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Conserved domains on  [gi|1710300832|ref|WP_143364361|]
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3'-5' exonuclease, partial [Escherichia coli]

Protein Classification

3'-5' exonuclease( domain architecture ID 10149829)

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

Gene Ontology:  GO:0008408|GO:0003677

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 1-153 3.81e-30

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: 107.77  E-value: 3.81e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLD-NTAEALEIGLTDAAGQVV----FETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVIIF 75
Cdd:cd06127     6 ETTGLDpKKDRIIEIGAVKVDGGIEiverFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGRVLVAH 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1710300832  76 NSRFDIRILKQTAAAHSDPadwLEEMTVYCAMELAAGYYGATNRYgtiSLASAASQAGLTWEGQAHSTIADARMAAGV 153
Cdd:cd06127    86 NASFDLRFLNRELRRLGGP---PLPNPWIDTLRLARRLLPGLRSH---RLGLLLAERYGIPLEGAHRALADALATAEL 157
 
Name Accession Description Interval E-value
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 1-153 3.81e-30

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: 107.77  E-value: 3.81e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLD-NTAEALEIGLTDAAGQVV----FETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVIIF 75
Cdd:cd06127     6 ETTGLDpKKDRIIEIGAVKVDGGIEiverFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGRVLVAH 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1710300832  76 NSRFDIRILKQTAAAHSDPadwLEEMTVYCAMELAAGYYGATNRYgtiSLASAASQAGLTWEGQAHSTIADARMAAGV 153
Cdd:cd06127    86 NASFDLRFLNRELRRLGGP---PLPNPWIDTLRLARRLLPGLRSH---RLGLLLAERYGIPLEGAHRALADALATAEL 157
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 1-162 3.94e-30

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 107.77  E-value: 3.94e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832    1 ETTGLDN-TAEALEIGLTDAAG---QVVFETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVIIFN 76
Cdd:smart00479   8 ETTGLDPgKDEIIEIAAVDVDGgeiIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGRILVAGN 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   77 S-RFDIRILKQTAAAHSDPADWLEEmtVYCAMELAAGYYGATNRYgtiSLASAASQAGLTWEGQAHSTIADARMAAGVVN 155
Cdd:smart00479  88 SaHFDLRFLKLEHPRLGIKQPPKLP--VIDTLKLARATNPGLPKY---SLKKLAKRLLLEVIQRAHRALDDARATAKLFK 162


                   ....*..
gi 1710300832  156 AIAAYHL 162
Cdd:smart00479 163 KLLERLE 169
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 1-159 1.06e-28

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 104.10  E-value: 1.06e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLD-NTAEALEIGLTDA-AGQVV--FETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVIIFN 76
Cdd:COG0847     8 ETTGLDpAKDRIIEIGAVKVdDGRIVetFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGAVLVAHN 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832  77 SRFDIRILKQTAAAHSDPADWleeMTVYCAMELAAGYYGATNRYgtiSLASAASQAGLTWEGqAHSTIADARMAAGVVNA 156
Cdd:COG0847    88 AAFDLGFLNAELRRAGLPLPP---FPVLDTLRLARRLLPGLPSY---SLDALCERLGIPFDE-RHRALADAEATAELFLA 160


                  ...
gi 1710300832 157 IAA 159
Cdd:COG0847   161 LLR 163
PRK09145 PRK09145
3'-5' exonuclease;
1-84 3.60e-10

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 56.45  E-value: 3.60e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLD-NTAEALEIGLTDAAGQVV-----FETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVII 74
Cdd:PRK09145   37 ETTGLDpRRAEIVSIAAVKIRGNRIltserLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFIGNRPLVG 116

                          90
                  ....*....|
gi 1710300832  75 FNSRFDIRIL 84
Cdd:PRK09145  117 YYLEFDVAML 126
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 1-153 2.56e-08

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: 50.81  E-value: 2.56e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLDN-TAEALEIG--LTDAAGQVV---FETRLKPTVA--IGAQAAAVHGISEQALCGAPSWTDVARQLRHAIG-DRP 71
Cdd:pfam00929   6 ETTGLDPeKDEIIEIAavVIDGGENEIgetFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFLRkGNL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832  72 VIIFNSRFDIRILKQTAAAHSdPADWLEEMTVYCAMELAAGYYgaTNRYGTiSLASAASQAGLTWEGQAHSTIADARMAA 151
Cdd:pfam00929  86 LVAHNASFDVGFLRYDDKRFL-KKPMPKLNPVIDTLILDKATY--KELPGR-SLDALAEKLGLEHIGRAHRALDDARATA 161


                  ..
gi 1710300832 152 GV 153
Cdd:pfam00929 162 KL 163
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 1-86 1.36e-07

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: 49.37  E-value: 1.36e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLDNTAEALEIGltdaAGQVV--------FETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPV 72
Cdd:TIGR00573  15 ETTGLYAGHDIIEIG----AVEIInrritgnkFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAEL 90

                          90
                  ....*....|....
gi 1710300832  73 IIFNSRFDIRILKQ 86
Cdd:TIGR00573  91 VIHNASFDVGFLNY 104
 
Name Accession Description Interval E-value
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 1-153 3.81e-30

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: 107.77  E-value: 3.81e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLD-NTAEALEIGLTDAAGQVV----FETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVIIF 75
Cdd:cd06127     6 ETTGLDpKKDRIIEIGAVKVDGGIEiverFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGRVLVAH 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1710300832  76 NSRFDIRILKQTAAAHSDPadwLEEMTVYCAMELAAGYYGATNRYgtiSLASAASQAGLTWEGQAHSTIADARMAAGV 153
Cdd:cd06127    86 NASFDLRFLNRELRRLGGP---PLPNPWIDTLRLARRLLPGLRSH---RLGLLLAERYGIPLEGAHRALADALATAEL 157
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 1-162 3.94e-30

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 107.77  E-value: 3.94e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832    1 ETTGLDN-TAEALEIGLTDAAG---QVVFETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVIIFN 76
Cdd:smart00479   8 ETTGLDPgKDEIIEIAAVDVDGgeiIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGRILVAGN 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   77 S-RFDIRILKQTAAAHSDPADWLEEmtVYCAMELAAGYYGATNRYgtiSLASAASQAGLTWEGQAHSTIADARMAAGVVN 155
Cdd:smart00479  88 SaHFDLRFLKLEHPRLGIKQPPKLP--VIDTLKLARATNPGLPKY---SLKKLAKRLLLEVIQRAHRALDDARATAKLFK 162


                   ....*..
gi 1710300832  156 AIAAYHL 162
Cdd:smart00479 163 KLLERLE 169
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 1-159 1.06e-28

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 104.10  E-value: 1.06e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLD-NTAEALEIGLTDA-AGQVV--FETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVIIFN 76
Cdd:COG0847     8 ETTGLDpAKDRIIEIGAVKVdDGRIVetFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGAVLVAHN 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832  77 SRFDIRILKQTAAAHSDPADWleeMTVYCAMELAAGYYGATNRYgtiSLASAASQAGLTWEGqAHSTIADARMAAGVVNA 156
Cdd:COG0847    88 AAFDLGFLNAELRRAGLPLPP---FPVLDTLRLARRLLPGLPSY---SLDALCERLGIPFDE-RHRALADAEATAELFLA 160


                  ...
gi 1710300832 157 IAA 159
Cdd:COG0847   161 LLR 163
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 1-168 5.90e-22

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 87.12  E-value: 5.90e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLD-NTAEALEIGltdAA----GQVV--FETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVI 73
Cdd:COG2176    16 ETTGLSpKKDEIIEIG---AVkvenGEIVdrFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLEFLGDAVLV 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832  74 IFNSRFDIRILKQTAAAHSDPADwleeMTVYCAMELAAGYYGATNRYgtiSLASAASQAGLTWEgQAHSTIADARMAAGV 153
Cdd:COG2176    93 AHNASFDLGFLNAALKRLGLPFD----NPVLDTLELARRLLPELKSY---KLDTLAERLGIPLE-DRHRALGDAEATAEL 164

                         170
                  ....*....|....*
gi 1710300832 154 VNAIaayhLELLQEQ 168
Cdd:COG2176   165 FLKL----LEKLEEK 175
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 6-157 8.63e-13

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 62.95  E-value: 8.63e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   6 DNTAEALEIGLT--DAAGQVV--FETRLKPTVaigaqaaavH-----------GISEQALCGAPSWTDVARQLRHAIGDR 70
Cdd:COG5018    21 GFPMEIIEIGAVkvDENGEIIdeFSSFVKPVR---------RpklspfcteltGITQEDVDSAPSFAEAIEDFKKWIGSE 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832  71 PVIIFN-SRFDIRILKQTAAAHSDPADWLEEM----TVYCAmelaagYYGATNRygtISLASAASQAGLTWEGQAHSTIA 145
Cdd:COG5018    92 DYILCSwGDYDRKQLERNCRFHGVPYPFGDRHinlkKLFAL------YFGLKKR---IGLKKALELLGLEFEGTHHRALD 162

                         170
                  ....*....|..
gi 1710300832 146 DARMAAGVVNAI 157
Cdd:COG5018   163 DARNTAKLFKKI 174
PRK09145 PRK09145
3'-5' exonuclease;
1-84 3.60e-10

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 56.45  E-value: 3.60e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLD-NTAEALEIGLTDAAGQVV-----FETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVII 74
Cdd:PRK09145   37 ETTGLDpRRAEIVSIAAVKIRGNRIltserLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFIGNRPLVG 116

                          90
                  ....*....|
gi 1710300832  75 FNSRFDIRIL 84
Cdd:PRK09145  117 YYLEFDVAML 126
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 41-154 8.23e-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: 54.44  E-value: 8.23e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832  41 AVHGISEQALCGAPSWTDVARQLRHAIGDRPVIIFNSRFDIRILKQTAAAHSDPADwleEMTVYCAMELAAGYYGATNRY 120
Cdd:cd06130    49 AIHGITPEDVADAPTFPEVWPEIKPFLGGSLVVAHNASFDRSVLRAALEAYGLPPP---PYQYLCTVRLARRVWPLLPNH 125

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1710300832 121 GtisLASAASQAGLTWegQAHSTIADARMAAGVV 154
Cdd:cd06130   126 K---LNTVAEHLGIEL--NHHDALEDARACAEIL 154
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 1-153 2.56e-08

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: 50.81  E-value: 2.56e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLDN-TAEALEIG--LTDAAGQVV---FETRLKPTVA--IGAQAAAVHGISEQALCGAPSWTDVARQLRHAIG-DRP 71
Cdd:pfam00929   6 ETTGLDPeKDEIIEIAavVIDGGENEIgetFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFLRkGNL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832  72 VIIFNSRFDIRILKQTAAAHSdPADWLEEMTVYCAMELAAGYYgaTNRYGTiSLASAASQAGLTWEGQAHSTIADARMAA 151
Cdd:pfam00929  86 LVAHNASFDVGFLRYDDKRFL-KKPMPKLNPVIDTLILDKATY--KELPGR-SLDALAEKLGLEHIGRAHRALDDARATA 161


                  ..
gi 1710300832 152 GV 153
Cdd:pfam00929 162 KL 163
PRK07942 PRK07942
DNA polymerase III subunit epsilon; Provisional
 1-166 3.87e-08

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 181176 [Multi-domain]  Cd Length: 232  Bit Score: 51.13  E-value: 3.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLD-NTAEALE--IGLTDAAGQVVFETRL--KPTVAIGAQAAAVHGIS-EQA-LCGAPSwTDVARQLRHAIGD---- 69
Cdd:PRK07942   14 ETTGVDpETARIVTaaLVVVDADGEVVESREWlaDPGVEIPEEASAVHGITtEYArAHGRPA-AEVLAEIADALREawar 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832  70 -RPVIIFNSRFDIRILKQTAAAHSDPAdwLEEMTVYCAMELAAgyygATNRY--GTISLASAASQAGLTWEGqAHSTIAD 146
Cdd:PRK07942   93 gVPVVVFNAPYDLTVLDRELRRHGLPS--LVPGPVIDPYVIDK----AVDRYrkGKRTLTALCEHYGVRLDN-AHEATAD 165

                         170       180
                  ....*....|....*....|
gi 1710300832 147 ARMAAGVVNAIAAYHLELLQ 166
Cdd:PRK07942  166 ALAAARVAWALARRFPELAA 185
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 1-110 4.39e-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: 49.84  E-value: 4.39e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLDNTA--EALEIG--------LTDAagqvVFETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDR 70
Cdd:cd06131     7 ETTGLDPREghRIIEIGcvelinrrLTGN----TFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIRGA 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1710300832  71 PVIIFNSRFDIRILKQTAAAHSDPADWLEEMTVYCAMELA 110
Cdd:cd06131    83 ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALA 122
PRK06722 PRK06722
exonuclease; Provisional
 5-154 5.97e-08

exonuclease; Provisional


Pssm-ID: 180670 [Multi-domain]  Cd Length: 281  Bit Score: 50.82  E-value: 5.97e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   5 LDNTAEALEIGLTDAAGQvvFETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVIIFNSRFDIRIL 84
Cdd:PRK06722   28 VDIGAVKIEASTMKVIGE--FSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQIIEKFIQFIGEDSIFVTWGKEDYRFL 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832  85 KQTAAAHSDPADWLEEMTVYCAMELAAGYYGATNRYgTISLASAASQAGLTWEGQAHSTIADARMAAGVV 154
Cdd:PRK06722  106 SHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEH-TPSLQSAVEQLGLIWEGKQHRALADAENTANIL 174
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 1-86 1.36e-07

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: 49.37  E-value: 1.36e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLDNTAEALEIGltdaAGQVV--------FETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPV 72
Cdd:TIGR00573  15 ETTGLYAGHDIIEIG----AVEIInrritgnkFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAEL 90

                          90
                  ....*....|....
gi 1710300832  73 IIFNSRFDIRILKQ 86
Cdd:TIGR00573  91 VIHNASFDVGFLNY 104
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 1-81 1.95e-06

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 46.01  E-value: 1.95e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLDNTAE--ALEIGLTDAAGQVV----FETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVII 74
Cdd:PRK05711   12 ETTGLNQREGhrIIEIGAVELINRRLtgrnFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDFIRGAELII 91


                  ....*..
gi 1710300832  75 FNSRFDI 81
Cdd:PRK05711   92 HNAPFDI 98
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 42-158 3.35e-06

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 45.93  E-value: 3.35e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832  42 VHGISEQALCGAPSWTDVARQLRHAIGDRPVIIFNSRFDIRILKQTAAAHSDPadwLEEMTVYCAMELAAGYYGATNRYG 121
Cdd:PRK06195   53 IHGIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDISVLRKTLELYNIP---MPSFEYICTMKLAKNFYSNIDNAR 129

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1710300832 122 TISLASAasqagLTWEGQAHSTIADARMAAGVVNAIA 158
Cdd:PRK06195  130 LNTVNNF-----LGYEFKHHDALADAMACSNILLNIS 161
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 1-149 7.10e-06

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 44.82  E-value: 7.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLDNTAE-ALEIGLTDAAGQVV---FETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVIIFN 76
Cdd:PRK06310   15 ETTGLDVKKDrIIEFAAIRFTFDEVidsVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFKEGDYIVGH 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1710300832  77 S-RFDIRILKQTAAAHSDPADwLEEMTVYCAMELAAGYYGATNRygtiSLASAASQAGLTWEGqAHSTIADARM 149
Cdd:PRK06310   95 SvGFDLQVLSQESERIGETFL-SKHYYIIDTLRLAKEYGDSPNN----SLEALAVHFNVPYDG-NHRAMKDVEI 162
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 1-171 1.32e-05

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


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 44.29  E-value: 1.32e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLDNTAEALEIGLTD-AAGQVV--FETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVIIFNS 77
Cdd:PRK07246   15 EATGAGPNASIIQVGIVIiEGGEIIdsYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDCIFVAHNV 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832  78 RFDIRILKQtaaahsdpADWLE--EM------TVycamELAAGYYGATNRYgtiSLASAASQAGLTWEgQAHSTIADARm 149
Cdd:PRK07246   95 KFDANLLAE--------ALFLEgyELrtprvdTV----ELAQVFFPTLEKY---SLSHLSRELNIDLA-DAHTAIADAR- 157

                         170       180
                  ....*....|....*....|..
gi 1710300832 150 aagvvnAIAAYHLELLQEQARL 171
Cdd:PRK07246  158 ------ATAELFLKLLQKIESL 173
PRK07983 PRK07983
exodeoxyribonuclease X; Provisional
 1-110 2.86e-05

exodeoxyribonuclease X; Provisional


Pssm-ID: 181186 [Multi-domain]  Cd Length: 219  Bit Score: 42.78  E-value: 2.86e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLDNTAeaLEIGLTDA-AGQVV--FETRLKPTVAIGAQAAAVHGISEQALCGAPsWTDVArqLRHAIGDRPVIIFNS 77
Cdd:PRK07983    8 ETCGLQGGI--VEIASVDViDGKIVnpMSHLVRPDRPISPQAMAIHRITEAMVADKP-WIEDV--IPHYYGSEWYVAHNA 82

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1710300832  78 RFDIRILKQTaaahsdPADWLeemtvyCAMELA 110
Cdd:PRK07983   83 SFDRRVLPEM------PGEWI------CTMKLA 103
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 44-154 4.12e-05

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: 41.82  E-value: 4.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832  44 GISEQALCGAPSWTDVARQLRHAIGDRPVIIF--NSRFDIRILKQTAAAHS--DPADWLEEMtvycaMELAAGYYGATNR 119
Cdd:cd06133    63 GITQEDVDNAPSFPEVLKEFLEWLGKNGKYAFvtWGDWDLKDLLQNQCKYKiiNLPPFFRQW-----IDLKKEFAKFYGL 137

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1710300832 120 YGTISLASAASQAGLTWEGQAHSTIADARMAAGVV 154
Cdd:cd06133   138 KKRTGLSKALEYLGLEFEGRHHRGLDDARNIARIL 172
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 1-92 4.73e-05

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 42.10  E-value: 4.73e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLD-NTAEALEIGLTDAAGQVVFETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVIIF--NS 77
Cdd:PRK06309   10 ETTGTQiDKDRIIEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTDNILVAhnND 89

                          90
                  ....*....|....*
gi 1710300832  78 RFDIRILKQTAAAHS 92
Cdd:PRK06309   90 AFDFPLLRKECRRHG 104
polC PRK00448
DNA polymerase III PolC; Validated
 1-86 1.49e-04

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 41.36  E-value: 1.49e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832    1 ETTGLDNT-AEALEIGltdaA-----GQVV--FETRLKPTVAIGAQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPV 72
Cdd:PRK00448   427 ETTGLSAVyDEIIEIG----AvkiknGEIIdkFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGDSIL 502

                           90
                   ....*....|....
gi 1710300832   73 IIFNSRFDIRILKQ 86
Cdd:PRK00448   503 VAHNASFDVGFINT 516
PRK06063 PRK06063
DEDDh family exonuclease;
1-157 1.53e-04

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 40.84  E-value: 1.53e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832   1 ETTGLDNTAE---ALEIGLTDAAGQVV--FETRLKPTVAIGAqaAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVIIF 75
Cdd:PRK06063   23 ETSGFRPGQAriiSLAVLGLDADGNVEqsVVTLLNPGVDPGP--THVHGLTAEMLEGQPQFADIAGEVAELLRGRTLVAH 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710300832  76 NSRFDIRILKQTAA-AHSD-PADWleemtVYCAMELAagyygatNRYG----TISLASAASQAGLTWEgQAHSTIADARM 149
Cdd:PRK06063  101 NVAFDYSFLAAEAErAGAElPVDQ-----VMCTVELA-------RRLGlglpNLRLETLAAHWGVPQQ-RPHDALDDARV 167


                  ....*...
gi 1710300832 150 AAGVVNAI 157
Cdd:PRK06063  168 LAGILRPS 175
 
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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