|
Name |
Accession |
Description |
Interval |
E-value |
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
8-170 |
1.17e-51 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 165.74 E-value: 1.17e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 8 PIVFFDLETTGTNINSDRIVEICYLKVYPNGNEESKTMRINPEMPIPAEASAVHGIYDADIADCPTFKEVARNIANDIEG 87
Cdd:COG0847 1 RFVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 88 CDLAGFNSnRFDIPVLAEEFLRAGvdIDMSRRKFVDVQVIFHKM----EQRTLSAAYKFYcGKNLEDAHTAEADTRATYE 163
Cdd:COG0847 81 AVLVAHNA-AFDLGFLNAELRRAG--LPLPPFPVLDTLRLARRLlpglPSYSLDALCERL-GIPFDERHRALADAEATAE 156
|
....*..
gi 492396467 164 VLMSQLD 170
Cdd:COG0847 157 LFLALLR 163
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
10-166 |
8.76e-43 |
|
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: 142.82 E-value: 8.76e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 10 VFFDLETTGTNINSDRIVEICYLKVYPNGN-EESKTMRINPEMPIPAEASAVHGIYDADIADCPTFKEVARNIANDIEGC 88
Cdd:cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEiVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 89 DLAGFNSNrFDIPVLAEEFLRAGvdIDMSRRKFVDVQVIFHKMEQRT----LSAAYKFYCGKNLEDAHTAEADTRATYEV 164
Cdd:cd06127 81 VLVAHNAS-FDLRFLNRELRRLG--GPPLPNPWIDTLRLARRLLPGLrshrLGLLLAERYGIPLEGAHRALADALATAEL 157
|
..
gi 492396467 165 LM 166
Cdd:cd06127 158 LL 159
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
9-165 |
4.23e-28 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 105.46 E-value: 4.23e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 9 IVFFDLETTGTNINSDRIVEICYLKVYPNGNEESKTMRINPEMPIPAEASAVHGIYDADIADCPTFKEVARNIANDIEGC 88
Cdd:smart00479 2 LVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 89 DLAGFNSNRFDIPVLAEEFLRAGvDIDMSRRKFVD----VQVIFHKMEQRTLSAAYKFYCGKNLEDAHTAEADTRATYEV 164
Cdd:smart00479 82 ILVAGNSAHFDLRFLKLEHPRLG-IKQPPKLPVIDtlklARATNPGLPKYSLKKLAKRLLLEVIQRAHRALDDARATAKL 160
|
.
gi 492396467 165 L 165
Cdd:smart00479 161 F 161
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
8-175 |
4.07e-26 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 101.98 E-value: 4.07e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 8 PIVFFDLETTGTNINSDRIVEICYLKVYPNGNE-ESKTMRINPEMPIPAEASAVHGIYD-------ADIAdcptfkEVAR 79
Cdd:PRK07942 7 PLAAFDLETTGVDPETARIVTAALVVVDADGEVvESREWLADPGVEIPEEASAVHGITTeyarahgRPAA------EVLA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 80 NIANDIEGCDLAG-----FNSnRFDIPVLAEEFLRAGVDiDMSRRKFVDVQVIFHKMEQ-----RTLSAAYKFYcGKNLE 149
Cdd:PRK07942 81 EIADALREAWARGvpvvvFNA-PYDLTVLDRELRRHGLP-SLVPGPVIDPYVIDKAVDRyrkgkRTLTALCEHY-GVRLD 157
|
170 180
....*....|....*....|....*.
gi 492396467 150 DAHTAEADTRATYEVLMSQLDRYPEL 175
Cdd:PRK07942 158 NAHEATADALAAARVAWALARRFPEL 183
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
10-165 |
2.69e-18 |
|
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;
Pssm-ID: 395743 [Multi-domain] Cd Length: 164 Bit Score: 79.32 E-value: 2.69e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 10 VFFDLETTGTNINSDRIVEICYLKVYPNGNEESKT--MRINPEMP--IPAEASAVHGIYDADIADCPTFKEVARNIANDI 85
Cdd:pfam00929 1 VVIDLETTGLDPEKDEIIEIAAVVIDGGENEIGETfhTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 86 E-GCDLAGFNsNRFDIPVLAEEFLRAGVDIDMSRRKFVD----VQVIFHKMEQRTLSAAYKFYCGKNLEDAHTAEADTRA 160
Cdd:pfam00929 81 RkGNLLVAHN-ASFDVGFLRYDDKRFLKKPMPKLNPVIDtlilDKATYKELPGRSLDALAEKLGLEHIGRAHRALDDARA 159
|
....*
gi 492396467 161 TYEVL 165
Cdd:pfam00929 160 TAKLF 164
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
12-169 |
2.09e-12 |
|
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA]
Pssm-ID: 129663 [Multi-domain] Cd Length: 217 Bit Score: 64.39 E-value: 2.09e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 12 FDLETTGTNINSDRIVEICYLKVYPNGNEESKTMRINPEMPIPAEASAVHGIYDADIADCPTFKEVARNIANDIEGCDLA 91
Cdd:TIGR00573 12 GDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELV 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 92 GFNSNrFDIPVLAEEFLRAGVDIDmSRRKFVDV----QVIF-----HKMeqRTLSAAYKFYCGKNLEDAHTAEADTRATY 162
Cdd:TIGR00573 92 IHNAS-FDVGFLNYEFSKLYKVEP-KTNDVIDTtdtlQYARpefpgKRN--TLDALCKRYEITNSHRALHGALADAFILA 167
|
....*..
gi 492396467 163 EVLMSQL 169
Cdd:TIGR00573 168 KLYLVMT 174
|
|
| ExoX-like_C |
pfam20600 |
Exodeoxyribonuclease X-like C-terminal; This short domain is found at the C-terminal of ... |
208-234 |
6.00e-08 |
|
Exodeoxyribonuclease X-like C-terminal; This short domain is found at the C-terminal of Exodeoxyribonuclease 10 (ExoX) from Escherichia coli (strain K12) and it is functionally uncharacterized. This domain is found in bacteria and eukaryotes There is a conserved FGKY/H sequence motif.
Pssm-ID: 466749 [Multi-domain] Cd Length: 28 Bit Score: 47.47 E-value: 6.00e-08
10 20
....*....|....*....|....*..
gi 492396467 208 FNFGKYKGMSVSDVLKRDPGYYSWILN 234
Cdd:pfam20600 1 FNFGKYKGKTLKEVAEIDPTYIEWCIE 27
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
207-235 |
1.52e-07 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 50.49 E-value: 1.52e-07
10 20
....*....|....*....|....*....
gi 492396467 207 VFNFGKYKGMSVSDVLKRDPGYYSWILNS 235
Cdd:PRK07983 173 TFTFGKYRGKAVSDVAERDPGYLRWLFNN 201
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
8-170 |
1.17e-51 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 165.74 E-value: 1.17e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 8 PIVFFDLETTGTNINSDRIVEICYLKVYPNGNEESKTMRINPEMPIPAEASAVHGIYDADIADCPTFKEVARNIANDIEG 87
Cdd:COG0847 1 RFVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 88 CDLAGFNSnRFDIPVLAEEFLRAGvdIDMSRRKFVDVQVIFHKM----EQRTLSAAYKFYcGKNLEDAHTAEADTRATYE 163
Cdd:COG0847 81 AVLVAHNA-AFDLGFLNAELRRAG--LPLPPFPVLDTLRLARRLlpglPSYSLDALCERL-GIPFDERHRALADAEATAE 156
|
....*..
gi 492396467 164 VLMSQLD 170
Cdd:COG0847 157 LFLALLR 163
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
10-166 |
8.76e-43 |
|
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: 142.82 E-value: 8.76e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 10 VFFDLETTGTNINSDRIVEICYLKVYPNGN-EESKTMRINPEMPIPAEASAVHGIYDADIADCPTFKEVARNIANDIEGC 88
Cdd:cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEiVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 89 DLAGFNSNrFDIPVLAEEFLRAGvdIDMSRRKFVDVQVIFHKMEQRT----LSAAYKFYCGKNLEDAHTAEADTRATYEV 164
Cdd:cd06127 81 VLVAHNAS-FDLRFLNRELRRLG--GPPLPNPWIDTLRLARRLLPGLrshrLGLLLAERYGIPLEGAHRALADALATAEL 157
|
..
gi 492396467 165 LM 166
Cdd:cd06127 158 LL 159
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
1-175 |
4.01e-39 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 134.12 E-value: 4.01e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 1 MKLNLKN-PIVFFDLETTGTNINSDRIVEICYLKVYpNGNEESK--TMrINPEMPIPAEASAVHGIYDADIADCPTFKEV 77
Cdd:COG2176 1 MSLDLEDlTYVVFDLETTGLSPKKDEIIEIGAVKVE-NGEIVDRfsTL-VNPGRPIPPFITELTGITDEMVADAPPFEEV 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 78 ARNIANDIEGCDLAGFNSNrFDIPVLAEEFLRAGVDIDmsrRKFVDV----QVIFHKMEQRTLSAAYKFYcGKNLEDAHT 153
Cdd:COG2176 79 LPEFLEFLGDAVLVAHNAS-FDLGFLNAALKRLGLPFD---NPVLDTlelaRRLLPELKSYKLDTLAERL-GIPLEDRHR 153
|
170 180
....*....|....*....|..
gi 492396467 154 AEADTRATYEVLMSQLDRYPEL 175
Cdd:COG2176 154 ALGDAEATAELFLKLLEKLEEK 175
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
9-165 |
4.23e-28 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 105.46 E-value: 4.23e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 9 IVFFDLETTGTNINSDRIVEICYLKVYPNGNEESKTMRINPEMPIPAEASAVHGIYDADIADCPTFKEVARNIANDIEGC 88
Cdd:smart00479 2 LVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 89 DLAGFNSNRFDIPVLAEEFLRAGvDIDMSRRKFVD----VQVIFHKMEQRTLSAAYKFYCGKNLEDAHTAEADTRATYEV 164
Cdd:smart00479 82 ILVAGNSAHFDLRFLKLEHPRLG-IKQPPKLPVIDtlklARATNPGLPKYSLKKLAKRLLLEVIQRAHRALDDARATAKL 160
|
.
gi 492396467 165 L 165
Cdd:smart00479 161 F 161
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
8-175 |
4.07e-26 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 101.98 E-value: 4.07e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 8 PIVFFDLETTGTNINSDRIVEICYLKVYPNGNE-ESKTMRINPEMPIPAEASAVHGIYD-------ADIAdcptfkEVAR 79
Cdd:PRK07942 7 PLAAFDLETTGVDPETARIVTAALVVVDADGEVvESREWLADPGVEIPEEASAVHGITTeyarahgRPAA------EVLA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 80 NIANDIEGCDLAG-----FNSnRFDIPVLAEEFLRAGVDiDMSRRKFVDVQVIFHKMEQ-----RTLSAAYKFYcGKNLE 149
Cdd:PRK07942 81 EIADALREAWARGvpvvvFNA-PYDLTVLDRELRRHGLP-SLVPGPVIDPYVIDKAVDRyrkgkRTLTALCEHY-GVRLD 157
|
170 180
....*....|....*....|....*.
gi 492396467 150 DAHTAEADTRATYEVLMSQLDRYPEL 175
Cdd:PRK07942 158 NAHEATADALAAARVAWALARRFPEL 183
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
9-236 |
2.29e-23 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 94.49 E-value: 2.29e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 9 IVFFDLETTGTNINSDRIVEICylkVYPNGNEESKTMRINPEMPIPAEASAVHGIYDADIADCPTFKEVARNIandIEGC 88
Cdd:PRK06309 4 LIFYDTETTGTQIDKDRIIEIA---AYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKF---IEFC 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 89 D----LAGFNSNRFDIPVLAEEFLRAGvdIDMSRRKFVD----VQVIFHKMEQRTLSAAYKFYcGKNLEDAHTAEADTRA 160
Cdd:PRK06309 78 GtdniLVAHNNDAFDFPLLRKECRRHG--LEPPTLRTIDslkwAQKYRPDLPKHNLQYLRQVY-GFEENQAHRALDDVIT 154
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 492396467 161 TYEVLMSQLDRYPELQndVAFLADYSSFNKnvdfagrmvyddkgVEVFNFGKYKGMSVSDVlkrDPGYYSWILNSD 236
Cdd:PRK06309 155 LHRVFSALVGDLSPQQ--VYDLLNESCHPR--------------IFKMPFGKYKGKPLSEV---PKSYIAWLEKQG 211
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
10-165 |
2.69e-18 |
|
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;
Pssm-ID: 395743 [Multi-domain] Cd Length: 164 Bit Score: 79.32 E-value: 2.69e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 10 VFFDLETTGTNINSDRIVEICYLKVYPNGNEESKT--MRINPEMP--IPAEASAVHGIYDADIADCPTFKEVARNIANDI 85
Cdd:pfam00929 1 VVIDLETTGLDPEKDEIIEIAAVVIDGGENEIGETfhTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 86 E-GCDLAGFNsNRFDIPVLAEEFLRAGVDIDMSRRKFVD----VQVIFHKMEQRTLSAAYKFYCGKNLEDAHTAEADTRA 160
Cdd:pfam00929 81 RkGNLLVAHN-ASFDVGFLRYDDKRFLKKPMPKLNPVIDtlilDKATYKELPGRSLDALAEKLGLEHIGRAHRALDDARA 159
|
....*
gi 492396467 161 TYEVL 165
Cdd:pfam00929 160 TAKLF 164
|
|
| TREX1_2 |
cd06136 |
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar ... |
10-161 |
3.40e-17 |
|
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins; Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TREX2 that point to different biological roles for these proteins. The main difference is the presence of about 70 amino acids at the C-terminus of TREX1. In addition, TREX1 has a nonrepetitive proline-rich region that is not present in the TREX2 protein. Furthermore, TREX2 contains a conserved DNA binding loop positioned adjacent to the active site that has a sequence distinct from the corresponding loop in TREX1. Truncations in the C-terminus of human TREX1 cause autosomal dominant retinal vasculopathy with cerebral leukodystrophy (RVCL), a neurovascular syndrome featuring a progressive loss of visual acuity combined with a variable neurological picture.
Pssm-ID: 99839 [Multi-domain] Cd Length: 177 Bit Score: 76.60 E-value: 3.40e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 10 VFFDLETTG-TNINSDRIVEICYLKVYPNGNEESK-------------TMRINPEMPIPAEASAVHGIYDADIADcptFK 75
Cdd:cd06136 2 VFLDLETTGlPKHNRPEITELCLVAVHRDHLLNTSrdkpalprvldklSLCFNPGRAISPGASEITGLSNDLLEH---KA 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 76 EVARNIANDIEG--------CDLAGFNSNRFDIPVLAEEFLRAGVDiDMSRRKFVDVQVIFHKMEQrTLSAAYKFYCGKN 147
Cdd:cd06136 79 PFDSDTANLIKLflrrqpkpICLVAHNGNRFDFPILRSELERLGTK-LPDDILCVDSLPAFRELDQ-SLGSLYKRLFGQE 156
|
170
....*....|....
gi 492396467 148 LEDAHTAEADTRAT 161
Cdd:cd06136 157 PKNSHTAEGDVLAL 170
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
9-121 |
7.34e-17 |
|
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: 75.65 E-value: 7.34e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 9 IVFFDLETTGTNINS-DRIVEI-C-----------YLKVYpngneesktmrINPEMPIPAEASAVHGIYDADIADCPTFK 75
Cdd:cd06131 1 QIVLDTETTGLDPREgHRIIEIgCvelinrrltgnTFHVY-----------INPERDIPEEAFKVHGITDEFLADKPKFA 69
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 492396467 76 EVARNIANDIEGCDLAGFNSNrFDIPVLAEEFLRAG-----------VD-IDMSRRKF 121
Cdd:cd06131 70 EIADEFLDFIRGAELVIHNAS-FDVGFLNAELSLLGlgkkiidfcrvIDtLALARKKF 126
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
1-123 |
1.21e-14 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 71.40 E-value: 1.21e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 1 MKLNLKNPIVFFDLETTGTNINSDRIVEICYLKVYPNGNEESKTMRINPEMPIPAEASAVHGIYDADIADCPTFKEVARN 80
Cdd:PRK06310 1 MSLLKDTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQ 80
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 492396467 81 IANDIEGCDLAGFNSNRFDIPVLAEEFLRAGVDIDMSRRKFVD 123
Cdd:PRK06310 81 IKGFFKEGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIID 123
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
13-171 |
1.01e-13 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 70.49 E-value: 1.01e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 13 DLETTGTNINSDRI-VEIcylkVYPNGNE--ESKTMRINPEMPIPAEASAVHGIYDADIADCPTFKEVARNIANDIEGCD 89
Cdd:PRK07246 13 DLEATGAGPNASIIqVGI----VIIEGGEiiDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDCI 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 90 LAGFNSnRFDIPVLAEEFLRAGVDIDMSRRKFVDV-QVIFHKMEQRTLSAAYKfYCGKNLEDAHTAEADTRATYEVL--- 165
Cdd:PRK07246 89 FVAHNV-KFDANLLAEALFLEGYELRTPRVDTVELaQVFFPTLEKYSLSHLSR-ELNIDLADAHTAIADARATAELFlkl 166
|
....*....
gi 492396467 166 ---MSQLDR 171
Cdd:PRK07246 167 lqkIESLPK 175
|
|
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
9-121 |
2.37e-13 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 67.58 E-value: 2.37e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 9 IVFfDLETTGTN-INSDRIVEI-C-----------YLKVYpngneesktmrINPEMPIPAEASAVHGIYDADIADCPTFK 75
Cdd:PRK05711 7 IVL-DTETTGLNqREGHRIIEIgAvelinrrltgrNFHVY-----------IKPDRLVDPEALAVHGITDEFLADKPTFA 74
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 492396467 76 EVARNIANDIEGCDLAGFNSNrFDIPVLAEEFLRAGVDID-------------MSRRKF 121
Cdd:PRK05711 75 EVADEFLDFIRGAELIIHNAP-FDIGFMDYEFALLGRDIPktntfckvtdtlaMARRMF 132
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
12-169 |
2.09e-12 |
|
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA]
Pssm-ID: 129663 [Multi-domain] Cd Length: 217 Bit Score: 64.39 E-value: 2.09e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 12 FDLETTGTNINSDRIVEICYLKVYPNGNEESKTMRINPEMPIPAEASAVHGIYDADIADCPTFKEVARNIANDIEGCDLA 91
Cdd:TIGR00573 12 GDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELV 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 92 GFNSNrFDIPVLAEEFLRAGVDIDmSRRKFVDV----QVIF-----HKMeqRTLSAAYKFYCGKNLEDAHTAEADTRATY 162
Cdd:TIGR00573 92 IHNAS-FDVGFLNYEFSKLYKVEP-KTNDVIDTtdtlQYARpefpgKRN--TLDALCKRYEITNSHRALHGALADAFILA 167
|
....*..
gi 492396467 163 EVLMSQL 169
Cdd:TIGR00573 168 KLYLVMT 174
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
10-166 |
5.02e-12 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 65.63 E-value: 5.02e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 10 VFFDLETTGTNINSDRIVEICYLKVYpNGNEESKTMR-INPEMPIPAEASAVHGIYDADIADCPTFKEVARNIANDIEGC 88
Cdd:PRK00448 422 VVFDVETTGLSAVYDEIIEIGAVKIK-NGEIIDKFEFfIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGDS 500
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 89 DLAGFNSNrFDIPVLAEEFLRAGVD------ID---MSRrkfvdvqVIFHKMEQRTLSAAYKFYcGKNLEDAHTAEADTR 159
Cdd:PRK00448 501 ILVAHNAS-FDVGFINTNYEKLGLEkiknpvIDtleLSR-------FLYPELKSHRLNTLAKKF-GVELEHHHRADYDAE 571
|
....*..
gi 492396467 160 ATYEVLM 166
Cdd:PRK00448 572 ATAYLLI 578
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
10-171 |
6.98e-12 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 64.97 E-value: 6.98e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 10 VFFDLETTGtniNS----DRIVEICYLKVyPNGN-EESKTMRINPEMPIPAEASAVHGIYDADIADCPTFKEVARNIAND 84
Cdd:PRK08074 6 VVVDLETTG---NSpkkgDKIIQIAAVVV-EDGEiLERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVEL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 85 IEGCDLAGFNSNrFDIPVLAEEFLRAGVD-IDMSRRKFVDV-QVIFHKMEQRTLSA-AYKFycgkNLE--DAHTAEADTR 159
Cdd:PRK08074 82 LEGAYFVAHNVH-FDLNFLNEELERAGYTeIHCPKLDTVELaRILLPTAESYKLRDlSEEL----GLEhdQPHRADSDAE 156
|
170
....*....|..
gi 492396467 160 ATYEVLMSQLDR 171
Cdd:PRK08074 157 VTAELFLQLLNK 168
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
10-198 |
6.29e-11 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 61.86 E-value: 6.29e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 10 VFFDLETTGTNINSDRIVEICYLKVypNGNE---ESKTMrINPEMPIPAEASAVHGIYDADIADCP-------TFKEVAR 79
Cdd:PRK07883 18 VVVDLETTGGSPAGDAITEIGAVKV--RGGEvlgEFATL-VNPGRPIPPFITVLTGITTAMVAGAPpieevlpAFLEFAR 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 80 niandieGCDLAGFNSnRFDIPVLAEEFLRAGVD---------IDMSRRKFVDVQVIFHKmeqrtLSAAYKFYcGKNLED 150
Cdd:PRK07883 95 -------GAVLVAHNA-PFDIGFLRAAAARCGYPwpgppvlctVRLARRVLPRDEAPNVR-----LSTLARLF-GATTTP 160
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 492396467 151 AHTAEADTRATYEVLMSQLDRypeLQN-DVAFLADYSSFNKNVDFAGRM 198
Cdd:PRK07883 161 THRALDDARATVDVLHGLIER---LGNlGVHTLEELLTYLPRVTPAQRR 206
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
8-163 |
3.41e-09 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 55.83 E-value: 3.41e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 8 PIVFFDLETTGTNI-NSDRIVEICYLKVypNGNE---ESKTMRINPEMPIPAEASAVHGIYDADIADCPTFKEVARNIAN 83
Cdd:PRK07740 60 PFVVFDLETTGFSPqQGDEILSIGAVKT--KGGEvetDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYA 137
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 84 DIEGCDLAGFNSnRFDipvlaEEFLRAGVDIDMSR---RKFVD----VQVIFHKMEQRTLSAAYKFYcGKNLEDAHTAEA 156
Cdd:PRK07740 138 FIGAGVLVAHHA-GHD-----KAFLRHALWRTYRQpftHRLIDtmflTKLLAHERDFPTLDDALAYY-GIPIPRRHHALG 210
|
....*..
gi 492396467 157 DTRATYE 163
Cdd:PRK07740 211 DALMTAK 217
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
13-171 |
6.99e-09 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 55.48 E-value: 6.99e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 13 DLETTGTNINSDRIVEICYLKVYPNGN-EESKTMRINPEM-PIPAEasaVHGIYDADIADCPTFKEVARNIANDIEGCDL 90
Cdd:PRK06063 21 DVETSGFRPGQARIISLAVLGLDADGNvEQSVVTLLNPGVdPGPTH---VHGLTAEMLEGQPQFADIAGEVAELLRGRTL 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 91 AGFNSNrFDIPVLAEEFLRAGVD---------IDMSRRkfVDVQVIFHKMEqrTLSAAYkfycGKNLEDAHTAEADTRAT 161
Cdd:PRK06063 98 VAHNVA-FDYSFLAAEAERAGAElpvdqvmctVELARR--LGLGLPNLRLE--TLAAHW----GVPQQRPHDALDDARVL 168
|
170
....*....|
gi 492396467 162 YEVLMSQLDR 171
Cdd:PRK06063 169 AGILRPSLER 178
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
9-165 |
1.11e-08 |
|
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: 52.90 E-value: 1.11e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 9 IVFFDLETTgtniNSDR-------IVEICylkvypNGNE-ESKTMRINPEMPIPAEASAVHGIYDADIADCPTFKEVARN 80
Cdd:cd06130 1 FVAIDFETA----NADRasacsigLVKVR------DGQIvDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPE 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 81 IANDIEGCDLAGFNSnRFDIPVLAEEFLRAGVDID---------MSRRKFVDVQVifHKMEqrTLSAaykfYCGKNLEDa 151
Cdd:cd06130 71 IKPFLGGSLVVAHNA-SFDRSVLRAALEAYGLPPPpyqylctvrLARRVWPLLPN--HKLN--TVAE----HLGIELNH- 140
|
170
....*....|....
gi 492396467 152 HTAEADTRATYEVL 165
Cdd:cd06130 141 HDALEDARACAEIL 154
|
|
| ExoX-like_C |
pfam20600 |
Exodeoxyribonuclease X-like C-terminal; This short domain is found at the C-terminal of ... |
208-234 |
6.00e-08 |
|
Exodeoxyribonuclease X-like C-terminal; This short domain is found at the C-terminal of Exodeoxyribonuclease 10 (ExoX) from Escherichia coli (strain K12) and it is functionally uncharacterized. This domain is found in bacteria and eukaryotes There is a conserved FGKY/H sequence motif.
Pssm-ID: 466749 [Multi-domain] Cd Length: 28 Bit Score: 47.47 E-value: 6.00e-08
10 20
....*....|....*....|....*..
gi 492396467 208 FNFGKYKGMSVSDVLKRDPGYYSWILN 234
Cdd:pfam20600 1 FNFGKYKGKTLKEVAEIDPTYIEWCIE 27
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
10-77 |
8.96e-08 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 52.12 E-value: 8.96e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 492396467 10 VFFDLETTGTNINSDRIVEICYLKVYPNGNEESKTMRINPEMPIPAEASAVHGIYDADIADCPTFKEV 77
Cdd:PRK06807 11 VVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEV 78
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
207-235 |
1.52e-07 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 50.49 E-value: 1.52e-07
10 20
....*....|....*....|....*....
gi 492396467 207 VFNFGKYKGMSVSDVLKRDPGYYSWILNS 235
Cdd:PRK07983 173 TFTFGKYRGKAVSDVAERDPGYLRWLFNN 201
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
10-171 |
4.24e-06 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 46.89 E-value: 4.24e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 10 VFFDLETTGTNINSDRIVEICYLKVypNGNEESKTMRI--------NPEMPIPAEASAVHGIYDADIADcPTFKEVArnI 81
Cdd:PRK09182 40 VILDTETTGLDPRKDEIIEIGMVAF--EYDDDGRIGDVldtfgglqQPSRPIPPEITRLTGITDEMVAG-QTIDPAA--V 114
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 82 ANDIEGCDL-----AGFNS---NRFDiPVLAEEFLRAGV-DIDMSRRKFVDvqvifHKMEQRTLSAAYkFYcgknleDAH 152
Cdd:PRK09182 115 DALIAPADLiiahnAGFDRpflERFS-PVFATKPWACSVsEIDWSARGFEG-----TKLGYLAGQAGF-FH------EGH 181
|
170
....*....|....*....
gi 492396467 153 TAEADTRATYEVLMSQLDR 171
Cdd:PRK09182 182 RAVDDCQALLELLARPLPE 200
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
10-135 |
6.10e-06 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 45.66 E-value: 6.10e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 10 VFFDLETTGTNINSDRIVEICYLKVypNGNE----ESKTMRINPEMPIPAEASAVHGIYDADIADCPTFKEVARNIANDI 85
Cdd:PRK09145 32 VALDCETTGLDPRRAEIVSIAAVKI--RGNRiltsERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFI 109
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 492396467 86 EGCDLAGFNSnRFDIPVLaEEFLRAGVDIDMSRRKfVDVQVIFH-KMEQRT 135
Cdd:PRK09145 110 GNRPLVGYYL-EFDVAML-NRYVRPLLGIPLPNPL-IEVSALYYdKKERHL 157
|
|
| ExoI_N |
cd06138 |
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar ... |
10-109 |
4.83e-05 |
|
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease 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. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Pssm-ID: 99841 [Multi-domain] Cd Length: 183 Bit Score: 43.02 E-value: 4.83e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 10 VFFDLETTGTNINSDRIVEICYLKVYPNGNEESKTM---RINPEMPIPAEASAVHGIYDADIADC-PTFKEVARNIANDI 85
Cdd:cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTDENFNEIEPFNifcRLPPDVLPSPEALIVTGITPQQLLKEgLSEYEFIAKIHRLF 80
|
90 100
....*....|....*....|....*..
gi 492396467 86 E---GCDLaGFNSNRFDipvlaEEFLR 109
Cdd:cd06138 81 NtpgTCIV-GYNNIRFD-----DEFLR 101
|
|
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
8-77 |
3.30e-04 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 41.06 E-value: 3.30e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 492396467 8 PIVFFDLETTGTNINSDRIVEICYL-----KVYPNgneESKTMRINPEMPIPAEASAVHGIYDADIADCPTFKEV 77
Cdd:PRK09146 48 PFVALDFETTGLDAEQDAIVSIGLVpftlqRIRCR---QARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERI 119
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
10-174 |
1.30e-03 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 39.23 E-value: 1.30e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 10 VFFDLETTGTNINSDRIVEICYLKVypNGNEESKTMRINPEMP-IPAEASAVHGIYDADIADCPTFKEVARN-------- 80
Cdd:PRK08517 71 CFVDIETNGSKPKKHQIIEIGAVKV--KNGEIIDRFESFVKAKeVPEYITELTGITYEDLENAPSLKEVLEEfrlflgds 148
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492396467 81 --IANDIegcdlagfnsnRFDIPVLAEEFLRAGVD---------IDMSRRKFvdvqvifhkMEQRTLSAAYKFYCGKNLE 149
Cdd:PRK08517 149 vfVAHNV-----------NFDYNFISRSLEEIGLGpllnrklctIDLAKRTI---------ESPRYGLSFLKELLGIEIE 208
|
170 180
....*....|....*....|....*
gi 492396467 150 DAHTAEADTRATYEVLMSQLDRYPE 174
Cdd:PRK08517 209 VHHRAYADALAAYEIFKICLLNLPS 233
|
|
| Orn |
cd06135 |
DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease ... |
9-30 |
2.72e-03 |
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DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. 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. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Pssm-ID: 99838 [Multi-domain] Cd Length: 173 Bit Score: 37.53 E-value: 2.72e-03
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