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Conserved domains on  [gi|1091029196|gb|OHP65067|]
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DNA polymerase III subunit epsilon [Staphylococcus sp. HMSC061G04]

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 ...
 5-157 4.52e-77

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: 227.01  E-value: 4.52e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   5 FIALDFETANGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKLPV 84
Cdd:cd06130     1 FVAIDFETANADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGSLV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1091029196  85 VAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTIDAYR-YGLKHLMKHYKLDFHgHHDALNDAKACAMI 157
Cdd:cd06130    81 VAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPnHKLNTVAEHLGIELN-HHDALEDARACAEI 153
 
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 ...
 5-157 4.52e-77

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: 227.01  E-value: 4.52e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   5 FIALDFETANGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKLPV 84
Cdd:cd06130     1 FVAIDFETANADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGSLV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1091029196  85 VAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTIDAYR-YGLKHLMKHYKLDFHgHHDALNDAKACAMI 157
Cdd:cd06130    81 VAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPnHKLNTVAEHLGIELN-HHDALEDARACAEI 153
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 5-163 3.62e-60

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 184.61  E-value: 3.62e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   5 FIALDFETANGKRT--SICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKL 82
Cdd:COG0847     2 FVVLDTETTGLDPAkdRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  83 PVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTI-DAYRYGLKHLMKHYKLDFHGHHDALNDAKACAMITFRL 161
Cdd:COG0847    82 VLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLpGLPSYSLDALCERLGIPFDERHRALADAEATAELFLAL 161


                  ..
gi 1091029196 162 LK 163
Cdd:COG0847   162 LR 163
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 5-157 1.25e-44

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 149.55  E-value: 1.25e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   5 FIALDFETANGKRTSICSVGMVKVVNNEIVESFYTLVNPFDY-FSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKLP 83
Cdd:PRK06195    3 FVAIDFETANEKRNSPCSIGIVVVKDGEIVEKVHYLIKPKEMrFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNNNL 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1091029196  84 VVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRT---IDayRYGLKHLMKHYKLDFHgHHDALNDAKACAMI 157
Cdd:PRK06195   83 VIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFysnID--NARLNTVNNFLGYEFK-HHDALADAMACSNI 156
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 5-165 3.20e-35

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 121.25  E-value: 3.20e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196    5 FIALDFETA--NGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKL 82
Cdd:smart00479   2 LVVIDCETTglDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   83 PVVAHN-AAFDMNVLHQSLKQLNIETPSMIYF-CSYQLAKRTI-DAYRYGLKHLMKHYKLDFHG-HHDALNDAKACAmit 158
Cdd:smart00479  82 ILVAGNsAHFDLRFLKLEHPRLGIKQPPKLPViDTLKLARATNpGLPKYSLKKLAKRLLLEVIQrAHRALDDARATA--- 158


                   ....*..
gi 1091029196  159 fRLLKHY 165
Cdd:smart00479 159 -KLFKKL 164
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 6-155 1.65e-24

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: 93.57  E-value: 1.65e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   6 IALDFETA--NGKRTSICSVGMVKVVN--NEIVESFYTLVNPFD--YFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:pfam00929   1 VVIDLETTglDPEKDEIIEIAAVVIDGgeNEIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  80 GKLPV-VAHNAAFDM-NVLHQSLKQLNIETPSMI-YFCSYQLAKRTI-DAYRYGLKHLMKHYKLDFHGH-HDALNDAKAC 154
Cdd:pfam00929  81 RKGNLlVAHNASFDVgFLRYDDKRFLKKPMPKLNpVIDTLILDKATYkELPGRSLDALAEKLGLEHIGRaHRALDDARAT 160


                  .
gi 1091029196 155 A 155
Cdd:pfam00929 161 A 161
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 2-173 1.40e-16

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: 74.02  E-value: 1.40e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   2 ENAFIALDFET-ANGKRTSICSVGMVKVVNN-EIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:TIGR00573   6 LDTETTGDNETtGLYAGHDIIEIGAVEIINRrITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYI 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  80 GKLPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFC----SYQLAKRTIDAYRYGLKHLMKHYKLDFHGH--HDALNDAKA 153
Cdd:TIGR00573  86 RGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIdttdTLQYARPEFPGKRNTLDALCKRYEITNSHRalHGALADAFI 165

                         170       180
                  ....*....|....*....|
gi 1091029196 154 CAMITFRLLKHYDNLQSMLQ 173
Cdd:TIGR00573 166 LAKLYLVMTGKQTKYGENEG 185
 
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 ...
 5-157 4.52e-77

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: 227.01  E-value: 4.52e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   5 FIALDFETANGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKLPV 84
Cdd:cd06130     1 FVAIDFETANADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGSLV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1091029196  85 VAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTIDAYR-YGLKHLMKHYKLDFHgHHDALNDAKACAMI 157
Cdd:cd06130    81 VAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPnHKLNTVAEHLGIELN-HHDALEDARACAEI 153
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 5-163 3.62e-60

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 184.61  E-value: 3.62e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   5 FIALDFETANGKRT--SICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKL 82
Cdd:COG0847     2 FVVLDTETTGLDPAkdRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  83 PVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTI-DAYRYGLKHLMKHYKLDFHGHHDALNDAKACAMITFRL 161
Cdd:COG0847    82 VLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLpGLPSYSLDALCERLGIPFDERHRALADAEATAELFLAL 161


                  ..
gi 1091029196 162 LK 163
Cdd:COG0847   162 LR 163
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 2-168 4.30e-48

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 154.53  E-value: 4.30e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   2 ENAFIALDFET--ANGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:COG2176     7 DLTYVVFDLETtgLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLEFL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  80 GKLPVVAHNAAFDMNVLHQSLKQLNIEtPSMIYFCSYQLAKRTI-DAYRYGLKHLMKHYKLDFHGHHDALNDAKACAMIT 158
Cdd:COG2176    87 GDAVLVAHNASFDLGFLNAALKRLGLP-FDNPVLDTLELARRLLpELKSYKLDTLAERLGIPLEDRHRALGDAEATAELF 165

                         170
                  ....*....|
gi 1091029196 159 FRLLKHYDNL 168
Cdd:COG2176   166 LKLLEKLEEK 175
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 6-157 1.23e-44

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: 145.14  E-value: 1.23e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   6 IALDFET--ANGKRTSICSVGMVKVVNN-EIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKL 82
Cdd:cd06127     1 VVFDTETtgLDPKKDRIIEIGAVKVDGGiEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1091029196  83 PVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTIDAYRYGLKH--LMKHYKLDFHGHHDALNDAKACAMI 157
Cdd:cd06127    81 VLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGllLAERYGIPLEGAHRALADALATAEL 157
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 5-157 1.25e-44

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 149.55  E-value: 1.25e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   5 FIALDFETANGKRTSICSVGMVKVVNNEIVESFYTLVNPFDY-FSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKLP 83
Cdd:PRK06195    3 FVAIDFETANEKRNSPCSIGIVVVKDGEIVEKVHYLIKPKEMrFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNNNL 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1091029196  84 VVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRT---IDayRYGLKHLMKHYKLDFHgHHDALNDAKACAMI 157
Cdd:PRK06195   83 VIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFysnID--NARLNTVNNFLGYEFK-HHDALADAMACSNI 156
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 5-165 3.20e-35

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 121.25  E-value: 3.20e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196    5 FIALDFETA--NGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKL 82
Cdd:smart00479   2 LVVIDCETTglDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   83 PVVAHN-AAFDMNVLHQSLKQLNIETPSMIYF-CSYQLAKRTI-DAYRYGLKHLMKHYKLDFHG-HHDALNDAKACAmit 158
Cdd:smart00479  82 ILVAGNsAHFDLRFLKLEHPRLGIKQPPKLPViDTLKLARATNpGLPKYSLKKLAKRLLLEVIQrAHRALDDARATA--- 158


                   ....*..
gi 1091029196  159 fRLLKHY 165
Cdd:smart00479 159 -KLFKKL 164
polC PRK00448
DNA polymerase III PolC; Validated
 5-163 3.23e-27

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 107.23  E-value: 3.23e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196    5 FIALDFETA--NGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKL 82
Cdd:PRK00448   421 YVVFDVETTglSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGDS 500

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   83 PVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTIDAY-RYGLKHLMKHYKLDFHGHHDALNDAKACAMITFRL 161
Cdd:PRK00448   501 ILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELkSHRLNTLAKKFGVELEHHHRADYDAEATAYLLIKF 580


                   ..
gi 1091029196  162 LK 163
Cdd:PRK00448   581 LK 582
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 6-155 1.65e-24

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: 93.57  E-value: 1.65e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   6 IALDFETA--NGKRTSICSVGMVKVVN--NEIVESFYTLVNPFD--YFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:pfam00929   1 VVIDLETTglDPEKDEIIEIAAVVIDGgeNEIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  80 GKLPV-VAHNAAFDM-NVLHQSLKQLNIETPSMI-YFCSYQLAKRTI-DAYRYGLKHLMKHYKLDFHGH-HDALNDAKAC 154
Cdd:pfam00929  81 RKGNLlVAHNASFDVgFLRYDDKRFLKKPMPKLNpVIDTLILDKATYkELPGRSLDALAEKLGLEHIGRaHRALDDARAT 160


                  .
gi 1091029196 155 A 155
Cdd:pfam00929 161 A 161
PRK08517 PRK08517
3'-5' exonuclease;
2-157 3.72e-24

3'-5' exonuclease;


Pssm-ID: 236281 [Multi-domain]  Cd Length: 257  Bit Score: 95.09  E-value: 3.72e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   2 ENAFIALDFETANGK--RTSICSVGMVKVVNNEIVESFYTLVnpFDYFSQTNI-EVHGITPEDVNDAPSFEYVFPYMMQF 78
Cdd:PRK08517   67 DQVFCFVDIETNGSKpkKHQIIEIGAVKVKNGEIIDRFESFV--KAKEVPEYItELTGITYEDLENAPSLKEVLEEFRLF 144

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1091029196  79 IGKLPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTIDAYRYGLKHLMKHYKLDFHGHHDALNDAKACAMI 157
Cdd:PRK08517  145 LGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYGLSFLKELLGIEIEVHHRAYADALAAYEI 223
PRK09145 PRK09145
3'-5' exonuclease;
2-163 5.42e-23

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 90.73  E-value: 5.42e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   2 ENAFIALDFETA--NGKRTSICSVGMVKVVNNEIV--ESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQ 77
Cdd:PRK09145   28 PDEWVALDCETTglDPRRAEIVSIAAVKIRGNRILtsERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLA 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  78 FIGKLPVVAHNAAFDMNVLHQSLKQL--------NIETPSMIYFCSY-QLAKRTIDAYrygLKHLMKHYKLDFHGHHDAL 148
Cdd:PRK09145  108 FIGNRPLVGYYLEFDVAMLNRYVRPLlgiplpnpLIEVSALYYDKKErHLPDAYIDLR---FDAILKHLDLPVLGRHDAL 184

                         170
                  ....*....|....*
gi 1091029196 149 NDAKACAMITFRLLK 163
Cdd:PRK09145  185 NDAIMAALIFLRLRK 199
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 1-174 4.73e-21

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 89.63  E-value: 4.73e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   1 MENAFIALDFET-----ANGKRtsICSVGMVKVVNNEIVESFYTLVNPfdyfsQTNI-----EVHGITPEDVNDAPSFEY 70
Cdd:PRK08074    1 MSKRFVVVDLETtgnspKKGDK--IIQIAAVVVEDGEILERFSSFVNP-----ERPIppfitELTGISEEMVKQAPLFED 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  71 VFPYMMQFIGKLPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAK---RTIDAYRygLKHLMKHYKLDFHGHHDA 147
Cdd:PRK08074   74 VAPEIVELLEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARillPTAESYK--LRDLSEELGLEHDQPHRA 151

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1091029196 148 LNDAKACAMITFRLLKH-----YDNLQSMLQI 174
Cdd:PRK08074  152 DSDAEVTAELFLQLLNKlerlpLVTLQQLRRL 183
PRK06807 PRK06807
3'-5' exonuclease;
5-157 9.18e-21

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 87.18  E-value: 9.18e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   5 FIALDFETA--NGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKL 82
Cdd:PRK06807   10 YVVIDFETTgfNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1091029196  83 PVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTI-DAYRYGLKHLMKHYKLDFHGhHDALNDAKACAMI 157
Cdd:PRK06807   90 VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMkHAPNHKLETLKRMLGIRLSS-HNAFDDCITCAAV 164
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 2-182 3.32e-19

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 81.80  E-value: 3.32e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   2 ENAFIALDFETA--NGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:PRK06310    6 DTEFVCLDCETTglDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFF 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  80 GKLP-VVAHNAAFDMNVLHQSLKQLNIETPSMIYFC--SYQLAKRTIDAYRYGLKHLMKHYKLDFHGHHDALNDAKACAM 156
Cdd:PRK06310   86 KEGDyIVGHSVGFDLQVLSQESERIGETFLSKHYYIidTLRLAKEYGDSPNNSLEALAVHFNVPYDGNHRAMKDVEINIK 165

                         170       180
                  ....*....|....*....|....*.
gi 1091029196 157 ITFRLLKHYDNLQSMLQIYGKNLKDK 182
Cdd:PRK06310  166 VFKHLCKRFRTLEQLKQILSKPIKMK 191
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
5-153 1.45e-18

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 82.27  E-value: 1.45e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   5 FIALDFETANGKRT--SICSVGMVKVVNNEIVESFYTLVNPfdyfsQTNIEVH-----GITPEDVNDAPSFEYVFPYMMQ 77
Cdd:PRK07883   17 FVVVDLETTGGSPAgdAITEIGAVKVRGGEVLGEFATLVNP-----GRPIPPFitvltGITTAMVAGAPPIEEVLPAFLE 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1091029196  78 FIGKLPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTI---DAYRYGLKHLMKHYKLDFHGHHDALNDAKA 153
Cdd:PRK07883   92 FARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLprdEAPNVRLSTLARLFGATTTPTHRALDDARA 170
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 5-167 3.59e-18

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 77.59  E-value: 3.59e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   5 FIALDFE-------TANGKRTSICSVGMVKV-VNNEIVESFYTLVNPfDYFSQTN---IEVHGITPEDVNDAPSFEYVFP 73
Cdd:COG5018     4 YLVIDLEatcwdgkPPPGFPMEIIEIGAVKVdENGEIIDEFSSFVKP-VRRPKLSpfcTELTGITQEDVDSAPSFAEAIE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  74 YMMQFIG-KLPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSyqLAKRTIDAY----RYGLKHLMKHYKLDFHG-HHDA 147
Cdd:COG5018    83 DFKKWIGsEDYILCSWGDYDRKQLERNCRFHGVPYPFGDRHIN--LKKLFALYFglkkRIGLKKALELLGLEFEGtHHRA 160

                         170       180
                  ....*....|....*....|
gi 1091029196 148 LNDakacAMITFRLLKHYDN 167
Cdd:COG5018   161 LDD----ARNTAKLFKKILG 176
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 2-173 1.40e-16

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: 74.02  E-value: 1.40e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   2 ENAFIALDFET-ANGKRTSICSVGMVKVVNN-EIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:TIGR00573   6 LDTETTGDNETtGLYAGHDIIEIGAVEIINRrITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYI 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  80 GKLPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFC----SYQLAKRTIDAYRYGLKHLMKHYKLDFHGH--HDALNDAKA 153
Cdd:TIGR00573  86 RGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIdttdTLQYARPEFPGKRNTLDALCKRYEITNSHRalHGALADAFI 165

                         170       180
                  ....*....|....*....|
gi 1091029196 154 CAMITFRLLKHYDNLQSMLQ 173
Cdd:TIGR00573 166 LAKLYLVMTGKQTKYGENEG 185
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 5-164 1.78e-16

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: 73.02  E-value: 1.78e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   5 FIALDFETANGKRTS-------ICSVGMVKVV--NNEIVESFYTLVNPFDYFSQTN--IEVHGITPEDVNDAPSFEYVFP 73
Cdd:cd06133     1 YLVIDFEATCWEGNSkpdypneIIEIGAVLVDvkTKEIIDTFSSYVKPVINPKLSDfcTELTGITQEDVDNAPSFPEVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  74 YMMQFIGKLpvvaHNAAF------DMNVLHQSLKQLNIETPSMiYFCSY-----QLAKRTIDAYRYGLKHLMKHYKLDFH 142
Cdd:cd06133    81 EFLEWLGKN----GKYAFvtwgdwDLKDLLQNQCKYKIINLPP-FFRQWidlkkEFAKFYGLKKRTGLSKALEYLGLEFE 155

                         170       180
                  ....*....|....*....|...
gi 1091029196 143 G-HHDALNDAKacamITFRLLKH 164
Cdd:cd06133   156 GrHHRGLDDAR----NIARILKR 174
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 1-163 2.33e-16

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


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 75.88  E-value: 2.33e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   1 MENAFIALDFE-TANGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:PRK07246    5 KLRKYAVVDLEaTGAGPNASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLI 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  80 GKLPVVAHNAAFDMNVLHQSLkqlnietpsmiYFCSYQLAKRTIDAY-----------RYGLKHLMKHYKLDFHGHHDAL 148
Cdd:PRK07246   85 EDCIFVAHNVKFDANLLAEAL-----------FLEGYELRTPRVDTVelaqvffptleKYSLSHLSRELNIDLADAHTAI 153

                         170
                  ....*....|....*
gi 1091029196 149 NDAKACAMITFRLLK 163
Cdd:PRK07246  154 ADARATAELFLKLLQ 168
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 6-152 2.69e-16

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: 72.18  E-value: 2.69e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   6 IALDFET-----ANGKRtsICSVGMVKVVNNEIV-ESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:cd06131     2 IVLDTETtgldpREGHR--IIEIGCVELINRRLTgNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  80 GKLPVVAHNAAFDMNVLHQSLKQLNIETPsMIYFC----SYQLAKRTIDAYRYGLKHLMKHYKLD-----FHGhhdALND 150
Cdd:cd06131    80 RGAELVIHNASFDVGFLNAELSLLGLGKK-IIDFCrvidTLALARKKFPGKPNSLDALCKRFGIDnshrtLHG---ALLD 155


                  ..
gi 1091029196 151 AK 152
Cdd:cd06131   156 AE 157
dnaQ_proteo TIGR01406
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ...
 6-151 3.29e-16

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: 73.20  E-value: 3.29e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   6 IALDFETANGKRTS---ICSVGMVKVVNNEIV-ESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGK 81
Cdd:TIGR01406   3 IILDTETTGLDPKGghrIVEIGAVELVNRMLTgDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFIGG 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1091029196  82 LPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSY----QLAKRTIDAYRYGLKHLMKHYKLDFHGH--HDALNDA 151
Cdd:TIGR01406  83 SELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVidtlAMARERFPGQRNSLDALCKRFKVDNSHRtlHGALLDA 158
PRK07740 PRK07740
hypothetical protein; Provisional
 5-181 7.18e-16

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 72.78  E-value: 7.18e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   5 FIALDFETA-----NGKRtsICSVGMVKVVNNEIV-ESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQF 78
Cdd:PRK07740   61 FVVFDLETTgfspqQGDE--ILSIGAVKTKGGEVEtDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYAF 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  79 IGKLPVVAHNAAFD---MN-VLHQSLKQ-LN---IETPSMIYFCSYQLAKRTIDAyryglkhLMKHYKLDFHGHHDALND 150
Cdd:PRK07740  139 IGAGVLVAHHAGHDkafLRhALWRTYRQpFThrlIDTMFLTKLLAHERDFPTLDD-------ALAYYGIPIPRRHHALGD 211

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1091029196 151 AKAcamiTFRLLKHYDNLQSMLQIYgkNLKD 181
Cdd:PRK07740  212 ALM----TAKLWAILLVEAQQRGIT--TLHD 236
PRK06063 PRK06063
DEDDh family exonuclease;
9-157 3.85e-12

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 63.18  E-value: 3.85e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   9 DFETANGKRTS--ICSVGMVKV-VNNEIVESFYTLVNPFDYFSQTNIevHGITPEDVNDAPSFEYVFPYMMQFIGKLPVV 85
Cdd:PRK06063   21 DVETSGFRPGQarIISLAVLGLdADGNVEQSVVTLLNPGVDPGPTHV--HGLTAEMLEGQPQFADIAGEVAELLRGRTLV 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1091029196  86 AHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRT---IDAYRygLKHLMKHYKLDFHGHHDALNDAKACAMI 157
Cdd:PRK06063   99 AHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLglgLPNLR--LETLAAHWGVPQQRPHDALDDARVLAGI 171
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 6-160 4.90e-11

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: 57.91  E-value: 4.90e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   6 IALDFE---TANGKRTSICsvGMVKVVN---NEIVESFytlVNPF----DYfsqtNIEVHGITPEDVNDAPSFEYVFPYM 75
Cdd:cd06144     1 VALDCEmvgVGPDGSESAL--ARVSIVNedgNVVYDTY---VKPQepvtDY----RTAVSGIRPEHLKDAPDFEEVQKKV 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  76 MQFI-GKLpVVAHNaafdmnvLHQSLKQLNIETPS-MIY-FCSYQLAKRTIDAYRYGLKHLMKHY-KLDFH-GHHDALND 150
Cdd:cd06144    72 AELLkGRI-LVGHA-------LKNDLKVLKLDHPKkLIRdTSKYKPLRKTAKGKSPSLKKLAKQLlGLDIQeGEHSSVED 143

                         170
                  ....*....|
gi 1091029196 151 AKAcAMITFR 160
Cdd:cd06144   144 ARA-AMRLYR 152
PRK07983 PRK07983
exodeoxyribonuclease X; Provisional
 8-177 8.68e-11

exodeoxyribonuclease X; Provisional


Pssm-ID: 181186 [Multi-domain]  Cd Length: 219  Bit Score: 58.58  E-value: 8.68e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   8 LDFETAnGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPymmQFIGKLPVVAH 87
Cdd:PRK07983    5 IDTETC-GLQGGIVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIP---HYYGSEWYVAH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  88 NAAFDMNVLhqslkqlnietPSMI--YFCSYQLAKRTIDAYRYGLKHLMKHYKLD------FHgHHDALNDakaCaMITF 159
Cdd:PRK07983   81 NASFDRRVL-----------PEMPgeWICTMKLARRLWPGIKYSNMALYKSRKLNvqtppgLH-HHRALYD---C-YITA 144

                         170       180
                  ....*....|....*....|...
gi 1091029196 160 RLLKHYDNL-----QSMLQIYGK 177
Cdd:PRK07983  145 ALLIDIMNTsgwtaEEMADITGR 167
PRK09146 PRK09146
DNA polymerase III subunit epsilon; Validated
 5-155 1.31e-10

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236392 [Multi-domain]  Cd Length: 239  Bit Score: 58.40  E-value: 1.31e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   5 FIALDFETA--NGKRTSICSVGMVKVVNNEIV--ESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVF-PYMMQFI 79
Cdd:PRK09146   49 FVALDFETTglDAEQDAIVSIGLVPFTLQRIRcrQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILdELLEALA 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  80 GKLPVVaHNAAFDMNVLHQSLKQL---NIETP---SMiyfcsyQLAKRTIDAYRYGL-KHLM-------------KHYKL 139
Cdd:PRK09146  129 GKVVVV-HYRRIERDFLDQALRNRigeGIEFPvidTM------EIEARIQRKQAGGLwNRLKgkkpesirladsrLRYGL 201

                         170
                  ....*....|....*.
gi 1091029196 140 DFHGHHDALNDAKACA 155
Cdd:PRK09146  202 PAYSPHHALTDAIATA 217
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 6-151 2.97e-10

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 57.18  E-value: 2.97e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   6 IALDFET-----ANGKRtsICSVGMVKVVNNEIV-ESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:PRK05711    7 IVLDTETtglnqREGHR--IIEIGAVELINRRLTgRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDFI 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1091029196  80 GKLPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFC----SYQLAKRTIDAYRYGLKHLMKHYKLDfHGH---HDALNDA 151
Cdd:PRK05711   85 RGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCkvtdTLAMARRMFPGKRNSLDALCKRYGID-NSHrtlHGALLDA 162
Rv2179c-like pfam16473
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease ...
 5-157 4.14e-10

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: 55.90  E-value: 4.14e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   5 FIALDFETANGKRTS-ICSVGMVKVV--NNEIVESFYTLVNP-FDYFSQTNIEVHGIT----------PEDVN-DAPSFE 69
Cdd:pfam16473   2 HLMIDIETLGNEPTApIVSIGAVFFDpeTGELGKEFYARIDLeSSMSAGATIDADTILwwlkqssearAQLLGdDAPSLP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  70 YVFPYMMQFIGK------LPVVAHNAAFDMNVLHQSLKQLNIETPsMIYF--CSYqlakRTIDAYRYGLKHLMKHYKLDF 141
Cdd:pfam16473  82 DALLDLNDFIRDngdpksLKVWGNGASFDNVILRAAFERGGLPAP-WKYWndRDV----RTIVALGPELGYDPKRDIPFE 156

                         170
                  ....*....|....*.
gi 1091029196 142 HGHHDALNDAKACAMI 157
Cdd:pfam16473 157 GVKHNALDDAIHQAKY 172
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 30-150 1.31e-09

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 55.20  E-value: 1.31e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  30 NNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKLPV-VAHNA-AFDMNVLHQSLKQLNIET 107
Cdd:PRK06309   28 NGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTDNIlVAHNNdAFDFPLLRKECRRHGLEP 107

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1091029196 108 PSMIYFCSYQLAKR-TIDAYRYGLKHLMKHYKLDFHGHHDALND 150
Cdd:PRK06309  108 PTLRTIDSLKWAQKyRPDLPKHNLQYLRQVYGFEENQAHRALDD 151
PRK07942 PRK07942
DNA polymerase III subunit epsilon; Provisional
 6-171 4.51e-08

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 181176 [Multi-domain]  Cd Length: 232  Bit Score: 51.13  E-value: 4.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   6 IALDFET--ANGKRTSICSVGMVKV-VNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDV--NDAPSFEyVFPYMMQFIG 80
Cdd:PRK07942    9 AAFDLETtgVDPETARIVTAALVVVdADGEVVESREWLADPGVEIPEEASAVHGITTEYAraHGRPAAE-VLAEIADALR 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  81 KL-----PVVAHNAAFDMNVLHQSLKQLNIETP-SMIYFCSYQLaKRTIDAYRYG---LKHLMKHYKLDFHGHHDALNDA 151
Cdd:PRK07942   88 EAwargvPVVVFNAPYDLTVLDRELRRHGLPSLvPGPVIDPYVI-DKAVDRYRKGkrtLTALCEHYGVRLDNAHEATADA 166

                         170       180
                  ....*....|....*....|
gi 1091029196 152 KACAMITFRLLKHYDNLQSM 171
Cdd:PRK07942  167 LAAARVAWALARRFPELAAL 186
PRK07748 PRK07748
3'-5' exonuclease KapD;
1-173 1.12e-07

3'-5' exonuclease KapD;


Pssm-ID: 236087  Cd Length: 207  Bit Score: 49.69  E-value: 1.12e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   1 MENAFIALDFE--------TANGKRTSICSVGMVKVVNNEIVESFYTLVNP--FDYFSQTNIEVHGITPEDVNDAPSFEy 70
Cdd:PRK07748    2 DEQQFLFLDFEftmpqhkkKPKGFFPEIIEVGLVSVVGCEVEDTFSSYVKPktFPSLTERCKSFLGITQEDVDKGISFE- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  71 vfpymmQFIGKLPVVAH----------NAafDMNVLHQSLKQLNIETP--------SMIYfcsyqlaKRTI-DAYRYGLK 131
Cdd:PRK07748   81 ------ELVEKLAEYDKrckptivtwgNM--DMKVLKHNCEKAGVPFPfkgqcrdlSLEY-------KKFFgERNQTGLW 145

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1091029196 132 HLMKHYKLDFHG-HHDALNDakacAMITFRLLKHYDNLQSMLQ 173
Cdd:PRK07748  146 KAIEEYGKEGTGkHHCALDD----AMTTYNIFKLVEKDKEYLV 184
PRK06722 PRK06722
exonuclease; Provisional
 1-165 6.90e-07

exonuclease; Provisional


Pssm-ID: 180670 [Multi-domain]  Cd Length: 281  Bit Score: 48.13  E-value: 6.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   1 MENA--FIALDFET-----ANGKRTSICSVGMVKV--VNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYV 71
Cdd:PRK06722    1 MENAthFIVFDIERnfrpyKSEDPSEIVDIGAVKIeaSTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196  72 FPYMMQFIGKLPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTIDAYRYGLKHL------MKHYKLDFHG-H 144
Cdd:PRK06722   81 IEKFIQFIGEDSIFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTpslqsaVEQLGLIWEGkQ 160

                         170       180
                  ....*....|....*....|.
gi 1091029196 145 HDALNDAKACAMItfrLLKHY 165
Cdd:PRK06722  161 HRALADAENTANI---LLKAY 178
PRK07247 PRK07247
3'-5' exonuclease;
1-90 9.36e-06

3'-5' exonuclease;


Pssm-ID: 180906 [Multi-domain]  Cd Length: 195  Bit Score: 44.00  E-value: 9.36e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196   1 MEN--AFIALD--FETANGKrTSICSVGMVKVVNNEIVESFYTLVN---PFDYFSQTnieVHGITPEDVNDAPSFEYVFP 73
Cdd:PRK07247    1 MKRleTYIAFDleFNTVNGV-SHIIQVSAVKYDDHKEVDSFDSYVYtdvPLQSFING---LTGITADKIADAPKVEEVLA 76

                          90
                  ....*....|....*..
gi 1091029196  74 YMMQFIGKLPVVAHNAA 90
Cdd:PRK07247   77 AFKEFVGELPLIGYNAQ 93
 
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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