NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1566446414|gb|QAZ79859|]
View 

3'-5' exonuclease (plasmid) [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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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) ...
 107-253 2.67e-32

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: 116.63  E-value: 2.67e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 107 LVLDTETTGLG-ERDQVIELAVTDIRG----AVLLCTRLRPTVEIDPQAMGVHGITETELSNEPTWTQVAPALARLLSGR 181
Cdd:cd06127     1 VVFDTETTGLDpKKDRIIEIGAVKVDGgieiVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1566446414 182 HLVIFNSSFDSRMLRQtasAFGDQLSWWQEQNCLCAMKLAADAFGSTNRHgtiSLADATCEAGVSWKGRAHS 253
Cdd:cd06127    81 VLVAHNASFDLRFLNR---ELRRLGGPPLPNPWIDTLRLARRLLPGLRSH---RLGLLLAERYGIPLEGAHR 146
 
Name Accession Description Interval E-value
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 107-253 2.67e-32

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: 116.63  E-value: 2.67e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 107 LVLDTETTGLG-ERDQVIELAVTDIRG----AVLLCTRLRPTVEIDPQAMGVHGITETELSNEPTWTQVAPALARLLSGR 181
Cdd:cd06127     1 VVFDTETTGLDpKKDRIIEIGAVKVDGgieiVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1566446414 182 HLVIFNSSFDSRMLRQtasAFGDQLSWWQEQNCLCAMKLAADAFGSTNRHgtiSLADATCEAGVSWKGRAHS 253
Cdd:cd06127    81 VLVAHNASFDLRFLNR---ELRRLGGPPLPNPWIDTLRLARRLLPGLRSH---RLGLLLAERYGIPLEGAHR 146
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 107-253 1.54e-30

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 112.19  E-value: 1.54e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 107 LVLDTETTGLG-ERDQVIELAVTDIRGAVL---LCTRLRPTVEIDPQAMGVHGITETELSNEPTWTQVAPALARLLSGRH 182
Cdd:COG0847     3 VVLDTETTGLDpAKDRIIEIGAVKVDDGRIvetFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGAV 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1566446414 183 LVIFNSSFDSRMLRQTASAFGDQLSWWQeqnCLCAMKLAADAFGSTNRHgtiSLADAtCEA-GVSWKGRaHS 253
Cdd:COG0847    83 LVAHNAAFDLGFLNAELRRAGLPLPPFP---VLDTLRLARRLLPGLPSY---SLDAL-CERlGIPFDER-HR 146
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 105-253 2.43e-24

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 96.22  E-value: 2.43e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414  105 EPLVLDTETTGLG-ERDQVIELAVTDIRG---AVLLCTRLRPTVEIDPQAMGVHGITETELSNEPTWTQVAPALARLLSG 180
Cdd:smart00479   1 TLVVIDCETTGLDpGKDEIIEIAAVDVDGgeiIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1566446414  181 RHLVIFNS-SFDSRMLRQTASAFGdqLSWWQEQNCLCAMKLAADAFGSTNRHgtiSLADATCEAGVSWKGRAHS 253
Cdd:smart00479  81 RILVAGNSaHFDLRFLKLEHPRLG--IKQPPKLPVIDTLKLARATNPGLPKY---SLKKLAKRLLLEVIQRAHR 149
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 108-191 3.40e-13

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 67.58  E-value: 3.40e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 108 VLDTETTGLGER--DQVIELavtdirGAVLLCTR----------LRPTVEIDPQAMGVHGITETELSNEPTWTQVAPALA 175
Cdd:PRK05711    8 VLDTETTGLNQRegHRIIEI------GAVELINRrltgrnfhvyIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFL 81

                          90
                  ....*....|....*.
gi 1566446414 176 RLLSGRHLVIFNSSFD 191
Cdd:PRK05711   82 DFIRGAELIIHNAPFD 97
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 107-191 8.76e-12

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: 63.24  E-value: 8.76e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 107 LVLDTETTGLGERDQVIE-LAVTDIRGAVLLC---TRLRPTVEIDPQAMGVHGITETELSNEPTWTQVAPALARLLSGRH 182
Cdd:TIGR00573  10 TTGDNETTGLYAGHDIIEiGAVEIINRRITGNkfhTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAE 89


                  ....*....
gi 1566446414 183 LVIFNSSFD 191
Cdd:TIGR00573  90 LVIHNASFD 98
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 107-203 4.85e-09

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: 54.28  E-value: 4.85e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 107 LVLDTETTGLG-ERDQVIELAVTDIRGAVLLC-----TRLRPTV--EIDPQAMGVHGITETELSNEPTWTQVAPALARLL 178
Cdd:pfam00929   1 VVIDLETTGLDpEKDEIIEIAAVVIDGGENEIgetfhTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100
                  ....*....|....*....|....*.
gi 1566446414 179 -SGRHLVIFNSSFDSRMLRQTASAFG 203
Cdd:pfam00929  81 rKGNLLVAHNASFDVGFLRYDDKRFL 106
 
Name Accession Description Interval E-value
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 107-253 2.67e-32

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: 116.63  E-value: 2.67e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 107 LVLDTETTGLG-ERDQVIELAVTDIRG----AVLLCTRLRPTVEIDPQAMGVHGITETELSNEPTWTQVAPALARLLSGR 181
Cdd:cd06127     1 VVFDTETTGLDpKKDRIIEIGAVKVDGgieiVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1566446414 182 HLVIFNSSFDSRMLRQtasAFGDQLSWWQEQNCLCAMKLAADAFGSTNRHgtiSLADATCEAGVSWKGRAHS 253
Cdd:cd06127    81 VLVAHNASFDLRFLNR---ELRRLGGPPLPNPWIDTLRLARRLLPGLRSH---RLGLLLAERYGIPLEGAHR 146
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 107-253 1.54e-30

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 112.19  E-value: 1.54e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 107 LVLDTETTGLG-ERDQVIELAVTDIRGAVL---LCTRLRPTVEIDPQAMGVHGITETELSNEPTWTQVAPALARLLSGRH 182
Cdd:COG0847     3 VVLDTETTGLDpAKDRIIEIGAVKVDDGRIvetFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGAV 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1566446414 183 LVIFNSSFDSRMLRQTASAFGDQLSWWQeqnCLCAMKLAADAFGSTNRHgtiSLADAtCEA-GVSWKGRaHS 253
Cdd:COG0847    83 LVAHNAAFDLGFLNAELRRAGLPLPPFP---VLDTLRLARRLLPGLPSY---SLDAL-CERlGIPFDER-HR 146
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 105-253 2.43e-24

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 96.22  E-value: 2.43e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414  105 EPLVLDTETTGLG-ERDQVIELAVTDIRG---AVLLCTRLRPTVEIDPQAMGVHGITETELSNEPTWTQVAPALARLLSG 180
Cdd:smart00479   1 TLVVIDCETTGLDpGKDEIIEIAAVDVDGgeiIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1566446414  181 RHLVIFNS-SFDSRMLRQTASAFGdqLSWWQEQNCLCAMKLAADAFGSTNRHgtiSLADATCEAGVSWKGRAHS 253
Cdd:smart00479  81 RILVAGNSaHFDLRFLKLEHPRLG--IKQPPKLPVIDTLKLARATNPGLPKY---SLKKLAKRLLLEVIQRAHR 149
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 97-250 6.04e-22

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 90.20  E-value: 6.04e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414  97 MAQRWVALEPLVLDTETTGL-GERDQVIELAVTDIRGAVLL---CTRLRPTVEIDPQAMGVHGITETELSNEPTWTQVAP 172
Cdd:COG2176     1 MSLDLEDLTYVVFDLETTGLsPKKDEIIEIGAVKVENGEIVdrfSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLP 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1566446414 173 ALARLLSGRHLVIFNSSFDSRMLRQTASAFGDQLswwqEQNCLCAMKLAADAFGSTNRHgtiSLADATCEAGVSWKGR 250
Cdd:COG2176    81 EFLEFLGDAVLVAHNASFDLGFLNAALKRLGLPF----DNPVLDTLELARRLLPELKSY---KLDTLAERLGIPLEDR 151
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 107-241 2.32e-14

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: 69.48  E-value: 2.32e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 107 LVLDTETTGLGER--DQVIELavtdirGAVLLCTR----------LRPTVEIDPQAMGVHGITETELSNEPTWTQVAPAL 174
Cdd:cd06131     2 IVLDTETTGLDPRegHRIIEI------GCVELINRrltgntfhvyINPERDIPEEAFKVHGITDEFLADKPKFAEIADEF 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1566446414 175 ARLLSGRHLVIFNSSFDSRMLRQTASAFGDQLSWWQEQNCLCAMKLAADAF-GSTNrhgtiSLaDATC 241
Cdd:cd06131    76 LDFIRGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFpGKPN-----SL-DALC 137
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 108-191 3.40e-13

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 67.58  E-value: 3.40e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 108 VLDTETTGLGER--DQVIELavtdirGAVLLCTR----------LRPTVEIDPQAMGVHGITETELSNEPTWTQVAPALA 175
Cdd:PRK05711    8 VLDTETTGLNQRegHRIIEI------GAVELINRrltgrnfhvyIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFL 81

                          90
                  ....*....|....*.
gi 1566446414 176 RLLSGRHLVIFNSSFD 191
Cdd:PRK05711   82 DFIRGAELIIHNAPFD 97
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 107-191 8.76e-12

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: 63.24  E-value: 8.76e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 107 LVLDTETTGLGERDQVIE-LAVTDIRGAVLLC---TRLRPTVEIDPQAMGVHGITETELSNEPTWTQVAPALARLLSGRH 182
Cdd:TIGR00573  10 TTGDNETTGLYAGHDIIEiGAVEIINRRITGNkfhTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAE 89


                  ....*....
gi 1566446414 183 LVIFNSSFD 191
Cdd:TIGR00573  90 LVIHNASFD 98
PRK06063 PRK06063
DEDDh family exonuclease;
96-221 1.18e-11

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 63.95  E-value: 1.18e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414  96 VMAQRWV--ALEP----LVLDTETTGLG-ERDQVIELAV--TDIRGAVL--LCTRLRPtvEIDPQAMGVHGITETELSNE 164
Cdd:PRK06063    1 MMSHTWGrpASHYprgwAVVDVETSGFRpGQARIISLAVlgLDADGNVEqsVVTLLNP--GVDPGPTHVHGLTAEMLEGQ 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1566446414 165 PTWTQVAPALARLLSGRHLVIFNSSFDSRMLRQTASAFGDQLSWWQEqncLCAMKLA 221
Cdd:PRK06063   79 PQFADIAGEVAELLRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQV---MCTVELA 132
PRK07983 PRK07983
exodeoxyribonuclease X; Provisional
 108-221 3.09e-11

exodeoxyribonuclease X; Provisional


Pssm-ID: 181186 [Multi-domain]  Cd Length: 219  Bit Score: 61.66  E-value: 3.09e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 108 VLDTETTGLgeRDQVIELAVTD-IRGAVL--LCTRLRPTVEIDPQAMGVHGITETELSNEPTWTQVAPalaRLLSGRHLV 184
Cdd:PRK07983    4 VIDTETCGL--QGGIVEIASVDvIDGKIVnpMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIP---HYYGSEWYV 78

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1566446414 185 IFNSSFDSRMLRQTASAfgdqlsWwqeqncLCAMKLA 221
Cdd:PRK07983   79 AHNASFDRRVLPEMPGE------W------ICTMKLA 103
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 108-203 5.37e-11

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: 59.83  E-value: 5.37e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 108 VLDTETTGlGERDQVIELAVTDIRGAVL---LCTRLRPTVEIDPQAMGVHGITETELSNEPTWTQVAPALARLLSGRHLV 184
Cdd:cd06130     3 AIDFETAN-ADRASACSIGLVKVRDGQIvdtFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGSLVV 81

                          90
                  ....*....|....*....
gi 1566446414 185 IFNSSFDSRMLRQTASAFG 203
Cdd:cd06130    82 AHNASFDRSVLRAALEAYG 100
PRK09145 PRK09145
3'-5' exonuclease;
101-195 9.48e-10

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 57.22  E-value: 9.48e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 101 WVALeplvlDTETTGLG-ERDQVIELAVTDIRGAVLLCT-----RLRPTVEIDPQAMGVHGITETELSNEPTWTQVAPAL 174
Cdd:PRK09145   31 WVAL-----DCETTGLDpRRAEIVSIAAVKIRGNRILTSerlelLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQL 105

                          90       100
                  ....*....|....*....|.
gi 1566446414 175 ARLLSGRHLVIFNSSFDSRML 195
Cdd:PRK09145  106 LAFIGNRPLVGYYLEFDVAML 126
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 107-203 4.85e-09

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: 54.28  E-value: 4.85e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 107 LVLDTETTGLG-ERDQVIELAVTDIRGAVLLC-----TRLRPTV--EIDPQAMGVHGITETELSNEPTWTQVAPALARLL 178
Cdd:pfam00929   1 VVIDLETTGLDpEKDEIIEIAAVVIDGGENEIgetfhTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100
                  ....*....|....*....|....*.
gi 1566446414 179 -SGRHLVIFNSSFDSRMLRQTASAFG 203
Cdd:pfam00929  81 rKGNLLVAHNASFDVGFLRYDDKRFL 106
dnaQ_proteo TIGR01406
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ...
 107-250 4.95e-09

DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 130473 [Multi-domain]  Cd Length: 225  Bit Score: 55.48  E-value: 4.95e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 107 LVLDTETTGLG--ERDQVIELavtdirGAVLLCTR----------LRPTVEIDPQAMGVHGITETELSNEPTWTQVAPAL 174
Cdd:TIGR01406   3 IILDTETTGLDpkGGHRIVEI------GAVELVNRmltgdnfhvyVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEF 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1566446414 175 ARLLSGRHLVIFNSSFDSRMLRQTASAFGDQLSWWQE-QNCLCAMKLAADAF-GSTNrhgtiSLaDATCEA-GVSWKGR 250
Cdd:TIGR01406  77 LDFIGGSELVIHNAAFDVGFLNYELERLGPTIKKIGEfCRVIDTLAMARERFpGQRN-----SL-DALCKRfKVDNSHR 149
PRK06807 PRK06807
3'-5' exonuclease;
97-203 1.11e-07

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 52.12  E-value: 1.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414  97 MAQRWVALEPLVLDTETTGLGE-RDQVIELAVTDIRGAVLL---CTRLRPTVEIDPQAMGVHGITETELSNEPTWTQVAP 172
Cdd:PRK06807    1 MGNISLPLDYVVIDFETTGFNPyNDKIIQVAAVKYRNHELVdqfVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLP 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1566446414 173 ALARLLSGRHLVIFNSSFDSRMLRQTASAFG 203
Cdd:PRK06807   81 LFLAFLHTNVIVAHNASFDMRFLKSNVNMLG 111
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 97-191 3.55e-07

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 51.49  E-value: 3.55e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414  97 MAQRWValeplVLDTETTGLGER--DQVIELAVTDIRGAVLL---CTRLRPTVEIDPQAMGVHGITETELSNEPTWTQVA 171
Cdd:PRK08074    1 MSKRFV-----VVDLETTGNSPKkgDKIIQIAAVVVEDGEILerfSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVA 75

                          90       100
                  ....*....|....*....|
gi 1566446414 172 PALARLLSGRHLVIFNSSFD 191
Cdd:PRK08074   76 PEIVELLEGAYFVAHNVHFD 95
PRK07942 PRK07942
DNA polymerase III subunit epsilon; Provisional
 107-203 1.94e-06

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 181176 [Multi-domain]  Cd Length: 232  Bit Score: 47.66  E-value: 1.94e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 107 LVLDTETTGLGERDQVI---ELAVTDIRGAVLLCTRL--RPTVEIDPQAMGVHGITeTELSNE------PTWTQVAPALA 175
Cdd:PRK07942    9 AAFDLETTGVDPETARIvtaALVVVDADGEVVESREWlaDPGVEIPEEASAVHGIT-TEYARAhgrpaaEVLAEIADALR 87

                          90       100
                  ....*....|....*....|....*....
gi 1566446414 176 RLL-SGRHLVIFNSSFDSRMLRQTASAFG 203
Cdd:PRK07942   88 EAWaRGVPVVVFNAPYDLTVLDRELRRHG 116
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
108-221 2.69e-06

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 48.38  E-value: 2.69e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 108 VLDTETTGLG-ERDQVIELAVTDIR-GAVL--LCTRLRPTVEIDPQAMGVHGITETELSNEPTWTQVAPALARLLSGRHL 183
Cdd:PRK07883   19 VVDLETTGGSpAGDAITEIGAVKVRgGEVLgeFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEFARGAVL 98

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1566446414 184 VIFNSSFDSRMLRQTASAFGDQlswWQEQNCLCAMKLA 221
Cdd:PRK07883   99 VAHNAPFDIGFLRAAAARCGYP---WPGPPVLCTVRLA 133
ExoI_N cd06138
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar ...
 110-198 2.03e-05

N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease 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. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.


Pssm-ID: 99841 [Multi-domain]  Cd Length: 183  Bit Score: 44.18  E-value: 2.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 110 DTETTGLG-ERDQVIELA--VTD-----IRGAVLLCtRLRPTVEIDPQAMGVHGIT----ETELSNEPTWTQvapALARL 177
Cdd:cd06138     4 DYETFGLNpSFDQILQFAaiRTDenfneIEPFNIFC-RLPPDVLPSPEALIVTGITpqqlLKEGLSEYEFIA---KIHRL 79

                          90       100
                  ....*....|....*....|....
gi 1566446414 178 LSGRHLVI--FNS-SFDSRMLRQT 198
Cdd:cd06138    80 FNTPGTCIvgYNNiRFDDEFLRFA 103
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 148-239 2.41e-04

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 42.07  E-value: 2.41e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 148 PQAMGVHGITETELSNEPTWTQVAPALARLLSGRHLVIFNSSFDSRMLRQTASAFGDQLSwwqEQNCLCAMKLAADAFGS 227
Cdd:PRK06195   48 PINIGIHGIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDISVLRKTLELYNIPMP---SFEYICTMKLAKNFYSN 124

                          90
                  ....*....|..
gi 1566446414 228 TNRHGTISLADA 239
Cdd:PRK06195  125 IDNARLNTVNNF 136
polC PRK00448
DNA polymerase III PolC; Validated
 108-197 1.22e-03

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 40.21  E-value: 1.22e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414  108 VLDTETTGLGER-DQVIELAVTDIR-GAVL--LCTRLRPTVEIDPQAMGVHGITETELSNEPTWTQVAPALARLLSGRHL 183
Cdd:PRK00448   423 VFDVETTGLSAVyDEIIEIGAVKIKnGEIIdkFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGDSIL 502

                           90
                   ....*....|....
gi 1566446414  184 VIFNSSFDSRMLRQ 197
Cdd:PRK00448   503 VAHNASFDVGFINT 516
PRK09182 PRK09182
DNA polymerase III subunit epsilon; Validated
 107-228 6.91e-03

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236397 [Multi-domain]  Cd Length: 294  Bit Score: 37.26  E-value: 6.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1566446414 107 LVLDTETTGLGER-DQVIELAVT----DIRGAVLLCT----RLR-PTVEIDPQAMGVHGITetelsNEPTWTQVAP--AL 174
Cdd:PRK09182   40 VILDTETTGLDPRkDEIIEIGMVafeyDDDGRIGDVLdtfgGLQqPSRPIPPEITRLTGIT-----DEMVAGQTIDpaAV 114

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1566446414 175 ARLLSGRHLVI-FNSSFDSRMLRQTASAFGDQlsWWQeqnclCAMK---LAADAFGST 228
Cdd:PRK09182  115 DALIAPADLIIaHNAGFDRPFLERFSPVFATK--PWA-----CSVSeidWSARGFEGT 165
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH