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Conserved domains on  [gi|2521008009|ref|WP_285813487|]
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MULTISPECIES: 3'-5' exonuclease [Staphylococcus]

Protein Classification

3'-5' exonuclease( domain architecture ID 10150019)

3'-5' exonuclease similar to DNA polymerase III subunit epsilon, which is a proofreading 3'-5' exonuclease and contains the editing function of the multichain enzyme responsible for most of the replicative synthesis in bacteria

CATH:  3.30.420.10
EC:  3.1.-.-
Gene Ontology:  GO:0008408|GO:0003676
PubMed:  11988770|11222749
SCOP:  4000547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 13-168 3.01e-72

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: 215.45  E-value: 3.01e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  13 YIALDFETANGKRTSICSVGMVKVINHQITETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFIDGLPV 92
Cdd:cd06130     1 FVAIDFETANADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGSLV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2521008009  93 VAHNAAFDMNVLHESIRAIGHKTPNLVYFCSLQLSRKTITNHR-YGLNYMMEYYNLDFKgHHDALNDAKACAMITYR 168
Cdd:cd06130    81 VAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPnHKLNTVAEHLGIELN-HHDALEDARACAEILLA 156
 
Name Accession Description Interval E-value
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 13-168 3.01e-72

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: 215.45  E-value: 3.01e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  13 YIALDFETANGKRTSICSVGMVKVINHQITETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFIDGLPV 92
Cdd:cd06130     1 FVAIDFETANADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGSLV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2521008009  93 VAHNAAFDMNVLHESIRAIGHKTPNLVYFCSLQLSRKTITNHR-YGLNYMMEYYNLDFKgHHDALNDAKACAMITYR 168
Cdd:cd06130    81 VAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPnHKLNTVAEHLGIELN-HHDALEDARACAEILLA 156
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 13-171 9.20e-58

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 178.83  E-value: 9.20e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  13 YIALDFETANGKRT--SICSVGMVKVINHQITETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFIDGL 90
Cdd:COG0847     2 FVVLDTETTGLDPAkdRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  91 PVVAHNAAFDMNVLHESIRAIGHKTPNLVYFCSLQLSRKTITNH-RYGLNYMMEYYNLDFKGHHDALNDAKACAMITYRL 169
Cdd:COG0847    82 VLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLpSYSLDALCERLGIPFDERHRALADAEATAELFLAL 161


                  ..
gi 2521008009 170 LK 171
Cdd:COG0847   162 LR 163
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 13-165 2.57e-40

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 138.76  E-value: 2.57e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  13 YIALDFETANGKRTSICSVGMVKVINHQITETFYTLVNPKDY-FSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFIDGLP 91
Cdd:PRK06195    3 FVAIDFETANEKRNSPCSIGIVVVKDGEIVEKVHYLIKPKEMrFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNNNL 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2521008009  92 VVAHNAAFDMNVLHESIRAIGHKTPNLVYFCSLQLSRKTITN-HRYGLNYMMEYYNLDFKgHHDALNDAKACAMI 165
Cdd:PRK06195   83 VIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNiDNARLNTVNNFLGYEFK-HHDALADAMACSNI 156
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 13-173 1.29e-27

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 101.99  E-value: 1.29e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009   13 YIALDFETA--NGKRTSICSVGMVKVINHQITETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFIDGL 90
Cdd:smart00479   2 LVVIDCETTglDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009   91 PVVAHN-AAFDMNVL-HESIRAIGHKTPNLVYFCSLQLSRKTITN-HRYGLNYMMEYYNLDFKG-HHDALNDAKACAmit 166
Cdd:smart00479  82 ILVAGNsAHFDLRFLkLEHPRLGIKQPPKLPVIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQrAHRALDDARATA--- 158


                   ....*..
gi 2521008009  167 yRLLKHY 173
Cdd:smart00479 159 -KLFKKL 164
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 14-163 3.08e-18

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 77.78  E-value: 3.08e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  14 IALDFETA--NGKRTSICSVGMVKVINHQ--ITETFYTLVNPKD--YFSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFI 87
Cdd:pfam00929   1 VVIDLETTglDPEKDEIIEIAAVVIDGGEneIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  88 DGLPV-VAHNAAFDM-NVLHESIRAIGHKTPNLV-YFCSLQLSRKTITNH-RYGLNYMMEYYNLDFKGH-HDALNDAKAC 162
Cdd:pfam00929  81 RKGNLlVAHNASFDVgFLRYDDKRFLKKPMPKLNpVIDTLILDKATYKELpGRSLDALAEKLGLEHIGRaHRALDDARAT 160


                  .
gi 2521008009 163 A 163
Cdd:pfam00929 161 A 161
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 28-171 6.03e-13

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: 64.78  E-value: 6.03e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  28 ICSVGMVKVINHQIT-ETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFIDGLPVVAHNAAFDMNVLHE 106
Cdd:TIGR00573  25 IIEIGAVEIINRRITgNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELVIHNASFDVGFLNY 104

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2521008009 107 SIRAIGHKTPNLVYFC----SLQLSRKTITNHRYGLNYMMEYYNLDfkGHHDALNDAKACAMITYRLLK 171
Cdd:TIGR00573 105 EFSKLYKVEPKTNDVIdttdTLQYARPEFPGKRNTLDALCKRYEIT--NSHRALHGALADAFILAKLYL 171
 
Name Accession Description Interval E-value
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 13-168 3.01e-72

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: 215.45  E-value: 3.01e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  13 YIALDFETANGKRTSICSVGMVKVINHQITETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFIDGLPV 92
Cdd:cd06130     1 FVAIDFETANADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGSLV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2521008009  93 VAHNAAFDMNVLHESIRAIGHKTPNLVYFCSLQLSRKTITNHR-YGLNYMMEYYNLDFKgHHDALNDAKACAMITYR 168
Cdd:cd06130    81 VAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPnHKLNTVAEHLGIELN-HHDALEDARACAEILLA 156
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 13-171 9.20e-58

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 178.83  E-value: 9.20e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  13 YIALDFETANGKRT--SICSVGMVKVINHQITETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFIDGL 90
Cdd:COG0847     2 FVVLDTETTGLDPAkdRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  91 PVVAHNAAFDMNVLHESIRAIGHKTPNLVYFCSLQLSRKTITNH-RYGLNYMMEYYNLDFKGHHDALNDAKACAMITYRL 169
Cdd:COG0847    82 VLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLpSYSLDALCERLGIPFDERHRALADAEATAELFLAL 161


                  ..
gi 2521008009 170 LK 171
Cdd:COG0847   162 LR 163
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 1-176 2.08e-47

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 152.99  E-value: 2.08e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009   1 MRKELHSMSdnaYIALDFET--ANGKRTSICSVGMVKVINHQITETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDI 78
Cdd:COG2176     1 MSLDLEDLT---YVVFDLETtgLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  79 VFPHMMNFIDGLPVVAHNAAFDMNVLHESIRAIGHKTPNLVYfCSLQLSRKTITNH-RYGLNYMMEYYNLDFKGHHDALN 157
Cdd:COG2176    78 VLPEFLEFLGDAVLVAHNASFDLGFLNAALKRLGLPFDNPVL-DTLELARRLLPELkSYKLDTLAERLGIPLEDRHRALG 156

                         170
                  ....*....|....*....
gi 2521008009 158 DAKACAMITYRLLKHYNDL 176
Cdd:COG2176   157 DAEATAELFLKLLEKLEEK 175
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 14-165 6.24e-42

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: 138.59  E-value: 6.24e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  14 IALDFET--ANGKRTSICSVGMVKVINH-QITETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFIDGL 90
Cdd:cd06127     1 VVFDTETtgLDPKKDRIIEIGAVKVDGGiEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2521008009  91 PVVAHNAAFDMNVLHESIRAIGHKTPNLVYFCSLQLSRKTI-TNHRYGLNYM-MEYYNLDFKGHHDALNDAKACAMI 165
Cdd:cd06127    81 VLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLpGLRSHRLGLLlAERYGIPLEGAHRALADALATAEL 157
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 13-165 2.57e-40

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 138.76  E-value: 2.57e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  13 YIALDFETANGKRTSICSVGMVKVINHQITETFYTLVNPKDY-FSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFIDGLP 91
Cdd:PRK06195    3 FVAIDFETANEKRNSPCSIGIVVVKDGEIVEKVHYLIKPKEMrFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNNNL 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2521008009  92 VVAHNAAFDMNVLHESIRAIGHKTPNLVYFCSLQLSRKTITN-HRYGLNYMMEYYNLDFKgHHDALNDAKACAMI 165
Cdd:PRK06195   83 VIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNiDNARLNTVNNFLGYEFK-HHDALADAMACSNI 156
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 13-173 1.29e-27

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 101.99  E-value: 1.29e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009   13 YIALDFETA--NGKRTSICSVGMVKVINHQITETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFIDGL 90
Cdd:smart00479   2 LVVIDCETTglDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009   91 PVVAHN-AAFDMNVL-HESIRAIGHKTPNLVYFCSLQLSRKTITN-HRYGLNYMMEYYNLDFKG-HHDALNDAKACAmit 166
Cdd:smart00479  82 ILVAGNsAHFDLRFLkLEHPRLGIKQPPKLPVIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQrAHRALDDARATA--- 158


                   ....*..
gi 2521008009  167 yRLLKHY 173
Cdd:smart00479 159 -KLFKKL 164
polC PRK00448
DNA polymerase III PolC; Validated
 8-194 2.97e-23

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 96.45  E-value: 2.97e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009    8 MSDNAYIALDFETA--NGKRTSICSVGMVKVINHQITETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMN 85
Cdd:PRK00448   416 LKDATYVVFDVETTglSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKE 495

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009   86 FIDGLPVVAHNAAFDMNVLHESIRAIGHKTPNLVYFCSLQLSRKTITNH-RYGLNYMMEYYNLDFKGHHDALNDAKACAM 164
Cdd:PRK00448   496 FCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELkSHRLNTLAKKFGVELEHHHRADYDAEATAY 575

                          170       180       190
                   ....*....|....*....|....*....|.
gi 2521008009  165 ITYRLLKHYNDLS-TMLNIYGKNLQDKDALK 194
Cdd:PRK00448   576 LLIKFLKDLKEKGiTNLDELNKKLGSEDAYK 606
PRK06807 PRK06807
3'-5' exonuclease;
7-165 4.19e-22

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 91.03  E-value: 4.19e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009   7 SMSDNaYIALDFETA--NGKRTSICSVGMVKVINHQITETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMM 84
Cdd:PRK06807    5 SLPLD-YVVIDFETTgfNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  85 NFIDGLPVVAHNAAFDMNVLHESIRAIGHKTPNLVYFCSLQLSRKT---ITNHRygLNYMMEYYNLDFKGhHDALNDAKA 161
Cdd:PRK06807   84 AFLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYmkhAPNHK--LETLKRMLGIRLSS-HNAFDDCIT 160


                  ....
gi 2521008009 162 CAMI 165
Cdd:PRK06807  161 CAAV 164
PRK08517 PRK08517
3'-5' exonuclease;
8-165 3.33e-19

3'-5' exonuclease;


Pssm-ID: 236281 [Multi-domain]  Cd Length: 257  Bit Score: 82.38  E-value: 3.33e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009   8 MSDNAYIALDFETANGK--RTSICSVGMVKVINHQITETFYTLVNPKD---YFSQqninVHGIHPDDVIHAPTFDIVFPH 82
Cdd:PRK08517   65 IKDQVFCFVDIETNGSKpkKHQIIEIGAVKVKNGEIIDRFESFVKAKEvpeYITE----LTGITYEDLENAPSLKEVLEE 140

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  83 MMNFIDGLPVVAHNAAFDMNVLHESIRAIGHK---TPNLvyfCSLQLSRKTITNHRYGLNYMMEYYNLDFKGHHDALNDA 159
Cdd:PRK08517  141 FRLFLGDSVFVAHNVNFDYNFISRSLEEIGLGpllNRKL---CTIDLAKRTIESPRYGLSFLKELLGIEIEVHHRAYADA 217


                  ....*.
gi 2521008009 160 KACAMI 165
Cdd:PRK08517  218 LAAYEI 223
PRK09145 PRK09145
3'-5' exonuclease;
10-171 1.74e-18

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 79.18  E-value: 1.74e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  10 DNAYIALDFETA--NGKRTSICSVGMVKVINHQI--TETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMN 85
Cdd:PRK09145   28 PDEWVALDCETTglDPRRAEIVSIAAVKIRGNRIltSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLA 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  86 FIDGLPVVAHNAAFDMNVLHESIRAI-GHKTPN-LVYFCSL-------QLSRKTITNHrygLNYMMEYYNLDFKGHHDAL 156
Cdd:PRK09145  108 FIGNRPLVGYYLEFDVAMLNRYVRPLlGIPLPNpLIEVSALyydkkerHLPDAYIDLR---FDAILKHLDLPVLGRHDAL 184

                         170
                  ....*....|....*
gi 2521008009 157 NDAKACAMITYRLLK 171
Cdd:PRK09145  185 NDAIMAALIFLRLRK 199
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 13-160 3.07e-18

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: 77.57  E-value: 3.07e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  13 YIALDFET-----ANGKRtsICSVGMVKVINHQIT-ETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMNF 86
Cdd:cd06131     1 QIVLDTETtgldpREGHR--IIEIGCVELINRRLTgNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDF 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  87 IDGLPVVAHNAAFDMNVLHESIRAIGHKTPnLVYFC----SLQLSRKTITNHRYGLNYMMEYYNLDfKGH---HDALNDA 159
Cdd:cd06131    79 IRGAELVIHNASFDVGFLNAELSLLGLGKK-IIDFCrvidTLALARKKFPGKPNSLDALCKRFGID-NSHrtlHGALLDA 156


                  .
gi 2521008009 160 K 160
Cdd:cd06131   157 E 157
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 14-163 3.08e-18

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 77.78  E-value: 3.08e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  14 IALDFETA--NGKRTSICSVGMVKVINHQ--ITETFYTLVNPKD--YFSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFI 87
Cdd:pfam00929   1 VVIDLETTglDPEKDEIIEIAAVVIDGGEneIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  88 DGLPV-VAHNAAFDM-NVLHESIRAIGHKTPNLV-YFCSLQLSRKTITNH-RYGLNYMMEYYNLDFKGH-HDALNDAKAC 162
Cdd:pfam00929  81 RKGNLlVAHNASFDVgFLRYDDKRFLKKPMPKLNpVIDTLILDKATYKELpGRSLDALAEKLGLEHIGRaHRALDDARAT 160


                  .
gi 2521008009 163 A 163
Cdd:pfam00929 161 A 161
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 10-176 2.08e-17

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 79.23  E-value: 2.08e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  10 DNAYIALDFET-----ANGKRtsICSVGMVKVINHQITETFYTLVNPKD---YFSQQninVHGIHPDDVIHAPTFDIVFP 81
Cdd:PRK08074    2 SKRFVVVDLETtgnspKKGDK--IIQIAAVVVEDGEILERFSSFVNPERpipPFITE---LTGISEEMVKQAPLFEDVAP 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  82 HMMNFIDGLPVVAHNAAFDMNVLHESIRAIGHKTPNLVYFCSLQLSRktI---TNHRYGLNYMMEYYNLDFKGHHDALND 158
Cdd:PRK08074   77 EIVELLEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELAR--IllpTAESYKLRDLSEELGLEHDQPHRADSD 154

                         170
                  ....*....|....*...
gi 2521008009 159 AKACAMITYRLLKHYNDL 176
Cdd:PRK08074  155 AEVTAELFLQLLNKLERL 172
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 11-176 1.73e-15

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


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 73.95  E-value: 1.73e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  11 NAYIALDFE-TANGKRTSICSVGMVKVINHQITETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFIDG 89
Cdd:PRK07246    7 RKYAVVDLEaTGAGPNASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIED 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  90 LPVVAHNAAFDMNVLHESIRAIGH--KTPNL-------VYFCSLQlsrktitnhRYGLNYMMEYYNLDFKGHHDALNDAK 160
Cdd:PRK07246   87 CIFVAHNVKFDANLLAEALFLEGYelRTPRVdtvelaqVFFPTLE---------KYSLSHLSRELNIDLADAHTAIADAR 157

                         170
                  ....*....|....*.
gi 2521008009 161 ACAMITYRLLKHYNDL 176
Cdd:PRK07246  158 ATAELFLKLLQKIESL 173
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
9-161 4.65e-14

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 69.56  E-value: 4.65e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009   9 SDNAYIALDFETANGKRT--SICSVGMVKVINHQITETFYTLVNPkdyfsQQNI-----NVHGIHPDDVIHAPTFDIVFP 81
Cdd:PRK07883   13 RDVTFVVVDLETTGGSPAgdAITEIGAVKVRGGEVLGEFATLVNP-----GRPIppfitVLTGITTAMVAGAPPIEEVLP 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  82 HMMNFIDGLPVVAHNAAFDMNVLHESIRAIGHKTPNLVYFCSLQLSRKTIT-----NHRygLNYMMEYYNLDFKGHHDAL 156
Cdd:PRK07883   88 AFLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPrdeapNVR--LSTLARLFGATTTPTHRAL 165


                  ....*
gi 2521008009 157 NDAKA 161
Cdd:PRK07883  166 DDARA 170
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 13-172 1.81e-13

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 65.27  E-value: 1.81e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  13 YIALDFE-------TANGKRTSICSVGMVKVINH-QITETFYTLVNPKdYFSQQN---INVHGIHPDDVIHAPTFDIVFP 81
Cdd:COG5018     4 YLVIDLEatcwdgkPPPGFPMEIIEIGAVKVDENgEIIDEFSSFVKPV-RRPKLSpfcTELTGITQEDVDSAPSFAEAIE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  82 HMMNFI-DGLPVVAHNAAFDMNVLHESIRAIGHKTPNLVYFCSLQLSRKTITN--HRYGLNYMMEYYNLDFKG-HHDALN 157
Cdd:COG5018    83 DFKKWIgSEDYILCSWGDYDRKQLERNCRFHGVPYPFGDRHINLKKLFALYFGlkKRIGLKKALELLGLEFEGtHHRALD 162

                         170
                  ....*....|....*
gi 2521008009 158 DakacAMITYRLLKH 172
Cdd:COG5018   163 D----ARNTAKLFKK 173
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 28-171 6.03e-13

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: 64.78  E-value: 6.03e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  28 ICSVGMVKVINHQIT-ETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFIDGLPVVAHNAAFDMNVLHE 106
Cdd:TIGR00573  25 IIEIGAVEIINRRITgNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELVIHNASFDVGFLNY 104

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2521008009 107 SIRAIGHKTPNLVYFC----SLQLSRKTITNHRYGLNYMMEYYNLDfkGHHDALNDAKACAMITYRLLK 171
Cdd:TIGR00573 105 EFSKLYKVEPKTNDVIdttdTLQYARPEFPGKRNTLDALCKRYEIT--NSHRALHGALADAFILAKLYL 171
PRK07740 PRK07740
hypothetical protein; Provisional
 8-189 6.71e-13

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 65.08  E-value: 6.71e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009   8 MSDNAYIALDFETA-----NGKRtsICSVGMVKVINHQI-TETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFP 81
Cdd:PRK07740   56 LTDLPFVVFDLETTgfspqQGDE--ILSIGAVKTKGGEVeTDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLH 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  82 HMMNFIDGLPVVAHNAAFDMNVLHESI-----RAIGHKtpnlvyFCSLQLSRKTITNHR--YGLNYMMEYYNLDFKGHHD 154
Cdd:PRK07740  134 RFYAFIGAGVLVAHHAGHDKAFLRHALwrtyrQPFTHR------LIDTMFLTKLLAHERdfPTLDDALAYYGIPIPRRHH 207

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2521008009 155 ALNDAKAcamiTYRLLKHYNDLSTMLNIYgkNLQD 189
Cdd:PRK07740  208 ALGDALM----TAKLWAILLVEAQQRGIT--TLHD 236
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 8-185 1.38e-12

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 64.08  E-value: 1.38e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009   8 MSDNAYIALDFETA--NGKRTSICSVGMVKVINHQITETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMN 85
Cdd:PRK06310    4 LKDTEFVCLDCETTglDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  86 FI-DGLPVVAHNAAFDMNVL-HESIRAIGHKTPNLVYFC-SLQLSRKTITNHRYGLNYMMEYYNLDFKGHHDALNDAKAC 162
Cdd:PRK06310   84 FFkEGDYIVGHSVGFDLQVLsQESERIGETFLSKHYYIIdTLRLAKEYGDSPNNSLEALAVHFNVPYDGNHRAMKDVEIN 163

                         170       180
                  ....*....|....*....|...
gi 2521008009 163 AMITYRLLKHYNDLSTMLNIYGK 185
Cdd:PRK06310  164 IKVFKHLCKRFRTLEQLKQILSK 186
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 13-172 1.42e-12

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: 63.01  E-value: 1.42e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  13 YIALDFETANGKRTS-------ICSVGMVKVINH--QITETFYTLVNPKdYFSQQN---INVHGIHPDDVIHAPTFDIVF 80
Cdd:cd06133     1 YLVIDFEATCWEGNSkpdypneIIEIGAVLVDVKtkEIIDTFSSYVKPV-INPKLSdfcTELTGITQEDVDNAPSFPEVL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  81 PHMMNFIDGLPvvahNAAF------DMNVLH--ESIRAIGHKTPNLVYFCSLQ--LSRKTITNHRYGLNYMMEYYNLDFK 150
Cdd:cd06133    80 KEFLEWLGKNG----KYAFvtwgdwDLKDLLqnQCKYKIINLPPFFRQWIDLKkeFAKFYGLKKRTGLSKALEYLGLEFE 155

                         170       180
                  ....*....|....*....|...
gi 2521008009 151 G-HHDALNDAKacamITYRLLKH 172
Cdd:cd06133   156 GrHHRGLDDAR----NIARILKR 174
dnaQ_proteo TIGR01406
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ...
 14-159 5.07e-12

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: 62.41  E-value: 5.07e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  14 IALDFETANGKRTS---ICSVGMVKVINHQIT-ETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFIDG 89
Cdd:TIGR01406   3 IILDTETTGLDPKGghrIVEIGAVELVNRMLTgDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFIGG 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2521008009  90 LPVVAHNAAFDMNVLHESIRAIGHKTPNLVYFCS----LQLSRKTITNHRYGLNYMMEYYNLDFKGH--HDALNDA 159
Cdd:TIGR01406  83 SELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRvidtLAMARERFPGQRNSLDALCKRFKVDNSHRtlHGALLDA 158
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 8-159 7.81e-11

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 59.10  E-value: 7.81e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009   8 MSDNAYIALDFET-----ANGKRtsICSVGMVKVINHQIT-ETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFP 81
Cdd:PRK05711    1 TAIMRQIVLDTETtglnqREGHR--IIEIGAVELINRRLTgRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVAD 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  82 HMMNFIDGLPVVAHNAAFDMNVLHESIRAIGHKTPNLVYFC----SLQLSRKTITNHRYGLNYMMEYYNLDfKGH---HD 154
Cdd:PRK05711   79 EFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCkvtdTLAMARRMFPGKRNSLDALCKRYGID-NSHrtlHG 157


                  ....*
gi 2521008009 155 ALNDA 159
Cdd:PRK05711  158 ALLDA 162
PRK06063 PRK06063
DEDDh family exonuclease;
41-165 2.42e-10

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 58.17  E-value: 2.42e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  41 ITETFYTLVNPKdyFSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFIDGLPVVAHNAAFDMNVL-HESIRAiGHKTPNLV 119
Cdd:PRK06063   48 VEQSVVTLLNPG--VDPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRGRTLVAHNVAFDYSFLaAEAERA-GAELPVDQ 124

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2521008009 120 YFCSLQLSRKT---ITNHRygLNYMMEYYNLDFKGHHDALNDAKACAMI 165
Cdd:PRK06063  125 VMCTVELARRLglgLPNLR--LETLAAHWGVPQQRPHDALDDARVLAGI 171
PRK07983 PRK07983
exodeoxyribonuclease X; Provisional
 16-185 3.07e-10

exodeoxyribonuclease X; Provisional


Pssm-ID: 181186 [Multi-domain]  Cd Length: 219  Bit Score: 57.42  E-value: 3.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  16 LDFETAnGKRTSICSVGMVKVINHQITETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMnfidGLPV-VA 94
Cdd:PRK07983    5 IDTETC-GLQGGIVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYY----GSEWyVA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  95 HNAAFDMNVLHESiraighktpNLVYFCSLQLSRKTITNHRYGLNYMMEYYNLDFKG-----HHDALNDakaCaMITYRL 169
Cdd:PRK07983   80 HNASFDRRVLPEM---------PGEWICTMKLARRLWPGIKYSNMALYKSRKLNVQTppglhHHRALYD---C-YITAAL 146

                         170       180
                  ....*....|....*....|.
gi 2521008009 170 LKHYNDLS-----TMLNIYGK 185
Cdd:PRK07983  147 LIDIMNTSgwtaeEMADITGR 167
PRK09146 PRK09146
DNA polymerase III subunit epsilon; Validated
 9-175 1.39e-09

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236392 [Multi-domain]  Cd Length: 239  Bit Score: 55.70  E-value: 1.39e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009   9 SDNAYIALDFETA--NGKRTSICSVGMVKVINHQI--TETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMM 84
Cdd:PRK09146   45 SEVPFVALDFETTglDAEQDAIVSIGLVPFTLQRIrcRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELL 124

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  85 NFIDGLPVVAH---------NAAFdMNVLHE----------SIRAIGHKTPNLVYF--------CSLQL--SRKtitnhR 135
Cdd:PRK09146  125 EALAGKVVVVHyrrierdflDQAL-RNRIGEgiefpvidtmEIEARIQRKQAGGLWnrlkgkkpESIRLadSRL-----R 198

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2521008009 136 YGLnymmEYYNldfkgHHDALNDAKACA-MITYRLLKHYND 175
Cdd:PRK09146  199 YGL----PAYS-----PHHALTDAIATAeLLQAQIAHHFSP 230
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 38-158 2.83e-09

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 54.82  E-value: 2.83e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  38 NHQITETFYTLVNPKDYFSQQNINVHGIHPDDVIHAPTFDIVFPHMMNFIDGLPV-VAHNA-AFDMNVLHESIRAIGHKT 115
Cdd:PRK06309   28 NGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTDNIlVAHNNdAFDFPLLRKECRRHGLEP 107

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2521008009 116 PNLVYFCSLQLSRKTITN-HRYGLNYMMEYYNLDFKGHHDALND 158
Cdd:PRK06309  108 PTLRTIDSLKWAQKYRPDlPKHNLQYLRQVYGFEENQAHRALDD 151
Rv2179c-like pfam16473
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease ...
 13-165 4.49e-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: 50.51  E-value: 4.49e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  13 YIALDFETANGKRTS-ICSVGMVKVI--NHQITETFYTLVNPKD--------------YFSQQNINVHGIHPDDviHAPT 75
Cdd:pfam16473   2 HLMIDIETLGNEPTApIVSIGAVFFDpeTGELGKEFYARIDLESsmsagatidadtilWWLKQSSEARAQLLGD--DAPS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  76 FDIVFPHMMNFI------DGLPVVAHNAAFDMNVLHESIRAIGHKTPNLVYfcsLQLSRKTITNHRYGLNYMMEYyNLDF 149
Cdd:pfam16473  80 LPDALLDLNDFIrdngdpKSLKVWGNGASFDNVILRAAFERGGLPAPWKYW---NDRDVRTIVALGPELGYDPKR-DIPF 155

                         170
                  ....*....|....*..
gi 2521008009 150 KG-HHDALNDAKACAMI 165
Cdd:pfam16473 156 EGvKHNALDDAIHQAKY 172
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 14-168 1.18e-06

DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins; This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins 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. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherchia coli RNase T.


Pssm-ID: 99847  Cd Length: 152  Bit Score: 46.35  E-value: 1.18e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  14 IALDFE---TANGKRTSICsvGMVKVIN---HQITETFytlVNPK----DYFSQqninVHGIHPDDVIHAPTFDIVFPHM 83
Cdd:cd06144     1 VALDCEmvgVGPDGSESAL--ARVSIVNedgNVVYDTY---VKPQepvtDYRTA----VSGIRPEHLKDAPDFEEVQKKV 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  84 MNFIDGLPVVAHNAAFDMNVLhesirAIGHKTPNLVYFCSLQLSRKTITNHRYGLNYMMEYY-NLDF-KGHHDALNDAKA 161
Cdd:cd06144    72 AELLKGRILVGHALKNDLKVL-----KLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLlGLDIqEGEHSSVEDARA 146


                  ....*..
gi 2521008009 162 cAMITYR 168
Cdd:cd06144   147 -AMRLYR 152
PRK07942 PRK07942
DNA polymerase III subunit epsilon; Provisional
 14-179 2.48e-06

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 181176 [Multi-domain]  Cd Length: 232  Bit Score: 46.12  E-value: 2.48e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  14 IALDFET--ANGKRTSICSVGMVKV--INHQITETFYtLVNPKDYFSQQNINVHGI-------H---PDDVIHAPTFDIV 79
Cdd:PRK07942    9 AAFDLETtgVDPETARIVTAALVVVdaDGEVVESREW-LADPGVEIPEEASAVHGItteyaraHgrpAAEVLAEIADALR 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  80 fphmMNFIDGLPVVAHNAAFDMNVLHESIRAIGHK--TPNLV---YFCSLQLSRktitnHRYG---LNYMMEYYNLDFKG 151
Cdd:PRK07942   88 ----EAWARGVPVVVFNAPYDLTVLDRELRRHGLPslVPGPVidpYVIDKAVDR-----YRKGkrtLTALCEHYGVRLDN 158

                         170       180
                  ....*....|....*....|....*...
gi 2521008009 152 HHDALNDAKACAMITYRLLKHYNDLSTM 179
Cdd:PRK07942  159 AHEATADALAAARVAWALARRFPELAAL 186
PRK07247 PRK07247
3'-5' exonuclease;
12-106 2.37e-05

3'-5' exonuclease;


Pssm-ID: 180906 [Multi-domain]  Cd Length: 195  Bit Score: 43.23  E-value: 2.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  12 AYIALD--FETANGKrTSICSVGMVKVINHQITETFYTLVNpKDYFSQQNIN-VHGIHPDDVIHAPTFDIVFPHMMNFID 88
Cdd:PRK07247    6 TYIAFDleFNTVNGV-SHIIQVSAVKYDDHKEVDSFDSYVY-TDVPLQSFINgLTGITADKIADAPKVEEVLAAFKEFVG 83

                          90
                  ....*....|....*....
gi 2521008009  89 GLPVVAHNAA-FDMNVLHE 106
Cdd:PRK07247   84 ELPLIGYNAQkSDLPILAE 102
PRK07748 PRK07748
3'-5' exonuclease KapD;
8-171 3.74e-05

3'-5' exonuclease KapD;


Pssm-ID: 236087  Cd Length: 207  Bit Score: 42.75  E-value: 3.74e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009   8 MSDNAYIALDFE--------TANGKRTSICSVGMVKVINHQITETFYTLVNPKDY--FSQQNINVHGIHPDDVIHAPTFD 77
Cdd:PRK07748    1 MDEQQFLFLDFEftmpqhkkKPKGFFPEIIEVGLVSVVGCEVEDTFSSYVKPKTFpsLTERCKSFLGITQEDVDKGISFE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2521008009  78 IVFPHMMNFIDGLP--VVAHNAAfDMNVLHESIRAIGHKTPNLVYFCSLQLSRKTI--TNHRYGLNYMMEYYNLDFKG-H 152
Cdd:PRK07748   81 ELVEKLAEYDKRCKptIVTWGNM-DMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFfgERNQTGLWKAIEEYGKEGTGkH 159

                         170
                  ....*....|....*....
gi 2521008009 153 HDALNDakacAMITYRLLK 171
Cdd:PRK07748  160 HCALDD----AMTTYNIFK 174
 
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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