NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2127481434|ref|WP_227658488|]
View 

MULTISPECIES: 3'-5' exonuclease [Enterobacterales]

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
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 2-142 3.22e-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: 107.57  E-value: 3.22e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   2 EIGLVNARGERI---FETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFNAEFDTRILKQTAA 78
Cdd:COG0847    21 EIGAVKVDDGRIvetFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGAVLVAHNAAFDLGFLNAELR 100

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2127481434  79 AHNDRaswLDSLTVYCAMRLAAGYYGPTNRYgtiSLSGAVSQAGLSWaGEAHSAVTDAVMTARV 142
Cdd:COG0847   101 RAGLP---LPPFPVLDTLRLARRLLPGLPSY---SLDALCERLGIPF-DERHRALADAEATAEL 157
 
Name Accession Description Interval E-value
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 2-142 3.22e-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: 107.57  E-value: 3.22e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   2 EIGLVNARGERI---FETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFNAEFDTRILKQTAA 78
Cdd:COG0847    21 EIGAVKVDDGRIvetFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGAVLVAHNAAFDLGFLNAELR 100

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2127481434  79 AHNDRaswLDSLTVYCAMRLAAGYYGPTNRYgtiSLSGAVSQAGLSWaGEAHSAVTDAVMTARV 142
Cdd:COG0847   101 RAGLP---LPPFPVLDTLRLARRLLPGLPSY---SLDALCERLGIPF-DERHRALADAEATAEL 157
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 2-142 6.19e-29

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: 104.30  E-value: 6.19e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   2 EIGLV----NARGERIFETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFNAEFDTRILKQTA 77
Cdd:cd06127    19 EIGAVkvdgGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGRVLVAHNASFDLRFLNREL 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2127481434  78 AAHNdraSWLDSLTVYCAMRLAAGYYGPTNRYgtiSLSGAVSQAGLSWAGEAHSAVTDAVMTARV 142
Cdd:cd06127    99 RRLG---GPPLPNPWIDTLRLARRLLPGLRSH---RLGLLLAERYGIPLEGAHRALADALATAEL 157
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 2-151 1.46e-25

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 95.83  E-value: 1.46e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434    2 EIGLVNARGERI---FETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFN-AEFDTRILKQTA 77
Cdd:smart00479  21 EIAAVDVDGGEIievFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGRILVAGNsAHFDLRFLKLEH 100

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2127481434   78 AAHNDRasWLDSLTVYCAMRLAAGYYGPTNRYgtiSLSGAVSQAGLSWAGEAHSAVTDAVMTARVVNNIAGYWR 151
Cdd:smart00479 101 PRLGIK--QPPKLPVIDTLKLARATNPGLPKY---SLKKLAKRLLLEVIQRAHRALDDARATAKLFKKLLERLE 169
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 1-75 7.95e-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: 60.93  E-value: 7.95e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2127481434   1 MEIGLVNARGERI----FETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFNAEFDTRILKQ 75
Cdd:TIGR00573  26 IEIGAVEIINRRItgnkFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELVIHNASFDVGFLNY 104
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 2-90 1.85e-10

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 57.18  E-value: 1.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   2 EIG---LVNAR--GeRIFETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFNAEFDT------ 70
Cdd:PRK05711   26 EIGaveLINRRltG-RNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDFIRGAELIIHNAPFDIgfmdye 104

                          90       100
                  ....*....|....*....|.
gi 2127481434  71 -RILKQTAAAHNDRASWLDSL 90
Cdd:PRK05711  105 fALLGRDIPKTNTFCKVTDTL 125
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 1-142 9.77e-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: 51.58  E-value: 9.77e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   1 MEIGLVNARGERI-----FETRLKPTV--GIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRP-LVIFNAEFDT-- 70
Cdd:pfam00929  18 IEIAAVVIDGGENeigetFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFLRKGNlLVAHNASFDVgf 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2127481434  71 ------RILKQTAAAHNDRaswLDSLtvycamRLAAGYYgpTNRYGTiSLSGAVSQAGLSWAGEAHSAVTDAVMTARV 142
Cdd:pfam00929  98 lryddkRFLKKPMPKLNPV---IDTL------ILDKATY--KELPGR-SLDALAEKLGLEHIGRAHRALDDARATAKL 163
 
Name Accession Description Interval E-value
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 2-142 3.22e-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: 107.57  E-value: 3.22e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   2 EIGLVNARGERI---FETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFNAEFDTRILKQTAA 78
Cdd:COG0847    21 EIGAVKVDDGRIvetFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGAVLVAHNAAFDLGFLNAELR 100

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2127481434  79 AHNDRaswLDSLTVYCAMRLAAGYYGPTNRYgtiSLSGAVSQAGLSWaGEAHSAVTDAVMTARV 142
Cdd:COG0847   101 RAGLP---LPPFPVLDTLRLARRLLPGLPSY---SLDALCERLGIPF-DERHRALADAEATAEL 157
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 2-142 6.19e-29

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: 104.30  E-value: 6.19e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   2 EIGLV----NARGERIFETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFNAEFDTRILKQTA 77
Cdd:cd06127    19 EIGAVkvdgGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGRVLVAHNASFDLRFLNREL 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2127481434  78 AAHNdraSWLDSLTVYCAMRLAAGYYGPTNRYgtiSLSGAVSQAGLSWAGEAHSAVTDAVMTARV 142
Cdd:cd06127    99 RRLG---GPPLPNPWIDTLRLARRLLPGLRSH---RLGLLLAERYGIPLEGAHRALADALATAEL 157
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 2-151 1.46e-25

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 95.83  E-value: 1.46e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434    2 EIGLVNARGERI---FETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFN-AEFDTRILKQTA 77
Cdd:smart00479  21 EIAAVDVDGGEIievFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGRILVAGNsAHFDLRFLKLEH 100

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2127481434   78 AAHNDRasWLDSLTVYCAMRLAAGYYGPTNRYgtiSLSGAVSQAGLSWAGEAHSAVTDAVMTARVVNNIAGYWR 151
Cdd:smart00479 101 PRLGIK--QPPKLPVIDTLKLARATNPGLPKY---SLKKLAKRLLLEVIQRAHRALDDARATAKLFKKLLERLE 169
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 2-142 9.56e-21

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 83.65  E-value: 9.56e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   2 EIGLVNARGERI---FETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFNAEFDTRILKQTAA 78
Cdd:COG2176    29 EIGAVKVENGEIvdrFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLEFLGDAVLVAHNASFDLGFLNAALK 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2127481434  79 AHNDRAswldSLTVYCAMRLAAGYYGPTNRYgtiSLSGAVSQAGLSWAgEAHSAVTDAVMTARV 142
Cdd:COG2176   109 RLGLPF----DNPVLDTLELARRLLPELKSY---KLDTLAERLGIPLE-DRHRALGDAEATAEL 164
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 3-93 9.64e-14

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: 64.84  E-value: 9.64e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   3 IGLVNARGERI---FETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFNAEFDTRILKQTAAA 79
Cdd:cd06130    19 IGLVKVRDGQIvdtFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGSLVVAHNASFDRSVLRAALEA 98

                          90
                  ....*....|....*..
gi 2127481434  80 HN---DRASWLDSLTVY 93
Cdd:cd06130    99 YGlppPPYQYLCTVRLA 115
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 2-142 1.89e-12

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: 61.39  E-value: 1.89e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   2 EIG---LVNAR-GERIFETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFNAEFD-------- 69
Cdd:cd06131    21 EIGcveLINRRlTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIRGAELVIHNASFDvgflnael 100

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2127481434  70 TRILKQTAAAHNDRasWLDSLTVycAMRLAAGyyGPTN------RYGtISLSGAvsqaglswagEAHSAVTDAVMTARV 142
Cdd:cd06131   101 SLLGLGKKIIDFCR--VIDTLAL--ARKKFPG--KPNSldalckRFG-IDNSHR----------TLHGALLDAELLAEV 162
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 2-148 6.57e-12

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 60.26  E-value: 6.57e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   2 EIGLV--NARGERI--FETRLKPTV--GIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFN-AEFDTRILK 74
Cdd:COG5018    28 EIGAVkvDENGEIIdeFSSFVKPVRrpKLSPFCTELTGITQEDVDSAPSFAEAIEDFKKWIGSEDYILCSwGDYDRKQLE 107

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2127481434  75 QTAAAHNDRASWLDS----LTVYCAmrlaagYYGPTNRygtISLSGAVSQAGLSWAGEAHSAVTDAVMTARVVNNIAG 148
Cdd:COG5018   108 RNCRFHGVPYPFGDRhinlKKLFAL------YFGLKKR---IGLKKALELLGLEFEGTHHRALDDARNTAKLFKKILG 176
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 1-75 7.95e-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: 60.93  E-value: 7.95e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2127481434   1 MEIGLVNARGERI----FETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFNAEFDTRILKQ 75
Cdd:TIGR00573  26 IEIGAVEIINRRItgnkFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELVIHNASFDVGFLNY 104
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 2-90 1.85e-10

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 57.18  E-value: 1.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   2 EIG---LVNAR--GeRIFETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFNAEFDT------ 70
Cdd:PRK05711   26 EIGaveLINRRltG-RNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDFIRGAELIIHNAPFDIgfmdye 104

                          90       100
                  ....*....|....*....|.
gi 2127481434  71 -RILKQTAAAHNDRASWLDSL 90
Cdd:PRK05711  105 fALLGRDIPKTNTFCKVTDTL 125
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 1-142 9.77e-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: 51.58  E-value: 9.77e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   1 MEIGLVNARGERI-----FETRLKPTV--GIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRP-LVIFNAEFDT-- 70
Cdd:pfam00929  18 IEIAAVVIDGGENeigetFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFLRKGNlLVAHNASFDVgf 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2127481434  71 ------RILKQTAAAHNDRaswLDSLtvycamRLAAGYYgpTNRYGTiSLSGAVSQAGLSWAGEAHSAVTDAVMTARV 142
Cdd:pfam00929  98 lryddkRFLKKPMPKLNPV---IDTL------ILDKATY--KELPGR-SLDALAEKLGLEHIGRAHRALDDARATAKL 163
PRK09145 PRK09145
3'-5' exonuclease;
3-140 1.13e-08

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 51.83  E-value: 1.13e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   3 IGLVNARGERI-----FETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFNAEFDTRILkqta 77
Cdd:PRK09145   51 IAAVKIRGNRIltserLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFIGNRPLVGYYLEFDVAML---- 126

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2127481434  78 aahnDRASWldsltVYCAMRLA-------AGYYGPTNRY---GTISLS-GAVSQA-GLSWAGeAHSAVTDAVMTA 140
Cdd:PRK09145  127 ----NRYVR-----PLLGIPLPnplievsALYYDKKERHlpdAYIDLRfDAILKHlDLPVLG-RHDALNDAIMAA 191
PRK07942 PRK07942
DNA polymerase III subunit epsilon; Provisional
 3-153 1.20e-08

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 181176 [Multi-domain]  Cd Length: 232  Bit Score: 52.29  E-value: 1.20e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   3 IGLVNARGERIFETRL--KPTVGIDPAAAAVHGISDDDLVSAPSWPD-----IAQQLQHHIGR-RPLVIFNAEFDTRILK 74
Cdd:PRK07942   30 LVVVDADGEVVESREWlaDPGVEIPEEASAVHGITTEYARAHGRPAAevlaeIADALREAWARgVPVVVFNAPYDLTVLD 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434  75 QTAAAHndRASWLDSLTVYCAM---RLAAGYygptnRYGTISLSGAVSQAGLSWAGeAHSAVTDAVMTARVVNNIAGYWR 151
Cdd:PRK07942  110 RELRRH--GLPSLVPGPVIDPYvidKAVDRY-----RKGKRTLTALCEHYGVRLDN-AHEATADALAAARVAWALARRFP 181


                  ..
gi 2127481434 152 EI 153
Cdd:PRK07942  182 EL 183
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 3-147 8.08e-08

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 50.16  E-value: 8.08e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   3 IGLVNARGERIFET-----RLKPTVgIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFNAEFDTRILKQTA 77
Cdd:PRK06195   21 IGIVVVKDGEIVEKvhyliKPKEMR-FMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDISVLRKTL 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434  78 AAHNDRaswLDSLTVYCAMRLAAGYYGPTNRYGTISLSGAvsqagLSWAGEAHSAVTDAVMTARVVNNIA 147
Cdd:PRK06195  100 ELYNIP---MPSFEYICTMKLAKNFYSNIDNARLNTVNNF-----LGYEFKHHDALADAMACSNILLNIS 161
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 2-143 1.18e-07

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: 48.76  E-value: 1.18e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   2 EIG--LVNARGERI---FETRLKPTV--GIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIF--NAEFDTRI 72
Cdd:cd06133    25 EIGavLVDVKTKEIidtFSSYVKPVInpKLSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKNGKYAFvtWGDWDLKD 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2127481434  73 LKQTAAAHNDR------ASWLDSLTVYCAmrlaagYYGPTNRygtISLSGAVSQAGLSWAGEAHSAVTDAVMTARVV 143
Cdd:cd06133   105 LLQNQCKYKIInlppffRQWIDLKKEFAK------FYGLKKR---TGLSKALEYLGLEFEGRHHRGLDDARNIARIL 172
PRK06722 PRK06722
exonuclease; Provisional
 1-143 1.44e-07

exonuclease; Provisional


Pssm-ID: 180670 [Multi-domain]  Cd Length: 281  Bit Score: 49.28  E-value: 1.44e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   1 MEIGLVNARGEriFETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFNAEFDTRILKQTAAAH 80
Cdd:PRK06722   35 IEASTMKVIGE--FSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQIIEKFIQFIGEDSIFVTWGKEDYRFLSHDCTLH 112

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2127481434  81 NDRASWLDSLTVYCAMRLAAGYYGPTNRYgTISLSGAVSQAGLSWAGEAHSAVTDAVMTARVV 143
Cdd:PRK06722  113 SVECPCMEKERRIDLQKFVFQAYEELFEH-TPSLQSAVEQLGLIWEGKQHRALADAENTANIL 174
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 1-90 6.51e-06

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 44.42  E-value: 6.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434   1 MEIGLVNARGERIFETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIF--NAEFDTRILKQTAA 78
Cdd:PRK06309   22 IEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTDNILVAhnNDAFDFPLLRKECR 101

                          90
                  ....*....|....*
gi 2127481434  79 AHN-DRASW--LDSL 90
Cdd:PRK06309  102 RHGlEPPTLrtIDSL 116
RNaseT cd06134
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ...
 17-150 8.27e-05

DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. 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. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.


Pssm-ID: 99837 [Multi-domain]  Cd Length: 189  Bit Score: 41.12  E-value: 8.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2127481434  17 RLKPTVG--IDPAAAAVHGIS-DDDLVSAPSWPDIAQQL---------QHHIGRRPLVIFNAEFDTRILKQTAAAHNDRA 84
Cdd:cd06134    49 HILPFEGanLDPAALEFNGIDpFHPFRFAVDEKEALKEIfkpirkalkAQGCTRAILVGHNAHFDLGFLNAAVARCKIKR 128

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2127481434  85 SWLDSLTVYCAMRLAAGYYGPTnrygtiSLSGAVSQAGLSWAG-EAHSAVTDAVMTARVVNNIAGYW 150
Cdd:cd06134   129 NPFHPFSTFDTATLAGLAYGQT------VLAKACQAAGIEFDNkEAHSALYDTQKTAELFCKIVNRW 189
PRK06063 PRK06063
DEDDh family exonuclease;
6-78 1.14e-04

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 41.22  E-value: 1.14e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2127481434   6 VNARG--ERIFETRLKPtvGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFNAEFDTRILKQTAA 78
Cdd:PRK06063   42 LDADGnvEQSVVTLLNP--GVDPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRGRTLVAHNVAFDYSFLAAEAE 114
PRK06807 PRK06807
3'-5' exonuclease;
14-74 2.13e-03

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 37.49  E-value: 2.13e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2127481434  14 FETRLKPTVGIDPAAAAVHGISDDDLVSAPSWPDIAQQLQHHIGRRPLVIFNAEFDTRILK 74
Cdd:PRK06807   44 FVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTNVIVAHNASFDMRFLK 104
 
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