|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
5-260 |
2.98e-137 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 387.84 E-value: 2.98e-137
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 5 LLHKDIQALIARLKHQDLSLGMLEKSLSRLIYD-EVNLEYLKACGLNFIETSENLITLKNLKTPLKDEVFSFIDLETTGS 83
Cdd:PRK08517 1 MLKQDIQALIAKLKKQSLSYGMLEKSLSRLLKDiDIDLELLKALGLPLVENKENLITLKTRFTPIKDQVFCFVDIETNGS 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 84 CPLKHEILEIGAVQVKGGEIINRFETLVKVKSVPDYIAELTGITYEDTLNAPSVHEALQELRLFLGNSVFVAHNANFDYN 163
Cdd:PRK08517 81 KPKKHQIIEIGAVKVKNGEIIDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEFRLFLGDSVFVAHNVNFDYN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 164 FLGRYFVEKLHCPLLNLKLCTLDLSKRAILSMRYSLSFLKELLGFGIEVSHRAYADALASYKLFEICLLNLPSYIKTTMD 243
Cdd:PRK08517 161 FISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYGLSFLKELLGIEIEVHHRAYADALAAYEIFKICLLNLPSYIKTTED 240
|
250
....*....|....*..
gi 727282424 244 LIDFSKCTNTLIKRPPR 260
Cdd:PRK08517 241 LIDFSKTAKTLKKKKPR 257
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
64-231 |
8.53e-60 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 188.04 E-value: 8.53e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 64 LKTPLKDEVFSFIDLETTGSCPLKHEILEIGAVQVKGGEIINRFETLVK-VKSVPDYIAELTGITYEDTLNAPSVHEALQ 142
Cdd:COG2176 1 MSLDLEDLTYVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVNpGRPIPPFITELTGITDEMVADAPPFEEVLP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 143 ELRLFLGNSVFVAHNANFDYNFLGRYFvEKLHCPLLNLKLCTLDLSKRAILSM-RYSLSFLKELLGFGIEVSHRAYADAL 221
Cdd:COG2176 81 EFLEFLGDAVLVAHNASFDLGFLNAAL-KRLGLPFDNPVLDTLELARRLLPELkSYKLDTLAERLGIPLEDRHRALGDAE 159
|
170
....*....|
gi 727282424 222 ASYKLFEICL 231
Cdd:COG2176 160 ATAELFLKLL 169
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
75-228 |
2.01e-47 |
|
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: 155.92 E-value: 2.01e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 75 FIDLETTGSCPLKHEILEIGAVQVKGG-EIINRFETLVKV-KSVPDYIAELTGITYEDTLNAPSVHEALQELRLFLGNSV 152
Cdd:cd06127 2 VFDTETTGLDPKKDRIIEIGAVKVDGGiEIVERFETLVNPgRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGRV 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 727282424 153 FVAHNANFDYNFLGRYFVEKLHCPLLNLKLCTLDLSKRAILSMRYSLSFLKELLGFGIEV--SHRAYADALASYKLFE 228
Cdd:cd06127 82 LVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLegAHRALADALATAELLL 159
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
73-235 |
4.47e-44 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 147.45 E-value: 4.47e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 73 FSFIDLETTGSCPLKHEILEIGAVQVKGGEIINRFETLVK-VKSVPDYIAELTGITYEDTLNAPSVHEALQELRLFLGNS 151
Cdd:smart00479 2 LVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKpDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 152 VFVAHN-ANFDYNFLGRYFVE-KLHCPLLNLKLCTLDLSKRAILSM-RYSLSFLKELLGFG-IEVSHRAYADALASYKLF 227
Cdd:smart00479 82 ILVAGNsAHFDLRFLKLEHPRlGIKQPPKLPVIDTLKLARATNPGLpKYSLKKLAKRLLLEvIQRAHRALDDARATAKLF 161
|
....*...
gi 727282424 228 EICLLNLP 235
Cdd:smart00479 162 KKLLERLE 169
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
75-227 |
6.59e-41 |
|
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: 139.41 E-value: 6.59e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 75 FIDLETTGSCPLKHEILEIGAVQVKGGE--IINRFETLVKVKS---VPDYIAELTGITYEDTLNAPSVHEALQELRLFLG 149
Cdd:pfam00929 2 VIDLETTGLDPEKDEIIEIAAVVIDGGEneIGETFHTYVKPTRlpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFLR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 150 -NSVFVAHNANFDYNFLGRYFVE--KLHCPLLNLKLCTLDLSKRAILS-MRYSLSFLKELLGF-GIEVSHRAYADALASY 224
Cdd:pfam00929 82 kGNLLVAHNASFDVGFLRYDDKRflKKPMPKLNPVIDTLILDKATYKElPGRSLDALAEKLGLeHIGRAHRALDDARATA 161
|
...
gi 727282424 225 KLF 227
Cdd:pfam00929 162 KLF 164
|
|
| dinG_rel |
TIGR01407 |
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ... |
72-226 |
2.79e-28 |
|
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273602 [Multi-domain] Cd Length: 850 Bit Score: 114.13 E-value: 2.79e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 72 VFSFIDLETTGSCPLKHEILEIGAVQVKGGEIINRFETLVKV-KSVPDYIAELTGITYEDTLNAPSVHEALQELRLFLGN 150
Cdd:TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPnEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLLED 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 727282424 151 SVFVAHNANFDYNFLGRYFVEKLHCPLLNLKLCTLDLSKRAILSMR-YSLSFLKELLGFGIEVSHRAYADALASYKL 226
Cdd:TIGR01407 81 GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEEsYQLSELSEALGLTHENPHRADSDAQATAEL 157
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
5-260 |
2.98e-137 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 387.84 E-value: 2.98e-137
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 5 LLHKDIQALIARLKHQDLSLGMLEKSLSRLIYD-EVNLEYLKACGLNFIETSENLITLKNLKTPLKDEVFSFIDLETTGS 83
Cdd:PRK08517 1 MLKQDIQALIAKLKKQSLSYGMLEKSLSRLLKDiDIDLELLKALGLPLVENKENLITLKTRFTPIKDQVFCFVDIETNGS 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 84 CPLKHEILEIGAVQVKGGEIINRFETLVKVKSVPDYIAELTGITYEDTLNAPSVHEALQELRLFLGNSVFVAHNANFDYN 163
Cdd:PRK08517 81 KPKKHQIIEIGAVKVKNGEIIDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEFRLFLGDSVFVAHNVNFDYN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 164 FLGRYFVEKLHCPLLNLKLCTLDLSKRAILSMRYSLSFLKELLGFGIEVSHRAYADALASYKLFEICLLNLPSYIKTTMD 243
Cdd:PRK08517 161 FISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYGLSFLKELLGIEIEVHHRAYADALAAYEIFKICLLNLPSYIKTTED 240
|
250
....*....|....*..
gi 727282424 244 LIDFSKCTNTLIKRPPR 260
Cdd:PRK08517 241 LIDFSKTAKTLKKKKPR 257
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
64-231 |
8.53e-60 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 188.04 E-value: 8.53e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 64 LKTPLKDEVFSFIDLETTGSCPLKHEILEIGAVQVKGGEIINRFETLVK-VKSVPDYIAELTGITYEDTLNAPSVHEALQ 142
Cdd:COG2176 1 MSLDLEDLTYVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVNpGRPIPPFITELTGITDEMVADAPPFEEVLP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 143 ELRLFLGNSVFVAHNANFDYNFLGRYFvEKLHCPLLNLKLCTLDLSKRAILSM-RYSLSFLKELLGFGIEVSHRAYADAL 221
Cdd:COG2176 81 EFLEFLGDAVLVAHNASFDLGFLNAAL-KRLGLPFDNPVLDTLELARRLLPELkSYKLDTLAERLGIPLEDRHRALGDAE 159
|
170
....*....|
gi 727282424 222 ASYKLFEICL 231
Cdd:COG2176 160 ATAELFLKLL 169
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
75-228 |
2.01e-47 |
|
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: 155.92 E-value: 2.01e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 75 FIDLETTGSCPLKHEILEIGAVQVKGG-EIINRFETLVKV-KSVPDYIAELTGITYEDTLNAPSVHEALQELRLFLGNSV 152
Cdd:cd06127 2 VFDTETTGLDPKKDRIIEIGAVKVDGGiEIVERFETLVNPgRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGRV 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 727282424 153 FVAHNANFDYNFLGRYFVEKLHCPLLNLKLCTLDLSKRAILSMRYSLSFLKELLGFGIEV--SHRAYADALASYKLFE 228
Cdd:cd06127 82 LVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLegAHRALADALATAELLL 159
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
73-227 |
1.12e-46 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 153.80 E-value: 1.12e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 73 FSFIDLETTGSCPLKHEILEIGAVQVKGGEIINRFETLVKV-KSVPDYIAELTGITYEDTLNAPSVHEALQELRLFLGNS 151
Cdd:COG0847 2 FVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVETFHTLVNPeRPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGA 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 727282424 152 VFVAHNANFDYNFLGRYFvEKLHCPLLNLK-LCTLDLSKRAILSM-RYSLSFLKELLGFGIEVSHRAYADALASYKLF 227
Cdd:COG0847 82 VLVAHNAAFDLGFLNAEL-RRAGLPLPPFPvLDTLRLARRLLPGLpSYSLDALCERLGIPFDERHRALADAEATAELF 158
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
73-235 |
4.47e-44 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 147.45 E-value: 4.47e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 73 FSFIDLETTGSCPLKHEILEIGAVQVKGGEIINRFETLVK-VKSVPDYIAELTGITYEDTLNAPSVHEALQELRLFLGNS 151
Cdd:smart00479 2 LVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKpDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 152 VFVAHN-ANFDYNFLGRYFVE-KLHCPLLNLKLCTLDLSKRAILSM-RYSLSFLKELLGFG-IEVSHRAYADALASYKLF 227
Cdd:smart00479 82 ILVAGNsAHFDLRFLKLEHPRlGIKQPPKLPVIDTLKLARATNPGLpKYSLKKLAKRLLLEvIQRAHRALDDARATAKLF 161
|
....*...
gi 727282424 228 EICLLNLP 235
Cdd:smart00479 162 KKLLERLE 169
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
75-227 |
6.59e-41 |
|
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: 139.41 E-value: 6.59e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 75 FIDLETTGSCPLKHEILEIGAVQVKGGE--IINRFETLVKVKS---VPDYIAELTGITYEDTLNAPSVHEALQELRLFLG 149
Cdd:pfam00929 2 VIDLETTGLDPEKDEIIEIAAVVIDGGEneIGETFHTYVKPTRlpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFLR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 150 -NSVFVAHNANFDYNFLGRYFVE--KLHCPLLNLKLCTLDLSKRAILS-MRYSLSFLKELLGF-GIEVSHRAYADALASY 224
Cdd:pfam00929 82 kGNLLVAHNASFDVGFLRYDDKRflKKPMPKLNPVIDTLILDKATYKElPGRSLDALAEKLGLeHIGRAHRALDDARATA 161
|
...
gi 727282424 225 KLF 227
Cdd:pfam00929 162 KLF 164
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
60-222 |
3.60e-37 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 138.51 E-value: 3.60e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 60 TLKNLKTPLKDEVFSFIDLETTGSCPLKHEILEIGAVQVKGGEIINRFETLVKV-KSVPDYIAELTGITYEDTLNAPSVH 138
Cdd:PRK07883 4 SFDDLGTPLRDVTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPgRPIPPFITVLTGITTAMVAGAPPIE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 139 EALQELRLFLGNSVFVAHNANFDYNFLgRYFVEKLHCPLLNLK-LCTLDLSKRaILSM----RYSLSFLKELLGFGIEVS 213
Cdd:PRK07883 84 EVLPAFLEFARGAVLVAHNAPFDIGFL-RAAAARCGYPWPGPPvLCTVRLARR-VLPRdeapNVRLSTLARLFGATTTPT 161
|
....*....
gi 727282424 214 HRAYADALA 222
Cdd:PRK07883 162 HRALDDARA 170
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
59-259 |
1.05e-36 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 138.82 E-value: 1.05e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 59 ITLKNLKTPLKDEVFSFIDLETTGSCPLKHEILEIGAVQVKGGEIINRFETLVKVK-SVPDYIAELTGITYEDTLNAPSV 137
Cdd:PRK00448 407 IVYNEVDRDLKDATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGhPLSAFTTELTGITDDMVKDAPSI 486
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 138 HEALQELRLFLGNSVFVAHNANFDYNFL----GRYFVEKLHCPLLNlklcTLDLSkRAILSM--RYSLSFLKELLGFGIE 211
Cdd:PRK00448 487 EEVLPKFKEFCGDSILVAHNASFDVGFIntnyEKLGLEKIKNPVID----TLELS-RFLYPElkSHRLNTLAKKFGVELE 561
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 727282424 212 VSHRAYADALASYKLFEICLLNLPSY-IKTTMDLIDFSKCTNTLIKRPP 259
Cdd:PRK00448 562 HHHRADYDAEATAYLLIKFLKDLKEKgITNLDELNKKLGSEDAYKKARP 610
|
|
| dinG_rel |
TIGR01407 |
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ... |
72-226 |
2.79e-28 |
|
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273602 [Multi-domain] Cd Length: 850 Bit Score: 114.13 E-value: 2.79e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 72 VFSFIDLETTGSCPLKHEILEIGAVQVKGGEIINRFETLVKV-KSVPDYIAELTGITYEDTLNAPSVHEALQELRLFLGN 150
Cdd:TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPnEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLLED 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 727282424 151 SVFVAHNANFDYNFLGRYFVEKLHCPLLNLKLCTLDLSKRAILSMR-YSLSFLKELLGFGIEVSHRAYADALASYKL 226
Cdd:TIGR01407 81 GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEEsYQLSELSEALGLTHENPHRADSDAQATAEL 157
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
73-233 |
5.97e-28 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 113.12 E-value: 5.97e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 73 FSFIDLETTGSCPLK-HEILEIGAVQVKGGEIINRFETLVKV-KSVPDYIAELTGITYEDTLNAPSVHEALQELRLFLGN 150
Cdd:PRK08074 5 FVVVDLETTGNSPKKgDKIIQIAAVVVEDGEILERFSSFVNPeRPIPPFITELTGISEEMVKQAPLFEDVAPEIVELLEG 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 151 SVFVAHNANFDYNFLGRYFVEKLHCPLLNLKLCTLDLSKraIL---SMRYSLSFLKELLGFGIEVSHRAYADALASYKLF 227
Cdd:PRK08074 85 AYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELAR--ILlptAESYKLRDLSEELGLEHDQPHRADSDAEVTAELF 162
|
....*.
gi 727282424 228 eICLLN 233
Cdd:PRK08074 163 -LQLLN 167
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
64-231 |
4.13e-24 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 97.43 E-value: 4.13e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 64 LKTPLKDEVFSFIDLETTGSCPLK-HEILEIGAVQVKGGEIINR-FETLVKVKS-VPDYIAELTGITYEDTLNAPSVHEA 140
Cdd:PRK07740 52 LDIPLTDLPFVVFDLETTGFSPQQgDEILSIGAVKTKGGEVETDtFYSLVKPKRpIPEHILELTGITAEDVAFAPPLAEV 131
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 141 LQELRLFLGNSVFVAHNANFDYNFLgRYFVEKLHCPLLNLKLctLDLSKRA-ILSMRYSLSFLKELLG-FGIEVS--HRA 216
Cdd:PRK07740 132 LHRFYAFIGAGVLVAHHAGHDKAFL-RHALWRTYRQPFTHRL--IDTMFLTkLLAHERDFPTLDDALAyYGIPIPrrHHA 208
|
170
....*....|....*
gi 727282424 217 YADALASYKLFEICL 231
Cdd:PRK07740 209 LGDALMTAKLWAILL 223
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
73-227 |
2.05e-22 |
|
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: 90.65 E-value: 2.05e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 73 FSFIDLETTgsCPLKHEILEIGAVQVKGGEIINRFETLVKVKSVPDYI-AELTGITYEDTLNAPSVHEALQELRLFLGNS 151
Cdd:cd06130 1 FVAIDFETA--NADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFnIAIHGITPEDVADAPTFPEVWPEIKPFLGGS 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 152 VFVAHNANFDYNFL----GRYFVEKLHCPLlnlkLCTLDLSKRAILSMR-YSLSFLKELLGFGIEvSHRAYADALASYKL 226
Cdd:cd06130 79 LVVAHNASFDRSVLraalEAYGLPPPPYQY----LCTVRLARRVWPLLPnHKLNTVAEHLGIELN-HHDALEDARACAEI 153
|
.
gi 727282424 227 F 227
Cdd:cd06130 154 L 154
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
73-230 |
1.35e-20 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 89.49 E-value: 1.35e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 73 FSFIDLETTGSCPLKHEILEIGAVQVKGGEIINRFETLVKVK-SVPDYIAELTGITYEDTLNAPSVHEALQELRLFLGNS 151
Cdd:PRK06807 10 YVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPErPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 152 VFVAHNANFDYNFLgRYFVEKLHCPLLNLKLC-TLDLSKRAILSM-RYSLSFLKELLGFGIEvSHRAYADALASYKLFEI 229
Cdd:PRK06807 90 VIVAHNASFDMRFL-KSNVNMLGLPEPKNKVIdTVFLAKKYMKHApNHKLETLKRMLGIRLS-SHNAFDDCITCAAVYQK 167
|
.
gi 727282424 230 C 230
Cdd:PRK06807 168 C 168
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
68-222 |
9.98e-20 |
|
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: 85.19 E-value: 9.98e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 68 LKDEVFSFIDLETTGScPLKHEILEIGAVQ-VKGGEIINRFETLVKV-KSVPDYIAELTGITYEDTLNAPSVHEALQELR 145
Cdd:TIGR00573 4 LVLDTETTGDNETTGL-YAGHDIIEIGAVEiINRRITGNKFHTYIKPdRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFA 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 146 LFLGNSVFVAHNANFDYNFLGRYFVEKLHCPLLNLKLCTLDLSKRAILSM----RYSLSFLKelLGFGIEVSHRAYADAL 221
Cdd:TIGR00573 83 DYIRGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEfpgkRNTLDALC--KRYEITNSHRALHGAL 160
|
.
gi 727282424 222 A 222
Cdd:TIGR00573 161 A 161
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
76-227 |
1.13e-17 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 82.81 E-value: 1.13e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 76 IDLETTGSCPlKHEILEIGAVQVKGGEIINRFETLVKV-KSVPDYIAELTGITYEDTLNAPSVHEALQELRLFLGNSVFV 154
Cdd:PRK07246 12 VDLEATGAGP-NASIIQVGIVIIEGGEIIDSYTTDVNPhEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDCIFV 90
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 727282424 155 AHNANFDYNFLGR-YFVEKlhCPLLNLKLCTLDLSKRAILSM-RYSLSFLKELLGFGIEVSHRAYADALASYKLF 227
Cdd:PRK07246 91 AHNVKFDANLLAEaLFLEG--YELRTPRVDTVELAQVFFPTLeKYSLSHLSRELNIDLADAHTAIADARATAELF 163
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
75-267 |
5.10e-17 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 77.93 E-value: 5.10e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 75 FIDLETTGSCPLKHEILEIGAVQVKGGEiinRFETLVKVK-SVPDYIAELTGITYEDTLNAPSVHEALQELRLFLGN-SV 152
Cdd:PRK06309 6 FYDTETTGTQIDKDRIIEIAAYNGVTSE---SFQTLVNPEiPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTdNI 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 153 FVAHNA-NFDYNFLGRYFVEKLHCPLLNLKLCTLDLSKRAILSM-RYSLSFLKELLGFGIEVSHRAYADALASYKLFEIC 230
Cdd:PRK06309 83 LVAHNNdAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLpKHNLQYLRQVYGFEENQAHRALDDVITLHRVFSAL 162
|
170 180 190
....*....|....*....|....*....|....*..
gi 727282424 231 LLNLPsyIKTTMDLIDFSkcTNTLIKRPPRSKYQETP 267
Cdd:PRK06309 163 VGDLS--PQQVYDLLNES--CHPRIFKMPFGKYKGKP 195
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
75-231 |
5.09e-15 |
|
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: 71.48 E-value: 5.09e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 75 FIDLETTgsCP-------LKHEILEIGAVQV--KGGEIINRFETLVKVKSVP---DYIAELTGITYEDTLNAPSVHEALQ 142
Cdd:cd06133 3 VIDFEAT--CWegnskpdYPNEIIEIGAVLVdvKTKEIIDTFSSYVKPVINPklsDFCTELTGITQEDVDNAPSFPEVLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 143 ELRLFLG---NSVFVAhNANFDYNFLGRYFVE-KLHCPL------LNLKLCtldLSKRAILSMRYSLSFLKELLGFGIEV 212
Cdd:cd06133 81 EFLEWLGkngKYAFVT-WGDWDLKDLLQNQCKyKIINLPpffrqwIDLKKE---FAKFYGLKKRTGLSKALEYLGLEFEG 156
|
170 180
....*....|....*....|
gi 727282424 213 S-HRAYADALASYKLFEICL 231
Cdd:cd06133 157 RhHRGLDDARNIARILKRLL 176
|
|
| KapD |
COG5018 |
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
75-227 |
6.03e-15 |
|
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];
Pssm-ID: 444042 [Multi-domain] Cd Length: 181 Bit Score: 71.04 E-value: 6.03e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 75 FIDLETTgsCP-------LKHEILEIGAVQV-KGGEIINRFETLVKVKSVP---DYIAELTGITYEDTLNAPSVHEALQE 143
Cdd:COG5018 6 VIDLEAT--CWdgkpppgFPMEIIEIGAVKVdENGEIIDEFSSFVKPVRRPklsPFCTELTGITQEDVDSAPSFAEAIED 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 144 LRLFLG--NSVFVA----------HNANF---DYNFLGRYfveklhcplLNLKLC---TLDLSKRaiLSMRYSLsflkEL 205
Cdd:COG5018 84 FKKWIGseDYILCSwgdydrkqleRNCRFhgvPYPFGDRH---------INLKKLfalYFGLKKR--IGLKKAL----EL 148
|
170 180
....*....|....*....|...
gi 727282424 206 LGFGIEVS-HRAYADALASYKLF 227
Cdd:COG5018 149 LGLEFEGThHRALDDARNTAKLF 171
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
75-221 |
2.63e-14 |
|
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: 69.10 E-value: 2.63e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 75 FIDLETTGSCPLK-HEILEIGAVqvkggEIINR------FETLVK-VKSVPDYIAELTGITYEDTLNAPSVHEALQELRL 146
Cdd:cd06131 3 VLDTETTGLDPREgHRIIEIGCV-----ELINRrltgntFHVYINpERDIPEEAFKVHGITDEFLADKPKFAEIADEFLD 77
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 727282424 147 FLGNSVFVAHNANFDYNFLGRYFvEKLHCPLLNLKLC----TLDLSKRAILSMRYSLSFLkeLLGFGIEVSHRAYADAL 221
Cdd:cd06131 78 FIRGAELVIHNASFDVGFLNAEL-SLLGLGKKIIDFCrvidTLALARKKFPGKPNSLDAL--CKRFGIDNSHRTLHGAL 153
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
73-250 |
7.03e-11 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 61.72 E-value: 7.03e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 73 FSFIDLETTGScpLKHEILEIGAVQVKGGEIINRFETLVKVKSV---PDYIAeLTGITYEDTLNAPSVHEALQELRLFLG 149
Cdd:PRK06195 3 FVAIDFETANE--KRNSPCSIGIVVVKDGEIVEKVHYLIKPKEMrfmPINIG-IHGIRPHMVEDELEFDKIWEKIKHYFN 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 150 NSVFVAHNANFDYNFLgRYFVEKLHCPLLNLK-LCTLDLSKRAILSM-RYSLSFLKELLGFGIEvSHRAYADALASYKLf 227
Cdd:PRK06195 80 NNLVIAHNASFDISVL-RKTLELYNIPMPSFEyICTMKLAKNFYSNIdNARLNTVNNFLGYEFK-HHDALADAMACSNI- 156
|
170 180
....*....|....*....|...
gi 727282424 228 eicLLNLPSYIKTTmDLIDFSKC 250
Cdd:PRK06195 157 ---LLNISKELNSK-DINEISKL 175
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
66-223 |
1.22e-10 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 59.53 E-value: 1.22e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 66 TPLKDEVFSfIDLETTGSCPLKHEILEIGAVQVKGGEII--NRFETLVKVKSVPDyiAE---LTGITYEDTLNAPSVHEA 140
Cdd:PRK09145 25 PPPPDEWVA-LDCETTGLDPRRAEIVSIAAVKIRGNRILtsERLELLVRPPQSLS--AEsikIHRLRHQDLEDGLSEEEA 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 141 LQELRLFLGNSVFVAHNANFDYNFLGRYFVEKLHCPLLN--LKLCTL--DLSKRAILSMRYSLSF---LKELlgfGIEVS 213
Cdd:PRK09145 102 LRQLLAFIGNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNplIEVSALyyDKKERHLPDAYIDLRFdaiLKHL---DLPVL 178
|
170
....*....|..
gi 727282424 214 --HRAYADALAS 223
Cdd:PRK09145 179 grHDALNDAIMA 190
|
|
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
77-221 |
1.33e-10 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 60.26 E-value: 1.33e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 77 DLETTGSCPLK-HEILEIGAVqvkggEIINRFET------LVK--VKSVPDYIAeLTGITYEDTLNAPSVHEALQELRLF 147
Cdd:PRK05711 10 DTETTGLNQREgHRIIEIGAV-----ELINRRLTgrnfhvYIKpdRLVDPEALA-VHGITDEFLADKPTFAEVADEFLDF 83
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 727282424 148 LGNSVFVAHNANFDYNFLGRYFvEKLHCPL-LNLKLC----TLDLSKRAILSMRYSLSFLKELlgFGIEVSHRAYADAL 221
Cdd:PRK05711 84 IRGAELIIHNAPFDIGFMDYEF-ALLGRDIpKTNTFCkvtdTLAMARRMFPGKRNSLDALCKR--YGIDNSHRTLHGAL 159
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
76-190 |
4.69e-10 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 59.33 E-value: 4.69e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 76 IDLETTGSCPLKHEILEIGAVQVK-GGEIINRFETLV--KVKSVPDYIAELTGITYEDtlnAPSVHEALQELRLFLGNSV 152
Cdd:PRK06063 20 VDVETSGFRPGQARIISLAVLGLDaDGNVEQSVVTLLnpGVDPGPTHVHGLTAEMLEG---QPQFADIAGEVAELLRGRT 96
|
90 100 110
....*....|....*....|....*....|....*....
gi 727282424 153 FVAHNANFDYNFLGR-YFVEKLHCPlLNLKLCTLDLSKR 190
Cdd:PRK06063 97 LVAHNVAFDYSFLAAeAERAGAELP-VDQVMCTVELARR 134
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
75-169 |
5.01e-10 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 58.83 E-value: 5.01e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 75 FIDLETTGSCPLKHEILEIGAVQVK----G--GEIINRFETLVK-VKSVPDYIAELTGITYEDTLNApSVHEAlqELRLF 147
Cdd:PRK09182 41 ILDTETTGLDPRKDEIIEIGMVAFEydddGriGDVLDTFGGLQQpSRPIPPEITRLTGITDEMVAGQ-TIDPA--AVDAL 117
|
90 100
....*....|....*....|...
gi 727282424 148 LGN-SVFVAHNANFDYNFLGRYF 169
Cdd:PRK09182 118 IAPaDLIIAHNAGFDRPFLERFS 140
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
73-219 |
6.73e-09 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 54.72 E-value: 6.73e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 73 FSFIDLETTGscpLKHEILEIGAVQVKGGEIINRFETLVK--VKSVPDYIAeLTGITYEDTLNAPSVHEALqelRLFLGN 150
Cdd:PRK07983 2 LRVIDTETCG---LQGGIVEIASVDVIDGKIVNPMSHLVRpdRPISPQAMA-IHRITEAMVADKPWIEDVI---PHYYGS 74
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 727282424 151 SVFVAHNANFDynflgRYFVEKLHCPLlnlkLCTLDLSKRAILSMRYSLSFLKELLGFGIEV-----SHRAYAD 219
Cdd:PRK07983 75 EWYVAHNASFD-----RRVLPEMPGEW----ICTMKLARRLWPGIKYSNMALYKSRKLNVQTppglhHHRALYD 139
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
68-228 |
1.38e-08 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 54.45 E-value: 1.38e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 68 LKDEVFSFIDLETTGSCPLKHEILEIGAVQVKGGEIINRFETLVKV-KSVPDYIAELTGITYEDTLNAPSVHEALQELRL 146
Cdd:PRK06310 4 LKDTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPeRVVSAESQRIHHISDAMLRDKPKIAEVFPQIKG 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 147 FLGNS-VFVAHNANFDYNFLGRYfVEKLHCPLL---NLKLCTLDLSKRAILSMRYSLSFLKELLGFGIEVSHRAYADALA 222
Cdd:PRK06310 84 FFKEGdYIVGHSVGFDLQVLSQE-SERIGETFLskhYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYDGNHRAMKDVEI 162
|
....*.
gi 727282424 223 SYKLFE 228
Cdd:PRK06310 163 NIKVFK 168
|
|
| PRK06722 |
PRK06722 |
exonuclease; Provisional |
89-220 |
4.95e-08 |
|
exonuclease; Provisional
Pssm-ID: 180670 [Multi-domain] Cd Length: 281 Bit Score: 53.13 E-value: 4.95e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 89 EILEIGAVQVKGG--EIINRFETLVKVKS-VPDYIAELTGITYEDTLNAPSVHEALQELRLFLG-NSVFVAHNANfDYNF 164
Cdd:PRK06722 26 EIVDIGAVKIEAStmKVIGEFSELVKPGArLTRHTTKLTGITKKDLIGVEKFPQIIEKFIQFIGeDSIFVTWGKE-DYRF 104
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 727282424 165 LGR----YFVEklhCPLLNlKLCTLDLSK------RAILSMRYSLSFLKELLGFGIE-VSHRAYADA 220
Cdd:PRK06722 105 LSHdctlHSVE---CPCME-KERRIDLQKfvfqayEELFEHTPSLQSAVEQLGLIWEgKQHRALADA 167
|
|
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
66-227 |
1.68e-07 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 51.08 E-value: 1.68e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 66 TPLKDEVFSFIDLETTGSCPLKHEILEIGAV-------QVKGGE--IINRFETLvKVKSVpdyiaELTGITYEDTLNAPS 136
Cdd:PRK09146 42 TPLSEVPFVALDFETTGLDAEQDAIVSIGLVpftlqriRCRQARhwVVKPRRPL-EEESV-----VIHGITHSELQDAPD 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 137 VHEALQELRLFLGNSVFVAHNANFDYNFLG----RYFVEKLHCPLLNlklcTLDLSKRaiLSMRYSLSFLKELLGFGIE- 211
Cdd:PRK09146 116 LERILDELLEALAGKVVVVHYRRIERDFLDqalrNRIGEGIEFPVID----TMEIEAR--IQRKQAGGLWNRLKGKKPEs 189
|
170 180 190
....*....|....*....|....*....|.
gi 727282424 212 ---------------VSHRAYADALASYKLF 227
Cdd:PRK09146 190 irladsrlryglpaySPHHALTDAIATAELL 220
|
|
| PRK07748 |
PRK07748 |
3'-5' exonuclease KapD; |
73-249 |
2.62e-07 |
|
3'-5' exonuclease KapD;
Pssm-ID: 236087 Cd Length: 207 Bit Score: 50.07 E-value: 2.62e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 73 FSFIDLETT---------GSCPlkhEILEIGAVQVKGGEIINRFETLVKVKSVPDYIAE---LTGITYEDTLNAPSVHEA 140
Cdd:PRK07748 6 FLFLDFEFTmpqhkkkpkGFFP---EIIEVGLVSVVGCEVEDTFSSYVKPKTFPSLTERcksFLGITQEDVDKGISFEEL 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 141 LQELRLF--LGNSVFVAHnANFDYNFLgRYFVEKLHCPLLNLKLCtLDLS---KRaILSMRYSLSFLKELLGFGIE---V 212
Cdd:PRK07748 83 VEKLAEYdkRCKPTIVTW-GNMDMKVL-KHNCEKAGVPFPFKGQC-RDLSleyKK-FFGERNQTGLWKAIEEYGKEgtgK 158
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 727282424 213 SHRAYADALASYKLFEIcLLNLPSYIKTTM-----DLIDFSK 249
Cdd:PRK07748 159 HHCALDDAMTTYNIFKL-VEKDKEYLVKPEpptigERVDFSK 199
|
|
| Rv2179c-like |
pfam16473 |
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease ... |
75-231 |
9.82e-07 |
|
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: 47.81 E-value: 9.82e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 75 FIDLETTG---SCPlkheILEIGAVQVKG--GEIINRFETLVKVKSVPDYIAELTGITYEDTL-------------NAPS 136
Cdd:pfam16473 4 MIDIETLGnepTAP----IVSIGAVFFDPetGELGKEFYARIDLESSMSAGATIDADTILWWLkqssearaqllgdDAPS 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 137 VHEALQELRLFLGNS------VFVAHNANFDYNFL----GRYFVEKLHCPLLNLKLCTLDLSKRAI-LSMRYSLSFLkel 205
Cdd:pfam16473 80 LPDALLDLNDFIRDNgdpkslKVWGNGASFDNVILraafERGGLPAPWKYWNDRDVRTIVALGPELgYDPKRDIPFE--- 156
|
170 180
....*....|....*....|....*.
gi 727282424 206 lgfgiEVSHRAYADALASYKLFEICL 231
Cdd:pfam16473 157 -----GVKHNALDDAIHQAKYVSAIW 177
|
|
| PRK07247 |
PRK07247 |
3'-5' exonuclease; |
87-158 |
2.32e-06 |
|
3'-5' exonuclease;
Pssm-ID: 180906 [Multi-domain] Cd Length: 195 Bit Score: 47.08 E-value: 2.32e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 727282424 87 KHEILEIGAVQVKGGEIINRFETLVKVkSVP--DYIAELTGITYEDTLNAPSVHEALQELRLFLGNSVFVAHNA 158
Cdd:PRK07247 20 VSHIIQVSAVKYDDHKEVDSFDSYVYT-DVPlqSFINGLTGITADKIADAPKVEEVLAAFKEFVGELPLIGYNA 92
|
|
| TREX1_2 |
cd06136 |
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar ... |
73-227 |
2.60e-04 |
|
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: 40.78 E-value: 2.60e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 73 FSFIDLETTGSCPLKH-EILEIGAVQVKGGEIINRFETLVKVKSVPDYI--------------AELTGItYEDTLN--AP 135
Cdd:cd06136 1 FVFLDLETTGLPKHNRpEITELCLVAVHRDHLLNTSRDKPALPRVLDKLslcfnpgraispgaSEITGL-SNDLLEhkAP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 136 SVHEALQELRLFL----GNSVFVAHNAN-FDYNFLgRYFVEKLHCPLLNLKLCtLDlSKRAILSMRYSLSFL-KELLGFG 209
Cdd:cd06136 80 FDSDTANLIKLFLrrqpKPICLVAHNGNrFDFPIL-RSELERLGTKLPDDILC-VD-SLPAFRELDQSLGSLyKRLFGQE 156
|
170
....*....|....*...
gi 727282424 210 IEVSHRAYADALASYKLF 227
Cdd:cd06136 157 PKNSHTAEGDVLALLKCA 174
|
|
| ExoI_N |
cd06138 |
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar ... |
75-226 |
1.05e-03 |
|
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: 39.17 E-value: 1.05e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 75 FIDLETTGSCPLKHEILEIGAVQV-KGGEIINRFETLVKVKsvPDYIAE-----LTGITYEDTL-NAPSVHEALQELRLF 147
Cdd:cd06138 2 FYDYETFGLNPSFDQILQFAAIRTdENFNEIEPFNIFCRLP--PDVLPSpealiVTGITPQQLLkEGLSEYEFIAKIHRL 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 148 LG--NSVFVAHNA-NFDYNFLGRYFVEKLHCP-------------LLNLKLCTLDLSKRAI---------LSMRysLSFL 202
Cdd:cd06138 80 FNtpGTCIVGYNNiRFDDEFLRFAFYRNLYDPytwewkngnsrwdLLDVVRAYYALRPDGIvwpknddgkPSFK--LEDL 157
|
170 180
....*....|....*....|....
gi 727282424 203 KELLGFGIEVSHRAYADALASYKL 226
Cdd:cd06138 158 AQANGIEHSNAHDALSDVEATIAL 181
|
|
| ISG20 |
cd06149 |
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ... |
116-228 |
1.91e-03 |
|
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins; Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 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. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and replication. It may carry out its function by degrading viral RNAs as part of the IFN-regulated antiviral response.
Pssm-ID: 99852 Cd Length: 157 Bit Score: 38.19 E-value: 1.91e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727282424 116 VPDYIAELTGITYEDTLNAPSVHEALQELRLFLGNSVFVAHNANFDYNFLgRYFVEKL------HCPLLNLKlctLDLSK 189
Cdd:cd06149 43 VTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGKVVVGHAIHNDFKAL-KYFHPKHmtrdtsTIPLLNRK---AGFPE 118
|
90 100 110 120
....*....|....*....|....*....|....*....|..
gi 727282424 190 RAILSMRySLSflKELLGFGIEVS---HRAYADALASYKLFE 228
Cdd:cd06149 119 NCRVSLK-VLA--KRLLHRDIQVGrqgHSSVEDARATMELYK 157
|
|
| |
