|
Name |
Accession |
Description |
Interval |
E-value |
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
105-265 |
9.24e-36 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 125.68 E-value: 9.24e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 105 LFLDTETTGLD-NTAEALEIGLTDV------AVFETRLKPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRP 177
Cdd:COG0847 3 VVLDTETTGLDpAKDRIIEIGAVKVddgrivETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGAV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 178 VIIFNARFDIRILKQTAAAHSDPADWleeMTVYCAMELAAGYYRATNRYgtiSLASAASQAGLTWEGlAHSAIADARMTA 257
Cdd:COG0847 83 LVAHNAAFDLGFLNAELRRAGLPLPP---FPVLDTLRLARRLLPGLPSY---SLDALCERLGIPFDE-RHRALADAEATA 155
|
....*...
gi 485779841 258 GVVNAIAA 265
Cdd:COG0847 156 ELFLALLR 163
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
105-259 |
1.58e-35 |
|
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: 124.72 E-value: 1.58e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 105 LFLDTETTGLD-NTAEALEIGLTDVA-------VFETRLKPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIGDR 176
Cdd:cd06127 1 VVFDTETTGLDpKKDRIIEIGAVKVDggieiveRFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 177 PVIIFNARFDIRILKQTAAAHSDPadwLEEMTVYCAMELAAGYYRATNRYgtiSLASAASQAGLTWEGLAHSAIADARMT 256
Cdd:cd06127 81 VLVAHNASFDLRFLNRELRRLGGP---PLPNPWIDTLRLARRLLPGLRSH---RLGLLLAERYGIPLEGAHRALADALAT 154
|
...
gi 485779841 257 AGV 259
Cdd:cd06127 155 AEL 157
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
105-268 |
5.13e-33 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 118.56 E-value: 5.13e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 105 LFLDTETTGLDN-TAEALEIGLTDVA------VFETRLKPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRP 177
Cdd:smart00479 3 VVIDCETTGLDPgKDEIIEIAAVDVDggeiieVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGRI 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 178 VIIFN-ARFDIRILKQTAAAHSDPADWLEEmtVYCAMELAAGYYRATNRYgtiSLASAASQAGLTWEGLAHSAIADARMT 256
Cdd:smart00479 83 LVAGNsAHFDLRFLKLEHPRLGIKQPPKLP--VIDTLKLARATNPGLPKY---SLKKLAKRLLLEVIQRAHRALDDARAT 157
|
170
....*....|..
gi 485779841 257 AGVVNAIAAYHL 268
Cdd:smart00479 158 AKLFKKLLERLE 169
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
105-259 |
2.51e-13 |
|
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: 66.22 E-value: 2.51e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 105 LFLDTETTGLDN-TAEALEIG--------LTDVAVFETRLKPTVAIGVQAAAV--HGISEQALCGAPSWTDVARQLRHAI 173
Cdd:pfam00929 1 VVIDLETTGLDPeKDEIIEIAavvidggeNEIGETFHTYVKPTRLPKLTDECTkfTGITQAMLDNKPSFEEVLEEFLEFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 174 G-DRPVIIFNARFDIRILKQTAAAHSdPADWLEEMTVYCAMELAAGYYraTNRYGTiSLASAASQAGLTWEGLAHSAIAD 252
Cdd:pfam00929 81 RkGNLLVAHNASFDVGFLRYDDKRFL-KKPMPKLNPVIDTLILDKATY--KELPGR-SLDALAEKLGLEHIGRAHRALDD 156
|
....*..
gi 485779841 253 ARMTAGV 259
Cdd:pfam00929 157 ARATAKL 163
|
|
| dnaQ_proteo |
TIGR01406 |
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ... |
107-192 |
9.55e-11 |
|
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: 60.10 E-value: 9.55e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 107 LDTETTGLDNTA--EALEIGLTDVA-------VFETRLKPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRP 177
Cdd:TIGR01406 5 LDTETTGLDPKGghRIVEIGAVELVnrmltgdNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFIGGSE 84
|
90
....*....|....*
gi 485779841 178 VIIFNARFDIRILKQ 192
Cdd:TIGR01406 85 LVIHNAAFDVGFLNY 99
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
91-257 |
1.30e-10 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 59.53 E-value: 1.30e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 91 RMARQAYDWLSLAP-----LFLDTETTGLD-NTAEALEIG---------LTDVAvFETRLKPTVAIGVQAAAVHGISEQA 155
Cdd:PRK09145 13 RLKDPRYAFLFEPPppdewVALDCETTGLDpRRAEIVSIAavkirgnriLTSER-LELLVRPPQSLSAESIKIHRLRHQD 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 156 LCGAPSWTDVARQLRHAIGDRPVIIFNARFDIRILKQTAAAHSD---PADwleemtvycAMELAAGYYRATNR-----YG 227
Cdd:PRK09145 92 LEDGLSEEEALRQLLAFIGNRPLVGYYLEFDVAMLNRYVRPLLGiplPNP---------LIEVSALYYDKKERhlpdaYI 162
|
170 180 190
....*....|....*....|....*....|.
gi 485779841 228 TISLASAASQAGL-TWEglAHSAIADARMTA 257
Cdd:PRK09145 163 DLRFDAILKHLDLpVLG--RHDALNDAIMAA 191
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
105-265 |
9.24e-36 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 125.68 E-value: 9.24e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 105 LFLDTETTGLD-NTAEALEIGLTDV------AVFETRLKPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRP 177
Cdd:COG0847 3 VVLDTETTGLDpAKDRIIEIGAVKVddgrivETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGAV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 178 VIIFNARFDIRILKQTAAAHSDPADWleeMTVYCAMELAAGYYRATNRYgtiSLASAASQAGLTWEGlAHSAIADARMTA 257
Cdd:COG0847 83 LVAHNAAFDLGFLNAELRRAGLPLPP---FPVLDTLRLARRLLPGLPSY---SLDALCERLGIPFDE-RHRALADAEATA 155
|
....*...
gi 485779841 258 GVVNAIAA 265
Cdd:COG0847 156 ELFLALLR 163
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
105-259 |
1.58e-35 |
|
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: 124.72 E-value: 1.58e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 105 LFLDTETTGLD-NTAEALEIGLTDVA-------VFETRLKPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIGDR 176
Cdd:cd06127 1 VVFDTETTGLDpKKDRIIEIGAVKVDggieiveRFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 177 PVIIFNARFDIRILKQTAAAHSDPadwLEEMTVYCAMELAAGYYRATNRYgtiSLASAASQAGLTWEGLAHSAIADARMT 256
Cdd:cd06127 81 VLVAHNASFDLRFLNRELRRLGGP---PLPNPWIDTLRLARRLLPGLRSH---RLGLLLAERYGIPLEGAHRALADALAT 154
|
...
gi 485779841 257 AGV 259
Cdd:cd06127 155 AEL 157
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
105-268 |
5.13e-33 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 118.56 E-value: 5.13e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 105 LFLDTETTGLDN-TAEALEIGLTDVA------VFETRLKPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRP 177
Cdd:smart00479 3 VVIDCETTGLDPgKDEIIEIAAVDVDggeiieVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGRI 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 178 VIIFN-ARFDIRILKQTAAAHSDPADWLEEmtVYCAMELAAGYYRATNRYgtiSLASAASQAGLTWEGLAHSAIADARMT 256
Cdd:smart00479 83 LVAGNsAHFDLRFLKLEHPRLGIKQPPKLP--VIDTLKLARATNPGLPKY---SLKKLAKRLLLEVIQRAHRALDDARAT 157
|
170
....*....|..
gi 485779841 257 AGVVNAIAAYHL 268
Cdd:smart00479 158 AKLFKKLLERLE 169
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
106-274 |
3.32e-26 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 101.37 E-value: 3.32e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 106 FLDTETTGLD-NTAEALEIGltdvAV----------FETRLKPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIG 174
Cdd:COG2176 12 VFDLETTGLSpKKDEIIEIG----AVkvengeivdrFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLEFLG 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 175 DRPVIIFNARFDIRILKQTAAAHSDPADwleeMTVYCAMELAAGYYRATNRYgtiSLASAASQAGLTWEGlAHSAIADAR 254
Cdd:COG2176 88 DAVLVAHNASFDLGFLNAALKRLGLPFD----NPVLDTLELARRLLPELKSY---KLDTLAERLGIPLED-RHRALGDAE 159
|
170 180
....*....|....*....|
gi 485779841 255 MTAGVVNAIaayhLELLQEQ 274
Cdd:COG2176 160 ATAELFLKL----LEKLEEK 175
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
105-259 |
2.51e-13 |
|
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: 66.22 E-value: 2.51e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 105 LFLDTETTGLDN-TAEALEIG--------LTDVAVFETRLKPTVAIGVQAAAV--HGISEQALCGAPSWTDVARQLRHAI 173
Cdd:pfam00929 1 VVIDLETTGLDPeKDEIIEIAavvidggeNEIGETFHTYVKPTRLPKLTDECTkfTGITQAMLDNKPSFEEVLEEFLEFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 174 G-DRPVIIFNARFDIRILKQTAAAHSdPADWLEEMTVYCAMELAAGYYraTNRYGTiSLASAASQAGLTWEGLAHSAIAD 252
Cdd:pfam00929 81 RkGNLLVAHNASFDVGFLRYDDKRFL-KKPMPKLNPVIDTLILDKATY--KELPGR-SLDALAEKLGLEHIGRAHRALDD 156
|
....*..
gi 485779841 253 ARMTAGV 259
Cdd:pfam00929 157 ARATAKL 163
|
|
| KapD |
COG5018 |
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
150-263 |
6.66e-13 |
|
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];
Pssm-ID: 444042 [Multi-domain] Cd Length: 181 Bit Score: 65.65 E-value: 6.66e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 150 GISEQALCGAPSWTDVARQLRHAIGDRPVIIFN-ARFDIRILKQTAAAHSDPADWLEEMtvycaMELAAGYYRATNRYGT 228
Cdd:COG5018 65 GITQEDVDSAPSFAEAIEDFKKWIGSEDYILCSwGDYDRKQLERNCRFHGVPYPFGDRH-----INLKKLFALYFGLKKR 139
|
90 100 110
....*....|....*....|....*....|....*
gi 485779841 229 ISLASAASQAGLTWEGLAHSAIADARMTAGVVNAI 263
Cdd:COG5018 140 IGLKKALELLGLEFEGTHHRALDDARNTAKLFKKI 174
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
147-260 |
9.47e-12 |
|
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: 61.76 E-value: 9.47e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 147 AVHGISEQALCGAPSWTDVARQLRHAIGDRPVIIFNARFDIRILKQTAAAHSDPADwleEMTVYCAMELAAGYYRATNRY 226
Cdd:cd06130 49 AIHGITPEDVADAPTFPEVWPEIKPFLGGSLVVAHNASFDRSVLRAALEAYGLPPP---PYQYLCTVRLARRVWPLLPNH 125
|
90 100 110
....*....|....*....|....*....|....
gi 485779841 227 GtisLASAASQAGLTWEglAHSAIADARMTAGVV 260
Cdd:cd06130 126 K---LNTVAEHLGIELN--HHDALEDARACAEIL 154
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
105-216 |
1.72e-11 |
|
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.
Pssm-ID: 99835 [Multi-domain] Cd Length: 167 Bit Score: 61.39 E-value: 1.72e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 105 LFLDTETTGLDNTA--EALEIGLTDVA-------VFETRLKPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIGD 175
Cdd:cd06131 2 IVLDTETTGLDPREghRIIEIGCVELInrrltgnTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIRG 81
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 485779841 176 RPVIIFNARFDIRILKQTAAAHSDPADWLEEMTVYCAMELA 216
Cdd:cd06131 82 AELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALA 122
|
|
| dnaQ_proteo |
TIGR01406 |
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ... |
107-192 |
9.55e-11 |
|
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: 60.10 E-value: 9.55e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 107 LDTETTGLDNTA--EALEIGLTDVA-------VFETRLKPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRP 177
Cdd:TIGR01406 5 LDTETTGLDPKGghRIVEIGAVELVnrmltgdNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFIGGSE 84
|
90
....*....|....*
gi 485779841 178 VIIFNARFDIRILKQ 192
Cdd:TIGR01406 85 LVIHNAAFDVGFLNY 99
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
91-257 |
1.30e-10 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 59.53 E-value: 1.30e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 91 RMARQAYDWLSLAP-----LFLDTETTGLD-NTAEALEIG---------LTDVAvFETRLKPTVAIGVQAAAVHGISEQA 155
Cdd:PRK09145 13 RLKDPRYAFLFEPPppdewVALDCETTGLDpRRAEIVSIAavkirgnriLTSER-LELLVRPPQSLSAESIKIHRLRHQD 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 156 LCGAPSWTDVARQLRHAIGDRPVIIFNARFDIRILKQTAAAHSD---PADwleemtvycAMELAAGYYRATNR-----YG 227
Cdd:PRK09145 92 LEDGLSEEEALRQLLAFIGNRPLVGYYLEFDVAMLNRYVRPLLGiplPNP---------LIEVSALYYDKKERhlpdaYI 162
|
170 180 190
....*....|....*....|....*....|.
gi 485779841 228 TISLASAASQAGL-TWEglAHSAIADARMTA 257
Cdd:PRK09145 163 DLRFDAILKHLDLpVLG--RHDALNDAIMAA 191
|
|
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
107-187 |
3.03e-10 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 59.10 E-value: 3.03e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 107 LDTETTGLDNTAE--ALEIGLtdVAVFETRL---------KPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIGD 175
Cdd:PRK05711 9 LDTETTGLNQREGhrIIEIGA--VELINRRLtgrnfhvyiKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDFIRG 86
|
90
....*....|..
gi 485779841 176 RPVIIFNARFDI 187
Cdd:PRK05711 87 AELIIHNAPFDI 98
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
108-272 |
1.20e-09 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 57.29 E-value: 1.20e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 108 DTETTGLDN------TAEALEIGLTDVAVFETRL--KPTVAIGVQAAAVHGIS-EQA-LCGAPSwTDVARQLRHAIGD-- 175
Cdd:PRK07942 12 DLETTGVDPetarivTAALVVVDADGEVVESREWlaDPGVEIPEEASAVHGITtEYArAHGRPA-AEVLAEIADALREaw 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 176 ---RPVIIFNARFDIRILKQTAAAHSDPAdwLEEMTVYCAMELAagyyRATNRY--GTISLASAASQAGLTWEGlAHSAI 250
Cdd:PRK07942 91 argVPVVVFNAPYDLTVLDRELRRHGLPS--LVPGPVIDPYVID----KAVDRYrkGKRTLTALCEHYGVRLDN-AHEAT 163
|
170 180
....*....|....*....|..
gi 485779841 251 ADARMTAGVVNAIAAYHLELLQ 272
Cdd:PRK07942 164 ADALAAARVAWALARRFPELAA 185
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
108-270 |
2.44e-09 |
|
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: 2.44e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 108 DTETTGLDNTAEALEIGLTDV-------AVFETRLKPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVII 180
Cdd:TIGR00573 13 DNETTGLYAGHDIIEIGAVEIinrritgNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELVI 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 181 FNARFDIRILKQtaaAHSDPADWLEEMTVYCAMELAAGYYRATNRYGTISLASAASQAGLTWEGLA-HSAIADARMTAGV 259
Cdd:TIGR00573 93 HNASFDVGFLNY---EFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRAlHGALADAFILAKL 169
|
170
....*....|.
gi 485779841 260 VNAIAAYHLEL 270
Cdd:TIGR00573 170 YLVMTGKQTKY 180
|
|
| PRK06722 |
PRK06722 |
exonuclease; Provisional |
115-260 |
1.68e-08 |
|
exonuclease; Provisional
Pssm-ID: 180670 [Multi-domain] Cd Length: 281 Bit Score: 54.29 E-value: 1.68e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 115 DNTAEALEIGLTDVAV--------FETRLKPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVIIFNARFD 186
Cdd:PRK06722 22 EDPSEIVDIGAVKIEAstmkvigeFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQIIEKFIQFIGEDSIFVTWGKED 101
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 485779841 187 IRILKQTAAAHSDPADWLEEMTVYCAMELAAGYYRATNRYgTISLASAASQAGLTWEGLAHSAIADARMTAGVV 260
Cdd:PRK06722 102 YRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEH-TPSLQSAVEQLGLIWEGKQHRALADAENTANIL 174
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
107-257 |
6.47e-08 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 52.03 E-value: 6.47e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 107 LDTETTGLDNTAeaLEIGLTDVA------VFETRLKPTVAIGVQAAAVHGISEQALCGAPsWTDVArqLRHAIGDRPVII 180
Cdd:PRK07983 5 IDTETCGLQGGI--VEIASVDVIdgkivnPMSHLVRPDRPISPQAMAIHRITEAMVADKP-WIEDV--IPHYYGSEWYVA 79
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 485779841 181 FNARFDIRILKQTaaahsdPADWLeemtvyCAMELAAGYYRATnRYGTISLASAASQAGLTWEGL-AHSAIADARMTA 257
Cdd:PRK07983 80 HNASFDRRVLPEM------PGEWI------CTMKLARRLWPGI-KYSNMALYKSRKLNVQTPPGLhHHRALYDCYITA 144
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
148-264 |
3.83e-07 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 50.55 E-value: 3.83e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 148 VHGISEQALCGAPSWTDVARQLRHAIGDRPVIIFNARFDIRILKQTAAAHSDPadwLEEMTVYCAMELAAGYYRATNRYG 227
Cdd:PRK06195 53 IHGIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDISVLRKTLELYNIP---MPSFEYICTMKLAKNFYSNIDNAR 129
|
90 100 110
....*....|....*....|....*....|....*..
gi 485779841 228 TISLASAasqagLTWEGLAHSAIADARMTAGVVNAIA 264
Cdd:PRK06195 130 LNTVNNF-----LGYEFKHHDALADAMACSNILLNIS 161
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
107-259 |
1.31e-06 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 48.29 E-value: 1.31e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 107 LDTETTGLD----NTAEALEIGLT---DVAVFETRLKPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVI 179
Cdd:PRK06310 12 LDCETTGLDvkkdRIIEFAAIRFTfdeVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFKEGDYI 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 180 I-FNARFDIRILKQTAAAHSDPADwLEEMTVYCAMELAAGYYRATNRygtiSLASAASQAGLTWEGlAHSAIADARMTAG 258
Cdd:PRK06310 92 VgHSVGFDLQVLSQESERIGETFL-SKHYYIIDTLRLAKEYGDSPNN----SLEALAVHFNVPYDG-NHRAMKDVEINIK 165
|
.
gi 485779841 259 V 259
Cdd:PRK06310 166 V 166
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
150-260 |
1.50e-06 |
|
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: 47.21 E-value: 1.50e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 150 GISEQALCGAPSWTDVARQLRHAIGDRPVIIF--NARFDIRILKQTAAAHS--DPADWLEEMtvycaMELAAGYYRATNR 225
Cdd:cd06133 63 GITQEDVDNAPSFPEVLKEFLEWLGKNGKYAFvtWGDWDLKDLLQNQCKYKiiNLPPFFRQW-----IDLKKEFAKFYGL 137
|
90 100 110
....*....|....*....|....*....|....*
gi 485779841 226 YGTISLASAASQAGLTWEGLAHSAIADARMTAGVV 260
Cdd:cd06133 138 KKRTGLSKALEYLGLEFEGRHHRGLDDARNIARIL 172
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
103-198 |
3.56e-06 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 47.11 E-value: 3.56e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 103 APLFLDTETTGL----DNTAEALEIGLTDVAVFETRLKPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPV 178
Cdd:PRK06309 3 ALIFYDTETTGTqidkDRIIEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTDNI 82
|
90 100
....*....|....*....|..
gi 485779841 179 IIF--NARFDIRILKQTAAAHS 198
Cdd:PRK06309 83 LVAhnNDAFDFPLLRKECRRHG 104
|
|
| Rv2179c-like |
pfam16473 |
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease ... |
105-263 |
9.72e-06 |
|
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: 45.11 E-value: 9.72e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 105 LFLDTETTGLDNTAEALEIGLTDV--------AVFETRLKPTVAIGVQAAAVHGISEQALC------------GAPSWTD 164
Cdd:pfam16473 3 LMIDIETLGNEPTAPIVSIGAVFFdpetgelgKEFYARIDLESSMSAGATIDADTILWWLKqssearaqllgdDAPSLPD 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 165 VARQLRHAIGDR-----PVIIFN-ARFDIRILKQTAAAHSDPADWLEEMT--VYCAMELA-AGYYRATNRygtislasaa 235
Cdd:pfam16473 83 ALLDLNDFIRDNgdpksLKVWGNgASFDNVILRAAFERGGLPAPWKYWNDrdVRTIVALGpELGYDPKRD---------- 152
|
170 180
....*....|....*....|....*...
gi 485779841 236 sqagLTWEGLAHSAIADARMTAGVVNAI 263
Cdd:pfam16473 153 ----IPFEGVKHNALDDAIHQAKYVSAI 176
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
108-257 |
1.44e-05 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 46.22 E-value: 1.44e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 108 DTETTGLDNTAEALEIGLTD------VAVFETRLKPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVIIF 181
Cdd:PRK07246 13 DLEATGAGPNASIIQVGIVIieggeiIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDCIFVAH 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 182 NARFDIRILKQtaaahsdpADWLE--EM------TVycamELAAGYYRATNRYgtiSLASAASQAGLTWEGlAHSAIADA 253
Cdd:PRK07246 93 NVKFDANLLAE--------ALFLEgyELrtprvdTV----ELAQVFFPTLEKY---SLSHLSRELNIDLAD-AHTAIADA 156
|
....
gi 485779841 254 RMTA 257
Cdd:PRK07246 157 RATA 160
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
108-192 |
9.97e-05 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 43.67 E-value: 9.97e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 108 DTETTGLDNT-AEALEIGLTD------VAVFETRLKPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVII 180
Cdd:PRK00448 425 DVETTGLSAVyDEIIEIGAVKikngeiIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGDSILVA 504
|
90
....*....|..
gi 485779841 181 FNARFDIRILKQ 192
Cdd:PRK00448 505 HNASFDVGFINT 516
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
148-263 |
3.42e-04 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 41.22 E-value: 3.42e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 148 VHGISEQALCGAPSWTDVARQLRHAIGDRPVIIFNARFDIRILKQTAA-AHSD-PADWleemtVYCAMELAagyyratNR 225
Cdd:PRK06063 67 VHGLTAEMLEGQPQFADIAGEVAELLRGRTLVAHNVAFDYSFLAAEAErAGAElPVDQ-----VMCTVELA-------RR 134
|
90 100 110 120
....*....|....*....|....*....|....*....|..
gi 485779841 226 YG----TISLASAASQAGLTWEGlAHSAIADARMTAGVVNAI 263
Cdd:PRK06063 135 LGlglpNLRLETLAAHWGVPQQR-PHDALDDARVLAGILRPS 175
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
108-274 |
4.31e-04 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 41.44 E-value: 4.31e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 108 DTETTGLDNTAEAL-EIGLTDV------AVFETRLKPTVAIGVQAAAVHGISEQALCGAPSWTDVARQLRHAIGDRPVII 180
Cdd:PRK07883 21 DLETTGGSPAGDAItEIGAVKVrggevlGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEFARGAVLVA 100
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485779841 181 FNARFDIRILKQTAAAHSDPadWLEEmTVYCAMELAAgyyRATNRYGTIS--LASAASQAGLTWEGlAHSAIADARMTAG 258
Cdd:PRK07883 101 HNAPFDIGFLRAAAARCGYP--WPGP-PVLCTVRLAR---RVLPRDEAPNvrLSTLARLFGATTTP-THRALDDARATVD 173
|
170
....*....|....*.
gi 485779841 259 VVNAIaayhLELLQEQ 274
Cdd:PRK07883 174 VLHGL----IERLGNL 185
|
|
| |
