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Conserved domains on  [gi|515630108|ref|WP_017062708|]
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MULTISPECIES: 3'-5' exonuclease [Vibrio]

Protein Classification

3'-5' exonuclease( domain architecture ID 10793152)

3'-5' exonuclease similar to DNA polymerase III subunit epsilon and exodeoxyribonuclease 10

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09145 PRK09145
3'-5' exonuclease;
1-202 1.87e-116

3'-5' exonuclease;


:

Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 329.56  E-value: 1.87e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108   1 MNRLVRYYWHHKLKGSLYQPLFTAPIDHEYVSLDCETTSLDPNQAELVTIAATKIIGNRIITSQPFEVRLRAPQSLDCNS 80
Cdd:PRK09145   2 MNWLRRLWWRRRLKDPRYAFLFEPPPPDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAES 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  81 IKIHRIRHQDLKHGIEEKQALIELLNFIGNRPLVGYHIRYDKKILDRACLKQLGFPLPNRLVEVSQLYQDKLERQLPNAY 160
Cdd:PRK09145  82 IKIHRLRHQDLEDGLSEEEALRQLLAFIGNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAY 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 515630108 161 FDLSMDAICRQLDLPiPVNKHDALQDAISAALIFVRLKHGDL 202
Cdd:PRK09145 162 IDLRFDAILKHLDLP-VLGRHDALNDAIMAALIFLRLRKGDA 202
 
Name Accession Description Interval E-value
PRK09145 PRK09145
3'-5' exonuclease;
1-202 1.87e-116

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 329.56  E-value: 1.87e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108   1 MNRLVRYYWHHKLKGSLYQPLFTAPIDHEYVSLDCETTSLDPNQAELVTIAATKIIGNRIITSQPFEVRLRAPQSLDCNS 80
Cdd:PRK09145   2 MNWLRRLWWRRRLKDPRYAFLFEPPPPDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAES 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  81 IKIHRIRHQDLKHGIEEKQALIELLNFIGNRPLVGYHIRYDKKILDRACLKQLGFPLPNRLVEVSQLYQDKLERQLPNAY 160
Cdd:PRK09145  82 IKIHRLRHQDLEDGLSEEEALRQLLAFIGNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAY 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 515630108 161 FDLSMDAICRQLDLPiPVNKHDALQDAISAALIFVRLKHGDL 202
Cdd:PRK09145 162 IDLRFDAILKHLDLP-VLGRHDALNDAIMAALIFLRLRKGDA 202
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 31-194 1.46e-36

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: 125.49  E-value: 1.46e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  31 VSLDCETTSLDPNQAELVTIAATKIIGNRIITSQpFEVRLRAPQSLDCNSIKIHRIRHQDLKHGIEEKQALIELLNFIGN 110
Cdd:cd06127    1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIVER-FETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108 111 RPLVGYHIRYDKKILDRACLKQLGFPLPNRLVEVSQLYQDKLERQLPNAYFDLsmdaICRQLDLPiPVNKHDALQDAISA 190
Cdd:cd06127   80 RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLL----LAERYGIP-LEGAHRALADALAT 154


                 ....
gi 515630108 191 ALIF 194
Cdd:cd06127  155 AELL 158
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 29-197 5.61e-34

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 118.74  E-value: 5.61e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  29 EYVSLDCETTSLDPNQAELVTIAATKIIGNRIITSqpFEVRLRAPQSLDCNSIKIHRIRHQDLKHGIEEKQALIELLNFI 108
Cdd:COG0847    1 RFVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVET--FHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108 109 GNRPLVGYHIRYDKKILDRAClKQLGFPLP-NRLVEVSQLYQdkleRQLPNAYfDLSMDAICRQLDLPIPvNKHDALQDA 187
Cdd:COG0847   79 GGAVLVAHNAAFDLGFLNAEL-RRAGLPLPpFPVLDTLRLAR----RLLPGLP-SYSLDALCERLGIPFD-ERHRALADA 151

                        170
                 ....*....|
gi 515630108 188 ISAALIFVRL 197
Cdd:COG0847  152 EATAELFLAL 161
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 29-198 1.75e-23

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 91.98  E-value: 1.75e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108    29 EYVSLDCETTSLDPNQAELVTIAATKIIGNRIITSqpFEVRLRAPQSLDCNSIKIHRIRHQDLKHGIEEKQALIELLNFI 108
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEV--FDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108   109 GNR-PLVGYHIRYDKKILDRACLKQLGFPLPNRLVevsqlyQD--KLERQLPNAYFDLSMDAICRQLDLPIPVNKHDALQ 185
Cdd:smart00479  79 RGRiLVAGNSAHFDLRFLKLEHPRLGIKQPPKLPV------IDtlKLARATNPGLPKYSLKKLAKRLLLEVIQRAHRALD 152

                          170
                   ....*....|...
gi 515630108   186 DAISAALIFVRLK 198
Cdd:smart00479 153 DARATAKLFKKLL 165
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 31-194 7.92e-18

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: 77.01  E-value: 7.92e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108   31 VSLDCETTSLDPNQAELVTIAATKIIGNRIITSQPFE--VRLRAPQSLDCNSIKIHRIRHQDLKHGIEEKQALIELLNFI 108
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGGENEIGETFHtyVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  109 G-NRPLVGYHIRYDKKILDRACLKQLGFPLPNRLVEVSQLYQDKLERQlpnAYFDLSMDAICRQLDLPIPVNKHDALQDA 187
Cdd:pfam00929  81 RkGNLLVAHNASFDVGFLRYDDKRFLKKPMPKLNPVIDTLILDKATYK---ELPGRSLDALAEKLGLEHIGRAHRALDDA 157


                  ....*..
gi 515630108  188 ISAALIF 194
Cdd:pfam00929 158 RATAKLF 164
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 30-197 1.26e-06

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: 47.44  E-value: 1.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108   30 YVSLDCETTSLDPNQaELVTIAATKIIGNRIITSQpFEVRLRAPQSLDCNSIKIHRIRHQDLKHGIEEKQALIELLNFIG 109
Cdd:TIGR00573   9 ETTGDNETTGLYAGH-DIIEIGAVEIINRRITGNK-FHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIR 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  110 NRPLVGYHIRYDKKILDRA----CLKQlgfPLPNRLVEVSQLYQdKLERQLPNAyfDLSMDAICRQLDLPipvNKHDALQ 185
Cdd:TIGR00573  87 GAELVIHNASFDVGFLNYEfsklYKVE---PKTNDVIDTTDTLQ-YARPEFPGK--RNTLDALCKRYEIT---NSHRALH 157

                         170
                  ....*....|..
gi 515630108  186 DAISAALIFVRL 197
Cdd:TIGR00573 158 GALADAFILAKL 169
 
Name Accession Description Interval E-value
PRK09145 PRK09145
3'-5' exonuclease;
1-202 1.87e-116

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 329.56  E-value: 1.87e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108   1 MNRLVRYYWHHKLKGSLYQPLFTAPIDHEYVSLDCETTSLDPNQAELVTIAATKIIGNRIITSQPFEVRLRAPQSLDCNS 80
Cdd:PRK09145   2 MNWLRRLWWRRRLKDPRYAFLFEPPPPDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAES 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  81 IKIHRIRHQDLKHGIEEKQALIELLNFIGNRPLVGYHIRYDKKILDRACLKQLGFPLPNRLVEVSQLYQDKLERQLPNAY 160
Cdd:PRK09145  82 IKIHRLRHQDLEDGLSEEEALRQLLAFIGNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAY 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 515630108 161 FDLSMDAICRQLDLPiPVNKHDALQDAISAALIFVRLKHGDL 202
Cdd:PRK09145 162 IDLRFDAILKHLDLP-VLGRHDALNDAIMAALIFLRLRKGDA 202
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 31-194 1.46e-36

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: 125.49  E-value: 1.46e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  31 VSLDCETTSLDPNQAELVTIAATKIIGNRIITSQpFEVRLRAPQSLDCNSIKIHRIRHQDLKHGIEEKQALIELLNFIGN 110
Cdd:cd06127    1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIVER-FETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108 111 RPLVGYHIRYDKKILDRACLKQLGFPLPNRLVEVSQLYQDKLERQLPNAYFDLsmdaICRQLDLPiPVNKHDALQDAISA 190
Cdd:cd06127   80 RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLL----LAERYGIP-LEGAHRALADALAT 154


                 ....
gi 515630108 191 ALIF 194
Cdd:cd06127  155 AELL 158
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 29-197 5.61e-34

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 118.74  E-value: 5.61e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  29 EYVSLDCETTSLDPNQAELVTIAATKIIGNRIITSqpFEVRLRAPQSLDCNSIKIHRIRHQDLKHGIEEKQALIELLNFI 108
Cdd:COG0847    1 RFVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVET--FHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108 109 GNRPLVGYHIRYDKKILDRAClKQLGFPLP-NRLVEVSQLYQdkleRQLPNAYfDLSMDAICRQLDLPIPvNKHDALQDA 187
Cdd:COG0847   79 GGAVLVAHNAAFDLGFLNAEL-RRAGLPLPpFPVLDTLRLAR----RLLPGLP-SYSLDALCERLGIPFD-ERHRALADA 151

                        170
                 ....*....|
gi 515630108 188 ISAALIFVRL 197
Cdd:COG0847  152 EATAELFLAL 161
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 27-197 2.79e-31

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 112.54  E-value: 2.79e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  27 DHEYVSLDCETTSLDPNQAELVTIAATKIIGNRIITSqpFEVRLRAPQSLDCNSIKIHRIRHQDLKHGIEEKQALIELLN 106
Cdd:COG2176    7 DLTYVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDR--FSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLE 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108 107 FIGNRPLVGYHIRYDKKILDRAClKQLGFPLPNRLVEVSQLYQdKLERQLPNAyfdlSMDAICRQLDLPIPVNkHDALQD 186
Cdd:COG2176   85 FLGDAVLVAHNASFDLGFLNAAL-KRLGLPFDNPVLDTLELAR-RLLPELKSY----KLDTLAERLGIPLEDR-HRALGD 157

                        170
                 ....*....|.
gi 515630108 187 AISAALIFVRL 197
Cdd:COG2176  158 AEATAELFLKL 168
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 29-198 1.75e-23

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 91.98  E-value: 1.75e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108    29 EYVSLDCETTSLDPNQAELVTIAATKIIGNRIITSqpFEVRLRAPQSLDCNSIKIHRIRHQDLKHGIEEKQALIELLNFI 108
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEV--FDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108   109 GNR-PLVGYHIRYDKKILDRACLKQLGFPLPNRLVevsqlyQD--KLERQLPNAYFDLSMDAICRQLDLPIPVNKHDALQ 185
Cdd:smart00479  79 RGRiLVAGNSAHFDLRFLKLEHPRLGIKQPPKLPV------IDtlKLARATNPGLPKYSLKKLAKRLLLEVIQRAHRALD 152

                          170
                   ....*....|...
gi 515630108   186 DAISAALIFVRLK 198
Cdd:smart00479 153 DARATAKLFKKLL 165
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 31-194 7.92e-18

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: 77.01  E-value: 7.92e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108   31 VSLDCETTSLDPNQAELVTIAATKIIGNRIITSQPFE--VRLRAPQSLDCNSIKIHRIRHQDLKHGIEEKQALIELLNFI 108
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGGENEIGETFHtyVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  109 G-NRPLVGYHIRYDKKILDRACLKQLGFPLPNRLVEVSQLYQDKLERQlpnAYFDLSMDAICRQLDLPIPVNKHDALQDA 187
Cdd:pfam00929  81 RkGNLLVAHNASFDVGFLRYDDKRFLKKPMPKLNPVIDTLILDKATYK---ELPGRSLDALAEKLGLEHIGRAHRALDDA 157


                  ....*..
gi 515630108  188 ISAALIF 194
Cdd:pfam00929 158 RATAKLF 164
PRK07740 PRK07740
hypothetical protein; Provisional
 16-191 8.47e-15

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 70.47  E-value: 8.47e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  16 SLYQPLFTAPIdheyVSLDCETTSLDPNQA-ELVTIAATKIIGNRIITSQPFE-VRLRAPQSLDCNSIKihRIRHQDLKH 93
Cdd:PRK07740  51 VLDIPLTDLPF----VVFDLETTGFSPQQGdEILSIGAVKTKGGEVETDTFYSlVKPKRPIPEHILELT--GITAEDVAF 124

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  94 GIEEKQALIELLNFIGNRPLVGYHIRYDKKILDRACLKQLGFPLPNRLVEVSqlyqdKLERQLPNAYFDLSMDAICRQLD 173
Cdd:PRK07740 125 APPLAEVLHRFYAFIGAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTM-----FLTKLLAHERDFPTLDDALAYYG 199

                        170
                 ....*....|....*...
gi 515630108 174 LPIPvNKHDALQDAISAA 191
Cdd:PRK07740 200 IPIP-RRHHALGDALMTA 216
PRK09146 PRK09146
DNA polymerase III subunit epsilon; Validated
 3-191 2.32e-14

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236392 [Multi-domain]  Cd Length: 239  Bit Score: 69.18  E-value: 2.32e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108   3 RLVRYYwhhklKGSLYQPlfTAPI-DHEYVSLDCETTSLDPNQAELVTIAATKIIGNRIITSQPFEVRLRAPQSLDCNSI 81
Cdd:PRK09146  28 RLKRFY-----AAGLVSP--DTPLsEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESV 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  82 KIHRIRHQDLKHGIEEKQALIELLNFIGNRPLVGYHIRYDKKILDRACLKQLG----FPLPNRLvEVSQLYQDKLERQLP 157
Cdd:PRK09146 101 VIHGITHSELQDAPDLERILDELLEALAGKVVVVHYRRIERDFLDQALRNRIGegieFPVIDTM-EIEARIQRKQAGGLW 179

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 515630108 158 NAYFDLSMDAI----CRQ-LDLPiPVNKHDALQDAISAA 191
Cdd:PRK09146 180 NRLKGKKPESIrladSRLrYGLP-AYSPHHALTDAIATA 217
polC PRK00448
DNA polymerase III PolC; Validated
 26-198 1.34e-12

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 66.01  E-value: 1.34e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108   26 IDHEYVSLDCETTSLDPNQAELVTIAATKIIGNRIITSqpFEVRLRAPQSLDCNSIKIHRIRHQDLKHGIEEKQALIELL 105
Cdd:PRK00448  417 KDATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDK--FEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFK 494

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  106 NFIGNRPLVGYHIRYDKKILDRACLKqLGFPlpnrlvEVSQLYQDKLE--RQLPNAYFDLSMDAICRQLDLpIPVNKHDA 183
Cdd:PRK00448  495 EFCGDSILVAHNASFDVGFINTNYEK-LGLE------KIKNPVIDTLElsRFLYPELKSHRLNTLAKKFGV-ELEHHHRA 566

                         170
                  ....*....|....*
gi 515630108  184 LQDAISAALIFVRLK 198
Cdd:PRK00448  567 DYDAEATAYLLIKFL 581
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 27-197 2.51e-11

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 61.00  E-value: 2.51e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  27 DHEYVSLDCETTSLDPNQAELVTIAATKIIGNRIITSqpFEVRLRAPQSLDCNSIKIHRIRHQDLKHGIEEKQALIELLN 106
Cdd:PRK06310   6 DTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDS--VEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKG 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108 107 FIGNRP-LVGYHIRYDKKILDRAClKQLGFP-LPNRLVEVSQLYQDKLERQLPNAyfdlSMDAICRQLDLPIPVNkHDAL 184
Cdd:PRK06310  84 FFKEGDyIVGHSVGFDLQVLSQES-ERIGETfLSKHYYIIDTLRLAKEYGDSPNN----SLEALAVHFNVPYDGN-HRAM 157

                        170
                 ....*....|...
gi 515630108 185 QDAISAALIFVRL 197
Cdd:PRK06310 158 KDVEINIKVFKHL 170
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 30-196 2.35e-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: 2.35e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  30 YVSLDCETTSLDPNQAelVTIAATKIIGNRIITSqpFEVRLRAPQSLDCNSIKIHRIRHQDLKHGIEEKQALIELLNFIG 109
Cdd:cd06130    1 FVAIDFETANADRASA--CSIGLVKVRDGQIVDT--FYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLG 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108 110 NRPLVGYHIRYDKKILdRACLKQLGFPLPNRLVEVS-QLYQdKLERQLPNAyfdlSMDAICRQLDlpIPVNKHDALQDAI 188
Cdd:cd06130   77 GSLVVAHNASFDRSVL-RAALEAYGLPPPPYQYLCTvRLAR-RVWPLLPNH----KLNTVAEHLG--IELNHHDALEDAR 148


                 ....*...
gi 515630108 189 SAALIFVR 196
Cdd:cd06130  149 ACAEILLA 156
PRK06807 PRK06807
3'-5' exonuclease;
29-194 3.27e-09

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 55.59  E-value: 3.27e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  29 EYVSLDCETTSLDPNQAELVTIAATKIIGNRIITSqpFEVRLRAPQSLDCNSIKIHRIRHQDLKHGIEEKQALIELLNFI 108
Cdd:PRK06807   9 DYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQ--FVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108 109 GNRPLVGYHIRYDKKILdRACLKQLGFPLPNRLVEVSQLYQDKLERQLPNAyfdlSMDAICRQLDlpIPVNKHDALQDAI 188
Cdd:PRK06807  87 HTNVIVAHNASFDMRFL-KSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNH----KLETLKRMLG--IRLSSHNAFDDCI 159


                 ....*.
gi 515630108 189 SAALIF 194
Cdd:PRK06807 160 TCAAVY 165
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 30-187 2.78e-08

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: 51.38  E-value: 2.78e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  30 YVSLDCETTSLDPNQAE-LVTIAATKIIgNRIITSQPFEVRLRAPQSLDCNSIKIHRIRHQDLKHGIEEKQALIELLNFI 108
Cdd:cd06131    1 QIVLDTETTGLDPREGHrIIEIGCVELI-NRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108 109 GNRPLVGYHIRYDKKILDRAcLKQLGFPLP----NRLVEVSQLYQDKLERQlPNayfdlSMDAICRQLDlpIPVNK---H 181
Cdd:cd06131   80 RGAELVIHNASFDVGFLNAE-LSLLGLGKKiidfCRVIDTLALARKKFPGK-PN-----SLDALCKRFG--IDNSHrtlH 150


                 ....*.
gi 515630108 182 DALQDA 187
Cdd:cd06131  151 GALLDA 156
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 30-197 1.26e-06

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: 47.44  E-value: 1.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108   30 YVSLDCETTSLDPNQaELVTIAATKIIGNRIITSQpFEVRLRAPQSLDCNSIKIHRIRHQDLKHGIEEKQALIELLNFIG 109
Cdd:TIGR00573   9 ETTGDNETTGLYAGH-DIIEIGAVEIINRRITGNK-FHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIR 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  110 NRPLVGYHIRYDKKILDRA----CLKQlgfPLPNRLVEVSQLYQdKLERQLPNAyfDLSMDAICRQLDLPipvNKHDALQ 185
Cdd:TIGR00573  87 GAELVIHNASFDVGFLNYEfsklYKVE---PKTNDVIDTTDTLQ-YARPEFPGK--RNTLDALCKRYEIT---NSHRALH 157

                         170
                  ....*....|..
gi 515630108  186 DAISAALIFVRL 197
Cdd:TIGR00573 158 GALADAFILAKL 169
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 86-203 7.16e-06

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 44.85  E-value: 7.16e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  86 IRHQDLKHGIEEKQALIELLNFIG--NRPLVGYHiRYDKKILDRAC-LKQLGFPLPNRLVEVSQLYqdKLERQLPNayfD 162
Cdd:COG5018   66 ITQEDVDSAPSFAEAIEDFKKWIGseDYILCSWG-DYDRKQLERNCrFHGVPYPFGDRHINLKKLF--ALYFGLKK---R 139

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 515630108 163 LSMDAICRQLDLPIPVNKHDALQDAISAALIFVR-LKHGDLP 203
Cdd:COG5018  140 IGLKKALELLGLEFEGTHHRALDDARNTAKLFKKiLGDKRLP 181
PRK08517 PRK08517
3'-5' exonuclease;
27-194 4.14e-05

3'-5' exonuclease;


Pssm-ID: 236281 [Multi-domain]  Cd Length: 257  Bit Score: 43.09  E-value: 4.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  27 DHEYVSLDCETTSLDPNQAELVTIAATKIIGNRIITSqpFEVRLRAPqSLDCNSIKIHRIRHQDLKHGIEEKQALIELLN 106
Cdd:PRK08517  67 DQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDR--FESFVKAK-EVPEYITELTGITYEDLENAPSLKEVLEEFRL 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108 107 FIGNRPLVGYHIRYDKKILDRAcLKQLGF-PLPNRLVEVSQLYQDKLERQlpnAYfdlSMDAICRQLDLPIPVNkHDALQ 185
Cdd:PRK08517 144 FLGDSVFVAHNVNFDYNFISRS-LEEIGLgPLLNRKLCTIDLAKRTIESP---RY---GLSFLKELLGIEIEVH-HRAYA 215


                 ....*....
gi 515630108 186 DAISAALIF 194
Cdd:PRK08517 216 DALAAYEIF 224
DNA_polA_I_Ecoli_like_exo cd06139
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial ...
 28-125 1.21e-04

DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D 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 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.


Pssm-ID: 176651 [Multi-domain]  Cd Length: 193  Bit Score: 41.35  E-value: 1.21e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  28 HEYVSLDCETTSLDPNQAELVTIaatkiignriitsqpfevrlrapqSLdcnSIKIHR-----IRHQDLKHGIEEKQALI 102
Cdd:cd06139    5 AKVFAFDTETTSLDPMQAELVGI------------------------SF---AVEPGEayyipLGHDYGGEQLPREEVLA 57

                         90       100
                 ....*....|....*....|....*
gi 515630108 103 ELLNFIGN--RPLVGYHIRYDKKIL 125
Cdd:cd06139   58 ALKPLLEDpsIKKVGQNLKFDLHVL 82
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 82-197 6.20e-04

DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing 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. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.


Pssm-ID: 99836 [Multi-domain]  Cd Length: 176  Bit Score: 39.13  E-value: 6.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  82 KIHRIRHQDLKHGIEEKQALIELLNFIGNRPLVGYHI-----RYDKKILDRACLKQLGFPLPNRLVEVSQLYQDKLERQL 156
Cdd:cd06133   60 ELTGITQEDVDNAPSFPEVLKEFLEWLGKNGKYAFVTwgdwdLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKK 139

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 515630108 157 PnayfdLSMDAICRQLDLPIPVNKHDALQDAISAALIFVRL 197
Cdd:cd06133  140 R-----TGLSKALEYLGLEFEGRHHRGLDDARNIARILKRL 175
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 30-193 9.59e-04

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 39.38  E-value: 9.59e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108  30 YVSLDCETTSLDPNQAelVTIAATKIIGNRIITSQPFEVRLRAPQSLDCNsIKIHRIRHQDLKHGIEEKQALIELLNFIG 109
Cdd:PRK06195   3 FVAIDFETANEKRNSP--CSIGIVVVKDGEIVEKVHYLIKPKEMRFMPIN-IGIHGIRPHMVEDELEFDKIWEKIKHYFN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515630108 110 NRPLVGYHIRYDKKILdRACLKQLGFPLPNRLVEVSQLYQDKLERQLPNAYFDLSMDAicrqldLPIPVNKHDALQDAIS 189
Cdd:PRK06195  80 NNLVIAHNASFDISVL-RKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNF------LGYEFKHHDALADAMA 152


                 ....
gi 515630108 190 AALI 193
Cdd:PRK06195 153 CSNI 156
 
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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