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Conserved domains on  [gi|1747860158|gb|QER78277|]
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DNA polymerase II large subunit, partial [Bacillus subtilis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
polC super family cl35100
DNA polymerase III PolC; Validated
 1-259 6.72e-157

DNA polymerase III PolC; Validated


The actual alignment was detected with superfamily member PRK00448:

Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 471.63  E-value: 6.72e-157
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158    1 DMGFLNVAYKKLlEVDKAKNPVIDTLELGRFLYPEFKNHRLNTLCKKFDIELTQHHRAIYDTEATAYLLLKMLKDAAEKG 80
Cdd:PRK00448   510 DVGFINTNYEKL-GLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELEHHHRADYDAEATAYLLIKFLKDLKEKG 588

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158   81 IQYHDELNENMGQSNAYQRSRPYHATLLAVNSTGLKNLFKLVSLSHIHYFYRVPRIPRSQLEKYREGLLIGSACDRGEVF 160
Cdd:PRK00448   589 ITNLDELNKKLGSEDAYKKARPKHATILVKNQVGLKNLFKLVSLSNTKYFYRVPRIPRSLLDKYREGLLIGSACEEGEVF 668

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158  161 EGMMQKSPEEVEDIASFYDYLEVQPPEVYRHLLELELVRDEKALKEIIANITKLGEKLNKPVVATGNVHYLNDEDKIYRK 240
Cdd:PRK00448   669 DAVLQKGDEELEEIAKFYDYIEIQPPANYQHLIERELVKDEEELKEIIKNLIELGKKLNKPVVATGDVHYLDPEDKIYRK 748

                          250
                   ....*....|....*....
gi 1747860158  241 ILISSQGGANPLNRHELPK 259
Cdd:PRK00448   749 ILVASQGGGNPLNRHPLPE 767
 
Name Accession Description Interval E-value
polC PRK00448
DNA polymerase III PolC; Validated
 1-259 6.72e-157

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 471.63  E-value: 6.72e-157
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158    1 DMGFLNVAYKKLlEVDKAKNPVIDTLELGRFLYPEFKNHRLNTLCKKFDIELTQHHRAIYDTEATAYLLLKMLKDAAEKG 80
Cdd:PRK00448   510 DVGFINTNYEKL-GLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELEHHHRADYDAEATAYLLIKFLKDLKEKG 588

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158   81 IQYHDELNENMGQSNAYQRSRPYHATLLAVNSTGLKNLFKLVSLSHIHYFYRVPRIPRSQLEKYREGLLIGSACDRGEVF 160
Cdd:PRK00448   589 ITNLDELNKKLGSEDAYKKARPKHATILVKNQVGLKNLFKLVSLSNTKYFYRVPRIPRSLLDKYREGLLIGSACEEGEVF 668

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158  161 EGMMQKSPEEVEDIASFYDYLEVQPPEVYRHLLELELVRDEKALKEIIANITKLGEKLNKPVVATGNVHYLNDEDKIYRK 240
Cdd:PRK00448   669 DAVLQKGDEELEEIAKFYDYIEIQPPANYQHLIERELVKDEEELKEIIKNLIELGKKLNKPVVATGDVHYLDPEDKIYRK 748

                          250
                   ....*....|....*....
gi 1747860158  241 ILISSQGGANPLNRHELPK 259
Cdd:PRK00448   749 ILVASQGGGNPLNRHPLPE 767
PHP_PolIIIA_POLC cd07435
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ...
 102-259 1.05e-89

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: 266.26  E-value: 1.05e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158 102 PYHATLLAVNSTGLKNLFKLVSLSHIHYFYRVPRIPRSQLEKYREGLLIGSACDRGEVFEGMMQKSPE-EVEDIASFYDY 180
Cdd:cd07435    70 PYHITILVKNQTGLKNLYKLVSLSHTKYFYRVPRIPKSELEKYREGLLIGSACENGELFEAALNKKSDeELEEIASFYDY 149

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1747860158 181 LEVQPPEVYRHLLELELVRDEKALKEIIANITKLGEKLNKPVVATGNVHYLNDEDKIYRKILISSQGGANPlNRHELPK 259
Cdd:cd07435   150 IEIQPLDNYQFLIEKGLIKSEEELKEINKRIIKLGKKLNKPVVATGDVHYLDPEDKIYREILLAGQGGGDG-RADEQPD 227
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 1-129 3.26e-42

exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA]


Pssm-ID: 129663 [Multi-domain]  Cd Length: 217  Bit Score: 143.36  E-value: 3.26e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158   1 DMGFLNVAYKKLLEVDKAKNPVIDTLELGRFLYPEFKNHRLNTLCKKFDIELTQHHRAIYDTEATAYLLLKMLKDAAEKG 80
Cdd:TIGR00573  98 DVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGALADAFILAKLYLVMTGKQ 177

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1747860158  81 IQYHdelnENMGqsnayQRSRPYHATLLAVNSTGLKNLFKLVSLSHIHY 129
Cdd:TIGR00573 178 TKYG----ENEG-----QQSRPYHAIKSIVKKDMLLKLIKAVSTELQAH 217
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 1-84 1.63e-32

DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 117.17  E-value: 1.63e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158   1 DMGFLNVAYKKLLEvdKAKNPVIDTLELGRFLYPEFKNHRLNTLCKKFDIELTQHHRAIYDTEATAYLLLKMLKDAAEKG 80
Cdd:COG2176    99 DLGFLNAALKRLGL--PFDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDRHRALGDAEATAELFLKLLEKLEEKG 176


                  ....
gi 1747860158  81 IQYH 84
Cdd:COG2176   177 ITTL 180
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 1-75 1.04e-17

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 78.11  E-value: 1.04e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1747860158    1 DMGFLNVAYKKLLEVDKAKNPVIDTLELGRFLYPEFKNHRLNTLCKKFDIELTQ-HHRAIYDTEATAYLLLKMLKD 75
Cdd:smart00479  92 DLRFLKLEHPRLGIKQPPKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQrAHRALDDARATAKLFKKLLER 167
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 1-69 2.27e-13

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 66.22  E-value: 2.27e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1747860158   1 DMGFLNVAYKKLLEVDKAK-NPVIDTLELGRFLYPEFKNHRLNTLCKKFDIELTQH-HRAIYDTEATAYLL 69
Cdd:pfam00929  94 DVGFLRYDDKRFLKKPMPKlNPVIDTLILDKATYKELPGRSLDALAEKLGLEHIGRaHRALDDARATAKLF 164
 
Name Accession Description Interval E-value
polC PRK00448
DNA polymerase III PolC; Validated
 1-259 6.72e-157

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 471.63  E-value: 6.72e-157
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158    1 DMGFLNVAYKKLlEVDKAKNPVIDTLELGRFLYPEFKNHRLNTLCKKFDIELTQHHRAIYDTEATAYLLLKMLKDAAEKG 80
Cdd:PRK00448   510 DVGFINTNYEKL-GLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELEHHHRADYDAEATAYLLIKFLKDLKEKG 588

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158   81 IQYHDELNENMGQSNAYQRSRPYHATLLAVNSTGLKNLFKLVSLSHIHYFYRVPRIPRSQLEKYREGLLIGSACDRGEVF 160
Cdd:PRK00448   589 ITNLDELNKKLGSEDAYKKARPKHATILVKNQVGLKNLFKLVSLSNTKYFYRVPRIPRSLLDKYREGLLIGSACEEGEVF 668

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158  161 EGMMQKSPEEVEDIASFYDYLEVQPPEVYRHLLELELVRDEKALKEIIANITKLGEKLNKPVVATGNVHYLNDEDKIYRK 240
Cdd:PRK00448   669 DAVLQKGDEELEEIAKFYDYIEIQPPANYQHLIERELVKDEEELKEIIKNLIELGKKLNKPVVATGDVHYLDPEDKIYRK 748

                          250
                   ....*....|....*....
gi 1747860158  241 ILISSQGGANPLNRHELPK 259
Cdd:PRK00448   749 ILVASQGGGNPLNRHPLPE 767
PHP_PolIIIA_POLC cd07435
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ...
 102-259 1.05e-89

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: 266.26  E-value: 1.05e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158 102 PYHATLLAVNSTGLKNLFKLVSLSHIHYFYRVPRIPRSQLEKYREGLLIGSACDRGEVFEGMMQKSPE-EVEDIASFYDY 180
Cdd:cd07435    70 PYHITILVKNQTGLKNLYKLVSLSHTKYFYRVPRIPKSELEKYREGLLIGSACENGELFEAALNKKSDeELEEIASFYDY 149

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1747860158 181 LEVQPPEVYRHLLELELVRDEKALKEIIANITKLGEKLNKPVVATGNVHYLNDEDKIYRKILISSQGGANPlNRHELPK 259
Cdd:cd07435   150 IEIQPLDNYQFLIEKGLIKSEEELKEINKRIIKLGKKLNKPVVATGDVHYLDPEDKIYREILLAGQGGGDG-RADEQPD 227
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 1-129 3.26e-42

exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA]


Pssm-ID: 129663 [Multi-domain]  Cd Length: 217  Bit Score: 143.36  E-value: 3.26e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158   1 DMGFLNVAYKKLLEVDKAKNPVIDTLELGRFLYPEFKNHRLNTLCKKFDIELTQHHRAIYDTEATAYLLLKMLKDAAEKG 80
Cdd:TIGR00573  98 DVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGALADAFILAKLYLVMTGKQ 177

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1747860158  81 IQYHdelnENMGqsnayQRSRPYHATLLAVNSTGLKNLFKLVSLSHIHY 129
Cdd:TIGR00573 178 TKYG----ENEG-----QQSRPYHAIKSIVKKDMLLKLIKAVSTELQAH 217
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 1-84 1.63e-32

DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 117.17  E-value: 1.63e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158   1 DMGFLNVAYKKLLEvdKAKNPVIDTLELGRFLYPEFKNHRLNTLCKKFDIELTQHHRAIYDTEATAYLLLKMLKDAAEKG 80
Cdd:COG2176    99 DLGFLNAALKRLGL--PFDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDRHRALGDAEATAELFLKLLEKLEEKG 176


                  ....
gi 1747860158  81 IQYH 84
Cdd:COG2176   177 ITTL 180
PHP_PolIIIA_DnaE3 cd12113
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ...
 99-235 2.96e-29

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: 111.38  E-value: 2.96e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158  99 RSRPYHATLLAVNSTGLKNLFKLVSLSHIHYFYRVPRIPRSQLEKYREGLLIGSACDRGEVFEGMMQKSPEEVEDIASFY 178
Cdd:cd12113    82 DKRYYHLVLLAKNEEGYRNLMKLVSLAYLEGFYYKPRIDKELLAKYSEGLIALSACLAGEIPQLLLNGDEEEAREAALEY 161

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1747860158 179 D--------YLEVQppevyRHLLELElvrdekalKEIIANITKLGEKLNKPVVATGNVHYLNDED 235
Cdd:cd12113   162 RdifgkdnfYLELQ-----DHGLPEQ--------KKVNEGLIELAKELGIPLVATNDVHYLNKED 213
DnaE COG0587
DNA polymerase III, alpha subunit [Replication, recombination and repair];
101-236 8.35e-27

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


Pssm-ID: 440352 [Multi-domain]  Cd Length: 1050  Bit Score: 109.00  E-value: 8.35e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158  101 RPYHATLLAVNSTGLKNLFKLVSLSHIHYFYR-VPRIPRSQLEKYREGLLIGSACDRGEVFEGMMQKSPEEVEDIASFYD 179
Cdd:COG0587     79 AGYHLVLLAKNREGYRNLCRLLSRAYLEGFYKgKPRIDLEDLAEHSEGLIALSGCLAGEVGQALLAGQYDEAEAALARLK 158

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1747860158  180 -------YLEVQppevyRHLLELELVRDEKALkeiianitKLGEKLNKPVVATGNVHYLNDEDK 236
Cdd:COG0587    159 difgdrfYLELQ-----RHGLPEDRRVNAALL--------ELARELGLPLVATNDVHYLNPEDA 209
polc TIGR00594
DNA-directed DNA polymerase III (polc); All proteins in this family for which functions are ...
 103-250 6.61e-26

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: 106.31  E-value: 6.61e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158  103 YHATLLAVNSTGLKNLFKLVSLSHIHYFYRVPRIPRSQLEKYREGLLIGSACDRGEVFEGMMQKSPEEVEDIASFYD--- 179
Cdd:TIGR00594   85 YHLILLAKNNTGYRNLMKLSSLAYLEGFYYKPRIDKELLEEHSEGLIALSACLSGEVPYLLLLGEERLAEEAALKYQeif 164

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1747860158  180 ----YLEVQppevyRHLLELELVRDEkalkeiiaNITKLGEKLNKPVVATGNVHYLNDEDKIYRKILISSQGGAN 250
Cdd:TIGR00594  165 gddyYLELQ-----DHGIPEQRVVNE--------ALLEISEELGIPLVATNDVHYINPEDAHAHEILLCIQTGKT 226
dnaE PRK06826
DNA polymerase III DnaE; Reviewed
 101-248 6.19e-24

DNA polymerase III DnaE; Reviewed


Pssm-ID: 235868 [Multi-domain]  Cd Length: 1151  Bit Score: 100.73  E-value: 6.19e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158  101 RPYHATLLAVNSTGLKNLFKLVSLSHIHYFYRVPRIPRSQLEKYREGLLIGSACDRGEVFEGMMQKSPEEVEDIASFYD- 179
Cdd:PRK06826    86 ETYHLVLLAKNETGYKNLMKIVSKAFTEGFYYKPRVDHELLKEHSEGLIALSACLAGEVPRYILKGNYEKAKEAALFYKd 165

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1747860158  180 -------YLEVQppevYRHLLELELVRDEkalkeiianITKLGEKLNKPVVATGNVHYLNDEDKIYRKILISSQGG 248
Cdd:PRK06826   166 ifgkenfYLELQ----DHGIPEQRKVNEE---------LIKLSKELGIPLVATNDVHYIRKEDAKAHDVLLCIQTG 228
dnaE PRK05673
DNA polymerase III subunit alpha; Validated
 101-235 1.29e-23

DNA polymerase III subunit alpha; Validated


Pssm-ID: 235554 [Multi-domain]  Cd Length: 1135  Bit Score: 99.79  E-value: 1.29e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158  101 RPYHATLLAVNSTGLKNLFKLVSLSHI--HYFYRvPRIPRSQLEKYREGLLIGSACDRGEVFEGMMQKSPEEVEDIASFY 178
Cdd:PRK05673    81 AYTHLTLLAKNETGYRNLFKLSSRAYLegQYGYK-PRIDREWLAEHSEGLIALSGCPSGEVGTALLAGQYDEAEEAAAEY 159

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1747860158  179 -----D--YLEVQppevyRHLLELElvrdekalKEIIANITKLGEKLNKPVVATGNVHYLNDED 235
Cdd:PRK05673   160 qeifgDrfYLELM-----RHGLPIE--------RRVEHALLELAKELGLPLVATNDVHYLTPED 210
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 1-74 2.26e-21

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 87.54  E-value: 2.26e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1747860158   1 DMGFLNVAYKKLlEVDKAKNPVIDTLELGRFLYPEFKNHRLNTLCKKFDIELTQHHRAIYDTEATAYLLLKMLK 74
Cdd:COG0847    91 DLGFLNAELRRA-GLPLPPFPVLDTLRLARRLLPGLPSYSLDALCERLGIPFDERHRALADAEATAELFLALLR 163
dnaE PRK07374
DNA polymerase III subunit alpha; Validated
 98-235 8.28e-21

DNA polymerase III subunit alpha; Validated


Pssm-ID: 168927 [Multi-domain]  Cd Length: 1170  Bit Score: 91.32  E-value: 8.28e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158   98 QRSRPYHATLLAVNSTGLKNLFKLVSLSHIH------YFYRvPRIPRSQLEKYREGLLIGSACDRGEVFEGMMQKSPEEV 171
Cdd:PRK07374    80 KKEKRYHLVVLAKNATGYKNLVKLTTISHLNgmrgrgIFSR-PCIDKELLKQYSEGLIVSTACLGGEIPQAILRGRPDVA 158

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1747860158  172 EDIASFYD-------YLEVQppevyrhllelelvrDEKALKEIIAN--ITKLGEKLNKPVVATGNVHYLNDED 235
Cdd:PRK07374   159 RDVAAWYKevfgddfYLEIQ---------------DHGSIEDRIVNveLVRIAKELGIKLIATNDAHYLSKND 216
PHP_PolIIIA_DnaE1 cd07433
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ...
 95-235 2.05e-18

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: 82.14  E-value: 2.05e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158  95 NAYQRSRPYHATLLAVNSTGLKNLFKLVSLSHIHYFYRV-PRIPRSQLEKYREGLLIGSACDRGEVFEGMMQKSPEEVED 173
Cdd:cd07433    70 NPDDADEPFRLTLLAQNEQGYKNLTELISRAYLEGQRNGgPHIKLEWLAEYSEGLIALSGGRDGDIGQLLLEGNPDLAEA 149

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1747860158 174 IASFYD-------YLEVQppevyRHLLELElvrdEKALKEIIanitKLGEKLNKPVVATGNVHYLNDED 235
Cdd:cd07433   150 LLQFLKkifpdrfYLELQ-----RHGRPEE----EAYEHALI----DLAYELGLPLVATNDVRFLKPED 205
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 1-75 1.04e-17

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 78.11  E-value: 1.04e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1747860158    1 DMGFLNVAYKKLLEVDKAKNPVIDTLELGRFLYPEFKNHRLNTLCKKFDIELTQ-HHRAIYDTEATAYLLLKMLKD 75
Cdd:smart00479  92 DLRFLKLEHPRLGIKQPPKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQrAHRALDDARATAKLFKKLLER 167
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 1-70 2.59e-16

DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.


Pssm-ID: 176648 [Multi-domain]  Cd Length: 159  Bit Score: 73.87  E-value: 2.59e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1747860158   1 DMGFLNVAYKKLLeVDKAKNPVIDTLELGRFLYPEFKNHRLNTL-CKKFDIELTQHHRAIYDTEATAYLLL 70
Cdd:cd06127    90 DLRFLNRELRRLG-GPPLPNPWIDTLRLARRLLPGLRSHRLGLLlAERYGIPLEGAHRALADALATAELLL 159
PRK09532 PRK09532
DNA polymerase III subunit alpha; Reviewed
 98-231 9.31e-15

DNA polymerase III subunit alpha; Reviewed


Pssm-ID: 181933 [Multi-domain]  Cd Length: 874  Bit Score: 73.62  E-value: 9.31e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158  98 QRSRPYHATLLAVNSTGLKNLFKLVSLSHIHYF-----YRVPRIPRSQLEKYREGLLIGSACDRGEVFEGMMQKSPEEVE 172
Cdd:PRK09532   78 KRRRKYHQVVLAKNTQGYKNLVKLTTISHLQGVqgkgiFARPCINKELLEQYHEGLIVTSACLGGEIPQAILSGRPDAAR 157

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1747860158 173 DIASFYD-------YLEVQppevyrhllelelvrDEKALKEIIAN--ITKLGEKLNKPVVATGNVHYL 231
Cdd:PRK09532  158 KVAKWYKklfgddfYLEIQ---------------DHGSQEDRIVNveIVKIARELGIKIIATNDSHFI 210
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 1-69 2.27e-13

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 66.22  E-value: 2.27e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1747860158   1 DMGFLNVAYKKLLEVDKAK-NPVIDTLELGRFLYPEFKNHRLNTLCKKFDIELTQH-HRAIYDTEATAYLL 69
Cdd:pfam00929  94 DVGFLRYDDKRFLKKPMPKlNPVIDTLILDKATYKELPGRSLDALAEKLGLEHIGRaHRALDDARATAKLF 164
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 1-73 2.91e-13

bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 69.21  E-value: 2.91e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1747860158   1 DMGFLNvaykKLLE---VDKAKNPVIDTLELGRFLYPEFKNHRLNTLCKKFDIELTQHHRAIYDTEATAYLLLKML 73
Cdd:PRK08074   95 DLNFLN----EELEragYTEIHCPKLDTVELARILLPTAESYKLRDLSEELGLEHDQPHRADSDAEVTAELFLQLL 166
PHP pfam02811
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ...
 99-184 6.30e-13

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


Pssm-ID: 460705 [Multi-domain]  Cd Length: 171  Bit Score: 64.87  E-value: 6.30e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158  99 RSRPYHATLLAVNSTGLKNLFKLVSLSHIHYFyrVPRIPRSQLEKYREGLLIGSACDRGEVFEGMMQKSP-EEVEDIASF 177
Cdd:pfam02811  77 LAKYFDLVLLAVHEVGYKNLIKLSSRAYLEGF--KPRIDKELLEEYFEGLIALSGCVLGHLDLILLAPGDyEEAEELAEE 154

                          90
                  ....*....|....*
gi 1747860158 178 YD--------YLEVQ 184
Cdd:pfam02811 155 YLeifgedgfYLEIN 169
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
1-87 2.59e-10

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 60.32  E-value: 2.59e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158   1 DMGFLNVAYKKLlEVDKAKNPVIDTLELGRFLYP--EFKNHRLNTLCKKFDIELTQHHRAIYDTEATAYLLLKMLKDAAE 78
Cdd:PRK07883  106 DIGFLRAAAARC-GYPWPGPPVLCTVRLARRVLPrdEAPNVRLSTLARLFGATTTPTHRALDDARATVDVLHGLIERLGN 184


                  ....*....
gi 1747860158  79 KGIQYHDEL 87
Cdd:PRK07883  185 LGVHTLEEL 193
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 23-70 4.51e-10

an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III; This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.


Pssm-ID: 99834 [Multi-domain]  Cd Length: 156  Bit Score: 56.75  E-value: 4.51e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1747860158  23 IDTLELGRFLYPEFKNHRLNTLCKKFDIELtQHHRAIYDTEATAYLLL 70
Cdd:cd06130   109 LCTVRLARRVWPLLPNHKLNTVAEHLGIEL-NHHDALEDARACAEILL 155
dinG_rel TIGR01407
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ...
 20-74 6.59e-10

DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273602 [Multi-domain]  Cd Length: 850  Bit Score: 59.05  E-value: 6.59e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1747860158  20 NPVIDTLELGRFLYPEFKNHRLNTLCKKFDIELTQHHRAIYDTEATAYLLLKMLK 74
Cdd:TIGR01407 109 KPRIDTVELAQIFFPTEESYQLSELSEALGLTHENPHRADSDAQATAELLLLLFE 163
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 19-74 2.41e-09

bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 57.39  E-value: 2.41e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1747860158  19 KNPVIDTLELGRFLYPEFKNHRLNTLCKKFDIELTQHHRAIYDTEATAYLLLKMLK 74
Cdd:PRK07246  113 RTPRVDTVELAQVFFPTLEKYSLSHLSRELNIDLADAHTAIADARATAELFLKLLQ 168
dnaE PRK06920
DNA polymerase III subunit alpha;
101-248 3.09e-09

DNA polymerase III subunit alpha;


Pssm-ID: 180749 [Multi-domain]  Cd Length: 1107  Bit Score: 57.11  E-value: 3.09e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158  101 RPYHATLLAVNSTGLKNLFKLVSLSHIHyfyRVPRIPRSQLEKYREGLLIGSACDRGEVFEGMMQKSPEEVEDIA----- 175
Cdd:PRK06920    76 KSYPLVLLAENEIGYQNLLKISSSIMTK---SKEGIPKKWLAHYAKGLIAISPGKDGEIEQLLLEDKESQAEEVArayqn 152

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1747860158  176 ---SFYDYLEVQPpevyrhllelelVRDEKALKEiiaNITKLGEKLNKPVVATGNVHYLNDEDKIYRKILISSQGG 248
Cdd:PRK06920   153 mfgNFYMSLQHHA------------IQDELLLQE---KLPEFSNRVNIPVVATNDVRYINQSDALVHECLLSVESG 213
PRK07740 PRK07740
hypothetical protein; Provisional
 1-81 4.52e-07

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 49.67  E-value: 4.52e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158   1 DMGFLNVAYKKLLEVdKAKNPVIDTLELGRFLYPEFKNHRLNTLCKKFDIELTQHHRAIYDTEATAYLLLKMLKDAAEKG 80
Cdd:PRK07740  152 DKAFLRHALWRTYRQ-PFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRRHHALGDALMTAKLWAILLVEAQQRG 230


                  .
gi 1747860158  81 I 81
Cdd:PRK07740  231 I 231
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 1-72 2.17e-06

DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.


Pssm-ID: 99835 [Multi-domain]  Cd Length: 167  Bit Score: 46.37  E-value: 2.17e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1747860158   1 DMGFLNVAYKKLLEVDKAKNP--VIDTLELGRFLYPEFKNHrLNTLCKKFDIELTQH--HRAIYDTEATAYLLLKM 72
Cdd:cd06131    92 DVGFLNAELSLLGLGKKIIDFcrVIDTLALARKKFPGKPNS-LDALCKRFGIDNSHRtlHGALLDAELLAEVYLEL 166
PRK06807 PRK06807
3'-5' exonuclease;
1-71 2.70e-05

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 44.42  E-value: 2.70e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1747860158   1 DMGFLNvAYKKLLEVDKAKNPVIDTLELGRFLYPEFKNHRLNTLCKKFDIELTQhHRAIYDTEATAYLLLK 71
Cdd:PRK06807   99 DMRFLK-SNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSS-HNAFDDCITCAAVYQK 167
PHP_PolIIIA cd07431
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; ...
 101-150 3.03e-04

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


Pssm-ID: 213986 [Multi-domain]  Cd Length: 179  Bit Score: 40.65  E-value: 3.03e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1747860158 101 RPYHATLLAVNSTGLKNLFKLVSLSHI-HYFYRVPRIPRSQLEKYREGLLI 150
Cdd:cd07431    71 EPYPLLLLAKNNEGYQNLLRLSTAAMLgEEKDGVPYLDLEELAEAASGLLV 121
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 23-116 4.46e-04

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 40.92  E-value: 4.46e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747860158  23 IDTLELGRFLYPEFKNHRLNTLCKKFDIELtQHHRAIYDTEATAYLLLKMLKDAAEKGIqyhDELNENMGqsnayqrsrp 102
Cdd:PRK06195  112 ICTMKLAKNFYSNIDNARLNTVNNFLGYEF-KHHDALADAMACSNILLNISKELNSKDI---NEISKLLG---------- 177

                          90
                  ....*....|....
gi 1747860158 103 yhATLLAVNSTGLK 116
Cdd:PRK06195  178 --VTLGYVNENGYK 189
PRK07983 PRK07983
exodeoxyribonuclease X; Provisional
 23-76 6.82e-04

exodeoxyribonuclease X; Provisional


Pssm-ID: 181186 [Multi-domain]  Cd Length: 219  Bit Score: 39.70  E-value: 6.82e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1747860158  23 IDTLELGRFLYPEFK--NHRLNTlCKKFDIELTQ---HHRAIYDTEATAYLLLKMLKDA 76
Cdd:PRK07983   97 ICTMKLARRLWPGIKysNMALYK-SRKLNVQTPPglhHHRALYDCYITAALLIDIMNTS 154
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 19-63 1.37e-03

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 39.04  E-value: 1.37e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1747860158  19 KNPVIDTLELGRfLYPEFKNHRLNTLCKKFDIELTQHHRAIYDTE 63
Cdd:PRK06310  118 HYYIIDTLRLAK-EYGDSPNNSLEALAVHFNVPYDGNHRAMKDVE 161
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 1-70 7.57e-03

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 36.76  E-value: 7.57e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1747860158   1 DMGFLNVAYKKLLEVDKAKNP---VIDTLELGRFLYPEFKNHrLNTLCKKFDIELT--QHHRAIYDTE--ATAYLLL 70
Cdd:PRK05711   97 DIGFMDYEFALLGRDIPKTNTfckVTDTLAMARRMFPGKRNS-LDALCKRYGIDNShrTLHGALLDAEilAEVYLAM 172
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 32-75 9.80e-03

3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 35.99  E-value: 9.80e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1747860158  32 LYPEFKNHR----LNTLCKKFDIELT-QHHRAIYDTEATAYLLLKMLKD 75
Cdd:COG5018   129 LFALYFGLKkrigLKKALELLGLEFEgTHHRALDDARNTAKLFKKILGD 177
 
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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