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Conserved domains on  [gi|2169825714|gb|UHO40005|]
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3'-5' exonuclease [Chryseobacterium capnotolerans]

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 ...
 3-159 8.58e-75

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: 221.23  E-value: 8.58e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   3 FCAIDFETATHEKSSACEMGICVVQDSKIVETKTWLIKPPsfPYFSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELMYGS 82
Cdd:cd06130     1 FVAIDFETANADRASACSIGLVKVRDGQIVDTFYTLIRPP--TRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGS 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2169825714  83 LMIAHNAGFDASVLRGCFEHYGIFPPKMNYLCSIQLAKKSWNYLPKYGLKPLAEYHQIQFNHHRAGADAEVCAKISL 159
Cdd:cd06130    79 LVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIELNHHDALEDARACAEILL 155
 
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 ...
 3-159 8.58e-75

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: 221.23  E-value: 8.58e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   3 FCAIDFETATHEKSSACEMGICVVQDSKIVETKTWLIKPPsfPYFSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELMYGS 82
Cdd:cd06130     1 FVAIDFETANADRASACSIGLVKVRDGQIVDTFYTLIRPP--TRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGS 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2169825714  83 LMIAHNAGFDASVLRGCFEHYGIFPPKMNYLCSIQLAKKSWNYLPKYGLKPLAEYHQIQFNHHRAGADAEVCAKISL 159
Cdd:cd06130    79 LVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIELNHHDALEDARACAEILL 155
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 1-177 6.41e-62

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 194.23  E-value: 6.41e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   1 MDFCAIDFETATHEKSSACEMGICVVQDSKIVETKTWLIKPPSFpYFSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELMY 80
Cdd:PRK06195    1 MNFVAIDFETANEKRNSPCSIGIVVVKDGEIVEKVHYLIKPKEM-RFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  81 GSLMIAHNAGFDASVLRGCFEHYGIFPPKMNYLCSIQLAKKSWNYLPKYGLKPLAEYHQIQFNHHRAGADAEVCAKISLL 160
Cdd:PRK06195   80 NNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFLGYEFKHHDALADAMACSNILLN 159

                         170
                  ....*....|....*..
gi 2169825714 161 AFEKLFITRNEEINESV 177
Cdd:PRK06195  160 ISKELNSKDINEISKLL 176
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 2-157 6.86e-52

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 163.43  E-value: 6.86e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   2 DFCAIDFETA--THEKSSACEMGICVVQDSKIVETKTWLIKPpsFPYFSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELM 79
Cdd:COG0847     1 RFVVLDTETTglDPAKDRIIEIGAVKVDDGRIVETFHTLVNP--ERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2169825714  80 YGSLMIAHNAGFDASVLRGCFEHYGIFPPKMNYLCSIQLAKKSWNYLPKYGLKPLAEYHQIQF-NHHRAGADAEVCAKI 157
Cdd:COG0847    79 GGAVLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPSYSLDALCERLGIPFdERHRALADAEATAEL 157
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 3-157 3.22e-23

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 90.44  E-value: 3.22e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714    3 FCAIDFETA--THEKSSACEMGICVVQDSKIVETKTWLIKPpsFPYFSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELMY 80
Cdd:smart00479   2 LVVIDCETTglDPGKDEIIEIAAVDVDGGEIIEVFDTYVKP--DRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLR 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   81 GSLMIAHN-AGFDASVLRGCFEHYGIFPPKMNY-LCSIQLAKKSWNYLPKYGLKPLAEYH--QIQFNHHRAGADAEVCAK 156
Cdd:smart00479  80 GRILVAGNsAHFDLRFLKLEHPRLGIKQPPKLPvIDTLKLARATNPGLPKYSLKKLAKRLllEVIQRAHRALDDARATAK 159


                   .
gi 2169825714  157 I 157
Cdd:smart00479 160 L 160
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 5-157 8.28e-20

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: 81.63  E-value: 8.28e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   5 AIDFETA--THEKSSACEMGICVVQDS--KIVETKTWLIKPPSFPYFSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELM- 79
Cdd:pfam00929   2 VIDLETTglDPEKDEIIEIAAVVIDGGenEIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFLr 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  80 YGSLMIAHNAGFDASVLRGCFEHYGIFP-PKMN-YLCSIQLAKKSWNYLPKYGLKPLAEYHQIQFN--HHRAGADAEVCA 155
Cdd:pfam00929  82 KGNLLVAHNASFDVGFLRYDDKRFLKKPmPKLNpVIDTLILDKATYKELPGRSLDALAEKLGLEHIgrAHRALDDARATA 161


                  ..
gi 2169825714 156 KI 157
Cdd:pfam00929 162 KL 163
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 3-164 7.74e-10

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: 55.92  E-value: 7.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   3 FCAIDFETATH-EKSSACEMGICVVQDSKIVETK-TWLIKPPSFpyFSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELMY 80
Cdd:TIGR00573   9 ETTGDNETTGLyAGHDIIEIGAVEIINRRITGNKfHTYIKPDRP--IDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIR 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  81 GSLMIAHNAGFDASVLRGCFEHYGIFPPKMNYLCSI-QLAKKSWNYLP--KYGLKPLAEYHQIQFNH---HRAGADAEVC 154
Cdd:TIGR00573  87 GAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTtDTLQYARPEFPgkRNTLDALCKRYEITNSHralHGALADAFIL 166

                         170
                  ....*....|
gi 2169825714 155 AKISLLAFEK 164
Cdd:TIGR00573 167 AKLYLVMTGK 176
 
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 ...
 3-159 8.58e-75

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: 221.23  E-value: 8.58e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   3 FCAIDFETATHEKSSACEMGICVVQDSKIVETKTWLIKPPsfPYFSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELMYGS 82
Cdd:cd06130     1 FVAIDFETANADRASACSIGLVKVRDGQIVDTFYTLIRPP--TRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGS 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2169825714  83 LMIAHNAGFDASVLRGCFEHYGIFPPKMNYLCSIQLAKKSWNYLPKYGLKPLAEYHQIQFNHHRAGADAEVCAKISL 159
Cdd:cd06130    79 LVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIELNHHDALEDARACAEILL 155
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 1-177 6.41e-62

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 194.23  E-value: 6.41e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   1 MDFCAIDFETATHEKSSACEMGICVVQDSKIVETKTWLIKPPSFpYFSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELMY 80
Cdd:PRK06195    1 MNFVAIDFETANEKRNSPCSIGIVVVKDGEIVEKVHYLIKPKEM-RFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  81 GSLMIAHNAGFDASVLRGCFEHYGIFPPKMNYLCSIQLAKKSWNYLPKYGLKPLAEYHQIQFNHHRAGADAEVCAKISLL 160
Cdd:PRK06195   80 NNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFLGYEFKHHDALADAMACSNILLN 159

                         170
                  ....*....|....*..
gi 2169825714 161 AFEKLFITRNEEINESV 177
Cdd:PRK06195  160 ISKELNSKDINEISKLL 176
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 2-157 6.86e-52

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 163.43  E-value: 6.86e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   2 DFCAIDFETA--THEKSSACEMGICVVQDSKIVETKTWLIKPpsFPYFSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELM 79
Cdd:COG0847     1 RFVVLDTETTglDPAKDRIIEIGAVKVDDGRIVETFHTLVNP--ERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2169825714  80 YGSLMIAHNAGFDASVLRGCFEHYGIFPPKMNYLCSIQLAKKSWNYLPKYGLKPLAEYHQIQF-NHHRAGADAEVCAKI 157
Cdd:COG0847    79 GGAVLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPSYSLDALCERLGIPFdERHRALADAEATAEL 157
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 1-165 2.86e-39

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 132.19  E-value: 2.86e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   1 MDFCAIDFET--ATHEKSSACEMGICVVQDSKIVETKTWLIKPP-SFPYFSkfnIAVHGIQPEDVQDAPTFDEIWYEAEE 77
Cdd:COG2176     8 LTYVVFDLETtgLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGrPIPPFI---TELTGITDEMVADAPPFEEVLPEFLE 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  78 LMYGSLMIAHNAGFDASVLRGCFEHYGIfPPKMNYLCSIQLAKKSWNYLPKYGLKPLAEYHQIQF-NHHRAGADAEVCAK 156
Cdd:COG2176    85 FLGDAVLVAHNASFDLGFLNAALKRLGL-PFDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLeDRHRALGDAEATAE 163


                  ....*....
gi 2169825714 157 ISLLAFEKL 165
Cdd:COG2176   164 LFLKLLEKL 172
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 4-157 7.98e-36

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: 122.41  E-value: 7.98e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   4 CAIDFETaT---HEKSSACEMGICVVQD-SKIVETKTWLIKPPSFPyfSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELM 79
Cdd:cd06127     1 VVFDTET-TgldPKKDRIIEIGAVKVDGgIEIVERFETLVNPGRPI--PPEATAIHGITDEMLADAPPFEEVLPEFLEFL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  80 YGSLMIAHNAGFDASVLRGCFEHYGIFPPKMNYLCSIQLAKKSWNYLPKYGLKPL--AEYHQIQFNHHRAGADAEVCAKI 157
Cdd:cd06127    78 GGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLlaERYGIPLEGAHRALADALATAEL 157
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 3-157 3.22e-23

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 90.44  E-value: 3.22e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714    3 FCAIDFETA--THEKSSACEMGICVVQDSKIVETKTWLIKPpsFPYFSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELMY 80
Cdd:smart00479   2 LVVIDCETTglDPGKDEIIEIAAVDVDGGEIIEVFDTYVKP--DRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLR 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   81 GSLMIAHN-AGFDASVLRGCFEHYGIFPPKMNY-LCSIQLAKKSWNYLPKYGLKPLAEYH--QIQFNHHRAGADAEVCAK 156
Cdd:smart00479  80 GRILVAGNsAHFDLRFLKLEHPRLGIKQPPKLPvIDTLKLARATNPGLPKYSLKKLAKRLllEVIQRAHRALDDARATAK 159


                   .
gi 2169825714  157 I 157
Cdd:smart00479 160 L 160
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 3-165 1.12e-22

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 94.25  E-value: 1.12e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   3 FCAIDFETATHEKSSACEM---GICVVQDSKIVETKTWLIKP--PSFPYFSKFNiavhGIQPEDVQDAPTFDEIWYEAEE 77
Cdd:PRK08074    5 FVVVDLETTGNSPKKGDKIiqiAAVVVEDGEILERFSSFVNPerPIPPFITELT----GISEEMVKQAPLFEDVAPEIVE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  78 LMYGSLMIAHNAGFDASVLRGCFEHYGIFPPKMNYLCSIQLAKKSWNYLPKYGLKPLAEYHQIQFNH-HRAGADAEVCAK 156
Cdd:PRK08074   81 LLEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEELGLEHDQpHRADSDAEVTAE 160


                  ....*....
gi 2169825714 157 ISLLAFEKL 165
Cdd:PRK08074  161 LFLQLLNKL 169
polC PRK00448
DNA polymerase III PolC; Validated
 20-185 2.81e-21

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 90.28  E-value: 2.81e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   20 EMGICVVQDSKIVETKTWLIKPpSFPyFSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELMYGSLMIAHNAGFDASVLRGC 99
Cdd:PRK00448   440 EIGAVKIKNGEIIDKFEFFIKP-GHP-LSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGDSILVAHNASFDVGFINTN 517

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  100 FEHYGIFPPKMNYLCSIQLAKKSWNYLPKYGLKPLAEYHQIQ-FNHHRAGADAEVCAKISLLAFEKLF---ITRNEEINE 175
Cdd:PRK00448   518 YEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVElEHHHRADYDAEATAYLLIKFLKDLKekgITNLDELNK 597

                          170
                   ....*....|
gi 2169825714  176 SVLKNYIKKL 185
Cdd:PRK00448   598 KLGSEDAYKK 607
PRK08517 PRK08517
3'-5' exonuclease;
2-165 6.71e-20

3'-5' exonuclease;


Pssm-ID: 236281 [Multi-domain]  Cd Length: 257  Bit Score: 83.92  E-value: 6.71e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   2 DFCAIDFET--ATHEKSSACEMGICVVQDSKIVETKTWLIKPPSFPYfskfNIA-VHGIQPEDVQDAPTFDEIWYEAEEL 78
Cdd:PRK08517   69 VFCFVDIETngSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAKEVPE----YITeLTGITYEDLENAPSLKEVLEEFRLF 144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  79 MYGSLMIAHNAGFDASVLRGCFEHYGIFPPKMNYLCSIQLAKKSWNYlPKYGLKPLAEYHQIQ-FNHHRAGADAEVCAKI 157
Cdd:PRK08517  145 LGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIES-PRYGLSFLKELLGIEiEVHHRAYADALAAYEI 223


                  ....*...
gi 2169825714 158 SLLAFEKL 165
Cdd:PRK08517  224 FKICLLNL 231
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 5-157 8.28e-20

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: 81.63  E-value: 8.28e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   5 AIDFETA--THEKSSACEMGICVVQDS--KIVETKTWLIKPPSFPYFSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELM- 79
Cdd:pfam00929   2 VIDLETTglDPEKDEIIEIAAVVIDGGenEIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFLr 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  80 YGSLMIAHNAGFDASVLRGCFEHYGIFP-PKMN-YLCSIQLAKKSWNYLPKYGLKPLAEYHQIQFN--HHRAGADAEVCA 155
Cdd:pfam00929  82 KGNLLVAHNASFDVGFLRYDDKRFLKKPmPKLNpVIDTLILDKATYKELPGRSLDALAEKLGLEHIgrAHRALDDARATA 161


                  ..
gi 2169825714 156 KI 157
Cdd:pfam00929 162 KL 163
PRK06063 PRK06063
DEDDh family exonuclease;
54-157 8.55e-14

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 67.80  E-value: 8.55e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  54 VHGIQPEDVQDAPTFDEIWYEAEELMYGSLMIAHNAGFDASVLRGCFEHYGIFPPKMNYLCSIQLAKKSWNYLPKYGLKP 133
Cdd:PRK06063   67 VHGLTAEMLEGQPQFADIAGEVAELLRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLET 146

                          90       100
                  ....*....|....*....|....*
gi 2169825714 134 LAEYHQI-QFNHHRAGADAEVCAKI 157
Cdd:PRK06063  147 LAAHWGVpQQRPHDALDDARVLAGI 171
PRK06807 PRK06807
3'-5' exonuclease;
2-159 1.19e-11

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 61.75  E-value: 1.19e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   2 DFCAIDFETATHEKSSACEMGICVVQ--DSKIVETKTWLIKPPSFpyFSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELM 79
Cdd:PRK06807    9 DYVVIDFETTGFNPYNDKIIQVAAVKyrNHELVDQFVSYVNPERP--IPDRITSLTGITNYRVSDAPTIEEVLPLFLAFL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  80 YGSLMIAHNAGFDASVLRGCFEHYGIFPPKMNYLCSIQLAKKSWNYLPKYGLKPLAEYHQIQFNHHRAGADAEVCAKISL 159
Cdd:PRK06807   87 HTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSSHNAFDDCITCAAVYQ 166
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 6-165 6.71e-11

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


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 60.09  E-value: 6.71e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   6 IDFE-TATHEKSSACEMGICVVQDSKIVETKTWLIKP--PsfpyFSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELMYGS 82
Cdd:PRK07246   12 VDLEaTGAGPNASIIQVGIVIIEGGEIIDSYTTDVNPheP----LDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDC 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  83 LMIAHNAGFDASVLRGC--FEHYGIFPPKMNylcSIQLAKKSWNYLPKYGLKPLAEYHQIQFNH-HRAGADAEVCAKISL 159
Cdd:PRK07246   88 IFVAHNVKFDANLLAEAlfLEGYELRTPRVD---TVELAQVFFPTLEKYSLSHLSRELNIDLADaHTAIADARATAELFL 164


                  ....*.
gi 2169825714 160 LAFEKL 165
Cdd:PRK07246  165 KLLQKI 170
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 3-164 7.74e-10

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: 55.92  E-value: 7.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   3 FCAIDFETATH-EKSSACEMGICVVQDSKIVETK-TWLIKPPSFpyFSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELMY 80
Cdd:TIGR00573   9 ETTGDNETTGLyAGHDIIEIGAVEIINRRITGNKfHTYIKPDRP--IDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIR 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  81 GSLMIAHNAGFDASVLRGCFEHYGIFPPKMNYLCSI-QLAKKSWNYLP--KYGLKPLAEYHQIQFNH---HRAGADAEVC 154
Cdd:TIGR00573  87 GAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTtDTLQYARPEFPgkRNTLDALCKRYEITNSHralHGALADAFIL 166

                         170
                  ....*....|
gi 2169825714 155 AKISLLAFEK 164
Cdd:TIGR00573 167 AKLYLVMTGK 176
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 1-157 1.35e-09

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 54.48  E-value: 1.35e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   1 MDFCAIDFETATHEKSS--ACEM-----GICVVQ-DSKIVETKTWLIKPPSFPYFSKFNIAVHGIQPEDVQDAPTFDEI- 71
Cdd:COG5018     2 MKYLVIDLEATCWDGKPppGFPMeiieiGAVKVDeNGEIIDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEAi 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  72 -----WYEAEELMYGSlmiahNAGFDASVL-RGCfEHYGIFPPKMNYLCSIQLAKKSWNYLPK-YGLKPLAEYHQIQF-- 142
Cdd:COG5018    82 edfkkWIGSEDYILCS-----WGDYDRKQLeRNC-RFHGVPYPFGDRHINLKKLFALYFGLKKrIGLKKALELLGLEFeg 155

                         170
                  ....*....|....*
gi 2169825714 143 NHHRAGADAEVCAKI 157
Cdd:COG5018   156 THHRALDDARNTAKL 170
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 53-147 4.73e-09

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 54.05  E-value: 4.73e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  53 AVHGIQPEDVQDAPTFDEIWYEAEELMYG-SLMIAHNA-GFDASVLRGCFEHYGIFPPKMNYLCSIQLAKKSWNYLPKYG 130
Cdd:PRK06309   51 KIHGITTDEVADAPKFPEAYQKFIEFCGTdNILVAHNNdAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHN 130

                          90
                  ....*....|....*...
gi 2169825714 131 LKPLAEYHQIQFNH-HRA 147
Cdd:PRK06309  131 LQYLRQVYGFEENQaHRA 148
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
3-152 9.79e-09

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 53.77  E-value: 9.79e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   3 FCAIDFETaTHEKSSAC---EMGICVVQDSKIVETKTWLIKPP-SFPYFskfnIAV-HGIQPEDVQDAPTFDEIWYEAEE 77
Cdd:PRK07883   17 FVVVDLET-TGGSPAGDaitEIGAVKVRGGEVLGEFATLVNPGrPIPPF----ITVlTGITTAMVAGAPPIEEVLPAFLE 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2169825714  78 LMYGSLMIAHNAGFDASVLRGCFEHYGIFPPKMNYLCSIQLAKK--SWNYLPKYGLKPLAEYHQI-QFNHHRAGADAE 152
Cdd:PRK07883   92 FARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRvlPRDEAPNVRLSTLARLFGAtTTPTHRALDDAR 169
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 52-121 1.02e-08

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: 52.15  E-value: 1.02e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2169825714  52 IAVHGIQPEDVQDAPTFDEIWYEAEELMYGSLMIAHNAGFDASVLRGCFEHYGIFPPKMNY---LCSIQLAKK 121
Cdd:cd06131    52 FKVHGITDEFLADKPKFAEIADEFLDFIRGAELVIHNASFDVGFLNAELSLLGLGKKIIDFcrvIDTLALARK 124
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 3-151 1.62e-08

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: 51.45  E-value: 1.62e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   3 FCAIDFEtATHEKSSAC--------EMGICVVQDS--KIVETKTWLIKPPSFPYFSKFNIAVHGIQPEDVQDAPTFDEIW 72
Cdd:cd06133     1 YLVIDFE-ATCWEGNSKpdypneiiEIGAVLVDVKtkEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  73 YEAEELM--YGSLMIAHNAGFDASVLRGCFEHYGI---FPPKMNYLCSIQLAKKSWNYLPKYGLKPLAEYHQIQFN--HH 145
Cdd:cd06133    80 KEFLEWLgkNGKYAFVTWGDWDLKDLLQNQCKYKIinlPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEgrHH 159


                  ....*.
gi 2169825714 146 RAGADA 151
Cdd:cd06133   160 RGLDDA 165
PRK07983 PRK07983
exodeoxyribonuclease X; Provisional
 6-155 2.85e-07

exodeoxyribonuclease X; Provisional


Pssm-ID: 181186 [Multi-domain]  Cd Length: 219  Bit Score: 48.56  E-value: 2.85e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   6 IDFETATHEkSSACEMGICVVQDSKIVETKTWLIKP--PsfpyFSKFNIAVHGIQPEDVQDAPTFDEiwyeAEELMYGS- 82
Cdd:PRK07983    5 IDTETCGLQ-GGIVEIASVDVIDGKIVNPMSHLVRPdrP----ISPQAMAIHRITEAMVADKPWIED----VIPHYYGSe 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  83 LMIAHNAGFDASVLrgcfehygifpPKMN--YLCSIQLAKKSWNYLpKYGLKPLAEYHQIQ------FNHHRAGADAEVC 154
Cdd:PRK07983   76 WYVAHNASFDRRVL-----------PEMPgeWICTMKLARRLWPGI-KYSNMALYKSRKLNvqtppgLHHHRALYDCYIT 143


                  .
gi 2169825714 155 A 155
Cdd:PRK07983  144 A 144
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 52-155 3.28e-06

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 45.62  E-value: 3.28e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  52 IAVHGIQPEDVQDAPTFDEIWYEAEELMYGSLMIAHNAGFDASVLRGCFEHYGIFPPKMNYLCSI----QLAKKSWnylP 127
Cdd:PRK05711   57 LAVHGITDEFLADKPTFAEVADEFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVtdtlAMARRMF---P 133

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2169825714 128 --KYGLKPLAEYHQIQfNHHRA--GA--DAEVCA 155
Cdd:PRK05711  134 gkRNSLDALCKRYGID-NSHRTlhGAllDAEILA 166
dnaQ_proteo TIGR01406
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ...
 54-160 3.42e-06

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: 45.85  E-value: 3.42e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  54 VHGIQPEDVQDAPTFDEIWYEAEELMYGSLMIAHNAGFDASVLRGCFEHYGIFPPKMNYLCS----IQLAKKSWnylP-- 127
Cdd:TIGR01406  55 VHGITDEFLADKPKFKEIADEFLDFIGGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRvidtLAMARERF---Pgq 131

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2169825714 128 KYGLKPLAEYHQIQFNH---HRAGADAEVCAKISLL 160
Cdd:TIGR01406 132 RNSLDALCKRFKVDNSHrtlHGALLDAHLLAEVYLA 167
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 23-157 3.01e-05

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 42.89  E-value: 3.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  23 ICVVQDSKIVETKTwLIKPPSfpYFSKFNIAVHGIQPEDVQDAPTFDEIWYEAEELMY-GSLMIAHNAGFDASVLRGCFE 101
Cdd:PRK06310   32 IRFTFDEVIDSVEF-LINPER--VVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFKeGDYIVGHSVGFDLQVLSQESE 108

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2169825714 102 HYGI-FPPKMNYLCSIQLAKKSWNYLPKYGLKPLAEYHQIQFN-HHRAGADAEVCAKI 157
Cdd:PRK06310  109 RIGEtFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYDgNHRAMKDVEINIKV 166
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 53-145 4.41e-04

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: 39.04  E-value: 4.41e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  53 AVHGIQPEDVQDAPTFDEIWYEAEELMYGSLMIAHNAGFDASVLRgcFEHygifPPKM-----NYLcsiQLAKKSWNYLP 127
Cdd:cd06144    49 AVSGIRPEHLKDAPDFEEVQKKVAELLKGRILVGHALKNDLKVLK--LDH----PKKLirdtsKYK---PLRKTAKGKSP 119

                          90       100
                  ....*....|....*....|.
gi 2169825714 128 kyGLKPLAEYH---QIQFNHH 145
Cdd:cd06144   120 --SLKKLAKQLlglDIQEGEH 138
PRK09146 PRK09146
DNA polymerase III subunit epsilon; Validated
 2-87 4.66e-04

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236392 [Multi-domain]  Cd Length: 239  Bit Score: 39.52  E-value: 4.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   2 DFCAIDFETAthekssacemGICVVQDSkIV---------------ETKTWLIKPPSfpYFSKFNIAVHGIQPEDVQDAP 66
Cdd:PRK09146   48 PFVALDFETT----------GLDAEQDA-IVsiglvpftlqrircrQARHWVVKPRR--PLEEESVVIHGITHSELQDAP 114

                          90       100
                  ....*....|....*....|.
gi 2169825714  67 TFDEIWYEAEELMYGSLMIAH 87
Cdd:PRK09146  115 DLERILDELLEALAGKVVVVH 135
Rv2179c-like pfam16473
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease ...
 62-157 5.72e-04

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: 38.95  E-value: 5.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  62 VQDAPTFDEIWYEAEE-LMYGSLM-----IAHNAGFDASVLRGCFEHYGIFPPKM--NYLC--SIQLAKKSWNYLPKYGL 131
Cdd:pfam16473  74 GDDAPSLPDALLDLNDfIRDNGDPkslkvWGNGASFDNVILRAAFERGGLPAPWKywNDRDvrTIVALGPELGYDPKRDI 153

                          90       100
                  ....*....|....*....|....*.
gi 2169825714 132 kplaeyhQIQFNHHRAGADAEVCAKI 157
Cdd:pfam16473 154 -------PFEGVKHNALDDAIHQAKY 172
PRK07748 PRK07748
3'-5' exonuclease KapD;
1-157 7.36e-04

3'-5' exonuclease KapD;


Pssm-ID: 236087  Cd Length: 207  Bit Score: 38.90  E-value: 7.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714   1 MDFCAIDFE-TATHEKSSA-------CEMGICVVQDSKIVETKTWLIKPPSFPYFSKFNIAVHGIQPEDVQDAPTFDEI- 71
Cdd:PRK07748    4 QQFLFLDFEfTMPQHKKKPkgffpeiIEVGLVSVVGCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEELv 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  72 --------WYEAEELMYGSLmiahnagfDASVLRGCFEHYGI-FPPKMNYlcsIQLAKKSWNYLPKYGL----KPLAEYH 138
Cdd:PRK07748   84 eklaeydkRCKPTIVTWGNM--------DMKVLKHNCEKAGVpFPFKGQC---RDLSLEYKKFFGERNQtglwKAIEEYG 152

                         170       180
                  ....*....|....*....|
gi 2169825714 139 QIQFN-HHRAGADAEVCAKI 157
Cdd:PRK07748  153 KEGTGkHHCALDDAMTTYNI 172
PRK09182 PRK09182
DNA polymerase III subunit epsilon; Validated
 53-163 5.27e-03

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236397 [Multi-domain]  Cd Length: 294  Bit Score: 36.49  E-value: 5.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2169825714  53 AVHGIQPEDVQDApTFDeiWYEAEELMY-GSLMIAHNAGFDasvlRGCFEHYG-IFPPKMnYLCSiqLAKKSWNYLPKYG 130
Cdd:PRK09182   95 RLTGITDEMVAGQ-TID--PAAVDALIApADLIIAHNAGFD----RPFLERFSpVFATKP-WACS--VSEIDWSARGFEG 164

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2169825714 131 LKP--LAEYHQIQFNHHRAGADAEvcAKISLLAFE 163
Cdd:PRK09182  165 TKLgyLAGQAGFFHEGHRAVDDCQ--ALLELLARP 197
 
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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