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Conserved domains on  [gi|1579911806|ref|WP_130536467|]
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3'-5' exonuclease [Thiomicrorhabdus indica]

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
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 150-324 4.37e-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: 112.96  E-value: 4.37e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 150 NIVCIDIEATNISTDPDAdIIQLSAC---DGEGKELFNQLINPGYDIPEN--DKHNITTEMVQDAPLLAKAWDEIHDTLR 224
Cdd:COG0847     1 RFVVLDTETTGLDPAKDR-IIEIGAVkvdDGRIVETFHTLVNPERPIPPEatAIHGITDEDVADAPPFAEVLPELLEFLG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 225 DADVVlAYSTESDFMYLEKSAEKkmLRFELDYNTWLDAAELSKDLIGAIRWHSermywfyktpkLTDAyAKVLDKPFpGD 304
Cdd:COG0847    80 GAVLV-AHNAAFDLGFLNAELRR--AGLPLPPFPVLDTLRLARRLLPGLPSYS-----------LDAL-CERLGIPF-DE 143

                         170       180
                  ....*....|....*....|
gi 1579911806 305 AHDALADAQATVELFNAMLK 324
Cdd:COG0847   144 RHRALADAEATAELFLALLR 163
 
Name Accession Description Interval E-value
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 150-324 4.37e-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: 112.96  E-value: 4.37e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 150 NIVCIDIEATNISTDPDAdIIQLSAC---DGEGKELFNQLINPGYDIPEN--DKHNITTEMVQDAPLLAKAWDEIHDTLR 224
Cdd:COG0847     1 RFVVLDTETTGLDPAKDR-IIEIGAVkvdDGRIVETFHTLVNPERPIPPEatAIHGITDEDVADAPPFAEVLPELLEFLG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 225 DADVVlAYSTESDFMYLEKSAEKkmLRFELDYNTWLDAAELSKDLIGAIRWHSermywfyktpkLTDAyAKVLDKPFpGD 304
Cdd:COG0847    80 GAVLV-AHNAAFDLGFLNAELRR--AGLPLPPFPVLDTLRLARRLLPGLPSYS-----------LDAL-CERLGIPF-DE 143

                         170       180
                  ....*....|....*....|
gi 1579911806 305 AHDALADAQATVELFNAMLK 324
Cdd:COG0847   144 RHRALADAEATAELFLALLR 163
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 152-320 3.54e-27

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: 105.08  E-value: 3.54e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 152 VCIDIEATNISTDPDaDIIQLSAC----DGEGKELFNQLINPGYDIPENDK--HNITTEMVQDAPLLAKAWDEIHDTLRD 225
Cdd:cd06127     1 VVFDTETTGLDPKKD-RIIEIGAVkvdgGIEIVERFETLVNPGRPIPPEATaiHGITDEMLADAPPFEEVLPEFLEFLGG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 226 aDVVLAYSTESDFMYLEKSAEKkmLRFELDYNTWLDAAELSKDLIGAIRWHsermywfyktpKLTDAYAKVLDKPFpGDA 305
Cdd:cd06127    80 -RVLVAHNASFDLRFLNRELRR--LGGPPLPNPWIDTLRLARRLLPGLRSH-----------RLGLLLAERYGIPL-EGA 144

                         170
                  ....*....|....*
gi 1579911806 306 HDALADAQATVELFN 320
Cdd:cd06127   145 HRALADALATAELLL 159
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 151-327 7.91e-22

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 90.82  E-value: 7.91e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806  151 IVCIDIEATniSTDPD-ADIIQLSA---CDGEGKELFNQLINPGYDIPE--NDKHNITTEMVQDAPLLAKAWDEIHDTLR 224
Cdd:smart00479   2 LVVIDCETT--GLDPGkDEIIEIAAvdvDGGEIIEVFDTYVKPDRPITDyaTEIHGITPEMLDDAPTFEEVLEELLEFLR 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806  225 DADVVLAYSTESDFMYLEKSAEKKMLRFELDyNTWLDAAELSKDLIGAIRWHSermywfyktpkLTDAyAKVLDKPFPGD 304
Cdd:smart00479  80 GRILVAGNSAHFDLRFLKLEHPRLGIKQPPK-LPVIDTLKLARATNPGLPKYS-----------LKKL-AKRLLLEVIQR 146

                          170       180
                   ....*....|....*....|...
gi 1579911806  305 AHDALADAQATVELFNAMLKRGE 327
Cdd:smart00479 147 AHRALDDARATAKLFKKLLERLE 169
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 146-325 3.47e-11

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 62.54  E-value: 3.47e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 146 LKGKNIVCIDIEATNIstDPDAD-IIQLSACDGEGKELFNQ---LINPGYDIPENDK--HNITTEMVQDAPLLAKAWDEI 219
Cdd:PRK06310    4 LKDTEFVCLDCETTGL--DVKKDrIIEFAAIRFTFDEVIDSvefLINPERVVSAESQriHHISDAMLRDKPKIAEVFPQI 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 220 HDTLRDADVVLAYSTESDFMYLEKSAEKKMLRFELDYNTWLDAAELSKDligairwhsermywFYKTPKLT-DAYAKVLD 298
Cdd:PRK06310   82 KGFFKEGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKE--------------YGDSPNNSlEALAVHFN 147

                         170       180
                  ....*....|....*....|....*..
gi 1579911806 299 KPFPGdAHDALADAQATVELFNAMLKR 325
Cdd:PRK06310  148 VPYDG-NHRAMKDVEINIKVFKHLCKR 173
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 152-319 1.70e-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: 56.21  E-value: 1.70e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 152 VCIDIEATNISTDPDAdIIQLSA--CDG---EGKELFNQLINPGYDIPENDK----HNITTEMVQDAPLLAKAWDEIHDT 222
Cdd:pfam00929   1 VVIDLETTGLDPEKDE-IIEIAAvvIDGgenEIGETFHTYVKPTRLPKLTDEctkfTGITQAMLDNKPSFEEVLEEFLEF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 223 LRDADVVLAYSTESDFMYLEKSAEKKMLRFELDYNTWLDAAELSKDLIGAIRWHSermywfyktpklTDAYAKVLDKPFP 302
Cdd:pfam00929  80 LRKGNLLVAHNASFDVGFLRYDDKRFLKKPMPKLNPVIDTLILDKATYKELPGRS------------LDALAEKLGLEHI 147

                         170
                  ....*....|....*..
gi 1579911806 303 GDAHDALADAQATVELF 319
Cdd:pfam00929 148 GRAHRALDDARATAKLF 164
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 199-328 4.94e-03

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: 37.81  E-value: 4.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 199 HNITTEMVQDAPLLAKAWDEIHDTLRDaDVVLAYSTESDFMYLeKSAEKKMLRFELDYNTWLDAAELSKDLIGAIRWHSE 278
Cdd:TIGR00573  61 HGITDDMLKDKPDFKEIAEDFADYIRG-AELVIHNASFDVGFL-NYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRN 138

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1579911806 279 RMYWFYKTPKLTDAYAKvldkpfpgdAHDALADAQATVELFNAMLKRGEQ 328
Cdd:TIGR00573 139 TLDALCKRYEITNSHRA---------LHGALADAFILAKLYLVMTGKQTK 179
 
Name Accession Description Interval E-value
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 150-324 4.37e-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: 112.96  E-value: 4.37e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 150 NIVCIDIEATNISTDPDAdIIQLSAC---DGEGKELFNQLINPGYDIPEN--DKHNITTEMVQDAPLLAKAWDEIHDTLR 224
Cdd:COG0847     1 RFVVLDTETTGLDPAKDR-IIEIGAVkvdDGRIVETFHTLVNPERPIPPEatAIHGITDEDVADAPPFAEVLPELLEFLG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 225 DADVVlAYSTESDFMYLEKSAEKkmLRFELDYNTWLDAAELSKDLIGAIRWHSermywfyktpkLTDAyAKVLDKPFpGD 304
Cdd:COG0847    80 GAVLV-AHNAAFDLGFLNAELRR--AGLPLPPFPVLDTLRLARRLLPGLPSYS-----------LDAL-CERLGIPF-DE 143

                         170       180
                  ....*....|....*....|
gi 1579911806 305 AHDALADAQATVELFNAMLK 324
Cdd:COG0847   144 RHRALADAEATAELFLALLR 163
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 152-320 3.54e-27

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: 105.08  E-value: 3.54e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 152 VCIDIEATNISTDPDaDIIQLSAC----DGEGKELFNQLINPGYDIPENDK--HNITTEMVQDAPLLAKAWDEIHDTLRD 225
Cdd:cd06127     1 VVFDTETTGLDPKKD-RIIEIGAVkvdgGIEIVERFETLVNPGRPIPPEATaiHGITDEMLADAPPFEEVLPEFLEFLGG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 226 aDVVLAYSTESDFMYLEKSAEKkmLRFELDYNTWLDAAELSKDLIGAIRWHsermywfyktpKLTDAYAKVLDKPFpGDA 305
Cdd:cd06127    80 -RVLVAHNASFDLRFLNRELRR--LGGPPLPNPWIDTLRLARRLLPGLRSH-----------RLGLLLAERYGIPL-EGA 144

                         170
                  ....*....|....*
gi 1579911806 306 HDALADAQATVELFN 320
Cdd:cd06127   145 HRALADALATAELLL 159
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 145-325 6.26e-25

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 99.45  E-value: 6.26e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 145 NLKGKNIVCIDIEATNISTDPDaDIIQLSAC---DGEGKELFNQLINPGYDIPEN--DKHNITTEMVQDAPLLAKAWDEI 219
Cdd:COG2176     4 DLEDLTYVVFDLETTGLSPKKD-EIIEIGAVkveNGEIVDRFSTLVNPGRPIPPFitELTGITDEMVADAPPFEEVLPEF 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 220 HDTLRDAdVVLAYSTESDFMYLEKSAEKKMLRFEldyNTWLDAAELSKDLIGairwhsermywFYKTPKLtDAYAKVLDK 299
Cdd:COG2176    83 LEFLGDA-VLVAHNASFDLGFLNAALKRLGLPFD---NPVLDTLELARRLLP-----------ELKSYKL-DTLAERLGI 146

                         170       180
                  ....*....|....*....|....*.
gi 1579911806 300 PFpGDAHDALADAQATVELFNAMLKR 325
Cdd:COG2176   147 PL-EDRHRALGDAEATAELFLKLLEK 171
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 151-327 7.91e-22

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 90.82  E-value: 7.91e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806  151 IVCIDIEATniSTDPD-ADIIQLSA---CDGEGKELFNQLINPGYDIPE--NDKHNITTEMVQDAPLLAKAWDEIHDTLR 224
Cdd:smart00479   2 LVVIDCETT--GLDPGkDEIIEIAAvdvDGGEIIEVFDTYVKPDRPITDyaTEIHGITPEMLDDAPTFEEVLEELLEFLR 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806  225 DADVVLAYSTESDFMYLEKSAEKKMLRFELDyNTWLDAAELSKDLIGAIRWHSermywfyktpkLTDAyAKVLDKPFPGD 304
Cdd:smart00479  80 GRILVAGNSAHFDLRFLKLEHPRLGIKQPPK-LPVIDTLKLARATNPGLPKYS-----------LKKL-AKRLLLEVIQR 146

                          170       180
                   ....*....|....*....|...
gi 1579911806  305 AHDALADAQATVELFNAMLKRGE 327
Cdd:smart00479 147 AHRALDDARATAKLFKKLLERLE 169
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 146-325 3.47e-11

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 62.54  E-value: 3.47e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 146 LKGKNIVCIDIEATNIstDPDAD-IIQLSACDGEGKELFNQ---LINPGYDIPENDK--HNITTEMVQDAPLLAKAWDEI 219
Cdd:PRK06310    4 LKDTEFVCLDCETTGL--DVKKDrIIEFAAIRFTFDEVIDSvefLINPERVVSAESQriHHISDAMLRDKPKIAEVFPQI 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 220 HDTLRDADVVLAYSTESDFMYLEKSAEKKMLRFELDYNTWLDAAELSKDligairwhsermywFYKTPKLT-DAYAKVLD 298
Cdd:PRK06310   82 KGFFKEGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKE--------------YGDSPNNSlEALAVHFN 147

                         170       180
                  ....*....|....*....|....*..
gi 1579911806 299 KPFPGdAHDALADAQATVELFNAMLKR 325
Cdd:PRK06310  148 VPYDG-NHRAMKDVEINIKVFKHLCKR 173
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 152-328 4.00e-11

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 64.59  E-value: 4.00e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 152 VCIDIEATNISTDPDADIIQLSAC---DGEGKELFNQLINPGYDIPE--NDKHNITTEMVQDAPLLAKAWDEIHDTLRDA 226
Cdd:PRK08074    6 VVVDLETTGNSPKKGDKIIQIAAVvveDGEILERFSSFVNPERPIPPfiTELTGISEEMVKQAPLFEDVAPEIVELLEGA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 227 DVVlAYSTESDFMYLEksAEKKMLRFELDYNTWLDAAELSKDLIGAIRwhsermywFYKTPKLTDAYAKVLDKPfpgdaH 306
Cdd:PRK08074   86 YFV-AHNVHFDLNFLN--EELERAGYTEIHCPKLDTVELARILLPTAE--------SYKLRDLSEELGLEHDQP-----H 149

                         170       180
                  ....*....|....*....|..
gi 1579911806 307 DALADAQATVELFNAMLKRGEQ 328
Cdd:PRK08074  150 RADSDAEVTAELFLQLLNKLER 171
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 152-319 1.70e-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: 56.21  E-value: 1.70e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 152 VCIDIEATNISTDPDAdIIQLSA--CDG---EGKELFNQLINPGYDIPENDK----HNITTEMVQDAPLLAKAWDEIHDT 222
Cdd:pfam00929   1 VVIDLETTGLDPEKDE-IIEIAAvvIDGgenEIGETFHTYVKPTRLPKLTDEctkfTGITQAMLDNKPSFEEVLEEFLEF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 223 LRDADVVLAYSTESDFMYLEKSAEKKMLRFELDYNTWLDAAELSKDLIGAIRWHSermywfyktpklTDAYAKVLDKPFP 302
Cdd:pfam00929  80 LRKGNLLVAHNASFDVGFLRYDDKRFLKKPMPKLNPVIDTLILDKATYKELPGRS------------LDALAEKLGLEHI 147

                         170
                  ....*....|....*..
gi 1579911806 303 GDAHDALADAQATVELF 319
Cdd:pfam00929 148 GRAHRALDDARATAKLF 164
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 151-323 2.75e-09

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: 55.69  E-value: 2.75e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 151 IVCIDIEAT----NISTDPDADIIQLSAC--DGEGKEL---FNQLINPgydiPENDK--------HNITTEMVQDAPLLA 213
Cdd:cd06133     1 YLVIDFEATcwegNSKPDYPNEIIEIGAVlvDVKTKEIidtFSSYVKP----VINPKlsdfctelTGITQEDVDNAPSFP 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 214 KAWDEIHDTLRD--ADVVLAYSTESDFMYLEKSAEKKMLRFELDYNTWLDAAELSKDLIGairwhsermywFYKTPKLTD 291
Cdd:cd06133    77 EVLKEFLEWLGKngKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYG-----------LKKRTGLSK 145

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1579911806 292 AyAKVLDKPFPGDAHDALADAQATVELFNAML 323
Cdd:cd06133   146 A-LEYLGLEFEGRHHRGLDDARNIARILKRLL 176
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 155-250 3.83e-08

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 53.28  E-value: 3.83e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 155 DIEATNISTDPDAdIIQLSACDGEGKELFNQLINPGYDIPENDK--HNITTEMVQDAPLLAKAWDEIHDTLRDADVVLAY 232
Cdd:PRK06309    8 DTETTGTQIDKDR-IIEIAAYNGVTSESFQTLVNPEIPIPAEASkiHGITTDEVADAPKFPEAYQKFIEFCGTDNILVAH 86

                          90
                  ....*....|....*....
gi 1579911806 233 STES-DFMYLEKSAEKKML 250
Cdd:PRK06309   87 NNDAfDFPLLRKECRRHGL 105
Rv2179c-like pfam16473
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease ...
 154-316 4.11e-08

3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease family. The proteins constitute a typical RNase fold, where the active site residues form a magnesium catalytic centre. The protein of the solved structure readily cleaves 3' overhangs in a time-dependent manner. It is similar to DEDD-type RNases and is an unusual ATP-binding protein that binds ATP and dATP. It forms a dimer in solution and both protomers in the asymmetric unit bind a magnesium ion through Asp-6 in SwissProt:P9WJ73. Proteins containing this domain also include 3'-5' exonuclease dexA from bacteriophage T4. It may play a role in the final step of host DNA degradation, by scavenging DNA into mononucleotides.


Pssm-ID: 406788  Cd Length: 177  Bit Score: 52.43  E-value: 4.11e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 154 IDIEAtnISTDPDADIIQLSAC-----DGEGKELFNQLINPGYDIP---ENDKHNITTEMVQDAPLLAKAWDEihDTLRD 225
Cdd:pfam16473   5 IDIET--LGNEPTAPIVSIGAVffdpeTGELGKEFYARIDLESSMSagaTIDADTILWWLKQSSEARAQLLGD--DAPSL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 226 ADVVLAYSTesdfmYLEKSAEKKMLRFELDY----NTWLDAAELSKDLIGAIRWHSERMYWFYKTPKLTDAYAKVLDKPF 301
Cdd:pfam16473  81 PDALLDLND-----FIRDNGDPKSLKVWGNGasfdNVILRAAFERGGLPAPWKYWNDRDVRTIVALGPELGYDPKRDIPF 155

                         170
                  ....*....|....*..
gi 1579911806 302 PGDAHDALADA--QATV 316
Cdd:pfam16473 156 EGVKHNALDDAihQAKY 172
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 151-319 4.46e-08

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: 51.74  E-value: 4.46e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 151 IVCIDIEATNisTDPDadiiqlSAC--------DGEGKELFNQLINP-GYDIPENDK-HNITTEMVQDAPLLAKAWDEIH 220
Cdd:cd06130     1 FVAIDFETAN--ADRA------SACsiglvkvrDGQIVDTFYTLIRPpTRFDPFNIAiHGITPEDVADAPTFPEVWPEIK 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 221 DTLrDADVVLAYSTESDFMYLEKSAEkkmlRFELDY--NTWLDAAELSKDLIGAIRWHsermywfyktpKLTDAyAKVLD 298
Cdd:cd06130    73 PFL-GGSLVVAHNASFDRSVLRAALE----AYGLPPppYQYLCTVRLARRVWPLLPNH-----------KLNTV-AEHLG 135

                         170       180
                  ....*....|....*....|.
gi 1579911806 299 KPFpgDAHDALADAQATVELF 319
Cdd:cd06130   136 IEL--NHHDALEDARACAEIL 154
polC PRK00448
DNA polymerase III PolC; Validated
 139-324 5.05e-08

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 54.84  E-value: 5.05e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806  139 LKEHAQNLKGKNIVCIDIEATNISTDPDaDIIQLSAC---DGEGKELFNQLINPGYDIPENDKH--NITTEMVQDAPLLA 213
Cdd:PRK00448   409 YNEVDRDLKDATYVVFDVETTGLSAVYD-EIIEIGAVkikNGEIIDKFEFFIKPGHPLSAFTTEltGITDDMVKDAPSIE 487

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806  214 KAWDEIHDTLRDAdVVLAYSTESDFMYLEKSAEK-KMLRFEldyNTWLDAAELSKDLigairwhsermYWFYKTPKLtDA 292
Cdd:PRK00448   488 EVLPKFKEFCGDS-ILVAHNASFDVGFINTNYEKlGLEKIK---NPVIDTLELSRFL-----------YPELKSHRL-NT 551

                          170       180       190
                   ....*....|....*....|....*....|...
gi 1579911806  293 YAKVLD-KPFpgDAHDALADAQATVELFNAMLK 324
Cdd:PRK00448   552 LAKKFGvELE--HHHRADYDAEATAYLLIKFLK 582
PRK07942 PRK07942
DNA polymerase III subunit epsilon; Provisional
 150-325 1.10e-07

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 181176 [Multi-domain]  Cd Length: 232  Bit Score: 51.90  E-value: 1.10e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 150 NIVCIDIEATniSTDPDADIIqLSAC------DGEGKELFNQLINPGYDIPEN--DKHNITTEMVQD-----APLLAKAW 216
Cdd:PRK07942    7 PLAAFDLETT--GVDPETARI-VTAAlvvvdaDGEVVESREWLADPGVEIPEEasAVHGITTEYARAhgrpaAEVLAEIA 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 217 DEIHDTLRDADVVLAYSTESDFMYLEKSAekkmLRF---ELDYNTWLDAAELSKdligairwHSERmywfYKTPK--LTD 291
Cdd:PRK07942   84 DALREAWARGVPVVVFNAPYDLTVLDREL----RRHglpSLVPGPVIDPYVIDK--------AVDR----YRKGKrtLTA 147

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1579911806 292 A---YAKVLDkpfpgDAHDALADAQATVELFNAMLKR 325
Cdd:PRK07942  148 LcehYGVRLD-----NAHEATADALAAARVAWALARR 179
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 149-327 4.23e-07

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 49.47  E-value: 4.23e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 149 KNIVCIDIEATNISTDP----DADIIQLSAC--DGEGKEL--FNQLINPGYDiPENDKH-----NITTEMVQDAPLLAKA 215
Cdd:COG5018     2 MKYLVIDLEATCWDGKPppgfPMEIIEIGAVkvDENGEIIdeFSSFVKPVRR-PKLSPFcteltGITQEDVDSAPSFAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 216 WDEIHDTLRDADVVLAYSTESDFMYLEKSAEKKMLRFELDYNtWLDAAELSKDLIGaIRwhsermywfyKTPKLTDAYaK 295
Cdd:COG5018    81 IEDFKKWIGSEDYILCSWGDYDRKQLERNCRFHGVPYPFGDR-HINLKKLFALYFG-LK----------KRIGLKKAL-E 147

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1579911806 296 VLDKPFPGDAHDALADAQATVELFNAMLKRGE 327
Cdd:COG5018   148 LLGLEFEGTHHRALDDARNTAKLFKKILGDKR 179
PRK07740 PRK07740
hypothetical protein; Provisional
 151-332 5.55e-06

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 46.97  E-value: 5.55e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 151 IVCIDIEATNISTDPDADIIQLSACDGEGKELFNQ----LINPGYDIPENDKH--NITTEMVQDAPLLAkawDEIHDTLR 224
Cdd:PRK07740   61 FVVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDtfysLVKPKRPIPEHILEltGITAEDVAFAPPLA---EVLHRFYA 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 225 --DADVVLAY--STESDFMyleKSAEKKMLRFELDYNTwLDAAELSKdligaIRWHSErmywfyKTPKLTDAYAkVLDKP 300
Cdd:PRK07740  138 fiGAGVLVAHhaGHDKAFL---RHALWRTYRQPFTHRL-IDTMFLTK-----LLAHER------DFPTLDDALA-YYGIP 201

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1579911806 301 fPGDAHDALADAQATVELFNAMLKRGEQSQVE 332
Cdd:PRK07740  202 -IPRRHHALGDALMTAKLWAILLVEAQQRGIT 232
PRK06063 PRK06063
DEDDh family exonuclease;
154-332 5.67e-06

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 47.39  E-value: 5.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 154 IDIEATNISTDPDAdIIQLSA----CDGEGKELFNQLINPGYDIPENDKHNITTEMVQDAPLLAKAWDEIHDTLRDAdVV 229
Cdd:PRK06063   20 VDVETSGFRPGQAR-IISLAVlgldADGNVEQSVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRGR-TL 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 230 LAYSTESDFMYLekSAEKKMLRFELDYNTWLDAAELSKDL---IGAIRWHSERMYWFYKTPKltdayakvldkpfpgdAH 306
Cdd:PRK06063   98 VAHNVAFDYSFL--AAEAERAGAELPVDQVMCTVELARRLglgLPNLRLETLAAHWGVPQQR----------------PH 159

                         170       180
                  ....*....|....*....|....*.
gi 1579911806 307 DALADAQATVELFNAMLKRGEQSQVE 332
Cdd:PRK06063  160 DALDDARVLAGILRPSLERARERDVW 185
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
152-325 2.05e-04

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 42.98  E-value: 2.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 152 VCIDIEATNISTDPDAdIIQLSA---CDGEGKELFNQLINPGYDIPENDKH--NITTEMVQDAPLLAKAWDEIHDTLRDA 226
Cdd:PRK07883   18 VVVDLETTGGSPAGDA-ITEIGAvkvRGGEVLGEFATLVNPGRPIPPFITVltGITTAMVAGAPPIEEVLPAFLEFARGA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 227 dVVLAYSTESDFMYLEKSAEkkmlRFELDY--NTWLDAAELSKDLI--GAIRWHsermywfyktpKLtDAYAKVLDKPFP 302
Cdd:PRK07883   97 -VLVAHNAPFDIGFLRAAAA----RCGYPWpgPPVLCTVRLARRVLprDEAPNV-----------RL-STLARLFGATTT 159

                         170       180
                  ....*....|....*....|...
gi 1579911806 303 GDaHDALADAQATVELFNAMLKR 325
Cdd:PRK07883  160 PT-HRALDDARATVDVLHGLIER 181
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 150-246 9.95e-04

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 40.53  E-value: 9.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 150 NIVCIDIEATNISTDPDADIIQLSACDGEGKELFNQLINPG--YDIPENDK-HNITTEMVQDAPLLAKAWDEIHDTLRDa 226
Cdd:PRK06195    2 NFVAIDFETANEKRNSPCSIGIVVVKDGEIVEKVHYLIKPKemRFMPINIGiHGIRPHMVEDELEFDKIWEKIKHYFNN- 80

                          90       100
                  ....*....|....*....|
gi 1579911806 227 DVVLAYSTESDFMYLEKSAE 246
Cdd:PRK06195   81 NLVIAHNASFDISVLRKTLE 100
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 199-328 4.94e-03

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: 37.81  E-value: 4.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 199 HNITTEMVQDAPLLAKAWDEIHDTLRDaDVVLAYSTESDFMYLeKSAEKKMLRFELDYNTWLDAAELSKDLIGAIRWHSE 278
Cdd:TIGR00573  61 HGITDDMLKDKPDFKEIAEDFADYIRG-AELVIHNASFDVGFL-NYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRN 138

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1579911806 279 RMYWFYKTPKLTDAYAKvldkpfpgdAHDALADAQATVELFNAMLKRGEQ 328
Cdd:TIGR00573 139 TLDALCKRYEITNSHRA---------LHGALADAFILAKLYLVMTGKQTK 179
PRK06807 PRK06807
3'-5' exonuclease;
150-210 7.88e-03

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 37.87  E-value: 7.88e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1579911806 150 NIVCIDIEATNISTDPDAdIIQLSACDGEGKEL---FNQLINPGYDIPEN--DKHNITTEMVQDAP 210
Cdd:PRK06807    9 DYVVIDFETTGFNPYNDK-IIQVAAVKYRNHELvdqFVSYVNPERPIPDRitSLTGITNYRVSDAP 73
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 183-269 9.74e-03

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: 36.36  E-value: 9.74e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579911806 183 FNQLINPGYDIPEN--DKHNITTEMVQDAPLLAKAWDEIHDTLRDADVVlAYSTESD--FMYLEKSAEKKMLRFElDYNT 258
Cdd:cd06131    37 FHVYINPERDIPEEafKVHGITDEFLADKPKFAEIADEFLDFIRGAELV-IHNASFDvgFLNAELSLLGLGKKII-DFCR 114

                          90
                  ....*....|.
gi 1579911806 259 WLDAAELSKDL 269
Cdd:cd06131   115 VIDTLALARKK 125
 
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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