167  81 PYLEAEIELLRPRVIVLLGKTAAKALLGLKK-ITKLRGkLIDLKGIPVLPTPHPSPLLR 138
Arch_udg NF040953
type-4 uracil-DNA glycosylase;
1-145 1.31e-22

type-4 uracil-DNA glycosylase;


Pssm-ID: 468884  Cd Length: 183  Bit Score: 94.56  E-value: 1.31e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362   1 MSCARC----GNREKVIGRGSLSPVILFIGLNPGVEEVRVGAPFVGPSGKLLDEWVKHWNLPNNAIAITNIVKCHTPNEA 76
Cdd:NF040953    9 RKCRKCplhkTRTNAVPGEGNPNAKIMFVGEAPGRNEDETGRPFVGAAGKLLTELLESIGLKREDVYITNVVKCRPPNNR 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1774765362  77 GVTGEMLQNCKEYLDRQIDYLKPDMIMSLGRLASEALKG----SSVNITKDIG-PY--EYKGVPLYTLP--HPSYYLR 145
Cdd:NF040953   89 DPTEEEIEACSPYLLRQIEIIKPKVIVTLGRHSTRYILSlaglEFESISKVRGkVYevEIGGGKVKVIPtyHPAAALY 166
UDG smart00986
Uracil DNA glycosylase superfamily;
14-150 4.30e-22

Uracil DNA glycosylase superfamily;


Pssm-ID: 214956  Cd Length: 156  Bit Score: 92.06  E-value: 4.30e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362   14 GRGSLSPVILFIGLNPGVEEVRVGAPFVGPSGKLLDEWVKHWNLPNNAIAITNIVKCHTPNEAG--VTGEMLQNC-KEYL 90
Cdd:smart00986   2 GTGDPNAKVLIVGQAPGASEEDRGGPFVGAAGLLLSVMLGVAGLPRLPPYLTNIVKCRPPDAGNrrPTSWELQGClLPWL 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1774765362   91 DRQIDYLKPDMIMSLGRLASEALKG--SSVNITKDIG---PYEYKGVPLYTLPHPSYYLRGGGDW 150
Cdd:smart00986  82 TVELALARPHLILLLGKFAAQALLGllRRPLVFGLRGrvaQLKGKGHRVLPLPHPSPLNRNFFPA 146
POLIIIAc smart00481
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ...
 165-229 1.78e-20

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: 84.63  E-value: 1.78e-20
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1774765362  165 HVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVTD 229
Cdd:smart00481   3 HVHSDYSLLDGALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYKAAKKAGIKPIIGLEANIVD 67
CehA_McbA_metalo NF038032
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ...
 165-209 1.07e-05

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: 47.32  E-value: 1.07e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1774765362 165 HVHSEYSvmDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQ 209
Cdd:NF038032    8 HIHTNHS--DGPTTPEELARAALAEGLDVIALTDHNTISGRAYFA 50
 
Name Accession Description Interval E-value
PHP_PolIIIA_DnaE3 cd12113
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ...
 165-438 1.34e-93

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: 283.95  E-value: 1.34e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 165 HVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVT------DTLNRENGDR 238
Cdd:cd12113     6 HVHTEYSLLDGAIRIKDLVKRAKELGMPALAITDHGNMFGAIEFYKAAKKAGIKPIIGCEVYVApgsrfdKKDKKGDKRY 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 239 YHLVLLAKDNIGLRNLFKLNHIAH-ENFYYKPRVTIDLISDYSEGLIASTACVGGVISRRIINGDFDIARDTLSDLKAIF 317
Cdd:cd12113    86 YHLVLLAKNEEGYRNLMKLVSLAYlEGFYYKPRIDKELLAKYSEGLIALSACLAGEIPQLLLNGDEEEAREAALEYRDIF 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 318 G-DDLYVEVQPHKFEEQVMVNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKAILFNKKVGESS---IEGDTYHLM 393
Cdd:cd12113   166 GkDNFYLELQDHGLPEQKKVNEGLIELAKELGIPLVATNDVHYLNKEDAEAHDVLLCIQTGKTLDDPNrmrFDTDEFYLK 245

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1774765362 394 RPDE---LFyagaeANIPpevmrRAMINTHRIARGCNAKIEFHSSVYP 438
Cdd:cd12113   246 SPEEmreLF-----PDVP-----EALENTLEIAERCNVELDFGKLHLP 283
DnaE COG0587
DNA polymerase III, alpha subunit [Replication, recombination and repair];
159-440 1.03e-82

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


Pssm-ID: 440352 [Multi-domain]  Cd Length: 1050  Bit Score: 274.64  E-value: 1.03e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  159 PTYTPIHVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVTDTLNRENGdr 238
Cdd:COG0587      3 PSFVHLHVHSEYSLLDGASRPEELVARAAELGMPALAITDHGNLFGAVRFYKAAKKAGIKPIIGCELYVAPGSRDDAG-- 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  239 YHLVLLAKDNIGLRNLFKLNHIAH-ENFYY-KPRVTIDLISDYSEGLIASTACVGGVISRRIINGDFDIARDTLSDLKAI 316
Cdd:COG0587     81 YHLVLLAKNREGYRNLCRLLSRAYlEGFYKgKPRIDLEDLAEHSEGLIALSGCLAGEVGQALLAGQYDEAEAALARLKDI 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  317 FGDDLYVEVQPHKFEEQVMVNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKAILFNKKVGE---SSIEGDTYHLM 393
Cdd:COG0587    161 FGDRFYLELQRHGLPEDRRVNAALLELARELGLPLVATNDVHYLNPEDAEAHDVLLCIRTGKTLDDpgrRRFANAERYLK 240

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|
gi 1774765362  394 RPDE---LFyagaeANIPpevmrRAMINTHRIARGCNAKIEFHSSVYPRF 440
Cdd:COG0587    241 SPEEmaeLF-----ADLP-----EALANTLEIAERCNFSLDLGKYQLPKF 280
dnaE PRK06826
DNA polymerase III DnaE; Reviewed
 165-440 5.12e-75

DNA polymerase III DnaE; Reviewed


Pssm-ID: 235868 [Multi-domain]  Cd Length: 1151  Bit Score: 254.43  E-value: 5.12e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  165 HVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYV-----TDTLNRENGDRY 239
Cdd:PRK06826     9 HVHTEYSLLDGSARIKDLIKRAKELGMDSIAITDHGVMYGVVDFYKAAKKQGIKPIIGCEVYVaprsrFDKEPDIDNETY 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  240 HLVLLAKDNIGLRNLFKLNHIAH-ENFYYKPRVTIDLISDYSEGLIASTACVGGVISRRIINGDFDIARDTLSDLKAIFG 318
Cdd:PRK06826    89 HLVLLAKNETGYKNLMKIVSKAFtEGFYYKPRVDHELLKEHSEGLIALSACLAGEVPRYILKGNYEKAKEAALFYKDIFG 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  319 -DDLYVEVQPHKFEEQVMVNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKAILFNKKVGES---SIEGDTYHLMR 394
Cdd:PRK06826   169 kENFYLELQDHGIPEQRKVNEELIKLSKELGIPLVATNDVHYIRKEDAKAHDVLLCIQTGKTVDDEnrmRFPSDEFYLKS 248

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|
gi 1774765362  395 PDE---LF-YAgaeanipPEvmrrAMINTHRIARGCNAKIEFHSSVYPRF 440
Cdd:PRK06826   249 PEEmyeLFsYV-------PE----ALENTVKIAERCNVEFEFGKSKLPKF 287
polc TIGR00594
DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are ...
 161-438 3.95e-73

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: 248.06  E-value: 3.95e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  161 YTPIHVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVTDTLN------RE 234
Cdd:TIGR00594    1 FVHLHVHSDYSLLDGAAKIKPLVKKAKELGMPALALTDHGNMFGAVEFYKACKKAGIKPIIGCEAYVAPGSRfdkkriSK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  235 NGDRYHLVLLAKDNIGLRNLFKLNHIAH-ENFYYKPRVTIDLISDYSEGLIASTACVGGVISRRIINGDFDIARDTLSDL 313
Cdd:TIGR00594   81 GKEAYHLILLAKNNTGYRNLMKLSSLAYlEGFYYKPRIDKELLEEHSEGLIALSACLSGEVPYLLLLGEERLAEEAALKY 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  314 KAIFGDDLYVEVQPHKFEEQVMVNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKAILFNKKVGESS---IEGDTY 390
Cdd:TIGR00594  161 QEIFGDDYYLELQDHGIPEQRVVNEALLEISEELGIPLVATNDVHYINPEDAHAHEILLCIQTGKTLSDPKrlkFYSDEF 240

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1774765362  391 HLMRPDE---LFyagaeANIPpevmrRAMINTHRIARGCNAKIEFHSSVYP 438
Cdd:TIGR00594  241 YLKSPEEmaeLF-----ADIP-----EALANTVEIAERCNLVDVKLGPPRL 281
dnaE PRK05673
DNA polymerase III subunit alpha; Validated
 161-440 6.15e-69

DNA polymerase III subunit alpha; Validated


Pssm-ID: 235554 [Multi-domain]  Cd Length: 1135  Bit Score: 237.31  E-value: 6.15e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  161 YTPIHVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVT--DTLNRENGDR 238
Cdd:PRK05673     2 FVHLHVHSEYSLLDGAAKIKPLVKKAAELGMPAVALTDHGNLFGAVEFYKAAKGAGIKPIIGCEAYVApeKKDDVSGGGA 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  239 Y-HLVLLAKDNIGLRNLFKLNHIAH-ENFY-YKPRVTIDLISDYSEGLIASTACVGGVISRRIINGDFDIARDTLSDLKA 315
Cdd:PRK05673    82 YtHLTLLAKNETGYRNLFKLSSRAYlEGQYgYKPRIDREWLAEHSEGLIALSGCPSGEVGTALLAGQYDEAEEAAAEYQE 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  316 IFGDDLYVEVQPHKFEEQVMVNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKAILFNKKVGESS---IEGDTYHL 392
Cdd:PRK05673   162 IFGDRFYLELMRHGLPIERRVEHALLELAKELGLPLVATNDVHYLTPEDAEAHEALLCIAEGKTLDDPDrfrFYSPEQYL 241

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1774765362  393 -----MRpdELFyagaeANIpPEvmrrAMINTHRIARGCNAKIEFHSSVYPRF 440
Cdd:PRK05673   242 ksaeeMR--ELF-----ADL-PE----ALDNTVEIAERCNVEVRLGKPFLPRF 282
dnaE PRK07374
DNA polymerase III subunit alpha; Validated
 161-440 2.94e-54

DNA polymerase III subunit alpha; Validated


Pssm-ID: 168927 [Multi-domain]  Cd Length: 1170  Bit Score: 195.33  E-value: 2.94e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  161 YTPIHVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVTdtlnreNGD--- 237
Cdd:PRK07374     3 FVPLHNHSDYSLLDGASQLPKMVERAKELGMPAIALTDHGVMYGAIELLKLCKGKGIKPIIGNEMYVI------NGSidd 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  238 -------RYHLVLLAKDNIGLRNLFKLNHIAHEN------FYYKPRVTIDLISDYSEGLIASTACVGGVISRRIINGDFD 304
Cdd:PRK07374    77 pqpkkekRYHLVVLAKNATGYKNLVKLTTISHLNgmrgrgIFSRPCIDKELLKQYSEGLIVSTACLGGEIPQAILRGRPD 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  305 IARDTLSDLKAIFGDDLYVEVQPHKFEEQVMVNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKAILFNKKVGESS 384
Cdd:PRK07374   157 VARDVAAWYKEVFGDDFYLEIQDHGSIEDRIVNVELVRIAKELGIKLIATNDAHYLSKNDVEAHDALLCVLTGKLISDEK 236

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1774765362  385 ---IEGDTYhLMRPDE---LFyagaEANIPPEVMRRAMINTHRIARgcnaKIE----FHSSVYPRF 440
Cdd:PRK07374   237 rlrYTGTEY-IKSEEEmlrLF----RDHLDPEVIQEAIANTVEVAE----KVEeydiLGTYRMPRF 293
PHP_PolIIIA_DnaE1 cd07433
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ...
 156-440 2.09e-51

Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. PolIIIA core enzyme catalyzes the reaction for polymerizing both DNA strands. dnaE1 is the longest compared to dnaE2 and dnaE3. A unique motif was also identified in dnaE1 and dnaE3 genes.


Pssm-ID: 213988 [Multi-domain]  Cd Length: 277  Bit Score: 174.59  E-value: 2.09e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 156 KFIPtytpIHVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVTDTLNREN 235
Cdd:cd07433     1 SFVH----LRVHSEYSLLDGAVRIKKLVKLAKEDGMPALAITDLSNLFGAVKFYKAASKAGIKPIIGADLNVANPDDADE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 236 gdRYHLVLLAKDNIGLRNLFKLNHIAHENFYY--KPRVTIDLISDYSEGLIASTACVGGVISRRIINGDFDIARDTLSDL 313
Cdd:cd07433    77 --PFRLTLLAQNEQGYKNLTELISRAYLEGQRngGPHIKLEWLAEYSEGLIALSGGRDGDIGQLLLEGNPDLAEALLQFL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 314 KAIFGDDLYVEVQPHKFEEQVMVNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKAIlfnkkvGESSIEGD----- 388
Cdd:cd07433   155 KKIFPDRFYLELQRHGRPEEEAYEHALIDLAYELGLPLVATNDVRFLKPEDFEAHEARVCI------AEGRTLDDprrpr 228

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1774765362 389 TY---HLMRPD----ELFyagaeANIPpevmrRAMINTHRIARGCNAKIEFHSSVYPRF 440
Cdd:cd07433   229 RYspqQYFKSAeemaELF-----ADLP-----EAIENTVEIAKRCNVRIELGKPFLPDF 277
PHP pfam02811
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ...
 165-328 1.55e-50

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


Pssm-ID: 460705 [Multi-domain]  Cd Length: 171  Bit Score: 168.88  E-value: 1.55e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 165 HVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVT----DTLNRENGDRYH 240
Cdd:pfam02811   3 HVHSEYSLLDGAARIEELVKRAKELGMPAIAITDHGNLFGAVEFYKAAKKAGIKPIIGCEVYVApgsrEETEKLLAKYFD 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 241 LVLLAKDNIGLRNLFKLNHIAHENfYYKPRVTIDLISDYSEGLIASTACVGGVISRRI-INGDFDIARDTLSDLKAIFGD 319
Cdd:pfam02811  83 LVLLAVHEVGYKNLIKLSSRAYLE-GFKPRIDKELLEEYFEGLIALSGCVLGHLDLILlAPGDYEEAEELAEEYLEIFGE 161

                         170
                  ....*....|
gi 1774765362 320 D-LYVEVQPH 328
Cdd:pfam02811 162 DgFYLEINTH 171
PHP_PolIIIA_POLC cd07435
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ...
 165-373 6.31e-46

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: 159.95  E-value: 6.31e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 165 HVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVTDTlnrengdrYHLVLL 244
Cdd:cd07435     5 HAHTKMSAMDGVTSVKELVKRAAEWGHKAIAITDHGVVQAFPEAYEAAKKNGIKVIYGVEAYLVDP--------YHITIL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 245 AKDNIGLRNLFKLNHIAH-ENFYYKPRVTIDLISDYSEGLIASTACVGGVISRRIINGDFDiardtlSDLKAI--FGDdl 321
Cdd:cd07435    77 VKNQTGLKNLYKLVSLSHtKYFYRVPRIPKSELEKYREGLLIGSACENGELFEAALNKKSD------EELEEIasFYD-- 148

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1774765362 322 YVEVQP-----HKFEEQVM--------VNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKA 373
Cdd:cd07435   149 YIEIQPldnyqFLIEKGLIkseeelkeINKRIIKLGKKLNKPVVATGDVHYLDPEDKIYREILLA 213
PRK09532 PRK09532
DNA polymerase III subunit alpha; Reviewed
 160-431 3.30e-43

DNA polymerase III subunit alpha; Reviewed


Pssm-ID: 181933 [Multi-domain]  Cd Length: 874  Bit Score: 162.60  E-value: 3.30e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 160 TYTPIHVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVT--DTLNRENGD 237
Cdd:PRK09532    2 SFVGLHIHSDYSLLDGASQLPALVDRAIELGMPAIALTDHGVMYGAIELLKVCRNKGIKPIIGNEMYVIngDIEKQKRRR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 238 RYHLVLLAKDNIGLRNLFKLNHIAH------ENFYYKPRVTIDLISDYSEGLIASTACVGGVISRRIINGDFDIARDTLS 311
Cdd:PRK09532   82 KYHQVVLAKNTQGYKNLVKLTTISHlqgvqgKGIFARPCINKELLEQYHEGLIVTSACLGGEIPQAILSGRPDAARKVAK 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 312 DLKAIFGDDLYVEVQPHKFEEQVMVNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKAILFNKKVGE------SSI 385
Cdd:PRK09532  162 WYKKLFGDDFYLEIQDHGSQEDRIVNVEIVKIARELGIKIIATNDSHFISCYDVEAHDALLCIQTGKLITEdkrlrySGT 241

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1774765362 386 E----GDTYHLMRPDELfyagaeaniPPEVMRRAMINTHRIArgcnAKIE 431
Cdd:PRK09532  242 EylksAEEMRLLFRDHL---------PDDVIAEAIANTLEVA----DKIE 278
UDG-F4_TTUDGA_SPO1dp_like cd10030
Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA ...
 3-145 1.69e-40

Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA polymerase, and similar proteins; Uracil DNA glycosylase family 4 includes Thermotoga maritima TTUDGA, a robust uracil DNA glycosylase that shares narrow substrate specificity and high catalytic efficiency with family 1, acting on double-stranded and single-stranded uracil-containing DNA. Members of this family possess four conserved cysteine residues required to coordinate the [4Fe-4S] iron-sulfur cluster. This family also includes the N-terminal domain of Bacillus phage SPO1 DNA polymerase. Bacteriophage SPO1 is one of a group of large, lytic, tailed bacteriophages of Bacillus subtilis, and contains hydroxymethyluracil (hmUra) in place of thymine in their DNA. It has been speculated that this UDG domain may help discriminate between hmUra containing SPO1 DNA and thymine-containing host DNA. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other.


Pssm-ID: 381680  Cd Length: 165  Bit Score: 142.20  E-value: 1.69e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362   3 CARCGNREK-VIGRGSLSPVILFIGLNPGVEEVRVGAPFVGPSGKLLDEWVKHWNLPNNAIAITNIVKCHTPNEAGVTGE 81
Cdd:cd10030     4 CPLSKTRTNvVFGEGNPDAKLMFIGEAPGAEEDRQGRPFVGRAGKLLDKMLAAIGLSREDVYITNVVKCRPPGNRTPTPE 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1774765362  82 MLQNCKEYLDRQIDYLKPDMIMSLGRLASEALKGSSVNITKDIG-PYEYK-GVPLYTLPHPSYYLR 145
Cdd:cd10030    84 EIAACRPFLDRQIELIKPKVIVTLGRTAAQALLGKDAPISKLRGkWHEYEkGIPVLPTYHPAALLR 149
Udg4 COG1573
Uracil-DNA glycosylase [Replication, recombination and repair];
2-145 3.03e-39

Uracil-DNA glycosylase [Replication, recombination and repair];


Pssm-ID: 441181  Cd Length: 189  Bit Score: 139.95  E-value: 3.03e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362   2 SCARCG---NREK-VIGRGSLSPVILFIGLNPGVEEVRVGAPFVGPSGKLLDEWVKHWNLPNNAIAITNIVKCHTPNEAG 77
Cdd:COG1573    19 ACRRCPlveTRTQpVFGEGDPDARLMIVGEAPGAGEDRTGRPFVGRAGQLLDKMLAAAGLAREDVYITNAVKCRPPGNRK 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  78 VTGEMLQNCKEYLDRQIDYLKPDMIMSLGRLASEALKGSSVNITKDIG-PYEYK-GVPLYTLPHPSYYLR 145
Cdd:COG1573    99 PTPEEIAACRPFLEREIALIRPKVIVALGATAAQALLGAGERITRLRGkWHELPgGIPLLPTYHPSYLLR 168
dnaE PRK06920
DNA polymerase III subunit alpha;
161-440 1.15e-34

DNA polymerase III subunit alpha;


Pssm-ID: 180749 [Multi-domain]  Cd Length: 1107  Bit Score: 137.62  E-value: 1.15e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  161 YTPIHVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVtdtLNRENGDRYH 240
Cdd:PRK06920     3 FVHLQCQTVFSLLKSACKIDELVVRAKELGYSSLAITDENVMYGVIPFYKACKKHGIHPIIGLTASI---FSEEEEKSYP 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  241 LVLLAKDNIGLRNLFKLNHIAHENfyYKPRVTIDLISDYSEGLIASTACVGGVISRRIINGDFDIARDTLSDLKAIFGdD 320
Cdd:PRK06920    80 LVLLAENEIGYQNLLKISSSIMTK--SKEGIPKKWLAHYAKGLIAISPGKDGEIEQLLLEDKESQAEEVARAYQNMFG-N 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  321 LYVEVQPHKFEEQVMVNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKAILFNKKVGESS---IEGDTYHLMRPDE 397
Cdd:PRK06920   157 FYMSLQHHAIQDELLLQEKLPEFSNRVNIPVVATNDVRYINQSDALVHECLLSVESGTKMTDPDrprLKTDQYYLKSSDE 236

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|...
gi 1774765362  398 LfyagaeANIPPEVmRRAMINTHRIARGCNAKIEFHSSVYPRF 440
Cdd:PRK06920   237 M------EALFSHV-PEAIYNTVEIAERCRVEIPFHVNQLPKF 272
PHP_PolIIIA cd07431
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ...
 162-373 2.69e-33

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: 123.47  E-value: 2.69e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 162 TPIHVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVTDtlnreNGDRYHL 241
Cdd:cd07431     1 AHLHVHSSYSLLDSAIRPEDLVARAKELGYSALALTDRNVLYGAVRFYKACKKAGIKPIIGLELTVEG-----DGEPYPL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 242 VLLAKDNIGLRNLFKLNHIAHENFYYKPRVTIDLIsdysegliastacvggvisrriingdfdiardtlsDLKAIFGDDL 321
Cdd:cd07431    76 LLLAKNNEGYQNLLRLSTAAMLGEEKDGVPYLDLE-----------------------------------ELAEAASGLL 120

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1774765362 322 YvevqphkfeeqVMVNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKA 373
Cdd:cd07431   121 V-----------VLLGPLLLLLAAEQGLPLVATNDVHYLNPEDAFAADVLTA 161
UDG_fam4 TIGR00758
uracil-DNA glycosylase, family 4; This well-conserved family of proteins is about 200 residues ...
 3-145 1.00e-30

uracil-DNA glycosylase, family 4; This well-conserved family of proteins is about 200 residues in length and homologous to the N-terminus of the DNA polymerase of phage SPO1 of Bacillus subtilis. The member from Thermus thermophilus HB8 is known to act as uracil-DNA glycosylase, an enzyme of DNA base excision repair. Its appearance as a domain of phage DNA polymerases could be consistent with uracil-DNA glycosylase activity. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129841  Cd Length: 173  Bit Score: 116.36  E-value: 1.00e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362   3 CARCGNREK----VIGRGSLSPVILFIGLNPGVEEVRVGAPFVGPSGKLLDEWVKHWNLPNNAIAITNIVKCHTPNEAGV 78
Cdd:TIGR00758   1 CRRCELHKTrtnaVPGDGNPDANIMFVGEAPGREEDRKGRPFVGRAGKLLDEMLAAIGLSRENVYITNVVKCRPPNNRDP 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1774765362  79 TGEMLQNCKEYLDRQIDYLKPDMIMSLGRLASEALKGSSVNITKDIG---PYEYKGVPLYTLP--HPSYYLR 145
Cdd:TIGR00758  81 TPEEVEACAPYLVKQIELIRPKVIICLGRTAAQSILGKNDGITKIRGrvfEYRYIGTKIKITAtyHPAALLR 152
UDG pfam03167
Uracil DNA glycosylase superfamily;
13-145 3.30e-30

Uracil DNA glycosylase superfamily;


Pssm-ID: 397331  Cd Length: 154  Bit Score: 114.37  E-value: 3.30e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  13 IGRGSLSPVILFIGLNPGVEEVRVGAPFVGPSGKLLDEWVKHWNLPNNA-----IAITNIVKCHTPNEAGVTGEMLQNCK 87
Cdd:pfam03167   1 PGFGPPNAKVLIVGEAPGADEDATGLPFVGRAGNLLWKLLNAAGLTRDLfspqgVYITNVVKCRPGNRRKPTSHEIDACW 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1774765362  88 EYLDRQIDYLKPDMIMSLGRLASEALKGSSVnITKDIG-PYEYKGVPLYTLPHPSYYLR 145
Cdd:pfam03167  81 PYLEAEIELLRPRVIVLLGKTAAKALLGLKK-ITKLRGkLIDLKGIPVLPTPHPSPLLR 138
Arch_udg NF040953
type-4 uracil-DNA glycosylase;
1-145 1.31e-22

type-4 uracil-DNA glycosylase;


Pssm-ID: 468884  Cd Length: 183  Bit Score: 94.56  E-value: 1.31e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362   1 MSCARC----GNREKVIGRGSLSPVILFIGLNPGVEEVRVGAPFVGPSGKLLDEWVKHWNLPNNAIAITNIVKCHTPNEA 76
Cdd:NF040953    9 RKCRKCplhkTRTNAVPGEGNPNAKIMFVGEAPGRNEDETGRPFVGAAGKLLTELLESIGLKREDVYITNVVKCRPPNNR 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1774765362  77 GVTGEMLQNCKEYLDRQIDYLKPDMIMSLGRLASEALKG----SSVNITKDIG-PY--EYKGVPLYTLP--HPSYYLR 145
Cdd:NF040953   89 DPTEEEIEACSPYLLRQIEIIKPKVIVTLGRHSTRYILSlaglEFESISKVRGkVYevEIGGGKVKVIPtyHPAAALY 166
UDG smart00986
Uracil DNA glycosylase superfamily;
14-150 4.30e-22

Uracil DNA glycosylase superfamily;


Pssm-ID: 214956  Cd Length: 156  Bit Score: 92.06  E-value: 4.30e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362   14 GRGSLSPVILFIGLNPGVEEVRVGAPFVGPSGKLLDEWVKHWNLPNNAIAITNIVKCHTPNEAG--VTGEMLQNC-KEYL 90
Cdd:smart00986   2 GTGDPNAKVLIVGQAPGASEEDRGGPFVGAAGLLLSVMLGVAGLPRLPPYLTNIVKCRPPDAGNrrPTSWELQGClLPWL 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1774765362   91 DRQIDYLKPDMIMSLGRLASEALKG--SSVNITKDIG---PYEYKGVPLYTLPHPSYYLRGGGDW 150
Cdd:smart00986  82 TVELALARPHLILLLGKFAAQALLGllRRPLVFGLRGrvaQLKGKGHRVLPLPHPSPLNRNFFPA 146
POLIIIAc smart00481
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ...
 165-229 1.78e-20

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: 84.63  E-value: 1.78e-20
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1774765362  165 HVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVTD 229
Cdd:smart00481   3 HVHSDYSLLDGALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYKAAKKAGIKPIIGLEANIVD 67
dnaE2 PRK05672
error-prone DNA polymerase; Validated
 159-374 1.06e-18

error-prone DNA polymerase; Validated


Pssm-ID: 235553 [Multi-domain]  Cd Length: 1046  Bit Score: 89.15  E-value: 1.06e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  159 PTYTPIHVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVTDTlNRENGDr 238
Cdd:PRK05672     3 PPYAELHCHSNFSFLDGASHPEELVERAARLGLRALAITDECGLAGVVRAAEAAKELGLRLVIGAELSLGPD-PDPGGP- 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  239 yHLVLLAKDNIGLRNLFKL---NHIAHENfyYKPRVTIDLISDYSEG-LIASTACVGG-VISRRIINGDFDIARDTLSDL 313
Cdd:PRK05672    81 -HLLVLARDREGYGRLSRLitrARLRAGK--GEYRLDLDDLAEPAGGhWAILTGCRKGfVILALPYGGDAAALAALAALL 157

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1774765362  314 KAIFGDDLYVEVQPHKFEEQVMVNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKAI 374
Cdd:PRK05672   158 DAFFADRVWLELTLHGRPDDDRRNARLAALAARAGVPLVATGDVHMHHRSRRRLQDAMTAI 218
polC PRK00448
DNA polymerase III PolC; Validated
 239-370 3.47e-18

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 87.59  E-value: 3.47e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  239 YHLVLLAKDNIGLRNLFKLNHIAH-ENFYYKPRVTIDLISDYSEGLIASTACVGGVISRRIINGDFDIARDtlsdlKAIF 317
Cdd:PRK00448   611 KHATILVKNQVGLKNLFKLVSLSNtKYFYRVPRIPRSLLDKYREGLLIGSACEEGEVFDAVLQKGDEELEE-----IAKF 685

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1774765362  318 GDdlYVEVQP-----H-------KFEEQVM-VNPKLIEYADEYDVEVVIGTDVHYNNRGDKFIYDV 370
Cdd:PRK00448   686 YD--YIEIQPpanyqHlierelvKDEEELKeIIKNLIELGKKLNKPVVATGDVHYLDPEDKIYRKI 749
UDG-like cd09593
uracil-DNA glycosylases (UDG) and related enzymes; Uracil-DNA glycosylases (UDGs) initiate ...
 22-142 2.05e-17

uracil-DNA glycosylases (UDG) and related enzymes; Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil may arise from misincorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations; thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. UDG family 1 is the most efficient uracil-DNA glycosylase (UDG, also known as UNG) and shows a specificity for uracil in DNA. UDG family 2 includes thymine DNA glycosylase which removes uracil and thymine from G:U and G:T mismatches, and mismatch-specific uracil DNA glycosylase (MUG) which in Escherichia coli is highly specific to G:U mismatches, but also repairs G:T mismatches at high enzyme concentration. UDG family 3 includes Human SMUG1 which can remove uracil and its oxidized pyrimidine derivatives from, single-stranded DNA and double-stranded DNA with a preference for single-stranded DNA. Pedobacter heparinus SMUG2, which is UDG family 3 SMUG1-like, displays catalytic activities towards DNA containing uracil or hypoxanthine/xanthine. UDG family 4 includes Thermotoga maritima TTUDGA, a robust UDG which like family 1, acts on double-stranded and single-stranded uracil-containing DNA. UDG family 5 (UDGb) includes Thermus thermophilus HB8 TTUDGB which acts on double-stranded uracil-containing DNA; it is a hypoxanthine DNA glycosylase acting on double-stranded hypoxanthine-containing DNA except for the C/I base pair, as well as a xanthine DNA glycosylase which acts on both double-stranded and single-stranded xanthine-containing DNA. UDG family 6 hypoxanthine-DNA glycosylase lacks any detectable UDG activity; it excises hypoxanthine. Other UDG families include one represented by Bradyrhizobium diazoefficiens Blr0248 which prefers single-stranded DNA and removes uracil, 5-hydroxymethyl-uracil or xanthine from it.


Pssm-ID: 381677  Cd Length: 125  Bit Score: 78.20  E-value: 2.05e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  22 ILFIGLNPGVEEVRVGAPFVGPSGKLLDEWVKH----WNLPNNAIAITNIVKCHTP-NEAGVTGEMLQNCKEYLDRQIDY 96
Cdd:cd09593     1 VLIVGQNPGPHGARAGGVPPGPSGNRLWRLLAAaggtPRLFRYGVGLTNTVPRGPPgAAAGSEKKELRFCGRWLRKLLEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1774765362  97 LKPDMIMSLGRLASEALKGSSVNITKdigpYEYKGVPLYTLPHPSY 142
Cdd:cd09593    81 LNPRVVVLLGKKAQEAYLAVLTSSKG----APGKGTEVLVLPHPSP 122
polC PRK00448
DNA polymerase III PolC; Validated
 165-229 9.05e-15

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 76.80  E-value: 9.05e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1774765362  165 HVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVTD 229
Cdd:PRK00448   338 HLHTKMSTMDAIPSVSELVKRAAKWGHKAIAITDHGVVQAFPEAYNAAKKAGIKVIYGVEANLVD 402
YciV COG0613
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ...
 165-363 1.65e-14

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


Pssm-ID: 440378 [Multi-domain]  Cd Length: 188  Bit Score: 71.48  E-value: 1.65e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 165 HVHSEYSvmDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFyvtDTlnRENGDRYHLVLL 244
Cdd:COG0613     7 HVHTTAS--DGSLSPEELVARAKAAGLDVLAITDHDTVAGYEEAAEAAKELGLLVIPGVEI---ST--RWEGREVHILGY 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 245 AKD--NIGLRNLFKLNHIAHENFYYKPRVTIDLISDYsegliastacvGGVIS-------RRIINGDFDIARDTLSDLKA 315
Cdd:COG0613    80 GIDpeDPALEALLGIPVEKAEREWLSLEEAIDLIREA-----------GGVAVlahpfryKRGRWLDDLLEELADAGLDG 148

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1774765362 316 IfgddlyvEV-QPHKFEEQvmvNPKLIEYADEYDVEVVIGTDVHYNNRG 363
Cdd:COG0613   149 I-------EVyNGRHSPED---NERAAELAEEYGLLATGGSDAHGPEKP 187
dnaE PRK07279
DNA polymerase III DnaE; Reviewed
 168-283 2.88e-13

DNA polymerase III DnaE; Reviewed


Pssm-ID: 180917 [Multi-domain]  Cd Length: 1034  Bit Score: 71.99  E-value: 2.88e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  168 SEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVTdtlnrENGDRYHLVLLAKD 247
Cdd:PRK07279     9 TVYSFMDSLIDLEKYVERAKELGYQTIGIMDKDNLYGAYHFIEGAQKNGLQPILGLELNIF-----VEEQEVTLRLIAKN 83

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1774765362  248 NIGLRNLFKLNhiaheNFYYKPRVTIDLISDYSEGL 283
Cdd:PRK07279    84 TQGYKNLLKIS-----TAKMSGKKQFSDLSQYLEGI 114
dnaE PRK07135
DNA polymerase III DnaE; Validated
 164-266 4.18e-13

DNA polymerase III DnaE; Validated


Pssm-ID: 235944 [Multi-domain]  Cd Length: 973  Bit Score: 71.64  E-value: 4.18e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 164 IHVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVtdtlnrengDRYHLVL 243
Cdd:PRK07135    6 LHTNTEYSFLSSTIKLDSLIKYAKENNLKTLVLTDHNNMFGVPKFYKLCKKNNIKPIIGLDLEV---------ENFRFIL 76

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1774765362 244 LAKDNIGLRNL------------FKLNHIAHENFY 266
Cdd:PRK07135   77 LAKNYSGYKLLnelsskksknkeIELNDLDSDNII 111
PHP_PolIIIA_DnaE2 cd07434
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ...
 161-427 2.48e-10

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


Pssm-ID: 213989 [Multi-domain]  Cd Length: 260  Bit Score: 60.93  E-value: 2.48e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 161 YTPIHVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGL---YDFQlncKKYKIKPIFGCEFYVTDtlnrenGD 237
Cdd:cd07434     1 YAELHCLSNFSFLRGASHPEELVARAAELGYRALAITDECSLAGVvraHAAA---KELGLKLIVGSELVLAD------GT 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 238 RyhLVLLAKDNIGLRNLFKL----NHIAHENFYykpRVTIDLISDYSEGLIastACVGGVISRRIINGDFDIARdtlsDL 313
Cdd:cd07434    72 R--LVLLARDRAGYGRLCRLitlgRRRAEKGEY---RLTLADLLAHAEGLL---LILLPPDRLPAAAALLAQLR----WL 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 314 KAIFGDDLYVEVQPH-------KFEEqvmvnpkLIEYADEYDVEVVIGTDVHYNNRGDKFIYDVVKAILFNKKVGESsie 386
Cdd:cd07434   140 ARAFPGRLWLALELHlggddarRLAR-------LAALAAALGLPLVATGDVLMHSPSRRPLQDVLTAIRLGTTVAEA--- 209

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1774765362 387 gdtyhlmrPDELFyAGAEANI-PPEVMRR-------AMINTHRIARGCN 427
Cdd:cd07434   210 --------GRRLA-ANAERHLrSPAELARlflyppeALAETLEIAARCT 249
PHP_HisPPase cd07432
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ...
 165-265 6.20e-10

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: 56.86  E-value: 6.20e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 165 HVHSEYSvMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVT-----DTLNRENGDRY 239
Cdd:cd07432     4 HIHSVFS-PDSDMTPEEIVERAIELGLDGIAITDHNTIDGAEEALKEAYKDGLLVIPGVEVTLVvlahpDRPSRYGLSDL 82

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1774765362 240 HLVLLAKDNIGL-----RNLFKLNHIAHENF 265
Cdd:cd07432    83 ILKPLIKNGDAIevnnsRLRYGLNNLAAKRY 113
PHP_HisPPase_AMP cd07438
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ...
 165-225 4.08e-08

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: 52.40  E-value: 4.08e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1774765362 165 HVHSEYSvmDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEF 225
Cdd:cd07438     4 HTHSTAS--DGTLSPEELVELAKEAGLKVLAITDHDTVAGLEEALAAAKELGIELIPGVEI 62
PHP cd07309
Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2 ...
 164-228 4.40e-08

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: 50.50  E-value: 4.40e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1774765362 164 IHVHSEYSVMDGIgSVESRVKAAAEMGFRSLALTDHGTLSGLYDF----QLNCKK----YKIKPIFGCEFYVT 228
Cdd:cd07309     3 LHTHTVFSDGDHA-KLTELVDKAKELGPDALAITDHGNLRGLAEFntagK*NHIKaaeaAGIKIIIGSEVNLT 74
UDG-F2_TDG_MUG cd10028
Uracil DNA glycosylase family 2, includes thymine DNA glycosylase, mismatch-specific uracil ...
 22-141 3.40e-06

Uracil DNA glycosylase family 2, includes thymine DNA glycosylase, mismatch-specific uracil DNA glycosylase and similar proteins; Uracil DNA glycosylase family 2 consists of thymine DNA glycosylase (TDG), which removes uracil and thymine from G:U and G:T mismatches in double-stranded DNA. It includes mismatch-specific uracil DNA glycosylase (MUG), the prokaryotic homolog of TDG. Escherichia coli MUG is highly specific to G:U mismatches but also repairs G:T mismatches at high enzyme concentration. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil in DNA can arise as a result of misincorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other..


Pssm-ID: 381679  Cd Length: 163  Bit Score: 47.09  E-value: 3.40e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  22 ILFIGLNPGVEEVRVGAPFVGP----------SGkLLDEWVK---HWNLPNNAIAITNIVKCHTPNEAGVT-GEMLQNCK 87
Cdd:cd10028    11 VLFCGINPGLRSAAVGHHYAHPgnrfwpllheSG-LTPRLLTpeeDRRLPEYGIGLTNLVKRPTASAAELSkAELRAGVP 89

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1774765362  88 EyLDRQIDYLKPDMIMSLGRLASEALKGsSVNITKDIGPYEYK---GVPLYTLPHPS 141
Cdd:cd10028    90 R-LLAKIARYRPRVVAFVGKGAYRAFFG-RLKKKAAYGLQPETgigGTRVFVLPSTS 144
HIS2 COG1387
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and ...
 165-200 4.46e-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: 47.46  E-value: 4.46e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1774765362 165 HVHSEYSvmDGIGSVESRVKAAAEMGFRSLALTDHG 200
Cdd:COG1387     6 HTHTTYS--DGEGTIEEMVEAAIELGLEYIAITDHS 39
PHP_PolX cd07436
Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal ...
 164-199 5.76e-06

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: 47.41  E-value: 5.76e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1774765362 164 IHVHSEYSvmDGIGSVESRVKAAAEMGFRSLALTDH 199
Cdd:cd07436     9 LHVHTTWS--DGRNSIEEMAEAARALGYEYIAITDH 42
CehA_McbA_metalo NF038032
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ...
 165-209 1.07e-05

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: 47.32  E-value: 1.07e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1774765362 165 HVHSEYSvmDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQ 209
Cdd:NF038032    8 HIHTNHS--DGPTTPEELARAALAEGLDVIALTDHNTISGRAYFA 50
dnaE PRK05898
DNA polymerase III subunit alpha;
164-264 1.73e-05

DNA polymerase III subunit alpha;


Pssm-ID: 135648 [Multi-domain]  Cd Length: 971  Bit Score: 47.14  E-value: 1.73e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362 164 IHVHSEYSVMDGIGSVESRVKAAAEMGFRSLALTDHGTLSGLYDFQLNCKKYKIKPIFGCEFYVTDTlnrengdRYHLVL 243
Cdd:PRK05898    5 LNTHSHYSLLSSTLSIDDIIKFALDNNQPYVCLTDLNNLYGCIEFYDKAKAHNLIPIIGLEIEYQST-------NATLVL 77

                          90       100
                  ....*....|....*....|.
gi 1774765362 244 LAKDNIGLRNLFKLNHIAHEN 264
Cdd:PRK05898   78 YAKNYNGYLNLIKISSFIMTN 98
UDG-F5_TTUDGB_like cd10031
Uracil DNA glycosylase family 5, includes Thermotoga maritima TTUDGB and similar proteins; ...
 16-113 2.51e-04

Uracil DNA glycosylase family 5, includes Thermotoga maritima TTUDGB and similar proteins; Uracil DNA glycosylase family 5 includes Thermus thermophilus HB8 TTUDGB (also called UDGb) which is not only a UDG acting on double-stranded uracil-containing DNA, but also a hypoxanthine DNA glycosylase acting on double-stranded hypoxanthine-containing DNA (except for the C/I base pair), as well as a xanthine DNA glycosylase acting on both, double-stranded and single-stranded xanthine-containing DNA. TTUDGB also excises thymine from G:T mismatched DNA, and removes analogs of uracil from DNA, including 5-hydroxymethyluracil (hmU) and 5-fluorouracil (fU). This subfamily also contains Bradyrhizobium diazoefficiens family 5 homolog Blr5068 (UdgB) which has been found to efficiently excise uracil from ssDNA and dsDNA. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Similar to family 4 UDGs, members of this family possess four conserved cysteine residues required to coordinate the [4Fe-4S] iron-sulfur cluster. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other.


Pssm-ID: 381681  Cd Length: 204  Bit Score: 42.07  E-value: 2.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774765362  16 GSLSPVILFIGLNPGVEEV-RVGAPFVG-PSGKLL-------------DEWVKHWNLPNNAIAITNIVKCHTPNEAgVTG 80
Cdd:cd10031    35 GDPNARLLIVGLAPAAHGGnRTGRPFTGdRSGDFLyralyeagfanqpTSESRDDGLELKDCYITAAVRCAPPQNK-PTP 113

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1774765362  81 EMLQNCKEYLDRQIDYLK-PDMIMSLGRLASEAL 113
Cdd:cd10031   114 EEIRNCRPFLEEELALLKnLKVILALGRIAFDAV 147
PRK07945 PRK07945
PHP domain-containing protein;
165-199 2.50e-03

PHP domain-containing protein;


Pssm-ID: 236135 [Multi-domain]  Cd Length: 335  Bit Score: 39.96  E-value: 2.50e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1774765362 165 HVHSEYSvmDGIGSVESRVKAAAEMGFRSLALTDH 199
Cdd:PRK07945  101 HTHSDWS--DGGSPIEEMARTAAALGHEYCALTDH 133
 
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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